Digital Commons Network^™

Unc-4 Acts To Promote Neuronal Identity And Development Of The Take-Off Circuit In The Drosophila Cns, Haluk Lacin, W. Ryan Williamson, Gwyneth M. Card, James B. Skeath, James W. Truman

Open Access Publications

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Single Cell Transcriptomics Identifies Focal Segmental Glomerulosclerosis Remission Endothelial Biomarker, Rajasree Menon, Sanjay Jain, Et Al

Open Access Publications

To define cellular mechanisms underlying kidney function and failure, the KPMP analyzes biopsy tissue in a multicenter research network to build cell-level process maps of the kidney. This study aimed to establish a single cell RNA sequencing strategy to use cell-level transcriptional profiles from kidney biopsies in KPMP to define molecular subtypes in glomerular diseases. Using multiple sources of adult human kidney reference tissue samples, 22,268 single cell profiles passed KPMP quality control parameters. Unbiased clustering resulted in 31 distinct cell clusters that were linked to kidney and immune cell types using specific cell markers. Focusing on endothelial cell phenotypes, …

Inflammatory Osteolysis Is Regulated By Site-Specific Isgylation Of The Scaffold Protein Nemo, Naga Suresh Adapala, Gaurav Swarnkar, Manoj Arra, Jie Shen, Gabriel Mbalaviele, Ke Ke, Yousef Abu-Amer

Open Access Publications

Inflammatory osteolysis is governed by exacerbated osteoclastogenesis. Ample evidence points to central role of NF-κB in such pathologic responses, yet the precise mechanisms underpinning specificity of these responses remain unclear. We propose that motifs of the scaffold protein IKKγ/NEMO partly facilitate such functions. As proof-of-principle, we used site-specific mutagenesis to examine the role of NEMO in mediating RANKL-induced signaling in mouse bone marrow macrophages, known as osteoclast precursors. We identified lysine (K)270 as a target regulating RANKL signaling as K270A substitution results in exuberant osteoclastogenesis in vitro and murine inflammatory osteolysis in vivo. Mechanistically, we discovered that K270A mutation disrupts …

Long Non-Coding Rna Graslnd Enhances Chondrogenesis Via Suppression Of The Interferon Type Ii Signaling Pathway, Nguyen P.T. Huynh, Catherine C. Gloss, Jeremiah Lorentz, Ruhang Tang, Jonathan M. Brunger, Audrey Mcalinden, Bo Zhang, Farshid Guilak

Open Access Publications

The roles of long noncoding RNAs (lncRNAs) in musculoskeletal development, disease, and regeneration remain poorly understood. Here, we identified the novel lncRNA

Abnormally Increased Carotid Intima Media-Thickness And Elasticity In Patients With Morquio A Disease, Raymond Y Wang, Kyle D Rudser, Donald R Dengel, Nicholas Evanoff, Julia Steinberger, Nina Movsesyan, Robert Garrett, Katherine Christensen, Deborah Boylan, Stephen R Braddock, Marwan Shinawi, Qi Gan, Adriana M Montaño

Open Access Publications

BACKGROUND: Cardiovascular disease frequently causes morbidity and mortality in mucopolysaccharidoses (MPS); however, cardiovascular anatomy and dysfunction in MPS IVA (Morquio A disease) is not well described. Consequently, the study aimed to compare carotid artery structure and elasticity of MPS IVA patients with other MPS patients and healthy control subjects, and quantitate frequency of MPS IVA cardiac structural and functional abnormalities.

METHODS: Prospective, multi-center echocardiogram and carotid ultrasound evaluations of 12 Morquio A patients were compared with other MPS and healthy control subjects. Average differences between groups were adjusted for age, sex, and height with robust variance estimation for confidence intervals …

Cerebrospinal Fluid Phospho-Tau T217 Outperforms T181 As A Biomarker For The Differential Diagnosis Of Alzheimer's Disease And Pet Amyloid-Positive Patient Identification, Nicolas R Barthélemy, Randall J Bateman, Christophe Hirtz, Philippe Marin, François Becher, Chihiro Sato, Audrey Gabelle, Sylvain Lehmann

Open Access Publications

BACKGROUND: Cerebrospinal fluid biomarker profiles characterized by decreased amyloid-beta peptide levels and increased total and phosphorylated tau levels at threonine 181 (pT181) are currently used to discriminate between Alzheimer's disease and other neurodegenerative diseases. However, these changes are not entirely specific to Alzheimer's disease, and it is noteworthy that other phosphorylated isoforms of tau, possibly more specific for the disease process, have been described in the brain parenchyma of patients. The precise detection of these isoforms in biological fluids remains however a challenge.

METHODS: In the present study, we used the latest quantitative mass spectrometry approach, which achieves a sensitive …

T Cell Response Kinetics Determines Neuroinfection Outcomes During Murine Hsv Infection, Aisha G Lee, Jason M Scott, Maria Rita Fabbrizi, Xiaoping Jiang, Dorothy K Sojka, Mark J Miller, Megan T Baldridge, Wayne M Yokoyama, Haina Shin

Open Access Publications

Herpes simplex virus-2 (HSV-2) and HSV-1 both can cause genital herpes, a chronic infection that establishes a latent reservoir in the nervous system. Clinically, the recurrence frequency of HSV-1 genital herpes is considerably less than HSV-2 genital herpes, which correlates with reduced neuronal infection. The factors dictating the disparate outcomes of HSV-1 and HSV-2 genital herpes are unclear. In this study, we show that vaginal infection of mice with HSV-1 leads to the rapid appearance of mature DCs in the draining lymph node, which is dependent on an early burst of NK cell-mediated IFN-γ production in the vagina that occurs …

Barrier-To-Autointegration Factor 1 Protects Against A Basal Cgas-Sting Response, Hongming Ma, Wei Qian, Monika Bambouskova, Patrick L Collins, Sofia I Porter, Andrea K Byrum, Rong Zhang, Maxim Artyomov, Eugene M Oltz, Nima Mosammaparast, Jonathan J Miner, Michael S Diamond

Open Access Publications

Although the pathogen recognition receptor pathways that activate cell-intrinsic antiviral responses are well delineated, less is known about how the host regulates this response to prevent sustained signaling and possible immune-mediated damage. Using a genome-wide CRISPR-Cas9 screening approach to identify host factors that modulate interferon-stimulated gene (ISG) expression, we identified the DNA binding protein Barrier-to-autointegration factor 1 (Banf1), a previously described inhibitor of retrovirus integration, as a modulator of basal cell-intrinsic immunity. Ablation of Banf1 by gene editing resulted in chromatin activation near host defense genes with associated increased expression of ISGs, including

Genome-Wide Association Study In Two Cohorts From A Multi-Generational Mouse Advanced Intercross Line Highlights The Difficulty Of Replication Due To Study-Specific Heterogeneity, Xinzhu Zhou, Celine L St Pierre, Natalia M Gonzales, Jennifer Zou, Riyan Cheng, Apurva S Chitre, Greta Sokoloff, Abraham A Palmer

Open Access Publications

There has been extensive discussion of the "Replication Crisis" in many fields, including genome-wide association studies (

Error-Corrected Sequencing Strategies Enable Comprehensive Detection Of Leukemic Mutations Relevant For Diagnosis And Minimal Residual Disease Monitoring, Erin L Crowgey, Nitin Mahajan, Wing Hing Wong, Anilkumar Gopalakrishnapillai, Sonali P Barwe, E Anders Kolb, Todd E Druley

2020-Current year OA Pubs

BACKGROUND: Pediatric leukemias have a diverse genomic landscape associated with complex structural variants, including gene fusions, insertions and deletions, and single nucleotide variants. Routine karyotype and fluorescence in situ hybridization (FISH) techniques lack sensitivity for smaller genomic alternations. Next-generation sequencing (NGS) assays are being increasingly utilized for assessment of these various lesions. However, standard NGS lacks quantitative sensitivity for minimal residual disease (MRD) surveillance due to an inherently high error rate.

METHODS: Primary bone marrow samples from pediatric leukemia (n = 32) and adult leukemia subjects (n = 5), cell line MV4-11, and an umbilical cord sample were utilized for …

Defining Stage-Specific Activity Of Potent New Inhibitors Of Cryptosporidium Parvum Growth In Vitro, Lisa J Funkhouser-Jones, Soumya Ravindran, L. David Sibley

Open Access Publications

No abstract provided.

Variant R94c In Tnnt2‐Encoded Troponin T Predisposes To Pediatric Restrictive Dardiomyopathy And Sudden Death Through Impaired Thin Filament Relaxation Resulting In Myocardial Diastolic Dysfunction, Jordan E Ezekian, Sarah R Clippinger, Jaquelin M Garcia, Qixin Yang, Susan Denfield, Aamir Jeewa, William J Dreyer, Wenxin Zou, Yuxin Fan, Hugh D Allen, Jeffrey J Kim, Michael J Greenberg, Andrew P Landstrom

Open Access Publications

Background Pediatric-onset restrictive cardiomyopathy (RCM) is associated with high mortality, but underlying mechanisms of disease are under investigated. RCM-associated diastolic dysfunction secondary to variants in

Acetate Coordinates Neutrophil And Ilc3 Responses Against C. Difficile Through Ffar2, José Luís Fachi, Cristiane Sécca, Blanda Di Luccia, Marco Colonna, Et Al

Open Access Publications

Antibiotic-induced dysbiosis is a key predisposing factor for Clostridium difficile infections (CDIs), which cause intestinal disease ranging from mild diarrhea to pseudomembranous colitis. Here, we examined the impact of a microbiota-derived metabolite, short-chain fatty acid acetate, on an acute mouse model of CDI. We found that administration of acetate is remarkably beneficial in ameliorating disease. Mechanistically, we show that acetate enhances innate immune responses by acting on both neutrophils and ILC3s through its cognate receptor free fatty acid receptor 2 (FFAR2). In neutrophils, acetate-FFAR2 signaling accelerates their recruitment to the inflammatory sites, facilitates inflammasome activation, and promotes the release of …

Glp-1 Notch-Lag-1 Csl Control Of The Germline Stem Cell Fate Is Mediated By Transcriptional Targets Lst-1 And Sygl-1, Jian Chen, Ariz Mohammad, Nanette Pazdernik, Huiyan Huang, Beth Bowman, Eric Tycksen, Tim Schedl

Open Access Publications

Stem cell systems are essential for the development and maintenance of polarized tissues. Intercellular signaling pathways control stem cell systems, where niche cells signal stem cells to maintain the stem cell fate/self-renewal and inhibit differentiation. In the C. elegans germline, GLP-1 Notch signaling specifies the stem cell fate, employing the sequence-specific DNA binding protein LAG-1 to implement the transcriptional response. We undertook a comprehensive genome-wide approach to identify transcriptional targets of GLP-1 signaling. We expected primary response target genes to be evident at the intersection of genes identified as directly bound by LAG-1, from ChIP-seq experiments, with genes identified as …

Modular Analysis Of The Control Of Flagellar Ca2+-Spike Trains Produced By Catsper And Cav Channels In Sea Urchin Sperm, Daniel A. Priego-Espinosa, Alberto Darszon, Adán Guerrero, Ana Laura González-Cota, Takuya Nishigaki, Gustavo Martínez-Mekler, Jorge Carneiro

Open Access Publications

Intracellular calcium ([Ca2+]i) is a basic and ubiquitous cellular signal controlling a wide variety of biological processes. A remarkable example is the steering of sea urchin spermatozoa towards the conspecific egg by a spatially and temporally orchestrated series of [Ca2+]i spikes. Although this process has been an experimental paradigm for reproduction and sperm chemotaxis studies, the composition and regulation of the signalling network underlying the cytosolic calcium fluctuations are hitherto not fully understood. Here, we used a differential equations model of the signalling network to assess which set of channels can explain the characteristic envelope and temporal organisation of the …

Modeling Cancer Genomic Data In Yeast Reveals Selection Against Atm Function During Tumorigenesis, Marcel Hohl, Aditya Mojumdar, Sarem Hailemariam, Vitaly Kuryavyi, Fiorella Ghisays, Kyle Sorenson, Matthew Chang, Barry S. Taylor, Dinshaw J. Patel, Peter M. Burgers, Jennifer A. Cobb, John H. J. Petrini

Open Access Publications

The DNA damage response (DDR) comprises multiple functions that collectively preserve genomic integrity and suppress tumorigenesis. The Mre11 complex and ATM govern a major axis of the DDR and several lines of evidence implicate that axis in tumor suppression. Components of the Mre11 complex are mutated in approximately five percent of human cancers. Inherited mutations of complex members cause severe chromosome instability syndromes, such as Nijmegen Breakage Syndrome, which is associated with strong predisposition to malignancy. And in mice, Mre11 complex mutations are markedly more susceptible to oncogene- induced carcinogenesis. The complex is integral to all modes of DNA double …

Platelet Activation In Experimental Murine Neonatal Pulmonary Hypertension, Pavel Davizon-Castillo, Ayed Allawzi, Matthew Sorrells, Susan Fisher, Kristina Baltrunaite, Keith Neeves, Eva Nozik-Grayck, Jorge Dipaola, Cassidy Delaney

Open Access Publications

Serotonin (5-HT) contributes to the pathogenesis of experimental neonatal pulmonary hypertension (PH) associated with bronchopulmonary dysplasia (BPD). Platelets are the primary source of circulating 5-HT and is released upon platelet activation. Platelet transfusions are associated with neonatal mortality and increased rates of BPD. As BPD is often complicated by PH, we tested the hypothesis that circulating platelets are activated and also increased in the lungs of neonatal mice with bleomycin-induced PH associated with BPD. Newborn wild-type mice received intraperitoneal bleomycin (3 units/kg) three times weekly for 3 weeks. Platelets from mice with experimental PH exhibited increased adhesion to collagen under …

Microbiome Restoration By Rbx2660 Does Not Preclude Recurrence Of Multidrug-Resistant Urinary Tract Infection Following Subsequent Antibiotic Exposure: A Case Report, Eric C. Keen, Preston Tasoff, Tiffany Hink, Kimberly A. Reske, Carey-Ann D. Burnham, Gautam Dantas, Jennie H. Kwon, Erik R. Dubberke

Open Access Publications

A 62-year-old woman received RBX2660, an investigational microbiome restoration therapeutic, for recurrent multidrug-resistant (MDR) urinary tract infection (UTI). RBX2660 increased gut microbiome diversity but did not eliminate uropathogen carriage, and MDR UTI recurred after subsequent antibiotic exposure. Thus, restoration of microbiome diversity does not preclude disease recurrence by residual MDR pathogens.

Tgfβ1 Orchestrates Renal Fibrosis Following Escherichia Coli Pyelonephritis, Teri N Hreha, Christina A Collins, Allyssa L Daugherty, Joy Twentyman, Nitin Paluri, David A Hunstad

Open Access Publications

Renal scarring after pyelonephritis is linked to long-term health risks for hypertension and chronic kidney disease. Androgen exposure increases susceptibility to, and severity of, uropathogenic Escherichia coli (UPEC) pyelonephritis and resultant scarring in both male and female mice, while anti-androgen therapy is protective against severe urinary tract infection (UTI) in these models. This work employed androgenized female C57BL/6 mice to elucidate the molecular mechanisms of post-infectious renal fibrosis and to determine how these pathways are altered by the presence of androgens. We found that elevated circulating testosterone levels primed the kidney for fibrosis by increasing local production of TGFβ1 before …

Proteoclade: A Taxonomic Toolkit For Multi-Species And Metaproteomic Analysis, Arshag D. Mooradian, Sjoerd Van Der Post, Kristen M. Naegle, Jason M. Held

Open Access Publications

We present ProteoClade, a Python toolkit that performs taxa-specific peptide assignment, protein inference, and quantitation for multi-species proteomics experiments. ProteoClade scales to hundreds of millions of protein sequences, requires minimal computational resources, and is open source, multi-platform, and accessible to non-programmers. We demonstrate its utility for processing quantitative proteomic data derived from patient-derived xenografts and its speed and scalability enable a novel de novo proteomic workflow for complex microbiota samples.

Impaired Tumor Necrosis Factor-Α Secretion By Cd4 T Cells During Respiratory Syncytial Virus Bronchiolitis Associated With Recurrent Wheeze, Maleewan Kitcharoensakkul, Leonard B Bacharier, Huiqing Yin-Declue, Jonathan S Boomer, Geneline Sajol, Marilyn K Leung, Brad Wilson, Kenneth B Schechtman, John P Atkinson, Jonathan M Green, Mario Castro

Open Access Publications

BACKGROUND: Infants with severe respiratory syncytial virus (RSV) bronchiolitis have an increased risk of recurrent wheezing and asthma. We aimed to evaluate the relationships between regulatory T cell (Treg) percentage and cytokine production of in vitro-stimulated CD4+ T cells during acute bronchiolitis and the development of recurrent wheezing in the first 3 years of life.

METHODS: We obtained peripheral blood from 166 infants hospitalized with their first episode of RSV-confirmed bronchiolitis. Granzyme B (GZB) expression, and interleukin-10, interferon-γ, tumor necrosis factor-α (TNF-α), IL-4, and IL-5 production by in vitro anti-CD3/CD28- and anti-CD3/CD46-activated CD4+ T cells, and percentage of peripheral Treg …

Long Non-Coding Rna Lcal62 / Linc00261 Is Associated With Lung Adenocarcinoma Prognosis, Ha X Dang, Nicole M White, Emily B Rozycki, Brooke M Felsheim, Mark A Watson, Ramaswamy Govindan, Jingqin Luo, Christopher A Maher

Open Access Publications

Background: More than half of non-small cell lung cancer (NSCLC) patients present with metastatic disease at initial diagnosis with an estimated five-year survival rate of ~5%. Despite advances in understanding primary lung cancer oncogenesis metastatic disease remains poorly characterized. Recent studies demonstrate important roles of long non-coding RNAs (lncRNAs) in tumor physiology and as prognostic markers. Therefore, we present the first transcriptome analysis to identify lncRNAs altered in metastatic lung adenocarcinoma leading to the discovery and characterization of the lncRNA

Patients and methods: RNA-Seq, microarray, nanoString expression, and clinical data from 1,116 LUAD patients across six independent cohorts and 83 …

The Dual-Specificity Kinase Dyrk1a Modulates The Levels Of Cyclin L2 To Control Hiv Replication In Macrophages, Javan K. Kisaka, Lee Ratner, George B. Kyei

Open Access Publications

HIV replication in macrophages contributes to the latent viral reservoirs, which are considered the main barrier to HIV eradication. Few cellular factors that facilitate HIV replication in latently infected cells are known. We previously identified cyclin L2 as a critical factor required by HIV-1 and found that depletion of cyclin L2 attenuates HIV-1 replication in macrophages. Here we demonstrate that cyclin L2 promotes HIV-1 replication through interactions with the dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A). Cyclin L2 and DYRK1A were colocalized in the nucleus and were found together in immunoprecipitation experiments. Knockdown or inhibition of DYRK1A increased HIV-1 replication in …

Endoscopic Retrograde Cholangiopancreatography (Ercp) Assisted Enucleation Of Deep Pancreatic Neuroendocrine Tumors (Pnets): A Novel Technique To Increase Procedure Safety And Decrease Risk Of Post-Operative Pancreatic Fistula, Adeel S. Khan, Mohamed A. Abdallah, Muslim Atiq, Daniel Mullady, Koushik K. Das, William C. Chapman, Maria B. Doyle

Open Access Publications

No abstract provided.

Regenerating Zebrafish Fin Epigenome Is Characterized By Stable Lineage-Specific Dna Methylation And Dynamic Chromatin Accessibility, Hyung Joo Lee, Yiran Hou, Yujie Chen, Zea Z Dailey, Aiyana Riddihough, Hyo Sik Jang, Ting Wang, Stephen L Johnson

2020-Current year OA Pubs

BACKGROUND: Zebrafish can faithfully regenerate injured fins through the formation of a blastema, a mass of proliferative cells that can grow and develop into the lost body part. After amputation, various cell types contribute to blastema formation, where each cell type retains fate restriction and exclusively contributes to regeneration of its own lineage. Epigenetic changes that are associated with lineage restriction during regeneration remain underexplored.

RESULTS: We produce epigenome maps, including DNA methylation and chromatin accessibility, as well as transcriptomes, of osteoblasts and other cells in uninjured and regenerating fins. This effort reveals regeneration as a process of highly dynamic …

Improving Characterization Of Understudied Human Microbiomes Using Targeted Phylogenetics, Bruce A Rosa, Kathie Mihindukulasuriya, Kymberlie Hallsworth-Pepin, Aye Wollam, John Martin, Caroline Snowden, William Michael Dunne Jr., George M Weinstock, Carey-Ann D. Burnham, Makedonka Mitreva

Open Access Publications

Whole-genome bacterial sequences are required to better understand microbial functions, niche-specific bacterial metabolism, and disease states. Although genomic sequences are available for many of the human-associated bacteria from commonly tested body habitats (e.g., feces), as few as 13% of bacterium-derived reads from other sites such as the skin map to known bacterial genomes. To facilitate a better characterization of metagenomic shotgun reads from underrepresented body sites, we collected over 10,000 bacterial isolates originating from 14 human body habitats, identified novel taxonomic groups based on full-length 16S rRNA gene sequences, clustered the sequences to ensure that no individual taxonomic group was …

The Plasmodium Falciparum Artemisinin Susceptibility-Associated Ap-2 Adaptin Μ Subunit Is Clathrin Independent And Essential For Schizont Maturation, Ryan C Henrici, Rachel L Edwards, Martin Zoltner, Donelly A Van Schalkwyk, Melissa N Hart, Franziska Mohring, Robert W Moon, Stephanie D Nofal, Avnish Patel, Christian Flueck, David A Baker, Audrey R Odom John, Mark C Field, Colin J Sutherland

Open Access Publications

The efficacy of current antimalarial drugs is threatened by reduced susceptibility of

Neural Mechanisms Of Economic Choices In Mice, Masaru Kuwabara, Ningdong Kang, Timothy E. Holy, Camillo Padoa-Schioppa

Open Access Publications

Economic choices entail computing and comparing subjective values. Evidence from primates indicates that this behavior relies on the orbitofrontal cortex. Conversely, previous work in rodents provided conflicting results. Here we present a mouse model of economic choice behavior, and we show that the lateral orbital (LO) area is intimately related to the decision process. In the experiments, mice chose between different juices offered in variable amounts. Choice patterns closely resembled those measured in primates. Optogenetic inactivation of LO dramatically disrupted choices by inducing erratic changes of relative value and by increasing choice variability. Neuronal recordings revealed that different groups of …

Agonist-Selective Recruitment Of Engineered Protein Probes And Of Grk2 By Opioid Receptors In Living Cells, Miriam Stoeber, Damien Jullié, Joy Li, Soumen Chakraborty, Susruta Majumdar, Nevin A. Lambert, Aashish Manglik, Mark Von Zastrow

Open Access Publications

G protein-coupled receptors (GPCRs) signal through allostery, and it is increasingly clear that chemically distinct agonists can produce different receptor-based effects. It has been proposed that agonists selectively promote receptors to recruit one cellular interacting partner over another, introducing allosteric 'bias' into the signaling system. However, the underlying hypothesis - that different agonists drive GPCRs to engage different cytoplasmic proteins in living cells - remains untested due to the complexity of readouts through which receptor-proximal interactions are typically inferred. We describe a cell-based assay to overcome this challenge, based on GPCR-interacting biosensors that are disconnected from endogenous transduction mechanisms. Focusing …

Pituitary Carcinoma: Two Case Reports And Review Of Literature, Lai Xu, Karam Khaddour, Jie Chen, Keith M. Rich, Richard J. Perrin, Jian Li Campian

Open Access Publications

BACKGROUND: Pituitary carcinoma is a rare type of malignancy that can be very difficult to diagnose and treat. Many cases were diagnosed at autopsy. Delays in diagnosis often adversely impact patients' outcomes. Even with prompt diagnosis, treatment decisions remain challenging in the absence of randomized controlled trials.

CASE SUMMARY: We report two cases of pituitary carcinoma in men with a history of pituitary adenoma. In the first case, a 55-year-old man was initially diagnosed with pituitary macroadenoma. He underwent subtotal debulking of the tumor followed by adjuvant radiotherapy. Subsequently, he developed relapsed disease and multifocal intracranial metastases and a diagnosis …