Yale Cancer Biology Institute Publications 2023

Mudumbi, K., Burns, E., Schodt, D., Petrova, Z., Kiyatkin, A., Kim, L., Mangiacapre, E., Ortiz-Caraveo, I., Rivera Ortiz, H., Hu, C., Ashtekar, K., Lidke, K., Lidke, D., Lemmon, M. (2023) Distinct interactions stabilize EGFR dimers and higher-order oligomers in cell membranes(Link is external). Cell Reports. doi: 10.1016/j.celrep.2023.113603. PMID: 38117650

Bergaggio, E., Tai, WT., Aroldi, A., Mecca, C., Landoni, E., Nüesch, M., Mota, I., Metovic, J., Molinaro, L., Ma, L., Alvarado, D., Ambrogio, C., Voena, C., Blasco, RB., Li, T., Klein, D., Irvine, DJ., Papotti, M., Savoldo, B., Dotti, G., Chiarle, R. (2023) ALK inhibitors increase ALK expression and sensitize neuroblastoma cells to ALK.CAR-T cells.(Link is external) Cancer Cell. doi: 10.1016/j.ccell.2023.11.004. PMID: 38039964

Huang, X., Gan, Z., Cui, H., Lan, T., Liu, Y., Caron, E., Shao, W. (2023) The SysteMHC Atlas v2.0, an updated resource for mass spectrometry-based immunopeptidomics.(Link is external) Nucleic Acids Research. doi: 10.1093/nar/gkad1068. PMID: 38000392

Walker, G., Brown, C., Ge, X., Kumar, S., Muzumdar, M., Gupta, K., Bhattacharyya, M. (2023) Oligomeric organization of membrane proteins from native membranes at nanoscale spatial and single-molecule resolution.(Link is external) Nature Nanotechnology. doi: 10.1038/s41565-023-01547-4. PMID: 38012273

Gui, Y., Palanza, Z., Gupta, P., Li, H., Pan, Y., Wang, Y., Hargis, G., Kreutzer, D., Wang, Y., Bastacky, S., Liu, Y., Liu, S., Zhou, D. (2023) Calponin 2 regulates ketogenesis to mitigate acute kidney injury.(Link is external) JCI Insight. doi: 10.1172/jci.insight.170521. PMID: 37751293

Chongsaritsinsuk, J., Steigmeyer, A., Mahoney, K., Rosenfeld, M., Lucas, T., Smith, C., Li, A., Ince, D., Kearns, F., Battison, A., Hollenhorst, M., Shon, J., Tiemeyer, K., Attah, V., Kwon, C., Bertozzi, C., Ferracane, M., Lemmon, M., Amaro, R., Malaker, S. (2023) Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE(Link is external)Nature Communications. PMID: 37794035 PMCID: PMC10550946 DOI: 10.1038/s41467-023-41756-y

Joo, Y., Black, E., Trier, I., Haakma, W., Zou, L., Kabeche, L. (2023) ATR promotes clearance of damaged DNA and damaged cells by rupturing micronuclei.(Link is external) Molecular Cell.  doi: 10.1016/j.molcel.2023.09.003. PMID: 37788673

Reilly, L., Lara, E., Ramos, D., Li, Z., Pantazis, C., Stadler, J., Santiana, M., Roberts, J., Faghri, F., Hao, Y., Nalls, M., Narayan, P., Liu, Y., Singleton, A., Cookson, M., Ward, M., Qi, Y. (2023) A fully automated FAIMS-DIA mass spectrometry-based proteomic pipeline(Link is external). Cell Reports Methods. PMID: 37729920 DOI: 10.1016/j.crmeth.2023.100593

Ruiz, C., Garcia, C., Jacox, J., Lawres, L., Muzumdar, M. (2023) Decoding the obesity-cancer connection: lessons from preclinical models of pancreatic adenocarcinoma.(Link is external) Life Science Alliance. doi: 10.26508/lsa.202302228 PMID: 37648285

Girish, V., Lakhani, A., Thompson, S., Scaduto, C., Brown, L., Hagenson, R., Sausville, E., Mendelson, B., Kandikuppa, P., Lukow, D., Yuan, M., Stevens, E., Lee, S., Schukken, K., Akalu, S., Vasudevan, A., Zou, C., Salovska, B., Li, W., Smith, J., Taylor, A., Martienssen, R., Liu, Y., Sun, R., Sheltzer, J. (2023) Oncogene-like addiction to aneuploidy in human cancers.(Link is external) Science. doi:10.1126/science.adg4521 PMID: 37410869

Zhou, W., Li, W., Wang, S., Salovska, B., Hu, Z., Tao, B., Di, Y., Punyamurtula, U., Turk, B., Sessa, W., Liu, Y. (2023) An optogenetic-phosphoproteomic study reveals dynamic Akt1 signaling profiles in endothelial cells.(Link is external) Nature Communications. doi: 10.1038/s41467-023-39514-1 PMID: 37365174

Trier, I., Black, E., Joo, Y., Kabeche, L. (2023) ATR protects centromere identity by promoting DAXX association with PML nuclear bodies.(Link is external) Cell Reports. doi: 10.1016/j.celrep.2023.112495 PMID: 37163376

Martin-Rufino, J., Castano, N., Pang, M., Grody, E., Joubran, S., Caulier, A., Wahlster, L., Li, T., Qiu, X., Riera-Escandell, A., Newby, G., Al’Khafaji, A., Chaudhary, S., Black, S., Weng, C., Munson, G., Liu, D., Wlodarski, M., Sims, K., Oakley, J., Fasano, R., Xavier, R., Lander, E., Klein, D., Sankaran, V. (2023) Massively parallel base editing to map variant effects in human hematopoiesis.(Link is external) Cell. doi: 10.1016/j.cell.2023.03.035. PMID: 37137305

Bali, A., Schaefer, S., Trier, I., Zhang, A., Kabeche, L., Paulsen, C. (2023) Molecular mechanism of hyperactivation conferred by a truncation of TRPA1(Link is external). Nature Communications. PMID: 37208332 DOI: 10.1038/s41467-023-38542-1

Perez-Pepe, M., Desotell, A., Li, H., Li, W., Han, B., Lin, Q., Klein, D., Liu, Y., Goodarzi, H., Alarcón, C. (2023) 7SK methylation by METTL3 promotes transcriptional activity.(Link is external) Science Advances. doi: 10.1126/sciadv.ade7500 PMID: 37163588

Berko, E., Witek, G., Matkar, S., Petrova, Z., Wu, M., Smith, C., Daniels, A., Kalna, J., Kennedy, A., Gostuski, I., Casey, C., Krytska, K., Gerelus, M., Pavlick, D., Ghazarian, S., Park, J., Marachelian, A., Maris, J., Goldsmith, K., Radhakrishnan, R., Lemmon, M., Mossé YP. (2023) Circulating tumor DNA reveals mechanisms of lorlatinib resistance in patients with relapsed/refractory ALK-driven neuroblastoma.(Link is external) Nature Communications. PMID: 37147298 doi: 10.1038/s41467-023-38195-0

McNamara, B., Harold, J., Manavella, D., Bellone, S., Mutlu, L., Hartwich, TMP., Zipponi, M., Yang-Hartwich, Y., Demirkiran, C., Verzosa MSZ, Yang, K., Choi, J., Dong, W., Buza, N., Hui, P., Altwerger, G., Huang, GS., Andikyan, V., Clark, M., Ratner, E., Azodi, M., Schwartz, PE., Burton, EA., Inagaki, H., Albers, A., Zhang, C., Bollag, G., Schlessinger, J., Santin, AD. (2023) Uterine leiomyosarcomas harboring MAP2K4 gene amplification are sensitive in vivo to PLX8725, a novel MAP2K4 inhibitor.(Link is external) Gynecologic Oncology. doi: 10.1016/j.ygyno.2023.03.009. PMID: 36958197

Krimmer, SG., Bertoletti, N., Suzuki, Y., Katic, L., Mohanty, J., Shu, S., Lee, S., Lax, I., Mi., W, Schlessinger, J. (2023) Cryo-EM analyses of KIT and oncogenic mutants reveal structural oncogenic plasticity and a target for therapeutic intervention.(Link is external) Proc. Natl. Acad. Sci. U.S.A. PMID: 36943885 DOI: 10.1073/pnas.2300054120

Grant, M., Aredo, J., Starrett, J., Stockhammer, P., van Alderwerelt van Rosenburgh, I., Wurtz, A., Piper-Valillo, A., Piotrowska, Z., Falcon, C., Yu, H., Aggarwal, C., Scholes, D., Patil, T., Nguyen, C., Phadke, M., Li, FY., Neal, J., Lemmon, M., Walther, Z., Politi, K., Goldberg, S. (2023) Efficacy of osimertinib in patients with lung cancer positive for uncommon EGFR exon 19 deletion mutations(Link is external)Clinical Cancer Research. PMID: 36913537 DOI: 10.1158/1078-0432.CCR-22-3497

Chen, Y., Ge, Y., Han, X., Hao, L., Huan, T., Li, L., Li, L., Li, W., Liang, X., Lin, Y., Liu, X., Liu, Y., Ma, S., Peng, J., Shou, W., Sun, L., Tao, AW., Tian, Y., Wang, KY., Wang, Y., Wu, R., Wu, S., Xia, J.,Yang, Z., Zhang, H., Zhang, H., Zhao, S., Weng, N., Huang, L. (2023) Meeting Report on the 2nd Chinese American Society for Mass Spectrometry Conference: Advancing Biological and Pharmaceutical Mass Spectrometry(Link is external)Molecular & Cellular Proteomics. PMID: 37105363 PMCID: PMC10245319 DOI: 10.1016/j.mcpro.2023.100559

Di, Y., Li, W., Salovska, B., Ba, Q., Hu, Z., Wang, S., Liu, Y. (2023) A basic phosphoproteomic-DIA workflow integrating precise quantification of phosphosites in systems biology(Link is external). Biophysics Reports. PMID: 37753060 PMCID: PMC10518521 DOI: 10.52601/bpr.2023.230007

Salovska, B., Gao, E., Müller-Dott, S., Li, W., Cordon, C., Wang, S., Dugourd, A., Rosenberger, G., Saez-Rodriguez, J., Liu, Y. (2023) Phosphoproteomic analysis of metformin signaling in colorectal cancer cells elucidates mechanism of action and potential therapeutic opportunities(Link is external)Clinical and Translational Medicine. PMID: 36781298 PMCID: PMC9925373 DOI: 10.1002/ctm2.1179

Salovska, B., Liu, Y. (2023) Post-translational modification and phenotype(Link is external)Proteomics. PMID: 36799530 DOI: 10.1002/pmic.202200535

Hu, Z., Chen, PH., Li, W., Douglas, T., Hines, J., Liu, Y., Crews, C. (2023) Targeted Dephosphorylation of Tau by Phosphorylation Targeting Chimeras (PhosTACs) as a Therapeutic Modality(Link is external). Journal of the American Chemical Society. PMID: 36753634 DOI: 10.1021/jacs.2c11706

An, S., Mohanty, J., Tome, F., Suzuki, Y., Lax, I., Schlessinger, J. (2023) Heparin is essential for optimal cell signaling by FGF21 and for regulation of βKlotho cellular stability(Link is external)Proc. Natl. Acad. Sci. USA. PMID: 36745784 DOI: 10.1073/pnas.2219128120

Ren, P., Peng, L., Yang, L., Suzuki, K., Fang, Z., Renauer, P., Lin, Q., Bai, M., Li, T., Clark, P., Klein, D., Chen, S. (2023) RAMIHM generates fully human monoclonal antibodies by rapid mRNA immunization of humanized mice and BCR-seq(Link is external). Cell Chemical Biology. PMID: 36640761 DOI: 10.1016/j.chembiol.2022.12.005