Epigenetic Modifications and Their Functional Implications

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Zhao, J., Gu, T., Gao, C., Miao, G., Palma-Gudiel, H., Yu, L., Yang, J., Wang, Y., Li, Y., Lim, J., Li, R., Yao, B., Wu, H., Schneider, J. A., Seyfried, N., Grodstein, F., De Jager, P. L., Jin, P., & Bennett, D. A. (2025). Brain 5-hydroxymethylcytosine alterations are associated with Alzheimer’s disease neuropathology. Nature Communications, 16(1). https://doi.org/10.1038/s41467-025-58159-w
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Naggayi, S. K., Kalibbala, D., Mboizi, V., Ssenkusu, J. M., Jin, Z., Rosano, C., Munube, D., Wambaka, B., Namazzi, R., Kasirye, P. G., Kabatabaazi, M., Nambatya, G., Murungi, S., Nabaggala, C., Nakafeero, M. R., Troidl, I. R., Opoka, R. O., Idro, R., Bangirana, P., & Green, N. S. (2025). Neurocognitive Gains Among Ugandan Children with Sickle Cell Anemia on Hydroxyurea: 18-month trial interim results. Blood Advances. https://doi.org/10.1182/bloodadvances.2024015073
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Yuan, F., Yang, J., Ma, F., Hu, Z., Malik, V., Zang, R., Li, D., Shi, X., Huang, X., Zhou, H., & Wang, J. (2025). Pluripotency factor Tex10 finetunes Wnt signaling for spermatogenesis and primordial germ cell development. Nature Communications, 16(1). https://doi.org/10.1038/s41467-025-57165-2
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Dharmadhikari, A. V., Abad, M. A., Khan, S., Maroofian, R., Sands, T. T., Ullah, F., Samejima, I., Shen, Y., Wear, M. A., Moore, K. E., Kondakova, E., Mitina, N., Schaub, T., Lee, G. K., Umandap, C. H., Berger, S. M., Iglesias, A. D., Popp, B., Abou Jamra, R., … Liao, J. (2025). RNA methyltransferase SPOUT1/CENP-32 links mitotic spindle organization with the neurodevelopmental disorder SpADMiSS. Nature Communications, 16(1). https://doi.org/10.1038/s41467-025-56876-w
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Ahn, J., Hwang, I.-S., Park, M.-R., Rosa-Velazquez, M., Cho, I.-C., Relling, A. E., Hwang, S., & Lee, K. (2025). Evolutionary lineage-specific genomic imprinting at the ZNF791 locus. PLOS Genetics, 21(1), e1011532. https://doi.org/10.1371/journal.pgen.1011532
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Karger, L. M., Webb, B. D., Edelmann, L., Liao, J., & Mehta, L. (2024). Familial RPL26 Variant Causing Congenital Anomalies Without Hematological Features of Diamond Blackfan Anemia. American Journal of Medical Genetics Part A. Portico. https://doi.org/10.1002/ajmg.a.63954
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Wadhwani, A. R., Goldberg, D., Wolk, D. A., Lee, E. B., Farrell, K. W., Crary, J. F., Bennett, D. A., De Jager, P. L., Schneider, J. A., Zhou, W., McMillan, C. T., & Group, P. W. (2024). Shared and Distinct Epigenetic Profiles in Primary Age‐Related Tauopathy and Alzheimer’s Disease: Insights into Tangle Formation and Spread. Alzheimer’s & Dementia, 20(S1). Portico. https://doi.org/10.1002/alz.092601
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Goldberg, D., Wadhwani, A. R., Wolk, D. A., Lee, E. B., Bennett, D. A., De Jager, P. L., Schneider, J. A., Zhou, W., & McMillan, C. T. (2024). DNA methylation associates with regional tau pathology beyond age and APOE. Alzheimer’s & Dementia, 20(S1). Portico. https://doi.org/10.1002/alz.092539
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Jeong, M.-S., Baek, S.-W., Yang, G.-E., Mun, J.-Y., Kim, J. A., Kim, T.-N., Nam, J.-K., Choi, Y.-H., Lee, J.-S., Chu, I.-S., & Leem, S.-H. (2025). Chemoresistance-motility signature of molecular evolution to chemotherapy in non-muscle-invasive bladder cancer and its clinical implications. Cancer Letters, 610, 217339. https://doi.org/10.1016/j.canlet.2024.217339
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Reisz, J. A., Earley, E. J., Nemkov, T., Key, A., Stephenson, D., Keele, G. R., Dzieciatkowska, M., Spitalnik, S. L., Hod, E. A., Kleinman, S., Roubinian, N. H., Gladwin, M. T., Hansen, K. C., Norris, P. J., Busch, M. P., Zimring, J. C., Churchill, G. A., Page, G. P., & D’Alessandro, A. (2024). Arginine metabolism is a biomarker of red blood cell and human aging. Aging Cell. Portico. https://doi.org/10.1111/acel.14388
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Shipman, G. A., Padilla, R., Horth, C., Hu, B., Bareke, E., Vitorino, F. N., Gongora, J. M., Garcia, B. A., Lu, C., & Majewski, J. (2024). Systematic perturbations of SETD2, NSD1, NSD2, NSD3, and ASH1L reveal their distinct contributions to H3K36 methylation. Genome Biology, 25(1). https://doi.org/10.1186/s13059-024-03415-3
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Zhang, Y., Karagiannis, D., Liu, H., Lin, M., Fang, Y., Jiang, M., Chen, X., Suresh, S., Huang, H., She, J., Shi, F., Liu, J., Luo, D., Angel, J. C., Lin, G., Yang, P., El-Rifai, W., Zaika, A., Oro, A. E., … Que, J. (2024). Epigenetic regulation of p63 blocks squamous-to-neuroendocrine transdifferentiation in esophageal development and malignancy. Science Advances, 10(41). https://doi.org/10.1126/sciadv.adq0479
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Savin, M. J., Wang, H., Pei, H., Aiello, A. E., Assuras, S., Caspi, A., Moffitt, T. E., Muenning, P. A., Ryan, C. P., Shi, B., Stern, Y., Sugden, K., Valeri, L., & Belsky, D. W. (2024). Association of a pace of aging epigenetic clock with rate of cognitive decline in the Framingham Heart Study Offspring Cohort. Alzheimer’s & Dementia: Diagnosis, Assessment & Disease Monitoring, 16(4). Portico. https://doi.org/10.1002/dad2.70038
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Su, S. H., Mitani, Y., Li, T., Sachdeva, U., Flashner, S., Klein-Szanto, A., Dunbar, K. J., Abrams, J., Nakagawa, H., & Gabre, J. (2024). Lactate Suppresses Growth of Esophageal Adenocarcinoma Patient-Derived Organoids through Alterations in Tumor NADH/NAD+ Redox State. Biomolecules, 14(9), 1195. https://doi.org/10.3390/biom14091195
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Elaimy, A. L., El-Derany, M. O., James, J., Wang, Z., Pearson, A. N., Holcomb, E. A., Huber, A. K., Gijón, M., Bell, H. N., Sanghvi, V. R., Frankel, T. L., Su, G. L., Tapper, E. B., Tai, A. W., Ramnath, N., Centonze, C. P., Dobrosotskaya, I., Moeller, J. A., Bryant, A. K., … Green, M. D. (2024). SLC4A11 mediates ammonia import and promotes cancer stemness in hepatocellular carcinoma. JCI Insight, 9(21). https://doi.org/10.1172/jci.insight.184826
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Shimonosono, M., Morimoto, M., Hirose, W., Tomita, Y., Matsuura, N., Flashner, S., Ebadi, M. S., Okayasu, E. H., Lee, C. Y., Britton, W. R., Martin, C., Wuertz, B. R., Parikh, A. S., Sachdeva, U. M., Ondrey, F. G., Atigadda, V. R., Elmets, C. A., Abrams, J. A., Muir, A. B., … Nakagawa, H. (2024). Modeling Epithelial Homeostasis and Perturbation in Three-Dimensional Human Esophageal Organoids. Biomolecules, 14(9), 1126. https://doi.org/10.3390/biom14091126
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Gretarsson, K. H., Abini-Agbomson, S., Gloor, S. L., Weinberg, D. N., McCuiston, J. L., Kumary, V. U. S., Hickman, A. R., Sahu, V., Lee, R., Xu, X., Lipieta, N., Flashner, S., Adeleke, O. A., Popova, I. K., Taylor, H. F., Noll, K., Windham, C. L., Maryanski, D. N., Venters, B. J., … Lu, C. (2024). Cancer-associated DNA hypermethylation of Polycomb targets requires DNMT3A dual recognition of histone H2AK119 ubiquitination and the nucleosome acidic patch. Science Advances, 10(35). https://doi.org/10.1126/sciadv.adp0975
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de Queiroz, R. M., Efe, G., Guzman, A., Hashimoto, N., Kawashima, Y., Tanaka, T., Rustgi, A. K., & Prives, C. (2024). Mdm2 requires Sprouty4 to regulate focal adhesion formation and metastasis independent of p53. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-51488-2
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Hassan, N., Yi, H., Malik, B., Gaspard-Boulinc, L., Samaraweera, S. E., Casolari, D. A., Seneviratne, J., Balachandran, A., Chew, T., Duly, A., Carter, D. R., Cheung, B. B., Norris, M., Haber, M., Kavallaris, M., Marshall, G. M., Zhang, X. D., Liu, T., Wang, J., … Wang, J. Y. (2024). Loss of the stress sensor GADD45A promotes stem cell activity and ferroptosis resistance in LGR4/HOXA9-dependent AML. Blood, 144(1), 84–98. https://doi.org/10.1182/blood.2024024072
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İş, Ö., Wang, X., Reddy, J. S., Min, Y., Yilmaz, E., Bhattarai, P., Patel, T., Bergman, J., Quicksall, Z., Heckman, M. G., Tutor-New, F. Q., Can Demirdogen, B., White, L., Koga, S., Krause, V., Inoue, Y., Kanekiyo, T., Cosacak, M. I., Nelson, N., … Ertekin-Taner, N. (2024). Gliovascular transcriptional perturbations in Alzheimer’s disease reveal molecular mechanisms of blood brain barrier dysfunction. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-48926-6
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Lu, Z., Wang, Y., Assumpção, A. L. F. V., Liu, P., Kopp, A., Saka, S., Mcilwain, S. J., Viny, A. D., Brand, M., & Pan, X. (2024). Yin Yang 1 regulates cohesin complex protein SMC3 in mouse hematopoietic stem cells. Blood Advances, 8(12), 3076–3091. https://doi.org/10.1182/bloodadvances.2023011411
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Li, Y., Li, J., Li, W., Liang, S., Wei, W., Chu, J., Lai, J., Lin, Y., Chen, H., Su, J., Hu, X., Wang, G., Meng, J., Jiang, J., Ye, L., & An, S. (2024). Scm6A: A Fast and Low-cost Method for Quantifying m6A Modifications at the Single-cell Level. Genomics, Proteomics & Bioinformatics. https://doi.org/10.1093/gpbjnl/qzae039
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Gilbertson, R. J., Behjati, S., Böttcher, A.-L., Bronner, M. E., Burridge, M., Clausing, H., Clifford, H., Danaher, T., Donovan, L. K., Drost, J., Eggermont, A. M. M., Emerson, C., Flores, M. G., Hamerlik, P., Jabado, N., Jones, A., Kaessmann, H., Kleinman, C. L., Kool, M., … Pfister, S. M. (2024). The Virtual Child. Cancer Discovery, 14(4), 663–668. https://doi.org/10.1158/2159-8290.cd-23-1500
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Wang, Y., Sarnowski, C., Lin, H., Pitsillides, A. N., Heard‐Costa, N. L., Choi, S. H., Wang, D., Bis, J. C., Blue, E. E., Boerwinkle, E., De Jager, P. L., Fornage, M., Wijsman, E. M., Seshadri, S., Dupuis, J., Peloso, G. M., & DeStefano, A. L. (2024). Key variants via the Alzheimer’s Disease Sequencing Project whole genome sequence data. Alzheimer’s & Dementia, 20(5), 3290–3304. Portico. https://doi.org/10.1002/alz.13705
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Fang, Y., Hua, X., Shan, C.-M., Toda, T., Qiao, F., Zhang, Z., & Jia, S. (2024). Coordination of histone chaperones for parental histone segregation and epigenetic inheritance. Genes & Development, 38(3–4), 189–204. https://doi.org/10.1101/gad.351278.123
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Sepich-Poore, G. D., McDonald, D., Kopylova, E., Guccione, C., Zhu, Q., Austin, G., Carpenter, C., Fraraccio, S., Wandro, S., Kosciolek, T., Janssen, S., Metcalf, J. L., Song, S. J., Kanbar, J., Miller-Montgomery, S., Heaton, R., Mckay, R., Patel, S. P., Swafford, A. D., … Knight, R. (2024). Robustness of cancer microbiome signals over a broad range of methodological variation. Oncogene, 43(15), 1127–1148. https://doi.org/10.1038/s41388-024-02974-w
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Galbraith, K., Vasudevaraja, V., Serrano, J., Shen, G., Tran, I., Abdallat, N., Wen, M., Patel, S., Movahed-Ezazi, M., Faustin, A., Spino-Keeton, M., Roberts, L. G., Maloku, E., Drexler, S. A., Liechty, B. L., Pisapia, D., Krasnozhen-Ratush, O., Rosenblum, M., Shroff, S., … Snuderl, M. (2023). Clinical utility of whole-genome DNA methylation profiling as a primary molecular diagnostic assay for central nervous system tumors—A prospective study and guidelines for clinical testing. Neuro-Oncology Advances, 5(1). https://doi.org/10.1093/noajnl/vdad076
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Mendelson, K., Martin, T. C., Nguyen, C. B., Hsu, M., Xu, J., Lang, C. C. V., Dummer, R., Saenger, Y., Messina, J. L., Sondak, V. K., Desman, G., Hasson, D., Bernstein, E., Parsons, R. E., & Celebi, J. T. (2024). Differential histone acetylation and super-enhancer regulation underlie melanoma cell dedifferentiation. JCI Insight. https://doi.org/10.1172/jci.insight.166611
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Kwak, S. H., Srinivasan, S., Chen, L., Todd, J., Mercader, J. M., Jensen, E. T., Divers, J., Mottl, A. K., Pihoker, C., Gandica, R. G., Laffel, L. M., Isganaitis, E., Haymond, M. W., Levitsky, L. L., Pollin, T. I., Florez, J. C., & Flannick, J. (2024). Genetic architecture and biology of youth-onset type 2 diabetes. Nature Metabolism, 6(2), 226–237. https://doi.org/10.1038/s42255-023-00970-0
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Columbia Affiliation
Sprinzen, L., Garcia, F., Mela, A., Lei, L., Upadhyayula, P., Mahajan, A., Humala, N., Manier, L., Caprioli, R., Quiñones-Hinojosa, A., Casaccia, P., & Canoll, P. (2024). EZH2 Inhibition Sensitizes IDH1R132H-Mutant Gliomas to Histone Deacetylase Inhibitor. Cells, 13(3), 219. https://doi.org/10.3390/cells13030219
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Mei, H., Simino, J., Li, L., Jiang, F., Bis, J. C., Davies, G., Hill, W. D., Xia, C., Gudnason, V., Yang, Q., Lahti, J., Smith, J. A., Kirin, M., De Jager, P., Armstrong, N. J., Ghanbari, M., Kolcic, I., Moran, C., Teumer, A., … Mosley, T. H. (2024). Multi-omics and pathway analyses of genome-wide associations implicate regulation and immunity in verbal declarative memory performance. Alzheimer’s Research & Therapy, 16(1). https://doi.org/10.1186/s13195-023-01376-6
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Giacomini, G., Piquet, S., Chevallier, O., Dabin, J., Bai, S.-K., Kim, B., Siddaway, R., Raught, B., Coyaud, E., Shan, C.-M., Reid, R. J. D., Toda, T., Rothstein, R., Barra, V., Wilhelm, T., Hamadat, S., Bertin, C., Crane, A., Dubois, F., … Polo, S. E. (2024). Aberrant DNA repair reveals a vulnerability in histone H3.3-mutant brain tumors. Nucleic Acids Research, 52(5), 2372–2388. https://doi.org/10.1093/nar/gkad1257
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Karagiannis, D., Wu, W., Li, A., Hayashi, M., Chen, X., Yip, M., Mangipudy, V., Xu, X., Sánchez-Rivera, F. J., Soto-Feliciano, Y. M., Ye, J., Papagiannakopoulos, T., & Lu, C. (2024). Metabolic reprogramming by histone deacetylase inhibition preferentially targets NRF2-activated tumors. Cell Reports, 43(1), 113629. https://doi.org/10.1016/j.celrep.2023.113629
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Hofmann, A., Haesler, L. M., Preische, O., Gräber‐Sultan, S., Obermüller, U., Vöglein, J., Levin, J., Laske, C., Fitzpatrick, C. D., Levin, R., Joseph‐Mathurin, N., Chen, C. D., Cruchaga, C., Goate, A., Allegri, R. F., Benzinger, T. L. S., Berman, S., Chui, H. C., Fagan, A. M., … Schultz, S. A. (2023). Refinement of Neurofilament light Dynamics in CSF and Blood for familial Alzheimer’s Disease. Alzheimer’s & Dementia, 19(S14). Portico. https://doi.org/10.1002/alz.078802
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Libby, J. B., Roshani, R., Seto, M., Wang, T., Nudelman, K. N. H., Buckley, R. F., Saykin, A. J., Mormino, E. C., Sperling, R. A., Mayeux, R., Dumitrescu, L. C., & Hohman, T. J. (2023). Genetically Regulated Telomere Length Relates to Brain Amyloidosis. Alzheimer’s & Dementia, 19(S12). Portico. https://doi.org/10.1002/alz.079903
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Chen, X., Li, Y., Zhu, F., Xu, X., Estrella, B., Pazos, M. A., McGuire, J. T., Karagiannis, D., Sahu, V., Mustafokulov, M., Scuoppo, C., Sánchez-Rivera, F. J., Soto-Feliciano, Y. M., Pasqualucci, L., Ciccia, A., Amengual, J. E., & Lu, C. (2023). Context-defined cancer co-dependency mapping identifies a functional interplay between PRC2 and MLL-MEN1 complex in lymphoma. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-39990-5
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Ray, N. R., Kunkle, B. W., Hamilton‐Nelson, K. L., Kurup, J. T., Cosacak, M. I., Kizil, C., Jean‐Francois, M., Cuccaro, M. L., Vance, J. M., Hendrie, H. C., Baiyewu, O., Ogunniyi, A., Martin, E. R., Wang, L., Beecham, G. W., Farrer, L. A., Haines, J. L., Byrd, G. S., … Schellenberg, G. D. (2023). Extended genome‐wide association study employing the African Genome Resources Panel identifies novel susceptibility loci for Alzheimer’s Disease in individuals of African ancestry. Alzheimer’s & Dementia, 19(S15). Portico. https://doi.org/10.1002/alz.078904
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Martino, J., Liu, Q., Vukojevic, K., Ke, J., Lim, T. Y., Khan, A., Gupta, Y., Perez, A., Yan, Z., Milo Rasouly, H., Vena, N., Lippa, N., Giordano, J. L., Saraga, M., Saraga-Babic, M., Westland, R., Bodria, M., Piaggio, G., Bendapudi, P. K., … Sanna-Cherchi, S. (2023). Mouse and human studies support DSTYK loss of function as a low-penetrance and variable expressivity risk factor for congenital urinary tract anomalies. Genetics in Medicine, 25(12), 100983. https://doi.org/10.1016/j.gim.2023.100983
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Upadhyayula, P. S., Higgins, D. M., Mela, A., Banu, M., Dovas, A., Zandkarimi, F., Patel, P., Mahajan, A., Humala, N., Nguyen, T. T. T., Chaudhary, K. R., Liao, L., Argenziano, M., Sudhakar, T., Sperring, C. P., Shapiro, B. L., Ahmed, E. R., Kinslow, C., Ye, L. F., … Canoll, P. (2023). Dietary restriction of cysteine and methionine sensitizes gliomas to ferroptosis and induces alterations in energetic metabolism. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-36630-w
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Naj, A. C., Rajabli, F., Reitz, C., Jun, G. R., Benchek, P., Tosto, G., Sha, J., Zhu, C., Kushch, N. A., Lee, W., Haut, J., Hamilton‐Nelson, K. L., Wheeler, N. R., Zhao, Y., Farrell, J., Grunin, M., Leung, Y. Y., Li, D., … da Fonseca, E. L. (2023). Multi‐Ancestry Genome‐wide Association Analysis of Late‐Onset Alzheimer’s Disease (LOAD) in 60,941 Individuals Identifies Multiple Novel Cross‐Ancestry Associations and Implicates Amyloid and Complement Pathways. Alzheimer’s & Dementia, 19(S12). Portico. https://doi.org/10.1002/alz.079401
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Sarnowski, C., Huan, T., Ma, Y., Joehanes, R., Beiser, A., DeCarli, C. S., Heard-Costa, N. L., Levy, D., Lin, H., Liu, C.-T., Liu, C., Meigs, J. B., Satizabal, C. L., Florez, J. C., Hivert, M.-F., Dupuis, J., De Jager, P. L., Bennett, D. A., Seshadri, S., & Morrison, A. C. (2023). Multi-tissue epigenetic analysis identifies distinct associations underlying insulin resistance and Alzheimer’s disease at CPT1A locus. Clinical Epigenetics, 15(1). https://doi.org/10.1186/s13148-023-01589-4
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Slowly, M., Domingo-Relloso, A., Santella, R. M., Haack, K., Fallin, D. M., Terry, M. B., Rhoades, D. A., Herreros-Martinez, M., Garcia-Esquinas, E., Cole, S. A., Tellez-Plaza, M., Navas-Acien, A., & Wu, H.-C. (2023). Blood DNA methylation and liver cancer in American Indians: evidence from the Strong Heart Study. Cancer Causes & Control, 35(4), 661–669. https://doi.org/10.1007/s10552-023-01822-8
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Xu, J. J., Chen, Y., Pantazi, J., Fernando, S., Alija, B., Sudunagunta, V., Bhagat, G., & Viny, A. D. (2023). Synergy of Stag2-Cohesin Loss Results in Expansion of Npm1c-Mutant Hematopoietic Stem and Progenitor Cells. Blood, 142(Supplement 1), 954–954. https://doi.org/10.1182/blood-2023-190627
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Hanna, R., Frangoul, H., McKinney, C., Pineiro, L., Mapara, M., Dalal, J., Chang, K.-H., Jaskolka, M., Kim, K., Farrington, D. L., Wally, M., Mei, B., Lawal, A., Afonja, O. O., & Walters, M. C. (2023). AsCas12a Gene Editing of HBG1/2 Promoters with EDIT-301 Results in Rapid and Sustained Normalization of Hemoglobin and Increased Fetal Hemoglobin in Patients with Severe Sickle Cell Disease and Transfusion-Dependent Beta-Thalassemia. Blood, 142(Supplement 1), 4996–4996. https://doi.org/10.1182/blood-2023-187397
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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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