Center Events

 Jun 27, 2025 @ 12:00 p.m.

Justin Brennan - Graduate Student

Defective viral genomes (DVGs) are truncated derivatives of their parental viral genomes that are incapable of productive infection in the absence of a co-infecting standard “helper” virus. Ubiquitous among RNA viruses, DVGs interfere with the genomic replication and packaging of standard viral genomes by competing for critical viral proteins and are well-documented triggers of the innate immune response. SARS-CoV-2 infection generates deletion-type DVGs that arise from non-homologous recombination events during viral genomic replication. Our group previously identified conserved “hotspots” (termed A, B and C) clustering with SARS-CoV-2 deletion DVG recombination sites in lung autopsy samples from COVID-19 patients and in vitro infections. Among the three “hotspots”, the DVG population arising from “hotspot” A (DVG-A) retains only the 5’ and 3’ UTRs and a fragment of the NSP1 gene, whereas the DVG population arising from “hotspot” B (DVG-B) bears a deletion ablating: ORF7a, ORF7b, ORF8, N, and ORF9b. To characterize the functions of DVG-A and DVG-B during infection, we generated virus-like particles specifically packaging either DVG-A or DVG-B genomes. We observed that DVG-B strongly induced types I and III interferon and ISG expression, relative to SARS-CoV-2 (Hong Kong strain) infection, in A549-ACE2 cells. DVG-B co-infection with SARS-CoV-2 attenuated viral gene expression and synergistically enhanced the expression of primary interferon, ISGs, and IL-6 compared to infections with DVG-B or SARS-CoV-2 alone. In contrast, DVG-A did not induce an antiviral response but attenuated viral gene expression, likely by competing for essential viral proteins. Because double-stranded RNA (dsRNA) is reportedly the primary trigger of interferon responses during coronavirus infection, we compared dsRNA levels and localization during DVG-B and SARS-CoV-2 infections. Despite its greater interferon induction, by immunofluorescence DVG-B infected cells exhibited lower dsRNA levels at 24 hours post-infection (hpi) compared to SARS-CoV-2. Interestingly, DVG-B derived dsRNA localized to discrete puncta throughout the cell, while SARS-CoV-2 dsRNA signal showed diffuse, juxtanuclear localization. Moreover, DVG-B infection induced significantly greater IRF-3 nuclear translocation than SARS-CoV-2, suggesting the activation of a RIG-I-like receptor (RLR). The addition of the RNA polymerase inhibitor remdesivir to DVG-B infection abolished viral genomic replication, dsRNA formation, and consequently IRF-3 nuclear translocation. To investigate whether the nucleoprotein impacts dsRNA levels and localization during DVG-B infection, veroE6 and veroE6 cells constitutively expressing the SARS-CoV-2 nucleoprotein (veroE6-N) were infected with DVG-B or SARS-CoV-2. In DVG-B infected veroE6-N cells, immunofluorescence revealed a partial restoration of the diffuse, juxtanuclear dsRNA signal phenotype typical of SARS-CoV-2. Overall, these findings suggest that the unique localization of DVG-B derived dsRNA and the absence of the nucleoprotein contribute to the activation of RLRs and the resulting interferon response. Ongoing experiments seek to identify the cellular sensor(s) responsible for DVG-B detection and to further elucidate the roles of the absent viral proteins (N, ORF9b) in mediating the DVG-B induced interferon response.

 May 08, 2025 @ 12:00 p.m.

 Medical Center | K307 (3-6408)

Host: Advisor: Yan Sun, Ph.D.

Sebastian Bosch - Graduate Student

Despite the transformation of HIV-1 infection into a chronic but manageable condition through combination anti-retroviral therapy (cART), HIV-associated neurocognitive disorders (HANDs) continue to affect as many as 45% of persons living with HIV. HANDs are defined as a spectrum of neurological impairments in people living with HIV, encompassing cognitive, motor and/or mood disorders. Microglia, the central nervous system (CNS) resident macrophages are the main cell type that HIV productively infects within the CNS, and in pathologic settings such as HANDs, can contribute to neuroinflammation and tissue damage. In contrast, astrocytes, a glial cell subtype that regulates blood brain barrier integrity, and supports synaptic maturation and plasticity, remain controversial in the literature, with conflicting reports on whether they may be productively infected by HIV-1. Yet, regardless of its mode of entry or subsequent life cycle, HIV-1 infection of the CNS contributes to astrocytic reactivity, leading to synaptic dysfunction through impaired glutamate clearance and reduced trophic support, disrupting neuronal communication and plasticity. At this time, no in vivo models that might allow real-time assessment of the role of human microglia and astrocytes in disease propagation, and neural function in the context of HIV-1 have been developed. To investigate how HIV-1 infection drives glial reactivity and neuroimmune dysfunction in the CNS, have begun to develop both in vitro and in vivo models for HIV-1 infection of human astrocytes and microglia.  As a first step, we have induced the differentiation of cultured WA09 human embryonic stem cells (hESCs) towards human glial progenitor cells (GPCs), which are subsequently differentiated to mature human astrocytes as evidenced by glial fibrillary acidic protein (GFAP+) staining. With use of the same hESC line, we have differentiated WA09s towards CD43⁺/CD235a⁺ human pluripotent stem cells (HPSCs).  We have then either: (A) engrafted the HPSCs into Rag2/IL2rg x human mCSF knock-in mice for development of a humanized microglial mouse model or (B) further differentiated the HPSCs in vitro, towards CD45/CD11b/CX3CR1/CSF1R⁺ human microglia. Differentiated hESC-derived human microglia are highly susceptible to infection by HIV-1 CCR5-tropic strain ADA. Furthermore, we show preliminary evidence of in vivo microglial infection in humanized mice, through colocalization of P2RY12+/human nuclei (hN+)/ and HIV-1 capsid protein (p24+). Ultimately, our goal is to leverage our in vitro and in vivo experimental models for HIV infection of human microglia and subsequent astrocytic reactivity, to characterize HIV-induced transcriptomic changes by fixed, single-cell RNA sequencing approaches considering the aforementioned cell types, as well as murine, corticostriatal medium spiny neurons (MSNs). Moreover, we wish to directly interrogate MSN synaptic pathology during HANDs in vivo, through mapping host neuronal dendritic networks via rabies viral tracing.

 May 01, 2025 @ 12:00 p.m.

 Medical Center | K307 (3-6408)

Host: Advisor: Stephen Dewhurst, Ph.D.

Chantelle Lehone White - Graduate Student

 Apr 28, 2025 @ 2:00 p.m.

 Medical Center | Ryan Case Method (1-9576)

Host: Advisor: Andrea Sant, PhD

Mojgan Naghavi, PhD - Professor, Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University

Our work has uncovered fundamental aspects of how HIV-1 regulates early infection by exploiting specialized microtubule (MT) plus-end tracking proteins (+TIPs). This includes recently discovering that HIV-1 capsids mimic a central MT regulator to bind several specialized +TIPs. Viral cores bind +TIPs in a manner distinct from other host cofactors, and this interaction relates to capsid pentamer organization and/or capsid curvature that provides insights into poorly understood aspects of core disassembly or uncoating. I will talk about how HIV-1 exploits +TIPs to alter MT behavior and regulate early infection.

 Apr 28, 2025 @ 12:00 p.m.

 Medical Center | Upper Aud. (3-7619)

Host: Yiping Zhu, Ph.D.

Ian Stone - Graduate Student

LECT-2/LECT2 is a secreted protein associated with antimicrobial immunity, inflammatory diseases, amyloidosis and neurite branching. It is conserved through evolution from nematodes to humans, but its function within the nervous system is still not completely understood. LECT-2 works as a cell non-autonomous regulator of dendrite branching of the PVD mechanosensory neurons in Caenorhabditis elegans (C. elegans). It accomplishes this through its interaction with the menorin complex, including the cell surface receptors SAX-7, MNR-1 and DMA-1. Surprisingly, I observed that LECT-2 is constitutively expressed throughout the lifespan of the animal and its expression was not restricted to areas important for PVD dendrite branching. These observations suggest that LECT-2 has other functions in the C. elegans nervous system aside from dendrite branching. This is congruent with my preliminary data, suggesting that LECT-2 is necessary for improved survivability for both genetic and environmental stressors. I have pursued a forward genetic approach using an endogenous, fluorescently tagged reporter of LECT-2 to identify mutants that affect its roles in the nervous system. In a small pilot screen, I have successfully identified 3 mutants with abnormal LECT-2 localization and will continue to screen and characterize mutants moving forward.

I have also interrogated the different roles of the menorin complex in dendrite maintenance, which has not been characterized. Interestingly, PVD dendrites are not static postdevelopment and continue growing through adulthood, including forming new branches. Using a combination of genetic mutants and feeding-based RNAi, I have determined that mnr-1 and sax-7 have unique, separable roles for dendrite maintenance. Importantly, this finding suggests that menorin complex members have distinct temporal and spatial roles for the regulation of dendrite branching. Additionally, knockdown of mnr-1 and sax-7 in adult animals reduced age-associated abnormal branching, suggesting that we can reverse neuronal aging and promote healthy neuronal functions in aging animals. The combination of both these studies will be important to better understand the role of cell non-autonomous cues on neuronal development and maintenance.

 Apr 24, 2025 @ 12:00 p.m.

 Medical Center | K307 (3-6408)

Host: Advisor: Carlos Diaz-Balzac, M.D., Ph.D.

Yolanda Huang, Ph.D. - Assistant Professor, Department of Microbiology and Immunology, University at Buffalo

The gut microbiota is important for human health, yet it remains difficult to predict how microbes colonize, grow, and survive in the gut environment. The Huang lab leverages functional genomics and DNA barcoding to connect genes to phenotypes in a high-throughput manner among an abundant group of gut bacteria, Bacteroidales. We demonstrated how an overexpression genomics platform using the prominent gut anaerobe, Bacteroides thetaiotaomicron, can advance our functional understanding of Bacteroidales. This talk will focus on current efforts in the lab to characterize pathways involved in tolerance to commonly encountered stressors in the gut and the extension of functional genomics to study interactions between anaerobes and their phages.

 Apr 14, 2025 @ 12:00 p.m.

 Medical Center | Upper Auditorium (3-7619)

Host: Steven Gill, Ph.D.

Gang Fan, Ph.D. - Assistant Professor, Department of Chemical Engineering, University of Rochester

For the green synthesis of polymers with defined sequences, we can take inspiration from cells, which have synthesized sequence-controlled polymers in the form of proteins, polysaccharides and nucleic acids for millions of years. Despite the promise of biosynthesis of polymers and significant progress in metabolic engineering, the reaction space available for cell-catalyzed transformations is still relatively limited compared to conventional synthetic chemistry. By integrating the advantages of bioengineering with chemical engineering, we have developed novel technologies for sustainable chemistry. In the first part of the talk, I will discuss the inherent activity of an electroactive microbe (Shewanella oneidensis) to control living radical polymerization. In the second part of my talk, I will introduce a cell-plastic embedment strategy that utilizes lipase-expressing Escherichia coli and polyester to enhance the biodegradability of common hydrolyzable plastics. Together, my work has demonstrated the immense power of biomolecules as Nature’s synthetic organic chemist.

 Mar 31, 2025 @ 12:00 p.m.

 Medical Center | Upper Auditorium (3-7619)

Host: Jacques Robert, Ph.D.

Kenny Jacoby - Graduate Student

Staphylococcus aureus is both commensal and pathogenic to humans. Over the last century, its evolution has led to increasing prevalence due to rising antibiotic resistance, which can cause infections ranging from asymptomatic colonization to life-threatening conditions, potentially causing sepsis, toxic shock, and endocarditis. Bacteriophages are viruses that only infect and replicate in bacteria. They coevolve with their hosts in a Coevolutionary Arms Race, where both agents develop new strategies to gain an advantage over the other. This evolutionary competition drives increasing specificity in phage-host interactions, yet the underlying host defense and anti-defense mechanisms in S. aureus remain poorly understood. Furthermore, the growing resistance to multiple antibiotics associated with these infections has necessitated a return to researching effective phage therapies. We studied the specificity between phages and bacterial hosts of S. aureus in terms of their variations in bacterial killing and susceptibility, respectively. This was done using a diverse collection of S. aureus clinical isolates from Duke University, generously provided to us by the Gill lab. Each bacterial strain was poly-lysogenic, so they were initially treated with Mitomycin-C to induce the production of lytic phage in the supernatant before being used for our host range experiments. After elucidating these patterns of phage-host specificity in S. aureus, we investigated the mechanisms underlying these inductions’ specificity. We attempted to isolate, propagate, and characterize individual phage populations responsible for the observed host range. To do this, an experiment was performed to assess the bacterial killing caused by the original wide-range inductions compared to the isolated phages. Our results have successfully elucidated the specificity of phage-host relationships in S. aureus at a massive scale, revealing the varying susceptibilities of 378 different strains to 378 phage-containing inductions. Moreover, our comparison of bacterial killing across 21 representative strains between the broad-specificity inductions and isolated phage populations produced unexpected results, suggesting an abortive infection (Abi) host defense mechanism could be at play that triggers widespread bacterial death upon phage infection. Future study will aim to characterize the mechanism of bacterial cell death caused by broad-specificity phage infection in S. aureus, potentially revealing a previously unrecognized aspect of phage specificity in the species. These findings may provide new insights into phage specificity in S. aureus and inform the development of more effective monophage therapies.

 Mar 27, 2025 @ 12:30 p.m.

 Medical Center | K307 (3-6408)

Host: Advisor: Andrew Varble, M.D.

Hannah Teets - Graduate Student

Commonly known as “forever chemicals,” per- and polyfluoroalkyl substances (PFAS) are a diverse class of synthetic organofluorine compounds that have been used in a variety of industrial applications and consumer products since the 1950s. Due to their unique chemical composition, PFAS are highly resistant to degradation, enabling them to persist in the environment and bioaccumulate, resulting in widespread human exposure. PFAS commonly co-occur as mixtures in both humans and the environment. Several studies have indicated that exposure to PFAS influences the immune system, yet the impact of exposure to PFAS mixtures on allergic airway immune responses remains unclear. In this study, a quaternary mixture of perfluorooctane sulfonate (PFOS), perfluorooctanoic acid (PFOA), perfluorohexane sulfonate (PFHxS), and perfluorononanoic acid (PFNA) was administered to dams via drinking water. Mature male and female offspring of dams given PFAS or control water were sensitized and challenged with house dust mite (HDM) extract; an established model of allergic airway inflammation. Immune response was examined using flow cytometry. In response to HDM, male offspring exposed to PFAS had fewer Th17 and Th1 cells, whereas female offspring had fewer eosinophils, monocytes, and macrophages compared to HDM-challenged offspring of control dams. These findings highlight the potential for early-life PFAS exposure to differentially alter allergic airway immune responses, particularly in a sex-dependent manner.

 Mar 27, 2025 @ 12:00 p.m.

 Medical Center | K307 (3-6408)

Host: Advisor: Paige Lawrence, M.D.

Julie Tobin - Graduate Student

The Poxviridae contain several medically relevant viruses including variola virus, the causative agent of smallpox, and monkeypox virus (MPXV), which is endemic in multiple African countries and currently circulating worldwide. The AT-rich (67%) dsDNA genome of Orthopoxviruses replicates entirely in the cytoplasm and encode many proteins that subvert both the adaptive and innate immune response. The ~200 kb linear genome is structured with conserved genes in the center and variable, host-adaptation genes at the periphery. While large DNA viruses like poxviruses are believed to have low mutation rates, they employ diverse mechanisms to rapidly adapt to host defenses and facilitate viral spillover events. Although RNA viruses achieve similar adaptability through high mutation rates, poxvirus mutation rates have not been thoroughly investigated. To determine the mutation rate for the prototypical poxvirus, vaccinia virus (VACV), we adapted a fluctuation test that scores reversion to fluorescence in mutant green fluorescent proteins (GFPnull) across 12 nucleotide mutational classes.  Recombinant VACV containing individual GFPnull mutations (vGFPnull) were created using an insertion vector targeting the intergenic site between peripheral genes B19R and WR201.  Fluctuation tests using vGFPnull will measure mutation rates of nucleotide substitutions— specifically C to A, G to A, and C to T—to explore mechanisms contributing to VACV’s high AT content. Additionally, these recombinant viruses will be used to investigate potential activity of APOBEC3G, a host restriction factor known to induce hypermutations in human  immunodeficiency virus (HIV-1), in VACV as it has been suggested to be a driver of rapid  evolution in MPXV. Ultimately, our studies will have critical implications for further vaccine development and antiviral strategies, and may clarify host-virus interactions that drive genetic variation during spillover events in emerging Orthopoxvirus species such as borealpox and zoonotic infections like MPXV.

 Mar 20, 2025 @ 12:30 p.m.

 Medical Center | K307 (3-6408)

Host: Advisor: Brian Ward, M.D.

Christine Li - Graduate Student

Vaccinia virus (VACV) is the prototypical poxvirus that is used as a model system to understand highly pathogenic orthopoxviruses such as variola virus, the causative agent of smallpox, and monkeypox, the causative agent of Mpox. Poxviruses have co-involved with mammalian hosts and shaped public health, particularly through its role as the live vaccine that was used to eradicate smallpox. The VACV genome (>200kb) has a large portion of early genes dedicated to immune evasion, highlighting how countering host defenses are critical for viral replication and pathogenesis. Despite this, cells are still able to detect VACV replication. RIG-I is a cytosolic pattern recognition receptor that senses viral dsRNA in the cytoplasm. Stimulation of HeLa cells by a synthetic dsRNA analog reduced VACV protein expression, suggesting a relationship between RIG-I activation and VACV infection. To interrogate this relationship, a RIG-I knock-out cell line was generated (ΔRIG-I). It was revealed that viral gene expression is significantly increased in ΔRIG-I cells compared to wild-type HeLa cells. Further, the deletion of RIG-I led to increased cell-to-cell spread and virus production. Future work will focus on determining how orthopoxviruses trigger the RIG-I pathway, and explore the downstream antiviral response on poxvirus replication.

 Mar 20, 2025 @ 12:00 p.m.

 Medical Center | K307 (3-6408)

Host: Advisor: Brian Ward, M.D.

James Jancovich, Ph.D. - Chair, Department of Biological Sciences, California State University San Marcos

Ranaviruses are an emerging infectious disease of economically and ecollogically important cold-blooded vertebrates world-wide. However, our understanding of how they infect, replicate and cause disease in such a wide varitey of ectothermic organisms is still not completely understood. Ranaviruses express approximately 100 proteins but the function of over half of these virally-encoded genes has yet to be determined. Therefore, we have developed a pipleline of experiements to better understand their role in viral replication and pathogenesis. During the course of these experiments we identified genomic elements and viral particle structural components that can be deleted allowing insertion of foreign protein-encoding DNA whilst attenuating the virus. By incorporating mammalian transcription and translation enhancement elements we have increased recombinant protein expression in mammalian cells in the absence of productive viral replication. Our in vitro and in vivo data suggest this attenuated amphibian virus may be a viable viral vector for therapeutic application.

 Mar 17, 2025 @ 12:00 p.m.

 Medical Center | Upper Auditorium (3-7619)

Host: Brian Ward, Ph.D., Co-Sponsored by the Pathogenesis Training Grant

Nicholas Miller - Graduate Student

Mycobacterium abscessus (Mab) is an emerging human pathogen that has a high rate of incidence in immunocompromised individuals. We have identified putative secondary metabolite pathway encoded in a gene cluster spanning MAB_0284c to 0305 within Mab which may be a key factor in its pathogenesis. This novel pathway is related to Streptomyces pathways producing the secondary metabolites streptonigrin and calcimycin. We constructed an in-frame deletion of the MAB_0295 (phzC) gene and tested its pathogenicity in our Xenopus laevis animal model. We have previously shown that X. laevis tadpoles, which have functional lungs and T cells, can serve as a reliable comparative model for persistent Mab infection and pathogenesis. Our study indicates that tadpoles intraperitoneally infected with the ∆phzC mutant exhibit decreased bacterial loads and have an increased chance of survival over 50 days. We also noted reduced transcript levels of several pro-inflammatory cytokines (IL-1β, TNF-α, iNOS, IFN-γ) in the liver and lungs of tadpoles infected with ∆phzC mutant Mab as compared with WT Mab. In addition, there was impaired macrophage recruitment and decreased macrophage infection in tadpoles infected with ∆phzC mutant by tail wound inoculation compared to WT bacteria as assayed by intravital confocal microscopy. These data underline the relevance and usefulness of X. laevis tadpoles as a novel comparative animal model to identify genetic determinants of Mab immune-pathogenesis and suggests a role for this novel and uncharacterized pathway in Mab pathogenesis and macrophage recruitment.

 Mar 06, 2025 @ 12:30 p.m.

 Medical Center | K307 (3-6408)

Host: Advisor: Jacques Robert, Ph.D.

Zhinian Zhou - Graduate Student

Vaccinia virus (VACV) is a large, enveloped, double-stranded DNA virus belonging to the Poxviridae family, the genus Orthopoxvirus. Vaccines derived from certain vaccinia viral strains provide protection against infections such as monkeypox, smallpox, and borealpox. Moreover, vaccinia is also used as a model to study these pathogens. Additional clinical applications of vaccinia include being used as a vaccine platform against other medically relevant viruses, such as HIV, and as a promising oncolytic virus in cancer immunotherapies. VACV replication cycle generates two infectious forms, a single-enveloped intracellular mature virus (IMV) that serves as a precursor for the formation of extracellular virus (EV), which is wrapped with an additional envelope derived from the trans-Golgi network (TGN). During infection, IMVs remain in the cell, and EVs are released, which is required for viral spread. F13 is a viral protein associated with the EV envelope and plays a critical role in EV production. How F13 functions in the formation of EVs is unclear. To determine F13’s role in EV envelopment, we utilized Bio-ID to identify proteins that potentially interact with F13 through proximity-dependent biotinylation. After infecting Hela cells with a recombinant virus expressing an F13-BirA fusion protein, biotinylated proteins were affinity captured and identified by mass spectrometry analysis. This analysis identified 125 cellular and viral proteins that were significantly abundant when compared with control infections, which were recognized as potential interacting partners of F13. Gene ontology revealed that several are involved in tethering and fusion of transport vesicles from the early endosome to the TGN. Consistent with these findings, previous research has suggested that F13 traffics from early endosomes to the TGN, where intracellular envelopment occurs. Additionally, an uncharacterized viral protein VACWR161, an EV-membrane protein E2, and its poorly characterized putative paralog O1 were also identified by our screen. Together, Bio-ID coupled with mass spectrometry identified cellular and viral proteins potentially interacting with F13 that may be essential to its role in EV production. Currently, we are verifying interactions between the identified proteins and F13 to determine their role in EV envelopment. 

 Mar 06, 2025 @ 12:00 p.m.

 Medical Center | K307 (3-6408)

Host: Advisor: Brian Ward, M.D.

Zhinian Zhou - Graduate Student

Vaccinia virus (VACV) is a large, enveloped, double-stranded DNA virus belonging to the Poxviridae family, the genus Orthopoxvirus. Vaccines derived from certain vaccinia viral strains provide protection against infections such as monkeypox, smallpox, and borealpox. Moreover, vaccinia is also used as a model to study these pathogens. Additional clinical applications of vaccinia include being used as a vaccine platform against other medically relevant viruses, such as HIV, and as a promising oncolytic virus in cancer immunotherapies. VACV replication cycle generates two infectious forms, a single-enveloped intracellular mature virus (IMV) that serves as a precursor for the formation of extracellular virus (EV), which is wrapped with an additional envelope derived from the trans-Golgi network (TGN). During infection, IMVs remain in the cell, and EVs are released, which is required for viral spread. F13 is a viral protein associated with the EV envelope and plays a critical role in EV production. How F13 functions in the formation of EVs is unclear. To determine F13’s role in EV envelopment, we utilized Bio-ID to identify proteins that potentially interact with F13 through proximity-dependent biotinylation. After infecting Hela cells with a recombinant virus expressing an F13-BirA fusion protein, biotinylated proteins were affinity captured and identified by mass spectrometry analysis. This analysis identified 125 cellular and viral proteins that were significantly abundant when compared with control infections, which were recognized as potential interacting partners of F13. Gene ontology revealed that several are involved in tethering and fusion of transport vesicles from the early endosome to the TGN. Consistent with these findings, previous research has suggested that F13 traffics from early endosomes to the TGN, where intracellular envelopment occurs. Additionally, an uncharacterized viral protein VACWR161, an EV-membrane protein E2, and its poorly characterized putative paralog O1 were also identified by our screen. Together, Bio-ID coupled with mass spectrometry identified cellular and viral proteins potentially interacting with F13 that may be essential to its role in EV production. Currently, we are verifying interactions between the identified proteins and F13 to determine their role in EV envelopment. 

 Mar 06, 2025 @ 12:00 p.m.

 Medical Center | K307 (3-6408)

Host: Advisor: Brian Ward, M.D.

Zirui Zhao - Graduate Student

The rise of antibiotic resistance is a critical global health challenge, underscoring the urgent need for novel strategies to re-sensitize resistant bacteria to treatment. Current antibiotic research approaches primarily rely on growth inhibition as the key metric for drug discovery and resistance assessment. However, emerging evidence suggests that bacterial metabolism, independent of growth, both influences and is influenced by antimicrobial resistance (AMR), revealing a potential new therapeutic avenue. However, despite its significance and potential clinical utility, the relationship between antibiotic resistance and metabolism remains poorly understood. To explore how metabolic adaptations contribute to AMR, we examined the metabolic dependencies of various antibiotics across multiple Staphylococcus aureus strains, including methicillin-resistant (MRSA) and methicillin-susceptible (MSSA) isolates. Our susceptibility profiling identified three distinct patterns of interaction between antibiotics and metabolic environments: (1) some antibiotics exhibited minimal metabolic dependency, (2) certain metabolites had little impact on antibiotic efficacy, and (3) most notably, specific drugs were strongly influenced by metabolites, while some metabolites had unique effects on different antibiotics. Importantly, the greatest variation in metabolic-antibiotic interaction profiles was observed in antibiotics to which MRSA strains were resistant, highlighting a clear link between resistance and metabolic effects. These findings emphasize the need to integrate metabolic factors into AMR assessment, which could enhance resistance prediction and inform more effective therapeutic strategies.

 Feb 27, 2025 @ 12:30 p.m.

 Medical Center | K307 (3-6408)

Host: Advisor: Allison Lopatkin, Ph.D.

Adam Tyrlik - Graduate Student

The BM microenvironment (BMME) serves as the milieu that maintains normal hematopoiesis via cell-cell interactions and secretory factors. A key component of the BMME are bone marrow stromal cells (BMSCs). BMSCs are a heterogeneous population of non-hematopoietic cells residing in several different niches of the bone marrow capable of multilineage differentiation, hematopoietic support, immunomodulation as well as efferocytosis. While efferocytosis is a homeostatic process, excessive efferocytosis by BMSCs can lead to significant metabolic stress, senescence and cell death. BMSC dysfunction has been reported to contribute to the development of hematological malignancies, including myelodysplastic syndrome (MDS) and leukemia. We were able to utilize single cell RNA-seq of Lin- CD271+ cells to capture a transcriptionally diverse pool of BMSCs from patients with MDS and healthy controls and identify a large population with high potential for hematopoietic support defined by expression of CXCL12, VCAM-1 and CSF1. We have observed a loss of heterogenicity in this supportive population complemented by broad transcriptional changes related to immunomodulatory and proliferative capacity in the context of MDS. Notably, these changes were conserved despite significant mutational heterogeneity across the patient population. We were also able to transcriptionally characterize efferocytic BMSCs by preforming a single cell RNA-seq analysis of a murine model. We identified a subset of efferocytic cells based on presence of Neutrophil and B cell specific transcripts and using this population were able to isolate efferocytic BMSC specific transcriptional profile which demonstrated loss of supportive ability in the efferocytic BMSC population as well as an activation of the pro-inflammatory cGAS-STING pathway.

 Feb 27, 2025 @ 12:00 p.m.

 Medical Center | K307 (3-6408)

Host: Advisor: Laura Calvi, M.D.

Raegan Myers - Graduate Student

Lymphangioleiomyomatosis (LAM) is a rare multisystemic disease almost exclusively found in genetic females. Patients develop thin walled cystic tumors that compromise airspace, causing breathing complications. These cysts appear to be caused by the abnormal proliferation of cells with a smooth muscle phenotype in the lungs. These tumor cells are estrogen sensitive and possess deleterious mutations in at least one of two in tuberous sclerosis (TSC1/2) complex genes, which leads to constituitive mTORC signaling, dysregulated protein synthesis, and cell proliferation. LAM tumor cells appear to be metastatic, as they can be found in the blood and lymph of LAM patients and have been shown to repopulate the lungs of LAM patients who have needed lung transplantation. Our laboratory hypothesized that the origin of LAM cells is the myometrium of the uterus, leading to the generation of a uterine specific TSC2 null mouse model. Here we describe a novel TSC2-null mouse myometrial cell line that was cultivated from these uterine-specific TSC2 null mice. These cells share nearly all characteristics of human LAM cells, including the expression of the melanocytic marker glycoprotein nonmetastatic melanoma protein B (GPNMB). Single cell RNA sequencing data on human lung samples confirm GPNMB upregulation in LAM core cells and macrophages. Notably, the extracellular domain of GPNMB can be released from the cell surface. While the role of GPNMB cleavage on LAM progression is not yet clear, we discovered that GPNMB levels are high in LAM patient serum, and are reduced with mTOR-inhibition therapy, demonstrating clinical potential of GPNMB as a biomarker for treatment response in LAM. Clinical observations of high cellular expression GPNMB levels across other malignancies such as melanoma and triple negative breast cancer are associated with poor prognosis, suggesting that GPNMB may be a driver of tumor progression. In support of this hypothesis, we find that, in rat TSC2 null cells, GPNMB down-regulation slows xenograft growth, implying the necessity to explore GPNMB expression and cleavage in TSC2 null models.  We will explore if GPNMB modulates cell proliferation, migration, and invasion in our novel TSC2 null mouse myometrial cell line.  Lastly will also explore the role of GPNMB cleavage in these functions, on LAM progression and its role in lung metastasis.

 Feb 20, 2025 @ 12:30 p.m.

 Medical Center | K307 (3-6408)

Host: Advisor: Stephen R. Hammes, M.D., Ph.D.

Zoe Matacchiera - Graduate Student

Influenza A virus (IAV) is a major cause of respiratory infections in both humans and animals worldwide. The host immune system relies on both innate and adaptive responses to combat the virus. A crucial component of the innate immune response is the ability of tissue-resident macrophages (TRMs) to sense pathogens and infection-induced tissue damage. TRMs are found in nearly all tissues and are defined by their embryonic origin and self-renewal capacity, making them independent of bone marrow progenitors.

In the lungs, two distinct populations of TRMs—alveolar and interstitial macrophages—are classified based on their location, function, and cell surface markers. However, the dynamics of these cells during IAV infection remain poorly understood. Our lab has recently demonstrated that intracellular pathogens capable of inducing IFN-γ drive the depletion of TRMs, leading to their replacement by monocyte-derived macrophages, which are generally better equipped to combat microbial and viral infections. Using multi-parameter flow cytometric analysis, we are investigating this phenomenon in alveolar and interstitial lung macrophages and assessing their role in immune defense against IAV. Our findings indicate that influenza infection leads to a significant infiltration of monocyte-derived alveolar and interstitial-like macrophages, while alveolar macrophages appear to be less impacted by IFN-γ responses triggered by IAV. Additionally, we have observed a shift in the phenotype of TRM populations during infection.

The primary aims of this project are to define the molecular mechanisms underlying these phenotypic shifts in lung macrophages and to elucidate their role in regulating adaptive immune responses, particularly CD4+ and CD8+ T cell-mediated immunity against influenza infection.

 Feb 20, 2025 @ 12:00 p.m.

 Medical Center | K307 (3-6408)

Host: Advisor: Felix Yarovinsky, M.D.

Ryan Hunter, Ph.D. - Associate Professor, Department of Microbiology and Immunology
University of Buffalo, Jacobs School of Medicine & Biomedical Sciences

Bacterial infections associated with chronic airway disease (cystic fibrosis, COPD, sinusitis) are composed of complex polymicrobial communities that incite persistent inflammation and airway damage.  Despite the surge in studies characterizing the composition of airway microbiota, a lack of effective therapeutics remains due to our limited understanding of how bacterial species interact with one another in vivo, how they adapt to the airway microenvironment, and their co-evolution over time. For example, nutrient sources that sustain bacterial growth in vivo are poorly understood. We have examined the role of airway mucus in shaping the ecophysiology of the cystic fibrosis lung microbiota. Despite mucins (the major macromolecular constituent of mucus) representing an abundant pool of bioavailable carbon, surprisingly, we have discovered that canonical airway pathogens (e.g. Pseudomonas aeruginosa and Staphylococcus aureus) inefficiently use mucins on their own. However, anaerobic “commensal” bacteria, more commonly associated with the oral cavity but found in abundance in airway mucus, can cross-feed and stimulate the growth and virulence of airway pathogens by degrading mucins and liberating nutritional byproducts. In this seminar, I will present our recent work supporting a keystone role of oral microbes in the development of chronic airway infections, a central role of mucin degradation and fermentation in CF pathogen colonization, and outside-the-box half-baked ideas for airway disease management.

 Feb 17, 2025 @ 12:00 p.m.

 Medical Center | Upper Auditorium (3-7619)

Host: Steven Gill, Ph.D.

Sophie Troyer - PhD Candidate

Childhood food allergy and atopic disease are becoming increasingly prevalent.  A significant goal in this field is to prevent food allergy development and halt the atopic march— the sequential progression of atopic diseases from atopic dermatitis (AD) and food allergy (FA) to asthma and allergic rhinitis. To do this, a greater understanding of the development of allergy in infancy is needed. Communities with farming lifestyles such as the Old Order Mennonite (OOM) community have decreased prevalence of food allergy and therefore serve as a model population for protection against allergic diseases. Studies have shown differences between farming and nonfarming communities in the innate immune system such as TLR expression that could explain an immune protective impact of farm exposure and may be due to alterations in endotoxin levels and microbiota exposures. To further explore this area of research, we will examine differences in innate immune response between the local OOM infant population and the Rochester urban/suburban infant population, which comprise our ZOOM1 cohort. To compare innate immune responses, we compare cytokine output of CBMCs and PBMCs after stimulation with various TLR agonists including LPS (TLR4 agonist, bacterial) and ssRNA40/LyoVec (TLR 7/8 agonist, viral). Thus far, we have optimized several stimulation conditions, including TLR agonist concentration, duration of stimulation, whether to rest cells before stimulation, and the use of PBMCs vs isolated CD14+ cells. These experiments will aid in understanding the role of innate immunity in farming lifestyle protection against allergic diseases.

 Feb 13, 2025 @ 12:30 p.m.

 Medical Center | K307 (3-6408)

Host: Advisor: Kirsi Järvinen-Seppo, M.D., Ph.D.

Thandolwethu Shabangu - PhD Candidate

Pseudouridine (Y) and N1-methyl-pseudouridine are crucial for mRNA stability, immunogenicity, and translational efficiency. While software for handling modified nucleotides is available, we currently do not have a comprehensive set of  Y and m1Y nearest neighbor parameters. We present a full set of nearest neighbor parameters for a folding alphabet of A, C, G, U and Y and a folding alphabet of A, C, G,U and m1Y which encompass both helix and loop formation. The parameters were derived from optical melting experiments conducted on oligonucleotides that have either a Y or a m1Y modification. Melting curves for each duplex were analyzed using a two-state model, and linear regression was used to fit the nearest neighbor parameters. RNAstructuture software functionality will be extended to use the thermodynamic parameters with Y and m1Y. Our findings show that Y and m1Y improve helix stability more effectively than U. Both Y and m1Y serve as stabilizing elements for Dangling ends, single mismatches, and terminal mismatches.  However, m1Y is less stabilizing compared to Y. The penalty for positioning Y at the end of the helix is similar to that of U. While a m1Y-A pair at the helix ends incurs a penalty, a m1Y-U pair does not. Additional evidence is needed to prove that the parameters improve prediction accuracy.

 Feb 13, 2025 @ 12:00 p.m.

 Medical Center | K307 (3-6408)

Host: David Mathews, M.D., Ph.D.

Kevin Li - PhD Candidate

Acute myeloid leukemia (AML) is a blood cancer disease that is usually a result of genetic alterations in hematopoietic stem cells (HSCs) or more differentiated myeloid progenitor cells in the bone marrow (BM). Mutations in the cells will generate leukemic stem cells (LSCs) that can further differentiate into AML blast cells which can proliferate uncontrollably. Many existing therapies failed to control the disease due to LSC residues in the BM. We believe T cells can generate specific anti-tumor immune responses to target these LSCs. However, existing T cell immunotherapies are ineffective due to immunosuppressive bone marrow microenvironment (BMME) that leads to T cell suppression and exhaustion. Hence, our first project is to unveil the T cell suppression/exhaustion mechanisms in the immunosuppressive BMME using high-resolution analysis like spectral flow cytometry and single-cell RNA (scRNA) sequencing and develop new therapeutic strategies to boost T cell functions. Our second project is to characterize the effect of CCL3 on T cell population and phenotype changes in AML BMME. CCL3 is a pro-inflammatory chemokine that has been shown to enhance AML progression. Previous studies have shown that blocking CCL3 in a murine model can control the disease. However, the interactions between CCL3 and T cells are poorly understood. Ultimately, we aim to study whether blocking the CCL3 signaling pathway in the AML murine model may reshape T cells to become anti-leukemic.

 Feb 06, 2025 @ 12:30 p.m.

 Medical Center | K307 (3-6408)

Host: Advisor: Benjamin Frisch, Ph.D. & Scott Gerber, Ph.D.

Abby He - PhD Candidate

Allergic diseases affect more than 25% of children in US, but so far there is no cure. During infancy and childhood, atopic dermatitis (AD), food allergy (FA), asthma, and allergic rhinitis typically develop sequentially in a temporal manner, which is called the atopic march. The presence and severity of AD and FA is strongly associated with increased risk of developing later allergic diseases. Th2 cells are key inducers of allergic responses, and recent studies have shown that an elevated pathogenic Th2A subpopulation exists in adults with AD, FA, and asthma. The function of pathogenic Th2 cells in the progression of the atopic march remains unknown. Our lab is conducting the “Zooming into Old Older Mennonites (OOM)” study, in which we compare pathogenic Th2 cells from urban Rochester infants and OOM infants, who maintain a farming lifestyle and have a lower risk of developing allergic diseases. Our study demonstrates that Th2A cells are elevated in infants with early allergic diseases. We also defined Th2B cells as a new subpopulation of pathogenic Th2 cells, which are enriched earlier than Th2A cells in allergic infants, and secret higher levels of pro-inflammatory cytokines. Overall, we identify two distinct pathogenic Th2 subpopulations during early development of allergic diseases. Future experiments will further characterize Th2A and Th2B in older allergic children, and investigate their power as biomarkers for preventing the progression of the atopic march.

 Feb 06, 2025 @ 12:00 p.m.

 Medical Center | K307 (3-6408)

Host: Advisor: Kirsi Järvinen-Seppo, M.D., Ph.D.

Yaxi Wang, Ph.D. - Postdoctoral Scholar and Acting Instructor, University of Washington, Seattle, WA

Patescibacteria is a large and diverse phylum of bacteria sharing unique features that distinguish them from most other bacteria. These features include ultrasmall cell size, highly streamlined genomes, and a general lack of de novo biosynthetic pathways for nucleotides, amino acids, and fatty acids. Interestingly, Patescibacteria generally appear to overcome their limited biosynthetic capabilities by living as obligate epibionts, attaching to and proliferating on the surface of host bacteria. Given their unique biology, Patescibacteria represent an untapped reservoir of novel biological mechanisms. A group of Patescibacteria prevalent in human oral microbiomes called Saccharibacteria (Sb) was the first to be cultivated. However, due to a lack of suitable tools, the genetic basis of their epibiotic lifestyle and other unique features of Sb and other Patescibacteria remained unexplored. We developed the first method for genetic manipulation of Sb, enabling an array of approaches that provided initial mechanistic insights into the mysterious biology of these bacteria. Building on this foundation, my ongoing and future work focuses on dissecting the molecular mechanisms underlying Sb-host interactions by identifying and characterizing factors within Sb and their host bacteria that govern these enigmatic epibiotic relationships. These factors include type IV pili in Sb and a novel threat-sensing pathway in host bacteria.

 Feb 03, 2025 @ 2:30 p.m.

 Medical Center | K307 (3-6408)

Host: Steve Gill, Ph.D.

Maedeh Aghahosseini; Sarah Eckl - PhD Candidate, Immunology, Microbiology, and Virology Ph.D. Program

Maedeh Aghahosseini

Mobile genetic elements (MGEs) such as phages, plasmids, and transposons play a crucial role in prokaryotic evolution and pathogenesis. Circular self-replicating RNAs, such as viroids, are a class of MGEs long thought to be limited to plants and fungi. However, recent reanalysis of metatranscriptomic data has identified self-replicating circular RNAs in the oral human microbiome. Streptococcus sanguinis is one member of the human oral microbiome which is postulated to be a host to these RNAs and have been named “obelisks” due to their long rod-shaped structure. While many related circular RNAs do not encode for gene products, obelisks have one or two open reading frames encoding proteins termed “oblins”. With bioinformatic evidence only suggesting the presence of obelisks in prokaryotes many questions remain about their function, host range, and stability. We have generated a reverse genetics system to express obelisks. Importantly, the open reading frame encoding Oblin1 and the secondary structure of the obelisk are critical for self-replication. Overall, understanding the biology of these novel circular RNAs will provide insight into the diversity and impact of MGEs in prokaryotic populations.

Sarah Eckl

Pancreatic ductal adenocarcinoma (PDAC) is the 3rd leading cause of cancer related deaths in the US with a dismal 13% 5-year survival rate. Few effective treatments exist for PDAC, highlighting the urgent need for novel approaches. The PDAC tumor microenvironment (TME) is exceptionally immunosuppressive, which contributes to poor outcomes and lack of effective treatments for this malignancy. This TME is a myeloid-driven immunosuppressive environment in which anti-tumor T cells exhibit an exhausted phenotype. T cell exhaustion exists along a spectrum and is described by the expression of inhibitory receptors, loss of effector function, and upregulation of master regulators of exhaustion. Our lab has developed a novel therapeutic that combines stereotactic body radiation therapy (SBRT) with the immunostimulatory cytokine interleukin-12 (IL-12). Our work demonstrates that SBRT/IL-12 treatment of PDAC in vivo results in significant survival improvements and cures that are mediated by a drastic repolarization of the TME. SBRT/IL-12 therapy reverses myeloid cell immunosuppression and reinvigorates exhausted T cells. Using an ex vivo model, we show that IL-12 downregulates T cell exhaustion markers, including master regulator Tox, and upregulates activation markers, including the potent anti-tumor cytokine IFN-γ. These preliminary data suggest that IL-12 reinvigorates T cells in the TME to result in extended survival and cures. Future experiments will determine the contributions of SBRT in conjunction with IL-12. Uncovering the mechanism by which SBRT/IL-12 modulates the PDAC TME provides potential targets for treatment and an avenue for improving anti-tumor immunity.

 Jan 30, 2025 @ 12:00 p.m.

 Medical Center | K307 (3-6408)

Host: Advisor: Andrew Varble, PhD and Advisor: Scott Gerber, PhD

Katya McDonald - PhD Candidate, Immunology, Microbiology and Virology PhD Program

Staphylococcus aureus, a human pathogen, is the leading cause of implant-associated osteomyelitis. It has a high reoccurrence rate and a low post-operative cure rate and can lead to sepsis, multiorgan failure, and death. Unfortunately, surgical interventions have high failure and reinfection rates (10-50%), indicating a need for future innovation in therapeutics and vaccines.

T cells are essential to orchestrating anti-S. aureus adaptive immunity and studies have demonstrated the dichotomous roles of protection vs. pathogenesis they play during S. aureus infections. The role of T cells during S. aureus osteomyelitis remains poorly understood. To study human T cell responses, we generated a humanized mouse model of osteomyelitis and found that Tbet+ type I T cells swarm to the site of bone infection. A deeper examination of these T cells using scRNAseq revealed remarkable heterogeneity in the bone niche. In particular, we observed that CD4 Th1/Th17 cells were a mixed population of effector, progenitor-exhausted, and terminally exhausted cells at 2 weeks post-infection, which is considered to be the initiation of the chronic phase of osteomyelitis. These results indicate that functional impairment of T cells could occur during chronic osteomyelitis. Thus, the central hypothesis of my work is that S. aureus drives human CD4+ Th1/Th17 cells toward functional exhaustion during chronic osteomyelitis and that this can be overcome by immune checkpoint blockade (ICB) adjuvant therapy. Ultimately, this work will provide novel mechanistic insights into bacteria-T cell interactions during S. aureus bone infections, an important component of disease pathogenesis.

 Jan 23, 2025 @ 12:00 p.m.

 Medical Center | K307 (3-6408)

Host: Advisor: Gowrishankar Muthukrishnan, Ph.D.

Stephanie Renner - PhD Candidate, Immunology, Microbiology, and Virology Ph.D. Program

Human Immunodeficiency Virus type 1 (HIV-1) is the causative agent of the HIV/AIDS global epidemic. With the advent of combination antiretroviral therapies (cART), which control HIV infection but cannot eliminate it, far fewer people succumb to HIV related issues, but the population of people living with HIV-1 continues to grow. The major obstacle in curing HIV-1 is latency. In cells with latent HIV-1, the viral DNA is integrated in the host genome and transcriptionally silenced. Thus, viral proteins are not produced, which enables infected cells to avoid immune recognition and clearance. A recent study showed that patients who have been on long-term cART have different integration profiles compared to their short-term ART or newly infected counterparts. Moreover, these integration profiles have shifted from active euchromatin regions to inactive heterochromatin regions. We are interested in understanding the mechanisms by which silencing is maintained in these heterochromatin regions, and more specifically the centromere region.

We have performed a CRISPR-Cas9 knockout screen in JLat82 cells, a CD4+ T cell line which contains an HIV-GFP DNA integrated in the centromere of chromosome 10. We assessed which host factors were required for silencing of the HIV-GFP reporter, and identified CENPB, SETDB1, and FAM60A. Knockout of these genes were able to relieve the silencing and activate the expression from HIV-1 DNA integrated in the centromere. Our current experiments seek to understand the mechanisms by which these host factors silence HIV-1 DNA.

 Jan 16, 2025 @ 12:00 p.m.

 Medical Center | K307 (3-6408)

Host: Advisor: Yiping Zhu, Ph.D.

Natalie Vance - PhD Candidate

Globally, the incidence of pediatric allergy is on the rise with the greatest increases occurring in high-income countries, where it is estimated that one in five children struggle with an allergic disease. CD4+ T cells and B cells play important roles in the allergic response as CD4+ T cells primed with allergen derived antigen interact with B cells to induce class switching, stimulating production of allergen specific immunoglobulin E (IgE). Though it is well documented that CD4+ T cells induce class switching in B cells, little is known about the development of CD4+ T cell and B cell populations in early life. Pediatric research is further limited by the difficulty in obtaining enough samples. This impairs development of robust and reproducible immune signatures. To investigate the immune cell heterogeneity among the pediatric population, we developed a reference single-cell RNA-sequencing dataset using publicly available data and advanced data-integration methods. The publicly available data was curated from peripheral blood mononuclear cells collected from children ages 0-16 at well child visits. We have further isolated and annotated eight CD4+ T cell subpopulations. To explore the CD4+ T cell subtypes implicated in food allergy (FA), we measured the proportion of cells with high FA response signature, developed from previously published studies, using a single-cell pathway score (scPS). We found that FA signatures were most notably enriched among a subtype of Th2 cells and Th17-like cells. To further investigate the immune cell heterogeneity among atopic and FA individuals, we mapped CD4+ T cells from these populations to our pediatric reference and saw an increased proportion of cells from allergic individuals mapping to the Th2 population. Further work will expand on this data to evaluate the differences in B cell heterogeneity. Overall, this work characterizes immune cell heterogeneity in both healthy and food allergic pediatric populations and aims to identify biomarkers of FA that can be used for early detection of allergic disease.

 Jan 09, 2025 @ 12:00 p.m.

 Medical Center | K307 (3-6408)

Host: Advisor: Juilee Thakar, Ph.D

Mark H. Kaplan, Ph.D. - Chair, Dept. Microbiology & Immunology, Indiana University School of Medicine

Chair, Department of Microbiology & Immunology
Director of Basic Sciences, Brown Center for Immunotherapy
Nicole Brown Professor of Immunology
Indiana University School of Medicine

 Jan 06, 2025 @ 12:00 p.m.

 Medical Center | Upper Auditorium (3-7619)