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BGG Student Marco Zocchi Defends Thesis!

Wednesday, October 15, 2025

Emily Berry Defends Thesis!

Thursday, September 4, 2025

Today, BGG Graduate Student Emily Berry held her thesis defense. Emily's research focused on the role of lncRNA Neat1 in maintaining cell identity. She conducted her thesis research in the laboratory of Stephano Spano Mello, Ph.D. -  Emily's thesis is titled "Examining the role of Neat1 in pancreatic exocrine cell identity". Her thesis abstract is below. 

Congratulations Dr. Emily Berry!

"The dysregulation of long noncoding RNAs (lncRNAs) has been widely found in many cancers, but the roles of lncRNA dysregulation in the development of pancreatic ductal adenocarcinoma (PDAC) remain elusive. The lncRNA NEAT1 is a target of the tumor suppressor TP53, and Neat1 absence in mouse models of PDAC increases the formation of preneoplastic lesions in the pancreas, suggesting that Neat1 functions as a tumor suppressor. Specifically, Neat1 null mice exhibit an increase in intraductal papillary mucinous neoplasm (IPMN) lesions, which are rarely seen in PDAC mice but observed in mouse models lacking functional SWItch/Sucrose nonfermenting (SWI/SNF) chromatin remodeling complexes. Both Neat1 and subunits of the SWI/SNF complex are implicated in the differentiation programs of other cell types, and are essential for the formation of paraspeckles, which are subnuclear ribonucleoprotein particles involved in the regulation of gene expression. These correlations could indicate a potential cooperation through paraspeckles to maintain exocrine pancreas cell identity. In this study, we utilized mouse models of PDAC to investigate the role of Neat1/paraspeckles and SWI/SNF in the pancreas. Neat1 and Arid1a null mouse models of PDAC exhibited similarities in increased preneoplastic lesion formation and decreased acinar cell population. Paraspeckle assembly was reduced in Neat1 and SWI/SNF deficient mouse PDAC cells, and the overexpression of SWI/SNF subunits increased paraspeckle abundance. The absence of Neat1 in exocrine cells redistributes SWI/SNF near the promoters of genes involved in pancreas identity pathways. Some of these genes are also significantly dysregulated in the absence of Neat1. Our findings presented here suggest that Neat1/paraspeckles and SWI/SNF cooperate to regulate the chromatin landscape as a means of maintaining exocrine pancreas identity."

University of Rochester Awarded Prestigious Aging Research Center Grant

Tuesday, July 15, 2025

The National Institutes of Health has awarded University of Rochester aging researcher Vera Gorbunova, PhD, a prestigious Nathan Shock Center grant. The grant will provide nearly $1 million per year over the next five years to establish the Upstate NY Comparative Biology of Aging Nathan Shock Center.

Lifespans vary widely—more than 100-fold—across the animal kingdom. The new center will compare the biology of various long- and short-lived animal species to identify biological mechanisms that promote longevity.

“It is about making people healthier overall,” says Gorbunova, the Doris Johns Cherry Professor of Biology, co-director of the Rochester Aging Research Center, and professor of Geriatrics/Aging at the University of Rochester Medical Center. “It really is about preventing all diseases.”

Gorbunova will lead a transdisciplinary team of faculty spanning the University and Medical Center, with expertise in veterinary biology, molecular biology, biochemistry, genetics, mass spectrometry, and bioinformatics.

“There are only eight centers like this in the country, so receiving this grant really puts us on the map in a more prominent way,” says Gorbunova.

Fatemeh Alimohammadi Earns Breast Cancer Coalition of Rochester Award!

Wednesday, June 18, 2025

On Tuesday June 17th, BGG student Fatemeh Alimohammadi (Harris Lab) earned the prestigious Pamela Delp Polashenski MD Breast Cancer Research Trainee Grant. With this award, the Breast Cancer Coalition of Rochester (BCCR) confers $25,000 of support towards Fatemeh’s doctoral studies. At the award reception, Fatemeh presented her research proposal "Understanding Glutathione-Related Dipeptide Metabolism in Triple Negative Breast Cancer" to the BCCR. This funding will help Fatemeh study antioxidant glutathione and its role in triple-negative breast cancer (TNBC). This may help develop potential new treatment options for TNBC.

We are grateful to the BCCR for its long history supporting our community.

Congratulations Fatemeh!

Why Don’t Bats Get Cancer? Researchers Discover Protection from Genes and Strong Immune Systems

Monday, June 9, 2025

UR scientists studying longevity are seeking to apply their findings to humans.

A study to look at why long-lived bats do not get cancer has broken new ground about the biological defenses that resist the disease.

Reported in the journal Nature Communications, a University of Rochester research team found that four common species of bats have superpowers allowing them to live up to 35 years, which is equal to about 180 human years, without cancer.

Vera Gorbunova, PhD, and Andrei Seluanov, PhD, members of the UR Department of Biology and Wilmot Cancer Institute, led the work. Their key discoveries on how bats prevent cancer:

• Bats and humans have a gene called p53, a tumor-suppressor that can shut down cancer. (Mutations in p53, limiting its ability act properly, occur in about half of all human cancers.) A species known as the “little brown” bat—found in Rochester and upstate New York—contain two copies of p53 and have elevated p53 activity compared to humans. High levels of p53 in the body can kill cancer cells before they become harmful in a process known as apoptosis. If levels of p53 are too high, however, this is bad because it eliminates too many cells. But bats have an enhanced system that balances apoptosis effectively.
• An enzyme, telomerase, is inherently active in bats, which allows their cells to proliferate indefinitely. This is an advantage in aging because it supports tissue regeneration during aging and injury. If cells divide uncontrollably, though, the higher p53 activity in bats compensates and can remove cancerous cells that may arise.
• Bats have an extremely efficient immune system, knocking out multiple deadly pathogens. This also contributes to bats’ anti-cancer abilities by recognizing and wiping out cancer cells, Gorbunova said. As humans age, the immune system slows, and people tend to get more inflammation (in joints and other organs), but bats are good at controlling inflammation, too. This intricate system allows them to stave off viruses and age-related diseases.

What Experts Want You to Know About Microplastics

Tuesday, May 20, 2025

Microbiologist Jacques Robert, PhD, told The New York Times (May 20) that his research shows tadpoles excreted about 60 percent to 70 percent of the microplastics they were fed. His studies also suggest that microplastics may weaken the immune system. While animal studies don’t always translate directly to humans, other research indicates that microplastics not excreted can enter the bloodstream and migrate to organs like the liver and brain.

BGG Student Brandon J. Park Successfully Defends His Thesis!

Thursday, March 6, 2025

Yesterday, on Wednesday, March 5th, BGG student Brandon J. Park successfully defended his thesis! During his time at the University of Rochester he was co-mentored Patrick J. Murphy, Ph.D. and Mitchell R. O'Connell, Ph.D. Brandon’s research focused the role of H2A.Z in epigenetic inheritance. His thesis is titled “Novel Chromatin Profiling Strategies to Assess Non-Coding Nucleic Acids”. We wish Bradon the best as he begins his post graduate career. You can read Brandon’s thesis abstract below...

Abstract: The proper regulation of gene expression is critically important in processes like organismal development and cellular responses to external stimuli, and aberrant gene expression patterns often cause disease. Many cellular factors can influence gene expression, including epigenetic factors and lncRNAs. Since the development of next-generation-sequencing, strategies for profiling the interactions between chromatin and RNA/proteins have drastically advanced, but many methods still have limitations that have made certain aspects of epigenetics and lncRNA biology difficult to study. Traditional ChIP-Seq techniques are biased against heterochromatic and sonication-resistant regions of the genome such as repetitive elements, and most modern techniques for mapping lncRNA-chromatin interactions suffer from a high cell number requirement that is not feasible for most rare cell types. Here, we investigate the potential of CUT&Tag for profiling chromatin modifications at heterochromatic regions of the genome, and propose a novel method called Cas-CUT&Tag for profiling lncRNA-chromatin interactions from a small number of cells. We find that CUT&Tag identifies H3K9me3 at many repetitive elements that are underrepresented in equivalent ChIP-Seq datasets, including many evolutionarily young LTR regions. CUT&Tag also detects H2A.Z at many IAPEz-int elements that are underrepresented in ChIP-Seq, and many proteins were identified in our study that are frequently discarded with the cellular debris pellet in traditional ChIP methods. Additionally, we find that our novel Cas-CUT&Tag method shows some degree of specificity for various lncRNA targets and cell types, but it also produces significant off-target effects that limit its current applicability. With further optimization of the Cas-CUT&Tag method and continued application of the standard CUT&Tag method across a variety of targets and cell types, our understanding of gene expression regulation via epigenetics and lncRNAs will undoubtedly continue to rapidly expand.

BGG Alum, Tom O'Connor featured on 'The Next Step' podcast!

Thursday, February 27, 2025

Tom O'Connor, Ph.D. is a former BGG student who pursued his doctoral research in Dr. Robert T. Dirksen’s laboratory. Tom defended his thesis in the summer of 2023 and is currently working as a Scientist at Roswell Park Cancer Center in Buffalo, New York. Yesterday, Tom discussed his experiences during the transition after gradate school with Jeff Koslofsky.

You can find more episodes of the next step podcast here.

Hongbo Liu, Ph.D. Publishes Kidney Disease Study in the Journal Science

Monday, February 17, 2025

Recently, BGG Program Faculty Member Hongbo Liu, Ph.D. published a study of genetic mutations related to Kidney Disease. Katalin Susztak, MD, Ph.D., from the University of Pennsylvania, co-authored this Science publication titled 'Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants'.

Read More: 'New Study Links Mystery Mutations to Kidney Disease, Unlocking Potential Therapies'

Brian J. Altman, Ph.D. Joins Scientific Leadership Committee

Saturday, February 1, 2025

BGG Program faculty member Brian J. Altman, Ph.D., will serve as assistant director for Education/Career Development for the Cancer Research Training and Education Coordination (CRTEC) team, and Scott Gerber, Ph.D., has been named co-leader of Wilmot's Cancer Microenvironment research program.

Read more on Brian and Scott's new roles on the URMC Intranet webpage: 'Brian Altman and Scott Gerber Join Scientific Leadership Committee'