Biography
Dr. Arun Kumar Ganesan obtained his Bachelor's degree in Biochemistry from Tiruvalluvar University and his Master's degree in Biomedical Genetics from the University of Madras, India. His research journey continued as he pursued his Ph.D. in Biomedical Genetics at the same institution, focusing on studying the roles of oncogenic and epithelial-mesenchymal transition/stemness-promoting microRNAs and long non-coding RNAs (lncRNAs) in oral squamous cell carcinoma.
As a postdoctoral fellow at the National Cancer Institute/NIH in Bethesda, Dr. Ganesan explored the role of oncogenic lncRNAs in mislocalizing centromere-specific protein A (CENP-A) to ectopic sites in cancers. His primary focus was on understanding how lncRNAs are involved in epigenetic control and chromosome integrity, with an explicit emphasis on the chromosome 8q24/cMYC locus, a common breakpoint in several cancers. In his research, Dr. Ganesan discovered that oncogenic lncRNAs could alter the epigenetic memory of this fragile chromosome locus, leading to its increased susceptibility to break in cancer cells.
Currently, as an Assistant Professor in the Department of Cell Biology and Physiology at the University of New Mexico and a full member of UNM Comprehensive Cancer Center, Dr. Ganesan's lab focuses on studying non-canonical pathways of chromosome instability and epigenetic regulations.
Personal Statement
Cancer remains difficult to treat due to its heterogeneity and the ability of tumor cells to develop resistance. Our long-term goal is to uncover the mechanisms driving these challenges and translate fundamental discoveries into the clinic, enabling more effective targeted therapies and personalized cancer treatment.
Areas of Specialty
LncRNA, Epigenetics, Chromatin Biology, Cancer Biology.
Achievements & Awards
2021 NIH Director's Award (2021).
CCR-FYI Colloquium - Outstanding presenter (2021).
NIH Fellows Award for Research Excellence (2020).
Key Publications
Journal Article
Ganesan, Arun Kumar, 2025 Oncogenic lncRNA transgene transcription modulates epigenetic memory at a naïve chromosomal locus. Nucleus https://www.tandfonline.com/doi/full/10.1080/19491034.2025.2534242?scroll=top&needAccess=true#abstract
Journal Article
Ganesan, Arun Kumar, 2026 MetaChrome: An Open-Source, User-Friendly Tool for Automated Metaphase Chromosome Analysis. Methods https://www.sciencedirect.com/science/article/pii/S1046202325002567?dgcid=coauthor#aep-article-footnote-id1
Journal Article
Ganesan, Arun Kumar, 2026 Linker Histone H1.5 Contributes to Centromere Integrity Nucleic Acid Research https://academic.oup.com/nar/article/54/1/gkaf1400/8418222?utm_source=authortollfreelink&utm_campaign=nar&utm_medium=email
Journal Article
Ganesan, Arun Kumar, Baek, Songjoon, Sturgill, David, Bui, Minh, Dalal, Yamini, 2022 Oncogenic lncRNAs alter epigenetic memory at a fragile chromosomal site in human cancer cells Science Advances, vol. 8, Issue 9
Journal Article
Ganesan, Arun Kumar, Anand, Shankar, Raksha, Partha, Dhamodharan, Shankar, Prasanna Srinivasa Rao, Harikrishnan, Subbiah, Shanmugam, Murugan, Avaniyapuram, Kannan Munirajan, Arasambattu, Kannan LncRNA OIP5-AS1 is overexpressed in undifferentiated oral tumors and integrated analysis identifies as a downstream effector of stemness-associated transcription factors Scientific Reports, vol. 8, Issue 1
Gender
Male
Languages
- English
- Tamil
Courses Taught
BIOM507
BIOM515
Research and Scholarship
Eukaryotic genomes are far more dynamic and complex than once appreciated, producing a vast repertoire of coding and non-coding RNAs that actively shape genome function. Our research program lies at the intersection of RNA biology, chromatin regulation, and environmental epigenetics, with a central goal of understanding how RNA-based mechanisms govern genome organization and drive chromosome instability in cancer.
RNA–Chromatin Interactions and Epigenetic Regulation:
LncRNAs regulate gene expression by guiding chromatin-modifying complexes and transcription regulators to specific genomic sites. In cancer, these interactions are often rewired. Our studies show oncogenic lncRNAs act as scaffolds or signals for histone chaperones and regulatory complexes, establishing abnormal epigenetic states. Notably, lncRNA-driven recruitment of CENP-A uncovers a new way RNA influences chromatin identity and stability.
Using integrative genomics, imaging, and computational approaches, we aim to uncover how RNA molecules reshape chromatin landscapes in normal and diseased cells and how these changes influence transcriptional programs and cell fate.
Chromosome Instability and Cancer:
Chromosome instability (CIN) is a hallmark of cancer, yet its underlying mechanisms remain incompletely understood. Our work uncovers how RNA-mediated chromatin perturbations contribute to CIN by altering both the epigenetic and biophysical properties of chromosomes. We investigate how mislocalization of histone variants, aberrant transcription, and RNA–DNA hybrid structures (R-loops) cooperate to destabilize genome integrity.
A major focus of the lab is understanding how ectopic CENP-A deposition is initiated, maintained, and how it impacts chromosome structure and transcription. We combine multi-omics approaches with quantitative imaging to link chromatin-level molecular changes to higher-order chromosome organization and mechanics.
Environmental Epigenetics and Genome Integrity:
Environmental stressors, particularly heavy metals such as hexavalent chromium [Cr(VI)], are potent disruptors of chromatin structure and genome stability. Our research demonstrates that low-dose exposure to such toxicants induces widespread changes in histone and RNA modifications and in R-loop formation, ultimately leading to chromosome instability.
We are particularly interested in how epitranscriptomic changes, including RNA modifications, influence chromatin accessibility and genome organization under stress conditions. By integrating epigenomic, transcriptomic, and biophysical analyses, we aim to define how environmental exposures reshape the genome and contribute to disease risk.
Overall, our lab seeks to uncover fundamental RNA-driven mechanisms that regulate chromatin architecture and genome stability, with the long-term goal of identifying new therapeutic vulnerabilities in cancer and environmentally induced diseases.