Center Events

Regina Rowe, MD, PhD - Assistant Professor, Pediatrics/Infectious Diseases

 Dec 08, 2023 @ 9:00 a.m.

 Kornberg Medical Research Building | 3-9624

Stephen Hammes, MD, PhD - Professor, Medicine/Endocrine/Metabolism

 Nov 17, 2023 @ 9:00 a.m.

 Kornberg Medical Research Building | 3-9624

Ian Stone - PhD Candidate, Immunology, Microbiology and Virology PhD Program

The elderly population are more susceptible to viral infections, in part due to increased dysregulation of immune responses, which are associated with increased age. Uncovering shared effector mechanisms between processes that regulate healthy aging and viral infection protection could represent novel pharmaceutical targets to decrease mortality rates. 

Caenorhabditis elegans (C. elegans) is an excellent model system for aging research, given its brief lifespan, short generation time, and high homology to human disease genes. Interestingly, C. elegans lack professional immune cells, allowing the study of innate immunity in isolation. Orsay virus (OV) is a natural viral pathogen of C. elegans, allowing for the genetic analysis of host-virus interactions in this model organism. I found older animals have decreased activation of innate immune pathways in response to OV infection and increased viral load over the course of infection compared to younger animals, suggesting they cannot adequately regulate viral replication. 

The mechanistic target of rapamycin (mTOR) is a major longevity pathway that controls aging and responds to cellular stress. mTOR forms two complexes, but mTORC1 has an important role in combating viral replication; downstream adaptive responses including autophagy and protein translation have been implicated in cellular stress responses to viral replication. I found that knockdown of TOR improved C. elegans resistance to OV infection, but the mechanisms underlying this resistance are still unknown. By continuing my study of requirements for mTOR-driven protection, I will be able to study the potential of mTORC1 as a therapeutic target for improving healthy aging and viral protection.

 Nov 16, 2023 @ 12:00 p.m.

 Medical Center | K-307 (3-6408)

Host: Andrew Samuelson, Ph.D. and Brian Ward, Ph.D. - Advisors

Gowri Muthukrishnan, PhD - Assistant Professor, Orthopaedics/CMSR

 Nov 10, 2023 @ 9:00 a.m.

 Kornberg Medical Research Building | 3-9624

Jennifer Anolik, MD, PhD - Professor, Medicine/Allergy, Immunology & Rheumatology

 Nov 03, 2023 @ 9:00 a.m.

 Kornberg Medical Research Building | 3-9624

Jeremiah Johnson, PhD - Associate Professor of Microbiology, University of Tennessee

Special Faculty Candidate Seminar

Campylobacter jejuni is the leading global cause of bacterial-derived gastroenteritis and induces neutrophil extracellular traps (NETs), which are structures comprised of DNA and antimicrobial proteins that can restrict pathogen growth and dissemination during infection. In a recent study, we identified a sirtuin encoded by C. jejuni that is secreted from the bacterium into human neutrophils where it associates with and deacetylates host histones to promote neutrophil activation and NET production. Using the murine model of campylobacteriosis, we found that a mutant of this sirtuin efficiently colonized the gastrointestinal tract, but was unable to induce cytokine production, gastrointestinal inflammation, and tissue pathology. These results suggest that secreted bacterial sirtuins are a previously unreported class of effector and that bacterial-mediated modification of host histones is responsible for the inflammation and pathology that occurs during campylobacteriosis.

Further, while NETs are efficient at limiting bacterial burden at the site of infection, numerous pathogens encode nucleases that degrade NETs to evade their antimicrobial effects. Because we found that C. jejuni viability is not impacted by human NETs, we hypothesized and found that unidentified C. jejuni nucleases promote the degradation and evasion of human NETs. Since the determinants required for C. jejuni nuclease production are poorly understood, we conducted a screen and identified a DNA glycolyase, called MugA, that promotes degradation and evasion of NETs. In addition, MugA-dependent NET degradation products promoted host inflammation through NLRP3-dependent inflammasome activation in adjacent macrophages. As such, while MugA assists the bacterium in evading NET killing, it promotes host inflammation. As a result, we found that a mugA mutant inconsistently colonizes and causes reduced inflammation when compared to wild-type-infection. These results suggest that nuclease-targeted therapeutics may be efficacious at reducing pathogen burden and disease within infected hosts.

 Nov 02, 2023 @ 2:30 p.m.

 Medical Center | Lower Adolph (1-7619)

Host: Department of Microbiology & Immunology

Andy Phan - PhD Candidate, Immunology, Microbiology, and Virology PhD Program

Human immunodeficiency virus 1 (HIV-1) is a pathogen responsible for an ongoing global epidemic, for which there is no curative therapy or protective vaccine.  Although there exists antiretroviral therapy (ART) which is effective in suppressing further HIV-1 replication, the virus cannot be eliminated from the patient, and cessation of ART would lead to rebound of viral replication.  The major obstacle towards an HIV-1 cure is the persistence of replication-competent viral DNA.  In infected cells, latent HIV-1 DNA is transcriptionally silenced and not susceptible to the host immune system or antiretroviral drugs.  Latency is commonly associated with the deposition of repressive epigenetic modifications and removal of active epigenetic modifications, which occurs through interactions with cellular proteins, but the exact mechanisms for silencing of viral DNA are not well understood.

By employing a CRISPR-Cas9 knockout screen, we assessed host factors to determine their potential in the silencing of viral gene expression, and identified the cohesin complex subunits SMC1A, SMC3, and RAD21 as cellular proteins responsible for silencing of HIV-1 DNA.  We show that depletion of these host factors leads to a significant increase in viral DNA expression.  We also assess the ability of Vpr, an HIV-1 accessory protein linked to enhancing viral gene expression, to counteract host-mediated silencing.  Our current experiments explore the mechanisms by which the cohesin complex may promote compaction of viral chromatin and therefore contribute to decreased viral gene expression, and the ability of HIV-1 to antagonize this silencing.  Expansion in this area of HIV-1 research will contribute to the progress of novel therapies to fully eliminate latent DNA in infected cells.

 Nov 02, 2023 @ 12:00 p.m.

 Medical Center | K-307 (3-6408)

Host: Yiping Zhu, PhD - Advisor

Ben Frisch, PhD - Assistant Professor, Pathology & Laboratory Medicine

 Oct 27, 2023 @ 9:00 a.m.

 Kornberg Medical Research Building | 3-9624

Adam Geber - PhD Candidate, Medical Scientist Training Program (MSTP)
Immunology, Microbiology and Virology PhD Program

The immune system is classically divided into two categories: innate and adaptive, where the former responds rapidly and nonspecifically and the latter does so more slowly, precisely, and with greater speed and specificity over time. These conceptual distinctions are most appropriate for adult humans, who have a substantial repertoire of mature naïve lymphocytes that can establish immunological memory to protect against reinfection. Because the infant immune system continues to develop after birth and does not yet have an archive of memory cells, it must be capable of rapid and often nonspecific responses to signals of danger and damage. T cells are crucial to proper functioning of the adaptive immune system and are responsible for recruiting and coordinating immune cells, shaping future responses, and directly killing infected or cancerous cells. CD8+ T cells are canonically known for their cytolytic functions but can also produce cytokines under certain inflammatory conditions. During the last two decades an array of lymphoid immune cells have been described as having innate-type functions and/or a strongly restricted capacity for recognizing foreign antigens. More recently, we have found evidence for a subset of CD8+ T cells that arise in utero during the second trimester, persist variably into adulthood, and behave in an innate-like manner. We report the initial flow cytometric characterization of the phenotype and function of putative fetal innate-like CD8+ T cells (FITs) derived from cord blood mononuclear cell samples.

 Oct 26, 2023 @ 12:00 p.m.

 Medical Center | K-307 (3-6408)

Host: David Topham, PhD - Advisor

Suryaram (Rham) Gummuluru, PhD - Professor & Vice-Chair, Department of Virology, Immunology & Microbiology, Director, Graduate Medical Sciences Immunology Training Program (ITP) Investigator, National Emerging Infectious Diseases Laboratory (NEIDL) Co-Director, Developmental Core, Providence/Boston Center for AIDS Research (Prov/Bos CFAR) Boston University

 Oct 23, 2023 @ 12:00 p.m.

 Medical Center | Upper Auditorium (3-7619)

Host: Steve Dewhurst, PhD

Juilee Thakar, PhD - Associate Professor, Microbiology & Immunology

 Oct 20, 2023 @ 9:00 a.m.

 Kornberg Medical Research Building | 3-9624

Ankit Dahal - Graduate Student, Immunology, Microbiology, and Virology Ph.D. Program

Cancer deaths is the 2nd leading cause of mortality worldwide, and the total number of cancer related deaths is anticipated to only increase. Emerging evidence suggests that the presence of polymorphonuclear (PMN) myeloid derived suppressor cells (MDSCs) with neutrophil-like phenotypes and morphologies play a major role in adverse clinical outcomes due in part to their contribution in establishing immunosuppressive tumor microenvironment (TME). Despite recent advances in our understanding of MDSC phenotypes and characteristics in the TME, the underlying molecular mechanisms by which classical neutrophils differentiate into MDSC within the TME remails largely unknown. 

To investigate the microenvironmental cues that regulate PMN-MDSC differentiation at the tumor site, we established several in vitro co-culture systems using multiple human and murine cancer cells and 3D spheroid conditions. With live cell migration microscopy, we first showed that neutrophils actively swarmed into the pancreatic cancer spheroids and stayed active for an extended period in the tumor. We further found that cancer cell culture supernatant significantly extended neutrophil survival and successfully differentiated neutrophils into MDSCs that exhibited increased arginase and suppressed CD8 cytotoxicity and proliferation. To identify the major macromolecules in the supernatant mediating MDSC differentiation, we selectively inactivated and depleted different classes of macromolecules and discovered that the loss of lipid signal from the cancer supernatant completely abrogated the ability of PMNs to differentiate into MDSCs. To further identify the specific lipid molecules mediating such effects, we utilized LC-MS lipidomic analysis to screen for major lipids secreted by both murine and human cancer cells and identified several arachidonic acid and other inflammatory lipid molecules including platelet activating factor (PAF). Meta transcriptional and survival analysis of human PDAC cancer highlights a strong negative association between the expression of PAF generating enzyme, LPCAT2, and patient survival, suggesting that PAF may be implicated in cancer progression and growth. Given that PAF is a strong neutrophil activator, we hypothesize that PAF mediated signaling may promote the differentiation of MDSCs in pancreatic cancer. 

 Oct 19, 2023 @ 12:00 p.m.

 Medical Center | K-307 (3-6408)

Host: Minsoo Kim, PhD - Advisor

Joseph E. Peters, PhD - Professor and Chair, Department of Microbiology
Cornell University

Transposon Tn7 and Tn7-like elements are notable for the control they exercise over where transposition events are directed. In these diverse elements one integration pathway recognizes a highly conserved attachment (att) site in the chromosome, while a second pathway specifically recognizes mobile plasmids that facilitate transfer of the element to new hosts. There has been a flood of recent work with these systems, including the discovery of five independent events were CRISPR-Cas systems have been coopted for natural guide RNA-directed transposition. New families of Tn7-like elements also include a variety of novel att sites in bacterial chromosomes where genome islands can form in important pathogens like Acinetobacter baumannii. I will present work from my lab that is expanding our understanding of Tn7-like elements, broadening our view of how genetic systems are repurposed and indicating potential new tools for genome modification and genomics.

 Oct 16, 2023 @ 12:00 p.m.

 Medical Center | Upper Auditorium (3-7619)

Host: Andrew Varble, PhD

Tim Flerlage, MD - Assistant Professor, Pediatrics/Infectious Diseases

 Oct 13, 2023 @ 9:00 a.m.

 Kornberg Medical Research Building | 3-9624

Hansol Im, PhD - Postdoctoral Fellow, Laboratory of Carlos J. Orihuela
University of Alabama at Birmingham

Streptococcus pneumoniae (Spn) is a Gram-positive bacterium and the leading cause of community-acquired pneumonia. In most instances, Spn resides in the nasopharynx asymptomatically. However, in infants or elders, those who are immunocompromised, or when a viral infection has damaged the airway, this opportunistic pathogen can cause infection of the lower airway and bloodstream. Annually, more than ten million individuals are hospitalized globally due to Spn infection, and as a result, hundreds of thousands die despite appropriate antimicrobial therapy. Thus, a better understanding of Spn-host interaction merits additional research to identify new therapeutic targets. In this series of studies, we observed that the physiology and virulence expression of the bacteria were highly dependent on where they were located within the host and surrounding carbon availability. Carbon metabolism and its alteration according to carbon availability are critical in determining the physiology and survival of Spn in the host. We evaluated carbon metabolic pathways involved in redox balance and its impact on downstream bacterial physiology and virulence phenotype. We found that NAD(H) redox balance during fermentation was vital for Spn energy generation, capsule production, in vivo fitness, and survival under antibiotic stresses. Moreover, targeting the NAD(H) metabolic pathway enhanced the susceptibility of multidrug-resistant Spn to antibiotics and prevented invasive disease in an animal infection model. Together, our results indicate carbon metabolism pathways are de novo targets for antibiotic development and a novel strategy to combat multidrug-resistant pathogens. Subsequently, better resolution in bacterial metabolic shifts during the course of disease will expand our understanding of the host-pathogen interactions at the foundation of Spn’s ability to cause disease, which can be valuable targets for novel therapeutics.

 Oct 12, 2023 @ 2:00 p.m.

 Medical Center | Lower Adolph Auditorium (1-7619)

Justin Brennan - Graduate Student, Immunology, Microbiology and Virology PhD Program

Defective viral genomes (DVGs) are truncated derivatives of their parental viral genomes unable to replicate without a full-length helper virus. DVGs have been observed in most RNA viruses and play critical roles in viral pathogenesis and evolution. During respiratory syncytial virus (RSV) infection, the copy-back type of DVGs (cbDVGs) potently induce the antiviral response. RSV is among the most consequential agents of pediatric respiratory illness and RSV cbDVGs correlate with antiviral responses in children; thus, cbDVGs are candidates for antivirals and vaccine adjuvants. Currently, little is known about the mechanisms of cbDVG generation or species-specific functions of cbDVGs, limiting our ability to use cbDVGs to mitigate viral pathogenesis. Our lab has shown that RSV cbDVG generation is not a stochastic process and identified three genomic “hotspots” (R1, R2 and R3) mediating the formation of cbDVGs. Moreover, the introduction of a poly-U mutation into R1 reduced its role in cbDVG formation, demonstrating that cbDVG generation is genetically manipulable. Here, our previous work was expanded on by generating a mutant virus with a similar mutation in R2 (10U). cbDVGs were enriched in WT and 10U viruses by high MOI passaging. Strikingly, the 10U virus had a two-passage delay in cbDVG generation compared to WT and this delay was recapitulated in a primary pediatric lung epithelial cell system. RNA-seq analysis of the cbDVG populations enriched in the WT and 10U viruses showed that the frequency of R2 cbDVGs was largely reduced by the 10U mutation, with R3 becoming the major rejoin hotspot. To examine the species-specific functions of R2 and R3 cbDVGs, the major WT (WT 1887) and 10U (10U 1563) cbDVGs were selected for further analysis. Compared to WT 1887, 10U 1563 had enhanced replication kinetics and, when transfected as naked RNA, induced significantly more interferon and ISG expression per cbDVG. Interestingly, this difference was minimized in the presence of the RSV nucleoprotein. Overall, these data support our previous findings and establish that various RSV cbDVG species have distinct replication kinetics and immunostimulatory capacities, and implicate the RSV nucleoprotein in mediating these functions.

 Oct 12, 2023 @ 12:00 p.m.

 Medical Center | K-307 (3-6408)

Host: Yan Sun, PhD - Advisor

Kathryn M. Kauffman, PhD - Assistant Professor, Department of Oral Biology School of Dental Medicine University at Buffalo

Viral predators and partners of bacteria (called phages) are present in essentially all microbial communities and shape their structure and function. Yet, understanding and predicting the impacts of phages on microbial communities remains a challenge. In this talk I highlight our work addressing this challenge through a focus on resolving phage-bacteria interactions in two model systems. In our marine model we focus on Vibrio, fast growing heterotrophs; establishing a collection of >250 phage-bacteria pairs, sequencing all genomes, and generating a complete all-by-all matrix of killing interactions. In our oral model we focus on Porphyromonas gingivalis, a keystone pathogen in periodontal disease; using bioinformatic approaches to investigate publicly available genomes. Take-aways include important considerations for development and deployment of phages in bioengineering, industry, and medicine, and a reminder that ecologically important phages can be missed even in well-studied host systems. For more details about our work please visit https://kauffmanlab.org/

 Oct 09, 2023 @ 12:00 p.m.

 Medical Center | Upper Auditorium (3-7619)

Host: Andrew Varble, PhD

Jennetta Hammond, PhD - Assistant Professor, Neurology/Neuroimmunology

 Oct 06, 2023 @ 9:00 a.m.

 Kornberg Medical Research Building | 3-9624

Kelli Connolly, PhD - Associate Research Scientist, Yale School of Medicine

We do not know if the lack of responses to checkpoint blockade immunotherapy (CPI) in some NSCLC subtypes is due to a lack of therapy-responsive T cells, or whether it is caused primarily by T cell-unrelated factors. Recently, utilizing a model of KP NSCLC, we discovered that a stable reservoir of TSL are maintained in tumor-draining lymph nodes (TDLN) throughout disease progression and migrate to the tumor over time, preserving the intratumoral CPI response. We hypothesize that TSL reservoirs are maintained within tdLNs of poorly responsive subtypes of NSCLC, such as KL, and that these cells can be leveraged to improve CPI responsiveness. To test this, I have developed genetically engineered mouse models of autochthonous KP, KPL, and KL NSCLC with inducible expression of a shared tumor neoantigen, thus allowing for direct comparisons of tumor-specific T cell responses in the context of these commonly occurring co-mutations.

NOTE: Dr. Connolly received her Ph.D. Degree in 2017 from UR in Microbiology and Immunology

 Oct 02, 2023 @ 12:00 p.m.

 Medical Center | Upper Auditorium (3-7619)

Host: Scott Gerber, PhD

Shannon Hilchey, PhD - Research Assistant Professor, Medicine/Nephrology

Bagels & Coffee available at 8:30 am in KMRB 3-9623

 Sep 29, 2023 @ 9:00 a.m.

 Kornberg Medical Research Building | 3.9624 East

Paige Lawrence, PhD - Professor, Department of Environmental Medicine

Breakfast Items & Coffee will still be available at 8:30 am in KMRB 3-9623

 Mar 31, 2023 @ 9:00 a.m.

M. Kerry O'Banion, MD, PhD - Professor, Department of Neuroscience

 Mar 24, 2023 @ 9:00 a.m.

 Kornberg Medical Research Building | 3-9624

Dave Topham, PhD - Professor, Center for Vaccine Biology & Immunology

Meeting ID: 976 3491 7477
Passcode: 664735

 Mar 17, 2023 @ 9:00 a.m.

 Kornberg Medical Research Building | 3-9624

The 2023 RNA Institute Symposium will be held March 16-17th at the University at Albany, in collaboration with the UR Center for RNA Biology.

Call for Abstracts

We are pleased to announce our upcoming 2023 Annual RNA Institute Symposium hosted by the RNA Institute at the University at Albany in collaboration with the RNA Center for Biology at the University of Rochester. This year's meeting will focus on strengthening connections between academia and industry, hosting invited speakers from New York State Biotech and Pharma Industries as well as academia.

Event Highlights

Speakers from NY Biotech & Pharma Industries and Academia
Networking Opportunities with Industry Scientists

Trainee Talks
Lightning Talks of Selected Posters

Poster Sessions
Cash Awards for trainee talks and Posters

Abstract submission and registrations are now open.

Abstract submission closes by February 3, 2023. Feel free to pass along the attached advertisement to your friends and colleagues.

Submit your abstract and register at the link below

Register Today

 Mar 16, 2023 @ 9:00 a.m.

Jerry Workman, PhD - Investigator; Director of Postdoc Affairs, Stowers Institute for Medical Research, Kansas City, MO

Our Keynote Retreat Speaker this year is Dr. Jerry Workman, Investigator; Director of Postdoc Affairs, Stowers Institute for Medical Research, Kansas City, MO. His talk title is “Signaling through Chromatin for Transcription and Metabolism”. His host is Dr. Jeff Hayes. The T32 Retreat this year will be co-sponsored by Graduate Women in Science (GWIS) and a supplement to the NIH NIGMS T32 in Cellular, Biochemical and Molecular Sciences.

New this year, there will be a Wellness and Resilience Panel following the Keynote, from 3:15 – 4:15 pm, moderated by Dr. Jeff Hayes. The featured panelists are:

• Brigid Cahill, PhD, Director, University Counseling Center,; Associate Professor of Clinical Psychiatry, University of Rochester
• Kermin Martínez-Hernández, PhD, Principal Facilitator, Center for the Improvement of Mentored Experiences in Research (CIMER); Associate Professor, Department of Chemistry, St. John Fisher University
• Susan H. McDaniel, PhD, Dr. Laurie Sands Distinguished Professor of Families & Health; Director, UR Medicine Physician Communication Coaching Program; Chief of Psychology and Director, Institute for the Family, Department of Psychiatry; Vice Chair, Department of Family Medicine, University of Rochester
• Adrienne Morgan, PhD, Vice President and Senior Associate Dean for Equity and Inclusion; Associate Professor, Department of Health Humanities and Bioethics; Associate Professor, Warner School of Education, University of Rochester.

 Mar 15, 2023 @ 1:00 p.m.

 Medical Center | Class of '62 Auditorium (G-9425)

Host: Dr. Jeffrey Hayes (co-sponsored by Graduate Women in Science GWIS)

Bing Li, PhD - Endowed Professor for Cancer Immunology, Professor of Pathology, Department of Pathology
University of Iowa, Iowa City, IA

 Mar 13, 2023 @ 12:00 p.m.

 Medical Center | WCI Formicola CR – 2-0727

Host: Minsoo Kim, PhD and Laura Calvi, MD

Ann Falsey, MD - Professor, Department of Medicine - Infectious Diseases

 Mar 10, 2023 @ 9:00 a.m.

 Kornberg Medical Research Building | 3-9624

Simon Foster, PhD - West Riding Professor of Microbiology, The Florey Institute, School of Biosciences, University of Sheffield

The shape and integrity of bacteria are determined by cell wall peptidoglycan, a single macromolecule that surrounds the cell.  The synthesis of peptidoglycan is also the site of action of important antibiotics such as penicillin and vancomycin.  Thus bacterial viability, growth and division are dependent on the architecture and dynamics of this essential polymer.  We use a combination of high-resolution microscopy approaches to reveal peptidoglycan architecture, and its dynamics, using the major human pathogen Staphylococcus aureus as our primary organism.  Atomic force microscopy has demonstrated a complex, nanoscale peptidoglycan architecture in diverse species, which meets the challenges of maintaining viability and growth within their environmental niches, by exploiting the bioengineering versatility of the polymer.  The application of super-resolution fluorescence microscopy, coupled with new chemical probes has begun to reveal how the polymer is synthesized and hydrolysed during growth and division.  We have also used these approaches to determine the mode of action of antibiotics and molecular mechanisms of antimicrobial resistance.

 Feb 27, 2023 @ 12:00 p.m.

Host: Edward Schwarz, PhD

Jim McGrath, PhD - Professor, Department of Biomedical Engineering

Meeting ID: 976 3491 7477
Passcode: 664735

 Feb 24, 2023 @ 9:00 a.m.

 Kornberg Medical Research Building | 3-9624

Taylor Jones - Graduate Student, Advisor: David Topham, PhD

Influenza and other respiratory viruses annually pose a global health and economic burden, leading to hospitalizations and even death. In order to formulate better treatments and vaccines, it’s imperative to understand the mechanisms that can reduce disease burden. Tissue- resident memory (Trm) CD8 T cells in the airway and lung are among the first line of defense against viral reinfection. The ability to provide surveillance at the primary site of infection distinguishes Trm from other CD8 memory T cells. Cell surface expression of CD69 has been used as a broad marker for Trm; however, the expression of integrins CD103 and CD49a distinguish subsets of Trm in the lung. CD49a binds to collagen IV, found in the basement membrane of the lung, and can be detected on CD8 T cells as early as 6-8 days post-infection. Functionally, CD49a has been implicated in Trm adherence, retention in the lung and airways, and motility within tissues. Anti-CD49a antibody blockade prior to secondary infection reduces Trm in the lung and is associated with increased mortality in mice. To further understand the functional relevance of CD49a in Trm, a transgenic OT-1 mouse-model was developed with a CD8 driven tamoxifen inducible CreERT2 recombinase crossed to loxP flanked Itga1 and tdTomato genes. Tamoxifen treatment leads to deletion loxP flanked genes, Itga1 (iCD8 Cre Itga1 tdTomato), which encodes CD49a. This model will be used to address how CD49a functions in tissue resident memory relating to motility, positioning within the tissues, and function. To test the model, splenocytes from iCD8 Cre Itga1 tdTomato mice were adoptively transferred into recipient B6 mice and infected the following day with X31-OVA influenza virus. Tamoxifen treatment was administered consecutively for 5 days beginning at day 32 post infection to trigger loss of CD49a. Flow cytometric analysis was done on the lungs, spleen, and mediastinal lymph node from these mice to measure changes in T cell localization. Treated mice had reduced CD49a+ memory CD8 T cells in the lung, suggesting the model works as expected. In the future, this model will be used to capture the cells’ potential to respond against secondary infection. The role of CD49a in motility within the airways will be examined by performing intravital multiphoton imaging of trachea using the adoptive transfer and infection model as before. The conditionality of this model will also allow us to prod the different time points that are essential for T cell memory. These experiments will help define the function of CD49a in local surveillance, retention, and antiviral immunity.

 Feb 23, 2023 @ 12:00 p.m.

 Medical Center | K-307 (3-6408)

Tom Mariani, PhD - Professor, Department of Pediatrics - Neonatology

Meeting ID: 976 3491 7477

Passcode: 664735

 Feb 17, 2023 @ 9:00 a.m.

 Kornberg Medical Research Building | 3-9624

Emily Britt - Graduate Student, Advisor: Steven Gill, PhD

Staphylococcus aureus is the most prevalent causative pathogen of prosthetic joint infections (PJIs). Obese-Type 2 Diabetics (Ob/T2D) are at an increased risk for post-operative infections due to immune dysfunction. Immune dysfunction is caused in part by gut microbiome dysbiosis that accompanies Ob/T2D. Microbial dysbiosis is characterized by altered community composition and abundance, which results in aberrant production of key gut microbe-derived metabolites. The balance of health and disease is dependent upon the synergistic interactions of these systems. Utilizing the Ob/T2D model, we can assess the contributions of both immune dysfunction and gut microbiome disturbances on infection severity. In our paradigm, we utilize a diet-induced Ob/T2D mouse model to study the impact of gut microbiome alterations on the immune response to infected surgical implants. Infections in Ob/T2D mice recapitulate increased severity seen in Ob/T2D humans compared to lean counterparts. Supplementation with dietary fiber oligofructose (OF) is known to alter the gut microbiome composition in humans and mice. We have shown that OF supplementation in our mouse model decreased infection severity in Ob/T2D mice. Targeted metabolomics revealed significantly increased polyamine output in Ob/T2D mice supplemented with OF. Supplementation with polyamines directly provided the same decrease in infection severity. I will perform dual-RNA sequencing of S. aureus-infected mouse tibia in our Ob/T2D model to determine the impact of dietary OF and polyamine supplementation on the host immune and S. aureus transcriptome responses in vivo. I will also complete in vitro assays to determine the mechanistic impacts of polyamines on macrophage gene expression and function as well as on S. aureus gene expression. I will present preliminary in vitro data that demonstrates the impact of polyamines on the expression of a key S. aureus host tissue adhesion factor. These experiments will give us better insight into how gut microbe-derived metabolites influence the immune response and ultimately the outcomes of infection, providing a glimpse at alternative methods to treat disease through modulation of host metabolism and immunity.  

 Feb 16, 2023 @ 12:30 p.m.

 Medical Center | K-307 (3-6408)

Zachary Boodoo - Graduate Student, Advisor: Meera Singh, PhD

As of 2021, approximately 38 million were living with HIV worldwide. The implementation and increased availability of combined antiretroviral therapy (cART) has both extended the lifespan and increased the quality of life for persons living with HIV (PLWH) while curtailing the rates of new infections (32% decline since 2010). These developments have made it possible for a significant population of HIV+ individuals to transition into middle and old age. Despite these advancements, PLWH exhibit an increased susceptibility to develop a vast number of comorbidities, which necessitates undertaking novel studies to address these concerns. One of these heightened disease states is cardiovascular disease, which is the subject of our research efforts.

Monocytes can be broadly classified into three subsets based on surface marker expression: classical (CD14+CD16-), intermediate (CD14+CD16+), and non-classical (CD14loCD16+). Although important in resolution of injury and homeostatic maintenance, non-classical monocytes, due to their pro-inflammatory phenotype, have been implicated in atherosclerosis (AS) by physically interacting with endothelial cells and contributing to plaque formation. Previous work done by our lab has demonstrated a higher percentage of these circulating non-classical monocytes in HIV+ individuals. Additionally, we observed a higher percentage of activated platelets in the same cohort, which have the propensity to form transient complexes with monocytes and induce their transition to the CD16+ subpopulation of interest. Platelet-monocyte complexes (PMCs) were found to be elevated in PLWH.

Platelets are the major source of circulating microparticles, which contain proteins, lipids, and RNA. Therefore, we hypothesize that platelet-monocyte complexes mediate efficient transfer of platelet-derived microparticles (PMPs), whose biomolecular contents induce monocyte maturation to the pro-inflammatory, CD16+ phenotype that is a major player in atherosclerosis and broader cardiovascular dysfunction. To investigate this, we will rely on human whole blood and plasma samples to isolate monocytes and platelet-derived microparticles, respectively, which were collected as part of a previously completed clinical study at the institution. Patients will be divided into subgroups based on HIV and AS status, with the latter determined by plaques revealed during carotid imaging data. Single-cell RNAseq and metabolic analysis will be performed on monocytes to construct a dynamic network model of gene expression that can identify differences in gene expression between patient groups. Concurrently, the miRNA and proteins enveloped within our isolated PMPs will be extracted and subject to small RNAseq and mass spectrometry analysis. miRNAs and proteins that differ between monocyte classes (platelet-complexed vs. non-complexed) or patient subgroups will be introduced into our network model to assess their ability to perturb monocytic signaling. Collectively, these sets of analyses will elucidate the impact of platelet-monocyte interactions on monocyte differentiation and function, and determine potential pathways that can be therapeutically targeted to prevent and treat AS.

As a preliminary experiment, platelet-derived microparticles were isolated from human plasma samples and incubated with both primary monocytes or U937 cells (a pro-monocytic cell line). Flow cytometry analysis demonstrated changes in cell surface marker expression between control and PMP-treated cells, however additional replicate experiments are needed to confirm these observations. 

 Feb 16, 2023 @ 12:00 p.m.

 Medical Center | K-307 (306408)

Mike O’Reilly, PhD - Professor, Department of Pediatrics - Neonatology

Zoom: https://rochester.zoom.us/j/97634917477?pwd=bjVvblg4RUoyY2o3MmFMTTVDQWE5QT09
Meeting ID: 976 3491 7477
Passcode: 664735

Breakfast Items & Coffee available at 8:30 am in KMRB 3-9623

 Feb 10, 2023 @ 9:00 a.m.

 Kornberg Medical Research Building | 3-9624

Ian Stone - Graduate Student, Advisor: Andrew Samuelson, PhD

Aging leads to the steady decline in a variety of factors associated with cellular health, resulting in the development of severe age-associated diseases. One such hallmark of aging is dysregulation of the proteome (loss of proteostasis), an important component of neurodegenerative conditions such as Alzheimer’s Disease (AD). SARS-CoV-2 infections have been associated with increased rates of death among AD patients, suggesting an important link between aging and viral infection. Many individual genes have now been identified that are able to singly affect lifespan by altering their activation levels. We hypothesized that genetic perturbations that extended longevity and preserved proteostasis would correlate with viral protection. To test this hypothesis, we approached it from the contrasting perspectives of mutations that extended longevity (increased lifespan) and the reverse, progeria (decreased lifespan). Caenorhabditis elegans (C. elegans) remains a powerful genetic model system for studying aging. Our laboratory uses two primary methods for assessing aging in C. elegans: longevity (knocking out a gene to increase lifespan) and progeria (knocking out a gene to reduce lifespan). We screened longevity mutants for viral resistance using a natural viral pathogen, Orsay virus (OV). We discovered that those with inactivated target of rapamycin (mTOR) complexes had a lower OV load and decreased activation of the intracellular pathogen response (IPR) pathway, suggesting that that these animals have enhanced viral resistance. Previous research from our laboratory identified a group of genes which, when inactivated, resulted in progeria in C. elegans. I tested this panel and found a subset that had reduced expression of the IPR during OV infection. These virally susceptible progeric (Visser) genes were tested for changes in viral pathogenicity using a reporter strain for intestinal shape; several genes were found to be important for viral protection as their inactivation resulted in intestinal bloating. Through dissecting both directions of aging and their relationship to viral immunity, our results have indicated that the longevity mutant mTOR has enhanced viral resistance, whereas some of the progeric mutants are more susceptible to viral infection. These findings suggest a potential inverse correlation for the role of genes in longevity and viral innate immunity. Through continuing our study of the temporal and tissue-specific requirements for mTOR pathway components, we will be able to identify necessary genes involved in connections between viral innate immunity and longevity mechanisms.

 Feb 09, 2023 @ 12:00 p.m.

 Medical Center | K-307 (3-6408)

Ke Du PhD - Assistant Professor of Chemical/Environmental Engineering, UC Riverside (Formerly RIT)

 Feb 08, 2023 @ 3:30 p.m.

 Kornberg Medical Research Building | 3.9624

Jordana Schmierer - Graduate Student, Advisor: Toru Takimoto, DVM, PhD

Pandemic Influenza A viruses (IAVs) have emerged due to genetic reassortment between human and avian or swine IAVs. Host adaptative mutations, particularly in the viral RNA-dependent RNA-polymerase (vRdRp), are required for productive infection and replication in mammals. Pandemic 2009 H1N1 (pH1N1) virus is a reassortant virus with two polymerase components, PA and PB2, originating from avian IAV, which typically does not function well in mammalian cells. Our previous research revealed that mutations in PA played a major role in mammalian host adaptation of pH1N1 and we have identified key mutations in both the N-terminal and C-terminal domains (CTD). However, the mechanisms of polymerase activation through these PA mutations are currently not known. The PA CTD is involved in interactions with viral nucleocapsid protein and host RNA polymerase II, and importantly, plays a key role in polymerase oligomer formation, essential for viral genome replication. We hypothesize that adaptive mutations in the PA CTD regulate viral genome replication kinetics. To test the effect of PA mutations in genome replication, we modified and optimized the Luciferase reporter gene assay to measure genome replication from a vRNA template to cRNA and vice versa. We characterized genome replication activity using polymerase complexes from pH1N1 virus isolated in 2009 with PA mutants containing key residues from either avian IAV (336L/356K) or from pH1N1 isolated in 2017 (321K/330V). We found that avian virus PA residues attenuated genome replication, while newly acquired mutations in the 2017 pH1N1 PA CTD led to increased genome replication. Furthermore, we rescued 2009 pH1N1 viruses with the PA CTD mutations and tested their effect on virus growth. As expected, the virus with avian PA residues attenuated genome replication and multi-step growth in cultured cells. Together, these data suggest that host adaptive mutations in PA CTD effect genome replication activity of the IAV polymerase. 

 Feb 02, 2023 @ 12:00 p.m.

 Medical Center | K-307 (3-6408)

Jacques Robert, PhD - Professor, Department of Microbiology & Immunology

 Jan 27, 2023 @ 9:00 a.m.

 Kornberg Medical Research Building | 3-9624

Adam Geber - Graduate Student, Advisor: David Topham, PhD

The immune system is classically divided into two categories: innate and adaptive, where the former responds rapidly and nonspecifically and the latter does so more slowly, precisely, and with greater speed and specificity over time. These conceptual distinctions are most appropriate for adult humans, who have a substantial repertoire of mature naïve lymphocytes that can establish immunological memory to protect against reinfection. Because the infant immune system continues to develop after birth and does not yet have an archive of memory cells, it must be capable of rapid and often nonspecific responses to signals of danger and damage. T cells are crucial to proper functioning of the adaptive immune system and are responsible for recruiting and coordinating immune cells, shaping future responses, and directly killing infected or cancerous cells. CD8+ T cells are canonically known for their cytolytic functions but can also produce cytokines under certain inflammatory conditions. During the last two decades an array of lymphoid immune cells have been described as having innate-type functions and/or a strongly restricted capacity for recognizing foreign antigens. More recently, we have found evidence for a subset of CD8+ T cells that arise in utero during the second trimester, persist variably into adulthood, and behave in an innate-like manner. This project aims to understand the stability of this cellular population, how it is activated, and how it might behave during in vivo infection. We plan to use flow cytometry to distinguish the phenotype of putative fetal innate-like CD8+ T cells (FITs) and single cell RNA-sequencing to compare their transcriptional repertoire to established profiles for conventional CD8+ T cells and other innate-type lymphoid cells. We also intend to use clinical samples collected at birth and in early childhood from a cohort with known respiratory infectious exposures to understand the ways that FITs might respond in vivo to coronaviruses (i.e. OC43, SARS-CoV-2). Our findings might help explain children’s lower COVID-19 disease severity and increased prevalence of post-infectious inflammatory conditions. Ultimately, FITs may serve as an immunomodulatory target for limiting immunopathology and enhancing vaccine efficacy in the vulnerable window of early life.

 Jan 26, 2023 @ 12:00 p.m.

 Medical Center | K-307 (3-6408)

Steve Gill, PhD - Professor, Center for Vaccine Biology & Immunology

 Jan 20, 2023 @ 9:00 a.m.

 Kornberg Medical Research Building | 3-9624

Ankit Dahal - Graduate Student, Advisor: Minsoo Kim, PhD

Pancreatic cancer is one of the deadliest malignancies with an average five-year survival of mere 2-9%. Emerging evidence suggests that the presence of polymorphonuclear (PMN) myeloid derived suppressor cells (MDSCs) with neutrophil-like phenotypes and morphologies play a major role in adverse clinical outcomes due in part to their contribution in establishing immunosuppressive tumor microenvironment (TME). Despite recent advances in our understanding of MDSC phenotypes and characteristics in the TME, the underlying molecular mechanisms by which classical neutrophils differentiate into MDSC within the TME remails largely unknown.

To investigate the microenvironmental cues that regulate PMN-MDSC differentiation at the tumor site, we established several in vitro co-culture systems using pancreatic cancer cells and 3D spheroid conditions. With live cell migration microscopy, we first showed that neutrophils actively swarmed into the pancreatic cancer spheroids and stayed active for an extended time period in the tumor. We further found that cancer cell culture supernatant significantly extended neutrophil survival and successfully differentiated neutrophils into MDSCs that exhibited decreased type 1 Interferon levels, increased arginase and ROS expression, and had the ability to suppress CD8 cytotoxicity. Additionally, when compared to other forms of neutrophil activators such as LPS and TNF, only tumor conditioned media enhanced neutrophil survival and MDSC differentiation. Our data suggest the presence of novel molecular processes that support MDSC differentiation at the tumor site. To identify the molecular regulators of MDSC formation, we have developed a CRISPR-Cas9 pooled library screen using the immortalized granulocyte-monocyte progenitor cell line, HoxB8. This study will further our understanding of MDSC differentiation and may help to develop therapeutics to limit MDSC development in the TME of pancreatic and other solid cancers.

 Jan 19, 2023 @ 12:00 p.m.

 Medical Center | K-307 (3-6408)

Minsoo Kim, PhD - Professor, Center for Vaccine Biology & Immunology

 Jan 13, 2023 @ 9:00 a.m.

 Kornberg Medical Research Building | 3-9624

Andy Phan - Graduate Student, Advisor: Yiping Zhu, PhD

Human immunodeficiency virus 1 (HIV-1) is a pathogen responsible for an ongoing global epidemic, for which there is no curative therapy or protective vaccine. Although there exists antiretroviral therapy (ART) which is effective in suppressing further HIV-1 replication, the virus cannot be eliminated from the patient, and cessation of ART would lead to rebound of viral replication. The major obstacle towards an HIV-1 cure is the persistence of replication-competent viral DNA. In infected cells, latent HIV-1 DNA is transcriptionally silenced and not susceptible to the host immune system or antiretroviral drugs. Latency is commonly associated with the deposition of repressive epigenetic modifications and removal of active epigenetic modifications, which occurs through interactions with cellular proteins, but the exact mechanisms for silencing of viral DNA are not well understood.

By employing a CRISPR-Cas9 knockout screen, we assessed host factors to determine their potential in the silencing of viral gene expression, and identified the cohesin complex subunits SMC1A, SMC3, and RAD21 as cellular proteins responsible for silencing of HIV-1 DNA. We show that depletion of these host factors leads to a significant increase in viral DNA expression. We also assess the ability of Vpr, an HIV-1 accessory protein linked to enhancing viral gene expression, to counteract host-mediated silencing. Our current experiments explore the mechanisms by which the cohesin complex may promote condensation of viral chromatin and therefore contribute to decreased viral gene expression, and the ability of HIV-1 to antagonize this silencing. Expansion in this area of HIV-1 research will contribute to the progress of novel therapies to fully eliminate latent DNA in infected cells.

 Jan 12, 2023 @ 12:00 p.m.

 Medical Center | K-307 (3-6408)

Michael M. Lutz - PhD Candidate, Advisor: Toru Takimoto, DVM,PhD

 Jan 11, 2023 @ 10:00 a.m.

Yuexuan Chen - Graduate Student, Advisor: Ruth Serra-Moreno, PhD

Three years into the COVID-19 pandemic and SARS-CoV-2 remains a biological threat due to the emergence of variants with increased transmissibility, more severe disease and/or better escape from neutralizing antibodies – which might render previous COVID-19 vaccines inefficient. Therefore, there is a need to develop antivirals to treat COVID-19. To reach this goal, a better understanding of the cellular factors essential for SARS-CoV-2 propagation can help identify targets for therapeutic intervention.

Here, we investigated the mechanism by which SARS-CoV-2 generates replication organelles (ROs). ROs are intracellular, membranous structures generated during the replication of all positive-sense RNA viruses. They provide a platform that allows the assembly of the virus polymerase for the successful replication and transcription of the viral genome, and as such, ROs are critical for virus replication. Previous studies reported that coronaviruses use the autophagy machinery to build their ROs, but recent findings have questioned this notion. Our work confirms that autophagy is dispensable to build ROs. Specifically, SARS-CoV-2 uses the non-structural protein NSP6 to recruit early endosomes for RO biogenesis in a clathrin- and COP-I-dependent manner, and that the virus also needs lipid droplets and mitochondria to meet its lipid demands for this massive membrane rewiring.

 Jan 05, 2023 @ 12:00 p.m.

 Medical Center | K-307 (3-6408)