Programs
Departments & Divisions
Institutes & Centers
Research Areas
Cancer Longevity & AgingMin Kyu Kim, PhD, MS
Assistant Professor
Currently seeking M.S. & Ph.D. students
Subspecialties: Large-scale Quantitative Proteomics; DNA Damage Response and DNA Repair Mechanisms; Cancer Systems and Protein interaction Network Biology
I am interested in profiling protein-protein interactions and post-translational modifications of proteins governing pathway deregulation in cancer and other human diseases using cutting-edge mass spectrometry-based proteomics. Particularly, my laboratory is studying how protein-protein interactions and various cellular signaling cascades (including phosphorylation, ubiquitylation, and methylation) regulate genome integrity during cellular DNA damage response. Given that many types of human cancer are caused by defects in executing DNA damage repair, identifying novel interaction partners and regulatory cues of DNA repair proteins will enable us to pinpoint novel cancer-associated genes and therapeutic vulnerabilities of cancer cells that could be targeted in the clinic for precision oncology.
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Professional Background
Education
- 2000 - PhD - Molecular Biology - Seoul National University, South Korea
- 1995 - MS - Molecular Biology - Seoul National University, South Korea
- 1992 - BSc - Biology - Korea Advanced Institute of Science and Technology, South Korea
Training
- 2009 - Postdoctoral Fellow - Biochemistry/Proteomics - Harvard Medical School
- 2001 - Postdoctoral Fellow - Molecular Biology - Seoul National University, South Korea
Highlights
2019 Prostate Cancer Program Pilot Funding Award, UCSF
2018 Breast Cancer Research Award, UCSF
2005 Charles A. King Trust Post-Doctoral Fellowship, the Medical Foundation, MA
2004 BCMP Discovery of the Year Award, Harvard Medical School
1992 Cum laude, Korea Advanced Institute of Science and Technology, Korea
Appointments
- 2023-04 - present - Assistant Professor - University of Texas Health Science Center, San Antonio
- 2015-01 - 2023-04 - Assistant Adjunct Professor - University of California San Francisco
- 2010-01 - 2014-12 - WCU Assistant Professor - Seoul National University, South Korea
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Research & Grants
I investigate physical and functional protein-protein interactions (PPIs) using large-scale proteomics methods to dissect functions of protein complexes and biological pathways.
For example, PPI mapping of DNA repair proteins (altered in many tumors) identifies many new DNA damage response (DDR)-associated proteins. One such protein, Spinophilin interacts with BRCA1 and regulates DNA double-strand break repair by dephosphorylating BRCA1 and other DDR proteins. Thus, the interactome study enables us to recognize novel regulatory mechanisms of DDR and provides a basis to build a hierarchy of DNA repair protein complexes and systems, for which new and effective therapeutic strategies could be developed to cure cancers.
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Service
School
2023 - present Mass Spectrometry Core Laboratory Associate Director
Service to the Profession
2023 - 2023 Florida Breast Cancer Foundation Grant Reviewer
National
2023 - 2023 NIH Study Section (Cancer Etiology) Early Career Reviewer
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Publications
Chou J, Robinson TM, Egusa EA, Lodha R, Zhang M, Badura M, Mikayelyan M, Delavan H, Swinderman J, Wilson C, Zhu J, Das R, Nguyen M, Loehr A, Golsorkhi T, Simmons A, Abida W, Chinnaiyan AM, Arkin MR, Small EJ, Quigley DA, Yang L, Kim M, Ashworth A, Feng FY. Synthetic Lethal Targeting of Cyclin Dependent Kinase-12-Deficient Prostate Cancer with PARP Inhibitors. Clin Cancer Res. 2024 Sep 25;. doi: 10.1158/1078-0432.CCR-23-3785. [Epub ahead of print] PubMed PMID: 39321214.
Jeelani I, Moon JS, da Cunha FF, Nasamran CA, Jeon S, Zhang X, Bandyopadhyay GK, Dobaczewska K, Mikulski Z, Hosseini M, Liu X, Kisseleva T, Brenner DA, Singh S, Loomba R, Kim M, Lee YS. HIF-2α drives hepatic Kupffer cell death and proinflammatory recruited macrophage activation in nonalcoholic steatohepatitis. Sci Transl Med. 2024 Sep 11;16(764):eadi0284. doi: 10.1126/scitranslmed.adi0284. Epub 2024 Sep 11. PubMed PMID: 39259813.
Yang Y, Badura ML, O'Leary PC, Delavan HM, Robinson TM, Egusa EA, Zhong X, Swinderman JT, Li H, Zhang M, Kim M, Ashworth A, Feng FY, Chou J, Yang L. Large tandem duplications in cancer result from transcription and DNA replication collisions. medRxiv. 2024 Jan 10;. doi: 10.1101/2023.05.17.23290140. PubMed PMID: 38260434; PubMed Central PMCID: PMC10802642.
Muralidharan M, Krogan NJ, Bouhaddou M, Kim M. Current proteomics methods applicable to dissecting the DNA damage response. NAR Cancer. 2023 Jun;5(2):zcad020. doi: 10.1093/narcan/zcad020. eCollection 2023 Jun. PubMed PMID: 37213254; PubMed Central PMCID: PMC10198729.
Kratz A*, Kim M*, Kelly MR, Zheng F, Koczor CA, Li J, Ono K, Qin Y, Churas C, Chen J, Pillich RT, Park J, Modak M, Collier R, Licon K, Pratt D, Sobol RW, Krogan NJ, Ideker T. A multi-scale map of protein assemblies in the DNA damage response. Cell Syst. 2023 May 16;. doi: 10.1016/j.cels.2023.04.007. [Epub ahead of print] PubMed PMID: 37220749. (*co-first author).
O'Leary PC, Chen H, Doruk YU, Williamson T, Polacco B, McNeal AS, Shenoy T, Kale N, Carnevale J, Stevenson E, Quigley DA, Chou J, Feng FY, Swaney DL, Krogan NJ, Kim M, Diolaiti ME, Ashworth A. Resistance to ATR Inhibitors Is Mediated by Loss of the Nonsense-Mediated Decay Factor UPF2. Cancer Res. 2022 Nov 2;82(21):3950-3961. doi: 10.1158/0008-5472.CAN-21-4335. PubMed PMID: 36273492; PubMed Central PMCID: PMC9633439.
Chen H, Diolaiti ME, O'Leary PC, Rojc A, Krogan NJ, Kim M, Ashworth A. A Whole-Genome CRISPR Screen Identifies AHR Loss as a Mechanism of Resistance to a PARP7 Inhibitor. Mol Cancer Ther. 2022 Jul 5;21(7):1076-1089. doi: 10.1158/1535-7163.MCT-21-0841. PubMed PMID: 35439318; PubMed Central PMCID: PMC9769698.
Kim M, Park J, Bouhaddou M, Kim K, Rojc A, Modak M, Soucheray M, McGregor MJ, O'Leary P, Wolf D, Stevenson E, Foo TK, Mitchell D, Herrington KA, Muñoz DP, Tutuncuoglu B, Chen KH, Zheng F, Kreisberg JF, Diolaiti ME, Gordan JD, Coppé JP, Swaney DL, Xia B, van 't Veer L, Ashworth A, Ideker T, Krogan NJ. A protein interaction landscape of breast cancer. Science. 2021 Oct;374(6563):eabf3066. doi: 10.1126/science.abf3066. Epub 2021 Oct 1. PubMed PMID: 34591612; PubMed Central PMCID: PMC9040556.
Swaney DL, Ramms DJ, Wang Z, Park J, Goto Y, Soucheray M, Bhola N, Kim K, Zheng F, Zeng Y, McGregor M, Herrington KA, O'Keefe R, Jin N, VanLandingham NK, Foussard H, Von Dollen J, Bouhaddou M, Jimenez-Morales D, Obernier K, Kreisberg JF, Kim M, Johnson DE, Jura N, Grandis JR, Gutkind JS, Ideker T, Krogan NJ. A protein network map of head and neck cancer reveals PIK3CA mutant drug sensitivity. Science. 2021 Oct;374(6563):eabf2911. doi: 10.1126/science.abf2911. Epub 2021 Oct 1. PubMed PMID: 34591642; PubMed Central PMCID: PMC9005332.
Zheng F, Kelly MR, Ramms DJ, Heintschel ML, Tao K, Tutuncuoglu B, Lee JJ, Ono K, Foussard H, Chen M, Herrington KA, Silva E, Liu SN, Chen J, Churas C, Wilson N, Kratz A, Pillich RT, Patel DN, Park J, Kuenzi B, Yu MK, Licon K, Pratt D, Kreisberg JF, Kim M, Swaney DL, Nan X, Fraley SI, Gutkind JS, Krogan NJ, Ideker T. Interpretation of cancer mutations using a multiscale map of protein systems. Science. 2021 Oct;374(6563):eabf3067. doi: 10.1126/science.abf3067. Epub 2021 Oct 1. PubMed PMID: 34591613; PubMed Central PMCID: PMC9126298.
Bouhaddou M, Memon D, Meyer B, White KM, Rezelj VV, Correa Marrero M, Polacco BJ, Melnyk JE, Ulferts S, Kaake RM, Batra J, Richards AL, Stevenson E, Gordon DE, Rojc A, Obernier K, Fabius JM, Soucheray M, Miorin L, Moreno E, Koh C, Tran QD, Hardy A, Robinot R, Vallet T, Nilsson-Payant BE, Hernandez-Armenta C, Dunham A, Weigang S, Knerr J, Modak M, Quintero D, Zhou Y, Dugourd A, Valdeolivas A, Patil T, Li Q, Hüttenhain R, Cakir M, Muralidharan M, Kim M, Jang G, Tutuncuoglu B, Hiatt J, Guo JZ, Xu J, Bouhaddou S, Mathy CJP, Gaulton A, Manners EJ, Félix E, Shi Y, Goff M, Lim JK, McBride T, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, De Wit E, Leach AR, Kortemme T, Shoichet B, Ott M, Saez-Rodriguez J, tenOever BR, Mullins RD, Fischer ER, Kochs G, Grosse R, García-Sastre A, Vignuzzi M, Johnson JR, Shokat KM, Swaney DL, Beltrao P, Krogan NJ. The Global Phosphorylation Landscape of SARS-CoV-2 Infection. Cell. 2020 Aug 6;182(3):685-712.e19. doi: 10.1016/j.cell.2020.06.034. Epub 2020 Jun 28. PubMed PMID: 32645325; PubMed Central PMCID: PMC7321036.
Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Meyer B, Roesch F, Vallet T, Mac Kain A, Miorin L, Moreno E, Naing ZZC, Zhou Y, Peng S, Shi Y, Zhang Z, Shen W, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Lyu J, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Rakesh R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Liboy-Lugo J, Lin Y, Huang XP, Liu Y, Wankowicz SA, Bohn M, Safari M, Ugur FS, Koh C, Savar NS, Tran QD, Shengjuler D, Fletcher SJ, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, Sharp PP, Wenzell NA, Kuzuoglu-Ozturk D, Wang HY, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Stroud RM, Frankel AD, Rosenberg OS, Verba KA, Agard DA, Ott M, Emerman M, Jura N, von Zastrow M, Verdin E, Ashworth A, Schwartz O, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor SN, Fraser JS, Gross JD, Sali A, Roth BL, Ruggero D, Taunton J, Kortemme T, Beltrao P, Vignuzzi M, García-Sastre A, Shokat KM, Shoichet BK, Krogan NJ. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. 2020 Jul;583(7816):459-468. doi: 10.1038/s41586-020-2286-9. Epub 2020 Apr 30. PubMed PMID: 32353859; PubMed Central PMCID: PMC7431030.
Bouhaddou M, Eckhardt M, Chi Naing ZZ, Kim M*, Ideker T*, Krogan NJ*. Mapping the protein-protein and genetic interactions of cancer to guide precision medicine. Curr Opin Genet Dev. 2019 Feb;54:110-117. doi: 10.1016/j.gde.2019.04.005. Epub 2019 Jul 6. Review. PubMed PMID: 31288129; PubMed Central PMCID: PMC6746583. (*co-corresponding authors)
Kim K, Heo DH, Kim I, Suh JY, Kim M. Exosome Cofactors Connect Transcription Termination to RNA Processing by Guiding Terminated Transcripts to the Appropriate Exonuclease within the Nuclear Exosome. J Biol Chem. 2016 Jun 17;291(25):13229-42. doi: 10.1074/jbc.M116.715771. Epub 2016 Apr 13. PubMed PMID: 27076633; PubMed Central PMCID: PMC4933236.
Park J, Kang M, Kim M. Unraveling the mechanistic features of RNA polymerase II termination by the 5'-3' exoribonuclease Rat1. Nucleic Acids Res. 2015 Mar 11;43(5):2625-37. doi: 10.1093/nar/gkv133. Epub 2015 Feb 26. PubMed PMID: 25722373; PubMed Central PMCID: PMC4357727.
Heo DH, Yoo I, Kong J, Lidschreiber M, Mayer A, Choi BY, Hahn Y, Cramer P, Buratowski S, Kim M. The RNA polymerase II C-terminal domain-interacting domain of yeast Nrd1 contributes to the choice of termination pathway and couples to RNA processing by the nuclear exosome. J Biol Chem. 2013 Dec 20;288(51):36676-90. doi: 10.1074/jbc.M113.508267. Epub 2013 Nov 6. PubMed PMID: 24196955; PubMed Central PMCID: PMC3868778.
Lunde BM, Reichow SL, Kim M, Suh H, Leeper TC, Yang F, Mutschler H, Buratowski S, Meinhart A, Varani G. Cooperative interaction of transcription termination factors with the RNA polymerase II C-terminal domain. Nat Struct Mol Biol. 2010 Oct;17(10):1195-201. doi: 10.1038/nsmb.1893. Epub 2010 Sep 5. PubMed PMID: 20818393; PubMed Central PMCID: PMC2950884.
Kim M, Suh H, Cho EJ, Buratowski S. Phosphorylation of the yeast Rpb1 C-terminal domain at serines 2, 5, and 7. J Biol Chem. 2009 Sep 25;284(39):26421-6. doi: 10.1074/jbc.M109.028993. Epub 2009 Aug 13. PubMed PMID: 19679665; PubMed Central PMCID: PMC2785330.
Vasiljeva L, Kim M, Mutschler H, Buratowski S, Meinhart A. The Nrd1-Nab3-Sen1 termination complex interacts with the Ser5-phosphorylated RNA polymerase II C-terminal domain. Nat Struct Mol Biol. 2008 Aug;15(8):795-804. doi: 10.1038/nsmb.1468. Epub 2008 Jul 27. PubMed PMID: 18660819; PubMed Central PMCID: PMC2597375.
Vasiljeva L, Kim M, Terzi N, Soares LM, Buratowski S. Transcription termination and RNA degradation contribute to silencing of RNA polymerase II transcription within heterochromatin. Mol Cell. 2008 Feb 15;29(3):313-23. doi: 10.1016/j.molcel.2008.01.011. PubMed PMID: 18280237; NIHMSID:NIHMS98684.
Dion MF, Kaplan T, Kim M, Buratowski S, Friedman N, Rando OJ. Dynamics of replication-independent histone turnover in budding yeast. Science. 2007 Mar 9;315(5817):1405-8. doi: 10.1126/science.1134053. PubMed PMID: 17347438.
Kim M, Vasiljeva L, Rando OJ, Zhelkovsky A, Moore C, Buratowski S. Distinct pathways for snoRNA and mRNA termination. Mol Cell. 2006 Dec 8;24(5):723-734. doi: 10.1016/j.molcel.2006.11.011. PubMed PMID: 17157255.
Liu CL, Kaplan T, Kim M, Buratowski S, Schreiber SL, Friedman N, Rando OJ. Single-nucleosome mapping of histone modifications in S. cerevisiae. PLoS Biol. 2005 Oct;3(10):e328. doi: 10.1371/journal.pbio.0030328. Epub 2005 Aug 30. PubMed PMID: 16122352; PubMed Central PMCID: PMC1195719.
Kim M, Krogan NJ, Vasiljeva L, Rando OJ, Nedea E, Greenblatt JF, Buratowski S. The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II. Nature. 2004 Nov 25;432(7016):517-22. doi: 10.1038/nature03041. PubMed PMID: 15565157.
Kim M, Ahn SH, Krogan NJ, Greenblatt JF, Buratowski S. Transitions in RNA polymerase II elongation complexes at the 3' ends of genes. EMBO J. 2004 Jan 28;23(2):354-64. doi: 10.1038/sj.emboj.7600053. Epub 2004 Jan 22. PubMed PMID: 14739930; PubMed Central PMCID: PMC1271760.
Ahn SH, Kim M, Buratowski S. Phosphorylation of serine 2 within the RNA polymerase II C-terminal domain couples transcription and 3' end processing. Mol Cell. 2004 Jan 16;13(1):67-76. doi: 10.1016/s1097-2765(03)00492-1. PubMed PMID: 14731395.
Nedea E, He X, Kim M, Pootoolal J, Zhong G, Canadien V, Hughes T, Buratowski S, Moore CL, Greenblatt J. Organization and function of APT, a subcomplex of the yeast cleavage and polyadenylation factor involved in the formation of mRNA and small nucleolar RNA 3'-ends. J Biol Chem. 2003 Aug 29;278(35):33000-10. doi: 10.1074/jbc.M304454200. Epub 2003 Jun 20. PubMed PMID: 12819204.
Krogan NJ*, Kim M*, Tong A, Golshani A, Cagney G, Canadien V, Richards DP, Beattie BK, Emili A, Boone C, Shilatifard A, Buratowski S, Greenblatt J. Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II. Mol Cell Biol. 2003 Jun;23(12):4207-18. doi: 10.1128/MCB.23.12.4207-4218.2003. PubMed PMID: 12773564; PubMed Central PMCID: PMC427527. (*equal contribution)
Kim MJ, Kim M, Park SD. Post-transcriptional regulation of ura4+ gene expression by glucose in Schizosaccharomyces pombe. Mol Cells. 2002 Dec 31;14(3):437-43. PubMed PMID: 12521309.
Krogan NJ, Kim M, Ahn SH, Zhong G, Kobor MS, Cagney G, Emili A, Shilatifard A, Buratowski S, Greenblatt JF. RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach. Mol Cell Biol. 2002 Oct;22(20):6979-92. doi: 10.1128/MCB.22.20.6979-6992.2002. PubMed PMID: 12242279; PubMed Central PMCID: PMC139818.
Jang YK, Kim M, Dai Park S. Fibrillarin binds to a 3' cis-regulatory element in pre-mRNA of uvi15+ in fission yeast. Biochem Biophys Res Commun. 2002 Jun 28;294(5):1184-90. doi: 10.1016/S0006-291X(02)00611-3. PubMed PMID: 12074602.
Cho EJ, Kobor MS, Kim M, Greenblatt J, Buratowski S. Opposing effects of Ctk1 kinase and Fcp1 phosphatase at Ser 2 of the RNA polymerase II C-terminal domain. Genes Dev. 2001 Dec 15;15(24):3319-29. doi: 10.1101/gad.935901. PubMed PMID: 11751637; PubMed Central PMCID: PMC312848.
Kim M, Lee W, Park J, Kim JB, Jang YK, Seong RH, Choe SY, Park SD. The stress-activated MAP kinase Sty1/Spc1 and a 3'-regulatory element mediate UV-induced expression of the uvi15(+) gene at the post-transcriptional level. Nucleic Acids Res. 2000 Sep 1;28(17):3392-402. doi: 10.1093/nar/28.17.3392. PubMed PMID: 10954610; PubMed Central PMCID: PMC110690.
Kim SH, Kim M, Lee JK, Kim MJ, Jin YH, Seong RH, Hong SH, Joe CO, Park SD. Identification and expression of uvi31+, a UV-inducible gene from Schizosaccharomyces pombe. Environ Mol Mutagen. 1997;30(1):72-81. doi: 10.1002/(sici)1098-2280(1997)30:1<72::aid-em10>3.0.co;2-n. PubMed PMID: 9258332.
Lee JK, Kim M, Choe J, Seong RH, Hong SH, Park SD. Characterization of uvi15+, a stress-inducible gene from Schizosaccharomyces pombe. Mol Gen Genet. 1995 Mar 20;246(6):663-70. doi: 10.1007/BF00290711. PubMed PMID: 7898433.