Fernández, E. C., Wang, J., Zhang, X., Wei, H.-J., Minns, H., Griffin, A., Obradovic, A., Vlahos, L., Martins, T., Becker, P., Crawford, J., Gartrell, R., Szalontay, L., Zacharoulis, S., Zhang, Z., Wechsler-Reya, R., Wu, C.-C., Califano, A., & Pavisic, J. (2023). DIPG-49. A SYSTEMS BIOLOGY APPROACH TO DEFINING AND TARGETING CELL STATE-SPECIFIC MASTER REGULATOR DEPENDENCIES IN DIFFUSE MIDLINE GLIOMA. Neuro-Oncology, 25(Supplement_1), i24–i24. https://doi.org/10.1093/neuonc/noad073.096

Liu, Y., Liu, Y., Ye, S., Feng, H., & Ma, L. (2023). A new ferroptosis-related signature model including messenger RNAs and long non-coding RNAs predicts the prognosis of gastric cancer patients. Journal of Translational Internal Medicine, 11(2), 145–155. https://doi.org/10.2478/jtim-2023-0089

Moore, C. E., Yalcindag, S. E., Czeladko, H., Ravindranathan, R., Wijesekara Hanthi, Y., Levy, J. C., Sannino, V., Schindler, D., Ciccia, A., Costanzo, V., & Elia, A. E. H. (2023). RFWD3 promotes ZRANB3 recruitment to regulate the remodeling of stalled replication forks. Journal of Cell Biology, 222(5). https://doi.org/10.1083/jcb.202106022

Li, Z., & Zhang, Z. (2023). Histone chaperones: A multinodal highway network inside the cell. Molecular Cell, 83(7), 1024–1026. https://doi.org/10.1016/j.molcel.2023.03.004

Su, Z., Kon, N., Yi, J., Zhao, H., Zhang, W., Tang, Q., Li, H., Kobayashi, H., Li, Z., Duan, S., Liu, Y., Olive, K. P., Zhang, Z., Honig, B., Manfredi, J. J., Rustgi, A. K., & Gu, W. (2023). Specific regulation of BACH1 by the hotspot mutant p53R175H reveals a distinct gain-of-function mechanism. Nature Cancer, 4(4), 564–581. https://doi.org/10.1038/s43018-023-00532-z

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

Langelier, M.-F., Lin, X., Zha, S., & Pascal, J. M. (2023). Clinical PARP inhibitors allosterically induce PARP2 retention on DNA. Science Advances, 9(12). https://doi.org/10.1126/sciadv.adf7175

Sohn, E. J., Goralsky, J. A., Shay, J. W., & Min, J. (2023). The Molecular Mechanisms and Therapeutic Prospects of Alternative Lengthening of Telomeres (ALT). Cancers, 15(7), 1945. https://doi.org/10.3390/cancers15071945

Savage, T. M., Vincent, R. L., Rae, S. S., Huang, L. H., Ahn, A., Pu, K., Li, F., de los Santos-Alexis, K., Coker, C., Danino, T., & Arpaia, N. (2023). Chemokines expressed by engineered bacteria recruit and orchestrate antitumor immunity. Science Advances, 9(10). https://doi.org/10.1126/sciadv.adc9436

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

Song, S., Su, Z., Kon, N., Chu, B., Li, H., Jiang, X., Luo, J., Stockwell, B. R., & Gu, W. (2023). ALOX5-mediated ferroptosis acts as a distinct cell death pathway upon oxidative stress in Huntington’s disease. Genes & Development, 37(5–6), 204–217. https://doi.org/10.1101/gad.350211.122

Ko, A., Hasanain, M., Oh, Y. T., D’Angelo, F., Sommer, D., Frangaj, B., Tran, S., Bielle, F., Pollo, B., Paterra, R., Mokhtari, K., Soni, R. K., Peyre, M., Eoli, M., Papi, L., Kalamarides, M., Sanson, M., Iavarone, A., & Lasorella, A. (2022). LZTR1Mutation Mediates Oncogenesis through Stabilization of EGFR and AXL. Cancer Discovery, 13(3), 702–723. https://doi.org/10.1158/2159-8290.cd-22-0376

Song, C., Zhang, Y., Li, Y., Bie, J., Wang, Z., Yang, X., Li, H., Zhu, L., Zhang, T., Chang, Q., & Luo, J. (2023). The phosphorylation of PHF5A by TrkA-ERK1/2-ABL1 cascade regulates centrosome separation. Cell Death & Disease, 14(2). https://doi.org/10.1038/s41419-023-05561-1

Kim, C., Wang, X.-D., Liu, Z., Zha, S., & Yu, Y. (2022). Targeting Scaffolding Functions of Enzymes Using PROTAC Approaches. Biochemistry, 62(3), 561–563. https://doi.org/10.1021/acs.biochem.2c00366

Migliozzi, S., Oh, Y. T., Hasanain, M., Garofano, L., D’Angelo, F., Najac, R. D., Picca, A., Bielle, F., Di Stefano, A. L., Lerond, J., Sarkaria, J. N., Ceccarelli, M., Sanson, M., Lasorella, A., & Iavarone, A. (2023). Integrative multi-omics networks identify PKCδ and DNA-PK as master kinases of glioblastoma subtypes and guide targeted cancer therapy. Nature Cancer, 4(2), 181–202. https://doi.org/10.1038/s43018-022-00510-x

Liu, D., Liang, C., Huang, B., Zhuang, X., Cui, W., Yang, L., Yang, Y., Zhang, Y., Fu, X., Zhang, X., Du, L., Gu, W., Wang, X., Yin, C., Chai, R., & Chu, B. (2023). Tryptophan Metabolism Acts as a New Anti‐Ferroptotic Pathway to Mediate Tumor Growth. Advanced Science, 10(6). Portico. https://doi.org/10.1002/advs.202204006

Zagelbaum, J., & Gautier, J. (2023). Double-strand break repair and mis-repair in 3D. DNA Repair, 121, 103430. https://doi.org/10.1016/j.dnarep.2022.103430

Zagelbaum, J., Schooley, A., Zhao, J., Schrank, B. R., Callen, E., Zha, S., Gottesman, M. E., Nussenzweig, A., Rabadan, R., Dekker, J., & Gautier, J. (2022). Multiscale reorganization of the genome following DNA damage facilitates chromosome translocations via nuclear actin polymerization. Nature Structural & Molecular Biology, 30(1), 99–106. https://doi.org/10.1038/s41594-022-00893-6

Deb, D., Wu, Y., Coker, C., Harimoto, T., Huang, R., & Danino, T. (2022). Design of combination therapy for engineered bacterial therapeutics in non-small cell lung cancer. Scientific Reports, 12(1). https://doi.org/10.1038/s41598-022-26105-1

Saeki, K., Qiu, W., Friedman, R. A., Pan, S., Lu, J., Ichimiya, S., Chio, I. I. C., Shawber, C. J., Kitajewski, J., Hu, J., & Su, G. H. (2022). Inactivation ofNotch4Attenuated Pancreatic Tumorigenesis in Mice. Cancer Research Communications, 2(12), 1601–1616. https://doi.org/10.1158/2767-9764.crc-22-0106

Mo, Y., Duan, S., Zhang, X., Hua, X., Zhou, H., Wei, H.-J., Watanabe, J., McQuillan, N., Su, Z., Gu, W., Wu, C.-C., Vakoc, C. R., Hashizume, R., Chang, K., & Zhang, Z. (2022). Epigenome Programming by H3.3K27M Mutation Creates a Dependence of Pediatric Glioma on SMARCA4. Cancer Discovery, 12(12), 2906–2929. https://doi.org/10.1158/2159-8290.cd-21-1492

Lee, S. B., Garofano, L., Ko, A., D’Angelo, F., Frangaj, B., Sommer, D., Gan, Q., Kim, K., Cardozo, T., Iavarone, A., & Lasorella, A. (2022). Regulated interaction of ID2 with the anaphase-promoting complex links progression through mitosis with reactivation of cell-type-specific transcription. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-29502-2

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

Xu, X., Duan, S., Hua, X., Li, Z., He, R., & Zhang, Z. (2022). Stable inheritance of H3.3-containing nucleosomes during mitotic cell divisions. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-30298-4

Paik, P. K., Luo, J., Ai, N., Kim, R., Ahn, L., Biswas, A., Coker, C., Ma, W., Wong, P., Buonocore, D. J., Lai, W. V., Chaft, J. E., Acharyya, S., Massagué, J., & Kris, M. G. (2022). Phase I trial of the TNF-α inhibitor certolizumab plus chemotherapy in stage IV lung adenocarcinomas. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-33719-6

Cordo’, V., Meijer, M. T., Hagelaar, R., de Goeij-de Haas, R. R., Poort, V. M., Henneman, A. A., Piersma, S. R., Pham, T. V., Oshima, K., Ferrando, A. A., Zaman, G. J. R., Jimenez, C. R., & Meijerink, J. P. P. (2022). Phosphoproteomic profiling of T cell acute lymphoblastic leukemia reveals targetable kinases and combination treatment strategies. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-28682-1

de Leval, L., Alizadeh, A. A., Bergsagel, P. L., Campo, E., Davies, A., Dogan, A., Fitzgibbon, J., Horwitz, S. M., Melnick, A. M., Morice, W. G., Morin, R. D., Nadel, B., Pileri, S. A., Rosenquist, R., Rossi, D., Salaverria, I., Steidl, C., Treon, S. P., Zelenetz, A. D., … Scott, D. W. (2022). Genomic profiling for clinical decision making in lymphoid neoplasms. Blood, 140(21), 2193–2227. https://doi.org/10.1182/blood.2022015854

Torres-Diz, M., Thomas-Tikhonenko, A., Reglero, C., Ferrando, A., Falkenstein, C. D., Tasian, S. K., Sehgal, P., Ang, Z., Barash, Y., & Radens, C. (2022). Non-Canonical Exon Usage in Pediatric Leukemia: Implications for Chemoresistance. Blood, 140(Supplement 1), 3264–3265. https://doi.org/10.1182/blood-2022-167006

Xu, X., Hua, X., Brown, K., Ren, X., & Zhang, Z. (2022). Mcm2 promotes stem cell differentiation via its ability to bind H3-H4. ELife, 11. CLOCKSS. https://doi.org/10.7554/elife.80917

Ye, S., Liu, Y., Zhang, T., Feng, H., Liu, Y., & Ma, L. (2022). Analysis of the correlation between non-alcoholic fatty liver disease and the risk of colorectal neoplasms. Frontiers in Pharmacology, 13. https://doi.org/10.3389/fphar.2022.1068432

Reglero, C., Dieck, C. L., Zask, A., Forouhar, F., Laurent, A. P., Lin, W.-H. W., Albero, R., Miller, H. I., Ma, C., Gastier-Foster, J. M., Loh, M. L., Tong, L., Stockwell, B. R., Palomero, T., & Ferrando, A. A. (2022). Pharmacologic Inhibition of NT5C2 Reverses Genetic and Nongenetic Drivers of 6-MP Resistance in Acute Lymphoblastic Leukemia. Cancer Discovery, 12(11), 2646–2665. https://doi.org/10.1158/2159-8290.cd-22-0010

Wendorff, A. A., Aidan Quinn, S., Alvarez, S., Brown, J. A., Biswas, M., Gunning, T., Palomero, T., & Ferrando, A. A. (2022). Epigenetic reversal of hematopoietic stem cell aging in Phf6-knockout mice. Nature Aging, 2(11), 1008–1023. https://doi.org/10.1038/s43587-022-00304-x

Minns, H., Padilla, O., Wei, H.-J., Webster-Carrion, A., Tazhibi, M., McQuillan, N., Zhang, X., Yeh, R., Zhang, Z., Szalontay, L., Pavisic, J., Garty, G., Garvin, J., Canoll, P., Vanpouille-Box, C., Menon, V., Olah, M., Rabadan, R., Wu, C.-C., & Gartrell, R. (2022). TMIC-68. EVALUATING FLASH AND CONVENTIONAL DOSE-RATE RADIATION AND IMMUNE RESPONSE WITH SINGLE-CELL SEQUENCING IN DIFFUSE MIDLINE GLIOMA (DMG). Neuro-Oncology, 24(Supplement_7), vii286–vii286. https://doi.org/10.1093/neuonc/noac209.1111

Du, W., Shi, G., Shan, C.-M., Li, Z., Zhu, B., Jia, S., Li, Q., & Zhang, Z. (2022). Mechanisms of chromatin-based epigenetic inheritance. Science China Life Sciences, 65(11), 2162–2190. https://doi.org/10.1007/s11427-022-2120-1

Lee, C. G., Lee, C., Lee, J., Nam, J. S., Kim, B., & Kwon, T. (2022). Dual‐Modulated Release of a Cytotoxic Photosensitizer Using Photogenerated Reactive Oxygen Species and Glutathione. Angewandte Chemie International Edition, 61(42). Portico. https://doi.org/10.1002/anie.202210623

Li, Y., Goldberg, E. M., Chen, X., Xu, X., McGuire, J. T., Leuzzi, G., Karagiannis, D., Tate, T., Farhangdoost, N., Horth, C., Dai, E., Li, Z., Zhang, Z., Izar, B., Que, J., Ciccia, A., Majewski, J., Yoon, A. J., Ailles, L., … Lu, C. (2022). Histone methylation antagonism drives tumor immune evasion in squamous cell carcinomas. Molecular Cell, 82(20), 3901-3918.e7. https://doi.org/10.1016/j.molcel.2022.09.007

Liu, Y., & Gu, W. (2022). The complexity of p53-mediated metabolic regulation in tumor suppression. Seminars in Cancer Biology, 85, 4–32. https://doi.org/10.1016/j.semcancer.2021.03.010

He, R., & Zhang, Z. (2022). Rad53 arrests leading and lagging strand DNA synthesis via distinct mechanisms in response to DNA replication stress. BioEssays, 44(9). Portico. https://doi.org/10.1002/bies.202200061

He, D., Feng, H., Sundberg, B., Yang, J., Powers, J., Christian, A. H., Wilkinson, J. E., Monnin, C., Avizonis, D., Thomas, C. J., Friedman, R. A., Kluger, M. D., Hollingsworth, M. A., Grandgenett, P. M., Klute, K. A., Toste, F. D., Chang, C. J., & Chio, I. I. C. (2022). Methionine oxidation activates pyruvate kinase M2 to promote pancreatic cancer metastasis. Molecular Cell, 82(16), 3045-3060.e11. https://doi.org/10.1016/j.molcel.2022.06.005

Zhang, H., Lin, X., & Zha, S. (2022). Revisiting PARP2 and PARP1 trapping through quantitative live-cell imaging. Biochemical Society Transactions, 50(4), 1169–1177. https://doi.org/10.1042/bst20220366

Liu, Y., Liu, Y., Ye, S., Feng, H., & Ma, L. (2022). Development and validation of cuproptosis-related gene signature in the prognostic prediction of liver cancer. Frontiers in Oncology, 12. https://doi.org/10.3389/fonc.2022.985484

Venkataramani, V., Yang, Y., Schubert, M. C., Reyhan, E., Tetzlaff, S. K., Wißmann, N., Botz, M., Soyka, S. J., Beretta, C. A., Pramatarov, R. L., Fankhauser, L., Garofano, L., Freudenberg, A., Wagner, J., Tanev, D. I., Ratliff, M., Xie, R., Kessler, T., Hoffmann, D. C., … Winkler, F. (2022). Glioblastoma hijacks neuronal mechanisms for brain invasion. Cell, 185(16), 2899-2917.e31. https://doi.org/10.1016/j.cell.2022.06.054

Akalu, Y. T., Mercau, M. E., Ansems, M., Hughes, L. D., Nevin, J., Alberto, E. J., Liu, X. N., He, L.-Z., Alvarado, D., Keler, T., Kong, Y., Philbrick, W. M., Bosenberg, M., Finnemann, S. C., Iavarone, A., Lasorella, A., Rothlin, C. V., & Ghosh, S. (2022). Tissue-specific modifier alleles determine Mertk loss-of-function traits. ELife, 11. CLOCKSS. https://doi.org/10.7554/elife.80530

Harimoto, T., Hahn, J., Chen, Y.-Y., Im, J., Zhang, J., Hou, N., Li, F., Coker, C., Gray, K., Harr, N., Chowdhury, S., Pu, K., Nimura, C., Arpaia, N., Leong, K. W., & Danino, T. (2022). A programmable encapsulation system improves delivery of therapeutic bacteria in mice. Nature Biotechnology, 40(8), 1259–1269. https://doi.org/10.1038/s41587-022-01244-y

Bal, E., Kumar, R., Hadigol, M., Holmes, A. B., Hilton, L. K., Loh, J. W., Dreval, K., Wong, J. C. H., Vlasevska, S., Corinaldesi, C., Soni, R. K., Basso, K., Morin, R. D., Khiabanian, H., Pasqualucci, L., & Dalla-Favera, R. (2022). Super-enhancer hypermutation alters oncogene expression in B cell lymphoma. Nature, 607(7920), 808–815. https://doi.org/10.1038/s41586-022-04906-8

Alvarez, S., da Silva Almeida, A. C., Albero, R., Biswas, M., Barreto-Galvez, A., Gunning, T. S., Shaikh, A., Aparicio, T., Wendorff, A., Piovan, E., Van Vlierberghe, P., Gygi, S., Gautier, J., Madireddy, A., & A. Ferrando, A. (2022). Functional mapping of PHF6 complexes in chromatin remodeling, replication dynamics, and DNA repair. Blood, 139(23), 3418–3429. https://doi.org/10.1182/blood.2021014103

Varn, F. S., Johnson, K. C., Martinek, J., Huse, J. T., Nasrallah, M. P., Wesseling, P., Cooper, L. A. D., Malta, T. M., Wade, T. E., Sabedot, T. S., Brat, D., Gould, P. V., Wöehrer, A., Aldape, K., Ismail, A., Sivajothi, S. K., Barthel, F. P., Kim, H., Kocakavuk, E., … Verhaak, R. GW. (2022). Glioma progression is shaped by genetic evolution and microenvironment interactions. Cell, 185(12), 2184-2199.e16. https://doi.org/10.1016/j.cell.2022.04.038

Webster Carrion, A., Wei, H.-J., McQuillan, N., Tazhibi, M., Kokossis, D., Berg, X., Minns, H., Zhang, X., Zhang, Z., Wang, J., Fernandez, E. C., Jan, C.-I., Padilla, O., Gartrell, R. D., Becher, O., Jr, J. H. G., Pavisic, J., Szalontay, L., Konofagou, E. E., … Wu, C.-C. (2022). MODL-24. Focused ultrasound-mediated blood-brain barrier opening and panobinostat in a thalamic syngeneic murine DMG model is feasible and safe. Neuro-Oncology, 24(Supplement_1), i174–i174. https://doi.org/10.1093/neuonc/noac079.647

McQuillan, N., Tazhibi, M., Wei, H.-J., Pouliopoulos, A., Bendau, E., Carrion, A. W., Berg, A., Kokossis, D., Zhang, X., Zhang, Z., Englander, Z., Yoh, N., Jan, C.-I., Gartrell, R. D., Garvin, J., Szalontay, L., Konofagou, E., Zacharoulis, S., & Wu, C.-C. (2022). MODL-25. Radiation and focused ultrasound–mediated blood–brain barrier opening for DMG: safety and feasibility of combinatorial therapy. Neuro-Oncology, 24(Supplement_1), i174–i174. https://doi.org/10.1093/neuonc/noac079.648

Fernández, E. C., Wang, J., Griffin, A., Minns, H., Wei, H.-J., Zhang, X., Szalontay, L., Mundi, P., Wu, C.-C., Gartrell, R., Zacharoulis, S., Califano, A., & Pavisic, J. (2022). DIPG-57. A systems biology approach to defining and targeting master regulator dependencies from bulk and single-Cell RNA-seq in diffuse midline glioma (DMG). Neuro-Oncology, 24(Supplement_1), i31–i32. https://doi.org/10.1093/neuonc/noac079.114