Cancer | Raunak Shrestha

An Atlas of Accessible Chromatin in Advanced Prostate Cancer Reveals the Epigenetic Evolution during Tumor Progression

Integration of a large cohort of transcriptome, whole genome, and ATAC-sequencing characterizes the chromatin accessibility changes in advanced prostate cancer and identifies therapy-resistant prostate cancer subtype-specific transcription factors that modulate oncogenic programs.

Raunak Shrestha, LN Chesner, M Zhang, S Zhou, A Foye, A Lundberg, AS Weinstein, M Sjostrom, X Zhu, T Moreno-Rodriguez, H Li, JJ Alumkal, R Aggarwal, EJ Small, M Lupien, DA Quigley, FY Feng

An Atlas of Accessible Chromatin in Advanced Prostate Cancer Reveals the Epigenetic Evolution during Tumor Progression

Integrated analyses highlight interactions between the three-dimensional genome and DNA, RNA and epigenomic alterations in metastatic prostate cancer

We discovered a group of metastatic prostate cancer patients with lower levels of DNA-DNA interactions around the Androgen Receptor (AR) gene, the main driver of prostate cancer. Interestingly, this group had an abundance of circular DNA outside of the chromosomes (extrachromosomal circular DNA (ecDNA)) that included parts of the AR gene resulting in AR gene amplification and become very active, which might explain why their cancer was resistant to treatment.

S Zhao, M Bootsma, S Zhou, Raunak Shrestha, T Moreno-Rodriguez, A Lundberg, C Pan, C Arlidge, J Hawley, A Foye, A Weinstein, M Sjostrom, M Zhang, H Li, LN Chesner, N Rydzewski, K Helzer, Y Shi, S Dehm, J Lang, J Alumkal, H He, A Wyatt, R Aggarwal, W Zwart, E Small, D Quigley, M Lupien, FY Feng

Integrated analyses highlight interactions between the three-dimensional genome and DNA, RNA and epigenomic alterations in metastatic prostate cancer

Integrative analysis of ultra-deep RNA-seq reveals alternative promoter usage as a mechanism of activating oncogenic programmes during prostate cancer progression

M Zhang, M Sjostrom, X Cui, A Foye, K Farh, Raunak Shrestha, A Lundberg, HX Dang, PG Febbo, R Aggarwal, J Alkumal, EJ Small, CA Maher, FY Feng, DA Quigley

HPV-mediated Cancers

Biomarkers of HPV-negative head and neck cancer

Oct 1, 2023

The genomic and epigenomic landscape of double-negative metastatic prostate cancer

A Lundberg, M Zhang, R Aggarwal, H Li, L Zhang, A Foye, M Sjostrom, J Chou, K Chang, T Moreno-Rodriguez, Raunak Shrestha, A Baskin, X Zhu, AS Weinstein, N Younger, JJ Alumkal, TM Beer, KN Chi, CP Evans, M Gleave, PN Lara, RE Reiter, MB Rettig, ON Witte, AW Wyatt, FY Feng, EJ Small, DA Quigley

The 5-Hydroxymethylcytosine Landscape of Prostate Cancer

M Sjostrom, SG Zhao, S Levy, M Zhang, Y Ning, Raunak Shrestha, A Lundberg, C Herberts, A Foye, R Aggarwal, JT Hua, H Li, A Bergamaschi, C Maurice-Dror, A Maheshwari, S Chen, SWS Ng, W Ye, J Petricca, M Fraser, L Chesner, MD Perry, T Moreno-Rodriguez, WS Chen, JJ Alumkal, J Chou, AK Morgans, TM Beer, GV Thomas, M Gleave, P Lloyd, T Phillips, E McCarthy, MC Haffner, A Zoubeidi, M Annala, RE Reiter, MB Rettig, ON Witte, L Fong, R Bose, FW Huang, J Luo, A Bjartell, JM Lang, NP Mahajan, PN Lara, CP Evans, PT Tran, EM Posadas, C He, X Cui, J Huang, W Zwart, LA Gilbert, CA Maher, PC Boutros, KN Chi, A Ashworth, EJ Small, HH He, AW Wyatt, DA Quigley, FY Feng

An integrated functional and clinical genomics approach reveals genes driving aggressive metastatic prostate cancer

R Das, M Sjostrom, Raunak Shrestha, C Yogodzinski, EA Egusa, L Chesner, WS Chen, J Chou, DK Dang, JT Swinderman, A Ge, JT Hua, S Kabir, DA Quigley, EJ Small, A Ashworth, FY Feng, LA Gilbert

Multiomics Characterization of Low-grade Serous Ovarian Carcinoma Identifies Potential Biomarkers of MEK-inhibitor Sensitivity and Therapeutic Vulnerability

LGSOC is a rare tumor subtype with high case fatality rates in patients with metastatic disease. Here, we use multiomics integration of whole-exome sequencing, RNA sequencing, and mass spectrometry–based proteomics on LGSOC cell lines to elucidate novel biomarkers and therapeutic vulnerabilities.

Raunak Shrestha, M Llaurado Fernandez, A Dawson, J Hoenisch, S Volik, Y Lin, S Anderson, H Kim, A Haegert, S Colborne, N Wong, B McConeghy, RH Bell, S Brahmbhatt, C Lee, GE DiMattia, S Le Bihan, GB Morin, CC Collins, MS Carey

Multiomics Characterization of Low-grade Serous Ovarian Carcinoma Identifies Potential Biomarkers of MEK-inhibitor Sensitivity and Therapeutic Vulnerability

Autoantibody landscape in patients with advanced prostate cancer

WS Chen, WA Haynes, R Waitz, K Kamath, A Vega-Crespo, Raunak Shrestha, A Foye, IB Carretero, IG Perez, M Zhang, SG Zhao, M Sjostrom, DA Quigley, J Chou, TM Beer, M Rettig, M Gleave, CP Evans, P Lara, KN Chi, RE Reiter, JJ Alumkal, R Aggarwal, EJ Small, PS Daugherty, A Ribas, DY Oh, JC Shon, FY Feng

Identification of Conserved Evolutionary Trajectories in Tumors

Delighted to share our paper describing an algorithm CONETT to identify Conserved Evolutionary Trajectory Tree from multiple tumors. This paper will be presented at the #ISMB2020 conference next week. @cenksahinalp https://t.

E Hodzic, Raunak Shrestha, S Malikic, CC Collins, K Litchfield, S Turajlic, SC Sahinalp