Scholars@Duke
So Young Kim

So Young Kim

Associate Research Professor in Molecular Genetics and Microbiology
Molecular Genetics and Microbiology
soyoung.kim@duke.edu
0050 CARL, Box 3053, Durham, NC 27710
213 Research Drive, 0050 CARL BX3053, Durham, NC 27710

Selected Publications

Abstract 6707: Direct in vivo CRISPR screen identifies BAP1 and FAT1 as potent tumor suppressors in sarcomagenesis

Conference Cancer Research · April 21, 2025 AbstractUndifferentiated pleomorphic sarcoma (UPS) is among the most common soft tissue sarcomas (STS) in adults. For decades, little therapeutic progress has been made for STSs, including UPSs. Targeted the ... Full text Cite

Human giant GTPase GVIN1 forms an antimicrobial coatomer around the intracellular bacterial pathogen Burkholderia thailandensis.

Journal Article bioRxiv · March 28, 2025 Several human pathogens exploit the kinetic forces generated by polymerizing actin to power their intracellular motility. Human cell-autonomous immune responses activated by the cytokine interferon-gamma (IFNγ) interfere with such microbial actin-based mot ... Full text Link to item Cite

Abstract A025: Direct in vivo CRISPR screen identifies BAP1 and FAT1 as potent tumor suppressors in sarcomagenesis

Conference Cancer Research · March 11, 2025 AbstractUndifferentiated pleomorphic sarcoma (UPS) is among the most common soft tissue sarcomas (STS) in adults. For decades, little therapeutic progress has been made for STSs, including UPSs. Targeted the ... Full text Cite

Abstract 1085: Exploiting bioenergetic vulnerabilities in chemotherapy resistant osteosarcoma

Conference Cancer Research · March 22, 2024 AbstractBACKGROUND: Osteosarcoma (OS) is the most common bone cancer in children and young adults. Standard treatment involves chemotherapy and surgical resection, yet nearly 4 in 10 patients experience dise ... Full text Cite

Pooled genetic screens to identify vulnerabilities in TERT-promoter-mutant glioblastoma.

Journal Article Oncogene · October 2023 Pooled genetic screens represent a powerful approach to identify vulnerabilities in cancer. Here we used pooled CRISPR/Cas9-based approaches to identify vulnerabilities associated with telomerase reverse transcriptase (TERT) promoter mutations (TPMs) found ... Full text Link to item Cite

MicroOrganoSpheres as a clinically applicable precision oncology platform for the discovery of novel therapies in colorectal cancer.

Conference Journal of Clinical Oncology · June 1, 2023 3592 Background: Patient-derived models of cancer, such as cell lines, patient-derived organoids, and patient-derived xenografts, are useful models of patient response in the clinic. However, these models are often not clinically ... Full text Cite

A synthetic lethal screen for Snail-induced enzalutamide resistance identifies JAK/STAT signaling as a therapeutic vulnerability in prostate cancer.

Journal Article Front Mol Biosci · 2023 Despite substantial improvements in the treatment landscape of prostate cancer, the evolution of hormone therapy-resistant and metastatic prostate cancer remains a major cause of cancer-related death globally. The mainstay of treatment for advanced prostat ... Full text Link to item Cite

Corrigendum: Psymberin, a marine-derived natural product, induces cancer cell growth arrest and protein translation inhibition.

Journal Article Front Med (Lausanne) · 2023 [This corrects the article DOI: 10.3389/fmed.2022.999004.]. ... Full text Link to item Cite

The bacterial effector GarD shields Chlamydia trachomatis inclusions from RNF213-mediated ubiquitylation and destruction.

Journal Article Cell Host Microbe · December 14, 2022 Chlamydia trachomatis is the leading cause of sexually transmitted bacterial infections and a major threat to women's reproductive health in particular. This obligate intracellular pathogen resides and replicates within a cellular compartment termed an inc ... Full text Link to item Cite

Steroid-sensitive nephrotic syndrome candidate gene CLVS1 regulates podocyte oxidative stress and endocytosis.

Journal Article JCI Insight · January 25, 2022 We performed next-generation sequencing in patients with familial steroid-sensitive nephrotic syndrome (SSNS) and identified a homozygous segregating variant (p.H310Y) in the gene encoding clavesin-1 (CLVS1) in a consanguineous family with 3 affected indiv ... Full text Link to item Cite

Psymberin, a marine-derived natural product, induces cancer cell growth arrest and protein translation inhibition.

Journal Article Front Med (Lausanne) · 2022 Colorectal cancer (CRC) is the third most prevalent form of cancer in the United States and results in over 50,000 deaths per year. Treatments for metastatic CRC are limited, and therefore there is an unmet clinical need for more effective therapies. In ou ... Full text Link to item Cite

Orthogonal genome-wide screens of bat cells identify MTHFD1 as a target of broad antiviral therapy.

Journal Article Proc Natl Acad Sci U S A · September 28, 2021 Bats are responsible for the zoonotic transmission of several major viral diseases, including those leading to the 2003 SARS outbreak and likely the ongoing COVID-19 pandemic. While comparative genomics studies have revealed characteristic adaptations of t ... Full text Link to item Cite

A Precision Medicine Drug Discovery Pipeline Identifies Combined CDK2 and 9 Inhibition as a Novel Therapeutic Strategy in Colorectal Cancer.

Journal Article Mol Cancer Ther · December 2020 Colorectal cancer is the third most common cancer in the United States and responsible for over 50,000 deaths each year. Therapeutic options for advanced colorectal cancer are limited, and there remains an unmet clinical need to identify new treatments for ... Full text Link to item Cite

A Comparative Oncology Drug Discovery Pipeline to Identify and Validate New Treatments for Osteosarcoma.

Journal Article Cancers (Basel) · November 11, 2020 BACKGROUND: Osteosarcoma is a rare but aggressive bone cancer that occurs primarily in children. Like other rare cancers, treatment advances for osteosarcoma have stagnated, with little improvement in survival for the past several decades. Developing new t ... Full text Link to item Cite

Development of a precision medicine pipeline to identify personalized treatments for colorectal cancer.

Journal Article BMC Cancer · June 24, 2020 BACKGROUND: Metastatic colorectal cancer (CRC) continues to be a major health problem, and current treatments are primarily for disease control and palliation of symptoms. In this study, we developed a precision medicine strategy to discover novel therapeu ... Full text Link to item Cite

From the Clinic to the Bench and Back Again in One Dog Year: How a Cross-Species Pipeline to Identify New Treatments for Sarcoma Illuminates the Path Forward in Precision Medicine.

Journal Article Front Oncol · 2020 Cancer drug discovery is an inefficient process, with more than 90% of newly-discovered therapies failing to gain regulatory approval. Patient-derived models of cancer offer a promising new approach to identify new treatments; however, for rare cancers, su ... Full text Link to item Cite

Genome-wide CRISPR Screen to Identify Genes that Suppress Transformation in the Presence of Endogenous KrasG12D.

Journal Article Sci Rep · November 20, 2019 Cooperating gene mutations are typically required to transform normal cells enabling growth in soft agar or in immunodeficient mice. For example, mutations in Kras and transformation-related protein 53 (Trp53) are known to transform a variety of mesenchyma ... Full text Open Access Link to item Cite

The whole-genome landscape of Burkitt lymphoma subtypes.

Journal Article Blood · November 7, 2019 Burkitt lymphoma (BL) is an aggressive, MYC-driven lymphoma comprising 3 distinct clinical subtypes: sporadic BLs that occur worldwide, endemic BLs that occur predominantly in sub-Saharan Africa, and immunodeficiency-associated BLs that occur primarily in ... Full text Link to item Cite

Identification of Novel Mast Cell Activators Using Cell-Based High-Throughput Screening.

Journal Article SLAS Discov · July 2019 Mast cells (MCs) are known to regulate innate and adaptive immunity. MC activators have recently been described as safe and effective vaccine adjuvants. Many currently known MC activators are inadequate for in vivo applications, however, and research on id ... Full text Link to item Cite

Comparative Loss-of-Function Screens Reveal ABCE1 as an Essential Cellular Host Factor for Efficient Translation of Paramyxoviridae and Pneumoviridae.

Journal Article mBio · May 14, 2019 Paramyxoviruses and pneumoviruses have similar life cycles and share the respiratory tract as a point of entry. In comparative genome-scale siRNA screens with wild-type-derived measles, mumps, and respiratory syncytial viruses in A549 cells, a human lung a ... Full text Link to item Cite

An Integrative Systems Biology and Experimental Approach Identifies Convergence of Epithelial Plasticity, Metabolism, and Autophagy to Promote Chemoresistance.

Journal Article J Clin Med · February 7, 2019 The evolution of therapeutic resistance is a major cause of death for cancer patients. The development of therapy resistance is shaped by the ecological dynamics within the tumor microenvironment and the selective pressure of the host immune system. These ... Full text Link to item Cite

bcSeq: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens.

Journal Article Bioinformatics · October 15, 2018 SUMMARY: CRISPR-Cas9 and shRNA high-throughput sequencing screens have abundant applications for basic and translational research. Methods and tools for the analysis of these screens must properly account for sequencing error, resolve ambiguous mappings am ... Full text Link to item Cite

A precision medicine strategy to identify the FGFR pathway as a novel target in colorectal cancer liver metastasis.

Conference Journal of Clinical Oncology · February 1, 2018 660 Background: Colorectal cancer liver metastasis (CRCLM) continues to be a major health problem and despite extensive efforts to develop new drugs, median survival remains at a mere 30 months. The purpose of our study is 1. Dev ... Full text Cite

A Testosterone Metabolite 19-Hydroxyandrostenedione Induces Neuroendocrine Trans-Differentiation of Prostate Cancer Cells via an Ectopic Olfactory Receptor.

Journal Article Front Oncol · 2018 Olfactory receptor OR51E2, also known as a Prostate Specific G-Protein Receptor, is highly expressed in prostate cancer but its function is not well understood. Through in silico and in vitro analyses, we identified 24 agonists and 1 antagonist for this re ... Full text Open Access Link to item Cite

Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma.

Journal Article Cell · October 5, 2017 Diffuse large B cell lymphoma (DLBCL) is the most common form of blood cancer and is characterized by a striking degree of genetic and clinical heterogeneity. This heterogeneity poses a major barrier to understanding the genetic basis of the disease and it ... Full text Link to item Cite

Synthesis of 4-Azido-N-acetylhexosamine Uridine Diphosphate Donors: Clickable Glycosaminoglycans.

Journal Article J Org Chem · September 15, 2017 Unnatural chemically modified nucleotide sugars UDP-4-N3-GlcNAc and UDP-4-N3-GalNAc were chemically synthesized for the first time. These unnatural UDP sugar products were then tested for incorporation into hyaluronan, heparosan, or chondroitin using polys ... Full text Link to item Cite

Pathogenesis and inhibition of flaviviruses from a carbohydrate perspective

Journal Article Pharmaceuticals · June 1, 2017 Flaviviruses are enveloped, positive single stranded ribonucleic acid (RNA) viruses with various routes of transmission. While the type and severity of symptoms caused by pathogenic flaviviruses vary from hemorrhagic fever to fetal abnormalities, their gen ... Full text Cite

The effects of PPARγ on the regulation of the TOMM40-APOE-C1 genes cluster.

Journal Article Biochim Biophys Acta Mol Basis Dis · March 2017 Chromosome 19q13.32 is a gene rich region, and has been implicated in multiple human phenotypes in adulthood including lipids traits, Alzheimer's disease, and longevity. Peroxisome Proliferator Activated Receptor Gamma (PPARγ) is a ligand-activated nuclear ... Full text Link to item Cite

Interaction of Zika Virus Envelope Protein with Glycosaminoglycans.

Journal Article Biochemistry · February 28, 2017 In February 2016, the World Health Organization declared a Public Health Emergency of International Concern on Zika Virus (ZIKV), because of its association with severe fetal anomalies of congenitally infected humans. This has led to urgent efforts by acad ... Full text Link to item Cite

Synthesis and biological evaluation of 5,7-dihydroxyflavanone derivatives as antimicrobial agents.

Journal Article Bioorg Med Chem Lett · July 1, 2016 A series of 5,7-dihydroxyflavanone derivatives were efficiently synthesized. Their antimicrobial efficacy on Gram-negative, Gram-positive bacteria and yeast were evaluated. Among these compounds, most of the halogenated derivatives exhibited the best antim ... Full text Link to item Cite

ACLY and ACC1 Regulate Hypoxia-Induced Apoptosis by Modulating ETV4 via α-ketoglutarate.

Journal Article PLoS Genet · October 2015 In order to propagate a solid tumor, cancer cells must adapt to and survive under various tumor microenvironment (TME) stresses, such as hypoxia or lactic acidosis. To systematically identify genes that modulate cancer cell survival under stresses, we perf ... Full text Open Access Link to item Cite

Abstract 1100: Functional genomics to investigate the genetic determinants of cell death induced by oxidative stresses

Conference Cancer Research · August 1, 2015 AbstractIncreased oxidative stress in the tumor microenvironments is a prominent stress that many tumor cells need to cope with during oncogenesis. The stress depletes intracellular glutathione, increases re ... Full text Cite

Abstract 3004: Contextual RNAi screen identifies ACLY and ACC1 as mediators of hypoxia-induced apoptosis through metabolic and transcriptional mechanisms

Conference Cancer Research · August 1, 2015 AbstractTo become established as a solid tumor, cancer cells must adapt to and survive under various tumor microenvironment (TME) stresses, such as hypoxia or lactic acidosis. While many stress-signaling mec ... Full text Cite

Abstract B38: p90RSK mediates resistance to PI3K-pathway inhibitors in breast cancer

Journal Article Molecular Cancer Therapeutics · July 1, 2015 AbstractThe PI3K signaling pathway regulates diverse cellular processes including proliferation, survival and metabolism and is aberrantly activated in human cancer. As such, numerous compounds targeting the ... Full text Cite

PRKACA mediates resistance to HER2-targeted therapy in breast cancer cells and restores anti-apoptotic signaling.

Journal Article Oncogene · April 16, 2015 Targeting HER2 with antibodies or small molecule inhibitors in HER2-positive breast cancer leads to improved survival, but resistance is a common clinical problem. To uncover novel mechanisms of resistance to anti-HER2 therapy in breast cancer, we performe ... Full text Link to item Cite

Abstract PR09: A genome-wide RNAi screen reveals a protective role of decreased lipogenesis under hypoxia

Conference Cancer Research · January 1, 2015 AbstractAs solid tumors form, a number of physiological changes occur within the tumor, including low oxygen levels (hypoxia) and an accumulation of lactic acid with concomitant lowered pH levels (lactic aci ... Full text Cite

Functional genomics approach for the identification of human host factors supporting dengue viral propagation.

Journal Article Methods Mol Biol · 2014 Dengue virus (DENV) is endemic throughout tropical regions of the world and there are no approved treatments or anti-transmission agents currently available. Consequently, there exists an enormous unmet need to treat the human diseases caused by DENV and b ... Full text Link to item Cite

Abstract P5-08-01: Systematic interrogation of resistance to HER2-directed therapy identifies a survival pathway activated by PRKACA and PIM1

Journal Article Cancer Research · December 15, 2013 AbstractAmplification and/or overexpression of the receptor tyrosine kinase HER2 occurs in 20-25% of breast cancers, and is associated with poor prognosis. Targeting of HER2 with drugs such as trastuzumab, l ... Full text Cite

Systematic interrogation of 3q26 identifies TLOC1 and SKIL as cancer drivers.

Journal Article Cancer Discov · September 2013 UNLABELLED: 3q26 is frequently amplified in several cancer types with a common amplified region containing 20 genes. To identify cancer driver genes in this region, we interrogated the function of each of these genes by loss- and gain-of-function genetic s ... Full text Link to item Cite

RSK3/4 mediate resistance to PI3K pathway inhibitors in breast cancer.

Journal Article J Clin Invest · June 2013 The PI3K signaling pathway regulates diverse cellular processes, including proliferation, survival, and metabolism, and is aberrantly activated in human cancer. As such, numerous compounds targeting the PI3K pathway are currently being clinically evaluated ... Full text Link to item Cite

Abstract A18: Genetic elements of cancer cell survival in tumor microenvironment stresses

Journal Article Molecular Cancer Therapeutics · May 1, 2013 AbstractAs solid human cancer tumors form there are a number of physiological changes that occur within the tumor itself, including low oxygen levels (hypoxia) and an accumulation of lactic acid with concomi ... Full text Cite

Abstract 5123: An integrated genomics approach to identify novel drivers of oncogenic pathway activity in human cancer

Journal Article Cancer Research · April 15, 2012 AbstractHuman cancers are defined by molecular and clinical heterogeneity. The molecular diversity of human tumors is a significant contributing factor to the inefficiency of current therapeutic regimens and ... Full text Cite

The JAK2/STAT3 signaling pathway is required for growth of CD44⁺CD24⁻ stem cell-like breast cancer cells in human tumors.

Journal Article J Clin Invest · July 2011 Intratumor heterogeneity is a major clinical problem because tumor cell subtypes display variable sensitivity to therapeutics and may play different roles in progression. We previously characterized 2 cell populations in human breast tumors with distinct p ... Full text Link to item Cite

COT drives resistance to RAF inhibition through MAP kinase pathway reactivation.

Journal Article Nature · December 16, 2010 Oncogenic mutations in the serine/threonine kinase B-RAF (also known as BRAF) are found in 50-70% of malignant melanomas. Pre-clinical studies have demonstrated that the B-RAF(V600E) mutation predicts a dependency on the mitogen-activated protein kinase (M ... Full text Link to item Cite

Metformin, independent of AMPK, inhibits mTORC1 in a rag GTPase-dependent manner.

Journal Article Cell Metab · May 5, 2010 Dysfunctional mTORC1 signaling is associated with a number of human pathologies owing to its central role in controlling cell growth, proliferation, and metabolism. Regulation of mTORC1 is achieved by the integration of multiple inputs, including those of ... Full text Link to item Cite

CK1epsilon is required for breast cancers dependent on beta-catenin activity.

Journal Article PLoS One · February 1, 2010 BACKGROUND: Aberrant beta-catenin signaling plays a key role in several cancer types, notably colon, liver and breast cancer. However approaches to modulate beta-catenin activity for therapeutic purposes have proven elusive to date. METHODOLOGY: To uncover ... Full text Link to item Cite

CK1ε is required for breast cancers dependent on β-catenin activity

Journal Article Plos One · February 1, 2010 Background: Aberrant β-catenin signaling plays a key role in several cancer types, notably colon, liver and breast cancer. However approaches to modulate β-catenin activity for therapeutic purposes have proven elusive to date. Methodology: To uncover genet ... Full text Cite

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1.

Journal Article Nature · November 5, 2009 The proto-oncogene KRAS is mutated in a wide array of human cancers, most of which are aggressive and respond poorly to standard therapies. Although the identification of specific oncogenes has led to the development of clinically effective, molecularly ta ... Full text Link to item Cite

SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas.

Journal Article Nat Genet · November 2009 Lineage-survival oncogenes are activated by somatic DNA alterations in cancers arising from the cell lineages in which these genes play a role in normal development. Here we show that a peak of genomic amplification on chromosome 3q26.33 found in squamous ... Full text Link to item Cite

AKT-independent signaling downstream of oncogenic PIK3CA mutations in human cancer.

Journal Article Cancer Cell · July 7, 2009 Dysregulation of the phosphatidylinositol 3-kinase (PI3K) signaling pathway occurs frequently in human cancer. PTEN tumor suppressor or PIK3CA oncogene mutations both direct PI3K-dependent tumorigenesis largely through activation of the AKT/PKB kinase. How ... Full text Link to item Cite

Integrative genomic approaches to understanding cancer.

Journal Article Biochim Biophys Acta · June 2009 Further advances in the prevention, diagnosis and treatment of cancer require a more complete knowledge of the molecular mechanisms that program the malignant state. Until recently, identifying and validating genetic alterations in tumors that contribute t ... Full text Link to item Cite

Synthetic lethal interaction between oncogenic KRAS dependency and STK33 suppression in human cancer cells.

Journal Article Cell · May 29, 2009 An alternative to therapeutic targeting of oncogenes is to perform "synthetic lethality" screens for genes that are essential only in the context of specific cancer-causing mutations. We used high-throughput RNA interference (RNAi) to identify synthetic le ... Full text Link to item Cite

CDK8 is a colorectal cancer oncogene that regulates beta-catenin activity.

Journal Article Nature · September 25, 2008 Aberrant activation of the canonical WNT/beta-catenin pathway occurs in almost all colorectal cancers and contributes to their growth, invasion and survival. Although dysregulated beta-catenin activity drives colon tumorigenesis, further genetic perturbati ... Full text Link to item Cite

Cancer genomics: integrating form and function.

Journal Article Carcinogenesis · July 2007 The sequencing of the human genome has formed the foundation with which to develop technologies and reagents to perform true genome-scale biological studies. In particular, the development and increasing application of these high-throughput genome-scale te ... Full text Link to item Cite

Integrative genomic approaches identify IKBKE as a breast cancer oncogene.

Journal Article Cell · June 15, 2007 The karyotypic chaos exhibited by human epithelial cancers complicates efforts to identify mutations critical for malignant transformation. Here we integrate complementary genomic approaches to identify human oncogenes. We show that activation of the ERK a ... Full text Link to item Cite

A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen.

Journal Article Cell · March 24, 2006 To enable arrayed or pooled loss-of-function screens in a wide range of mammalian cell types, including primary and nondividing cells, we are developing lentiviral short hairpin RNA (shRNA) libraries targeting the human and murine genomes. The libraries cu ... Full text Link to item Cite

Amino acids mediate mTOR/raptor signaling through activation of class 3 phosphatidylinositol 3OH-kinase.

Journal Article Proc Natl Acad Sci U S A · October 4, 2005 During the evolution of metazoans and the rise of systemic hormonal regulation, the insulin-controlled class 1 phosphatidylinositol 3OH-kinase (PI3K) pathway was merged with the primordial amino acid-driven mammalian target of rapamycin (mTOR) pathway to c ... Full text Link to item Cite

Multiple cell-type-specific elements regulate Myc protein stability.

Journal Article Oncogene · May 6, 2004 Myc is a highly unstable transcription factor that is destroyed by ubiquitin (Ub)-mediated proteolysis. We have previously identified an amino-terminal 'degron' within Myc that signals its destruction; this degron spans the transcriptional activation domai ... Full text Link to item Cite

Skp2 regulates Myc protein stability and activity.

Journal Article Mol Cell · May 2003 Myc is an oncoprotein transcription factor that plays a prominent role in cancer. Like many transcription factors, Myc is an unstable protein that is destroyed by ubiquitin (Ub)-mediated proteolysis. Here, we report that the oncoprotein and Ub ligase Skp2 ... Full text Link to item Cite

Human origin recognition complex large subunit is degraded by ubiquitin-mediated proteolysis after initiation of DNA replication.

Journal Article Mol Cell · March 2002 Eukaryotic cells possess overlapping mechanisms to ensure that DNA replication is restricted to the S phase of the cell cycle. The levels of hOrc1p, the largest subunit of the human origin recognition complex, vary during the cell division cycle. In rapidl ... Full text Link to item Cite

Destruction of Myc by ubiquitin-mediated proteolysis: cancer-associated and transforming mutations stabilize Myc.

Journal Article EMBO J · February 1, 1999 The human proto-oncogene c-myc encodes a highly unstable transcription factor that promotes cell proliferation. Although the extreme instability of Myc plays an important role in preventing its accumulation in normal cells, little is known about how Myc is ... Full text Link to item Cite