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Min Kyu Kim, PhD, MS

Title(s)Assistant Professor, Cellular Molecular Pharmacology
SchoolSchool of Medicine
Address1700 4th Street
San Francisco CA 94158
Phone415-476-3068
ORCID ORCID Icon0000-0002-1139-2279 Additional info
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    Collapse Biography 
    Collapse Education and Training
    KAISTB.Sc.1992Biology
    Seoul National UniversityM.S.1995Molecular Biology
    Seoul National UniversityPh.D.2000Biological Sciences
    Seoul National University PostDoc2001Biological Sciences
    Harvard Medical SchoolPostDoc2009Biological Chemistry and Molecular Pharmacology
    Collapse Awards and Honors
    KAIST1992Cum laude
    Korea Research Foundation1995  - 1996Pre-doctoral Fellowship for Future Researchers
    Harvard Medical School2004BCMP Discovery of the Year
    The Medical Foundation2005  - 2007Charles A. King Trust Postdoctoral Fellowship
    Helen Diller Family Comprehensive Cancer Center, UCSF2016  - 2017Martha and Bruce Atwater Breast Cancer Research Award
    UCSF2016  - 2017Program for Breakthrough Biomedical Research (PBBR) Award
    Helen Diller Family Comprehensive Cancer Center, UCSF2018  - 2019Give Breast Cancer The Boot Award
    UCSF Wolfe Meningioma Program2018  - 2019Wolfe Meningioma Program Project Award
    Helen Diller Family Comprehensive Cancer Center, UCSF2018  - 2021Martha and Bruce Atwater Breast Cancer Research Award
    UCSF Prostate Cancer Program2019  - 2019Prostate Cancer Program Research Pilot Funding Award
    Helen Diller Family Comprehensive Cancer Center, UCSF2020  - 2020Benioff Initiative for Prostate Cancer Research Funding

    Collapse Overview 
    Collapse Overview
    Physical and Genetic Interaction Networks Governing Pathway Deregulation in Cancer

    A central question in cancer genetics is how variations in DNA sequence (genotypic heterogeneity), dispersed across a multitude of genes and proteins, elicit similar phenotypes and patient outcomes. However, different genetic drivers of a trait often aggregate, rather than randomly located, in the molecular networks such as those that underlie protein complexes or signaling pathways, emphasizing the importance of network-based approaches in cancer research. We investigates protein-protein and genetic interactions, using the large-scale proteomics and genomics, to dissect functions of protein complexes and biological pathways during cellular proliferation and/or tumorigenesis as they are formed and turned on. Indeed, our analysis identifies novel PIK3CA-interacting proteins which repress AKT signaling, and UBE2N emerges as a BRCA1 interactor predictive of clinical response to inhibition of PARP in the context of the I-SPY 2 clinical trial. Thus, cancer protein interaction landscapes provide a framework to recognize oncogenic drivers and drug vulnerabilities, for which new and effective therapeutic strategies could be developed.


    Functional Interactome of DNA Damage Response-Deficient Breast Cancer

    The DNA damage response (DDR) requires the interaction of proteins involved in DNA repair, and that the coordinated regulation of these interactions is fundamental to maintain genome stability. To define functional DDR interactome, we identified 240 proteins that physically interact with 10 breast cancer susceptible DNA repair proteins (BRCA1, BRCA2, BRIP1, CHEK2, PALB2, RAD51C, RAD51D, MLH1, MSH2, XPC), and assessed the role of these interacting proteins in DDR by analyzing cellular response to DDR-targeting drugs (cisplatin and olaparib) upon knocking these genes out by CRISPR/Cas9. These efforts uncovered multiple novel “BRCAness” genes (ARAF, UBE2N, RRP9, SAFB, CDCA5, MCM10, etc) to which current BRCA-targeted therapy could be applied. Furthermore, this approach identified a novel protein (Spinophilin) which interacts with BRCA1. Knockdown of Spinophilin led to significant impairment in DNA double-strand break repair by both homologous recombination and single-strand annealing pathways, establishing that this protein has a defined role in DNA repair. Further analysis indicates that Spinophilin dephosphorylates and thus modulate BRCA1 functions via direct interaction. Importantly, Spinophilin is frequently amplified in ~8% (87 out of 1093) of sequenced breast cancer patient tumors (TCGA Study), which is higher than the alteration frequency of BRCA1 (3%) and BRCA2 (4%). Our finding suggests that Spinophilin-amplified tumors may arise due to abnormal regulation of DDR.


    Rational Repurposing of Kinase Inhibitors for SARS-CoV-2 Combination Therapy

    The development of therapeutic strategies against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an urgent global research priority. Identifying host targets of SARS-CoV-2 offers the potential to develop efficient therapies with a fast development timeline by avoiding viral escape mechanisms and utilizing repurposed FDA-approved drugs. We recently identified 332 host factors that interact with SARS-CoV-2, including 66 that are targeted by 109 FDA-approved drugs, investigational new drugs (INDs), and preclinical compounds. Among these, inhibitors of mRNA translation and predicted regulators of the Sigma1 and Sigma2 receptors demonstrated antiviral activity in vitro. To obtain additional potential drug targets, we utilized the orthogonal approach of global phosphorylation proteomic profiling upon SARS-CoV-2 infection in Vero E6 cells to gain a snapshot of signaling pathways that are rewired during virus infection. Profiling of differentially regulated kinase activities and pathways revealed 87 kinase inhibitors, with inhibitors of p38, CK2, CDKs, AXL, and PIKFYVE kinases all showing in vitro antiviral activity. We will further expand on the portfolio of pharmacological interventions and drug repurposing by analyzing the proteome-wide impact of SARS-CoV-2 on protein abundance and phosphorylation over a clinically relevant time-course of infection in human cells.

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. The Global Phosphorylation Landscape of SARS-CoV-2 Infection. Cell. 2020 08 06; 182(3):685-712.e19. 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. PMID: 32645325.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    2. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. 2020 07; 583(7816):459-468. 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. PMID: 32353859.
      View in: PubMed   Mentions: 218     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    3. Mapping the protein-protein and genetic interactions of cancer to guide precision medicine. Curr Opin Genet Dev. 2019 02; 54:110-117. Bouhaddou M, Eckhardt M, Chi Naing ZZ, Kim M, Ideker T, Krogan NJ. PMID: 31288129.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    4. 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. Kim K, Heo DH, Kim I, Suh JY, Kim M. PMID: 27076633.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    5. 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. Park J, Kang M, Kim M. PMID: 25722373.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    6. 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. Heo DH, Yoo I, Kong J, Lidschreiber M, Mayer A, Choi BY, Hahn Y, Cramer P, Buratowski S, Kim M. PMID: 24196955.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    7. Cooperative interaction of transcription termination factors with the RNA polymerase II C-terminal domain. Nat Struct Mol Biol. 2010 Oct; 17(10):1195-201. Lunde BM, Reichow SL, Kim M, Suh H, Leeper TC, Yang F, Mutschler H, Buratowski S, Meinhart A, Varani G. PMID: 20818393.
      View in: PubMed   Mentions: 62     Fields:    Translation:HumansCells
    8. Phosphorylation of the yeast Rpb1 C-terminal domain at serines 2, 5, and 7. J Biol Chem. 2009 Sep 25; 284(39):26421-6. Kim M, Suh H, Cho EJ, Buratowski S. PMID: 19679665.
      View in: PubMed   Mentions: 70     Fields:    Translation:AnimalsCells
    9. 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. Vasiljeva L, Kim M, Mutschler H, Buratowski S, Meinhart A. PMID: 18660819.
      View in: PubMed   Mentions: 135     Fields:    Translation:AnimalsCells
    10. Transcription termination and RNA degradation contribute to silencing of RNA polymerase II transcription within heterochromatin. Mol Cell. 2008 Feb 15; 29(3):313-23. Vasiljeva L, Kim M, Terzi N, Soares LM, Buratowski S. PMID: 18280237.
      View in: PubMed   Mentions: 72     Fields:    Translation:AnimalsCells
    11. Dynamics of replication-independent histone turnover in budding yeast. Science. 2007 Mar 09; 315(5817):1405-8. Dion MF, Kaplan T, Kim M, Buratowski S, Friedman N, Rando OJ. PMID: 17347438.
      View in: PubMed   Mentions: 291     Fields:    Translation:AnimalsCells
    12. Distinct pathways for snoRNA and mRNA termination. Mol Cell. 2006 Dec 08; 24(5):723-734. Kim M, Vasiljeva L, Rando OJ, Zhelkovsky A, Moore C, Buratowski S. PMID: 17157255.
      View in: PubMed   Mentions: 98     Fields:    Translation:AnimalsCells
    13. Single-nucleosome mapping of histone modifications in S. cerevisiae. PLoS Biol. 2005 Oct; 3(10):e328. Liu CL, Kaplan T, Kim M, Buratowski S, Schreiber SL, Friedman N, Rando OJ. PMID: 16122352.
      View in: PubMed   Mentions: 248     Fields:    Translation:AnimalsCells
    14. The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II. Nature. 2004 Nov 25; 432(7016):517-22. Kim M, Krogan NJ, Vasiljeva L, Rando OJ, Nedea E, Greenblatt JF, Buratowski S. PMID: 15565157.
      View in: PubMed   Mentions: 213     Fields:    Translation:AnimalsCells
    15. Transitions in RNA polymerase II elongation complexes at the 3' ends of genes. EMBO J. 2004 Jan 28; 23(2):354-64. Kim M, Ahn SH, Krogan NJ, Greenblatt JF, Buratowski S. PMID: 14739930.
      View in: PubMed   Mentions: 159     Fields:    Translation:Cells
    16. 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. Ahn SH, Kim M, Buratowski S. PMID: 14731395.
      View in: PubMed   Mentions: 219     Fields:    Translation:AnimalsCells
    17. 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. Nedea E, He X, Kim M, Pootoolal J, Zhong G, Canadien V, Hughes T, Buratowski S, Moore CL, Greenblatt J. PMID: 12819204.
      View in: PubMed   Mentions: 94     Fields:    Translation:AnimalsCells
    18. 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. 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. PMID: 12773564.
      View in: PubMed   Mentions: 287     Fields:    Translation:AnimalsCells
    19. Post-transcriptional regulation of ura4+ gene expression by glucose in Schizosaccharomyces pombe. Mol Cells. 2002 Dec 31; 14(3):437-43. Kim MJ, Kim M, Park SD. PMID: 12521309.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    20. RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach. Mol Cell Biol. 2002 Oct; 22(20):6979-92. Krogan NJ, Kim M, Ahn SH, Zhong G, Kobor MS, Cagney G, Emili A, Shilatifard A, Buratowski S, Greenblatt JF. PMID: 12242279.
      View in: PubMed   Mentions: 237     Fields:    Translation:AnimalsCells
    21. 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. Jang YK, Kim M, Dai Park S. PMID: 12074602.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    22. 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. Cho EJ, Kobor MS, Kim M, Greenblatt J, Buratowski S. PMID: 11751637.
      View in: PubMed   Mentions: 180     Fields:    Translation:AnimalsCells
    23. 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 01; 28(17):3392-402. Kim M, Lee W, Park J, Kim JB, Jang YK, Seong RH, Choe SY, Park SD. PMID: 10954610.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    24. Identification and expression of uvi31+, a UV-inducible gene from Schizosaccharomyces pombe. Environ Mol Mutagen. 1997; 30(1):72-81. Kim SH, Kim M, Lee JK, Kim MJ, Jin YH, Seong RH, Hong SH, Joe CO, Park SD. PMID: 9258332.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    25. Characterization of uvi15+, a stress-inducible gene from Schizosaccharomyces pombe. Mol Gen Genet. 1995 Mar 20; 246(6):663-70. Lee JK, Kim M, Choe J, Seong RH, Hong SH, Park SD. PMID: 7898433.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
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