• 
  Paudel, R., Sorger, L., Hufnagel, A., Pasemann, M., Hove, T., Marquardt, A., Kneitz, S., Schlosser, A., Kisker, C., Kuper, J., & Meierjohann, S.Anti-tumorigenic properties by trichothiodystrophy mutations in melanocytic cellsNAR Cancer, 7(3). https://doi.org/10.1093/narcan/zcaf026.
  • [ DOI ]

• 
  Meinert, M., Jessen, C., Hufnagel, A., Kreß, J.K.C., Burnworth, M., Däubler, T., Gallasch, T., Xavier da Silva, T.N., dos Santos, A.F., Ade, C.P., Schmitz, W., Kneitz, S., Friedmann Angeli, J.P., & Meierjohann, S.Thiol starvation triggers melanoma state switching in an ATF4 and NRF2-dependent mannerRedox Biology, 70: 103011.
  • [ DOI ]
• 
  Schartl, M., Woltering, J.M., Irisarri, I., Du, K., Kneitz, S., Pippel, M., Brown, T., Franchini, P., Li, J., Li, M., Adolfi, M., Winkler, S., de Freitas Sousa, J., Chen, Z., Jacinto, S., Kvon, E.Z., Correa de Oliveira, L.R., Monteiro, E., Baia Amaral, D., et al.The genomes of all lungfish inform on genome expansion and tetrapod evolutionNature, 634(8032): 96–103.
  • [ Abstract ]
  • [ DOI ]
  The genomes of living lungfishes can inform on the molecular-developmental basis of the Devonian sarcopterygian fish--tetrapod transition. We de novo sequenced the genomes of the African (Protopterus annectens) and South American lungfishes (Lepidosiren paradoxa). The Lepidosiren genome (about 91\thinspaceGb, roughly 30 times the human genome) is the largest animal genome sequenced so far and more than twice the size of the Australian (Neoceratodus forsteri)1 and African2 lungfishes owing to enlarged intergenic regions and introns with high repeat content (about 90{\%}). All lungfish genomes continue to expand as some transposable elements (TEs) are still active today. In particular, Lepidosiren's genome grew extremely fast during the past 100 million years (Myr), adding the equivalent of one human genome every 10\thinspaceMyr. This massive genome expansion seems to be related to a reduction of PIWI-interacting RNAs and C2H2 zinc-finger and Kr\"u}ppel-associated box (KRAB)-domain protein genes that suppress TE expansions. Although TE abundance facilitates chromosomal rearrangements, lungfish chromosomes still conservatively reflect the ur-tetrapod karyotype. Neoceratodus' limb-like fins still resemble those of their extinct relatives and remained phenotypically static for about 100\thinspaceMyr. We show that the secondary loss of limb-like appendages in the Lepidosiren--Protopterus ancestor was probably due to loss of sonic hedgehog limb-specific enhancers.
• 
  Münch, L., Helmprobst, F., Volff, J.-N., Chalopin, D., Schartl, M., & Kneitz, S.Transposable Element Expression Profiles in Premalignant Pigment Cell Lesions and Melanoma of XiphophorusGenes, 15(5): 620.
  • [ DOI ]

• 
  Fetiva, M.C., Liss, F., Gertzmann, D., Thomas, J., Gantert, B., Vogl, M., Sira, N., Weinstock, G., Kneitz, S., Ade, C., & Gaubatz, S.Oncogenic YAP mediates changes in chromatin accessibility and activity that drive cell cycle gene expression and cell migrationNucleic Acids Research, 51(9): 4266–4283.
  • [ DOI ]
• 
  Kotlyar, M.J., Krebs, M., Solimando, A.G., Marquardt, A., Burger, M., Kübler, H., Bargou, R., Kneitz, S., Otto, W., Breyer, J., Vergho, D.C., Kneitz, B., & Kalogirou, C.Critical Evaluation of a microRNA-Based Risk Classifier Predicting Cancer-Specific Survival in Renal Cell Carcinoma with Tumor Thrombus of the Inferior Vena CavaCancers, 15(7): 1981.
  • [ DOI ]
• 
  Lu, Y., Rice, E., Du, K., Kneitz, S., Naville, M., Dechaud, C., Volff, J.-N., Boswell, M., Boswell, W., Hillier, L., Tomlinson, C., Milin, K., Walter, R.B., Schartl, M., & Warren, W.C.High resolution genomes of multiple Xiphophorusspecies provide new insights into microevolution, hybrid incompatibility, and epistasisGenome Research, 33(4): 557–571.
  • [ DOI ]

• 
  Dedukh, D., da Cruz, I., Kneitz, S., Marta, A., Ormanns, J., Tichop\’a}d, T., Lu, Y., Alsheimer, M., Janko, K., & Schartl, M.Achiasmatic meiosis in the unisexual Amazon molly, Poecilia formosaChromosome Research, 30(4): 443–457.
  • [ Abstract ]
  • [ DOI ]
  Unisexual reproduction, which generates clonal offspring, is an alternative strategy to sexual breeding and occurs even in vertebrates. A wide range of non-sexual reproductive modes have been described, and one of the least understood questions is how such pathways emerged and how they mechanistically proceed. The Amazon molly, Poecilia formosa, needs sperm from males of related species to trigger the parthenogenetic development of diploid eggs. However, the mechanism, of how the unreduced female gametes are produced, remains unclear. Cytological analyses revealed that the chromosomes of primary oocytes initiate pachytene but do not proceed to bivalent formation and meiotic crossovers. Comparing ovary transcriptomes of P. formosa and its sexual parental species revealed expression levels of meiosis-specific genes deviating from P. mexicana but not from P. latipinna. Furthermore, several meiosis genes show biased expression towards one of the two alleles from the parental genomes. We infer from our data that in the Amazon molly diploid oocytes are generated by apomixis due to a failure in the synapsis of homologous chromosomes. The fact that this failure is not reflected in the differential expression of known meiosis genes suggests the underlying molecular mechanism may be dysregulation on the protein level or misexpression of a so far unknown meiosis gene, and/or hybrid dysgenesis because of compromised interaction of proteins from diverged genomes.
• 
  Tamihardja, J., Zehner, L., Hartrampf, P., Lisowski, D., Kneitz, S., Cirsi, S., Razinskas, G., Flentje, M., & Polat, B.Salvage Nodal Radiotherapy as Metastasis-Directed Therapy for Oligorecurrent Prostate Cancer Detected by Positron Emission Tomography Shows Favorable Outcome in Long-Term Follow-UpCancers, 14(15): 3766.
  • [ DOI ]
• 
  Martinez-Bengochea, A.L., Kneitz, S., Herpin, A., N\’o}brega, R.H., Adolfi, M.C., & Schartl, M.Sexual development dysgenesis in interspecific hybrids of Medaka fishScientific Reports, 12(1): 5408.
  • [ Abstract ]
  • [ DOI ]
  Fish are amongst vertebrates the group with the highest diversity of known sex-determining genes. Particularly, the genus Oryzias is a suitable taxon to understand how different sex determination genetic networks evolved in closely related species. Two closely related species, O. latipes and O. curvinotus, do not only share the same XX/XY sex chromosome system, but also the same male sex-determining gene, dmrt1bY. We performed whole mRNA transcriptomes and morphology analyses of the gonads of hybrids resulting from reciprocal crosses between O. latipes and O. curvinotus. XY male hybrids, presenting meiotic arrest and no production of sperm were sterile, and about 30\% of the XY hybrids underwent male-to-female sex reversal. Both XX and XY hybrid females exhibited reduced fertility and developed ovotestis while aging. Transcriptome data showed that male-related genes are upregulated in the XX and XY female hybrids. The transcriptomes of both types of female and of the male gonads are characterized by upregulation of meiosis and germ cell differentiation genes. Differences in the parental species in the downstream pathways of sexual development could explain sex reversal, sterility, and the development of intersex gonads in the hybrids. We hypothesize that male-to-female sex reversal may be connected to a different development time between species at which dmrt1bY expression starts. Our results provide molecular clues for the proximate mechanisms of hybrid incompatibility and Haldane's rule.
• 
  Du, K., Pippel, M., Kneitz, S., Feron, R., da Cruz, I., Winkler, S., Wilde, B., Avila Luna, E.G., Myers, G., Guiguen, Y., Macias Garcia, C., & Schartl, M.Genome biology of the darkedged splitfin, Girardinichthys multiradiatus, and the evolution of sex chromosomes and placentationGenome Research, 32(3): 583–594.
  • [ DOI ]

• 
  Schartl, M., Kneitz, S., Ormanns, J., Schmidt, C., Anderson, J.L., Amores, A., Catchen, J., Wilson, C., Geiger, D., Du, K., Garcia-Olazábal, M., Sudaram, S., Winkler, C., Hedrich, R., Warren, W.C., Walter, R., Meyer, A., & Postlethwait, J.H.The Developmental and Genetic Architecture of the Sexually Selected Male Ornament of SwordtailsCurrent Biology, 31(5): 911–922.e4.
  • [ DOI ]
• 
  Adolfi, M.C., Amaury, H., Martinez-Bengochea, A., Kneitz, S., Martina, R., Grunwald, D.J., & Schartl, M.Crosstalk Between Retinoic Acid and Sex-Related Genes Controls Germ Cell Fate and Gametogenesis in MedakaFrontiers in Cell and Developmental Biology, 8: 613497.
  • [ DOI ]
• 
  Adolfi, M.C., Herpin, A., Martinez-Bengochea, A., Kneitz, S., Regensburger, M., Grunwald, D.J., & Schartl, M.Crosstalk Between Retinoic Acid and Sex-Related Genes Controls Germ Cell Fate and Gametogenesis in MedakaFrontiers in Cell and Developmental Biology, Volume 8 - 2020. https://doi.org/10.3389/fcell.2020.613497.
  • [ Abstract ]
  • [ DOI ]
  Sex determination (SD) is a highly diverse and complex mechanism. In vertebrates one of the first morphological differences between the sexes is the timing of initiation of the first meiosis, where its initiation occurs first in female and later in male. Thus, SD is intimately related to the responsiveness of the germ cells to undergo meiosis in a sex-specific manner. In some vertebrates, it has been reported that the timing for meiosis entry would be under control of retinoic acid (RA), through activation of Stra8. In this study, we used a fish model species for sex determination and lacking the stra8 gene, the Japanese medaka (Oryzias latipes), to investigate the connection between RA and the sex determination pathway. Exogenous RA treatments act as a stress factor inhibiting germ cell differentiation probably by activation of dmrt1a and amh. Disruption of the RA degrading enzyme gene cyp26a1 induced precocious meiosis and oogenesis in embryos/hatchlings of female and even some males. Transcriptome analyzes of cyp26a1 -/- adult gonads revealed upregulation of genes related to germ cell differentiation and meiosis, in both ovaries and testes. Our findings show that germ cells respond to RA in a stra8 independent model species. The responsiveness to RA is conferred by sex-related genes, restricting its action to the sex differentiation period in both sexes.
• 
  Meyer, A., Schloissnig, S., Franchini, P., Du, K., Woltering, J.M., Irisarri, I., Wong, W.Y., Nowoshilow, S., Kneitz, S., Kawaguchi, A., Fabrizius, A., Xiong, P., Dechaud, C., Spaink, H.P., Volff, J.-N., Simakov, O., Burmester, T., Tanaka, E.M., & Schartl, M.Giant lungfish genome elucidates the conquest of land by vertebratesNature, 590(7845): 284–289.
  • [ Abstract ]
  • [ DOI ]
  Lungfishes belong to lobe-fined fish (Sarcopterygii) that, in the Devonian period, `conquered' the land and ultimately gave rise to all land vertebrates, including humans1--3. Here we determine the chromosome-quality genome of the Australian lungfish (Neoceratodus forsteri), which is known to have the largest genome of any animal. The vast size of this genome, which is about 14\texttimes larger than that of humans, is attributable mostly to huge intergenic regions and introns with high repeat content (around 90{\%}), the components of which resemble those of tetrapods (comprising mainly long interspersed nuclear elements) more than they do those of ray-finned fish. The lungfish genome continues to expand independently (its transposable elements are still active), through mechanisms different to those of the enormous genomes of salamanders. The 17 fully assembled lungfish macrochromosomes maintain synteny to other vertebrate chromosomes, and all microchromosomes maintain conserved ancient homology with the ancestral vertebrate karyotype. Our phylogenomic analyses confirm previous reports that lungfish occupy a key evolutionary position as the closest living relatives to tetrapods4,5, underscoring the importance of lungfish for understanding innovations associated with terrestrialization. Lungfish preadaptations to living on land include the gain of limb-like expression in developmental genes such as hoxc13 and sall1 in their lobed fins. Increased rates of evolution and the duplication of genes associated with obligate air-breathing, such as lung surfactants and the expansion of odorant receptor gene families (which encode proteins involved in detecting airborne odours), contribute to the tetrapod-like biology of lungfishes. These findings advance our understanding of this major transition during vertebrate evolution.
• 
  Feron, R., Pan, Q., Wen, M., Imarazene, B., Jouanno, E., Anderson, J., Herpin, A., Journot, L., Parrinello, H., Klopp, C., Kottler, V.A., Roco, A.S., Du, K., Kneitz, S., Adolfi, M., Wilson, C.A., McCluskey, B., Amores, A., Desvignes, T., et al.RADSex: A computational workflow to study sex determination using restriction site‐associated DNA sequencing dataMolecular Ecology Resources, 21(5): 1715–1731.
  • [ DOI ]
• 
  Helmprobst, F., Kneitz, S., Klotz, B., Naville, M., Dechaud, C., Volff, J.-N., & Schartl, M.Differential expression of transposable elements in the medaka melanoma modelPLOS ONE, 16(10): 1–17.
  • [ Abstract ]
  • [ DOI ]
  Malignant melanoma incidence is rising worldwide. Its treatment in an advanced state is difficult, and the prognosis of this severe disease is still very poor. One major source of these difficulties is the high rate of metastasis and increased genomic instability leading to a high mutation rate and the development of resistance against therapeutic approaches. Here we investigate as one source of genomic instability the contribution of activation of transposable elements (TEs) within the tumor. We used the well-established medaka melanoma model and RNA-sequencing to investigate the differential expression of TEs in wildtype and transgenic fish carrying melanoma. We constructed a medaka-specific TE sequence library and identified TE sequences that were specifically upregulated in tumors. Validation by qRT- PCR confirmed a specific upregulation of a LINE and an LTR element in malignant melanomas of transgenic fish.
• 
  Adolfi, M.C., Du, K., Kneitz, S., Cabau, C., Zahm, M., Klopp, C., Feron, R., Paix\~a}o, R.V., Varela, E.S., de Almeida, F.L., de Oliveira, M.A., N\’o}brega, R.H., Lopez-Roques, C., Iampietro, C., Lluch, J., Kloas, W., Wuertz, S., Schaefer, F., St\"o}ck, M., et al.A duplicated copy of id2b is an unusual sex-determining candidate gene on the Y chromosome of arapaima (Arapaima gigas)Scientific Reports, 11(1): 21544.
  • [ Abstract ]
  • [ DOI ]
  Arapaima gigas is one of the largest freshwater fish species of high ecological and economic importance. Overfishing and habitat destruction are severe threats to the remaining wild populations. By incorporating a chromosomal Hi-C contact map, we improved the arapaima genome assembly to chromosome-level, revealing an unexpected high degree of chromosome rearrangements during evolution of the bonytongues (Osteoglossiformes). Combining this new assembly with pool-sequencing of male and female genomes, we identified id2bbY, a duplicated copy of the inhibitor of DNA binding 2b (id2b) gene on the Y chromosome as candidate male sex-determining gene. A PCR-test for id2bbY was developed, demonstrating that this gene is a reliable male-specific marker for genotyping. Expression analyses showed that this gene is expressed in juvenile male gonads. Its paralog, id2ba, exhibits a male-biased expression in immature gonads. Transcriptome analyses and protein structure predictions confirm id2bbY as a prime candidate for the master sex-determiner. Acting through the TGF$\beta$ signaling pathway, id2bbY from arapaima would provide the first evidence for a link of this family of transcriptional regulators to sex determination. Our study broadens our current understanding about the evolution of sex determination genetic networks and provide a tool for improving arapaima aquaculture for commercial and conservation purposes.
• 
  Vardapour, R., Kehl, T., Kneitz, S., Ludwig, N., Meese, E., Lenhof, H.-P., & Gessler, M.The DGCR8 E518K mutation found in Wilms tumors leads to a partial miRNA processing defect that alters gene expression patterns and biological processesCarcinogenesis, 43(2): 82–93.
  • [ DOI ]
• 
  Buschhart, A.-L., Bolten, L., Volzke, J., Ekat, K., Kneitz, S., Mikkat, S., Kreikemeyer, B., & Müller-Hilke, B.Periodontal pathogens alter the synovial proteome. Periodontal pathogens do not exacerbate macroscopic arthritis but alter the synovial proteome in micePLOS ONE, 15(12): 1–18.
  • [ Abstract ]
  • [ DOI ]
  Rheumatoid arthritis (RA) and periodontitis (PD) are chronic inflammatory diseases that appear to occur in tandem. However, the mutual impact PD exerts on RA and vice versa has not yet been defined. To address this issue, we set up an animal model and analyzed how two prime inducers of periodontitis—Porphyromonas gingivalis (Pg) and Aggregatibacter actinomycetemcomitans (Aa)–differ in their pathogenic potential. Our experimental setup included collagen induced arthritis (CIA) in the mouse, oral inoculation with Pg or Aa to induce alveolar bone loss and the combination of both diseases in inverted orders of events. Neither pathobiont impacted on macroscopic arthritis and arthritis did not exacerbate alveolar bone loss. However, there were subtle differences between Pg and Aa with the former inducing more alveolar bone loss if PD was induced before CIA. On a molecular level, Pg and Aa led to differential expression patterns in the synovial membranes that were reminiscent of cellular and humoral immune responses, respectively. The Pg and Aa specific signatures in the synovial proteomes suggest a role for oral pathogens in shaping disease subtypes and setting the stage for subsequent therapy response.

• 
  Jessen, C., Kre\ss}, J.K.C., Baluapuri, A., Hufnagel, A., Schmitz, W., Kneitz, S., Roth, S., Marquardt, A., Appenzeller, S., Ade, C.P., Glutsch, V., Wobser, M., Friedmann-Angeli, J.P., Mosteo, L., Goding, C.R., Schilling, B., Geissinger, E., Wolf, E., & Meierjohann, S.The transcription factor NRF2 enhances melanoma malignancy by blocking differentiation and inducing COX2 expressionOncogene, 39(44): 6841–6855.
  • [ Abstract ]
  • [ DOI ]
  The transcription factor NRF2 is the major mediator of oxidative stress responses and is closely connected to therapy resistance in tumors harboring activating mutations in the NRF2 pathway. In melanoma, such mutations are rare, and it is unclear to what extent melanomas rely on NRF2. Here we show that NRF2 suppresses the activity of the melanocyte lineage marker MITF in melanoma, thereby reducing the expression of pigmentation markers. Intriguingly, we furthermore identified NRF2 as key regulator of immune-modulating genes, linking oxidative stress with the induction of cyclooxygenase 2 (COX2) in an ATF4-dependent manner. COX2 is critical for the secretion of prostaglandin E2 and was strongly induced by H2O2 or TNF$\alpha$ only in presence of NRF2. Induction of MITF and depletion of COX2 and PGE2 were also observed in NRF2-deleted melanoma cells in vivo. Furthermore, genes corresponding to the innate immune response such as RSAD2 and IFIH1 were strongly elevated in absence of NRF2 and coincided with immune evasion parameters in human melanoma datasets. Even in vitro, NRF2 activation or prostaglandin E2 supplementation blunted the induction of the innate immune response in melanoma cells. Transcriptome analyses from lung adenocarcinomas indicate that the observed link between NRF2 and the innate immune response is not restricted to melanoma.
• 
  Du, K., St\"o}ck, M., Kneitz, S., Klopp, C., Woltering, J.M., Adolfi, M.C., Feron, R., Prokopov, D., Makunin, A., Kichigin, I., Schmidt, C., Fischer, P., Kuhl, H., Wuertz, S., Gessner, J., Kloas, W., Cabau, C., Iampietro, C., Parrinello, H., et al.The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidizationNature Ecology \& Evolution, 4(6): 841–852.
  • [ Abstract ]
  • [ DOI ]
  Sturgeons seem to be frozen in time. The archaic characteristics of this ancient fish lineage place it in a key phylogenetic position at the base of the \textasciitilde30,000 modern teleost fish species. Moreover, sturgeons are notoriously polyploid, providing unique opportunities to investigate the evolution of polyploid genomes. We assembled a high-quality chromosome-level reference genome for the sterlet, Acipenser ruthenus. Our analysis revealed a very low protein evolution rate that is at least as slow as in other deep branches of the vertebrate tree, such as that of the coelacanth. We uncovered a whole-genome duplication that occurred in the Jurassic, early in the evolution of the entire sturgeon lineage. Following this polyploidization, the rediploidization of the genome included the loss of whole chromosomes in a segmental deduplication process. While known adaptive processes helped conserve a high degree of structural and functional tetraploidy over more than 180 million years, the reduction of redundancy of the polyploid genome seems to have been remarkably random.
• 
  Krebs, M., Solimando, A.G., Kalogirou, C., Marquardt, A., Frank, T., Sokolakis, I., Hatzichristodoulou, G., Kneitz, S., Bargou, R., Kübler, H., Schilling, B., Spahn, M., & Kneitz, B.miR-221-3p Regulates VEGFR2 Expression in High-Risk Prostate Cancer and Represents an Escape Mechanism from Sunitinib In VitroJournal of Clinical Medicine, 9(3): 670.
  • [ DOI ]
• 
  Kottler, V.A., Feron, R., Nanda, I., Klopp, C., Du, K., Kneitz, S., Helmprobst, F., Lamatsch, D.K., Lopez-Roques, C., Lluch, J., Journot, L., Parrinello, H., Guiguen, Y., & Schartl, M.Independent Origin of XY and ZW Sex Determination Mechanisms in Mosquitofish Sister SpeciesGenetics, 214(1): 193–209.
  • [ DOI ]
• 
  Lu, Y., Sandoval, A., Voss, S., Lai, Z., Kneitz, S., Boswell, W., Boswell, M., Savage, M., Walter, C., Warren, W., Schartl, M., & Walter, R.Oncogenic allelic interaction in Xiphophorus highlights hybrid incompatibilityProceedings of the National Academy of Sciences, 117(47): 29786–29794.
  • [ Abstract ]
  • [ DOI ]
  The Bateson–Dobzhansky–Muller (BDM) model describes negative epistatic interactions that occur between genes with a different evolutionary history to account for hybrid incompatibility and is a central theory explaining genetic mechanisms underlying speciation. Since the early 1900 s when the BDM model was forwarded examples of BDM incompatibility have been described in only a few nonvertebrate cases. This study reports the only vertebrate system, with clearly defined interacting loci, that supports the BDM model. In addition, this study also poses that tumorigenesis serves as a novel mechanism that accounts for postzygotic isolation. Mixing genomes of different species by hybridization can disrupt species-specific genetic interactions that were adapted and fixed within each species population. Such disruption can predispose the hybrids to abnormalities and disease that decrease the overall fitness of the hybrids and is therefore named as hybrid incompatibility. Interspecies hybridization between southern platyfish and green swordtails leads to lethal melanocyte tumorigenesis. This occurs in hybrids with tumor incidence following progeny ratio that is consistent with two-locus interaction, suggesting melanoma development is a result of negative epistasis. Such observations make Xiphophorus one of the only two vertebrate hybrid incompatibility examples in which interacting genes have been identified. One of the two interacting loci has been characterized as a mutant epidermal growth factor receptor. However, the other locus has not been identified despite over five decades of active research. Here we report the localization of the melanoma regulatory locus to a single gene, rab3d, which shows all expected features of the long-sought oncogene interacting locus. Our findings provide insights into the role of egfr regulation in regard to cancer etiology. Finally, they provide a molecular explainable example of hybrid incompatibility.
• 
  Schmidt, C.J., Wenndorf, K., Ebbers, M., Volzke, J., Müller, M., Strübing, J., Kriebel, K., Kneitz, S., Kreikemeyer, B., & Müller-Hilke, B.Infection With Clostridioides difficile Attenuated Collagen-Induced Arthritis in Mice and Involved Mesenteric Treg and Th2 PolarizationFrontiers in Immunology, Volume 11 - 2020. https://doi.org/10.3389/fimmu.2020.571049.
  • [ Abstract ]
  • [ DOI ]
  Objectives: Rheumatoid arthritis is an autoimmune disease with multifactorial etiopathogenesis. Among the environmental factors, mucosal infections and the inducing pathobionts are gaining increasing attention. We here set out to explore the gut-joint-axis and the impact of Clostridioides difficile infection on subsequent arthritis. Methods: We combined C. difficile infection in DBA/1J × B10.Q F1 mice with collagen induced arthritis (CIA). Mice were infected via oral gavage and infection was monitored by weight loss, colonic histology and antibodies against bacteria. Scoring of arthritis was performed macroscopically. Intestinal microbiomes were analyzed and immune responses were monitored via quantification of transcription factor-specific mRNA isolated from the inguinal and mesenteric lymphnodes. Results: Infection with C. difficile VPI 10463 resulted in significant weight loss and severe colitis yet accelerated the reversal towards the original microbiome after antibiotic treatment. Spontaneous clearance of VPI 10463 infection reduced the incidence of subsequent CIA and led to mesenteric Treg plasticity that involved Th2 polarization. However, this attenuating effect was abrogated if VPI 10463 was eradicated via vancomycin followed by fecal microbiota transplantation. Moreover, VPI 10463 infection following the onset of CIA lacked therapeutic potential. Conclusion: Our results demonstrate that infection with C. difficile VPI10463 induced an inflammation of the gut that protected from subsequent arthritis development in mice. Both, microbial changes to the gut and immune cell mobilization and/or polarization may have contributed to arthritis protection. The prospect of potential therapeutic benefits resulting from C. difficile infections or some byproduct thereof call for further experiments that help elucidate exact mechanisms.
• 
  Phan, Q.T., Tan, W.H., Liu, R., Sundaram, S., Buettner, A., Kneitz, S., Cheong, B., Vyas, H., Mathavan, S., Schartl, M., & Winkler, C.Cxcl9l and Cxcr3.2 regulate recruitment of osteoclast progenitors to bone matrix in a medaka osteoporosis modelProceedings of the National Academy of Sciences, 117(32): 19276–19286.
  • [ Abstract ]
  • [ DOI ]
  Bone remodeling requires a balanced interplay of osteoblasts and osteoclasts. While the intercellular signaling that triggers bone cell differentiation is well understood, it remains unclear how bone progenitor cells are recruited to remodeling sites. Various chemokines are upregulated under osteoporotic conditions. However, whether they are involved in progenitor recruitment or instead have inflammatory roles is unknown. Here we used a medaka fish osteoporosis model to identify the chemokine ligand Cxcl9l and receptor Cxcr3.2 as essential to control osteoclast progenitor recruitment and differentiation at bone resorption sites. Cxcr3.2 activity can be blocked by small-molecule inhibitors that protect bone from osteoporotic insult. Our study demonstrates the potential of fish for osteoporosis drug discovery and opens avenues for future osteoporosis therapy. Bone homeostasis requires continuous remodeling of bone matrix to maintain structural integrity. This involves extensive communication between bone-forming osteoblasts and bone-resorbing osteoclasts to orchestrate balanced progenitor cell recruitment and activation. Only a few mediators controlling progenitor activation are known to date and have been targeted for intervention of bone disorders such as osteoporosis. To identify druggable pathways, we generated a medaka (Oryzias latipes) osteoporosis model, where inducible expression of receptor-activator of nuclear factor kappa-Β ligand (Rankl) leads to ectopic formation of osteoclasts and excessive bone resorption, which can be assessed by live imaging. Here we show that upon Rankl induction, osteoblast progenitors up-regulate expression of the chemokine ligand Cxcl9l. Ectopic expression of Cxcl9l recruits mpeg1-positive macrophages to bone matrix and triggers their differentiation into osteoclasts. We also demonstrate that the chemokine receptor Cxcr3.2 is expressed in a distinct subset of macrophages in the aorta-gonad-mesonephros (AGM). Live imaging revealed that upon Rankl induction, Cxcr3.2-positive macrophages get activated, migrate to bone matrix, and differentiate into osteoclasts. Importantly, mutations in cxcr3.2 prevent macrophage recruitment and osteoclast differentiation. Furthermore, Cxcr3.2 inhibition by the chemical antagonists AMG487 and NBI-74330 also reduced osteoclast recruitment and protected bone integrity against osteoporotic insult. Our data identify a mechanism for progenitor recruitment to bone resorption sites and Cxcl9l and Cxcr3.2 as potential druggable regulators of bone homeostasis and osteoporosis.

• 
  Lu, Y., Boswell, W., Boswell, M., Klotz, B., Kneitz, S., Regneri, J., Savage, M., Mendoza, C., Postlethwait, J., Warren, W.C., Schartl, M., & Walter, R.B.Application of the Transcriptional Disease Signature (TDSs) to Screen Melanoma-Effective Compounds in a Small Fish ModelScientific Reports, 9(1): 530.
  • [ Abstract ]
  • [ DOI ]
  Cell culture and protein target-based compound screening strategies, though broadly utilized in selecting candidate compounds, often fail to eliminate candidate compounds with non-target effects and/or safety concerns until late in the drug developmental process. Phenotype screening using intact research animals is attractive because it can help identify small molecule candidate compounds that have a high probability of proceeding to clinical use. Most FDA approved, first-in-class small molecules were identified from phenotypic screening. However, phenotypic screening using rodent models is labor intensive, low-throughput, and very expensive. As a novel alternative for small molecule screening, we have been developing gene expression disease profiles, termed the Transcriptional Disease Signature (TDS), as readout of small molecule screens for therapeutic molecules. In this concept, compounds that can reverse, or otherwise affect known disease-associated gene expression patterns in whole animals may be rapidly identified for more detailed downstream direct testing of their efficacy and mode of action. To establish proof of concept for this screening strategy, we employed a transgenic strain of a small aquarium fish, medaka (Oryzias latipes), that overexpresses the malignant melanoma driver gene xmrk, a mutant egfr gene, that is driven by a pigment cell-specific mitf promoter. In this model, melanoma develops with 100\% penetrance. Using the transgenic medaka malignant melanoma model, we established a screening system that employs the NanoString nCounter platform to quantify gene expression within custom sets of TDS gene targets that we had previously shown to exhibit differential transcription among xmrk-transgenic and wild-type medaka. Compound-modulated gene expression was identified using an internet-accessible custom-built data processing pipeline. The effect of a given drug on the entire TDS profile was estimated by comparing compound-modulated genes in the TDS using an activation Z-score and Kolmogorov-Smirnov statistics. TDS gene probes were designed that target common signaling pathways that include proliferation, development, toxicity, immune function, metabolism and detoxification. These pathways may be utilized to evaluate candidate compounds for potential favorable, or unfavorable, effects on melanoma-associated gene expression. Here we present the logistics of using medaka to screen compounds, as well as, the development of a user-friendly NanoString data analysis pipeline to support feasibility of this novel TDS drug-screening strategy.
• 
  Pattschull, G., Walz, S., Gründl, M., Schwab, M., Rühl, E., Baluapuri, A., Cindric-Vranesic, A., Kneitz, S., Wolf, E., Ade, C.P., Rosenwald, A., von Eyss, B., & Gaubatz, S.The Myb-MuvB Complex Is Required for YAP-Dependent Transcription of Mitotic GenesCell Reports, 27(12): 3533 – 3546.e7.
  • [ Abstract ]
  • [ DOI ]
  Summary YAP and TAZ, downstream effectors of the Hippo pathway, are important regulators of proliferation. Here, we show that the ability of YAP to activate mitotic gene expression is dependent on the Myb-MuvB (MMB) complex, a master regulator of genes expressed in the G2/M phase of the cell cycle. By carrying out genome-wide expression and binding analyses, we found that YAP promotes binding of the MMB subunit B-MYB to the promoters of mitotic target genes. YAP binds to B-MYB and stimulates B-MYB chromatin association through distal enhancer elements that interact with MMB-regulated promoters through chromatin looping. The cooperation between YAP and B-MYB is critical for YAP-mediated entry into mitosis. Furthermore, the expression of genes coactivated by YAP and B-MYB is associated with poor survival of cancer patients. Our findings provide a molecular mechanism by which YAP and MMB regulate mitotic gene expression and suggest a link between two cancer-relevant signaling pathways.
• 
  Blanco-Redondo, B., Nuwal, N., Kneitz, S., Nuwal, T., Halder, P., Liu, Y., Ehmann, N., Scholz, N., Mayer, A., Kleber, J., Kähne, T., Schmitt, D., Sadanandappa, M.K., Funk, N., Albertova, V., Helfrich-Förster, C., Ramaswami, M., Hasan, G., Kittel, R.J., et al.Implications of the Sap47 null mutation for synapsin phosphorylation, longevity, climbing, and behavioural plasticity in adult DrosophilaJournal of Experimental Biology. https://doi.org/10.1242/jeb.203505.
  • [ DOI ]
• 
  Reuter, I., Jäckels, J., Kneitz, S., Kuper, J., Lesch, K.-P., & Lillesaar, C.Fgf3 is crucial for the generation of monoaminergic cerebrospinal fluid contacting cells in zebrafishBiology Open. https://doi.org/10.1242/bio.040683.
  • [ DOI ]
• 
  Schartl, M., Kneitz, S., Volkoff, H., Adolfi, M., Schmidt, C., Fischer, P., Minx, P., Tomlinson, C., Meyer, A., & Warren, W.C.The Piranha Genome Provides Molecular Insight Associated to Its Unique Feeding Behavior (E. Betran, Ed.)Genome Biology and Evolution, 11(8): 2099–2106.
  • [ DOI ]
• 
  Du, K., Wuertz, S., Adolfi, M., Kneitz, S., St\"o}ck, M., Oliveira, M., N\’o}brega, R., Ormanns, J., Kloas, W., Feron, R., Klopp, C., Parrinello, H., Journot, L., He, S., Postlethwait, J., Meyer, A., Guiguen, Y., & Schartl, M.The genome of the arapaima (Arapaima gigas) provides insights into gigantism, fast growth and chromosomal sex determination systemScientific Reports, 9(1): 5293.
  • [ Abstract ]
  • [ DOI ]
  We have sequenced the genome of the largest freshwater fish species of the world, the arapaima. Analysis of gene family dynamics and signatures of positive selection identified genes involved in the specific adaptations and unique features of this iconic species, in particular it's large size and fast growth. Genome sequences from both sexes combined with RAD-tag analyses from other males and females led to the isolation of male-specific scaffolds and supports an XY sex determination system in arapaima. Whole transcriptome sequencing showed that the product of the gland-like secretory organ on the head surface of males and females may not only provide nutritional fluid for sex-unbiased parental care, but that the organ itself has a more specific function in males, which engage more in parental care.
• 
  Herpin, A., Schmidt, C., Kneitz, S., Gobé, C., Regensburger, M., Le Cam, A., Montfort, J., Adolfi, M.C., Lillesaar, C., Wilhelm, D., Kraeussling, M., Mourot, B., Porcon, B., Pannetier, M., Pailhoux, E., Ettwiller, L., Dolle, D., Guiguen, Y., & Schartl, M.A novel evolutionary conserved mechanism of RNA stability regulates synexpression of primordial germ cell-specific genes prior to the sex-determination stage in medakaPLOS Biology, 17(4): 1–29.
  • [ Abstract ]
  • [ DOI ]
  Dmrt1 is a highly conserved transcription factor, which is critically involved in regulation of gonad development of vertebrates. In medaka, a duplicate of dmrt1—acting as master sex-determining gene—has a tightly timely and spatially controlled gonadal expression pattern. In addition to transcriptional regulation, a sequence motif in the 3′ UTR (D3U-box) mediates transcript stability of dmrt1 mRNAs from medaka and other vertebrates. We show here that in medaka, two RNA-binding proteins with antagonizing properties target this D3U-box, promoting either RNA stabilization in germ cells or degradation in the soma. The D3U-box is also conserved in other germ-cell transcripts, making them responsive to the same RNA binding proteins. The evolutionary conservation of the D3U-box motif within dmrt1 genes of metazoans—together with preserved expression patterns of the targeting RNA binding proteins in subsets of germ cells—suggest that this new mechanism for controlling RNA stability is not restricted to fishes but might also apply to other vertebrates.
• 
  Krebs, M., Behrmann, C., Kalogirou, C., Sokolakis, I., Kneitz, S., Kruithof-de Julio, M., Zoni, E., Rech, A., Schilling, B., Kübler, H., Spahn, M., & Kneitz, B.miR-221 Augments TRAIL-Mediated Apoptosis in Prostate Cancer Cells by Inducing Endogenous TRAIL Expression and Targeting the Functional Repressors SOCS3 and PIK3R1BioMed Research International, 2019: 1–11.
  • [ DOI ]
• 
  Klotz, B., Kneitz, S., Lu, Y., Boswell, W., Postlethwait, J., Warren, W., Walter, R.B., & Schartl, M.Expression Signatures of Cisplatin- and Trametinib-Treated Early-Stage Medaka MelanomasG3 Genes|Genomes|Genetics, 9(7): 2267–2276.
  • [ DOI ]
• 
  L\"u}bcke, P.M., Ebbers, M.N.B., Volzke, J., Bull, J., Kneitz, S., Engelmann, R., Lang, H., Kreikemeyer, B., & M\"u}ller-Hilke, B.Periodontal treatment prevents arthritis in mice and methotrexate ameliorates periodontal bone lossScientific Reports, 9(1): 8128.
  • [ Abstract ]
  • [ DOI ]
  Recent studies indicate a causal relationship between the periodontal pathogen P. gingivalis and rheumatoid arthritis involving the production of autoantibodies against citrullinated peptides. We therefore postulated that therapeutic eradication P. gingivalis may ameliorate rheumatoid arthritis development and here turned to a mouse model in order to challenge our hypothesis. F1 (DBA/1 x B10.Q) mice were orally inoculated with P. gingivalis before collagen-induced arthritis was provoked. Chlorhexidine or metronidazole were orally administered either before or during the induction phase of arthritis and their effects on arthritis progression and alveolar bone loss were compared to intraperitoneally injected methotrexate. Arthritis incidence and severity were macroscopically scored and alveolar bone loss was evaluated via microcomputed tomography. Serum antibody titres against P. gingivalis were quantified by ELISA and microbial dysbiosis following oral inoculation was monitored in stool samples via microbiome analyses. Both, oral chlorhexidine and metronidazole reduced the incidence and ameliorated the severity of collagen-induced arthritis comparable to methotrexate. Likewise, all three therapies attenuated alveolar bone loss. Relative abundance of Porphyromonadaceae was increased after oral inoculation with P. gingivalis and decreased after treatment. This is the first study to describe beneficial effects of non-surgical periodontal treatment on collagen-induced arthritis in mice and suggests that mouthwash with chlorhexidine or metronidazole may also be beneficial for patients with rheumatoid arthritis and a coexisting periodontitis. Methotrexate ameliorated periodontitis in mice, further raising the possibility that methotrexate may also positively impact on the tooth supporting tissues of patients with rheumatoid arthritis.

• 
  Tiwarekar, V., Wohlfahrt, J., Fehrholz, M., Scholz, C.-J., Kneitz, S., & Schneider-Schaulies, J.APOBEC3G-Regulated Host Factors Interfere with Measles Virus Replication: Role of REDD1 and Mammalian TORC1 Inhibition (R. E. Dutch, Ed.)Journal of Virology, 92(17). https://doi.org/10.1128/jvi.00835-18.
  • [ DOI ]
• 
  Lu, Y., Boswell, M., Boswell, W., Kneitz, S., Hausmann, M., Klotz, B., Regneri, J., Savage, M., Amores, A., Postlethwait, J., Warren, W., Schartl, M., & Walter, R.Comparison of Xiphophorus and human melanoma transcriptomes reveals conserved pathway interactionsPigment Cell &Amp; Melanoma Research, 31(4): 496–508.
  • [ DOI ]
• 
  Klotz, B., Kneitz, S., Regensburger, M., Hahn, L., Dannemann, M., Kelso, J., Nickel, B., Lu, Y., Boswell, W., Postlethwait, J., Warren, W., Kunz, M., Walter, R.B., & Schartl, M.Expression signatures of early-stage and advanced medaka melanomasComparative Biochemistry and Physiology Part C: Toxicology &Amp; Pharmacology, 208: 20–28.
  • [ DOI ]
• 
  Anelli, V., Ordas, A., Kneitz, S., Sagredo, L.M., Gourain, V., Schartl, M., Meijer, A.H., & Mione, M.Ras-Induced miR-146a and 193a Target Jmjd6 to Regulate Melanoma ProgressionFrontiers in Genetics, Volume 9 - 2018. https://doi.org/10.3389/fgene.2018.00675.
  • [ Abstract ]
  • [ DOI ]
  Ras genes are among the most commonly mutated genes in human cancer; yet our understanding of their oncogenic activity at the molecular mechanistic level is incomplete. To identify downstream events that mediate ras-induced cellular transformation in vivo, we analyzed global microRNA expression in three different models of Ras-induction and tumor formation in zebrafish. Six microRNAs were found increased in Ras-induced melanoma, glioma and in an inducible model of ubiquitous Ras expression. The upregulation of the microRNAs depended on the activation of the ERK and AKT pathways and to a lesser extent, on mTOR signaling. Three Ras-induced microRNAs (miR-146a, 146b, and 193a) target Jmjd6, inducing downregulation of its mRNA and protein levels at the onset of Ras expression. However, at later stages of melanoma progression, Jmjd6 levels were elevated. The dynamic of Jmjd6 levels during progression of melanoma in the zebrafish model suggests that upregulation of the microRNAs targeting Jmjd6 may be part of an anti-cancer response. Indeed, triple transgenic fish engineered to express a microRNA-resistant Jmjd6 from the onset of melanoma have increased tumor burden, higher infiltration of leukocytes and shorter melanoma-free survival. The connection miR146/193-JMJD6 is conserved in human melanoma, indicating that the up-regulation of Jmjd6 is a critical event in melanoma progression.
• 
  Regneri, J., Klotz, B., Wilde, B., Kottler, V.A., Hausmann, M., Kneitz, S., Regensburger, M., Maurus, K., Götz, R., Lu, Y., Walter, R.B., Herpin, A., & Schartl, M.Analysis of the putative tumor suppressor gene cdkn2ab in pigment cells and melanoma of Xiphophorus and medakaPigment Cell &Amp; Melanoma Research, 32(2): 248–258.
  • [ DOI ]
• 
  Kunz, M., L\"o}ffler-Wirth, H., Dannemann, M., Willscher, E., Doose, G., Kelso, J., Kottek, T., Nickel, B., Hopp, L., Landsberg, J., Hoffmann, S., T\"u}ting, T., Zigrino, P., Mauch, C., Utikal, J., Ziemer, M., Schulze, H.-J., H\"o}lzel, M., Roesch, A., et al.RNA-seq analysis identifies different transcriptomic types and developmental trajectories of primary melanomasOncogene, 37(47): 6136–6151.
  • [ Abstract ]
  • [ DOI ]
  Recent studies revealed trajectories of mutational events in early melanomagenesis, but the accompanying changes in gene expression are far less understood. Therefore, we performed a comprehensive RNA-seq analysis of laser-microdissected melanocytic nevi (n{\thinspace}={\thinspace}23) and primary melanoma samples (n{\thinspace}={\thinspace}57) and characterized the molecular mechanisms of early melanoma development. Using self-organizing maps, unsupervised clustering, and analysis of pseudotime (PT) dynamics to identify evolutionary trajectories, we describe here two transcriptomic types of melanocytic nevi (N1 and N2) and primary melanomas (M1 and M2). N1/M1 lesions are characterized by pigmentation-type and MITF gene signatures, and a high prevalence of NRAS mutations in M1 melanomas. N2/M2 lesions are characterized by inflammatory-type and AXL gene signatures with an equal distribution of wild-type and mutated BRAF and low prevalence of NRAS mutations in M2 melanomas. Interestingly, N1 nevi and M1 melanomas and N2 nevi and M2 melanomas, respectively, cluster together, but there is no clustering in a stage-dependent manner. Transcriptional signatures of M1 melanomas harbor signatures of BRAF/MEK inhibitor resistance and M2 melanomas harbor signatures of anti-PD-1 antibody treatment resistance. Pseudotime dynamics of nevus and melanoma samples are suggestive for a switch-like immune-escape mechanism in melanoma development with downregulation of immune genes paralleled by an increasing expression of a cell cycle signature in late-stage melanomas. Taken together, the transcriptome analysis identifies gene signatures and mechanisms underlying development of melanoma in early and late stages with relevance for diagnostics and therapy.
• 
  Kruber, P., Angay, O., Winkler, A., Bösl, M.R., Kneitz, S., Heinze, K.G., & Gessler, M.Loss or oncogenic mutation of DROSHA impairs kidney development and function, but is not sufficient for Wilms tumor formationInternational Journal of Cancer, 144(6): 1391–1400.
  • [ DOI ]
• 
  Lu, Y., Boswell, M., Boswell, W., Kneitz, S., Klotz, B., Savage, M., Salinas, R., Marks, R., Regneri, J., Postlethwait, J., Warren, W.C., Schartl, M., & Walter, R.Gene expression variation and parental allele inheritance in a Xiphophorus interspecies hybridization modelPLOS Genetics, 14(12): 1–16.
  • [ Abstract ]
  • [ DOI ]
  Understanding the genetic mechanisms underlying segregation of phenotypic variation through successive generations is important for understanding physiological changes and disease risk. Tracing the etiology of variation in gene expression enables identification of genetic interactions, and may uncover molecular mechanisms leading to the phenotypic expression of a trait, especially when utilizing model organisms that have well-defined genetic lineages. There are a plethora of studies that describe relationships between gene expression and genotype, however, the idea that global variations in gene expression are also controlled by genotype remains novel. Despite the identification of loci that control gene expression variation, the global understanding of how genome constitution affects trait variability is unknown. To study this question, we utilized Xiphophorus fish of different, but tractable genetic backgrounds (inbred, F1 interspecies hybrids, and backcross hybrid progeny), and measured each individual’s gene expression concurrent with the degrees of inter-individual expression variation. We found, (a) F1 interspecies hybrids exhibited less variability than inbred animals, indicting gene expression variation is not affected by the fraction of heterozygous loci within an individual genome, and (b), that mixing genotypes in backcross populations led to higher levels of gene expression variability, supporting the idea that expression variability is caused by heterogeneity of genotypes of cis or trans loci. In conclusion, heterogeneity of genotype, introduced by inheritance of different alleles, accounts for the largest effects on global phenotypical variability.
• 
  Warren, W.C., Garc\’i}a-P{\’e}rez, R., Xu, S., Lampert, K.P., Chalopin, D., St\"o}ck, M., Loewe, L., Lu, Y., Kuderna, L., Minx, P., Montague, M.J., Tomlinson, C., Hillier, L.W., Murphy, D.N., Wang, J., Wang, Z., Garcia, C.M., Thomas, G.C.W., Volff, J.-N., et al.Clonal polymorphism and high heterozygosity in the celibate genome of the Amazon mollyNature Ecology \& Evolution, 2(4): 669–679.
  • [ Abstract ]
  • [ DOI ]
  The extreme rarity of asexual vertebrates in nature is generally explained by genomic decay due to absence of meiotic recombination, thus leading to extinction of such lineages. We explore features of a vertebrate asexual genome, the Amazon molly, Poecilia formosa, and find few signs of genetic degeneration but unique genetic variability and ongoing evolution. We uncovered a substantial clonal polymorphism and, as a conserved feature from its interspecific hybrid origin, a 10-fold higher heterozygosity than in the sexual parental species. These characteristics seem to be a principal reason for the unpredicted fitness of this asexual vertebrate. Our data suggest that asexual vertebrate lineages are scarce not because they are at a disadvantage, but because the genomic combinations required to bypass meiosis and to make up a functioning hybrid genome are rarely met in nature.

• 
  Maurus, K., Hufnagel, A., Geiger, F., Graf, S., Berking, C., Heinemann, A., Paschen, A., Kneitz, S., Stigloher, C., Geissinger, E., Otto, C., Bosserhoff, A., Schartl, M., & Meierjohann, S.The AP-1 transcription factor FOSL1 causes melanocyte reprogramming and transformationOncogene, 36(36): 5110–5121.
  • [ Abstract ]
  • [ DOI ]
  The MAPK pathway is activated in the majority of melanomas and is the target of therapeutic approaches. Under normal conditions, it initiates the so-called immediate early response, which encompasses the transient transcription of several genes belonging to the AP-1 transcription factor family. Under pathological conditions, such as continuous MAPK pathway overactivation due to oncogenic alterations occurring in melanoma, these genes are constitutively expressed. The consequences of a permanent expression of these genes are largely unknown. Here, we show that FOSL1 is the main immediate early AP-1 member induced by melanoma oncogenes. We first examined its role in established melanoma cells. We found that FOSL1 is involved in melanoma cell migration as well as cell proliferation and anoikis-independent growth, which is mediated by the gene product of its target gene HMGA1, encoding a multipotent chromatin modifier. As FOSL1 expression is increased in patient melanoma samples compared to nevi, we investigated the effect of enhanced FOSL1 expression on melanocytes. Intriguingly, we found that FOSL1 acts oncogenic and transforms melanocytes, enabling subcutaneous tumor growth in vivo. During the process of transformation, FOSL1 reprogrammed the melanocytes and downregulated MITF in a HMGA1-dependent manner. At the same time, AXL was upregulated, leading to a shift in the MITF/AXL balance. Furthermore, FOSL1 re-enforced pro-tumorigenic transcription factors MYC, E2F3 and AP-1. Together, this led to the enhancement of several growth-promoting processes, such as ribosome biogenesis, cellular detachment and pyrimidine metabolism. Overall, we demonstrate that FOSL1 is a novel reprogramming factor for melanocytes with potent tumor transformation potential.
• 
  Silva-Vilches, C., Pletinckx, K., Lohnert, M., Pavlovic, V., Ashour, D., John, V., Vendelova, E., Kneitz, S., Zhou, J., Chen, R., Reinheckel, T., Mueller, T.D., Bodem, J., & Lutz, M.B.Low doses of cholera toxin and its mediator cAMP induce CTLA-2 secretion by dendritic cells to enhance regulatory T cell conversionPLOS ONE, 12(7): 1–20.
  • [ Abstract ]
  • [ DOI ]
  Immature or semi-mature dendritic cells (DCs) represent tolerogenic maturation stages that can convert naive T cells into Foxp3+ induced regulatory T cells (iTreg). Here we found that murine bone marrow-derived DCs (BM-DCs) treated with cholera toxin (CT) matured by up-regulating MHC-II and costimulatory molecules using either high or low doses of CT (CThi, CTlo) or with cAMP, a known mediator CT signals. However, all three conditions also induced mRNA of both isoforms of the tolerogenic molecule cytotoxic T lymphocyte antigen 2 (CTLA-2α and CTLA-2β). Only DCs matured under CThi conditions secreted IL-1β, IL-6 and IL-23 leading to the instruction of Th17 cell polarization. In contrast, CTlo- or cAMP-DCs resembled semi-mature DCs and enhanced TGF-β-dependent Foxp3+ iTreg conversion. iTreg conversion could be reduced using siRNA blocking of CTLA-2 and reversely, addition of recombinant CTLA-2α increased iTreg conversion in vitro. Injection of CTlo- or cAMP-DCs exerted MOG peptide-specific protective effects in experimental autoimmune encephalomyelitis (EAE) by inducing Foxp3+ Tregs and reducing Th17 responses. Together, we identified CTLA-2 production by DCs as a novel tolerogenic mediator of TGF-β-mediated iTreg induction in vitro and in vivo. The CT-induced and cAMP-mediated up-regulation of CTLA-2 also may point to a novel immune evasion mechanism of Vibrio cholerae.
• 
  Hupe, M., Li, M.X., Kneitz, S., Davydova, D., Yokota, C., Kele, J., Hot, B., Stenman, J.M., & Gessler, M.Gene expression profiles of brain endothelial cells during embryonic development at bulk and single-cell levelsScience Signaling, 10(487). https://doi.org/10.1126/scisignal.aag2476.
  • [ DOI ]
• 
  Lu, Y., Boswell, M., Boswell, W., Kneitz, S., Hausmann, M., Klotz, B., Regneri, J., Savage, M., Amores, A., Postlethwait, J., Warren, W., Schartl, M., & Walter, R.Molecular genetic analysis of the melanoma regulatory locus in Xiphophorus interspecies hybridsMolecular Carcinogenesis, 56(8): 1935–1944.
  • [ DOI ]

• 
  Nekova, T.S., Kneitz, S., Einsele, H., Bargou, R., & Stuhler, G.Silencing of CDK2, but not CDK1, separates mitogenic from anti-apoptotic signaling, sensitizing p53 defective cells for synthetic lethalityCell Cycle, 15(23): 3203–3209.
  • [ DOI ]
• 
  Endres, M., Kneitz, S., Orth, M.F., Perera, R.K., Zernecke, A., & Butt, E.Regulation of matrix metalloproteinases (MMPs) expression and secretion in MDA-MB-231 breast cancer cells by LIM and SH3 protein 1 (LASP1)Oncotarget, 7(39): 64244–64259.
  • [ DOI ]
• 
  Kneitz, S., Mishra, R.R., Chalopin, D., Postlethwait, J., Warren, W.C., Walter, R.B., & Schartl, M.Germ cell and tumor associated piRNAs in the medaka and Xiphophorus melanoma modelsBMC Genomics, 17(1): 357.
  • [ Abstract ]
  • [ DOI ]
  A growing number of studies report an abnormal expression of Piwi-interacting RNAs (piRNAs) and the piRNA processing enzyme Piwi in many cancers. Whether this finding is an epiphenomenon of the chaotic molecular biology of the fast dividing, neoplastically transformed cells or is functionally relevant to tumorigenesisis is difficult to discern at present. To better understand the role of piRNAs in cancer development small laboratory fish models can make a valuable contribution. However, little is known about piRNAs in somatic and neoplastic tissues of fish.

• 
  Weber, D., Heisig, J., Kneitz, S., Wolf, E., Eilers, M., & Gessler, M.Mechanisms of epigenetic and cell-type specific regulation of Hey target genes in ES cells and cardiomyocytesJournal of Molecular and Cellular Cardiology, 79: 79–88.
  • [ DOI ]
• 
  Kang, J.H., Manousaki, T., Franchini, P., Kneitz, S., Schartl, M., & Meyer, A.Transcriptomics of two evolutionary novelties: how to make a sperm‐transfer organ out of an anal fin and a sexually selected “sword” out of a caudal finEcology and Evolution, 5(4): 848–864.
  • [ DOI ]
• 
  Leikam, C., Hufnagel, A.L., Otto, C., Murphy, D.J., M\"u}hling, B., Kneitz, S., Nanda, I., Schmid, M., Wagner, T.U., Haferkamp, S., Br\"o}cker, E.-B., Schartl, M., & Meierjohann, S.In vitro evidence for senescent multinucleated melanocytes as a source for tumor-initiating cellsCell Death \& Disease, 6(4): e1711-e1711.
  • [ Abstract ]
  • [ DOI ]
  Oncogenic signaling in melanocytes results in oncogene-induced senescence (OIS), a stable cell-cycle arrest frequently characterized by a bi- or multinuclear phenotype that is considered as a barrier to cancer progression. However, the long-sustained conviction that senescence is a truly irreversible process has recently been challenged. Still, it is not known whether cells driven into OIS can progress to cancer and thereby pose a potential threat. Here, we show that prolonged expression of the melanoma oncogene N-RAS61K in pigment cells overcomes OIS by triggering the emergence of tumor-initiating mononucleated stem-like cells from senescent cells. This progeny is dedifferentiated, highly proliferative, anoikis-resistant and induces fast growing, metastatic tumors. Our data describe that differentiated cells, which are driven into senescence by an oncogene, use this senescence state as trigger for tumor transformation, giving rise to highly aggressive tumor-initiating cells. These observations provide the first experimental in vitro evidence for the evasion of OIS on the cellular level and ensuing transformation.
• 
  Simon, C.M., Rauskolb, S., Gunnersen, J.M., Holtmann, B., Drepper, C., Dombert, B., Braga, M., Wiese, S., Jablonka, S., P\"u}hringer, D., Zielasek, J., Hoeflich, A., Silani, V., Wolf, E., Kneitz, S., Sommer, C., Toyka, K.V., & Sendtner, M.Dysregulated IGFBP5 expression causes axon degeneration and motoneuron loss in diabetic neuropathyActa Neuropathologica, 130(3): 373–387.
  • [ Abstract ]
  • [ DOI ]
  Diabetic neuropathy (DNP), afflicting sensory and motor nerve fibers, is a major complication in diabetes. The underlying cellular mechanisms of axon degeneration are poorly understood. IGFBP5, an inhibitory binding protein for insulin-like growth factor 1 (IGF1) is highly up-regulated in nerve biopsies of patients with DNP. We investigated the pathogenic relevance of this finding in transgenic mice overexpressing IGFBP5 in motor axons and sensory nerve fibers. These mice develop motor axonopathy and sensory deficits similar to those seen in DNP. Motor axon degeneration was also observed in mice in which the IGF1 receptor (IGF1R) was conditionally depleted in motoneurons, indicating that reduced activity of IGF1 on IGF1R in motoneurons is responsible for the observed effect. These data provide evidence that elevated expression of IGFBP5 in diabetic nerves reduces the availability of IGF1 for IGF1R on motor axons, thus leading to progressive neurodegeneration. Inhibition of IGFBP5 could thus offer novel treatment strategies for DNP.
• 
  Wegert, J., Ishaque, N., Vardapour, R., Geörg, C., Gu, Z., Bieg, M., Ziegler, B., Bausenwein, S., Nourkami, N., Ludwig, N., Keller, A., Grimm, C., Kneitz, S., Williams, R., Chagtai, T., Pritchard-Jones, K., van Sluis, P., Volckmann, R., Koster, J., et al.Mutations in the SIX1/2 Pathway and the DROSHA/DGCR8 miRNA Microprocessor Complex Underlie High-Risk Blastemal Type Wilms TumorsCancer Cell, 27(2): 298–311.
  • [ DOI ]

• 
  Vergho, D.C., Kneitz, S., Kalogirou, C., Burger, M., Krebs, M., Rosenwald, A., Spahn, M., Löser, A., Kocot, A., Riedmiller, H., & Kneitz, B.Impact of miR-21, miR-126 and miR-221 as Prognostic Factors of Clear Cell Renal Cell Carcinoma with Tumor Thrombus of the Inferior Vena CavaPLOS ONE, 9(10): 1–11.
  • [ Abstract ]
  • [ DOI ]
  Clear cell renal cell carcinoma (ccRCC) characterized by a tumor thrombus (TT) extending into the inferior vena cava (IVC) generally indicates poor prognosis. Nevertheless, the risk for tumor recurrence after nephrectomy and thrombectomy varies. An applicable and accurate prediction system to select ccRCC patients with TT of the IVC (ccRCC/TT) at high risk after nephrectomy is urgently needed, but has not been established up to now. To our knowledge, a possible role of microRNAs (miRs) for the development of ccRCC/TT or their impact as prognostic markers in ccRCC/TT has not been explored yet. Therefore, we analyzed the expression of the previously described onco-miRs miR-200c, miR-210, miR-126, miR-221, let-7b, miR-21, miR-143 and miR-141 in a study collective of 74 ccRCC patients. Using the expression profiles of these eight miRs we developed classification systems that accurately differentiate ccRCC from non-cancerous renal tissue and ccRCC/TT from tumors without TT. In the subgroup of 37 ccRCC/TT cases we found that miR-21, miR-126, and miR-221 predicted cancer related death (CRD) accurately and independently from other clinico-pathological features. Furthermore, a combined risk score based on the expression of miR-21, miR-126 and miR-221 was developed and showed high sensitivity and specificity to predict cancer specific survival (CSS) in ccRCC/TT. Using the combined risk score we were able to classify ccRCC/TT patients correctly into high and low risk cases. The risk stratification by the combined risk score (CRS) will benefit from further cohort validation and might have potential for clinical application as a molecular prediction system to identify high- risk ccRCC/TT patients.
• 
  Saal, L., Briese, M., Kneitz, S., Glinka, M., & Sendtner, M.Subcellular transcriptome alterations in a cell culture model of spinal muscular atrophy point to widespread defects in axonal growth and presynaptic differentiationRNA, 20(11): 1789–1802.
  • [ DOI ]
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  Mishra, R.R., Kneitz, S., & Schartl, M.Comparative analysis of melanoma deregulated miRNAs in the medaka and Xiphophorus pigment cell cancer modelsComparative Biochemistry and Physiology Part C: Toxicology &Amp; Pharmacology, 163: 64–76.
  • [ DOI ]
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  Nekova, T.S., Kneitz, S., Einsele, H., & Stuhler, G.Silencing of Dicer1 temporally separates pro- and anti-apoptotic signaling and confers susceptibility to chemotherapy in p53 mutated cellsCell Cycle, 13(14): 2192–2198.
  • [ DOI ]
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  Morton, C.O., Fliesser, M., Dittrich, M., Mueller, T., Bauer, R., Kneitz, S., Hope, W., Rogers, T.R., Einsele, H., & Loeffler, J.Gene Expression Profiles of Human Dendritic Cells Interacting with Aspergillus fumigatus in a Bilayer Model of the Alveolar Epithelium/Endothelium InterfacePLOS ONE, 9(5): 1–12.
  • [ Abstract ]
  • [ DOI ]
  The initial stages of the interaction between the host and Aspergillus fumigatus at the alveolar surface of the human lung are critical in the establishment of aspergillosis. Using an in vitro bilayer model of the alveolus, including both the epithelium (human lung adenocarcinoma epithelial cell line, A549) and endothelium (human pulmonary artery epithelial cells, HPAEC) on transwell membranes, it was possible to closely replicate the in vivo conditions. Two distinct sub-groups of dendritic cells (DC), monocyte-derived DC (moDC) and myeloid DC (mDC), were included in the model to examine immune responses to fungal infection at the alveolar surface. RNA in high quantity and quality was extracted from the cell layers on the transwell membrane to allow gene expression analysis using tailored custom-made microarrays, containing probes for 117 immune-relevant genes. This microarray data indicated minimal induction of immune gene expression in A549 alveolar epithelial cells in response to germ tubes of A. fumigatus. In contrast, the addition of DC to the system greatly increased the number of differentially expressed immune genes. moDC exhibited increased expression of genes including CLEC7A, CD209 and CCL18 in the absence of A. fumigatus compared to mDC. In the presence of A. fumigatus, both DC subgroups exhibited up-regulation of genes identified in previous studies as being associated with the exposure of DC to A. fumigatus and exhibiting chemotactic properties for neutrophils, including CXCL2, CXCL5, CCL20, and IL1B. This model closely approximated the human alveolus allowing for an analysis of the host pathogen interface that complements existing animal models of IA.
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  Kneitz, B., Krebs, M., Kalogirou, C., Schubert, M., Joniau, S., van Poppel, H., Lerut, E., Kneitz, S., Scholz, C.J., Ströbel, P., Gessler, M., Riedmiller, H., & Spahn, M.Survival in Patients with High-Risk Prostate Cancer Is Predicted by miR-221, Which Regulates Proliferation, Apoptosis, and Invasion of Prostate Cancer Cells by Inhibiting IRF2 and SOCS3Cancer Research, 74(9): 2591–2603.
  • [ DOI ]
• 
  Leikam, C., Hufnagel, A., Walz, S., Kneitz, S., Fekete, A., M\"u}ller, M.J., Eilers, M., Schartl, M., & Meierjohann, S.Cystathionase mediates senescence evasion in melanocytes and melanoma cellsOncogene, 33(6): 771–782.
  • [ Abstract ]
  • [ DOI ]
  The development of malignant melanoma is a highly complex process, which is still poorly understood. A majority of human melanomas are found to express a few oncogenic proteins, such as mutant RAS and BRAF variants. However, these oncogenes are also found in nevi, and it is now a well-accepted fact that their expression alone leads to senescence. This renders the understanding of senescence escape mechanisms an important point to understand tumor development. Here, we approached the question of senescence evasion by expressing the transcription factor v-myc myelocytomatosis viral oncogene homolog (c-MYC), which is known to act synergistically with many oncogenes, in melanocytes. We observed that MYC drives the evasion of reactive-oxygen stress-induced melanocyte senescence, caused by activated receptor tyrosine kinase signaling. Conversely, MIZ1, the growth suppressing interaction partner of MYC, is involved in mediating melanocyte senescence. Both, MYC overexpression and Miz1 knockdown led to a strong reduction of endogenous reactive-oxygen species (ROS), DNA damage and senescence. We identified the cystathionase (CTH) gene product as mediator of the ROS-related MYC and MIZ1 effects. Blocking CTH enzymatic activity in MYC-overexpressing and Miz1 knockdown cells increased intracellular stress and senescence. Importantly, pharmacological inhibition of CTH in human melanoma cells also reconstituted senescence in the majority of cell lines, and CTH knockdown reduced tumorigenic effects such as proliferation, H2O2 resistance and soft agar growth. Thus, we identified CTH as new MYC target gene with an important function in senescence evasion.
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  Vergho, D., Kneitz, S., Rosenwald, A., Scherer, C., Spahn, M., Burger, M., Riedmiller, H., & Kneitz, B.Combination of expression levels of miR-21 and miR-126 is associated with cancer-specific survival in clear-cell renal cell carcinomaBMC Cancer, 14(1): 25.
  • [ Abstract ]
  • [ DOI ]
  Renal cell carcinoma (RCC) is marked by high mortality rate. To date, no robust risk stratification by clinical or molecular prognosticators of cancer-specific survival (CSS) has been established for early stages. Transcriptional profiling of small non-coding RNA gene products (miRNAs) seems promising for prognostic stratification. The expression of miR-21 and miR-126 was analysed in a large cohort of RCC patients; a combined risk score (CRS)-model was constructed based on expression levels of both miRNAs.

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  Gohlke, J., Scholz, C.-J., Kneitz, S., Weber, D., Fuchs, J., Hedrich, R., & Deeken, R.DNA Methylation Mediated Control of Gene Expression Is Critical for Development of Crown Gall TumorsPLOS Genetics, 9(2): 1–12.
  • [ Abstract ]
  • [ DOI ]
  Crown gall tumors develop after integration of the T-DNA of virulent Agrobacterium tumefaciens strains into the plant genome. Expression of the T-DNA–encoded oncogenes triggers proliferation and differentiation of transformed plant cells. Crown gall development is known to be accompanied by global changes in transcription, metabolite levels, and physiological processes. High levels of abscisic acid (ABA) in crown galls regulate expression of drought stress responsive genes and mediate drought stress acclimation, which is essential for wild-type-like tumor growth. An impact of epigenetic processes such as DNA methylation on crown gall development has been suggested; however, it has not yet been investigated comprehensively. In this study, the methylation pattern of Arabidopsis thaliana crown galls was analyzed on a genome-wide scale as well as at the single gene level. Bisulfite sequencing analysis revealed that the oncogenes Ipt, IaaH, and IaaM were unmethylated in crown galls. Nevertheless, the oncogenes were susceptible to siRNA–mediated methylation, which inhibited their expression and subsequently crown gall growth. Genome arrays, hybridized with methylated DNA obtained by immunoprecipitation, revealed a globally hypermethylated crown gall genome, while promoters were rather hypomethylated. Mutants with reduced non-CG methylation developed larger tumors than the wild-type controls, indicating that hypermethylation inhibits plant tumor growth. The differential methylation pattern of crown galls and the stem tissue from which they originate correlated with transcriptional changes. Genes known to be transcriptionally inhibited by ABA and methylated in crown galls became promoter methylated upon treatment of A. thaliana with ABA. This suggests that the high ABA levels in crown galls may mediate DNA methylation and regulate expression of genes involved in drought stress protection. In summary, our studies provide evidence that epigenetic processes regulate gene expression, physiological processes, and the development of crown gall tumors.
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  Huang, B., Belharazem, D., Li, L., Kneitz, S., Schnabel, P., Rieker, R., Körner, D., Nix, W., Schalke, B., Müller-Hermelink, H.K., Ott, G., Rosenwald, A., Ströbel, P., & Marx, A.Anti-Apoptotic Signature in Thymic Squamous Cell Carcinomas – Functional Relevance of Anti-Apoptotic BIRC3 Expression in the Thymic Carcinoma Cell Line 1889cFrontiers in Oncology, Volume 3 - 2013. https://doi.org/10.3389/fonc.2013.00316.
  • [ Abstract ]
  • [ DOI ]
  The molecular pathogenesis of thymomas and thymic carcinomas (TCs) is poorly understood and results of adjuvant therapy are unsatisfactory in case of metastatic disease and tumor recurrence. For these clinical settings, novel therapeutic strategies are urgently needed. Recently, limited sequencing efforts revealed that a broad spectrum of genes that play key roles in various common cancers are rarely affected in thymomas and thymic carcinomas, suggesting that other oncogenic principles might be important. This made us re-analyze historic expression data obtained in a spectrum of thymomas and thymic squamous cell carcinomas (TSCC) with a custom made cDNA microarray. By cluster analysis, different anti-apoptotic signatures were detected in type B3 thymoma and TSCC, including overexpression of BIRC3 in TSCCs. This was confirmed by qRT-PCR in the original and an independent validation set of tumors. In contrast to several other cancer cell lines, the BIRC3-positive TSCC cell line, 1889c showed spontaneous apoptosis after BIRC3 knock-down. Targeting apoptosis genes is worth testing as therapeutic principle in TSCC.
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  Bauer, H., Ache, P., Lautner, S., Fromm, J., Hartung, W., Al-Rasheid, K., Sonnewald, S., Sonnewald, U., Kneitz, S., Lachmann, N., Mendel, R., Bittner, F., Hetherington, A., & Hedrich, R.The Stomatal Response to Reduced Relative Humidity Requires Guard Cell-Autonomous ABA SynthesisCurrent Biology, 23(1): 53–57.
  • [ DOI ]
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  Riedel, A., Mofolo, B., Avota, E., Schneider-Schaulies, S., Meintjes, A., Mulder, N., & Kneitz, S.Accumulation of Splice Variants and Transcripts in Response to PI3K Inhibition in T CellsPLOS ONE, 8(2): 1–12.
  • [ Abstract ]
  • [ DOI ]
  Background Measles virus (MV) causes T cell suppression by interference with phosphatidylinositol-3-kinase (PI3K) activation. We previously found that this interference affected the activity of splice regulatory proteins and a T cell inhibitory protein isoform was produced from an alternatively spliced pre-mRNA. Hypothesis Differentially regulated and alternatively splice variant transcripts accumulating in response to PI3K abrogation in T cells potentially encode proteins involved in T cell silencing. Methods To test this hypothesis at the cellular level, we performed a Human Exon 1.0 ST Array on RNAs isolated from T cells stimulated only or stimulated after PI3K inhibition. We developed a simple algorithm based on a splicing index to detect genes that undergo alternative splicing (AS) or are differentially regulated (RG) upon T cell suppression. Results Applying our algorithm to the data, 9% of the genes were assigned as AS, while only 3% were attributed to RG. Though there are overlaps, AS and RG genes differed with regard to functional regulation, and were found to be enriched in different functional groups. AS genes targeted extracellular matrix (ECM)-receptor interaction and focal adhesion pathways, while RG genes were mainly enriched in cytokine-receptor interaction and Jak-STAT. When combined, AS/RG dependent alterations targeted pathways essential for T cell receptor signaling, cytoskeletal dynamics and cell cycle entry. Conclusions PI3K abrogation interferes with key T cell activation processes through both differential expression and alternative splicing, which together actively contribute to T cell suppression.
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  Schubert, M., Spahn, M., Kneitz, S., Scholz, C.J., Joniau, S., Stroebel, P., Riedmiller, H., & Kneitz, B.Distinct microRNA Expression Profile in Prostate Cancer Patients with Early Clinical Failure and the Impact of let-7 as Prognostic Marker in High-Risk Prostate CancerPLOS ONE, 8(6): 1–14.
  • [ Abstract ]
  • [ DOI ]
  Background The identification of additional prognostic markers to improve risk stratification and to avoid overtreatment is one of the most urgent clinical needs in prostate cancer (PCa). MicroRNAs, being important regulators of gene expression, are promising biomarkers in various cancer entities, though the impact as prognostic predictors in PCa is poorly understood. The aim of this study was to identify specific miRNAs as potential prognostic markers in high-risk PCa and to validate their clinical impact. Methodology and Principal Findings We performed miRNA-microarray analysis in a high-risk PCa study group selected by their clinical outcome (clinical progression free survival (CPFS) vs. clinical failure (CF)). We identified seven candidate miRNAs (let-7a/b/c, miR-515-3p/5p, -181b, -146b, and -361) that showed differential expression between both groups. Further qRT-PCR analysis revealed down-regulation of members of the let-7 family in the majority of a large, well-characterized high-risk PCa cohort (n = 98). Expression of let-7a/b/and -c was correlated to clinical outcome parameters of this group. While let-7a showed no association or correlation with clinical relevant data, let-7b and let-7c were associated with CF in PCa patients and functioned partially as independent prognostic marker. Validation of the data using an independent high-risk study cohort revealed that let-7b, but not let-7c, has impact as an independent prognostic marker for BCR and CF. Furthermore, we identified HMGA1, a non-histone protein, as a new target of let-7b and found correlation of let-7b down-regulation with HMGA1 over-expression in primary PCa samples. Conclusion Our findings define a distinct miRNA expression profile in PCa cases with early CF and identified let-7b as prognostic biomarker in high-risk PCa. This study highlights the importance of let-7b as tumor suppressor miRNA in high-risk PCa and presents a basis to improve individual therapy for high-risk PCa patients.
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  Weißflog, L., Scholz, C.-J., Jacob, C.P., Nguyen, T.T., Zamzow, K., Groß-Lesch, S., Renner, T.J., Romanos, M., Rujescu, D., Walitza, S., Kneitz, S., Lesch, K.-P., & Reif, A.KCNIP4 as a candidate gene for personality disorders and adult ADHDEuropean Neuropsychopharmacology, 23(6): 436–447.
  • [ DOI ]
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  Jazbutyte, V., Fiedler, J., Kneitz, S., Galuppo, P., Just, A., Holzmann, A., Bauersachs, J., & Thum, T.MicroRNA-22 increases senescence and activates cardiac fibroblasts in the aging heartAGE, 35(3): 747–762.
  • [ Abstract ]
  • [ DOI ]
  MicroRNAs (miRs) are small non- coding RNA molecules controlling a plethora of biological processes such as development, cellular survival and senescence. We here determined miRs differentially regulated during cardiac postnatal development and aging. Cardiac function, morphology and miR expression profiles were determined in neonatal, 4 weeks, 6 months and 19 months old normotensive male healthy C57/Bl6N mice. MiR-22 was most prominently upregulated during cardiac aging. Cardiac expression of its bioinformatically predicted target mimecan (osteoglycin, OGN) was gradually decreased with advanced age. Luciferase reporter assays validated mimecan as a bona fide miR-22 target. Both, miR-22 and its target mimecan were co- expressed in cardiac fibroblasts and smooth muscle cells. Functionally, miR-22 overexpression induced cellular senescence and promoted migratory activity of cardiac fibroblasts. Small interference RNA-mediated silencing of mimecan in cardiac fibroblasts mimicked the miR-22-mediated effects. Rescue experiments revealed that the effects of miR-22 on cardiac fibroblasts were only partially mediated by mimecan. In conclusion, miR-22 upregulation in the aging heart contributed at least partly to accelerated cardiac fibroblast senescence and increased migratory activity. Our results suggest an involvement of miR-22 in age-associated cardiac changes, such as cardiac fibrosis.
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  Bauer, H., Ache, P., Wohlfart, F., Al-Rasheid, K.A., Sonnewald, S., Sonnewald, U., Kneitz, S., Hetherington, A.M., & Hedrich, R.How Do Stomata Sense Reductions in Atmospheric Relative Humidity?Molecular Plant, 6(5): 1703–1706.
  • [ DOI ]
• 
  Kalogirou, C., Spahn, M., Krebs, M., Joniau, S., Lerut, E., Burger, M., Scholz, C.-J., Kneitz, S., Riedmiller, H., & Kneitz, B.MiR-205 Is Progressively Down-Regulated in Lymph Node Metastasis but Fails as a Prognostic Biomarker in High-Risk Prostate CancerInternational Journal of Molecular Sciences, 14(11): 21414–21434.
  • [ DOI ]

• 
  Langenhorst, D., Gogishvili, T., Ribechini, E., Kneitz, S., McPherson, K., Lutz, M.B., & Hünig, T.Sequential Induction of Effector Function, Tissue Migration and Cell Death during Polyclonal Activation of Mouse Regulatory T-CellsPLOS ONE, 7(11): 1–11.
  • [ Abstract ]
  • [ DOI ]
  The ability of CD4+Foxp3+ regulatory T-cells (Treg) to produce interleukin (IL)-10 is important for the limitation of inflammation at environmental interfaces like colon or lung. Under steady state conditions, however, few Tregs produce IL-10 ex vivo. To investigate the origin and fate of IL-10 producing Tregs we used a superagonistic mouse anti-mouse CD28 mAb (CD28SA) for polyclonal in vivo stimulation of Tregs, which not only led to their numeric expansion but also to a dramatic increase in IL-10 production. IL-10 secreting Tregs strongly upregulated surface receptors associated with suppressive function as compared to non-producing Tregs. Furthermore, polyclonally expanding Tregs shifted their migration receptor pattern after activation from a CCR7+CCR5− lymph node-seeking to a CCR7−CCR5+ inflammation-seeking phenotype, explaining the preferential recruitment of IL-10 producers to sites of ongoing immune responses. Finally, we observed that IL-10 producing Tregs from CD28SA stimulated mice were more apoptosis-prone in vitro than their IL-10 negative counterparts. These findings support a model where prolonged activation of Tregs results in terminal differentiation towards an IL-10 producing effector phenotype associated with a limited lifespan, implicating built-in termination of immunosuppression.
• 
  Frantz, S., Hofmann, U., Fraccarollo, D., Schäfer, A., Kranepuhl, S., Hagedorn, I., Nieswandt, B., Nahrendorf, M., Wagner, H., Bayer, B., Pachel, C., Schön, M.P., Kneitz, S., Bobinger, T., Weidemann, F., Ertl, G., & Bauersachs, J.Monocytes/macrophages prevent healing defects and left ventricular thrombus formation after myocardial infarctionThe FASEB Journal, 27(3): 871–881.
  • [ DOI ]
• 
  Arias-Loza, P.-A., Kreissl, M.C., Kneitz, S., Kaiser, F.R., Israel, I., Hu, K., Frantz, S., Bayer, B., Fritzemeier, K.-H., Korach, K.S., & Pelzer, T.The Estrogen Receptor-α Is Required and Sufficient to Maintain Physiological Glucose Uptake in the Mouse HeartHypertension, 60(4): 1070–1077.
  • [ DOI ]
• 
  Schartl, M., Kneitz, S., Wilde, B., Wagner, T., Henkel, C.V., Spaink, H.P., & Meierjohann, S.Conserved Expression Signatures between Medaka and Human Pigment Cell TumorsPLOS ONE, 7(5): 1–10.
  • [ Abstract ]
  • [ DOI ]
  Aberrations in gene expression are a hallmark of cancer cells. Differential tumor-specific transcript levels of single genes or whole sets of genes may be critical for the neoplastic phenotype and important for therapeutic considerations or useful as biomarkers. As an approach to filter out such relevant expression differences from the plethora of changes noted in global expression profiling studies, we searched for changes of gene expression levels that are conserved. Transcriptomes from massive parallel sequencing of different types of melanoma from medaka were generated and compared to microarray datasets from zebrafish and human melanoma. This revealed molecular conservation at various levels between fish models and human tumors providing a useful strategy for identifying expression signatures strongly associated with disease phenotypes and uncovering new melanoma molecules.
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  Heisig, J., Weber, D., Englberger, E., Winkler, A., Kneitz, S., Sung, W.-K., Wolf, E., Eilers, M., Wei, C.-L., & Gessler, M.Target Gene Analysis by Microarrays and Chromatin Immunoprecipitation Identifies HEY Proteins as Highly Redundant bHLH RepressorsPLOS Genetics, 8(5): 1–14.
  • [ Abstract ]
  • [ DOI ]
  HEY bHLH transcription factors have been shown to regulate multiple key steps in cardiovascular development. They can be induced by activated NOTCH receptors, but other upstream stimuli mediated by TGFß and BMP receptors may elicit a similar response. While the basic and helix-loop-helix domains exhibit strong similarity, large parts of the proteins are still unique and may serve divergent functions. The striking overlap of cardiac defects in HEY2 and combined HEY1/HEYL knockout mice suggested that all three HEY genes fulfill overlapping function in target cells. We therefore sought to identify target genes for HEY proteins by microarray expression and ChIPseq analyses in HEK293 cells, cardiomyocytes, and murine hearts. HEY proteins were found to modulate expression of their target gene to a rather limited extent, but with striking functional interchangeability between HEY factors. Chromatin immunoprecipitation revealed a much greater number of potential binding sites that again largely overlap between HEY factors. Binding sites are clustered in the proximal promoter region especially of transcriptional regulators or developmental control genes. Multiple lines of evidence suggest that HEY proteins primarily act as direct transcriptional repressors, while gene activation seems to be due to secondary or indirect effects. Mutagenesis of putative DNA binding residues supports the notion of direct DNA binding. While class B E-box sequences (CACGYG) clearly represent preferred target sequences, there must be additional and more loosely defined modes of DNA binding since many of the target promoters that are efficiently bound by HEY proteins do not contain an E-box motif. These data clearly establish the three HEY bHLH factors as highly redundant transcriptional repressors in vitro and in vivo, which explains the combinatorial action observed in different tissues with overlapping expression.
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  Schubert, M., Joniau, S., Gontero, P., Kneitz, S., Scholz, C.-J. rgen, Kneitz, B., Briganti, A., Karnes, R.J., Tombal, B., Walz, J., Hsu, C.-Y., Marchioro, G., Bader, P., Bangma, C., Frohneberg, D., Graefen, M., Schröder, F., van Cangh, P., van Poppel, H., et al.The Role of Adjuvant Hormonal Treatment after Surgery for Localized High-Risk Prostate Cancer: Results of a Matched Multiinstitutional AnalysisAdvances in Urology, 2012: 1–6.
  • [ DOI ]

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  Fraccarollo, D., Berger, S., Galuppo, P., Kneitz, S., Hein, L., Schütz, G., Frantz, S., Ertl, G., & Bauersachs, J.Deletion of Cardiomyocyte Mineralocorticoid Receptor Ameliorates Adverse Remodeling After Myocardial InfarctionCirculation, 123(4): 400–408.
  • [ DOI ]
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  Beyrich, C., Löffler, J., Kobsar, A., Speer, C.P., Kneitz, S., & Eigenthaler, M.Infection of Human Coronary Artery Endothelial Cells by Group B Streptococcus Contributes to Dysregulation of Apoptosis, Hemostasis, and Innate Immune ResponsesMediators of Inflammation, 2011: 1–8.
  • [ DOI ]
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  Seher, A., Joachim, N., Mueller, T.D., Kneitz, S., Gebhardt, S., Meyer ter Vehn, T., Schlunck, G., & Sebald, W.Gene expression profiling of connective tissue growth factor (CTGF) stimulated primary human tenon fibroblasts reveals an inflammatory and wound healing response in vitroMol Vis, 8(17): 53–62.
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  Morton, C.O., Varga, J.J., Hornbach, A., Mezger, M., Sennefelder, H., Kneitz, S., Kurzai, O., Krappmann, S., Einsele, H., Nierman, W.C., Rogers, T.R., & Loeffler, J.The Temporal Dynamics of Differential Gene Expression in Aspergillus fumigatus Interacting with Human Immature Dendritic Cells In VitroPLOS ONE, 6(1): 1–18.
  • [ Abstract ]
  • [ DOI ]
  Dendritic cells (DC) are the most important antigen presenting cells and play a pivotal role in host immunity to infectious agents by acting as a bridge between the innate and adaptive immune systems. Monocyte-derived immature DCs (iDC) were infected with viable resting conidia of Aspergillus fumigatus (Af293) for 12 hours at an MOI of 5; cells were sampled every three hours. RNA was extracted from both organisms at each time point and hybridised to microarrays. iDC cell death increased at 6 h in the presence of A. fumigatus which coincided with fungal germ tube emergence; >80% of conidia were associated with iDC. Over the time course A. fumigatus differentially regulated 210 genes, FunCat analysis indicated significant up-regulation of genes involved in fermentation, drug transport, pathogenesis and response to oxidative stress. Genes related to cytotoxicity were differentially regulated but the gliotoxin biosynthesis genes were down regulated over the time course, while Aspf1 was up-regulated at 9 h and 12 h. There was an up-regulation of genes in the subtelomeric regions of the genome as the interaction progressed. The genes up-regulated by iDC in the presence of A. fumigatus indicated that they were producing a pro-inflammatory response which was consistent with previous transcriptome studies of iDC interacting with A. fumigatus germ tubes. This study shows that A. fumigatus adapts to phagocytosis by iDCs by utilising genes that allow it to survive the interaction rather than just up-regulation of specific virulence genes.
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  Wegert, J., Bausenwein, S., Kneitz, S., Roth, S., Graf, N., Geissinger, E., & Gessler, M.Retinoic acid pathway activity in wilms tumors and characterization of biological responses in vitroMolecular Cancer, 10(1): 136.
  • [ Abstract ]
  • [ DOI ]
  Wilms tumor (WT) is one of the most common malignancies in childhood. With current therapy protocols up to 90\% of patients can be cured, but there is still a need to improve therapy for patients with aggressive WT and to reduce treatment intensity where possible. Prior data suggested a deregulation of the retinoic acid (RA) signaling pathway in high-risk WT, but its mode of action remained unclear.
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  Van den Hove, D., Jakob, S.B., Schraut, K.-G., Kenis, G., Schmitt, A.G., Kneitz, S., Scholz, C.-J., Wiescholleck, V., Ortega, G., Prickaerts, J., Steinbusch, H., & Lesch, K.-P.Differential Effects of Prenatal Stress in 5-Htt Deficient Mice: Towards Molecular Mechanisms of Gene × Environment InteractionsPLOS ONE, 6(8): 1–16.
  • [ Abstract ]
  • [ DOI ]
  Prenatal stress (PS) has been shown to influence the development of the fetal brain and to increase the risk for the development of psychiatric disorders in later life. Furthermore, the variation of human serotonin transporter (5-HTT, SLC6A4) gene was suggested to exert a modulating effect on the association between early life stress and the risk for depression. In the present study, we used a 5-Htt×PS paradigm to investigate whether the effects of PS are dependent on the 5-Htt genotype. For this purpose, the effects of PS on cognition, anxiety- and depression-related behavior were examined using a maternal restraint stress paradigm of PS in C57BL6 wild-type (WT) and heterozygous 5-Htt deficient (5-Htt +/−) mice. Additionally, in female offspring, a genome-wide hippocampal gene expression profiling was performed using the Affymetrix GeneChip® Mouse Genome 430 2.0 Array. 5-Htt +/− offspring showed enhanced memory performance and signs of reduced anxiety as compared to WT offspring. In contrast, exposure of 5-Htt +/− mice to PS was associated with increased depressive-like behavior, an effect that tended to be more pronounced in female offspring. Further, 5-Htt genotype, PS and their interaction differentially affected the expression of numerous genes and related pathways within the female hippocampus. Specifically, MAPK and neurotrophin signaling were regulated by both the 5-Htt +/− genotype and PS exposure, whereas cytokine and Wnt signaling were affected in a 5-Htt genotype×PS manner, indicating a gene×environment interaction at the molecular level. In conclusion, our data suggest that although the 5-Htt +/− genotype shows clear adaptive capacity, 5-Htt +/− mice –particularly females– at the same time appear to be more vulnerable to developmental stress exposure when compared to WT offspring. Moreover, hippocampal gene expression profiles suggest that distinct molecular mechanisms mediate the behavioral effects of the 5-Htt genotype, PS exposure, and their interaction.
• 
  Pletinckx, K., Stijlemans, B., Pavlovic, V., Laube, R., Brandl, C., Kneitz, S., Beschin, A., De Baetselier, P., & Lutz, M.B.Similar inflammatory DC maturation signatures induced by TNF or Trypanosoma brucei antigens instruct default Th2‐cell responsesEuropean Journal of Immunology, 41(12): 3479–3494.
  • [ DOI ]
• 
  Bartl, J., Scholz, C.-J., Hinterberger, M., Jungwirth, S., Wichart, I., Rainer, M.K., Kneitz, S., Danielczyk, W., Tragl, K.H., Fischer, P., Riederer, P., & Gr\"u}nblatt, E.Disorder-specific effects of polymorphisms at opposing ends of the Insulin Degrading EnzymegeneBMC Medical Genetics, 12(1): 151.
  • [ Abstract ]
  • [ DOI ]
  Insulin-degrading enzyme (IDE) is the ubiquitously expressed enzyme responsible for insulin and amyloid beta (A$\beta$) degradation. IDE gene is located on chromosome region 10q23-q25 and exhibits a well-replicated peak of linkage with Type 2 diabetes mellitus (T2DM). Several genetic association studies examined IDE gene as a susceptibility gene for Alzheimer's disease (AD), however with controversial results.
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  Fiedler, J., Jazbutyte, V., Kirchmaier, B.C., Gupta, S.K., Lorenzen, J., Hartmann, D., Galuppo, P., Kneitz, S., Pena, J.T., Sohn-Lee, C., Loyer, X., Soutschek, J., Brand, T., Tuschl, T., Heineke, J., Martin, U., Schulte-Merker, S., Ertl, G., Engelhardt, S., et al.MicroRNA-24 Regulates Vascularity After Myocardial InfarctionCirculation, 124(6): 720–730.
  • [ DOI ]

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  Fleissner, F., Jazbutyte, V., Fiedler, J., Gupta, S.K., Yin, X., Xu, Q., Galuppo, P., Kneitz, S., Mayr, M., Ertl, G., Bauersachs, J., & Thum, T.Short Communication: Asymmetric Dimethylarginine Impairs Angiogenic Progenitor Cell Function in Patients With Coronary Artery Disease Through a MicroRNA-21–Dependent MechanismCirculation Research, 107(1): 138–143.
  • [ DOI ]
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  Scholz, C., Jacob, C.P., Buttenschon, H.N., Kittel‐Schneider, S., Boreatti‐Hümmer, A., Zimmer, M., Walter, U., Lesch, K., Mors, O., Kneitz, S., Deckert, J., & Reif, A.Functional variants of TSPAN8 are associated with bipolar disorder and schizophreniaAmerican Journal of Medical Genetics Part B: Neuropsychiatric Genetics, 153B(4): 967–972.
  • [ DOI ]
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  Spahn, M., Kneitz, S., Scholz, C., Stenger, N., Rüdiger, T., Ströbel, P., Riedmiller, H., & Kneitz, B.Expression of microRNA‐221 is progressively reduced in aggressive prostate cancer and metastasis and predicts clinical recurrenceInternational Journal of Cancer, 127(2): 394–403.
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  ENGELMANN, J.C., RAHMANN, S., WOLF, M., SCHULTZ, J., FRITZILAS, E., KNEITZ, S., DANDEKAR, T., & MÜLLER, T.Modelling cross‐hybridization on phylogenetic DNA microarrays increases the detection power of closely related speciesMolecular Ecology Resources, 9(1): 83–93.
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  Mezger, M., Kneitz, S., Wozniok, I., Kurzai, O., Einsele, H., & Loeffler, J.Proinflammatory Response of Immature Human Dendritic Cells is Mediated by Dectin‐1 after Exposure toAspergillus fumigatusGerm TubesThe Journal of Infectious Diseases, 197(6): 924–931.
  • [ DOI ]
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  Meisner, F., Scheller, C., Kneitz, S., Sopper, S., Neuen-Jacob, E., Riederer, P., Meulen, V. ter, Koutsilieri, E., & for the German Competence Network HIV/AIDS.Memantine Upregulates BDNF and Prevents Dopamine Deficits in SIV-Infected Macaques: A Novel Pharmacological Action of MemantineNeuropsychopharmacology, 33(9): 2228–2236.
  • [ Abstract ]
  • [ DOI ]
  N-methyl-D-aspartate (NMDA) receptor activation is involved in the pathogenetic cascades of neurodegenerative disorders including human immunodeficiency virus (HIV) dementia. Memantine, an uncompetitive NMDA receptor antagonist, which has been recently approved for the treatment of Alzheimer's disease, is being discussed as a potential adjunctive therapeutic substance for HIV dementia. We used simian immunodeficiency virus-infected rhesus macaques to assess the effects of memantine on brain dysfunction and brain pathology within 3–5 months after initial infection during early asymptomatic stage of disease. We had shown previously that within this time frame, marked changes were evident in the dopaminergic systems. Memantine was administered two weeks post infection, at peak viremia, in order to prevent early NMDA receptor activation due to immune mediators. We found that memantine prevented onset of dopamine deficits in the brains of SIV-infected macaques, without affecting early brain pathology or peripheral course of infection. Memantine specifically upregulated mRNA and protein expression of the neurotrophic factor brain-derived neurotrophic factor (BDNF), suggesting that the protective effect of memantine on dopamine function may be mechanistically remote from NMDA receptor antagonism. This novel pharmacological action of memantine may also be relevant for other neurodegenerative disorders and supports the involvement of neurotrophic factors in adult brain neuroprotection.
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  Fraccarollo, D., Galuppo, P., Schraut, S., Kneitz, S., van Rooijen, N., Ertl, G., & Bauersachs, J.Immediate Mineralocorticoid Receptor Blockade Improves Myocardial Infarct Healing by Modulation of the Inflammatory ResponseHypertension, 51(4): 905–914.
  • [ DOI ]
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  Schön, M., Wienrich, B.G., Kneitz, S., Sennefelder, H., Amschler, K., Vöhringer, V., Weber, O., Stiewe, T., Ziegelbauer, K., & Schön, M.P.KINK-1, a Novel Small-Molecule Inhibitor of IKKβ, and the Susceptibility of Melanoma Cells to Antitumoral TreatmentJNCI: Journal of the National Cancer Institute, 100(12): 862–875.
  • [ DOI ]

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  Thum, T., Galuppo, P., Wolf, C., Fiedler, J., Kneitz, S., van Laake, L.W., Doevendans, P.A., Mummery, C.L., Borlak, J., Haverich, A., Gross, C., Engelhardt, S., Ertl, G., & Bauersachs, J.MicroRNAs in the Human Heart: A Clue to Fetal Gene Reprogramming in Heart FailureCirculation, 116(3): 258–267.
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  Lukashova v.Zangen, I., Kneitz, S., Monoranu, C.-M., Rutkowski, S., Hinkes, B., Vince, G.H., Huang, B., & Roggendorf, W.Ependymoma gene expression profiles associated with histological subtype, proliferation, and patient survivalActa Neuropathologica, 113(3): 325–337.
  • [ Abstract ]
  • [ DOI ]
  Ependymomas are primary tumors of the central nervous system that typically originate from the walls of the cerebral ventricles or from the spinal canal. The pathogenesis of these tumors is poorly understood, and prognostic assessment based on histologic features and clinical parameters is difficult. The aim of this study was to investigate the molecular heterogeneity of ependymomas. We used cDNA microarrays and RT-PCR to examine gene expression in 47 ependymomas. We present results for five comparisons: (1) tumors from children and adults with poor versus favorable outcome, (2) tumors from children with poor versus favorable outcome, (3) tumors with high versus low proliferation indices, (4) subependymomas versus myxopapillary ependymomas, and (5) spinal versus intracranial ependymomas. For patients with an overall survival >10 years after diagnosis, we identified 27 genes associated with favorable prognosis. In contrast, overexpression of BNIP3, MRC1, EPHB3, GLIS3, CDK4, COL4A2, EBP, NRCAM, and CCNA1 genes in tumors with high proliferation indices was associated with a poor outcome. Thirty genes, including ETV6, YWHAE, TOP2A, TLR2, IRAK1, TIA1, and UFD1L were found to be highly expressed in subependymomas but not myxopapillary ependymomas. Also, 30 genes were differentially expressed in spinal versus intracranial ependymomas. There was no relationship between expression profiles and tumor grade, patient age, and patient gender. Our results provide insight into specific molecular events underlying ependymoma tumorigenesis and may contribute to more accurate diagnosis and prediction of clinical outcome.
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  Kneitz, S., Meisner, F., Sopper, S., Kaiser, F., Grünblatt, E., Scheller, C., Riederer, P., Meulen, V. ter, & Koutsilieri, E.Biostatistical analysis of gene microarrays reveals diverse expression clusters between macaque subspecies in brain SIV infectionIn Neuropsychiatric Disorders An Integrative Approach, 317–322 Vienna: Springer Vienna.
  • [ Abstract ]
  In this study we investigated differences in the gene expression profiling of the brains of rhesus macaques that were uninfected or infected with SIV in the asymptomatic stage or AIDS. The main aim was to use biostatistical methods to classify brain gene expression following SIV infection, without consideration of the biological significance of the individual genes. We also used data from animals treated with different pharmacological substances such as dopaminergic drags, N-methyl-D-aspartate (NMDA) antagonists or antioxidants during the early stage of infection as these animals exhibited an accelerated or attenuated neuropsychiatrie disease progression.

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  Muenzner, P., Rohde, M., Kneitz, S., & Hauck, C.R.CEACAM engagement by human pathogens enhances cell adhesion and counteracts bacteria-induced detachment of epithelial cellsThe Journal of Cell Biology, 170(5): 825–836.
  • [ DOI ]

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  Smolenski, A., Schultess, J., Danielewski, O., Garcia Arguinzonis, M.I., Thalheimer, P., Kneitz, S., Walter, U., & Lohmann, S.M.Quantitative analysis of the cardiac fibroblast transcriptome—implications for NO/cGMP signalingGenomics, 83(4): 577–587.
  • [ DOI ]

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  Zavadil, J., Bitzer, M., Liang, D., Yang, Y.-C., Massimi, A., Kneitz, S., Piek, E., & Böttinger, E.P.Genetic programs of epithelial cell plasticity directed by transforming growth factor-βProceedings of the National Academy of Sciences, 98(12): 6686–6691.
  • [ DOI ]

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  Park, J.H., Dixit, M.P., Onuchic, L.F., Wu, G., Goncharuk, A.N., Kneitz, S., Santarina, L.B., Hayashi, T., Avner, E.D., Guay-Woodford, L., Zerres, K., Germino, G.G., & Somlo, S.A 1-Mb BAC/PAC-Based Physical Map of the Autosomal Recessive Polycystic Kidney Disease Gene (PKHD1) Region on Chromosome 6Genomics, 57(2): 249–255.
  • [ DOI ]
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  Ruschenburg, I., Kneitz, S., Brinck, U., Korabiowska, M., Harms, H., & Droese, M.Myoepithelial sialadenitis versus low-grade non-Hodgkin’s lymphoma of the salivary gland in FNAB: is discrimination by means of an image processing system possible?In Vivo (Athens, Greece), 13(6): 515–518.

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  Kneitz, S., Ott, G., Albert, R., Müller-Hermelink, H.K., & Harms, H.Differentiation of low-grade non-Hodgkin’s lymphomas using paraffin sections by image processingCytometry, 34(2): 75–81.
  • [ Abstract ]
  • [ DOI ]
  Abstract In a previous study, we were able to demonstrate that the differentiation of low-grade non-Hodgkin's lymphomas (NHLs) using digital image analysis of touch imprints obtained from native tumor tissue is feasible. The availability of touch imprints in routine diagnostics, however, is restricted. Therefore, we extended our studies toward paraffin sections being used as routine material for histological diagnoses. To identify five types of NHL classified according to the Revised European American Lymphoma classification, paraffin sections (n = 53) of NHL and 9 reactive lymphoid tissues (RLTs) were scanned with a color-video-based microscope system and analyzed by digital image processing. A reliable division between benign and neoplastic lymphoproliferations was achieved. We were able to identify 78\% of RLTs as benign and 94\% of NHLs as neoplastic. The average probability of correct identification into the six subgroups was 66\%. In detail, 78\% of RLTs, 50\% of chronic lymphocytic lymphomas and MALT-type lymphomas, 72\% of mantle cell lymphomas, and 67\% of follicle center cell lymphoma were classified correctly. Although the method of subclassifying or identifying NHLs on the basis of a computer-mediated assay is still not usable in daily practice, we show that a reliable differentiation between reactive and neoplastic lymphoproliferative lesions can be achieved by analysis of paraffin sections with high-resolution image analysis and that it is possible to define nuclear structures by identifying subtypes of NHL. Cytometry (Comm. Clin. Cytometry) 34:75–81, 1998. © 1998 Wiley-Liss, Inc.

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  and Kneitz, S., Ott, G., Albert, Schindewolf, T., Müller-Hermelink, H.K., & Harms, H.Differentiation of low grade non-Hodgkin’s lymphoma by digital image processingAnalytical and Quantitative Cytology and Histology, 18(2): 121–128.
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  Albert, R., Müller, J.G., Kristen, P., Schindewolf, T., Kneitz, S., & Harms, H.New method of nuclear grading of tissue sections by means of digital image analysis with prognostic significance for node-negative breast cancer patientsCytometry, 24(2): 140–150.
  • [ Abstract ]
  • [ DOI ]
  Abstract To optimize treatment of the individual patient with node-negative breast cancer, objective, reproducible, and standardized prognostic criteria are required. A number of factors have been studied in recent years, but until now it has been possible to obtain information about the risk of recurrence only for some patients belonging to subgroups with special characteristics. We report the establishment of an image analysis method for nuclear grading as an attempt to solve this problem. In a retrospective analysis, we used routine hematoxylin and eosin-stained paraffin sections from 54 node-negative patients with surgery between 1980 and 1985. Cell scenes of primary tumors were scanned in a light microscope in successive focus positions to obtain three-dimensional information. After automatic image segmentation, nuclear features were calculated as input for a first binary classification tree to differentiate between tumor and nontumor cells. Tumor nuclei from patients with or without relapse were defined as high-risk or low-risk nuclei, respectively, and were separated with a second tree. Feature values of the measured tumor nuclei from each patient were examined with this second tree to analyze whether the majority of nuclei for each patient were classified as high-risk or low-risk nuclei. Correct classification rates in the two binary cell classification trees were 88.0\% and 83.8\%, respectively. In the learning sample of our study, all patients with a relapse had the majority of nuclei in the high-risk group, most with more than 80\%. Therefore, it seems to be possible to develop an image analytical risk profile system for nuclear grading to provide information on individual prognosis. © 1996 Wiley-Liss, Inc.