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Our EstroGene browser is launched to the public!

We are pleased to introduce the EstroGene Project -a comprehensive multi-omic NGS database focusing on estrogen receptor function in breast cancer. It aims to document and integrate the majority of publicly available estrogen-stimulated next generation sequencing data sets (including RNA-seq, microarray, ChIP-seq, ATAC-seq, ChIA-PET, Hi-C, GRO-seq, etc), and establish a comprehensive database to allow users’ customized data mining and visualization. We have curated 136 published NGS data sets from 2004-2022 across 19 breast cancer cell lines and generated a browser for simplified queries.

Features of EstroGene:

-A uniformly processed and crowd-sourced multi-omic database with detailed experimental documentation summary.

-A browser allowing single gene-based visualization of E2-induced expressional changes and ER proximal binding at users’ selected genes of interest.

-A browser supporting statistical cutoff-based gene list query function to export genes regulated by E2 under users’ defined contexts.

-An ER and breast cancer-centered database for dissecting the biological and technical diversity and variation of estrogen receptor-relevant NGS experiments and the confound ER regulomes in breast cancer.

We have summarized all of the curated datasets in this google form. We are crowd-sourcing additional datasets that may not be available in the public domain but are available within laboratories. If you have such a dataset please don’t hesitate to fill in the google form and we will contact you back.

We would appreciate it if you could operate the website and give us feedbacks to improve it and continue notify us about new data sets via the google form.

The BioRxiv manuscript of this project will be deposit after receiving feedbacks from the research community!

For any queries please email Nadine Ryan (ryann@upmc.edu)

Dr. Steffi Oesterreich and the lab’s latest collaborative publication in JNCI featured in the Pittsburgh Post Gazette!

Research publication: Clinicopathological Features and Outcomes Comparing Patients With Invasive Ductal and Lobular Breast Cancer

https://www.post-gazette.com/news/health/2022/10/17/breast-cancer-invasive-lobular-cancer-ilc-idc-steffi-oesterreich/stories/202210170073

Congrats to Neil Carleton on his new publication in Nature Reviews Clinical Oncology!

Congrats to lab member Neil Carleton and surgeon / lab collaborator Dr. Priscilla McAuliffe on their recent publication in Nature Reviews Clinical Oncology! This comment explores how chronological age cutoffs in clinical oncology guidelines are defined. Using the case of breast cancer in older women, the authors discuss why the age at which individuals transition from ‘younger’ to ‘older’ has been defined in a heterogeneous, unstandardized, arbitrary and disparate manner. 

Read the full article here: https://www.nature.com/articles/s41571-022-00684-4.  

Our paper about ESR1 mutations and breast cancer metastasis is now published in Cancer Research! 

https://cancerres.aacrjournals.org/content/early/2022/01/25/0008-5472.CAN-21-2576
Zheqi (Vaciry) Li, Ph.D.

This study was led by former graduate student Vaciry Li with great efforts from many intra- and inter-group collaborations. Congratulations to all! 

In this study, we showed that context and allele-dependent transcriptome and cistrome reprogramming in ESR1 mutation cell models, which elicit diverse metastatic phenotypes related to cell-cell adhesion, cell-ECM adhesion and migration driven by increased desmosome/gap junctions, dampened TIMP3-MMP axis and Wnt pathway. Importantly, some of these pathways can pharmacologically targeted and reveals novel therapeutic strategies.  

Our new review is out now in The Lancet Healthy Longevity!

Led by PhD student Neil Carleton and senior authors Adrian Lee, Priscilla McAuliffe, and Steffi Oesterreich, we review key considerations for “right-sizing” therapy options for older women with ER+ breast cancer. With contributions from radiation, pathology, surgical oncology, radiation oncology, and medical oncology from the UPMC / Magee Women’s Hospital breast cancer group, this collaborative effort touches on optimizing quality of life along with new translational studies that may impact future treatment of these patients. 

Check it out at: https://www.thelancet.com/journals/lanhl/article/PIIS2666-7568(21)00280-4/fulltext.  

Congrats to Neil and the lab on their recent paper studying treatment regimens for elderly breast cancer – out now in JAMA Network Open!

Update (7/16/2021): Check out the 21 news stories written on our recent publication!
https://jamanetwork.altmetric.com/details/103966504/news

Led by Neil Carleton with significant contributions from others in the lab (Osama Shah & Fangyuan (Chelsea) Chen), we studied trends of use of two interventions, sentinel lymph node biopsy (SLNB) and radiation therapy (RT), in elderly women with ER+, clinically node-negative breast cancer. Despite two national guidelines recommending against their use, trends of use by surgical oncologists and radiation oncologists remain quite high. We used propensity score matching to control for confounding and biases in retrospective analysis. Significantly, we found that omitting either SLNB or RT was a feasible approach to care and did not compromise recurrence free survival. Our results bolster the existing clinical guidelines recommending for de-implementation of these interventions.

This was a highly collaborative projects with input from authors in biostatistics, radiation oncology, surgical oncology, medical oncology, and specialists in women’s cancer.

Excitingly, this paper received quite a bit of attention in the media and in the field at large! We were thrilled to see Dr. Lee appear on multiple local TV news stations and Dr. McAuliffe making a number of radio appearances!

Link to paper on journal website: https://jamanetwork.com/journals/jamanetworkopen/fullarticle/2778563

Link to Hillman Cancer Center Press Release press release: https://hillmanresearch.upmc.edu/breast-cancer-treatment-study/

Link to Adrian’s KDKA segment: https://pittsburgh.cbslocal.com/video/5495249-upmc-study-not-all-breast-cancer-should-be-treated/

Link to Adrian’s WTAE segment: https://www.wtae.com/article/sometimes-less-is-better-study-looks-at-treatment-of-breast-cancer-patients-over-70/36159559

Ashuvinee Elangovan wins the GRC and BGSA travel awards!

Congrats to Ashuvinee Elangovan for winning the GRC and BGSA travel awards!

Ashuvinee Elangovan
Graduate Student

Ashuvinee Elangovan, a 2nd year graduate student in the lab won travel awards from the Gordon Research (GRC) Conferences and the Biomedical Graduate Student Association (BGSA) for the upcoming Gordon conference on IGF and Insulin System in Physiology and Disease in Ventura, CA.

Congrats to Dr. Tasdemir and colleagues on their new BioRxiv pre-print!

Congratulations to Nilgun Tasdemir on her new publication!

Proteomic and Transcriptomic Profiling Identifies Mediators of Anchorage-Independent Growth and Roles of Inhibitor of Differentiation Proteins in Invasive Lobular Breast Cancer – biorxiv.org

Abstract. BACKGROUND: Invasive lobular carcinoma (ILC) is a histological subtype of breast cancer with distinct molecular and clinical features from the more common subtype invasive lobular carcinoma (IDC).www.biorxiv.org