The Quigley Lab studies tumor genomes to understand how urological cancers develop and respond to therapy. Our lab is part of the Department of Urology and the Helen Diller Family Comprehensive Cancer Center at the University of California, San Francisco. Our lab collaborates with the West Coast Dream Team consortium to define the landscape of of metastatic prostate cancer.
For an overview of research in our group, visit the About the Lab page.
Recent work from our team
- Integrated Hi-C analysis of metastatic prostate tumor biopsies (Zhao et al. Nature Genetics 2024)
- An Atlas of Accessible Chromatin in Advanced Prostate Cancer Reveals the Epigenetic Evolution during Tumor Progression. (Shrestha et al. Cancer Research 2024)
- Alternative promoter use evolves as tumors develop resistance to androgen-targeted therapy (Zhang et al. Nature Cell Biology 2024)
- The genomic and epigenomic landscape of double-negative prostate tumors (Lundberg et al. Cancer Research 2023)
News
July 2024
- We welcome Biomedical Informatics graduate student Siddharth Mahesh to the Quigley lab!
- Congratulations to postdoc Raunak Shrestha on the publication of An Atlas of Accessible Chromatin in Advanced Prostate Cancer Reveals the Epigenetic Evolution during Tumor Progression in Cancer Research. This work produced chromatin accessibility maps linked to the binding of lineage-specific transcription factors (TF) by performing ATAC sequencing on 70 mCRPC tissue biopsies integrated with transcriptome and whole genome sequencing.
June 2024
- Congratulations to postdoc Meng Zhang on the publication of Integrative analysis of ultra-deep RNA-seq reveals alternative promoter usage as a mechanism of activating oncogenic programmes during prostate cancer progression in Nature Cell Biology. This work showed Alternative Promoters (APs) become increasingly important as prostate cells evolve into metastatic tumors. Many groups (including us!) tend to focus on canonical gene promoters in genome-wide studies of mCRPC. Meng used very deep RNA-sequencing to interrogate all annotated promoters in benign, localized, and mCRPC biopsies. Meng found AP use changes as tumors develop therapy resistance and she linked these changes to binding activity of key disease drivers. Meng then linked changes in AP activity to epigenomic alterations at specific AP sites.
May 2024
- David Quigley received the UCSF 2024 Outstanding Faculty Mentorship Award, chosen by the Associated Students of the Graduate Division. Dr. Quigley was honored to accept this award while standing on the same stage as Professor Allan Balmain (pictured below), his first UCSF mentor and supervisor for many years.
January 2024
- The Quigley lab has been awarded a $1,000,000 three year Data Science Award from the Department of Defense's Prostate Cancer Research Program. Metastatic castration-resistant prostate cancer (mCRPC) is unfortunately a lethal disease because most patients develop resistance to available therapies. Some mCRPC tumors resist therapy by becoming more efficient at processing androgen and remain androgen-dependent. However, a substantial number of mCRPC tumors change their behavior to reduce or eliminate their reliance on androgen signaling. This award will fund computational analysis into the transcriptional drivers of treatment-resistant mCRPC subtypes.
- Congratulations to Dr. Xiaolin Zhu on receiving a Physician Research Award from the Department of Defense's Prostate Cancer Research Program. Dr. Zhu will be co-mentored by Felix Feng and David Quigley on this four year, $750,000 award.
- We welcome UCSF Biomedical Informatics rotation student Siddharth Mahesh for a Winter rotation in the lab.
December 2023
- David Quigley presented a lecture on Quigley lab's recent study The genomic and epigenomic landscape of double-negative metastatic prostate cancer to the VA Precision Oncology Program for Cancer of the Prostate (POPCaP) program.
August 2023
- Congratulations to postdoc Thaidy Moreno on the publication of AARDVARK: An Automated Reversion Detector for Variants Affecting Resistance Kinetics in Bioinformatics. AARDVARK automatically detects and annotates mutations that cause resistance to PARP inhibitor and platinum therapy by analyzing tumor sequence data. You can download the AARDVARK R package on Github.
- UroToday Interview: David Quigley and Andrea Miyahira (Prostate Cancer Foundation) discuss the lab's recent paper on UroToday.
June 2023
- Congratulations to postdoc Arian Lundberg on the publication of The genomic and epigenomic landscape of double-negative metastatic prostate cancer in Cancer Research. In this work from our lab, presented at AACR Prostate Cancer 2023, we used unbiased analysis of 134 metastatic tumor biopsies from the West Coast Dream Team collaboration to dig into the transcription factors that drive different subtypes of therapy-resistance disease.
March 2023
February 2023
- David Quigley and postdoc Meng Zhang will be presenting talks the upcoming AACR Prostate Cancer meeting in March.
January 2023
- Congratulations to postdocs Arian Lundberg and Thaidy Moreno-Rodriguez on receiving UCSF Cancer Center Travel Awards to present their research at the upcoming AACR Prostate Cancer meeting in March!
October 2022
- We welcome Joaquín Magaña as a Fall rotation student from the UCSF Bioinformatics program.
- Congratulations to HemOnc fellow Xiaolin Zhu and postdoc Raunak Shrestha on receiving Prostate Cancer Foundation Young Investigator awards!
September 2022
- Congratulations to postdoc Martin Sjöeström and the West Coast Dream Team collaboration on the publication of The 5-Hydroxymethylcytosine Landscape of Prostate Cancer, now out in Cancer Research.
- Check out our latest commentary in Cancer Discovery, led by postdocs Thaidy Moreno-Rodriguez and Meng Zhang.
May 2022
- Meng Zhang received a travel award to attend the Society for Basic Urological Research annual meeting in November.