Suhn Kyong Rhie, PhD

Dr. Rhie received her B.S. in Biochemistry, magna cum laude from the University of California, Los Angeles. She earned her Ph.D. degree in Genetic, Molecular and Cellular Biology from the University of Southern California in 2013. She completed her postdoctoral training in the laboratories of Dr. Peter Laird and Dr. Peggy Farnham. Dr. Rhie participated in Genome-Wide Association Studies (GWAS) in different cancer types, unraveling mechanisms that explain how genetic variants affect disease risks. Dr. Rhie characterized heterogeneous tumor tissues as a leader of DNA methylation analysis for The Cancer Genome Atlas (TCGA) Consortium and discovered how genetic alterations such as somatic mutations, fusions, copy number variations are associated with epigenetic changes in cancer. She has also led epigenomic data analysis to investigate how transcription factors act at regulatory elements in a 3D nucleome structure in cancer and psychiatric diseases as part of the ENCODE and PsychENCODE Consortia.
Her current research interests are to characterize key transcription factor and understand roles of regulatory elements activated in different types of cancers and neurodevelopmental diseases. By using both molecular biology and bioinformatics to address how genes are regulated in 3D nucleome structure (e.g. ChIP-seq, RNA-seq, whole genome sequencing, whole genome bisulfite sequencing, NOMe-seq, DNA methylation, Hi-C, CRISPR/Cas9, dCas9-ED systems), her lab is discovering new molecular mechanisms of human diseases that can aid in the development of therapeutics to enhance quality of life for patients.

• NCI Career Development Award, 2018-2021
• Women for Change, 2007
• Ethel Terry McCoy Award for Excellence in Chemistry and Biochemistry, 2007

• m6A epitranscriptome analysis reveals differentially methylated transcripts that drive early chemoresistance in bladder cancer NAR Cancer. 2023 Dec; 5(4):zcad054. . View in PubMed
• Correction: Characterizing chromatin interactions of regulatory elements and nucleosome positions, using Hi-C, Micro-C, and promoter capture Micro-C Epigenetics Chromatin. 2023 Jun 07; 16(1):22. . View in PubMed
• Cell-free DNA Methylation as a Predictive Biomarker of Response to Neoadjuvant Chemotherapy for Patients with Muscle-invasive Bladder Cancer in SWOG S1314 Eur Urol Oncol. 2023 10; 6(5):516-524. . View in PubMed
• Evidence of Novel Susceptibility Variants for Prostate Cancer and a Multiancestry Polygenic Risk Score Associated with Aggressive Disease in Men of African Ancestry Eur Urol. 2023 07; 84(1):13-21. . View in PubMed
• Florida-California Cancer Research, Education and Engagement (CaRE2) Health Equity Center: Structure, Innovations, and Initial Outcomes Cancer Control. 2023 Jan-Dec; 30:10732748231197878. . View in PubMed
• Genomic, epigenomic, and transcriptomic signatures of prostate cancer between African American and European American patients Front Oncol. 2023; 13:1079037. . View in PubMed
• Validation of Myc-Associated Protein X (MAX) regulation in growth hormone secreting and nonfunctional pituitary adenoma PLoS One. 2023; 18(4):e0284949. . View in PubMed
• Phosphorylation and stabilization of EZH2 by DCAF1/VprBP trigger aberrant gene silencing in colon cancer Nat Commun. 2023 04 17; 14(1):2140. . View in PubMed
• Radiogenomic Associations Clear Cell Renal Cell Carcinoma: An Exploratory Study Oncology. 2023; 101(6):375-388. . View in PubMed
• Characterizing and Targeting Genes Regulated by Transcription Factor MYBL2 in Lung Adenocarcinoma Cells Cancers (Basel). 2022 Oct 11; 14(20). . View in PubMed
• CT-based radiomics stratification of tumor grade and TNM stage of clear cell renal cell carcinoma Eur Radiol. 2022 Apr; 32(4):2552-2563. . View in PubMed
• FOXC1 Binds Enhancers and Promotes Cisplatin Resistance in Bladder Cancer Cancers (Basel). 2022 Mar 28; 14(7). . View in PubMed
• MMP-9 drives the melanomagenic transcription program through histone H3 tail proteolysis Oncogene. 2022 01; 41(4):560-570. . View in PubMed
• Characterizing chromatin interactions of regulatory elements and nucleosome positions, using Hi-C, Micro-C, and promoter capture Micro-C Epigenetics Chromatin. 2022 12 21; 15(1):41. . View in PubMed
• Methylation Subtypes of Primary Prostate Cancer Predict Poor Prognosis Cancer Epidemiol Biomarkers Prev. 2022 07 01; 31(7):1473-1482. . View in PubMed
• Feasibility of using CT radiomic signatures for predicting CD8-T cell infiltration and PD-L1 expression in renal cell carcinoma Eur J Radiol Open. 2022; 9:100440. . View in PubMed
• Epigenetic dysregulation in meningiomas Neurooncol Adv. 2022 Jan-Dec; 4(1):vdac084. . View in PubMed
• Genetic discovery and risk characterization in type 2 diabetes across diverse populations HGG Adv. 2021 Apr 08; 2(2). . View in PubMed
• VprBP directs epigenetic gene silencing through histone H2A phosphorylation in colon cancer Mol Oncol. 2021 10; 15(10):2801-2817. . View in PubMed
• Discovery and fine-mapping of height loci via high-density imputation of GWASs in individuals of African ancestry Am J Hum Genet. 2021 04 01; 108(4):564-582. . View in PubMed
• Molecular and computational approaches to map regulatory elements in 3D chromatin structure Epigenetics Chromatin. 2021 03 19; 14(1):14. . View in PubMed
• Role of KCNAB2 expression in modulating hormone secretion in somatotroph pituitary adenoma J Neurosurg. 2020 Feb 28; 134(3):787-793. . View in PubMed
• TENET 20: Identification of key transcriptional regulators and enhancers in lung adenocarcinoma. PLoS Genet. 2020 09; 16(9):e1009023. . View in PubMed
• Parallel PRC2/cPRC1 and vPRC1 pathways silence lineage-specific genes and maintain self-renewal in mouse embryonic stem cells Sci Adv. 2020 04; 6(14):eaax5692. . View in PubMed
• Epigenetic plasticity potentiates a rapid cyclical shift to and from an aggressive cancer phenotype Int J Cancer. 2020 06 01; 146(11):3065-3076. . View in PubMed
• Ezh2-dCas9 and KRAB-dCas9 enable engineering of epigenetic memory in a context-dependent manner Epigenetics Chromatin. 2019 May 03; 12(1):26. . View in PubMed
• The Enigmatic HOX Genes: Can We Crack Their Code? Cancers (Basel). 2019 Mar 07; 11(3).. View in PubMed
• The prostate cancer risk variant rs55958994 regulates multiple gene expression through extreme long-range chromatin interaction to control tumor progression Sci Adv. 2019 07; 5(7):eaaw6710. . View in PubMed
• A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome Nat Commun. 2019 09 12; 10(1):4154. . View in PubMed
• Revealing the brain’s molecular architecture Science. 2018 Dec 14; 362(6420):1262-1263. . View in PubMed
• ZFX acts as a transcriptional activator in multiple types of human tumors by binding downstream of transcription start sites at the majority of CpG island promoters Genome Res. 2018 Feb 02. . View in PubMed
• Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation Sci Adv. 2018 12; 4(12):eaav8550. . View in PubMed
• Positional integration of lung adenocarcinoma susceptibility loci with primary human alveolar epithelial cell epigenomes Epigenomics. 2018 09; 10(9):1167-1187. . View in PubMed
• Comprehensive functional genomic resource and integrative model for the human brain Science. 2018 12 14; 362(6420). . View in PubMed
• Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder Science. 2018 12 14; 362(6420). . View in PubMed
• Integrative functional genomic analysis of human brain development and neuropsychiatric risks Science. 2018 12 14; 362(6420). . View in PubMed
• Transcriptome and epigenome landscape of human cortical development modeled in organoids Science. 2018 12 14; 362(6420). . View in PubMed
• CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops Genome Biol. 2018 10 08; 19(1):160. . View in PubMed
• Defining Regulatory Elements in the Human Genome Using Nucleosome Occupancy and Methylome Sequencing (NOMe-Seq) Methods Mol Biol. 2018; 1766:209-229. . View in PubMed
• A Prostate Cancer Risk Element Functions as a Repressive Loop that Regulates HOXA13 Cell Rep. 2017 Nov 07; 21(6):1411-1417. . View in PubMed
• Characterizing Genetic Susceptibility to Breast Cancer in Women of African Ancestry Cancer Epidemiol Biomarkers Prev. 2017 07; 26(7):1016-1026. . View in PubMed
• Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles Cell Rep. 2017 06 27; 19(13):2878-2880. . View in PubMed
• Comparison of Breast Cancer Molecular Features and Survival by African and European Ancestry in The Cancer Genome Atlas JAMA Oncol. 2017 12 01; 3(12):1654-1662. . View in PubMed
• Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles Cell Rep. 2017 03 14; 18(11):2780-2794. . View in PubMed
• Identification of activated enhancers and linked transcription factors in breast, prostate, and kidney tumors by tracing enhancer networks using epigenetic traits Epigenetics Chromatin. 2016; 9:50. . View in PubMed
• The Molecular Taxonomy of Primary Prostate Cancer Cell. 2015 Nov 05; 163(4):1011-25. . View in PubMed
• Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer Cell. 2015 Oct 08; 163(2):506-19. . View in PubMed
• Cell-type-specific enrichment of risk-associated regulatory elements at ovarian cancer susceptibility loci Hum Mol Genet. 2015 Jul 01; 24(13):3595-607. . View in PubMed
• A comprehensive examination of breast cancer risk loci in African American women Hum Mol Genet. 2014 Oct 15; 23(20):5518-26. . View in PubMed
• Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin Cell. 2014 Aug 14; 158(4):929-944. . View in PubMed
• Nucleosome positioning and histone modifications define relationships between regulatory elements and nearby gene expression in breast epithelial cells BMC Genomics. 2014 May 02; 15:331. . View in PubMed
• Comprehensive functional annotation of 77 prostate cancer risk loci PLoS Genet. 2014 Jan; 10(1):e1004102. . View in PubMed
• The Cancer Genome Atlas Pan-Cancer analysis project Nat Genet. 2013 Oct; 45(10):1113-20. . View in PubMed
• A meta-analysis identifies new loci associated with body mass index in individuals of African ancestry Nat Genet. 2013 Jun; 45(6):690-6. . View in PubMed
• Genome-wide association studies identify four ER negative-specific breast cancer risk loci Nat Genet. 2013 Apr; 45(4):392-8398e1-2. . View in PubMed
• A genome-wide association study of breast cancer in women of African ancestry Hum Genet. 2013 Jan; 132(1):39-48. . View in PubMed
• Comprehensive functional annotation of seventy-one breast cancer risk Loci PLoS One. 2013; 8(5):e63925. . View in PubMed
• A meta-analysis of genome-wide association studies of breast cancer identifies two novel susceptibility loci at 6q14 and 20q11 Hum Mol Genet. 2012 Dec 15; 21(24):5373-84. . View in PubMed
• FunciSNP: an R/bioconductor tool integrating functional non-coding data sets with genetic association studies to identify candidate regulatory SNPs Nucleic Acids Res. 2012 Oct; 40(18):e139. . View in PubMed
• Myogenic Akt signaling upregulates the utrophin-glycoprotein complex and promotes sarcolemma stability in muscular dystrophy Hum Mol Genet. 2009 Jan 15; 18(2):318-27. . View in PubMed
• A case of pulmonary cysticercosis Korean J Intern Med. 1991 Jan; 6(1):38-43. . View in PubMed

• Farnham, Peggy
• Haiman, Christopher
• Liang, Gangning
• Lenz, Heinz-Josef
• An, Woojin