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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. Clinical and Translational Medicine. PMID: 36781298 PMCID: PMC9925373 DOI: 10.1002/ctm2.1179
 
Salovska, B., Liu, Y. (2023) Post-translational modification and phenotype. 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. 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. 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. Cell Chemical Biology. PMID: 36640761 DOI: 10.1016/j.chembiol.2022.12.005