Faculty

김홍숙 (Hong Sook Kim)  직함  전공  연구실  전화  사무실  이메일    조교수   분자생물학   분자시스템생물학연구실   031-290-7003   제2과학관 32110   hongkim@skku.edu

 Research Background                                                                                                                                                                                     

1. Epigenetics and Disease

▶ Cancer Epigenomics

- 폐암, 대장암에서의 유전체, 전사체 데이터 및 다양한 후성유전학 NGS 데이터를 이용하여 암 발생 및 암 진행에 관련된 작용 기전을 이해하고 임상적 의의를 규명하고자 함.

- 새롭게 구축된 알고리즘을 이용하여 발암 유전자를 발굴하고, 그것의 작용 기전 및 기능을 in vivo/in vitro 실험을 통해 증명함. 

- TCGA 데이터 분석을 통해 식별된 새로운 유전자 변이의 후성유전학적 조절 메커니즘을 연구하고, 그것의 기능을 규명함.

▶ Epigenetic regulation of Pluripotency and Differentiation

- 배아줄기세포의 pluripotency 단계에 따른 chromatin dynamics 연구.

- 배아줄기세포의 분화과정에서의 다이나믹한 후성유전체적 변화 연구.

 

2.Precision Medicine

▶ 암아형 분류 및 암아형의 분자적 특징 이해

-  암 유전체, 전사체, 임상 데이터 분석을 통한 암 아형 분류.

-  다양한 통계적 방법, computational 분석 tool 을 이용하여 암 아형에서의 분자적 특징 이해.

▶ 암 치료제 반응성 예측 바이오마커 발굴 및 작용 기전의 이해

-  병원과의 협력 연구, 또는 다양한 open database 를 이용하여 암 환자 치료제 반응성 임상 데이터 및 유전체, 전사체 데이터 수집하고, 치료 약물에 대한 반응성 예측 바이오 마커 발굴.

-  다양한 NGS 수행 및 분석, 분자생물학적 실험, in vivo/in vitro 실험을 통해 작용 기전 이해.

 

3.Molecular Biomarkers

-  암 외에도 다양한 human disease 가 존재하며, 이들 중 많은 수가 아직 진단, 치료 바이오 마커도 없는 상태이다. 질병의 상태 파악만이 가능하기 때문에 보통 침습성 방법을 통해 조직의 일부를 채취하여 질병 검사를 수행하게 되며, 그럴 경우 환자에게 큰 고통을 줄 뿐만 아니라, 부작용의 위험도 존재한다. 따라서, 비침습성 방법ㅡblood, urine-을 이용하여 질병을 진단할 수 있는 바이오 마커에 대한 연구를 수행중이다. 더 나아가, 치료 반응 정도를 모니터링 할 수 있는 바이오마커로의 적용까지 확대 연구 중이다.

 

 Academic Employments and Educcation                                                                                                                                                           

2020 -             Assostamt Professor, Dept.of Biological Sciences, Sungkyunkwan University, Korea

2018 - 2020      Senior Researcher, Dept.of Biological Sciences, Sungkyunkwan University, Korea

2013 - 2018      Assistant Project Scientist, Department of Medicine, University of California--San Diego, CA, USA

2009 - 2013      Postdoc Fellow, Department of Medicine, University of California-San Diego, CA, USA

2008 - 2009      Postdoc Fellow, Department of Medicine, University of California-Los Angeles, CA, USA

2007 - 2008      Postdoc Fellow, Department of Medicine, Seoul National University College Of Medicine, Seoul, Korea          

2003 - 2007      M.S., Dept. of Microbiology, Seoul National University College of Medicine, Seoul, Korea          

1998 - 2003      B.S., in Microbiological engineering Department of Engineering, KomKuk University, Seoul Korea          

 Research Publications                                                                                                                                                                                   

1.  Desitici E, Zhu Fm Tran S, Preissl S, Farah EN, Zhang Y, Hou X, Poiron OB, Lee AY, Grinstein JD, Bloomekatz J, Kim HS, Hu R, Evens SM, Ren B, Benner C, Chi N (2022) Human-gained heart enhancers are associate with species-specific cardiac attributes Nature Cardiovascular Research, accepted

2.  Bae GH, Kim YS, Park JY, Lee M, Lee SK, Kim JC, Kim JG, Shin YJ, Lee H, Kim SY, Bae YS, Zabel BA, Kim HS, Bae YS (2022) Unique characteristics of lung-resident neutrophils are maintained by PGE2/PKA/Tgm2-mediated signaling. Blood. 140(8):889-899.

3.  Yun JW*, Lee S*, Chun S, Lee KW, Kim J, Kim HS (2021) Comprehensive analysis of oncogenic signatures and consequent repurposed drugs in TMPRSS2:ERG fusion-positive prostate cancer Clinical and Translational Medicine, 11(5):e420

4.  Lee S, Cho S, Yoon Y, Pang C, Sohn J, Jeong J, Jeon B, Jang M, An C, Lee S, Kim Y, Kim G, Kim S, Kim Y, Lee G. Lee E, Lee E, Kim S, Kim HS, Kim Y, Kim H, Yang H, Kim S, Kim S, Chung H, Moon MH, Nam MH, Kwon JY, Won S, Park J, Weinstock GM, Lee C, Yoon KW, Park H (2021) Bifidobacterium bifidum strains synergize with immune checkpoint inhibitors to reduce tumour burden in mice Nature microbiology

5.  Kim HK, Joung JG, Choi YL, Lee SH, Park BJ, Choi YS, Ryu D, Nam JY, Lee MS, Park WY, Hwang S, Cha H, Kim HS, Lee S, Jung Y, Lee JE, Doh J, Paik S, Kang JH, Lee J, Kim J (2020) Earlier-Phased Cancer Immunity Cycle Strongly Influences Cancer Immunity in Operable Never-Smoker Lung Adenocarcinoma iSciecne

6.  Shim JH*, Kim HS*, Cha H*, Kim S, Kim TM, Anagnostou V, Choi YL, Jung HA, Sun JM, Ahn JS, Ahn MJ, Park K, Park WY, Lee SH (2020) HLA-corrected tumor mutation burden and homologous recombination deficiency for the prediction of response to PD-(L)1 blockade in advanced non-small-cell lung cancer patients Annals of Oncology (*co-first author)

7.  Kim K*, Kim HS*, Kim JY, Jung H, Sun J, Ahn JS, Ahn M, Park K, Lee SH, Choi JK (2020) Predicting clinical benefit of immunotherapy by antigenic or functional mutations affecting tumor immunogenicity Nature communications 11 (*co-first author)

8.  Lee J*, Kim HS*, Lee B, Kim HK, Sun J, Ahn JS, Ahn M, Park K, Lee SH (2020) Genomic landscape of acquired resistance to third-generation EGFR tyrosine kinase inhibitors in EGFR T790M-mutant non-small cell lung cancer Cancer (*co-first author)

9.  Almenar-Queralt A, Merkurjev D, Kim HS, Navarro M, Ma Q, Chaves RS, Alleque C, Driscoll SP, Chen AG, Kohlnhofer B, Fong LK, Woodruff G, Mackintosh C, Bohaciakova D, Hruska-Plochan M, Tadokoro T, Young JE, Hajj NE, Dittrich M, Marsala M, Goldstein LSB, Garcia-Bassets I (2019) Chromatin establishes an immature version of neuronal protocadherin selection during the naïve to primed conversion of pluripotent stem cells Nature genetics 51, 1691-1701

10.  Jung H*, Kim HS*, Kim JY, Sun J, Ahn JS, Ahn M, Park K, Esteller M, Lee S, Choi JK (2019) DNA methylation loss promotes immune evasion of tumours with high mutation and copy number load Nature communications 10: 4278 (*co-first author)

11.  Kim HS*, Cha H*, Kim J, Park W, Choi Y. Sun J, Ahn JS, Ahn M. Park K, Lee S (2019) Genomic scoring to determine clinical benefit of immunotherapy by targeted sequencing European journal of Cancer 120, 65-74 (*co-first author)

12.  Kim Y*, Kim CH*, Lee HY*, Lee S*, Kim HS, Lee S. Cha H, Hong S, Kim K, Seo SW, Sun J, Ahn M, Ahn JS, Park K (2019) Comprehensive Clinical and Genetic Characterization of Hyperprogression Based on Volumetry in Advanced Non-Small Cell Lung Cancer Treated with Immune Checkpoint Inhibitor Journal of Thoracic Oncology 14(9), 1608-161

13.  Cho JG, Choi JS, Lee JH, Cho MG, Kim HS, Noh HD, Lim KH, Park B, Kim JO, Park SG (2019) MED28 Over-Expression Shortens the Cell Cycle and Induces Genomic Instability Int. J. Mol. Sci 20(7), 1746

14.  Kim HS#, Tan Y, Ma W, Merkujev D, Destici E, Ma Q, Suter T, Ohgi K, Friedman M, Krawczyk D, Rosenfeld MG# (2018) Pluripotency factors functionally premark cell-type-restricted enhancers in ES cells. Nature doi:10.1038/s41586-018-0048-8 (#co-coresponding author)

15.  Cho JG, Park S, Lim CH, Kim HS, Song SY, Roh TY, Sung JH, Suh W, Ham SJ, Lim KH, Park SG (2016) ZNF224, Kruppel like zinc finger protein, induces cell growth and apoptosis-resistance by down-regulation of p21 and p53 via miR-663a. Oncotarget 7(21):31177-90

16.  Kim HS, Kim BH, Jung JE, Lee CS, Lee HG, Lee JW, Lee KH, You HJ, Chung MH, Ye SK (2016) Potential role of 8-oxoguanine DNA glycosylase 1 as a STAT1 coactivator in endotoxin-induced inflammatory response. Free Radic Biol Med 93:12-22

17.  Li W, Notani D, Ma Q, Tanasa B, Nunez E, Chen AY, Merkurjev D, Zhang J, Ohgi K, Song X, Oh S, Kim HS, Glass CK, Rosenfeld MG. (2013) Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation. Nature 498(7455):516-20.

18.  Tachdjian R, Al Khatib S, Schwinglshackl A, Kim HS, Chen A, Blasioli J, Mathias C, Kim HY, Umetsu DT, Oettgen HC, Chatila TA. (2010) In vivo regulation of the allergic response by the IL-4 receptor alpha chain immunoreceptor tyrosine-based inhibitory motif. J Allergy Clin Immunol 125(5):1128-113

19.  Shin YJ, Han CS, Lee CS, Kim HS, Ko SH, Hwang SK, Ko SG, Shin JW, Ye SK, Chung MH. (2010) Zeolite 4A, a synthetic silicate, suppresses melanogenesis through the degradation of microphthalmia-associated transcription factor by extracellular signal-regulated kinase activation in B16F10 melanoma cells. Biol Pharm Bull 33(1):72-6.

20.  Engelhardt KR, McGhee S, Winkler S, Sassi A, Woellner C, Lopez-Herrera G, Chen A, Kim HS, Lloret MG, Schulze I, Ehl S, Thiel J, Pfeifer D, Veelken H, Niehues T, Siepermann K, Weinspach S, Reisli I, Keles S, Genel F, Kutukculer N, Camcioğlu Y, Somer A, Karakoc-Aydiner E, Barlan I, Gennery A, Metin A, Degerliyurt A, Pietrogrande MC, Yeganeh M, Baz Z, Al-Tamemi S, Klein C, Puck JM, Holland SM, McCabe ER, Grimbacher B, Chatila TA. (2009) Large deletions and point mutations involving the dedicator of cytokinesis 8 (DOCK8) in the autosomal-recessive form of hyper-IgE syndrome. J Allergy Clin Immunol 124(6):1289-302

21.  Tachdjian R, Mathias C, Al Khatib S, Bryce PJ, Kim HS, Blaeser F, O'Connor BD, Rzymkiewicz D, Chen A, Holtzman MJ, Hershey GK, Garn H, Harb H, Renz H, Oettgen HC, Chatila TA. (2009) Pathogenicity of a disease-associated human IL-4 receptor allele in experimental asthma. J Exp Med 206(10):2191-204.       

22.  Kim JE*, Kim HS*, Shin YJ, Lee CS, Won C, Lee SA, Lee JW, Kim Y, Kang JS, Ye SK, Chung MH. (2008) LYR71, a derivative of trimeric resveratrol, inhibits tumorigenesis by blocking STAT3-mediated matrix metalloproteinase 9 expression. Exp Mol Med 40(5):514-22. (*co-first author)        

23.  Jung JE, Kim HS, Lee CS, Shin YJ, Kim YN, Kang GH, Kim TY, Chun YS, Kim SJ, Park JW, Ye SK, Chung MH. (2008) STAT3 inhibits the degradation of HIF-1alpha by pVHL-mediated ubiquitination. Exp Mol Med 40(5):479-85.        

24.  Kim HS, Cho IH, Kim JE, Shin YJ, Jeon JH, Kim Y, Yang YM, Lee KH, Lee JW, Lee WJ, Ye SK, Chung MH. (2008) Ethyl pyruvate has an anti-inflammatory effect by inhibiting ROS-dependent STAT signaling in activated microglia. Free Radic Biol Med 45(7):950-63       

25.  Jung JE, Kim HS, Lee CS, Park DH, Kim YN, Lee MJ, Lee JW, Park JW, Kim MS, Ye SK, Chung MH (2007) Caffeic Acid and its Synthetic Derivative CADPE Suppress Tumor Angiogenesis by Blocking STAT3-mediated VEGF Expression in Human Renal Carcinoma Cells. Carcinogenesis       

26.  Kim DH, Cho IH, Kim HS, Jung JE, Kim JE, Lee KH, Park T, Yang YM, Seong SY, Ye SK, Chung MH (2006) Anti-inflammatory effects of 8-hydroxydeoxyguanosine in LPS-induced microglia activation: suppression of STAT3-mediated intercellular adhesion molecule-1 expression. Exp Mol Med 38, 417-427       

27.  Kim HS, Ye SK, Cho IH, Jung JE, Kim DH, Choi S, Kim YS, Park CG, Kim TY, Lee JW, Chung MH (2006) 8-hydroxydeoxyguanosine suppresses NO production and COX-2 activity via Rac1/STATs signaling in LPS-induced brain microglia. Free Radic Biol Med 41, 1392-1403       

28.  Kim DH, Yoon BH, Jung JE, Kim HS, Ko SH, Choi EY, Lee KH, Kim K, Ye SK, Chung MH (2005) Interleukin-7 receptor is indispensable for proliferation and survival in thymic gammadelta T cell development. Immune Network 5, 23-29