Digital Commons Network^™

High-Throughput Deconvolution Of 3d Organoid Dynamics At Cellular Resolution For Cancer Pharmacology With Cellos., Patience Mukashyaka, Pooja A Kumar, David J Mellert, Shadae Nicholas, Javad Noorbakhsh, Mattia Brugiolo, Elise T Courtois, Olga Anczuków, Edison Liu, Jeffrey Chuang

Faculty Research 2023

Three-dimensional (3D) organoid cultures are flexible systems to interrogate cellular growth, morphology, multicellular spatial architecture, and cellular interactions in response to treatment. However, computational methods for analysis of 3D organoids with sufficiently high-throughput and cellular resolution are needed. Here we report Cellos, an accurate, high-throughput pipeline for 3D organoid segmentation using classical algorithms and nuclear segmentation using a trained Stardist-3D convolutional neural network. To evaluate Cellos, we analyze ~100,000 organoids with ~2.35 million cells from multiple treatment experiments. Cellos segments dye-stained or fluorescently-labeled nuclei and accurately distinguishes distinct labeled cell populations within organoids. Cellos can recapitulate traditional luminescence-based drug response …

Combining The Tyrosine Kinase Inhibitor Cabozantinib And The Mtorc1/2 Inhibitor Sapanisertib Blocks Erk Pathway Activity And Suppresses Tumor Growth In Renal Cell Carcinoma., Yige Wu, Siqi Chen, Xiaolu Yang, Kazuhito Sato, Preet Lal, Yuefan Wang, Andrew T Shinkle, Michael C Wendl, Tina M Primeau, Yanyan Zhao, Alanna Gould, Hua Sun, Jacqueline L Mudd, Jeremy Hoog, R Jay Mashl, Matthew A Wyczalkowski, Chia-Kuei Mo, Ruiyang Liu, John M Herndon, Sherri R Davies, Di Liu, Xi Ding, Yvonne A Evrard, Bryan E Welm, David Lum, Mei Yee Koh, Alana L Welm, Jeffrey Chuang, Jeffrey A Moscow, Funda Meric-Bernstam, Ramaswamy Govindan, Shunqiang Li, James Hsieh, Ryan C Fields, Kian-Huat Lim, Cynthia X Ma, Hui Zhang, Li Ding, Feng Chen

Faculty Research 2023

UNLABELLED: Current treatment approaches for renal cell carcinoma (RCC) face challenges in achieving durable tumor responses due to tumor heterogeneity and drug resistance. Combination therapies that leverage tumor molecular profiles could offer an avenue for enhancing treatment efficacy and addressing the limitations of current therapies. To identify effective strategies for treating RCC, we selected ten drugs guided by tumor biology to test in six RCC patient-derived xenograft (PDX) models. The multitargeted tyrosine kinase inhibitor (TKI) cabozantinib and mTORC1/2 inhibitor sapanisertib emerged as the most effective drugs, particularly when combined. The combination demonstrated favorable tolerability and inhibited tumor growth or induced …

The Medical Action Ontology: A Tool For Annotating And Analyzing Treatments And Clinical Management Of Human Disease., Leigh Carmody, Michael Gargano, Sabrina Toro, Nicole A Vasilevsky, Margaret P Adam, Hannah Blau, Lauren E Chan, David Gomez-Andres, Rita Horvath, Megan L Kraus, Markus S Ladewig, David Lewis-Smith, Hanns Lochmüller, Nicolas A Matentzoglu, Monica C Munoz-Torres, Catharina Schuetz, Berthold Seitz, Morgan N Similuk, Teresa N Sparks, Timmy Strauss, Emilia M Swietlik, Rachel Thompson, Xingmin Aaron Zhang, Christopher J Mungall, Melissa A Haendel, Peter N Robinson

Faculty Research 2023

BACKGROUND: Navigating the clinical literature to determine the optimal clinical management for rare diseases presents significant challenges. We introduce the Medical Action Ontology (MAxO), an ontology specifically designed to organize medical procedures, therapies, and interventions.

METHODS: MAxO incorporates logical structures that link MAxO terms to numerous other ontologies within the OBO Foundry. Term development involves a blend of manual and semi-automated processes. Additionally, we have generated annotations detailing diagnostic modalities for specific phenotypic abnormalities defined by the Human Phenotype Ontology (HPO). We introduce a web application, POET, that facilitates MAxO annotations for specific medical actions for diseases using the Mondo …

Deletion Of Vβ3, Cheng Ye, Sadie A Clements, Weihong Gu, Aron M Geurts, Clayton E Mathews, David V. Serreze, Yi-Guang Chen, John P Driver

Faculty Research 2023

In both humans and NOD mice, type 1 diabetes (T1D) develops from the autoimmune destruction of pancreatic beta cells by T cells. Interactions between both helper CD4

Young Infants Display Heterogeneous Serological Responses And Extensive But Reversible Transcriptional Changes Following Initial Immunizations., Nima Nouri, Raquel Giacomelli Cao, Eleonora Bunsow, Djamel Nehar-Belaid, Radu Marches, Zhaohui Xu, Bennett Smith, Santtu Heinonen, Sara Mertz, Amy Leber, Gaby Smits, Fiona Van Der Klis, Asunción Mejías, Jacques Banchereau, Virginia Pascual, Octavio Ramilo

Faculty Research 2023

Infants necessitate vaccinations to prevent life-threatening infections. Our understanding of the infant immune responses to routine vaccines remains limited. We analyzed two cohorts of 2-month-old infants before vaccination, one week, and one-month post-vaccination. We report remarkable hetero- geneity but limited antibody responses to the different antigens. Whole-blood transcriptome analysis in an initial cohort showed marked overexpression of interferon-stimulated genes (ISGs) and to a lesser extent of inflammation- genes at day 7, which normalized one month post-vaccination. Single-cell RNA sequencing in peripheral blood mononuclear cells from a second cohort identified at baseline a predominantly naive immune landscape including ISGhi cells. On …

Systematic Evaluation Of Aml-Associated Antigens Identifies Anti-U5 Snrnp200 Therapeutic Antibodies For The Treatment Of Acute Myeloid Leukemia., Katherine Knorr, Jahan Rahman, Caroline Erickson, Eric Wang, Mara Monetti, Zhuoning Li, Juliana Ortiz-Pacheco, Andrew Jones, Sydney X Lu, Robert F Stanley, Maria Baez, Nina Fox, Cynthia Castro, Alessandra E Marino, Caroline Jiang, Alex Penson, Simon J Hogg, Xiaoli Mi, Hideaki Nakajima, Hiroyoshi Kunimoto, Koutarou Nishimura, Daichi Inoue, Benjamin Greenbaum, David Knorr, Jeffrey Ravetch, Omar Abdel-Wahab

Faculty Research 2023

Despite recent advances in the treatment of acute myeloid leukemia (AML), there has been limited success in targeting surface antigens in AML, in part due to shared expression across malignant and normal cells. Here, high-density immunophenotyping of AML coupled with proteogenomics identified unique expression of a variety of antigens, including the RNA helicase U5 snRNP200, on the surface of AML cells but not on normal hematopoietic precursors and skewed Fc receptor distribution in the AML immune microenvironment. Cell membrane localization of U5 snRNP200 was linked to surface expression of the Fcγ receptor IIIA (FcγIIIA, also known as CD32A) and correlated …

Term-Blast-Like Alignment Tool For Concept Recognition In Noisy Clinical Texts., Tudor Groza, Honghan Wu, Marcel E Dinger, Daniel Danis, Coleman Hilton, Anita Bagley, Jon R Davids, Ling Luo, Zhiyong Lu, Peter N Robinson

Faculty Research 2023

MOTIVATION: Methods for concept recognition (CR) in clinical texts have largely been tested on abstracts or articles from the medical literature. However, texts from electronic health records (EHRs) frequently contain spelling errors, abbreviations, and other nonstandard ways of representing clinical concepts.

RESULTS: Here, we present a method inspired by the BLAST algorithm for biosequence alignment that screens texts for potential matches on the basis of matching k-mer counts and scores candidates based on conformance to typical patterns of spelling errors derived from 2.9 million clinical notes. Our method, the Term-BLAST-like alignment tool (TBLAT) leverages a gold standard corpus for typographical …

Generation Of Four Gene-Edited Human Induced Pluripotent Stem Cell Lines With Mutations In The Atm Gene To Model Ataxia-Telangiectasia., Wasifa Nurieva, Elena Ivanova, Sanabel Chehab, Parth Singh, Marina Reichlmeir, Karoly Szuhai, Georg W J Auburger, William C Skarnes, Zoltán Ivics

Faculty Research 2023

Ataxia-Telangiectasia (A-T) is an autosomal recessive multi-system disorder caused by mutations in the ataxia-telangiectasia mutated (ATM) gene, resulting, among other symptoms, in neurological dysfunction. ATM is known to be a master controller of signal transduction for DNA damage response, with additional functions that are poorly understood. CRISPR/Cas9 technology was used to introduce biallelic mutations at selected sites of the ATM gene in human induced pluripotent stem cells (hiPSCs). This panel of hiPSCs with nonsense and missense mutations in ATM can help understand the molecular basis of A-T.

The Alliance Of Genome Resources: Transforming Comparative Genomics., Carol J Bult, Paul W Sternberg

Faculty Research 2023

Comparing genomic and biological characteristics across multiple species is essential to using model systems to investigate the molecular and cellular mechanisms underlying human biology and disease and to translate mechanistic insights from studies in model organisms for clinical applications. Building a scalable knowledge commons platform that supports cross-species comparison of rich, expertly curated knowledge regarding gene function, phenotype, and disease associations available for model organisms and humans is the primary mission of the Alliance of Genome Resources (the Alliance). The Alliance is a consortium of seven model organism knowledgebases (mouse, rat, yeast, nematode, zebrafish, frog, fruit fly) and the Gene …

Aging And Urinary Control: Alterations In The Brain-Bladder Axis., Cara C Hardy, Ron Korstanje

Faculty Research 2023

Age-associated alterations in bladder control affect millions of older adults, with a heavy burden added to families both economically and in quality of life. Therapeutic options are limited with poor efficacy in older adults, lending to a growing need to address the gaps in our current understanding of urinary tract aging. This review summarizes the current knowledge of age-associated alterations in the structure and function of the brain-bladder axis and identifies important gaps in the field that have yet to be addressed. Urinary aging is associated with decreased tissue responsiveness, decreased control over the voiding reflex, signaling dysfunction along the …

Discovery Of Ferm Domain Protein-Protein Interaction Inhibitors For Msn And Cd44 As A Potential Therapeutic Approach For Alzheimer's Disease., Yuhong Du, William J Bradshaw, Tina M Leisner, Joel K Annor-Gyamfi, Kun Qian, Frances M Bashore, Arunima Sikdar, Felix O Nwogbo, Andrey A Ivanov, Stephen V Frye, Opher Gileadi, Paul E Brennan, Allan I Levey, The Emory-Sage-Sgc Treat-Ad Center, Alison D Axtman, Kenneth H Pearce, Haian Fu, Vittorio L Katis

Faculty Research 2023

Proteomic studies have identified moesin (MSN), a protein containing a four-point-one, ezrin, radixin, moesin (FERM) domain, and the receptor CD44 as hub proteins found within a coexpression module strongly linked to Alzheimer's disease (AD) traits and microglia. These proteins are more abundant in Alzheimer's patient brains, and their levels are positively correlated with cognitive decline, amyloid plaque deposition, and neurofibrillary tangle burden. The MSN FERM domain interacts with the phospholipid phosphatidylinositol 4,5-bisphosphate (PIP

Generation Of Glucocorticoid-Producing Cells Derived From Human Pluripotent Stem Cells., Gerard Ruiz-Babot, Ariane Eceiza, Fernando Abollo-Jiménez, Maria Malyukov, Diana L Carlone, Kleiton Borges, Alexandra Rodrigues Da Costa, Shamma Qarin, Takuya Matsumoto, Ryuji Morizane, William C Skarnes, Barbara Ludwig, Paul J Chapple, Leonardo Guasti, Helen L Storr, Stefan R Bornstein, David T Breault

Faculty Research 2023

Adrenal insufficiency is a life-threatening condition resulting from the inability to produce adrenal hormones in a dose- and time-dependent manner. Establishing a cell-based therapy would provide a physiologically responsive approach for the treatment of this condition. We report the generation of large numbers of human-induced steroidogenic cells (hiSCs) from human pluripotent stem cells (hPSCs). Directed differentiation of hPSCs into hiSCs recapitulates the initial stages of human adrenal development. Following expression of steroidogenic factor 1, activation of protein kinase A signaling drives a steroidogenic gene expression profile most comparable to human fetal adrenal cells, and leads to dynamic secretion of steroid …

Efficacy Of Futibatinib, An Irreversible Fibroblast Growth Factor Receptor Inhibitor, In Fgfr-Altered Breast Cancer., Turcin Saridogan, Argun Akcakanat, Ming Zhao, Kurt W Evans, Erkan Yuca, Stephen Scott, Bryce P Kirby, Xiaofeng Zheng, Min Jin Ha, Huiqin Chen, Patrick Ks Ng, Timothy P Diperi, Gordon B Mills, Jordi Rodon Ahnert, Senthil Damodaran, Funda Meric-Bernstam

Faculty Research 2023

Several alterations in fibroblast growth factor receptor (FGFR) genes have been found in breast cancer; however, they have not been well characterized as therapeutic targets. Futibatinib (TAS-120; Taiho) is a novel, selective, pan-FGFR inhibitor that inhibits FGFR1-4 at nanomolar concentrations. We sought to determine futibatinib's efficacy in breast cancer models. Nine breast cancer patient-derived xenografts (PDXs) with various FGFR1-4 alterations and expression levels were treated with futibatinib. Antitumor efficacy was evaluated by change in tumor volume and time to tumor doubling. Alterations indicating sensitization to futibatinib in vivo were further characterized in vitro. FGFR gene expression between patient tumors and …

Human Mcts1-Dependent Translation Of Jak2 Is Essential For Ifn-Γ Immunity To Mycobacteria., Jonathan Bohlen, Qinhua Zhou, Quentin Philippot, Masato Ogishi, Darawan Rinchai, Tea Nieminen, Simin Seyedpour, Nima Parvaneh, Nima Rezaei, Niloufar Yazdanpanah, Mana Momenilandi, Clément Conil, Anna-Lena Neehus, Carltin Schmidt, Carlos A Arango-Franco, Tom Le Voyer, Taushif Khan, Rui Yang, Julia Puchan, Lucia Erazo, Mykola Roiuk, Taja Vatovec, Zarah Janda, Ivan Bagarić, Marie Materna, Adrian Gervais, Hailun Li, Jérémie Rosain, Jessica N Peel, Yoann Seeleuthner, Ji Eun Han, Anne-Sophie L'Honneur, Marcela Moncada-Vélez, Marta Martin-Fernandez, Michael E Horesh, Tatiana Kochetkov, Monika Schmidt, Mohammed A Alshehri, Eeva Salo, Harri Saxen, Gehad Elghazali, Ahmad Yatim, Camille Soudée, Federica Sallusto, Armin Ensser, Nico Marr, Peng Zhang, Dusan Bogunovic, Aurélie Cobat, Mohammad Shahrooei, Vivien Béziat, Laurent Abel, Xiaochuan Wang, Stéphanie Boisson-Dupuis, Aurelio A Teleman, Jacinta Bustamante, Qian Zhang, Jean-Laurent Casanova

Faculty Research 2023

Human inherited disorders of interferon-gamma (IFN-γ) immunity underlie severe mycobacterial diseases. We report X-linked recessive MCTS1 deficiency in men with mycobacterial disease from kindreds of different ancestries (from China, Finland, Iran, and Saudi Arabia). Complete deficiency of this translation re-initiation factor impairs the translation of a subset of proteins, including the kinase JAK2 in all cell types tested, including T lymphocytes and phagocytes. JAK2 expression is sufficiently low to impair cellular responses to interleukin-23 (IL-23) and partially IL-12, but not other JAK2-dependent cytokines. Defective responses to IL-23 preferentially impair the production of IFN-γ by innate-like adaptive mucosal-associated invariant T cells …

Meeting Report Of The Annual Workshop On Principles And Techniques For Improving Preclinical To Clinical Translation In Alzheimer's Disease Research., Michael Sasner, Paul R Territo, Stacey J Sukoff Rizzo

Faculty Research 2023

INTRODUCTION: The second annual 5-day workshop on Principles and Techniques for Improving Preclinical to Clinical Translation in Alzheimer's Disease Research was held October 7-11, 2019, at The Jackson Laboratory in Bar Harbor, Maine, USA, and included didactic lectures and hands-on training. Participants represented a broad range of research across the Alzheimer's disease (AD) field, and varied in career stages from trainees and early stage investigators to established faculty, with attendance from the United States, Europe, and Asia.

METHODS: In line with the National Institutes of Health (NIH) initiative on rigor and reproducibility, the workshop aimed to address training gaps in …

Harnessing Large Language Models (Llms) For Candidate Gene Prioritization And Selection., Mohammed Toufiq, Darawan Rinchai, Eleonore Bettacchioli, Basirudeen Syed Ahamed Kabeer, Taushif Khan, Bishesh Subba, Olivia White, Marina Yurieva, Joshy George, Noemie Jourde-Chiche, Laurent Chiche, Karolina Palucka, Damien Chaussabel

Faculty Research 2023

BACKGROUND: Feature selection is a critical step for translating advances afforded by systems-scale molecular profiling into actionable clinical insights. While data-driven methods are commonly utilized for selecting candidate genes, knowledge-driven methods must contend with the challenge of efficiently sifting through extensive volumes of biomedical information. This work aimed to assess the utility of large language models (LLMs) for knowledge-driven gene prioritization and selection.

METHODS: In this proof of concept, we focused on 11 blood transcriptional modules associated with an Erythroid cells signature. We evaluated four leading LLMs across multiple tasks. Next, we established a workflow leveraging LLMs. The steps consisted …

A Transcriptomic Appreciation Of Childhood Meningococcal And Polymicrobial Sepsis From A Pro-Inflammatory And Trajectorial Perspective, A Role For Vascular Endothelial Growth Factor A And B Modulation?, Asrar Rashid, Berit S Brusletto, Feras Al-Obeidat, Mohammed Toufiq, Govind Benakatti, Joe Brierley, Zainab A Malik, Zain Hussain, Hoda Alkhazaimi, Javed Sharief, Raziya Kadwa, Amrita Sarpal, Damien Chaussabel, Rayaz A Malik, Nasir Quraishi, Praveen Khilnani, Syed A Zaki, Rashid Nadeem, Guftar Shaikh, Ahmed Al-Dubai, Wael Hafez, Amir Hussain

Faculty Research 2023

This study investigated the temporal dynamics of childhood sepsis by analyzing gene expression changes associated with proinflammatory processes. Five datasets, including four meningococcal sepsis shock (MSS) datasets (two temporal and two longitudinal) and one polymicrobial sepsis dataset, were selected to track temporal changes in gene expression. Hierarchical clustering revealed three temporal phases: early, intermediate, and late, providing a framework for understanding sepsis progression. Principal component analysis supported the identification of gene expression trajectories. Differential gene analysis highlighted consistent upregulation of vascular endothelial growth factor A (VEGF-A) and nuclear factor κB1 (NFKB1), genes involved in inflammation, across the sepsis datasets. NFKB1 …

Distinct Roles Of Estrone And Estradiol In Endothelial Colony-Forming Cells., Alicia Ivory, Andrew S Greene

Faculty Research 2023

Our current understanding of the relationship between estrogen and human endothelial colony-forming cell (hECFC) function is based almost exclusively on studies investigating estradiol action at nuclear estrogen receptors. In the current study the hypothesis was tested that the less potent estrogen receptor agonist, estrone, affects hECFC proliferation, migration, secretion, and tube formation in a way that is unique from that of estradiol. The relationship between the estrogens, estradiol and estrone, is clinically important, particularly in postmenopausal women where estradiol levels wane and estrone becomes the predominant estrogen. Cultured hECFCs from peripheral blood mononuclear cell fractions were treated with concentrations of …

A Universal Method For Generating Knockout Mice In Multiple Genetic Backgrounds Using Zygote Electroporation., Tomohiro Tamari, Yoshihisa Ikeda, Kento Morimoto, Keiko Kobayashi, Saori Mizuno-Iijima, Shinya Ayabe, Akihiro Kuno, Seiya Mizuno, Atsushi Yoshiki

Faculty Research 2023

Genetically engineered mouse models are essential tools for understanding mammalian gene functions and disease pathogenesis. Genome editing allows the generation of these models in multiple inbred strains of mice without backcrossing. Zygote electroporation dramatically removed the barrier for introducing the CRISPR-Cas9 complex in terms of cost and labour. Here, we demonstrate that the generalised zygote electroporation method is also effective for generating knockout mice in multiple inbred strains. By combining in vitro fertilisation and electroporation, we obtained founders for knockout alleles in eight common inbred strains. Long-read sequencing analysis detected not only intended mutant alleles but also differences in read …

Isscr Standards For The Use Of Human Stem Cells In Basic Research., Tenneille E Ludwig, Peter W Andrews, Ivana Barbaric, Nissim Benvenisty, Anita Bhattacharyya, Jeremy M Crook, Laurence M Daheron, Jonathan S Draper, Lyn E Healy, Meritxell Huch, Maneesha S Inamdar, Kim B Jensen, Andreas Kurtz, Madeline A Lancaster, Prisca Liberali, Matthias P Lutolf, Christine L Mummery, Martin Pera, Yoji Sato, Noriko Shimasaki, Austin G Smith, Jihwan Song, Claudia Spits, Glyn Stacey, Christine A Wells, Tongbiao Zhao, Jack T Mosher

Faculty Research 2023

The laboratory culture of human stem cells seeks to capture a cellular state as an in vitro surrogate of a biological system. For the results and outputs from this research to be accurate, meaningful, and durable, standards that ensure reproducibility and reliability of the data should be applied. Although such standards have been previously proposed for repositories and distribution centers, no widely accepted best practices exist for laboratory research with human pluripotent and tissue stem cells. To fill that void, the International Society for Stem Cell Research has developed a set of recommendations, including reporting criteria, for scientists in basic …

Pkhd1, Chaozhe Yang, Naoe Harafuji, Ljubica Caldovic, Weiying Yu, Ravindra Boddu, Surajit Bhattacharya, Hayk Barseghyan, Heather Gordish-Dressman, Oded Foreman, Zsuzsa Bebok, Eva M Eicher, Lisa M Guay-Woodford

Faculty Research 2023

Autosomal-recessive polycystic kidney disease (ARPKD; MIM #263200) is a severe, hereditary, hepato-renal fibrocystic disorder that causes early childhood morbidity and mortality. Mutations in the polycystic kidney and hepatic disease 1 (PKHD1) gene, which encodes the protein fibrocystin/polyductin complex (FPC), cause all typical forms of ARPKD. Several mouse lines carrying diverse, genetically engineered disruptions in the orthologous Pkhd1 gene have been generated, but none expresses the classic ARPKD renal phenotype. In the current study, we characterized a spontaneous mouse Pkhd1 mutation that is transmitted as a recessive trait and causes cysticliver (cyli), similar to the hepato-biliary disease in ARPKD, but which …

Bridging Mouse And Human Anatomies; A Knowledge-Based Approach To Comparative Anatomy For Disease Model Phenotyping., Jesús Ruberte, Paul N Schofield, John P Sundberg, Alfonso Rodriguez-Baeza, Ana Carretero, Colin Mckerlie

Faculty Research 2023

The laboratory mouse is the foremost mammalian model used for studying human diseases and is closely anatomically related to humans. Whilst knowledge about human anatomy has been collected throughout the history of mankind, the first comprehensive study of the mouse anatomy was published less than 60 years ago. This has been followed by the more recent publication of several books and resources on mouse anatomy. Nevertheless, to date, our understanding and knowledge of mouse anatomy is far from being at the same level as that of humans. In addition, the alignment between current mouse and human anatomy nomenclatures is far …

Modeling Islet Enhancers Using Deep Learning Identifies Candidate Causal Variants At Loci Associated With T2d And Glycemic Traits., Sanjarbek Hudaiberdiev, D Leland Taylor, Wei Song, Narisu Narisu, Redwan M Bhuiyan, Henry J Taylor, Xuming Tang, Tingfen Yan, Amy J Swift, Lori L Bonnycastle, Diamante Consortium, Shuibing Chen, Michael L. Stitzel, Michael R Erdos, Ivan Ovcharenko, Francis S Collins

Faculty Research 2023

Genetic association studies have identified hundreds of independent signals associated with type 2 diabetes (T2D) and related traits. Despite these successes, the identification of specific causal variants underlying a genetic association signal remains challenging. In this study, we describe a deep learning (DL) method to analyze the impact of sequence variants on enhancers. Focusing on pancreatic islets, a T2D relevant tissue, we show that our model learns islet-specific transcription factor (TF) regulatory patterns and can be used to prioritize candidate causal variants. At 101 genetic signals associated with T2D and related glycemic traits where multiple variants occur in linkage disequilibrium, …

Assessment Of The Glycan-Binding Profile Of Pseudomonas Aeruginosa Pao1., Hector Sanchez, George A O'Toole, Brent Berwin

Faculty Research 2023

Pseudomonas aeruginosa is an opportunistic pathogen that can establish acute and chronic infections in individuals who lack fully functional innate immunity. In particular, phagocytosis by neutrophils and macrophages is a key mechanism that modulates host control and clearance of P. aeruginosa. Individuals with neutropenia or cystic fibrosis are highly susceptible to P. aeruginosa infection, thus underscoring the importance of the host innate immune response. Cell-to-cell contact between host innate immune cells and the pathogen, a first step in phagocytic uptake, is facilitated by simple and complex glycan structures present at the host cell surface. We have previously shown that endogenous …

High-Throughput Bioprinting Of The Nasal Epithelium Using Patient-Derived Nasal Epithelial Cells., I Deniz Derman, Miji Yeo, Diana Cadena, Megan Callender, Mian Horvath, Zengshuo Mo, Ruoyun Xiong, Elizabeth Fleming, Phylip Chen, Mark E Peeples, Karolina Palucka, Julia Oh, Ibrahim T Ozbolat

Faculty Research 2023

Progenitor human nasal epithelial cells (hNECs) are an essential cell source for the reconstruction of the respiratory pseudostratified columnar epithelium composed of multiple cell types in the context of infection studies and disease modeling. Hitherto, manual seeding has been the dominant method for creating nasal epithelial tissue models through biofabrication. However, this approach has limitations in terms of achieving the intricate three-dimensional (3D) structure of the natural nasal epithelium. 3D bioprinting has been utilized to reconstruct various epithelial tissue models, such as cutaneous, intestinal, alveolar, and bronchial epithelium, but there has been no attempt to use of 3D bioprinting technologies …

Genetically Diverse Mouse Models Of Sars-Cov-2 Infection Reproduce Clinical Variation In Type I Interferon And Cytokine Responses In Covid-19., Shelly J Robertson, Olivia Bedard, Kristin L Mcnally, Carl Shaia, Chad S Clancy, Matthew Lewis, Rebecca M Broeckel, Abhilash I Chiramel, Jeffrey G Shannon, Gail L Sturdevant, Rebecca Rosenke, Sarah L Anzick, Elvira Forte, Christoph Preuss, Candice N Baker, Jeffrey M. Harder, Catherine Brunton, Steven C. Munger, Daniel P Bruno, Justin B Lack, Jacqueline M Leung, Amirhossein Shamsaddini, Paul Gardina, Daniel E Sturdevant, Jian Sun, Craig Martens, Steven M Holland, Nadia Rosenthal, Sonja M Best

Faculty Research 2023

Inflammation in response to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection drives severity of coronavirus disease 2019 (COVID-19) and is influenced by host genetics. To understand mechanisms of inflammation, animal models that reflect genetic diversity and clinical outcomes observed in humans are needed. We report a mouse panel comprising the genetically diverse Collaborative Cross (CC) founder strains crossed to human ACE2 transgenic mice (K18-hACE2) that confers susceptibility to SARS-CoV-2. Infection of CC x K18-hACE2 resulted in a spectrum of survival, viral replication kinetics, and immune profiles. Importantly, in contrast to the K18-hACE2 model, early type I interferon (IFN-I) and regulated …

Cancer-Associated Mesothelial Cells Are Regulated By The Anti-Müllerian Hormone Axis., M Chauvin, M-C Meinsohn, S Dasari, P May, S Iyer, N M P Nguyen, E Oliva, Z Lucchini, N Nagykery, A Kashiwagi, R Mishra, Richard S. Maser, Julie Wells, Carol J Bult, A K Mitra, Patricia K Donahoe, D Pépin

Faculty Research 2023

Cancer-associated mesothelial cells (CAMCs) in the tumor microenvironment are thought to promote growth and immune evasion. We find that, in mouse and human ovarian tumors, cancer cells express anti-Mullerian hormone (AMH) while CAMCs express its receptor AMHR2, suggesting a paracrine axis. Factors secreted by cancer cells induce AMHR2 expression during their reprogramming into CAMCs in mouse and human in vitro models. Overexpression of AMHR2 in the Met5a mesothelial cell line is sufficient to induce expression of immunosuppressive cytokines and growth factors that stimulate ovarian cancer cell growth in an AMH- dependent way. Finally, syngeneic cancer cells implanted in transgenic mice …

Carbamoylated Erythropoietin-Induced Cerebral Blood Perfusion And Vascular Gene Regulation., Jayanarayanan Sadanandan, Monica Sathyanesan, Yutong Liu, Neeraj K Tiwari, Samuel S Newton

Faculty Research 2023

Cerebral hypoperfusion is associated with enhanced cognitive decline and increased risk of neuropsychiatric disorders. Erythropoietin (EPO) is a neurotrophic factor known to improve cognitive function in preclinical and clinical studies of neurodegenerative and psychiatric disorders. However, the clinical application of EPO is limited due to its erythropoietic activity that can adversely elevate hematocrit in non-anemic populations. Carbamoylated erythropoietin (CEPO), a chemically engineered non-erythropoietic derivative of EPO, does not alter hematocrit and maintains neurotrophic and behavioral effects comparable to EPO. Our study aimed to investigate the role of CEPO in cerebral hemodynamics. Magnetic resonance imaging (MRI) analysis indicated increased blood perfusion …

Gbmdeconvoluter Accurately Infers Proportions Of Neoplastic And Immune Cell Populations From Bulk Glioblastoma Transcriptomics Data., Shoaib Ajaib, Disha Lodha, Steven Pollock, Gemma Hemmings, Martina A Finetti, Arief Gusnanto, Aruna Chakrabarty, Azzam Ismail, Erica Wilson, Frederick S Varn, Bethany Hunter, Andrew Filby, Asa A Brockman, David Mcdonald, Roel G W Verhaak, Rebecca A Ihrie, Lucy F Stead

Faculty Research 2023

BACKGROUND: Characterizing and quantifying cell types within glioblastoma (GBM) tumors at scale will facilitate a better understanding of the association between the cellular landscape and tumor phenotypes or clinical correlates. We aimed to develop a tool that deconvolutes immune and neoplastic cells within the GBM tumor microenvironment from bulk RNA sequencing data.

METHODS: We developed an IDH wild-type (IDHwt) GBM-specific single immune cell reference consisting of B cells, T-cells, NK-cells, microglia, tumor associated macrophages, monocytes, mast and DC cells. We used this alongside an existing neoplastic single cell-type reference for astrocyte-like, oligodendrocyte- and neuronal progenitor-like and mesenchymal GBM cancer cells …

Robustness Of Single-Cell Rna-Seq For Identifying Differentially Expressed Genes., Yong Liu, Jing Huang, Rajan Pandey, Pengyuan Liu, Bhavika Therani, Qiongzi Qiu, Sridhar Rao, Aron M Geurts, Allen W Cowley, Andrew S Greene, Mingyu Liang

Faculty Research 2023

BACKGROUND: A common feature of single-cell RNA-seq (scRNA-seq) data is that the number of cells in a cell cluster may vary widely, ranging from a few dozen to several thousand. It is not clear whether scRNA-seq data from a small number of cells allow robust identification of differentially expressed genes (DEGs) with various characteristics.

RESULTS: We addressed this question by performing scRNA-seq and poly(A)-dependent bulk RNA-seq in comparable aliquots of human induced pluripotent stem cells-derived, purified vascular endothelial and smooth muscle cells. We found that scRNA-seq data needed to have 2,000 or more cells in a cluster to identify the …