Epigenetic Modifications and Their Functional Implications

Displaying 51 - 99 of 99CSV
Trauernicht, M., Rastogi, C., Manzo, S. G., Bussemaker, H. J., & van Steensel, B. (2023). Optimisation of TP53 reporters by systematic dissection of synthetic TP53 response elements. Nucleic Acids Research, 51(18), 9690–9702. https://doi.org/10.1093/nar/gkad718
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Li, A. M., He, B., Karagiannis, D., Li, Y., Jiang, H., Srinivasan, P., Ramirez, Y., Zhou, M.-N., Curtis, C., Gruber, J. J., Lu, C., Rankin, E. B., & Ye, J. (2023). Serine starvation silences estrogen receptor signaling through histone hypoacetylation. Proceedings of the National Academy of Sciences, 120(38). https://doi.org/10.1073/pnas.2302489120
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Abini-Agbomson, S., Gretarsson, K., Shih, R. M., Hsieh, L., Lou, T., De Ioannes, P., Vasilyev, N., Lee, R., Wang, M., Simon, M. D., Armache, J.-P., Nudler, E., Narlikar, G., Liu, S., Lu, C., & Armache, K.-J. (2023). Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1. Molecular Cell, 83(16), 2872-2883.e7. https://doi.org/10.1016/j.molcel.2023.07.020
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Thomas, J. F., Valencia-Sánchez, M. I., Tamburri, S., Gloor, S. L., Rustichelli, S., Godínez-López, V., De Ioannes, P., Lee, R., Abini-Agbomson, S., Gretarsson, K., Burg, J. M., Hickman, A. R., Sun, L., Gopinath, S., Taylor, H. F., Sun, Z.-W., Ezell, R. J., Vaidya, A., Meiners, M. J., … Armache, K.-J. (2023). Structural basis of histone H2A lysine 119 deubiquitination by Polycomb repressive deubiquitinase BAP1/ASXL1. Science Advances, 9(32). https://doi.org/10.1126/sciadv.adg9832
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Wang, E., Wang, M., Guo, L., Fullard, J. F., Micallef, C., Bendl, J., Song, W., Ming, C., Huang, Y., Li, Y., Yu, K., Peng, J., Bennett, D. A., De Jager, P. L., Roussos, P., Haroutunian, V., & Zhang, B. (2023). Genome‐wide methylomic regulation of multiscale gene networks in Alzheimer’s disease. Alzheimer’s & Dementia, 19(8), 3472–3495. Portico. https://doi.org/10.1002/alz.12969
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Chung, J., Sun, X., Schmidt, M. A., Song, Y. E., Grunin, M., Palmer, E. L., Bush, W. S., Naj, A. C., Rajabli, F., Hamilton‐Nelson, K. L., Zhang, X., Leung, Y. Y., Wang, L., Mayeux, R., Schellenberg, G. D., Vance, M. A., Haines, J. L., Farrer, L. A., Kunkle, B. W., & Martin, E. R. (2023). Variants near X‐Chromosome Genes NLGN4X and PTCHD1 are Significantly Associated with Alzheimer’s Disease Risk. Alzheimer’s & Dementia, 19(S1). Portico. https://doi.org/10.1002/alz.067117
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Columbia Affiliation
Morin, A., Thompson, E. E., Helling, B. A., Shorey-Kendrick, L. E., Faber, P., Gebretsadik, T., Bacharier, L. B., Kattan, M., O’Connor, G. T., Rivera-Spoljaric, K., Wood, R. A., Barnes, K. C., Mathias, R. A., Altman, M. C., Hansen, K., McEvoy, C. T., Spindel, E. R., Hartert, T., Jackson, D. J., … Ober, C. (2023). A functional genomics pipeline to identify high-value asthma and allergy CpGs in the human methylome. Journal of Allergy and Clinical Immunology, 151(6), 1609–1621. https://doi.org/10.1016/j.jaci.2022.12.828
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Frankel, E., Podder, A., Sharifi, M., Pillai, R., Belnap, N., Ramsey, K., Dodson, J., Venugopal, P., Brzezinski, M., Llaci, L., Gerald, B., Mills, G., Sanchez-Castillo, M., Balak, C. D., Szelinger, S., Jepsen, W. M., Siniard, A. L., Richholt, R., Naymik, M., … Rangasamy, S. (2023). Genetic and Protein Network Underlying the Convergence of Rett-Syndrome-like (RTT-L) Phenotype in Neurodevelopmental Disorders. Cells, 12(10), 1437. https://doi.org/10.3390/cells12101437
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Becerra, C. Y., Wells, R. K., Kunihiro, B. P., Lee, R. H., Umeda, L., Allan, N. P., Rubas, N. C., McCracken, T. A., Nunokawa, C. K. L., Lee, M.-H., Pidlaoan, F. G. S., Phankitnirondorn, K., Dye, C. K., Yamamoto, B. Y., Peres, R., Juarez, R., & Maunakea, A. K. (2023). Examining the immunoepigenetic-gut microbiome axis in the context of self-esteem among Native Hawaiians and other Pacific Islanders. Frontiers in Genetics, 14. https://doi.org/10.3389/fgene.2023.1125217
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Wang, Y.-C., Kelso, A. A., Karamafrooz, A., Chen, Y.-H., Chen, W.-K., Cheng, C.-T., Qi, Y., Gu, L., Malkas, L., Taglialatela, A., Kung, H.-J., Moldovan, G.-L., Ciccia, A., Stark, J. M., & Ann, D. K. (2023). Arginine shortage induces replication stress and confers genotoxic resistance by inhibiting histone H4 translation and promoting PCNA ubiquitination. Cell Reports, 42(4), 112296. https://doi.org/10.1016/j.celrep.2023.112296
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Vlasevska, S., Garcia-Ibanez, L., Duval, R., Holmes, A. B., Jahan, R., Cai, B., Kim, A., Mo, T., Basso, K., Soni, R. K., Bhagat, G., Dalla-Favera, R., & Pasqualucci, L. (2023). KMT2D acetylation by CREBBP reveals a cooperative functional interaction at enhancers in normal and malignant germinal center B cells. Proceedings of the National Academy of Sciences, 120(11). https://doi.org/10.1073/pnas.2218330120
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Liao, X., Kennel, P. J., Liu, B., Nash, T. R., Zhuang, R. Z., Godier-Furnemont, A. F., Xue, C., Lu, R., Colombo, P. C., Uriel, N., Reilly, M. P., Marx, S. O., Vunjak-Novakovic, G., & Topkara, V. K. (2023). Effect of mechanical unloading on genome-wide DNA methylation profile of the failing human heart. JCI Insight, 8(4). https://doi.org/10.1172/jci.insight.161788
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Fine, R. L., Mao, Y., Dinnen, R., Rosal, R. V., Raffo, A., Hochfeld, U., Senatus, P., Bruce, J. N., Nichols, G., Wang, H., Li, Y., & Brandt-Rauf, P. W. (2023). C-Terminal p53 Palindromic Tetrapeptide Restores Full Apoptotic Function to Mutant p53 Cancer Cells In Vitro and In Vivo. Biomedicines, 11(1), 137. https://doi.org/10.3390/biomedicines11010137
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Ding, L., Gao, L., Lee, H., & Goodman, J. (2023). 3050 – AN EPITRANSCRIPTOMIC PROGRAM DISTINGUISHES HEMATOPOIETIC STEM CELL NICHE GENERATION FROM MAINTENANCE. Experimental Hematology, 124, S75. https://doi.org/10.1016/j.exphem.2023.06.157
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Sturm, G., Monzel, A. S., Karan, K. R., Michelson, J., Ware, S. A., Cardenas, A., Lin, J., Bris, C., Santhanam, B., Murphy, M. P., Levine, M. E., Horvath, S., Belsky, D. W., Wang, S., Procaccio, V., Kaufman, B. A., Hirano, M., & Picard, M. (2022). A multi-omics longitudinal aging dataset in primary human fibroblasts with mitochondrial perturbations. Scientific Data, 9(1). https://doi.org/10.1038/s41597-022-01852-y
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Tanagala, K. K. K., Morin-Baxter, J., Carvajal, R., Cheema, M., Dubey, S., Nakagawa, H., Yoon, A., Cheng, Y.-S. L., Taylor, A., Nickerson, J., Mintz, A., & Momen-Heravi, F. (2022). SP140 inhibits STAT1 signaling, induces IFN-γ in tumor-associated macrophages, and is a predictive biomarker of immunotherapy response. Journal for ImmunoTherapy of Cancer, 10(12), e005088. https://doi.org/10.1136/jitc-2022-005088
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Filippone, M. G., Gaglio, D., Bonfanti, R., Tucci, F. A., Ceccacci, E., Pennisi, R., Bonanomi, M., Jodice, G., Tillhon, M., Montani, F., Bertalot, G., Freddi, S., Vecchi, M., Taglialatela, A., Romanenghi, M., Romeo, F., Bianco, N., Munzone, E., Sanguedolce, F., … Pece, S. (2022). CDK12 promotes tumorigenesis but induces vulnerability to therapies inhibiting folate one-carbon metabolism in breast cancer. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-30375-8
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Kulminski, A. M., Jain‐Washburn, E., Philipp, I., He, L., Loika, Y., Loiko, E., Bagley, O., Ukraintseva, S., Yashin, A., Arbeev, K., Stallard, E., Feitosa, M. F., Schupf, N., Christensen, K., & Culminskaya, I. (2022). APOE ɛ4 allele and TOMM40‐APOC1 variants jointly contribute to survival to older ages. Aging Cell, 21(12). Portico. https://doi.org/10.1111/acel.13730
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Columbia Affiliation
Baran, N., Lodi, A., Dhungana, Y., Herbrich, S., Collins, M., Sweeney, S., Pandey, R., Skwarska, A., Patel, S., Tremblay, M., Kuruvilla, V. M., Cavazos, A., Kaplan, M., Warmoes, M. O., Veiga, D. T., Furudate, K., Rojas-Sutterin, S., Haman, A., Gareau, Y., … Konopleva, M. (2022). Inhibition of mitochondrial complex I reverses NOTCH1-driven metabolic reprogramming in T-cell acute lymphoblastic leukemia. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-30396-3
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Zhou, R. W., Xu, J., Martin, T. C., Zachem, A. L., He, J., Ozturk, S., Demircioglu, D., Bansal, A., Trotta, A. P., Giotti, B., Gryder, B., Shen, Y., Wu, X., Carcamo, S., Bosch, K., Hopkins, B., Tsankov, A., Steinhagen, R., Jones, D. R., … Parsons, R. E. (2022). A local tumor microenvironment acquired super-enhancer induces an oncogenic driver in colorectal carcinoma. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-33377-8
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Locatelli, F., Lang, P., Li, A., Corbacioglu, S., de la Fuente, J., Wall, D. A., Liem, R., Meisel, R., Mapara, M. Y., Shah, A. J., Cappellini, M. D. D., Kattamis, A., Sheth, S., Bobruff, Y., Bower, L., Zhang, L., Sharma, A., Song, Y., Hobbs, W., & Frangoul, H. (2022). Efficacy and Safety of a Single Dose of Exagamglogene Autotemcel for Transfusion-Dependent β-Thalassemia. Blood, 140(Supplement 1), 4899–4901. https://doi.org/10.1182/blood-2022-166881
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Estrella, B., Pazos, M. A., Ricker, E. C., Ryu, Y. K., Piorczynski, T. B., Liu, Y., Tolu, S., & Amengual, J. E. (2022). First-in-Class Histone Acetyltransferase (HAT) Activator, YF2, Modulates Immune Evasion in DLBCL, Enhancing the Effects of Immune Checkpoint Blockade. Blood, 140(Supplement 1), 358–359. https://doi.org/10.1182/blood-2022-166929
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McAlpine, C. S., Kiss, M. G., Zuraikat, F. M., Cheek, D., Schiroli, G., Amatullah, H., Huynh, P., Bhatti, M. Z., Wong, L.-P., Yates, A. G., Poller, W. C., Mindur, J. E., Chan, C. T., Janssen, H., Downey, J., Singh, S., Sadreyev, R. I., Nahrendorf, M., Jeffrey, K. L., … Swirski, F. K. (2022). Sleep exerts lasting effects on hematopoietic stem cell function and diversity. Journal of Experimental Medicine, 219(11). https://doi.org/10.1084/jem.20220081
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Shen, Y., Singh, J., Sah, B., Chen, Z., Ha, W., Henzler, C., Su, T., Xie, L., Deng, Y., Li, G., Guo, H., Hibshoosh, H., & Liu, L. (2022). The Histone Demethylase HR Suppresses Breast Cancer Development through Enhanced CELF2 Tumor Suppressor Activity. Cancers, 14(19), 4648. https://doi.org/10.3390/cancers14194648
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Ahn, J., Lee, J., Kim, D.-H., Hwang, I.-S., Park, M.-R., Cho, I.-C., Hwang, S., & Lee, K. (2022). Loss of Monoallelic Expression of IGF2 in the Adult Liver Via Alternative Promoter Usage and Chromatin Reorganization. Frontiers in Genetics, 13. https://doi.org/10.3389/fgene.2022.920641
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Torrini, C., Nguyen, T. T. T., Shu, C., Mela, A., Humala, N., Mahajan, A., Seeley, E. H., Zhang, G., Westhoff, M.-A., Karpel-Massler, G., Bruce, J. N., Canoll, P., & Siegelin, M. D. (2022). Lactate is an epigenetic metabolite that drives survival in model systems of glioblastoma. Molecular Cell, 82(16), 3061-3076.e6. https://doi.org/10.1016/j.molcel.2022.06.030
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Eckhardt, C. M., Wu, H., Prada, D., Vokonas, P. S., Sparrow, D., Hou, L., Schwartz, J., & Baccarelli, A. A. (2022). Predicting risk of lung function impairment and all-cause mortality using a DNA methylation-based classifier of tobacco smoke exposure. Respiratory Medicine, 200, 106896. https://doi.org/10.1016/j.rmed.2022.106896
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Jain, P., Binder, A. M., Chen, B., Parada, H., Gallo, L. C., Alcaraz, J., Horvath, S., Bhatti, P., Whitsel, E. A., Jordahl, K., Baccarelli, A. A., Hou, L., Stewart, J. D., Li, Y., Justice, J. N., & LaCroix, A. Z. (2022). Analysis of Epigenetic Age Acceleration and Healthy Longevity Among Older US Women. JAMA Network Open, 5(7), e2223285. https://doi.org/10.1001/jamanetworkopen.2022.23285
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Basseville, A., Violet, P.-C., Safari, M., Sourbier, C., Linehan, W. M., Robey, R. W., Levine, M., Sackett, D. L., & Bates, S. E. (2022). A Histone Deacetylase Inhibitor Induces Acetyl-CoA Depletion Leading to Lethal Metabolic Stress in RAS-Pathway Activated Cells. Cancers, 14(11), 2643. https://doi.org/10.3390/cancers14112643
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Cambuli, F., Foletto, V., Alaimo, A., De Felice, D., Gandolfi, F., Palumbieri, M. D., Zaffagni, M., Genovesi, S., Lorenzoni, M., Celotti, M., Bertossio, E., Mazzero, G., Bertossi, A., Bisio, A., Berardinelli, F., Antoccia, A., Gaspari, M., Barbareschi, M., Fiorentino, M., … Lunardi, A. (2022). Intra‐epithelial non‐canonical Activin A signaling safeguards prostate progenitor quiescence. EMBO Reports, 23(5). Portico. https://doi.org/10.15252/embr.202154049
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Chen, H., Hu, B., Horth, C., Bareke, E., Rosenbaum, P., Kwon, S. Y., Sirois, J., Weinberg, D. N., Robison, F. M., Garcia, B. A., Lu, C., Pastor, W. A., & Majewski, J. (2022). H3K36 dimethylation shapes the epigenetic interaction landscape by directing repressive chromatin modifications in embryonic stem cells. Genome Research. https://doi.org/10.1101/gr.276383.121
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Antoszewski, M., Fournier, N., Ruiz Buendía, G. A., Lourenco, J., Liu, Y., Sugrue, T., Dubey, C., Nkosi, M., Pritchard, C. E. J., Huijbers, I. J., Segat, G. C., Alonso-Moreno, S., Serracanta, E., Belver, L., Ferrando, A. A., Ciriello, G., Weng, A. P., Koch, U., & Radtke, F. (2022). Tcf1 is essential for initiation of oncogenic Notch1-driven chromatin topology in T-ALL. Blood, 139(16), 2483–2498. https://doi.org/10.1182/blood.2021012077
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Columbia Affiliation
Li, Z., Guo, W., Ding, S., Feng, K., Lu, L., Huang, T., & Cai, Y. (2022). Detecting Blood Methylation Signatures in Response to Childhood Cancer Radiotherapy via Machine Learning Methods. Biology, 11(4), 607. https://doi.org/10.3390/biology11040607
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Galán-Díez, M., Borot, F., Ali, A. M., Zhao, J., Gil-Iturbe, E., Shan, X., Luo, N., Liu, Y., Huang, X.-P., Bisikirska, B., Labella, R., Kurland, I., Roth, B. L., Quick, M., Mukherjee, S., Rabadán, R., Carroll, M., Raza, A., & Kousteni, S. (2022). Subversion of Serotonin Receptor Signaling in Osteoblasts by Kynurenine Drives Acute Myeloid Leukemia. Cancer Discovery, 12(4), 1106–1127. https://doi.org/10.1158/2159-8290.cd-21-0692
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Zhang, W., Ruan, X., Li, Y., Zhi, J., Hu, L., Hou, X., Shi, X., Wang, X., Wang, J., Ma, W., Gu, P., Zheng, X., & Gao, M. (2022). KDM1A promotes thyroid cancer progression and maintains stemness through the Wnt/β-catenin signaling pathway. Theranostics, 12(4), 1500–1517. https://doi.org/10.7150/thno.66142
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Rousová, D., Nivsarkar, V., Altmannova, V., Raina, V. B., Funk, S. K., Liedtke, D., Janning, P., Müller, F., Reichle, H., Vader, G., & Weir, J. R. (2021). Novel mechanistic insights into the role of Mer2 as the keystone of meiotic DNA break formation. ELife, 10. CLOCKSS. https://doi.org/10.7554/elife.72330
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Wang, Z., Fan, X., Shen, Y., Pagadala, M. S., Signer, R., Cygan, K. J., Fairbrother, W. G., Carter, H., Chung, W. K., & Huang, K. (2021). Non-cancer-related pathogenic germline variants and expression consequences in ten-thousand cancer genomes. Genome Medicine, 13(1). https://doi.org/10.1186/s13073-021-00964-1
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Kremer, D. M., Nelson, B. S., Lin, L., Yarosz, E. L., Halbrook, C. J., Kerk, S. A., Sajjakulnukit, P., Myers, A., Thurston, G., Hou, S. W., Carpenter, E. S., Andren, A. C., Nwosu, Z. C., Cusmano, N., Wisner, S., Mbah, N. E., Shan, M., Das, N. K., Magnuson, B., … Lyssiotis, C. A. (2021). GOT1 inhibition promotes pancreatic cancer cell death by ferroptosis. Nature Communications, 12(1). https://doi.org/10.1038/s41467-021-24859-2
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Tate, T., Xiang, T., Wobker, S. E., Zhou, M., Chen, X., Kim, H., Batourina, E., Lin, C.-S., Kim, W. Y., Lu, C., Mckiernan, J. M., & Mendelsohn, C. L. (2021). Pparg signaling controls bladder cancer subtype and immune exclusion. Nature Communications, 12(1). https://doi.org/10.1038/s41467-021-26421-6
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Ricker, E. C., Estrella, B., Pazos, M. A., & Amengual, J. E. (2021). Dual Targeting of EZH2 and HDAC with Tazemetostat and Belinostat Promotes Immunogenicity in GC-DLBCL. Blood, 138(Supplement 1), 2410–2410. https://doi.org/10.1182/blood-2021-153460
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Park, S., Rong, L., Owczarek, T. B., Bernardo, M. D., Shoulson, R. L., Chua, C.-W., Kim, J. Y., Lankarani, A., Chakrapani, P., Syed, T., McKiernan, J. M., Solit, D. B., Shen, M. M., Al-Ahmadie, H. A., & Abate-Shen, C. (2021). Novel Mouse Models of Bladder Cancer Identify a Prognostic Signature Associated with Risk of Disease Progression. Cancer Research, 81(20), 5161–5175. https://doi.org/10.1158/0008-5472.can-21-1254
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Lu, J., Cao, L., Xu, Y., Huang, X., Cho, S.-J., Ashktorab, H., Smoot, D. T., Li, P., Zheng, C., Kim, J.-W., Ryeom, S. W., Yoon, S. S., Yoon, C., & Huang, C. (2021). WITHDRAWN: FOXC1 modulates stem-like cell properties and chemoresistance through hedgehog and EMT signaling in gastric adenocarcinoma. Molecular Therapy. https://doi.org/10.1016/j.ymthe.2021.09.009
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