Digital Commons Network^™

Factors, Enablers And Challenges For Covid-19 Vaccine Development, Jean-Louis Excler, Melanie Saville, Lois Privor-Dumm, Sarah Gilbert, Peter J Hotez, Didi Thompson, Salim Abdool-Karim, Jerome H Kim

Faculty, Staff and Students Publications

The COVID-19 pandemic triggered a sense of vulnerability and urgency that led to concerted actions by governments, funders, regulators and industry to overcome traditional challenges for the development of vaccine candidates and to reach authorisation. Unprecedented financial investments, massive demand, accelerated clinical development and regulatory reviews were among the key factors that contributed to accelerating the development and approval of COVID-19 vaccines. The rapid development of COVID-19 vaccines benefited of previous scientific innovations such as mRNA and recombinant vectors and proteins. This has created a new era of vaccinology, with powerful platform technologies and a new model for vaccine development. …

Gpr43 Stimulation On Tcrαβ+ Intraepithelial Colonic Lymphocytes Inhibits The Recruitment Of Encephalitogenic T-Cells Into The Central Nervous System And Attenuates The Development Of Autoimmunity, Carolina Prado, Alexandra Espinoza, J Eduardo Martínez-Hernández, Joseph Petrosino, Erick Riquelme, Alberto J M Martin, Rodrigo Pacheco

Faculty, Staff and Students Publications

INTRODUCTION: Gut microbiota plays a critical role in the regulation of immune homeostasis. Accordingly, several autoimmune disorders have been associated with dysbiosis in the gut microbiota. Notably, the dysbiosis associated with central nervous system (CNS) autoimmunity involves a substantial reduction of bacteria belonging to Clostridia clusters IV and XIVa, which constitute major producers of short-chain fatty acids (SCFAs). Here we addressed the role of the surface receptor-mediated effects of SCFAs on mucosal T-cells in the development of CNS autoimmunity.

METHODS: To induce CNS autoimmunity, we used the mouse model of experimental autoimmune encephalomyelitis (EAE) induced by immunization with the myelin …

Dual-Target Deep Brain Stimulation For Obsessive-Compulsive Disorder And Tourette Syndrome, Ricardo A Najera, Nicole Provenza, Huy Dang, Kalman A Katlowitz, Alyssa Hertz, Sandesh Reddy, Ben Shofty, Steven T Bellows, Eric A Storch, Wayne K Goodman, Sameer A Sheth

Faculty, Staff and Students Publications

No abstract provided.

Genotypic And Phenotypic Spectrum Of Infantile Liver Failure Due To Pathogenic Trmu Variants, Georg F Vogel, Yael Mozer-Glassberg, Yuval E Landau, Lea D Schlieben, Holger Prokisch, René G Feichtinger, Johannes A Mayr, Heiko Brennenstuhl, Julian Schröter, Agnes Pechlaner, Fowzan S Alkuraya, Joshua J Baker, Giulia Barcia, Ivo Baric, Nancy Braverman, Birute Burnyte, John Christodoulou, Elzbieta Ciara, David Coman, Anibh M Das, Niklas Darin, Adela Della Marina, Felix Distelmaier, Erik A Eklund, Melike Ersoy, Weiyan Fang, Pauline Gaignard, Rebecca D Ganetzky, Emmanuel Gonzales, Caoimhe Howard, Joanne Hughes, Vassiliki Konstantopoulou, Melis Kose, Marina Kerr, Aneal Khan, Dominic Lenz, Robert Mcfarland, Merav Gil Margolis, Kevin Morrison, Thomas Müller, Kei Murayama, Emanuele Nicastro, Alessandra Pennisi, Heidi Peters, Dorota Piekutowska-Abramczuk, Agnès Rötig, René Santer, Fernando Scaglia, Manuel Schiff, Mohmmad Shagrani, Mark Sharrard, Claudia Soler-Alfonso, Christian Staufner, Imogen Storey, Michael Stormon, Robert W Taylor, David R Thorburn, Elisa Leao Teles, Jian-She Wang, Daniel Weghuber, Saskia Wortmann

Faculty, Staff and Students Publications

Purpose: This study aimed to define the genotypic and phenotypic spectrum of reversible acute liver failure (ALF) of infancy resulting from biallelic pathogenic TRMU variants and determine the role of cysteine supplementation in its treatment.

Methods: Individuals with biallelic (likely) pathogenic variants in TRMU were studied within an international retrospective collection of de-identified patient data.

Results: In 62 individuals, including 30 previously unreported cases, we described 47 (likely) pathogenic TRMU variants, of which 17 were novel, and 1 intragenic deletion. Of these 62 individuals, 42 were alive at a median age of 6.8 (0.6-22) years after a median follow-up of …

Association Of Area Deprivation Index With Severity Of Covid-19 In Pediatric Patients: A Multisite Study Of Racially And Ethnically Diverse Children, Sebastian Acosta, Srinivasan Suresh, Anna K Ettinger, Fabio Savorgnan, Ananth Annapragada, Nirupama Kannikeswaran, Usha Sethuraman

Faculty, Staff and Students Publications

Area deprivation index (ADI) is associated with the risk of severe COVID-19 in adults. However, this association has not been established in children. Information on ADI, demographics, clinical features, disease severity, and outcomes was analyzed for 3434 children with COVID-19. A multivariate logistic regression revealed that non-Hispanic Asians, extremes of weight, and higher ADI were associated with severe disease.

Tumour Infiltrating Lymphocytes (Tils) And Immune Composition In Breast Cancer Patients From Kenya: Spatial Distributions And Associations With Risk Factors And Tumour Characteristics, Shahin Sayed, Hela Koka, Mustapha Abubakar, Kevin Gardner, Roberto Salgado, Zahir Moloo, Ambar Beatriz Caban-Ureña, Daniel Rosen, Patricia Castro, Mansoor Saleh, Asim Jamal Shaikh, Jasmit Shah, Jonine Figueroa, Francis Makokha, Hien Khanh Ha, Zhong Wang, Pumza Magangane, Richard Naidoo, Veronica Ngundo, Xiaohong Rose Yang, Dhirendra Govender

Faculty, Staff and Students Publications

Background: The immune landscape of breast cancer (BC) in patients from Sub Saharan Africa is understudied. Our aims were to describe the distribution of Tumour Infiltrating Lymphocytes (TILs) within the intratumoural stroma (sTILs) and the leading/invasive edge stroma (LE-TILs), and to evaluate TILs across BC subtypes with established risk factors and clinical characteristics in Kenyan women.

Methods: Visual quantification of sTILs and LE-TILs were performed on Haematoxylin and eosin -stained pathologically confirmed BC cases based on the International TIL working group guidelines. Tissue Microarrays were constructed and stained with immunohistochemistry (IHC) for CD3, CD4, CD8, CD68, CD20, and FOXP3. Linear …

Magnesium Increases Numbers Of Foxp3+ Treg Cells And Reduces Arthritis Severity And Joint Damage In An Il-10-Dependent Manner Mediated By The Intestinal Microbiome, Teresina Laragione, Carolyn Harris, Nasim Azizgolshani, Christine Beeton, Gerold Bongers, Percio S Gulko

Faculty, Staff and Students Publications

BACKGROUND: Rheumatoid arthritis (RA) is a common autoimmune disease with emerging environmental and microbiome risk factors. The western diet is typically deficient in magnesium (Mg), and there is some evidence suggesting that Mg may have anti-inflammatory properties. But the actual role of Mg supplementation in arthritis or in T cell subsets has not been explored.

METHODS: We investigated the role of a high Mg diet in two different mouse models of RA induced with the KRN serum, and collagen-induced arthritis. We also characterized the phenotypes of splenocytes, gene expression, and an extensive intestinal microbiome analyses including fecal material transplantation (FMT). …

Forging New Therapeutic Targets: Efforts Of Tumor Derived Exosomes To Prepare The Pre-Metastatic Niche For Cancer Cell Dissemination And Dormancy, Ranvir Bhatia, Joanna Chang, Jessian L Munoz, Nykia D Walker

Faculty, Staff and Students Publications

Tumor-derived exosomes play a multifaceted role in preparing the pre-metastatic niche, promoting cancer dissemination, and regulating cancer cell dormancy. A brief review of three types of cells implicated in metastasis and an overview of other types of extracellular vesicles related to metastasis are described. A central focus of this review is on how exosomes influence cancer progression throughout metastatic disease. Exosomes are crucial mediators of intercellular communication by transferring their cargo to recipient cells, modulating their behavior, and promoting tumor pro-gression. First, their functional role in cancer cell dissemination in the peripheral blood by facilitating the establishment of a pro-angiogenic …

Alterations In The Circulating Proteome Associated With Albuminuria, Elizabeth Kiernan, Aditya Surapaneni, Linda Zhou, Pascal Schlosser, Keenan A Walker, Eugene P Rhee, Christie M Ballantyne, Rajat Deo, Ruth F Dubin, Peter Ganz, Josef Coresh, Morgan E Grams

Faculty, Staff and Students Publications

Significance statement: We describe circulating proteins associated with albuminuria in a population of African American Study of Kidney Disease and Hypertension with CKD (AASK) using the largest proteomic platform to date: nearly 7000 circulating proteins, representing approximately 2000 new targets. Findings were replicated in a subset of a general population cohort with kidney disease (ARIC) and a population with CKD Chronic Renal Insufficiency Cohort (CRIC). In cross-sectional analysis, 104 proteins were significantly associated with albuminuria in the Black group, of which 67 of 77 available proteins were replicated in ARIC and 68 of 71 available proteins in CRIC. LMAN2, TNFSFR1B, …

Behavioral And Biologic Characteristics Of Cancer-Related Cognitive Impairment Biotypes, Michele M Mulholland, Sarah Prinsloo, Elizabeth Kvale, Adrienne N Dula, Oxana Palesh, Shelli R Kesler

Faculty, Staff and Students Publications

Psychiatric diagnosis is moving away from symptom-based classification and towards multi-dimensional, biologically-based characterization, or biotyping. We previously identified three biotypes of chemotherapy-related cognitive impairment based on functional brain connectivity. In this follow-up study of 80 chemotherapy-treated breast cancer survivors and 80 non-cancer controls, we evaluated additional factors to help explain biotype expression: neurofunctional stability, brain age, apolipoprotein (APOE) genotype, and psychoneurologic symptoms. We also compared the discriminative ability of a traditional, symptom-based cognitive impairment definition with that of biotypes. We found significant differences in cortical brain age (F = 10.50, p <  0.001), neurofunctional stability (F = 2.83, p = 0.041), APOE e4 genotype (X2 = 7.68, p = 0.050), and psychoneurological symptoms (Pillai = 0.378, p <  0.001) across the three biotypes. The more resilient Biotype 2 demonstrated significantly higher neurofunctional stability compared to the other biotypes. Symptom-based classification of cognitive impairment did not differentiate biologic or other behavioral variables, suggesting that traditional categorization of cancer-related cognitive effects may miss important characteristics which could inform targeted treatment strategies. Additionally, biotyping, but not symptom-typing, was able to distinguish survivors with cognitive versus psychological effects. Our results suggest that Biotype 1 survivors might benefit from first addressing symptoms of anxiety and fatigue, Biotype 3 might benefit from a treatment plan which includes sleep hygiene, and Biotype 2 might benefit most from cognitive skills training or rehabilitation. Future research should include additional demographic and clinical information to further investigate biotype expression related to risk and resilience and examine integration of more clinically feasible imaging approaches.

Comprehensive Ecg Reference Intervals In C57bl/6n Substrains Provide A Generalizable Guide For Cardiac Electrophysiology Studies In Mice, Manuela A Oestereicher, Janine M Wotton, Shinya Ayabe, Ghina Bou About, Tsz Kwan Cheng, Jae-Hoon Choi, Dave Clary, Emily M Dew, Lahcen Elfertak, Alain Guimond, Hamed Haseli Mashhadi, Jason D Heaney, Lois Kelsey, Piia Keskivali-Bond, Federico Lopez Gomez, Susan Marschall, Michael Mcfarland, Hamid Meziane, Violeta Munoz Fuentes, Ki-Hoan Nam, Zuzana Nichtová, Dale Pimm, Lynette Bower, Jan Prochazka, Jan Rozman, Luis Santos, Michelle Stewart, Nobuhiko Tanaka, Christopher S Ward, Amelia M E Willett, Robert Wilson, Robert E Braun, Mary E Dickinson, Ann M Flenniken, Yann Herault, K C Kent Lloyd, Ann-Marie Mallon, Colin Mckerlie, Stephen A Murray, Lauryl M J Nutter, Radislav Sedlacek, Je Kyung Seong, Tania Sorg, Masaru Tamura, Sara Wells, Elida Schneltzer, Helmut Fuchs, Valerie Gailus-Durner, Martin Hrabe De Angelis, Jacqueline K White, Nadine Spielmann

Faculty, Staff and Students Publications

Reference ranges provide a powerful tool for diagnostic decision-making in clinical medicine and are enormously valuable for understanding normality in pre-clinical scientific research that uses in vivo models. As yet, there are no published reference ranges for electrocardiography (ECG) in the laboratory mouse. The first mouse-specific reference ranges for the assessment of electrical conduction are reported herein generated from an ECG dataset of unprecedented scale. International Mouse Phenotyping Consortium data from over 26,000 conscious or anesthetized C57BL/6N wildtype control mice were stratified by sex and age to develop robust ECG reference ranges. Interesting findings include that heart rate and key …

Three-Dimensional Microct Imaging Of Mouse Heart Development From Early Post-Implantation To Late Fetal Stages, Nanbing Li-Villarreal, Tara L Rasmussen, Audrey E Christiansen, Mary E Dickinson, Chih-Wei Hsu

Faculty, Staff and Students Publications

Comprehensive detailed characterization of new mouse models can be challenging due to the individual focus involved in developing these models. Often models are engineered to test a specific hypothesis in a limited number of tissues, stages, and/or other contexts. Whether or not the model produces the desired phenotypes, phenotyping beyond the desired context can be extremely work intensive and these studies are often not undertaken. However, the general information resulting from broader phenotyping can be invaluable to the wider scientific community. The International Mouse Phenotyping Consortium (IMPC) and its subsidiaries, like the Knockout Mouse Project (KOMP), has made great strides …

Mouse Models Of Spontaneous Atrial Fibrillation, Joshua A Keefe, Mohit M Hulsurkar, Svetlana Reilly, Xander H T Wehrens

Faculty, Staff and Students Publications

Atrial fibrillation (AF) is the most common arrhythmia in adults, with a prevalence increasing with age. Current clinical management of AF is focused on tertiary prevention (i.e., treating the symptoms and sequelae) rather than addressing the underlying molecular pathophysiology. Robust animal models of AF, particularly those that do not require supraphysiologic stimuli to induce AF (i.e., showing spontaneous AF), enable studies that can uncover the underlying mechanisms of AF. Several mouse models of AF have been described to exhibit spontaneous AF, but pathophysiologic drivers of AF differ among models. Here, we describe relevant AF mechanisms and provide an overview of …

Beyond Diversity And Inclusion: Developing A Research Agenda For Anti-Racism In Emergency Medicine Education, Edgardo Ordonez, Cassandra Bradby, Jennifer Carey, Sanjey Gupta, Katherine M Hiller, Danielle Miller, Ava Pierce, Kathryn Wiesendanger, Shannon Moffett

Faculty, Staff and Students Publications

BACKGROUND: Addressing racism in emergency medicine education is vital for providing optimal training and assessment of physicians in the specialty, developing physicians with the skills necessary to advocate for their patients, and recruiting and retaining a diverse group of physicians. To form a prioritized research agenda, the Society of Academic Emergency Medicine (SAEM) conducted a consensus conference at the annual meeting in May 2022 on addressing racism in emergency medicine, which included a subgroup on education.

METHODS: The education workgroup worked on summarizing the current literature on addressing racism in emergency medicine education, identifying critical knowledge gaps, and creating a …

Genetic Studies Of Paired Metabolomes Reveal Enzymatic And Transport Processes At The Interface Of Plasma And Urine, Pascal Schlosser, Nora Scherer, Franziska Grundner-Culemann, Sara Monteiro-Martins, Stefan Haug, Inga Steinbrenner, Burulça Uluvar, Matthias Wuttke, Yurong Cheng, Arif B Ekici, Gergely Gyimesi, Edward D Karoly, Fruzsina Kotsis, Johanna Mielke, Maria F Gomez, Bing Yu, Morgan E Grams, Josef Coresh, Eric Boerwinkle, Michael Köttgen, Florian Kronenberg, Heike Meiselbach, Robert P Mohney, Shreeram Akilesh, Gckd Investigators, Miriam Schmidts, Matthias A Hediger, Ulla T Schultheiss, Kai-Uwe Eckardt, Peter J Oefner, Peggy Sekula, Yong Li, Anna Köttgen

Faculty, Staff and Students Publications

The kidneys operate at the interface of plasma and urine by clearing molecular waste products while retaining valuable solutes. Genetic studies of paired plasma and urine metabolomes may identify underlying processes. We conducted genome-wide studies of 1,916 plasma and urine metabolites and detected 1,299 significant associations. Associations with 40% of implicated metabolites would have been missed by studying plasma alone. We detected urine-specific findings that provide information about metabolite reabsorption in the kidney, such as aquaporin (AQP)-7-mediated glycerol transport, and different metabolomic footprints of kidney-expressed proteins in plasma and urine that are consistent with their localization and function, including the …

Physiological Age By Artificial Intelligence-Enhanced Electrocardiograms As A Novel Risk Factor Of Mortality In Kidney Transplant Candidates, Elizabeth C Lorenz, Isabella Zaniletti, Bradley K Johnson, Tanya M Petterson, Walter K Kremers, Carrie A Schinstock, Hatem Amer, Andrea L Cheville, Nathan K Lebrasseur, Wolfgang C Winkelmayer, Sankar D Navaneethan, Abraham Baez-Suarez, Zachi I Attia, Francisco Lopez-Jimenez, Paul A Friedman, Cassie C Kennedy, Andrew D Rule

Faculty, Staff and Students Publications

BACKGROUND: Mortality risk assessment before kidney transplantation (KT) is imperfect. An emerging risk factor for death in nontransplant populations is physiological age as determined by the application of artificial intelligence to the electrocardiogram (ECG). The aim of this study was to examine the relationship between ECG age and KT waitlist mortality.

METHODS: We applied a previously developed convolutional neural network to the ECGs of KT candidates evaluated 2014 to 2019 to determine ECG age. We used a Cox proportional hazard model to examine whether ECG age was associated with waitlist mortality.

RESULTS: Of the 2183 patients evaluated, 59.1% were male, …

A Short-Term Method To Evaluate Anti-Leishmania Drugs By Inhibition Of Stage Differentiation In Leishmania Mexicana Using Flow Cytometry, Christian Florian Teh-Poot, Victor Manuel Dzul-Huchim, Jonathan M Mercado, Liliana Estefanía Villanueva-Lizama, Maria Elena Bottazzi, Kathryn M Jones, Francis T F Tsai, Julio Vladimir Cruz-Chan

Faculty, Staff and Students Publications

Leishmaniasis is a vector-borne neglected tropical disease caused by the Leishmania spp. Parasite. The disease is transmitted to humans and animals by the bite of infected female sandflies during the ingestion of bloodmeal. Because current drug treatments induce toxicity and parasite resistance, there is an urgent need to evaluate new drugs. Most therapeutics target the differentiation of promastigotes to amastigotes, which is necessary to maintain Leishmania infection. However, in vitro assays are laborious, time-consuming, and depend on the experience of the technician. In this study, we aimed to establish a short-term method to assess the differentiation status of Leishmania mexicana …

Long Non-Coding Rnas: Definitions, Functions, Challenges And Recommendations, John S Mattick, Paulo P Amaral, Piero Carninci, Susan Carpenter, Howard Y Chang, Ling-Ling Chen, Runsheng Chen, Caroline Dean, Marcel E Dinger, Katherine A Fitzgerald, Thomas R Gingeras, Mitchell Guttman, Tetsuro Hirose, Maite Huarte, Rory Johnson, Chandrasekhar Kanduri, Philipp Kapranov, Jeanne B Lawrence, Jeannie T Lee, Joshua T Mendell, Timothy R Mercer, Kathryn J Moore, Shinichi Nakagawa, John L Rinn, David L Spector, Igor Ulitsky, Yue Wan, Jeremy E Wilusz, Mian Wu

Faculty, Staff and Students Publications

Genes specifying long non-coding RNAs (lncRNAs) occupy a large fraction of the genomes of complex organisms. The term 'lncRNAs' encompasses RNA polymerase I (Pol I), Pol II and Pol III transcribed RNAs, and RNAs from processed introns. The various functions of lncRNAs and their many isoforms and interleaved relationships with other genes make lncRNA classification and annotation difficult. Most lncRNAs evolve more rapidly than protein-coding sequences, are cell type specific and regulate many aspects of cell differentiation and development and other physiological processes. Many lncRNAs associate with chromatin-modifying complexes, are transcribed from enhancers and nucleate phase separation of nuclear condensates …

Dementias Among Older Males And Females In The U.S. Medicare System With And Without Hiv, Xiaoying Yu, Yong-Fang Kuo, Mukaila A Raji, Abbey B Berenson, Jacques Baillargeon, Thomas P Giordano

Faculty, Staff and Students Publications

Background: Despite the growing concern that people with HIV (PWH) will experience a disproportionate burden of dementia as they age, very few studies have examined the sex-specific prevalence of dementia, including Alzheimer disease and related dementias (AD/ADRD) among older PWH versus people without HIV (PWOH) using large national samples.

Methods: We constructed successive cross-sectional cohorts including all PWH aged 65+ years from U.S. Medicare enrollees and PWOH in a 5% national sample of Medicare data from 2007 to 2019. All AD/ADRD cases were identified by ICD-9-CM/ICD-10-CM diagnosis codes. Prevalence of AD/ADRD was calculated for each calendar year by sex-age strata. …

Splendid Isolation, Dimitrios Laurin Wagner, Maksim Mamonkin

Faculty, Staff and Students Publications

No abstract provided.

Synapse-Specific Changes In Arc And Bdnf In Rat Hippocampus Following Chronic Temporal Lobe Epilepsy, Daniel L Egbenya, Suleman Hussain, Yi-Chen Lai, Anne E Anderson, Svend Davanger

Faculty, Staff and Students Publications

Expression of immediate early genes (IEGs) in the brain is important for synaptic plasticity, and probably also in neurodegenerative conditions. To understand the cellular mechanisms of the underlying neuropathophysiological processes in epilepsy, we need to pinpoint changes in concentration of synaptic plasticity-related proteins at subsynaptic levels. In this study, we examined changes in synaptic expression of Activity-regulated cytoskeleton-associated (Arc) and Brai Derived Neurotrophic Factor (BDNF) in a rat model of kainate-induced temporal lobe epilepsy (TLE). Western blotting showed reduced concentrations of Arc and increased concentrations of BDNF in hippocampal synaptosomes in chronic TLE rats. Then, using quantitative electron microscopy, we …

A Scalable Platform For Fabricating Biodegradable Microparticles With Pulsatile Drug Release, Tyler P Graf, Sherry Yue Qiu, Dhruv Varshney, Mei-Li Laracuente, Erin M Euliano, Pujita Munnangi, Brett H Pogostin, Tsvetelina Baryakova, Arnav Garyali, Kevin J Mchugh

Faculty, Staff and Students Publications

Pulsatile drug delivery systems have the potential to improve patient adherence and therapeutic efficacy by providing a sequence of doses in a single injection. Herein, a novel platform, termed Particles Uniformly Liquified and Sealed to Encapsulate Drugs (PULSED) is developed, which enables the high-throughput fabrication of microparticles exhibiting pulsatile release. In PULSED, biodegradable polymeric microstructures with an open cavity are formed using high-resolution 3D printing and soft lithography, filled with drug, and sealed using a contactless heating step in which the polymer flows over the orifice to form a complete shell around a drug-loaded core. Poly(lactic-co-glycolic acid) particles with this …

Functional Response To A Microbial Synbiotic In The Gastrointestinal System Of Children: A Randomized Clinical Trial, Braden T Tierney, James Versalovic, Alessio Fasano, Joseph F Petrosino, Bruno P Chumpitazi, Emeran A Mayer, Jared Boetes, Gerard Smits, Shanthi G Parkar, Noah Voreades, Ece Kartal, Gabriel A Al-Ghalith, Marco Pane, Peter A Bron, Gregor Reid, Raja Dhir, Christopher E Mason

Faculty, Staff and Students Publications

BACKGROUND: Oral microbial therapy has been studied as an intervention for a range of gastrointestinal disorders. Though research suggests that microbial exposure may affect the gastrointestinal system, motility, and host immunity in a pediatric population, data have been inconsistent, with most prior studies being in neither a randomized nor placebo-controlled setting. The aim of this randomized, placebo-controlled study was to evaluate the efficacy of a synbiotic on increasing weekly bowel movements (WBMs) in constipated children.

METHODS: Sixty-four children (3-17 years of age) were randomized to receive a synbiotic (n = 33) comprising mixed-chain length oligosaccharides and nine microbial strains, or …

Clinical Spectrum And Genetic Causes Of Mitochondrial Hepatopathy Phenotype In Children, James E Squires, Alexander G Miethke, C Alexander Valencia, Kieran Hawthorne, Lisa Henn, Johan L K Van Hove, Robert H Squires, Kevin Bove, Simon Horslen, Rohit Kohli, Jean P Molleston, Rene Romero, Estella M Alonso, Jorge A Bezerra, Stephen L Guthery, Evelyn Hsu, Saul J Karpen, Kathleen M Loomes, Vicky L Ng, Philip Rosenthal, Krupa Mysore, Kasper S Wang, Marisa W Friederich, John C Magee, Ronald J Sokol, Childhood Liver Disease Research Network (Children)

Faculty, Staff and Students Publications

BACKGROUND: Alterations in both mitochondrial DNA (mtDNA) and nuclear DNA genes affect mitochondria function, causing a range of liver-based conditions termed mitochondrial hepatopathies (MH), which are subcategorized as mtDNA depletion, RNA translation, mtDNA deletion, and enzymatic disorders. We aim to enhance the understanding of pathogenesis and natural history of MH.

METHODS: We analyzed data from patients with MH phenotypes to identify genetic causes, characterize the spectrum of clinical presentation, and determine outcomes.

RESULTS: Three enrollment phenotypes, that is, acute liver failure (ALF, n = 37), chronic liver disease (Chronic, n = 40), and post-liver transplant (n = 9), were analyzed. …

Conjugated Bile Acids Are Nutritionally Re-Programmable Antihypertensive Metabolites, Saroj Chakraborty, Anju Lulla, Xi Cheng, Ji-Youn Yeo, Juthika Mandal, Tao Yang, Xue Mei, Piu Saha, Rachel M Golonka, Beng San Yeoh, Blair Mell, Wei Jia, Vasanta Putluri, Danthasinghe Waduge Badrajee Piyarathna, Nagireddy Putluri, Arun Sreekumar, Katie Meyer, Matam Vijay-Kumar, Bina Joe

Faculty, Staff and Students Publications

BACKGROUND: Hypertension is the largest risk factor affecting global mortality. Despite available medications, uncontrolled hypertension is on the rise, whereby there is an urgent need to develop novel and sustainable therapeutics. Because gut microbiota is now recognized as an important entity in blood pressure regulation, one such new avenue is to target the gut-liver axis wherein metabolites are transacted via host-microbiota interactions. Knowledge on which metabolites within the gut-liver axis regulate blood pressure is largely unknown.

METHOD: To address this, we analyzed bile acid profiles of human, hypertensive and germ-free rat models and report that conjugated bile acids are inversely …

Bi-Allelic Variants In Hmgcr Cause An Autosomal-Recessive Progressive Limb-Girdle Muscular Dystrophy, Joel A Morales-Rosado, Tanya L Schwab, Sarah K Macklin-Mantia, A Reghan Foley, Filippo Pinto E Vairo, Davut Pehlivan, Sandra Donkervoort, Jill A Rosenfeld, Grace E Boyum, Ying Hu, Anh T Q Cong, Timothy E Lotze, Carrie A Mohila, Dimah Saade, Diana Bharucha-Goebel, Katherine R Chao, Christopher Grunseich, Christine C Bruels, Hannah R Littel, Elicia A Estrella, Lynn Pais, Peter B Kang, Michael T Zimmermann, James R Lupski, Brendan Lee, Matthew J Schellenberg, Karl J Clark, Klaas J Wierenga, Carsten G Bönnemann, Eric W Klee

Faculty, Staff and Students Publications

Statins are a mainstay intervention for cardiovascular disease prevention, yet their use can cause rare severe myopathy. HMG-CoA reductase, an essential enzyme in the mevalonate pathway, is the target of statins. We identified nine individuals from five unrelated families with unexplained limb-girdle like muscular dystrophy and bi-allelic variants in HMGCR via clinical and research exome sequencing. The clinical features resembled other genetic causes of muscular dystrophy with incidental high CPK levels (>1,000 U/L), proximal muscle weakness, variable age of onset, and progression leading to impaired ambulation. Muscle biopsies in most affected individuals showed non-specific dystrophic changes with non-diagnostic immunohistochemistry. …

Discordant Calls Across Genotype Discovery Approaches Elucidate Variants With Systematic Errors, Elizabeth G Atkinson, Mykyta Artomov, Alexander A Loboda, Heidi L Rehm, Daniel G Macarthur, Konrad J Karczewski, Benjamin M Neale, Mark J Daly

Faculty, Staff and Students Publications

Large-scale high-throughput sequencing data sets have been transformative for informing clinical variant interpretation and for use as reference panels for statistical and population genetic efforts. Although such resources are often treated as ground truth, we find that in widely used reference data sets such as the Genome Aggregation Database (gnomAD), some variants pass gold-standard filters, yet are systematically different in their genotype calls across genotype discovery approaches. The inclusion of such discordant sites in study designs involving multiple genotype discovery strategies could bias results and lead to false-positive hits in association studies owing to technological artifacts rather than a true …

The Voltage-Gated Sodium Channel In Drosophila, Para, Localizes To Dendrites As Well As Axons In Mechanosensitive Chordotonal Neurons, Thomas A Ravenscroft, Ashleigh Jacobs, Mingxue Gu, Daniel F Eberl, Hugo J Bellen

Faculty, Staff and Students Publications

The fruit fly Drosophila melanogaster has provided important insights into how sensory information is transduced by transient receptor potential (TRP) channels in the peripheral nervous system (PNS). However, TRP channels alone have not been able to completely model mechanosensitive transduction in mechanoreceptive chordotonal neurons (CNs). Here, we show that, in addition to TRP channels, the sole voltage-gated sodium channel (NaV) in Drosophila, Para, is localized to the dendrites of CNs. Para is localized to the distal tip of the dendrites in all CNs, from embryos to adults, and is colocalized with the mechanosensitive TRP channels No mechanoreceptor potential C …

Snv/Indel Hypermutator Phenotype In Biallelic Rad51c Variant: Fanconi Anemia, Roni Zemet, Haowei Du, Tomasz Gambin, James R Lupski, Pengfei Liu, Paweł Stankiewicz

Faculty, Staff and Students Publications

We previously reported a fetus with Fanconi anemia (FA), complementation group O due to compound heterozygous variants involving RAD51C. Interestingly, the trio exome sequencing analysis also detected eight apparent de novo mosaic variants with variant allele fraction (VAF) ranging between 11.5 and 37%. Here, using whole genome sequencing and a 'home-brew' variant filtering pipeline and DeepMosaic module, we investigated the number and signature of de novo heterozygous and mosaic variants and the hypothesis of a rare phenomenon of hypermutation. Eight-hundred-thirty apparent de novo SNVs and 21 de novo indels had VAFs below 37.41% and were considered postzygotic somatic mosaic variants. …

The Nanoflow Repository, Jessie E Arce, Joshua A Welsh, Sean Cook, John Tigges, Ionita Ghiran, Jennifer C Jones, Andrew Jackson, Matthew Roth, Aleksandar Milosavljevic

Faculty, Staff and Students Publications

Motivation

Extracellular particles (EPs) are the focus of a rapidly growing area of exploration due to the widespread interest in understanding their roles in health and disease. However, despite the general need for EP data sharing and established community standards for data reporting, no standard repository for EP flow cytometry data captures rigor and minimum reporting standards such as those defined by MIFlowCyt-EV (https://doi.org/10.1080/20013078.2020.1713526). We sought to address this unmet need by developing the NanoFlow Repository.

Results

We have developed The NanoFlow Repository to provide the first implementation of the MIFlowCyt-EV framework.

Availability and implementation

The NanoFlow Repository …