About

Dr. Ratnakar Singh is a Research Assistant Professor in the Department of Comparative Biosciences at the University of Illinois Urbana-Champaign. His research focuses on the molecular and epigenetic mechanisms that drive cancer progression and therapeutic response, with an emphasis on developing more effective and personalized treatments. He uses a multidisciplinary approach that integrates molecular biology, epigenomics, transcriptomics, and translational models to identify pathways that govern sensitivity or resistance to chemotherapy and targeted therapies. During his postdoctoral training at MD Anderson Cancer Center, Dr. Singh identified biomarkers predicting responses to mitotic and PI3K/mTOR inhibitors in head and neck and lung cancers, contributing to the initiation of a clinical trial in head and neck squamous cell carcinoma. At Illinois, his work centers on testicular germ cell tumors (TGCTs), where he has defined critical roles for polycomb signaling and DNA methylation in shaping cisplatin response. His recent discoveries include that TGCTs overexpress DNA methyltransferase 3B and are more sensitive to low doses of DNA hypomethylating agents than somatic cancer cells, leading to a phase 1b clinical trial testing demethylation therapy for cisplatin-resistant testicular cancer patients. His group has also validated polycomb-targeted therapies for cisplatin-refractory testicular cancer, suggesting promising second epigenetic treatment options for chemotherapy-resistant cases. Dr. Singh aims to translate molecular insights into new therapeutic strategies that improve outcomes for patients with refractory cancers. He is actively involved in teaching biochemistry, mentoring students, and contributing to interdisciplinary initiatives, while also engaging in editorial work and professional organizations to support the broader scientific community.

Research topics

• Biology
• Cancer research
• Bioinformatics
• Genetics
• Oncology
• Medicine
• Computational biology
• Internal medicine
• Endocrinology
• Chemistry
• Molecular biology

Selected publications

• Comparative Analysis of the Transcriptomic Response to Cisplatin in Drug-Sensitive and Drug-Resistant Testicular Germ Cell Tumors

  Cancers · 2026-02-10

  articleOpen accessCorresponding

  Background/Objectives: Testicular germ cell tumors (TGCTs) are uniquely curable with cisplatin-based therapies even when widely metastatic; however, cisplatin resistance does occur, resulting in very poor prognosis. The mechanisms to explain TGCT hypersensitivity to cisplatin and mechanisms of resistance are not well-understood. Methods: The global transcriptional response to acute cisplatin treatment (24 h after a 6 h pulse of cisplatin) was assessed in three parental embryonal carcinoma TGCT cells lines compared to multiple isogenic, stable, cisplatin-resistant clonal lines from these parental cells. Results: Cisplatin treatment of parental cells consistently showed a more robust overall transcriptional response to cisplatin compared to their cisplatin-resistant cellular counterparts for a common set of genes and pathways including the upregulation of genes associated with histone modifications and p53, EMT, and KRAS signaling and the downregulation of genes normally upregulated by MYC. Focusing on genes exclusively altered in parental cells revealed upregulated genes known to be induced by p53 and downregulated by MYC and the transferrin receptor, TFRC1. Several of these p53/MYC/TFRC1 targets were associated with a higher instance of disease-free survival in a cohort of TGCT patients. Conclusions: Cisplatin resistance in TGCT cells is associated with a diminished alteration in cisplatin-responsive genes, especially genes known to be regulated by p53, MYC and TFRC1, that may be linked to cisplatin hypersensitivity and survival in TGCTs.

  PublisherOA PDFDOI

• A critical review of consolidation processes for ODS steels: Development as clad tube materials in Gen-IV nuclear reactors

  Critical reviews in solid state and materials sciences/CRC critical reviews in solid state and materials sciences · 2025-07-16 · 2 citations

  review1st authorCorresponding
  PublisherDOI

• The role of lipid metabolism and peroxisome proliferator activation in mediating pro-cancer phenotypes of poly- and perfluoroalkyl substances in testicular cancer

  Environmental Toxicology and Pharmacology · 2025-11-16 · 2 citations

  articleOpen accessSenior author

  Poly- and perfluoroalkyl substances (PFAS) are of human health concern as epidemiological studies show significant associations with testicular germ cell tumors (TGCTs). Here, the effects of perfluorooctanesulfonic acid (PFOS), lithium bis(trifluoromethylsulfonyl)imide (HQ-115), and hexafluoropropylene oxide dimer acid (GenX) on TGCT cells were investigated. Concentrations (10 nM to 1 µM) modelled PFAS doses in relevant human exposure ranges and acute and short-term timepoints (18 h and 4 days) captured proximal mechanisms of action. Metabolomic studies revealed that HQ-115 altered metabolites associated with steroid biosynthesis and lipid metabolism. Peroxisome-proliferator activation receptor (PPAR) target gene expression was altered upon HQ-115 and GenX exposure. Lastly, PFAS exposure altered the activity of PPARs, in TGCT cells, with the most prominent effects being antagonist activity toward PPARγ. These data support that PFAS may act as fatty acid mimics to modulate fatty acid metabolic and steroidogenic endocrine outcome leading to pro-cancer phenotypes in TGCTs.

  PublisherDOI

• A study on creep behavior of superalloy 617 M using a Wilshire approach

  Engineering Failure Analysis · 2025-04-09 · 2 citations

  articleOpen accessCorresponding

  • Creep tests attaining equal rupture life at 650⁰C, 700⁰C and 750⁰C are investigated. • Extended creep at 700⁰C is illustrated using TEM. • Creep data analysis was carried out using a Wilshire approach. • Creep activation energy obtained close to activation energy for self-diffusion. • This is in contrast to high creep activation energy reported in literature. Tensile creep tests were performed on forged 617 M alloy. Classical creep characterized by an extended steady-state (secondary stage) is exhibited during creep at 650°C. Formation of dislocation entanglements limit creep elongation (∼1.5 %). In contrast, limited secondary creep and extended tertiary creep was observed in samples tested at 700°C/750°C. All these samples exhibited extensive creep elongation (7 to 25 %). At 272 MPa/700°C, local climb dominates, increasing dislocation length and enhancing dislocation-precipitate interactions. Instability in dislocation structure prevails as outcome of intensified dislocation interactions during short-term creep. During long-term creep at 190 MPa/700°C, significant growth of precipitates and carbides takes place, facilitating dislocation cross-slip and looping which accounts for extended tertiary creep. At 750°C, precipitate instability causes prolonged tertiary creep. Moderate creep strength reduction on increasing the temperature from 650°C to 700°C reflects microstructural stability at 700°C and a sharp drop at 750°C is ascribed to microstructural degradation. Analysis of creep data was carried out using Wilshire approach. Creep activation energy is calculated to be ∼ 259 kJ/mole which is shown to be consistent with activation energy for self-diffusion. The Wilshire equation predicted stresses for creep life of 1,00,000 h to be 130 MPa at 710°C and 101.5 MPa at 750°C.

  PublisherDOI

• Abstract 6687: Micromanaging resistance: microRNA expression and chemoresistance in testicular germ cell tumors

  Cancer Research · 2025-04-21

  article1st authorCorresponding

  Abstract Testicular germ cell tumors (TGCTs) are the most common type of cancer among young men, and incidence has increased over the past 40 years. Approximately 80% of patients with metastatic TGCTs can be cured with chemotherapy; however, those patients that develop resistance to treatment often have a poor prognosis. Despite efforts to identify clear genetic factors that determine chemotherapy sensitivity and resistance in TGCTs, recent research has shifted focus toward the role of epigenetics in maintaining sensitivity to drugs like cisplatin and decitabine. Epigenetic mechanisms, including DNA methylation, histone modifications, and microRNAs (miRNAs), play a crucial role in regulating gene expression. Prior studies in somatic cancers have linked differential expressions of miRNAs to drug resistance. In this study, we hypothesized that the response of TGCTs to cisplatin and decitabine is partially influenced by miRNA expression. Through miRNA sequencing analysis followed by RT-qPCR validation, we identified distinct patterns of miRNA expression that correlate with resistance to cisplatin and decitabine in TGCTs. Consistent with our previous findings on protein coding gene expression, we observed that 54 miRNAs were reciprocally expressed between cells resistant to decitabine and those resistant to cisplatin. In follow-up analysis, we selected a subset of these reciprocally regulated miRNAs and predicted their target genes using miRDB and TargetScan. Downstream miRNA-RNA interactive analysis, enrichment analysis, and validation assays are ongoing and will be presented. Together, our study aims to elucidate the mechanistic roles of miRNAs in chemosensitivity and chemoresistance in TGCTs. The findings from this study will also support precise diagnosis and personalized treatment strategies for patients with TGCTs. Citation Format: Ratnakar Singh, Kelly Kries, Aayush Gupta, Amy Li, Zeeshan Fazal, Doha Shokry, Raya Boyd, Brayden Rennels, Sarah J. Freemantle, Michael J. Spinella. Micromanaging resistance: microRNA expression and chemoresistance in testicular germ cell tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 6687.

  PublisherDOI

• Refractory testicular germ cell tumors are highly sensitive to the targeting of polycomb pathway demethylases KDM6A and KDM6B

  Research Square · 2024-10-18

  preprintOpen accessSenior author
  PublisherOA PDFDOI

• Refractory testicular germ cell tumors are highly sensitive to the targeting of polycomb pathway demethylases KDM6A and KDM6B

  Cell Communication and Signaling · 2024-10-31 · 10 citations

  articleOpen accessSenior author

  Testicular germ cell tumors (TGCTs) can be treated with cisplatin-based therapy. However, a clinically significant number of cisplatin-resistant patients die from progressive disease as no effective alternatives exist. Curative cisplatin therapy results in acute and life-long toxicities in the young TGCT patient population providing a rationale to decrease cisplatin exposure. In contrast to genetic alterations, recent evidence suggests that epigenetics is a major driving factor for TGCT formation, progression, and response to chemotherapy. Hence, targeting epigenetic pathways with "epidrugs" is one potential relatively unexplored strategy to advance TGCT treatment beyond cisplatin. In this report, we demonstrate for the first time that targeting polycomb demethylases KDM6A and KDM6B with epidrug GSK-J4 can treat both cisplatin-sensitive and -resistant TGCTs. While GSK-J4 had minimal effects alone on TGCT tumor growth in vivo, it dramatically sensitized cisplatin-sensitive and -resistant TGCTs to cisplatin. We validated KDM6A/KDM6B as the target of GSK-J4 since KDM6A/KDM6B genetic depletion had a similar effect to GSK-J4 on cisplatin-mediated anti-tumor activity and transcriptome alterations. Pharmacologic and genetic targeting of KDM6A/KDM6B potentiated or primed the p53-dominant transcriptional response to cisplatin, with also evidence for basal activation of p53. Further, several chromatin modifier genes, including BRD4, lysine demethylases, chromodomain helicase DNA binding proteins, and lysine methyltransferases, were repressed with cisplatin only in KDM6A/KDM6B-targeted cells, implying that KDM6A/KDM6B inhibition sets the stage for extensive chromatin remodeling of TGCT cells upon cisplatin treatment. Our findings demonstrate that targeting polycomb demethylases is a new potent pharmacologic strategy for treating cisplatin resistant TGCTs that warrants clinical development.

  PublisherOA PDFDOI

• Evolution of Microstructure during Creep Deformation in a Forged 617 Superalloy

  Advanced Engineering Materials · 2024-11-27 · 3 citations

  articleOpen access

  Creep tests are conducted on forged 617 M superalloy samples at 650, 700, and 750 °C at stresses ranging from 115 to 320 MPa. At 650 °C, a significant steady‐state secondary creep is observed, while at 700 and 750 °C limited secondary creep and prolonged tertiary creep are observed. Creep data analysis using power‐law creep approach estimates high‐stress exponents ( n ≈ 13.4 at 650 °C, ≈11.5 at 700 °C, and ≈9.7 at 750 °C) and activation energy ( Q ≈ 530.6 kJ mole −1 ). After incorporating threshold stress, the activation energy for creep is found to be ≈261 kJ mole −1 . This is consistent with the activation energy for lattice self‐diffusion in the alloy. Transmission electron microscopy provides evidences affirming that climb‐controlled dislocation creep may be the operative creep mechanism. Ni 3 (Al, Ti) (γ′) precipitates and M 23 C 6 carbides evolve during exposure at operating temperatures. These are observed to lead to enhanced creep resistance at 700 °C. Significant coarsening rate of γ′ precipitates are noted during exposure at 750 °C. This intensifies recovery processes and lowers creep threshold stress drastically. Extended tertiary creep prevails near the service conditions of this alloy, which is ascribed to instability in microstructure during creep.

  PublisherOA PDFDOI

• Abstract 4561: Mechanism of histone H3K27me3 demethylase therapy for restoring cisplatin sensitivity in refractory testicular cancer

  Cancer Research · 2024-03-22

  article

  Abstract Testicular germ cell tumors (TGCTs) can be cured at a high rate with standard cisplatin-based chemotherapy, but 15% of metastatic patients are cisplatin resistant/refractory and die from progressive disease. In prior work, we used de novo pharmacogenetic approaches leveraging a series of unique cisplatin resistant cell models that uncovered an important role for polycomb and histone H3K27me3 methylation in mediating TGCT sensitivity and resistance to cisplatin. Importantly, we demonstrated that pharmacological inhibition of H3K27 methylation with the EZH2 inhibitor GSK-126 conferred cisplatin resistance to parental cells while induction of H3K27 methylation with the histone lysine demethylase inhibitor GSK-J4 resulted in a high degree of cisplatin sensitization of TGCT tumors including cisplatin resistant TGCT cells. In order to elucidate mechanisms that account for the remarkable cisplatin sensitization effects of GSKJ4 in TGCTs, we used two distinct cisplatin resistant TGCT cell lines 2102EP-C1 and NT2D1-A4. Cells were pretreated for three days with either vehicle control or 1µM GSK-J4 to modulate H3K27me3 followed by treatment with vehicle control or 0.5µM cisplatin for 6 hours. RNA was extracted from cells after 24 hours of cisplatin removal. This treatment protocol was designed to capture “early” transcriptional responses to GSKJ4 sensitization before the onset of cell death. RNA-seq transcriptomic profiling and differential gene expression analysis revealed as expected a severely attenuated transcriptional response to cisplatin in cisplatin refractory cells that was restored with GSKJ4 pretreatment. Interestingly GSKJ4 alone resulted in a robust transcriptional response with a large overlap with gene changed with cisplatin alone, despite the fact that GSKJ4 alone did not affect cell proliferation or survival. However, GSKJ4 uniquely regulated a subset of genes and uniquely restored cisplatin response to a subset of genes which are candidates for driving the remarkable cisplatin sensitizing effects of GSKJ4 in TGCTs. Further enrichment and biological classification analysis of these distinct gene subsets are ongoing and will be presented. In summary, our data suggests mechanisms to account for why directly targeting H3K27 methylation with GSKJ4 appear highly effective in treating cisplatin resistant/refractory TGCTs and may provide biomarkers for future clinical investigation of this strategy. Citation Format: Doha Naguib Ahmed Mohamed Shokry, Ratnakar Singh, Mehwish Khan, Zeeshan Fazal, Raya Boyd, Christine Powell, Sarah J. Freemantle, Michael J. Spinella. Mechanism of histone H3K27me3 demethylase therapy for restoring cisplatin sensitivity in refractory testicular cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4561.

  PublisherDOI

• Perfluorooctanesulfonic Acid Alters Pro-Cancer Phenotypes and Metabolic and Transcriptional Signatures in Testicular Germ Cell Tumors

  Toxics · 2024-03-22 · 14 citations

  articleOpen accessCorresponding

  The potential effects of poly- and perfluoroalkyl substances (PFAS) are a recently emergent human and environmental health concern. There is a consistent link between PFAS exposure and cancer, but the mechanisms are poorly understood. Although epidemiological evidence supporting PFAS exposure and cancer in general is conflicting, there is relatively strong evidence linking PFAS and testicular germ cell tumors (TGCTs). However, no mechanistic studies have been performed to date concerning PFAS and TGCTs. In this report, the effects of the legacy PFAS perfluorooctanesulfonic acid (PFOS) and the newer "clean energy" PFAS lithium bis(trifluoromethylsulfonyl)imide (LiTFSi, called HQ-115), on the tumorigenicity of TGCTs in mice, TGCT cell survival, and metabolite production, as well as gene regulation were investigated. In vitro, the proliferation and survival of both chemo-sensitive and -resistant TGCT cells were minimally affected by a wide range of PFOS and HQ-115 concentrations. However, both chemicals promoted the growth of TGCT cells in mouse xenografts at doses consistent with human exposure but induced minimal acute toxicity, as assessed by total body, kidney, and testis weight. PFOS, but not HQ-115, increased liver weight. Transcriptomic alterations of PFOS-exposed normal mouse testes were dominated by cancer-related pathways and gene expression alterations associated with the H3K27me3 polycomb pathway and DNA methylation, epigenetic pathways that were previously showed to be critical for the survival of TGCT cells after cisplatin-based chemotherapy. Similar patterns of PFOS-mediated gene expression occurred in PFOS-exposed cells in vitro. Metabolomic studies revealed that PFOS also altered metabolites associated with steroid biosynthesis and fatty acid metabolism in TGCT cells, consistent with the proposed ability of PFAS to mimic fatty acid-based ligands controlling lipid metabolism and the proposed role of PFAS as endocrine disrupters. Our data, is the first cell and animal based study on PFAS in TGCTs, support a pro-tumorigenic effect of PFAS on TGCT biology and suggests epigenetic, metabolic, and endocrine disruption as potential mechanisms of action that are consistent with the non-mutagenic nature of the PFAS class.

  PublisherOA PDFDOI

Frequent coauthors

• Faye M. Johnson

  The University of Texas MD Anderson Cancer Center

  46 shared

• Jing Wang

  The University of Texas MD Anderson Cancer Center

  41 shared

• Shaohua Peng

  Central South University

  40 shared

• Vaishnavi Sambandam

  National Comprehensive Cancer Network

  39 shared

• Pan Tong

  National Defense Medical Center

  39 shared

• Mitchell J. Frederick

  37 shared

• Tuhina Mazumdar

  The University of Texas MD Anderson Cancer Center

  37 shared

• Curtis R. Pickering

  Yale University

  37 shared

Labs

• Comparative BiosciencesPI

Education

• PhD, Biochemistry

  All India Institute of Medical Sciences

  2014

• Master of Science (Medical Biochemistry), Biochemistry

  Jawaharlal Institute of Post Graduate Medical Education

  2008

• Bachelor of Science (Medical Laboratory Technology)

  Jawaharlal Institute of Post Graduate Medical Education

  2005

Awards & honors

• The Jeffrey Lee Cousin Fellowship
• Award of Excellence, Carcinogenesis Foundation, New Delhi, I…
• Nature Publishing Group Award for best poster ‘Cell Death’ G…
• Travel Grant 2012 from the Department of Science and Technol…
• Senior Research Fellow (2011 - 2014) by Department of Biotec…