eScholarship@UMassChan Repository at UMass Chan Medical School


Sherman Center building at UMass Chan Medical School at night

eScholarship@UMassChan is a digital repository for UMass Chan Medical School's research and scholarship, including journal articles, theses, datasets and more. We welcome submissions from our faculty, staff, and students. eScholarship@UMassChan is a service of the Lamar Soutter Library, Worcester, MA, USA. See also our open access journal publishing services.

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  • Apheresis practice variation during the COVID-19 pandemic: Results of a survey

    Tanhehco, Yvette C; Alsammak, Mohamed; Chhibber, Vishesh; Ibeh, Nnaemeka; Li, Yanhua; Stephens, Laura D; Noland, Daniel K; Wu, Ding Wen; Zantek, Nicole D; DeChristopher, Phillip J; et al. (2024-06-01)
    Background: The COVID-19 pandemic affected healthcare delivery across all specialties including apheresis. To describe the changes in apheresis service practices that occurred during the pandemic, the American Society for Apheresis (ASFA) Apheresis Medicine Attending Physician Subcommittee conducted a survey study. Study design and methods: A 32-question survey was designed and distributed to 400 ASFA physician members on September 7, 2022. Attending physicians responded to questions about whether and how apheresis service practices changed during the COVID-19 pandemic compared with the time period prior to the pandemic in terms of: (1) procedure types and volumes, (2) patient consultation workflow, and (3) the use of telemedicine. Descriptive analyses were reported as number and frequency of responses. Results: The survey response rate was 13.8% (55/400). Of these respondents, 96.4% (53/55) were attending physicians. The majority of respondents (42/53, 79.2%) indicated that the types of procedures performed during COVID-19 compared to pre-pandemic did not change. Most frequently for apheresis procedure volume, respondents reported: no change in their monthly inpatient volume (21/47, 44.7%) and a decrease in their monthly outpatient volume (28/46, 60.9%). Prior to COVID-19, 75.0% (30/40) of respondents performed consultations at bedside for inpatients and 67.4% (29/43) performed consultations at bedside for outpatients. Bedside consultations decreased in both settings during the pandemic but were still most frequently performed by attending physicians. At the same time, the use of telemedicine increased for 15.4% of survey respondents during COVID-19. Conclusion: Some, but not all, respondents observed or made changes to their apheresis service during the COVID-19 pandemic. A subset of changes, such as increased utilization of telemedicine, may persist.
  • Kinetics of Pre-mRNA 3’ End Cleavage

    Torres Ulloa, Leslie (2024-05-31)
    3’ end cleavage and polyadenylation are required steps in pre-mRNA maturation. The rate at which 3’ end cleavage occurs can determine the temporal availability of mRNA for subsequent function throughout the cell and is likely tightly regulated. While there are numerous high-throughput methods for global profiling of RNA maturation rates, the study of pre-mRNA 3’ end cleavage kinetics has remained limited to low-throughput approaches, and the temporal regulation of polyadenylation site choice that determines the composition of the 3’ UTRs of mRNAs remains poorly understood. This research project seeks to address this gap by introducing a novel genome-wide, site-specific methodology for estimating rates of pre-mRNA 3’ end cleavage, using metabolic labeling of nascent RNA, high-throughput sequencing, and mathematical modeling. Using in-silico simulations of nascent RNA-seq data, we show that our approach can accurately and precisely estimate cleavage half-lives for both constitutive and alternative sites. In Drosophila melanogaster S2 cells, we find that cleavage rates are fast but highly variable across sites, with alternative events being slowest. This variability in rates is underpinned by distinctive sequence elements, where an A-rich region upstream of the cleavage site, a U-rich element downstream of the cleavage site, and a higher density of polyadenylation signals, lead to faster cleavage reactions. Assessment of Polymerase II dynamics around cleavage sites reveals that cleavage rates are associated with the localization of RNA Polymerase II at the end of a gene and faster cleavage leads to quicker degradation of downstream read-through RNA. This approach for estimating pre-mRNA 3’ end cleavage kinetics opens new possibilities in the study of co-transcriptional regulation of mRNA expression and transcription termination across cellular states.
  • Variation in Depth of Sedation Targeted and Achieved among Mechanically Ventilated Patients and Associated Outcomes

    Rucci, Justin M (2024-05-30)
    Introduction: Sedative agents are commonly administered to patients receiving mechanical ventilation (MV). Practice guidelines recommend provision of light sedation within validated scoring systems (e.g., Richmond Agitation Sedation Scale [RASS]), but recognize some circumstances require deeper sedation. The real-world approaches to depth of sedation, and the impact of hospital sedation practices on patient outcomes, remain uncharacterized. Methods: We used the US based eICU collaborative research database to identify adult patients who received MV > 24 hours, who did not have a diagnosis that may require sedatives for indications other than facilitating MV, and who had recorded RASS goals and scores. We used mixed effects regression models to determine factors associated with initial RASS goals and rates of RASS score-goal concordance. We organized hospitals into quartiles of risk-adjusted RASS score-goal concordance, and used g-computation to evaluate differences in ventilator free days (VFD) at hospital day 28. Results: We identified a study sample of 1,650 adult patients (at 21 hospitals) who met inclusion/exclusion criteria. Hospital-level risk-adjusted initial RASS goals ranged from -1.4 to 0.2, and hospital-level risk-adjusted RASS score-goal concordance ranged from 27% to 64%. Patients admitted to hospitals in the highest quartile of score-goal concordance (quartile 4) were generally targeted for deeper sedation (median RASS goal -1.31) than patients admitted to hospitals in the lowest quartile (quartile 1) (median RASS goal -0.58). Compared to patients admitted to quartile 1 hospitals, patients at quartile 4 hospitals experienced fewer VFDs (adjusted incidence risk difference -2.4, 95% CI -4.26 to -0.36). Conclusion: US hospitals prescribe RASS goals in line with guideline recommendations for light sedation, but there is wide variation in achieving these RASS goals. Hospitals with higher RASS score-goal concordance typically prescribed deeper RASS goals, and patients admitted to these hospitals experienced fewer VFD.
  • SARS-CoV-2 infection is associated with an increase in new diagnoses of schizophrenia spectrum and psychotic disorder: A study using the US national COVID cohort collaborative (N3C)

    Rahman, Asif; Russell, Michael; Zheng, Wanhong; Eckrich, Daniel; Ahmed, Imtiaz (2024-05-30)
    Amid the ongoing global repercussions of SARS-CoV-2, it is crucial to comprehend its potential long-term psychiatric effects. Several recent studies have suggested a link between COVID-19 and subsequent mental health disorders. Our investigation joins this exploration, concentrating on Schizophrenia Spectrum and Psychotic Disorders (SSPD). Different from other studies, we took acute respiratory distress syndrome (ARDS) and COVID-19 lab-negative cohorts as control groups to accurately gauge the impact of COVID-19 on SSPD. Data from 19,344,698 patients, sourced from the N3C Data Enclave platform, were methodically filtered to create propensity matched cohorts: ARDS (n = 222,337), COVID-19 positive (n = 219,264), and COVID-19 negative (n = 213,183). We systematically analyzed the hazard rate of new-onset SSPD across three distinct time intervals: 0-21 days, 22-90 days, and beyond 90 days post-infection. COVID-19 positive patients consistently exhibited a heightened hazard ratio (HR) across all intervals [0-21 days (HR: 4.6; CI: 3.7-5.7), 22-90 days (HR: 2.9; CI: 2.3 -3.8), beyond 90 days (HR: 1.7; CI: 1.5-1.)]. These are notably higher than both ARDS and COVID-19 lab-negative patients. Validations using various tests, including the Cochran Mantel Haenszel Test, Wald Test, and Log-rank Test confirmed these associations. Intriguingly, our data indicated that younger individuals face a heightened risk of SSPD after contracting COVID-19, a trend not observed in the ARDS and COVID-19 negative groups. These results, aligned with the known neurotropism of SARS-CoV-2 and earlier studies, accentuate the need for vigilant psychiatric assessment and support in the era of Long-COVID, especially among younger populations.
  • Disparities in Palliative Care Use for Patients With Blood Cancer Who Died in the Hospital

    Hsieh, Tien-Chan; Yeo, Yee Hui; Zou, Guangchen; Zhou, Chan; Ash, Arlene S. (2024-05-27)
    Background: Palliative care can enhance quality of life during a terminal hospitalization. Despite advances in diagnostic and treatment tools, blood cancers lag behind solid malignancies in palliative use. It is not clear what factors affect palliative care use in blood cancer. Methods: We used the 2016 to 2019 National Inpatient Sample to identify demographic and socioeconomic factors associated with receiving palliative care among patients over age 18 with any malignant hematological diagnosis during a terminal hospitalization lasting at least 3 days, excluding those receiving a stem cell transplant. Results: Palliative care use was documented 54% of the time among 49,720 weighted cases (9944 distinct individual hospitalizations), approximately evenly distributed across the years 2016-2019. Palliative care use was lowest in 2016 (51%) and highest in 2018 (58%), and increased with age, reaching 58% for those 80 years and older. Men and women were similarly likely to receive care. Patients of Hispanic ethnicity and African Americans received less palliative care (47% and 49%, respectively), as did those insured by Medicaid (48%), and those admitted to small or rural hospitals (52% and 47%, respectively). Charges for hospitalizations with palliative care were 19% lower than for those without it. Conclusions: This study highlights disparities in palliative care use among blood-cancer patients who died in the hospital. It seems likely that many of the 46% who did not receive palliative care could have benefitted from it. Interventions are likely needed to achieve equitable access to ideal levels of palliative care services in late-stage blood cancer.
  • SLIGHT shield dataset on effect of chest shielding during phototherapy in premature infants on the incidence of patent ductus arteriosus

    Amin, Sanjiv; Mannan, Javed (2024-05-23)
    The SLIGHT shield dataset reflects the results from a double blind randomized trial on the effect of chest shielding during phototherapy in premature infants on the incidence of patent ductus arteriosus. All preterm infants ≤ 29 weeks GA or weighing ≤1000 grams at birth admitted to our neonatal intensive care unit (NICU) within the first 24 hours of life were eligible for the study and randomized to chest shield placement or sham shield placement during phototherapy treatment. Enrollment occurred from August 1, 2015 to April 13, 2018. The primary outcome was the incidence of sPDA diagnosed via clinical parameters by the investigator team during the period from 24 hours after initiating phototherapy to 3 days after stopping phototherapy. Secondary outcomes consistent of echo based parameters : 1) ductal diameter with a left to right or bidirectional shunt across the PDA 2) left atrium (LA) to aortic root (AO) diameter ratio (LA/AO) and 3) LA volume. Additional secondary outcomes included the following: 1) surgical ligation of PDA, 2) chronic lung disease (CLD), 3) retinopathy of prematurity (ROP), 4) intraventricular hemorrhage (IVH), 5) peak levels of total serum bilirubin and 6) duration of phototherapy. Baseline/demographc data as well as clinical data were also obtained. Study participants self-reported three items assessing religiosity: strength/comfort from religion, petition prayers for health, and awareness of intercessory prayers by others. All cause-mortality within 2-years of hospital discharge was ascertained by review of medical records at participating study hospitals and from death certificates. Cox proportional hazards models were used to estimate the multivariable adjusted risk of 2-year all-cause mortality.
  • Spatial Transcriptomics Reconstruction of Mouse Olfactory System

    Wang, I-Hao (2024-05-20)
    The olfactory system is crucial for animals in tasks such as foraging, mate selection, and predator avoidance due to its ability to detect and distinguish a vast array of environmental chemicals. Mice detect these chemicals via olfactory receptor (OR) proteins, which are uniquely expressed by olfactory sensory neurons (OSNs); each OSN expresses only one OR type. OSNs with the same OR converge their axons to a specific location in the olfactory bulb (OB), forming a structure known as a glomerulus. This precise organization ensures a consistent, spatially invariant pattern of glomerular activation for each odorant, playing a likely role in the brain's decoding of odor identities. Nevertheless, the exact locations of most glomeruli are unknown, and the mechanisms that create consistent glomerular maps across different animals are not fully understood. In this study, we leveraged spatial transcriptomics and machine learning to map the majority of glomerular positions within the mouse OB. Furthermore, single-cell RNA sequencing revealed distinct transcriptional profiles for each OSN type, characterized not only by their OR gene but also by a unique set of axon guidance genes. These profiles can predict the eventual location of each OSN's glomerulus within the olfactory bulb. We also identified a correlation between the spatial distribution of glomeruli and the characteristics of their corresponding ORs, suggesting a chemotopic arrangement in the mouse olfactory system. Additionally, we probed the complexity of the OB by creating a spatially resolved cell atlas through spatial single-cell transcriptomics, revealing the identity and distribution of neuron subtypes that contribute to odor perception.
  • Working Together to Mint DOIs on Demand for a DSpace Repository

    Grynoch, Tess; Palmer, Lisa A. (2024-05-20)
    Background: Digital Object Identifiers (DOIs) are a key persistent identifier in the publishing landscape to ensure discoverability and citation of research products. Minting DOIs can be a time-consuming task for repository librarians. This process can be automated since the metadata for DOIs is already in the repository record and DataCite, a DOI minting organization, and Open Repository, a DSpace repository platform, both have application programming interfaces (APIs). Previous software has enabled bulk DOI minting. However, the institutional repository contains a mixture of original materials (dissertations, reports, data, etc.) and previously published materials such as journal articles and preprints. Description: An institutional repository librarian and her librarian colleague with Python experience embarked on a pair programming project to create a script to mint DOIs on demand in DataCite for individual items in the institution’s Open Repository instance. The pair met for one hour each week to develop and test the script. The institutional repository librarian lent invaluable insight into both platforms and the metadata variations the code would need to account for. The project was also a great learning opportunity for both librarians to improve their Python coding skills. This project will be evaluated in terms of how the time spent creating the code compares to the time it takes to mint DOIs manually as well as metadata enhancements and accuracy in DataCite. Program Conclusion: This poster will share the final Python script and highlight the takeaways from this approach for both the institutional repository librarian and the coding librarian. Final evaluation is forthcoming.
  • Exploring the relationship between school-supervised asthma therapy and social determinants of health in pediatric asthma care

    Al-Halbouni, Layana; Ryan, Grace W; Radu, Sonia; Spano, Michelle; Sabnani, Reshma; Phipatanakul, Wanda; Gerald, Lynn B; Garg, Arvin; Pbert, Lori; Trivedi, Michelle (2024-05-16)
    Background: Social determinants of health (SDoH), including access to care, economic stability, neighborhood factors, and social context, strongly influence pediatric asthma outcomes. School-supervised asthma therapy (SST) is an evidence-based strategy that improves asthma outcomes, particularly for historically marginalized children, by providing support for daily medication adherence in school. However, little is known about the relationship between these programs and the adverse SDoH commonly affecting underrepresented minority and marginalized children with asthma. Methods: We examined qualitative data from interviews (n = 52) conducted between 2017 and 2020 with diverse multi-level partners involved in Asthma Link, a SST intervention. Participants included end-users (children and their parents), deliverers (school nurses and pediatric providers), and systems-level partners (e.g., insurers, legislators, and state officials). We used inductive coding to determine themes and subthemes and deductive coding using the Healthy People 2030 SDoH framework. Results: Three themes emerged: (1) SST mitigates adverse SDoH (improves access to preventive healthcare and asthma health literacy), (2) SST benefits children experiencing specific adverse SDoH (provides a consistent medication routine to children with unstable family/housing situations) and (3) specific adverse SDoH impede SST implementation (economic instability, culture and language barriers). Conclusion: This study suggests an important relationship between SDoH and SST that warrants further evaluation in our future work on this community-based asthma intervention. Moreover, our findings underscore the importance of measuring SDoH in the implementation and evaluation of pediatric asthma interventions, particularly given the strong influence of these social factors on child health outcomes.
  • UMCCTS Newsletter, May 2024

    UMass Center for Clinical and Translational Science (2024-05-06)
    This is the May 2024 issue of the UMass Center for Clinical and Translational Science Newsletter containing news and events of interest.
  • Dominant negative mutations in yeast Hsp90 reveal triage decision mechanism targeting client proteins for degradation [preprint]

    Flynn, Julia M; Joyce, Margot E; Bolon, Daniel N A (2024-04-30)
    Most of the fundamental processes of cells are mediated by proteins. However, the biologically-relevant mechanism of most proteins are poorly understood. Dominant negative mutations have provided a valuable tool for investigating protein mechanisms but can be difficult to isolate because of their toxic effects. We used a mutational scanning approach to identify dominant negative mutations in yeast Hsp90. Hsp90 is a chaperone that forms dynamic complexes with many co-chaperones and client proteins. In vitro analyses have elucidated some key biochemical states and structures of Hsp90, co-chaperones, and clients; however, the biological mechanism of Hsp90 remains unclear. For example, high throughput studies have found that many E3 ubiquitin ligases bind to Hsp90, but it is unclear if these are primarily clients or acting to tag other clients for degradation. We introduced a library of all point mutations in the ATPase domain of Hsp90 into yeast and noticed that 176 were more than 10-fold depleted at the earliest point that we could analyze. There were two hot spot regions of the depleted mutations that were located at the hinges of a loop that closes over ATP. We quantified the dominant negative growth effects of mutations in the hinge regions using a library of mutations driven by an inducible promoter. We analyzed individual dominant negative mutations in detail and found that addition of the E33A mutation that prevents ATP hydrolysis by Hsp90 abrogated the dominant negative phenotype. Pull-down experiments did not reveal any stable binding partners, indicating that the dominant effects were mediated by dynamic complexes. DN Hsp90 decreased the expression level of two model Hsp90 clients, glucocorticoid receptor (GR) and v-src kinase. Using MG132, we found that GR was rapidly destabilized in a proteasome-dependent fashion. These findings provide evidence that the binding of E3 ligases to Hsp90 may serve a quality control function fundamental to eukaryotes.
  • Identifying Therapeutic Oligonucleotide-Induced Neurotoxicity and Methods for Safe Delivery to the Central Nervous System

    Miller, Rachael (2024-04-29)
    Huntington’s disease (HD) is a hereditary neurodegenerative disorder caused by an autosomal dominant mutation in Exon 1 of the Huntingtin gene (Htt). There are no approved treatments for HD. Oligonucleotide therapeutics (ASOs and siRNAs) offer a new strategy to treat genetically defined CNS diseases. These therapeutics aim to attenuate disease pathogenesis by targeting Htt mRNA to reduce the toxic mutant protein. Recent technological advancements now enable robust distribution and efficacy throughout mouse, sheep, and NHP brains. However, oligonucleotides can cause acute neurotoxicity when injected directly into the CSF. This dissertation aims to optimize oligonucleotide delivery for the treatment of HD by addressing safety issues across species. We used electroencephalography (EEG) and electromyography (EMG) in awake animals to confirm that direct CSF injection of oligonucleotides induces seizures. We hypothesized that this was due to the negatively charged oligonucleotides changing the delicate balance of divalent cations in the CSF. To address this issue, we developed an artificial CSF (aCSF) buffer supplemented with Ca2+ alone, Mg2+ alone, or Ca2+ and Mg2+ in the injected solution to prevent the imbalance. Real-time EEG monitoring in awake mice and lambs confirmed the absence of seizures when oligonucleotides were delivered in the new aCSF buffer. In summary, this dissertation identified a potential cause of oligonucleotide-induced acute neurotoxicity, developed a method to safely deliver oligonucleotides to the CNS with Ca2+/Mg2+-enriched buffers, and demonstrated the viability of this formulation in a large animal model. These findings support a new method for safely delivering oligonucleotides to the CNS to treat neurological diseases.
  • Epigenetic Enablers of Meningioma Growth

    Berry, Bethany C (2024-04-26)
    Meningiomas are the most common primary intracranial brain tumor, often causing significant disability and sometimes even death. The most aggressive meningiomas commonly exhibit extensive genomic disruption that can lead to genotoxic and proteotoxic stress, but the mechanisms that enable these tumors to thrive are unknown. To date, meningiomas have no effective chemotherapy. This study used a high-throughput bioactive small molecule screen of established meningioma cell lines and RNA-sequencing of patient meningiomas to identify EHMT2/G9a inhibitors as potent cytotoxic agents in meningioma in vitro. Further, studies using the small molecule EHMT2/G9a inhibitor, UNC0631 demonstrated reduced tumor growth in an orthotopic xenograft mouse model of meningioma in vivo. We used CUT&Tag and transcriptomic analyses of established meningioma cell lines after EHMT2/G9a inhibition to identify the unfolded protein response (UPR) and endoplasmic reticulum (ER) stress apoptotic signaling pathway as key factors in EHMT2/G9a-mediated meningioma cell death. After EHMT2/G9a inhibition, we observed a collapse of heat shock protein expression and hypothesized that downregulation of a deacetylase, Sirtuin 1 (SirT1), may be responsible. Consistent with decreased SirT1 activity, Heat Shock Factor 1 exhibited increased lysine acetylation and decreased DNA binding at the promoters of downregulated heat shock proteins. Overexpression of SirT1 or shRNA-mediated knockdown of the ER stress response mediators, ATF4 or CHOP/DDIT3, decreased meningioma cell death caused by EHMT2/G9a inhibition. The molecular chaperone and ER stress inhibitor, 4-phenylbutyric acid, abrogated meningioma cell death occurring after EHMT2/G9a inhibition. In conclusion, epigenetic maintenance of heat shock protein activity and suppression of the UPR/ER stress apoptotic signaling pathway by EHMT2/G9a and SirT1 are essential for aggressive meningioma growth.
  • Advancing Oligonucleotide Technologies for Malignant Brain Tumors and Other Central Nervous System Diseases

    Sarli, Samantha L (2024-04-26)
    Oligonucleotides are a class of synthetic, nucleic acid-based drugs that modulate the expression of disease-causing genes. These drugs are chemically modified to ensure safe and effective activity in relevant tissues in vivo. However, in complex tissues such as the brain, oligonucleotides can show striking differences in activity across cell types. Determining the activity profile of an oligonucleotide in distinct cell types can inform on mechanism of action and is key in moving these drugs towards the clinic. In this thesis, I broadly focused on developing tools to measure efficacy and improve the safety of gene-silencing oligonucleotides in the central nervous system (CNS). Much of this work was dedicated to glioblastoma multiforme (GBM), a universally lethal brain tumor that is largely resistant to current surgical and drug interventions. To this end, I designed a method to measure gene silencing by oligonucleotides in GBM xenografts versus normal brain tissue in vivo. I assessed the impact of conjugates on oligonucleotide activity patterns in tumor and normal brain cells and identified conjugates with potential GBM applications. In addition, I studied formulation as a strategy to mitigate acute neurotoxicity induced by antisense oligonucleotides (ASOs) delivery to the CNS. I also optimized immunostaining methods for a phosphorothioate-specific antibody to characterize biodistribution of monovalent and multivalent ASOs. In summary, this thesis expands the frameworks used in the rational design of these drugs and further
  • Deciphering Splicing Anomalies in Pancreatic Islets and Cancer Cells

    MacMillan, Hannah J (2024-04-25)
    Efficient splicing hinges upon an intricate balance between splice site choice accuracy and temporal coordination. It is well known that splicing programs are widely dysregulated in disease contexts such as diabetes and cancer, but the mechanism and consequence is not always clear. Here, we investigate splicing outcomes in the context of SNPs and splicing factor mutations. Specifically, we examine back-splicing of the antisense non-coding RNA in the INK locus (ANRIL) in cardiometabolic disease and then query the consequences of recurrent splicing factor mutations SF3B1K700E and U2AF1S34F in cancer. We characterize consistent circular ANRIL isoforms across dozens of pancreatic islet donors and find that individuals with a Type II Diabetes T2D risk-SNP in exon 2 of ANRIL produce more circANRIL. We also find that a higher circular:linear ANRIL isoform ratio is associated with decreased beta cell proliferation, drawing an association between back-splicing and disease phenotype. Outside of transcriptomic variation due to individual SNPs relating to cardiometabolic disease, we investigate the consequences of missense mutations within core splicing factors in cancer. Through a combination of nascent and steady state RNA sequencing and mathematical modeling, we find that both highly prevalent mutations in MDS and leukemias, SF3B1K700E and U2AF1S34F, cause a significant global alteration in splicing rate. Our result suggests that prevalent spliceosomal mutation not only contributes to disease progression in the form of select mis-spliced transcripts as previously reported, but also through a global disruption in the temporal coordination of mRNA processing. Together, our research sheds further light on the interplay between aberrant splicing mechanisms and the progression of disease phenotypes.
  • Translation-dependent and -independent mRNA decay occur through mutually exclusive pathways defined by ribosome density during T cell activation

    Mercier, Blandine C; Labaronne, Emmanuel; Cluet, David; Guiguettaz, Laura; Fontrodona, Nicolas; Bicknell, Alicia; Corbin, Antoine; Wencker, Mélanie; Aube, Fabien; Modolo, Laurent; et al. (2024-04-25)
    mRNA translation and decay are tightly interconnected processes both in the context of mRNA quality-control pathways and for the degradation of functional mRNAs. Cotranslational mRNA degradation through codon usage, ribosome collisions, and the recruitment of specific proteins to ribosomes is an important determinant of mRNA turnover. However, the extent to which translation-dependent mRNA decay (TDD) and translation-independent mRNA decay (TID) pathways participate in the degradation of mRNAs has not been studied yet. Here we describe a comprehensive analysis of basal and signal-induced TDD and TID in mouse primary CD4+ T cells. Our results indicate that most cellular transcripts are decayed to some extent in a translation-dependent manner. Our analysis further identifies the length of untranslated regions, the density of ribosomes, and GC3 content as important determinants of TDD magnitude. Consistently, all transcripts that undergo changes in ribosome density within their coding sequence upon T cell activation display a corresponding change in their TDD level. Moreover, we reveal a dynamic modulation in the relationship between GC3 content and TDD upon T cell activation, with a reversal in the impact of GC3- and AU3-rich codons. Altogether, our data show a strong and dynamic interconnection between mRNA translation and decay in mammalian primary cells.
  • Mechanisms of Interferon-α/β Receptor (IFNAR) Dependent and Independent Autoimmune Diabetes in LEW.1WR1 Rats

    Arowosegbe, Adediwura (2024-04-22)
    Type 1 diabetes (T1D) is an autoimmune disease characterized by the destruction of insulin-producing pancreatic β cells by immune cells, leading to insulin deficiency. T1D is driven by intricate interactions between the innate and adaptive immune mechanism, and autoreactive T-cells perpetuate destruction of islets cells following priming by proinflammatory cytokines and chemokines. Although the primary risk factor for T1D is genetic, environmental factors have been implicated as possible triggers or accelerators in the pathogenesis of T1D. Viral infections, especially enteroviruses have been implicated in the pathogenesis of T1D. Mechanisms proposed for such association include virus-induced innate immune responses including type I interferon (IFN) that unmask β-cells for recognition by autoreactive T-cells. Type I IFN has been implicated in the early stages of T1D autoimmunity and previous studies in our rat model highlight the essential role of virus-induced, type I IFN responses as rats lacking type I IFN signaling (Ifnar1-/- LEW.1WR1 rats) have delayed onset and up to 50% reduction in the incidence of autoimmune diabetes. The goal of my thesis research is to delineate type I IFN dependent and independent mechanisms that drive autoimmune diabetes using LEW.1WR1 rats, models in which autoimmune diabetes can be induced with combined poly I:C and virus infection. I hypothesize that in Ifnar1-/- LEW.1WR1 rats, type II IFN and non-interferon innate immune responses compensate for type I IFN responses and drive the adaptive immune cells to mediate autoimmune diabetes. Transcriptome profiles of wild type (WT) and Ifnar1-/- LEW.1WR1 rat islets over a time course were analyzed to define temporal transcriptional events that lead to autoimmune diabetes in prediabetic LEW.1WR1 rats following poly I:C and KRV treatment. Pancreatic sections of treated rats were also analyzed using RNA-in situ hybridization (RNA-ISH) to spatially map islet cells inflammation and to correlate with local islet T cell recruitment. In WT LEW.1WR1 rats, a transcriptional signature characterized by interferon-stimulated genes, chemokines, major histocompatibility class I, and genes for the ubiquitin-proteasome system was identified in subsets of β and α cells. These signature cells increased in frequency over time and correlated with local islet T cell recruitment. Type I IFN genes as well as genes for the ubiquitin-proteasome system are largely suppressed in poly I:C + KRV treated Ifnar1-/- rats compared to control Ifnar1-/- rats, while MHC class I genes were upregulated in poly I:C + KRV treated Ifnar1-/- rats compared to control Ifnar1-/- rats. Cytokine analysis reveal an increase in levels of IFNγ in poly I:C + KRV treated Ifnar1-/- rats compared to WT rats. Blocking IL-1R does not protect from diabetes in WT and Ifnar1-/- treated rats although both are protected with depletion of CD8+ T cells. Infiltration of immune cells in WT rats was accompanied with extensive islet damage while infiltration in Ifnar1-/- rats was less destructive. Inhibition of the JAK signaling pathway confirmed the requirement of the JAK-STAT signaling pathway and CD8+ T cells in progression to diabetes in the WT rats and further testing to confirm this requirement in Ifnar1-/- rats is ongoing. Although CCL proteins were expressed on immune cells, blockade of CCR5 had no effect on diabetes incidence. Collectively, the results from these studies provided mechanistic insights into the essential role of virus-induced, innate immune responses in the early phase of autoimmune diabetes pathogenesis.
  • BNST GluN2D-containing NMDARs contribute to ethanol intake but not negative affective behaviors in female mice [preprint]

    Doyle, Marie A; Salimando, Gregory J; Altemus, Megan E; Badt, Justin K; Bedenbaugh, Michelle N; Vardy, Alexander S; Adank, Danielle N; Park, Anika S; Winder, Danny G (2024-04-21)
    Alcohol use disorder (AUD) is a chronic, relapsing disease, highly comorbid with anxiety and depression. The bed nucleus of the stria terminalis (BNST), and Crh + neurons in this region are thought to play a key role in chronic ethanol-induced increases in volitional ethanol intake. This role has been hypothesized to be driven by emergent BNST-dependent negative affective behaviors. Indeed, we report here that in female mice undergoing a home cage chronic drinking forced abstinence model (CDFA), excitatory transmission undergoes time-dependent upregulation in BNST Crh + cells. Excitatory NMDA receptors (NMDARs) are a major target of ethanol, and chronic ethanol exposure has been shown to regulate NMDAR function and expression. GluN2D subunit-containing NMDARs have emerged as a target of interest due to their limited distribution and potential roles in affective behavior. We find that knockdown of dorsal BNST (dBNST) GluN2D expression significantly decreases ethanol intake in female, but not male, mice. While BNST Grin2b expression was significantly increased in protracted abstinence following CDFA, no differences in Grin2d expression were observed in dBNST or specifically in dBNST Crh + neurons. Finally, to determine the impact of GluN2D expression on negative affective behaviors, open field, elevated zero maze, and forced swim tasks were used to measure anxiety- and depressive-like behaviors in constitutive and conditional BNST GluN2D knockout mice. Surprisingly, we find that deletion of GluN2D fails to alter negative affect in ethanol-naïve female mice. Together, these data suggest a role for BNST GluN2D-containing NMDARs in ethanol drinking behaviors but not abstinence from ethanol, highlighting potential sex differences and behavioral specificity in the context of AUD behaviors. Overall, these data further suggest roles for BNST synaptic signaling in volitional ethanol intake that are partially independent of actions on affective behavior.
  • Teachers' Perceptions of the Impact of the COVID-19 Pandemic and Their Implementation of an Evidence-based HIV Prevention Program in the Bahamas

    Schieber, Elizabeth; Cottrell, Lesley; Deveaux, Lynette; Li, Xiaoming; Taylor, Marcellus; Adderley, Richard; Marshall, Sharon; Forbes, Nikkiah; Wang, Bo (2024-04-20)
    Information on how school-based programs is implemented and sustained during crises is limited. In this study, we assessed the impact of the COVID-19 pandemic on the implementation of a HIV prevention intervention in The Bahamas. Data were collected from 139 Grade 6 teachers in 2021-2022. Teachers attended virtual training and received implementation monitoring from coordinators. On average, teachers taught 26.4 (SD = 9.2) of the 35 core activities, and 7.4 (SD = 2.4) out of 9 sessions. More than half (58.3%) of teachers completed 28 or more core activities; 69.1% covered eight or all nine sessions, which is equivalent to 80% of the HIV intervention curriculum. Almost half of the teachers (43%) reported that the pandemic negatively impacted their ability to teach the program; 72% of teachers maintained that the program remained "very important" during times of crisis. Greater self-efficacy and supports increased implementation fidelity.
  • Building a Community of Practice to Improve Dissemination of Disability Research

    Wnuk, Jean (2024-04-18)
    A Community of Practice brings together groups of people who share a concern, a set of problems, a passion about a topic, and who deepen their knowledge and expertise in this area by interacting on an ongoing basis. In 2022, the Center on Knowledge Translation for Employment Research (CeKTER) developed of a Community of Practice on "S.M.A.R.T. Social Media for Employment Research Dissemination,” This CoP was developed to respond to NIDILRR disability research grantees who have a collective desire to enhance their social media effectiveness. This CoP continues as of April 2024. Using our experience with the "S.M.A.R.T. Social Media for Employment Research Dissemination" CoP this tip sheet offers others guidance on how to develop and sustain a successful CoP.

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