Selected Recent Publications

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Selected Recent Publications

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Zhuang, X., Wang, Q., Joost, S., Ferrena, A., Humphreys, D. T., Li, Z., Blum, M., Krause, K., Ding, S., Landais, Y., Zhan, Y., Zhao, Y., Chaligne, R., Lee, J. H., Carrasco, S. E., Bhanot, U. K., Koche, R. P., Bott, M. J., Katajisto, P., Soto-Feliciano, Y. M., Pisanic, T., Thomas, T., Zheng, D., Wong, E. S., & Tammela, T. (2025). Ageing limits stemness and tumorigenesis by reprogramming iron homeostasis. Nature, 637(8044), 184-194.

Pakula, A., El Nagar, S., Bayin, N. S., Christensen, J. B., Stephen, D. N., Reid, A. J., Koche, R., & Joyner, A. L. (2025). An increase in reactive oxygen species underlies neonatal cerebellum repair. bioRxiv. https://doi.org/10.1101/2024.10.14.618368

Nichols, A., Norman, R., Chen, Y., Choi, Y., Striepen, J., Salataj, E., Toufektchan, E., Koche, R., & Maciejowski, J. (2025). Mitotic transcription ensures ecDNA inheritance through chromosomal tethering. bioRxiv. https://doi.org/10.1101/2025.02.12.637945

Delamarre, A., Bailey, B., Yavid, J., Koche, R., Mohibullah, N., & Whitehouse, I. (2025). Chromatin architecture mapping by multiplex proximity tagging. bioRxiv. https://doi.org/10.1101/2024.11.12.623258

Hei Yu KK, Abou-Mrad Z, Törkenczy K, Schulze I, Gantchev J, Baquer G, Hopland K, Bander ED, Tosi U, Brennan C, Moss NS, Hamard PJ, Koche R, Lareau C, Agar NYR, Merghoub T, Tabar V (2025). A pathogenic subpopulation of human glioma associated macrophages linked to glioma progression. bioRxiv. https://doi: 10.1101/2025.02.12.637857.

Prescott NA, Biaco T, Mansisidor A, Bram Y, Rendleman J, Faulkner SC, Lemmon AA, Lim C, Tiersky R, Salataj E, Garcia-Martinez L, Borges RL, Morey L, Hamard PJ, Koche RP, Risca VI, Schwartz RE, David Y (2025). A nucleosome switch primes hepatitis B virus infection. Cell, Feb 16:S0092-8674(25)00102-3.

Brodeur MN, Dopeso H, Zhu Y, Longhini ALF, Gazzo A, Sun S, Koche RP, Qu R, Rosenberg L, Hamard PJ, Bykov Y, Green H, Gusain L, Chiappinelli KB, Ozsoy MA, Chui MH, Basili T, Gardner R, Walderich S, DeStanchina E, Greenbaum B, Gönen M, Vabret N, Weigelt B, Zamarin D (2024). Interferon response and epigenetic modulation by SMARCA4 mutations drive ovarian tumor immunogenicity. Sci Adv. Dec 6;10(49).

Tong X, Remsik J, Brook J, Petrova B, Xu L, Li MJ, Snyder J, Chabot K, Estrera R, Osei-Gyening I, Nobre AR, Wang H, Osman AM, Wong AYL, Sidharta M, Piedrafita-Ortiz S, Manoranjan B, Zhou T, Murali R, Hamard PJ, Koche R, He Y, Kanarek N, Boire A (2024). Retinoid X Receptor Signaling Mediates Cancer Cell Lipid Metabolism in the Leptomeninges.  bioRxiv. https://doi: 10.1101/2024.10.13.618083.

Wong EWP, Sahin M, Yang R, Lee U, Zhan YA, Misra R, Tomas F, Alomran N, Polyzos A, Lee CJ, Trieu T, Fundichely AM, Wiesner T, Rosowicz A, Cheng S, Liu C, Lallo M, Merghoub T, Hamard PJ, Koche R, Khurana E, Apostolou E, Zheng D, Chen Y, Leslie CS, Chi P (2024). TAD hierarchy restricts poised LTR activation and loss of TAD hierarchy promotes LTR co-option in cancer. bioRxiv.. https://doi: 10.1101/2024.05.31.596845.

Waarts, M. R., Mowla, S., Boileau, M., Martinez Benitez, A. R., Sango, J., Bagish, M., Fernández-Maestre, I., Shan, Y., Eisman, S. E., Park, Y. C., Wereski, M., Csete, I., O’Connor, K., Romero-Vega, A. C., Miles, L. A., Xiao, W., Wu, X., Koche, R. P., Armstrong, S. A., Shih, A. H., Papapetrou, E. P., Butler, J. M., Cai, S. F., Bowman, R. L., & Levine, R. L. (2024). CRISPR Dependency Screens in Primary Hematopoietic Stem Cells Identify KDM3B as a Genotype-specific Vulnerability in IDH2- and TET2-mutant Cells. Cancer Discov, 14(10), 1860-1878.

Tsanov, K. M., Barriga, F. M., Ho, Y. J., Alonso-Curbelo, D., Livshits, G., Koche, R. P., Baslan, T., Simon, J., Tian, S., Wuest, A. N., Luan, W., Wilkinson, J. E., Masilionis, I., Dimitrova, N., Iacobuzio-Donahue, C. A., Chaligné, R., Pe’er, D., Massagué, J., & Lowe, S. W. (2024). Metastatic site influences driver gene function in pancreatic cancer. bioRxiv. https://doi.org/10.1101/2024.03.17.585402

Tiedje, V., Vela, P. S., Yang, J. L., Untch, B. R., Boucai, L., Stonestrom, A. J., Costa, A. B., Expósito, S. F., Srivastava, A., Kerpelev, M., Greenberg, J., Wereski, M., Kulick, A., Chen, K., Qin, T., Im, S. Y., Krishnan, A., Martinez Benitez, A. R., Pluvinet, R., Sahin, M., Menghrajani, K., Krishnamoorthy, G. P., de Stanchina, E., Zehir, A., Satija, R., Knauf, J., Bowman, R. L., Esteller, M., Devlin, S., Berger, M. F., Koche, R. P., Fagin, J. A., & Levine, R. L. (2024). Targetable treatment resistance in thyroid cancer with clonal hematopoiesis. bioRxiv. https://doi.org/10.1101/2024.10.10.617685

Stöber, M. C., Chamorro González, R., Brückner, L., Conrad, T., Wittstruck, N., Szymansky, A., Eggert, A., Schulte, J. H., Koche, R. P., Henssen, A. G., Schwarz, R. F., & Haase, K. (2024). Intercellular extrachromosomal DNA copy-number heterogeneity drives neuroblastoma cell state diversity. Cell Rep, 43(9), 114711.

Redin, E., Sridhar, H., Zhan, Y. A., Pereira Mello, B., Zhong, H., Durani, V., Sabet, A., Manoj, P., Linkov, I., Qiu, J., Koche, R. P., de Stanchina, E., Astorkia, M., Betel, D., Quintanal-Villalonga, Á., & Rudin, C. M. (2024). SMARCA4 controls state plasticity in small cell lung cancer through regulation of neuroendocrine transcription factors and REST splicing. J Hematol Oncol, 17(1), 58.

Quintanal-Villalonga, A., Kawasaki, K., Redin, E., Uddin, F., Rakhade, S., Durani, V., Sabet, A., Shafer, M., Karthaus, W. R., Zaidi, S., Zhan, Y. A., Manoj, P., Sridhar, H., Kinyua, D., Zhong, H., Mello, B. P., Ciampricotti, M., Bhanot, U. K., Linkov, I., Qiu, J., Patel, R. A., Morrissey, C., Mehta, S., Barnes, J., Haffner, M. C., Socci, N. D., Koche, R. P., de Stanchina, E., Molina-Pinelo, S., Salehi, S., Yu, H. A., Chan, J. M., & Rudin, C. M. (2024). CDC7 inhibition impairs neuroendocrine transformation in lung and prostate tumors through MYC degradation. Signal Transduct Target Ther, 9(1), 189.

Lee, J. H., Sánchez-Rivera, F. J., He, L., Basnet, H., Chen, F. X., Spina, E., Li, L., Torner, C., Chan, J. E., Yarlagadda, D. V. K., Park, J. S., Sussman, C., Rudin, C. M., Lowe, S. W., Tammela, T., Macias, M. J., Koche, R. P., & Massagué, J. (2024). TGF-β and RAS jointly unmask primed enhancers to drive metastasis. Cell, 187(22), 6182-6199.e6129.

Jain, N., Zhao, Z., Koche, R. P., Antelope, C., Gozlan, Y., Montalbano, A., Brocks, D., Lopez, M., Dobrin, A., Shi, Y., Gunset, G., Giavridis, T., & Sadelain, M. (2024). Disruption of SUV39H1-Mediated H3K9 Methylation Sustains CAR T-cell Function. Cancer Discov, 14(1), 142-157.

Glenn, R. A., Do, S. C., Guruvayurappan, K., Corrigan, E. K., Santini, L., Medina-Cano, D., Singer, S., Cho, H., Liu, J., Broman, K., Czechanski, A., Reinholdt, L., Koche, R., Furuta, Y., Kunz, M., & Vierbuchen, T. (2024). A pluripotent stem cell platform for in vitro systems genetics studies of mouse development. bioRxiv. https://doi.org/10.1101/2024.06.06.597758

Giurgiu, M., Wittstruck, N., Rodriguez-Fos, E., Chamorro González, R., Brückner, L., Krienelke-Szymansky, A., Helmsauer, K., Hartebrodt, A., Euskirchen, P., Koche, R. P., Haase, K., Reinert, K., & Henssen, A. G. (2024). Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil. Genome Res, 34(9), 1355-1364.

Dunbar, A. J., Bowman, R. L., Park, Y. C., O’Connor, K., Izzo, F., Myers, R. M., Karzai, A., Zaroogian, Z., Kim, W. J., Fernández-Maestre, I., Waarts, M. R., Nazir, A., Xiao, W., Codilupi, T., Brodsky, M., Farina, M., Cai, L., Cai, S. F., Wang, B., An, W., Yang, J. L., Mowla, S., Eisman, S. E., Hanasoge Somasundara, A. V., Glass, J. L., Mishra, T., Houston, R., Guzzardi, E., Martinez Benitez, A. R., Viny, A. D., Koche, R. P., Meyer, S. C., Landau, D. A., & Levine, R. L. (2024). Jak2V617F Reversible Activation Shows Its Essential Requirement in Myeloproliferative Neoplasms. Cancer Discov, 14(5), 737-751.

Codilupi, T., Szybinski, J., Arunasalam, S., Jungius, S., Dunbar, A. C., Stivala, S., Brkic, S., Albrecht, C., Vokalova, L., Yang, J. L., Buczak, K., Ghosh, N., Passweg, J. R., Rovo, A., Angelillo-Scherrer, A., Pankov, D., Dirnhofer, S., Levine, R. L., Koche, R., & Meyer, S. C. (2024). Development of Resistance to Type II JAK2 Inhibitors in MPN Depends on AXL Kinase and Is Targetable. Clin Cancer Res, 30(3), 586-599.

Ciceri, G., Baggiolini, A., Cho, H. S., Kshirsagar, M., Benito-Kwiecinski, S., Walsh, R. M., Aromolaran, K. A., Gonzalez-Hernandez, A. J., Munguba, H., Koo, S. Y., Xu, N., Sevilla, K. J., Goldstein, P. A., Levitz, J., Leslie, C. S., Koche, R. P., & Studer, L. (2024). An epigenetic barrier sets the timing of human neuronal maturation. Nature, 626(8000), 881-890.

Blawski, R., Vokshi, B. H., Guo, X., Kittane, S., Sallaku, M., Chen, W., Gjyzari, M., Cheung, T., Zhang, Y., Simpkins, C., Zhou, W., Kulick, A., Zhao, P., Wei, M., Shivashankar, P., Prioleau, T., Razavi, P., Koche, R., Rebecca, V. W., de Stanchina, E., Castel, P., Chan, H. M., Scaltriti, M., Cocco, E., Ji, H., Luo, M., & Toska, E. (2024). Methylation of the chromatin modifier KMT2D by SMYD2 contributes to therapeutic response in hormone-dependent breast cancer. Cell Rep, 43(5), 114174.

Bei, Y., Bramé, L., Kirchner, M., Fritsche-Guenther, R., Kunz, S., Bhattacharya, A., Rusu, M. C., Gürgen, D., Dubios, F. P. B., Köppke, J. K. C., Proba, J., Wittstruck, N., Sidorova, O. A., Chamorro González, R., Dorado Garcia, H., Brückner, L., Xu, R., Giurgiu, M., Rodriguez-Fos, E., Yu, Q., Spanjaard, B., Koche, R. P., Schmitt, C. A., Schulte, J. H., Eggert, A., Haase, K., Kirwan, J., Hagemann, A. I. H., Mertins, P., Dörr, J. R., & Henssen, A. G. (2024). Passenger Gene Coamplifications Create Collateral Therapeutic Vulnerabilities in Cancer. Cancer Discov, 14(3), 492-507.

Zhu, C., Soto-Feliciano, Y. M., Morris, J. P., Huang, C. H., Koche, R. P., Ho, Y. J., Banito, A., Chen, C. W., Shroff, A., Tian, S., Livshits, G., Chen, C. C., Fennell, M., Armstrong, S. A., Allis, C. D., Tschaharganeh, D. F., & Lowe, S. W. (2023). MLL3 regulates the CDKN2A tumor suppressor locus in liver cancer. Elife, 12.

Tagore, M., Hergenreder, E., Perlee, S. C., Cruz, N. M., Menocal, L., Suresh, S., Chan, E., Baron, M., Melendez, S., Dave, A., Chatila, W. K., Nsengimana, J., Koche, R. P., Hollmann, T. J., Ideker, T., Studer, L., Schietinger, A., & White, R. M. (2023). GABA Regulates Electrical Activity and Tumor Initiation in Melanoma. Cancer Discov, 13(10), 2270-2291.

Sun, Z., Lin, Y., Islam, M. T., Koche, R., Hedehus, L., Liu, D., Huang, C., Vierbuchen, T., Sawyers, C. L., & Helin, K. (2023). Chromatin regulation of transcriptional enhancers and cell fate by the Sotos syndrome gene NSD1. Mol Cell, 83(14), 2398-2416.e2312.

Schvartzman, J. M., Forsyth, G., Walch, H., Chatila, W., Taglialatela, A., Lee, B. J., Zhu, X., Gershik, S., Cimino, F. V., Santella, A., Menghrajani, K., Ciccia, A., Koche, R., Sánchez-Vega, F., Zha, S., & Thompson, C. B. (2023). Oncogenic IDH mutations increase heterochromatin-related replication stress without impacting homologous recombination. Mol Cell, 83(13), 2347-2356.e2348.

Sanghrajka, R. M., Koche, R., Medrano, H., El Nagar, S., Stephen, D. N., Lao, Z., Bayin, N. S., Ge, K., & Joyner, A. L. (2023). KMT2D suppresses Sonic hedgehog-driven medulloblastoma progression and metastasis. iScience, 26(10), 107831.

Rodriguez-Fos, E., Planas-Fèlix, M., Burkert, M., Puiggròs, M., Toedling, J., Thiessen, N., Blanc, E., Szymansky, A., Hertwig, F., Ishaque, N., Beule, D., Torrents, D., Eggert, A., Koche, R. P., Schwarz, R. F., Haase, K., Schulte, J. H., & Henssen, A. G. (2023). Mutational topography reflects clinical neuroblastoma heterogeneity. Cell Genom, 3(10), 100402.

Radzisheuskaya, A., Peña-Rømer, I., Lorenzini, E., Koche, R., Zhan, Y., Shliaha, P. V., Cooper, A. J., Fan, Z., Shlyueva, D., Johansen, J. V., Hendrickson, R. C., & Helin, K. (2023). An alternative NURF complex sustains acute myeloid leukemia by regulating the accessibility of insulator regions. Embo j, 42(24), e114221.

Quintanal-Villalonga, A., Durani, V., Sabet, A., Redin, E., Kawasaki, K., Shafer, M., Karthaus, W. R., Zaidi, S., Zhan, Y. A., Manoj, P., Sridhar, H., Shah, N. S., Chow, A., Bhanot, U. K., Linkov, I., Asher, M., Yu, H. A., Qiu, J., de Stanchina, E., Patel, R. A., Morrissey, C., Haffner, M. C., Koche, R. P., Sawyers, C. L., & Rudin, C. M. (2023). Exportin 1 inhibition prevents neuroendocrine transformation through SOX2 down-regulation in lung and prostate cancers. Sci Transl Med, 15(707), eadf7006.

Jain, N., Zhao, Z., Feucht, J., Koche, R., Iyer, A., Dobrin, A., Mansilla-Soto, J., Yang, J., Zhan, Y., Lopez, M., Gunset, G., & Sadelain, M. (2023). TET2 guards against unchecked BATF3-induced CAR T cell expansion. Nature, 615(7951), 315-322.

Falvo, D. J., Grimont, A., Zumbo, P., Fall, W. B., Yang, J. L., Osterhoudt, A., Pan, G., Rendeiro, A. F., Meng, Y., Wilkinson, J. E., Dündar, F., Elemento, O., Yantiss, R. K., Hissong, E., Koche, R., Betel, D., & Chandwani, R. (2023). A reversible epigenetic memory of inflammatory injury controls lineage plasticity and tumor initiation in the mouse pancreas. Dev Cell, 58(24), 2959-2973.e2957.

Dunbar, A. J., Kim, D., Lu, M., Farina, M., Bowman, R. L., Yang, J. L., Park, Y., Karzai, A., Xiao, W., Zaroogian, Z., O’Connor, K., Mowla, S., Gobbo, F., Verachi, P., Martelli, F., Sarli, G., Xia, L., Elmansy, N., Kleppe, M., Chen, Z., Xiao, Y., McGovern, E., Snyder, J., Krishnan, A., Hill, C., Cordner, K., Zouak, A., Salama, M. E., Yohai, J., Tucker, E., Chen, J., Zhou, J., McConnell, T., Migliaccio, A. R., Koche, R., Rampal, R., Fan, R., Levine, R. L., & Hoffman, R. (2023). CXCL8/CXCR2 signaling mediates bone marrow fibrosis and is a therapeutic target in myelofibrosis. Blood, 141(20), 2508-2519.

Chamorro González, R., Conrad, T., Stöber, M. C., Xu, R., Giurgiu, M., Rodriguez-Fos, E., Kasack, K., Brückner, L., van Leen, E., Helmsauer, K., Dorado Garcia, H., Stefanova, M. E., Hung, K. L., Bei, Y., Schmelz, K., Lodrini, M., Mundlos, S., Chang, H. Y., Deubzer, H. E., Sauer, S., Eggert, A., Schulte, J. H., Schwarz, R. F., Haase, K., Koche, R. P., & Henssen, A. G. (2023). Parallel sequencing of extrachromosomal circular DNAs and transcriptomes in single cancer cells. Nat Genet, 55(5), 880-890.

Burdziak, C., Alonso-Curbelo, D., Walle, T., Reyes, J., Barriga, F. M., Haviv, D., Xie, Y., Zhao, Z., Zhao, C. J., Chen, H. A., Chaudhary, O., Masilionis, I., Choo, Z. N., Gao, V., Luan, W., Wuest, A., Ho, Y. J., Wei, Y., Quail, D. F., Koche, R., Mazutis, L., Chaligné, R., Nawy, T., Lowe, S. W., & Pe’er, D. (2023). Epigenetic plasticity cooperates with cell-cell interactions to direct pancreatic tumorigenesis. Science, 380(6645), eadd5327.

Agustinus, A. S., Al-Rawi, D., Dameracharla, B., Raviram, R., Jones, B., Stransky, S., Scipioni, L., Luebeck, J., Di Bona, M., Norkunaite, D., Myers, R. M., Duran, M., Choi, S., Weigelt, B., Yomtoubian, S., McPherson, A., Toufektchan, E., Keuper, K., Mischel, P. S., Mittal, V., Shah, S. P., Maciejowski, J., Storchova, Z., Gratton, E., Ly, P., Landau, D., Bakhoum, M. F., Koche, R. P., Sidoli, S., Bafna, V., David, Y., & Bakhoum, S. F. (2023). Epigenetic dysregulation from chromosomal transit in micronuclei. Nature, 619(7968), 176-183.

Ogura, K., Elkrief, A., Bowman, A. S., Koche, R. P., de Stanchina, E., Benayed, R., Mauguen, A., Mattar, M. S., Khodos, I., Meyers, P. A., Healey, J. H., Tap, W. D., Hameed, M., Zehir, A., Shukla, N., Sawyers, C., Bose, R., Slotkin, E., & Ladanyi, M. (2022). Prospective Clinical Genomic Profiling of Ewing Sarcoma: ERF and FGFR1 Mutations as Recurrent Secondary Alterations of Potential Biologic and Therapeutic Relevance. JCO Precis Oncol, 6, e2200048.

Li, L., Kim, J. H., Lu, W., Williams, D. M., Kim, J., Cope, L., Rampal, R. K., Koche, R. P., Xian, L., Luo, L. Z., Vasiljevic, M., Matson, D. R., Zhao, Z. J., Rogers, O., Stubbs, M. C., Reddy, K., Romero, A. R., Psaila, B., Spivak, J. L., Moliterno, A. R., & Resar, L. M. S. (2022). HMGA1 chromatin regulators induce transcriptional networks involved in GATA2 and proliferation during MPN progression. Blood, 139(18), 2797-2815.

Li, B., An, W., Wang, H., Baslan, T., Mowla, S., Krishnan, A., Xiao, W., Koche, R. P., Liu, Y., Cai, S. F., Xiao, Z., Derkach, A., Iacobucci, I., Mullighan, C. G., Helin, K., Lowe, S. W., Levine, R. L., & Rampal, R. K. (2022). BMP2/SMAD pathway activation in JAK2/p53-mutant megakaryocyte/erythroid progenitors promotes leukemic transformation. Blood, 139(25), 3630-3646.

Asimomitis, G., Deslauriers, A. G., Kotini, A. G., Bernard, E., Esposito, D., Olszewska, M., Spyrou, N., Arango Ossa, J., Mortera-Blanco, T., Koche, R., Nannya, Y., Malcovati, L., Ogawa, S., Cazzola, M., Aaronson, S. A., Hellström-Lindberg, E., Papaemmanuil, E., & Papapetrou, E. P. (2022). Patient-specific MDS-RS iPSCs define the mis-spliced transcript repertoire and chromatin landscape of SF3B1-mutant HSPCs. Blood Adv, 6(10), 2992-3005.