Digital Commons Network^™

High-Resolution Transcriptional And Morphogenetic Profiling Of Cells From Micropatterned Human Esc Gastruloid Cultures, Kyaw Thu Minn, Yuheng C. Fu, Shenghua He, Sabine Dietmann, Steven C. George, Mark A. Anastasio, Samantha A. Morris, Lilianna Solnica-Krezel

Open Access Publications

During mammalian gastrulation, germ layers arise and are shaped into the body plan while extraembryonic layers sustain the embryo. Human embryonic stem cells, cultured with BMP4 on extracellular matrix micro-discs, reproducibly differentiate into gastruloids, expressing markers of germ layers and extraembryonic cells in radial arrangement. Using single-cell RNA sequencing and cross-species comparisons with mouse, cynomolgus monkey gastrulae, and post-implantation human embryos, we reveal that gastruloids contain cells transcriptionally similar to epiblast, ectoderm, mesoderm, endoderm, primordial germ cells, trophectoderm, and amnion. Upon gastruloid dissociation, single cells reseeded onto micro-discs were motile and aggregated with the same but segregated from distinct cell …

Full-Length Trkb Variant In Nsclc Is Associated With Brain Metastasis, Mariangela Lombardi, Michela D'Ascanio, Stefania Scarpino, Davide Scozzi, Marco Giordano, Leopoldo Costarelli, Enrico Rathina Raj, Rita Mancini, Giuseppe Cardillo, Vittorio Cardaci, Marta Innammorato, Andrea Vecchione, Alberto Ricci

Open Access Publications

Despite remarkable therapeutic advances have been made in the last few decades, non-small cell lung cancer (NSCLC) is still one of the leading causes of death worldwide. Brain metastases are a common complication of a wide range of human malignancies and in particular NSCLC. Brain-derived neurotrophic factor (BDNF), binding its high-affinity tyrosine kinase B receptor, has been shown to promote cancer progression and metastasis. We hereby investigated the expression of the BDNF and its TrkB receptor in its full-length and truncated isoform T1, in samples from primary adenocarcinomas (ADKs) of the lung and in their metastasis to evaluate if their …

Structure Of The Receptor Binding Domain Of Envp(B)1, An Endogenous Retroviral Envelope Protein Expressed In Human Tissues, Kevin R Mccarthy, Joseph L Timpona, Simon Jenni, Louis-Marie Bloyet, Vesna Brusic, Welkin E Johnson, Sean P J Whelan, Lindsey R Robinson-Mccarthy

Open Access Publications

EnvP(b)1 is an endogenous retroviral envelope gene found in human and other primate genomes. We report EnvP(b)1 sequences in primate genomes consistent with an integration event between 40 and 71 million years ago. Using a highly specific polyclonal antiserum raised against the putative receptor binding domain (RBD) of human EnvP(b)1, we detected expression in human placenta, ovaries, and thymus. We found that EnvP(b)1 is proteolytically processed, and using cell-cell fusion assays in multiple primate cell lines, we demonstrated that extant EnvP(b)1 proteins from a variety of primate genomes are fusogenic. This work supports the idea that EnvP(b)1 is under purifying …

Increased Mtor Activity And Metabolic Efficiency In Mouse And Human Cells Containing The African-Centric Tumor-Predisposing P53 Variant Pro47ser, Keerthana Gnanapradeepan, Julia I-Ju Leu, Subhasree Basu, Thibaut Barnoud, Madeline Good, Joyce V. Lee, William J. Quinn, Che-Pei Kung, Rexford Ahima, Joseph A. Baur, Kathryn E. Wellen, Qin Liu, Zachary T. Schug, Donna L. George, Maureen E. Murphy

Open Access Publications

The Pro47Ser variant of p53 (S47) exists in African-descent populations and is associated with increased cancer risk in humans and mice. Due to impaired repression of the cystine importer

Tfeb Transcriptional Responses Reveal Negative Feedback By Bhlhe40 And Bhlhe41, Kimberly L Carey, Geraldine L C Paulus, Lingfei Wang, Dale R Balce, Jessica W Luo, Phil Bergman, Ianina C Ferder, Lingjia Kong, Nicole Renaud, Shantanu Singh, Maria Kost-Alimova, Beat Nyfeler, Kara G Lassen, Herbert W Virgin, Ramnik J Xavier

Open Access Publications

Transcription factor EB (TFEB) activates lysosomal biogenesis genes in response to environmental cues. Given implications of impaired TFEB signaling and lysosomal dysfunction in metabolic, neurological, and infectious diseases, we aim to systematically identify TFEB-directed circuits by examining transcriptional responses to TFEB subcellular localization and stimulation. We reveal that steady-state nuclear TFEB is sufficient to activate transcription of lysosomal, autophagy, and innate immunity genes, whereas other targets require higher thresholds of stimulation. Furthermore, we identify shared and distinct transcriptional signatures between mTOR inhibition and bacterial autophagy. Using a genome-wide CRISPR library, we find TFEB targets that protect cells from or sensitize …

Kir6.1- And Sur2-Dependent Katp Over-Activity Disrupts Intestinal Motility In Murine Models Of Cantu Syndrome, Nathaniel W York, Helen Parker, Zili Xie, David Tyus, Maham A Waheed, Zihan Yan, Dorothy K Grange, Maria S Remedi, Sarah K England, Hongzhen Hu, Colin G Nichols

Open Access Publications

Cantύ Syndrome (CS), caused by gain-of-function (GOF) mutations in pore-forming (Kir6.1, KCNJ8) and accessory (SUR2, ABCC9) ATP-sensitive potassium (KATP) channel subunit genes, is frequently accompanied by gastrointestinal (GI) dysmotility, and we describe one CS patient who required an implanted intestinal irrigation system for successful stooling. We used gene-modified mice to assess the underlying KATP channel subunits in gut smooth muscle, and to model the consequences of altered KATP channels in CS gut. We show that Kir6.1/SUR2 subunits underlie smooth muscle KATP channels throughout the small intestine and colon. Knock-in mice, carrying human KCNJ8 and ABCC9 CS mutations in the endogenous …

Treatment Of Epithelial Ovarian Cancer, Lindsay Kuroki, Saketh R Guntupalli

Open Access Publications

Ovarian cancer is the third most common gynecologic malignancy worldwide but accounts for the highest mortality rate among these cancers. A stepwise approach to assessment, diagnosis, and treatment is vital to appropriate management of this disease process. An integrated approach with gynecologic oncologists as well as medical oncologists, pathologists, and radiologists is of paramount importance to improving outcomes. Surgical cytoreduction to R0 is the mainstay of treatment, followed by adjuvant chemotherapy. Genetic testing for gene mutations that affect treatment is the standard of care for all women with epithelial ovarian cancer. Nearly all women will have a recurrence, and the …

Myh3-Associated Distal Arthrogryposis Zebrafish Model Is Normalized With Para-Aminoblebbistatin, Julia Whittle, Lilian Antunes, Mya Harris, Zachary Upshaw, Diane S Sepich, Aaron N Johnson, Mayssa Mokalled, Lilianna Solnica-Krezel, Matthew B Dobbs, Christina A Gurnett

Open Access Publications

Distal arthrogryposis (DA) is group of syndromes characterized by congenital joint contractures. Treatment development is hindered by the lack of vertebrate models. Here, we describe a zebrafish model in which a common MYH3 missense mutation (R672H) was introduced into the orthologous zebrafish gene smyhc1 (slow myosin heavy chain 1) (R673H). We simultaneously created a smyhc1 null allele (smyhc1

Moonshots For Aging, Sandeep Kumar, Timothy R Peterson

Open Access Publications

As the global population ages, there is increased interest in living longer and improving one's quality of life in later years. However, studying aging - the decline in body function - is expensive and time-consuming. And despite research success to make model organisms live longer, there still aren't really any feasible solutions for delaying aging in humans. With space travel, scientists and engineers couldn't know what it would take to get to the moon. They had to extrapolate from theory and shorter-range tests. Perhaps with aging, we need a similar moonshot philosophy. And though "shot" might imply medicine, perhaps we …

Blood Plasma Phosphorylated-Tau Isoforms Track Cns Change In Alzheimer's Disease, Nicolas R. Barthélemy, Kanta Horie, Chihiro Sato, Randall J. Bateman

Open Access Publications

Highly sensitive and specific plasma biomarkers for Alzheimer's disease (AD) have the potential to improve diagnostic accuracy in the clinic and facilitate research studies including enrollment in prevention and treatment trials. We recently reported CSF tau hyperphosphorylation, especially on T217, is an accurate predictor of β-amyloidosis at asymptomatic and symptomatic stages. In the current study, we determine by mass spectrometry the potential utility of plasma p-tau isoforms to detect AD pathology and investigate CSF and plasma tau isoforms' profile relationships. Plasma tau was truncated as previously described in CSF. CSF and plasma measures of p-tau-217 and p-tau-181 were correlated. No …

Prospective, Randomized, Double-Blind, Placebo-Controlled Evaluation Of The Pharmacokinetics, Safety And Efficacy Of Recombinant Antithrombin Versus Placebo In Preterm Preeclampsia, Michael J Paidas, George A Macones, Et Al

Open Access Publications

BACKGROUND: Despite expectant management, preeclampsia remote from term usually results in preterm delivery. Antithrombin, which displays antiinflammatory and anticoagulant properties, may have a therapeutic role in treating preterm preeclampsia, a disorder characterized by endothelial dysfunction, inflammation, and activation of the coagulation system.

OBJECTIVE: This randomized, placebo-controlled clinical trial aimed to evaluate whether intravenous recombinant human antithrombin could prolong gestation and therefore improve maternal and fetal outcomes.

STUDY DESIGN: We performed a double-blind, placebo-controlled trial at 23 hospitals. Women were eligible if they had a singleton pregnancy, early-onset or superimposed preeclampsia at 23 0/7 to 30 0/7 weeks' gestation, and planned …

Implications Of Pneumonitis After Chemoradiation And Durvalumab For Locally Advanced Non-Small Cell Lung Cancer, Comron Hassanzadeh, Timothy Sita, Rohan Savoor, Pamela P Samson, Jeffrey Bradley, Michelle Gentile, Michael Roach, Nisha Mohindra, Saiama Waqar, Timothy J Kruser, Clifford Robinson

Open Access Publications

Background: Consolidation durvalumab improved overall survival (OS) in locally advanced non-small cell lung cancer (LA-NSCLC) treated with chemoradiotherapy (CRT) in the PACIFIC trial; however, pneumonitis was increased with durvalumab. We sought to examine real-world outcomes with the PACIFIC paradigm, especially factors associated with pneumonitis, using a multi-institutional review.

Methods: Patients with LA-NSCLC treated with CRT followed by durvalumab from January 2017-February 2019 were identified at 2 institutions. We characterized demographics, tumor factors, radiotherapy, and duration of durvalumab. We examined pneumonitis outcomes including re-challenge success, with secondary endpoints of progression-free survival (PFS) and OS.

Results: Thirty-four patients were included with median …

Sarm1 Depletion Rescues Nmnat1-Dependent Photoreceptor Cell Death And Retinal Degeneration, Yo Sasaki, Hiroki Kakita, Shunsuke Kubota, Abdoulaye Sene, Tae Jun Lee, Norimitsu Ban, Zhenyu Dong, Joseph B. Lin, Sanford L. Boye, Aaron Diantonio, Shannon E. Boye, Rajendra S. Apte, Jeffrey Milbrandt

Open Access Publications

Leber congenital amaurosis type nine is an autosomal recessive retinopathy caused by mutations of the NAD

Role Of Endothelial Nitric Oxide Synthase In Isoflurane Conditioning-Induced Neurovascular Protection In Subarachnoid Hemorrhage, Umeshkumar Athiraman, Keshav Jayaraman, Meizi Liu, Tusar Giri, Jane Yuan, Gregory J Zipfel

Open Access Publications

Background Delayed cerebral ischemia remains a common and profound risk factor for poor outcome after subarachnoid hemorrhage (SAH). The aim of our current study is to define the role of endothelial nitric oxide synthase (eNOS) in isoflurane conditioning-induced neurovascular protection after SAH. Methods and Results Ten- to 14-week-old male wild-type mice (C57BL/6) as controls and eNOS knockout male mice (strain # 002684) were obtained for the study. Animals underwent either sham surgery, SAH surgery, or SAH with isoflurane conditioning. Anesthetic post conditioning was performed with isoflurane 2% for 1 hour, 1 hour after SAH. Normothermia was maintained with the homeothermic …

The Fgf8 Subfamily (Fgf8, Fgf17 And Fgf18) Is Required For Closure Of The Embryonic Ventral Body Wall, Michael Boylan, Matthew J Anderson, David M Ornitz, Mark Lewandoski

Open Access Publications

The closure of the embryonic ventral body wall in amniotes is an important morphogenetic event and is essential for life. Defects in human ventral wall closure are a major class of birth defect and a significant health burden. Despite this, very little is understood about how the ventral body wall is formed. Here, we show that fibroblast growth factor (FGF) ligands FGF8, FGF17 and FGF18 are essential for this process. Conditional mouse mutants for these genes display subtle migratory defects in the abdominal muscles of the ventral body wall and an enlarged umbilical ring, through which the internal organs are …

Burst Mitofusin Activation Reverses Neuromuscular Dysfunction In Murine Cmt2a, Antonietta Franco, Xiawei Dang, Emily K. Walton, Joshua N. Ho, Barbara Zablocka, Cindy Ly, Timothy M. Miller, Robert H. Baloh, Michael E. Shy, Andrew S. Yoo, Gerald W. Dorn

Open Access Publications

Charcot-Marie-Tooth disease type 2A (CMT2A) is an untreatable childhood peripheral neuropathy caused by mutations of the mitochondrial fusion protein, mitofusin (MFN) 2. Here, pharmacological activation of endogenous normal mitofusins overcame dominant inhibitory effects of CMT2A mutants in reprogrammed human patient motor neurons, reversing hallmark mitochondrial stasis and fragmentation independent of causal

Acute Kidney Injury Pathology And Pathophysiology: A Retrospective Review, Joseph P. Gaut, Helen Liapis

Open Access Publications

Acute kidney injury (AKI) is the clinical term used for decline or loss of renal function. It is associated with chronic kidney disease (CKD) and high morbidity and mortality. However, not all causes of AKI lead to severe consequences and some are reversible. The underlying pathology can be a guide for treatment and assessment of prognosis. The Kidney Disease: Improving Global Outcomes guidelines recommend that the cause of AKI should be identified if possible. Renal biopsy can distinguish specific AKI entities and assist in patient management. This review aims to show the pathology of AKI, including glomerular and tubular diseases.

Argonaut: A Web Platform For Collaborative Multi-Omic Data Visualization And Exploration, Dain R Brademan, Ian J Miller, Nicholas W Kwiecien, David J Pagliarini, Michael S Westphall, Joshua J Coon, Evgenia Shishkova

Open Access Publications

Researchers now generate large multi-omic datasets using increasingly mature mass spectrometry techniques at an astounding pace, facing new challenges of "Big Data" dissemination, visualization, and exploration. Conveniently, web-based data portals accommodate the complexity of multi-omic experiments and the many experts involved. However, developing these tailored companion resources requires programming expertise and knowledge of web server architecture-a substantial burden for most. Here, we describe Argonaut, a simple, code-free, and user-friendly platform for creating customizable, interactive data-hosting websites. Argonaut carries out real-time statistical analyses of the data, which it organizes into easily sharable projects. Collaborating researchers worldwide can explore the results, visualized …

Proceedings From The Fourth International Symposium On Sigma-2 Receptors: Role In Health And Disease, Nicholas J Izzo, Martí Colom-Cadena, Aladdin A Riad, Jinbin Xu, Meharvan Singh, Carmen Abate, Michael A Cahill, Tara L Spires-Jones, Wayne D Bowen, Robert H Mach, Susan M Catalano

Open Access Publications

The sigma-2 receptor (S2R) complex has been implicated in central nervous system disorders ranging from anxiety and depression to neurodegenerative disorders such as Alzheimer's disease (AD). The proteins comprising the S2R complex impact processes including autophagy, cholesterol synthesis, progesterone signaling, lipid membrane-bound protein trafficking, and receptor stabilization at the cell surface. While there has been much progress in understanding the role of S2R in cellular processes and its potential therapeutic value, a great deal remains unknown. The

The Glycoprotease Cpaa Secreted By Medically Relevant Acinetobacter Species Targets Multiple O-Linked Host Glycoproteins, M Florencia Haurat, Nichollas E Scott, Gisela Di Venanzio, Juvenal Lopez, Benjamin Pluvinage, Alisdair B Boraston, Michael J Ferracane, Mario F Feldman

Open Access Publications

Glycans decorate proteins and affect their biological function, including protection against proteolytic degradation. However, pathogenic, and commensal bacteria have evolved specific glycoproteases that overcome the steric impediment posed by carbohydrates, cleaving glycoproteins precisely at their glycosylation site(s). Medically relevant

Isg15 Connects Autophagy And Ifn-Γ-Dependent Control Of Toxoplasma Gondii Infection In Human Cells, Jaya Bhushan, Joshua B Radke, Yi-Chieh Perng, Michael Mcallaster, Deborah J Lenschow, Herbert W Virgin, L David Sibley

Open Access Publications

The intracellular protozoan parasite

Alternative Splicing During The Chlamydomonas Reinhardtii Cell Cycle, Manishi Pandey, Gary D Stormo, Susan K Dutcher

Open Access Publications

Genome-wide analysis of transcriptome data in

Identifying And Validating Subtypes Within Major Psychiatric Disorders Based On Frontal-Posterior Functional Imbalance Via Deep Learning, Miao Chang, Fay Y Womer, Xiaohong Gong, Weixiong Zhang, Et Al

Open Access Publications

Converging evidence increasingly implicates shared etiologic and pathophysiological characteristics among major psychiatric disorders (MPDs), such as schizophrenia (SZ), bipolar disorder (BD), and major depressive disorder (MDD). Examining the neurobiology of the psychotic-affective spectrum may greatly advance biological determination of psychiatric diagnosis, which is critical for the development of more effective treatments. In this study, ensemble clustering was developed to identify subtypes within a trans-diagnostic sample of MPDs. Whole brain amplitude of low-frequency fluctuations (ALFF) was used to extract the low-dimensional features for clustering in a total of 944 participants: 581 psychiatric patients (193 with SZ, 171 with BD, and 217 …

Neurofibromatosis 1 - Mutant Microglia Exhibit Sexually-Dimorphic Cyclic Amp-Dependent Purinergic Defects, Nirmeen Elmadany, Francesca Logiacco, Alice Buonfiglioli, Verena C Haage, Elizabeth C Wright-Jin, Alexander Schattenberg, Roxane M Papawassiliou, Helmut Kettenmann, Marcus Semtner, David H Gutmann

Open Access Publications

As critical regulators of brain homeostasis, microglia are influenced by numerous factors, including sex and genetic mutations. To study the impact of these factors on microglia biology, we employed genetically engineered mice that model Neurofibromatosis type 1 (NF1), a disorder characterized by clinically relevant sexually dimorphic differences. While microglia phagocytic activity was reduced in both male and female heterozygous Nf1 mutant (Nf1+/-) mice, purinergic control of phagocytosis was only affected in male Nf1+/- mice. ATP-induced P2Y-mediated membrane currents and P2RY12-dependent laser lesion-induced accumulation of microglial processes were also only impaired in male, but not female Nf1+/-, microglia. These defects resulted …

A Molecular Understanding Of Alphavirus Entry, Autumn C. Holmes, Katherine Basore, Daved H. Fremont, Michael S. Diamond

Open Access Publications

Alphaviruses cause severe human illnesses including persistent arthritis and fatal encephalitis. As alphavirus entry into target cells is the first step in infection, intensive research efforts have focused on elucidating aspects of this pathway, including attachment, internalization, and fusion. Herein, we review recent developments in the molecular understanding of alphavirus entry both in vitro and in vivo and how these advances might enable the design of therapeutics targeting this critical step in the alphavirus life cycle.

Spontaneous Restoration Of Functional Β-Cell Mass In Obese Sm/J Mice, Mario A Miranda, Caryn Carson, Celine L St Pierre, Juan F Macias-Velasco, Jing W Hughes, Marcus Kunzmann, Heather Schmidt, Jessica P Wayhart, Heather A Lawson

Open Access Publications

Maintenance of functional β-cell mass is critical to preventing diabetes, but the physiological mechanisms that cause β-cell populations to thrive or fail in the context of obesity are unknown. High fat-fed SM/J mice spontaneously transition from hyperglycemic-obese to normoglycemic-obese with age, providing a unique opportunity to study β-cell adaptation. Here, we characterize insulin homeostasis, islet morphology, and β-cell function during SM/J's diabetic remission. As they resolve hyperglycemia, obese SM/J mice dramatically increase circulating and pancreatic insulin levels while improving insulin sensitivity. Immunostaining of pancreatic sections reveals that obese SM/J mice selectively increase β-cell mass but not α-cell mass. Obese SM/J …

Adaptation Of Arginine Synthesis Among Uropathogenic Branches Of The Escherichia Coli Phylogeny Reveals Adjustment To The Urinary Tract Habitat, Michael E Hibbing, Karen W Dodson, Vasilios Kalas, Swaine L Chen, Scott J Hultgren

Open Access Publications

Urinary tract infections (UTIs) are predominantly caused by uropathogenic

Digenic Variants In The Fgf21 Signaling Pathway Associated With Severe Insulin Resistance And Pseudoacromegaly, Stephen I Stone, Daniel J Wegner, Jennifer A Wambach, F Sessions Cole, Fumihiko Urano, David M Ornitz

Open Access Publications

Insulin-mediated pseudoacromegaly (IMPA) is a rare disease of unknown etiology. Here we report a 12-year-old female with acanthosis nigricans, hirsutism, and acromegalic features characteristic of IMPA. The subject was noted to have normal growth hormone secretion, with extremely elevated insulin levels. Studies were undertaken to determine a potential genetic etiology for IMPA. The proband and her family members underwent whole exome sequencing. Functional studies were undertaken to validate the pathogenicity of candidate variant alleles. Whole exome sequencing identified monoallelic, predicted deleterious variants in genes that mediate fibroblast growth factor 21 (FGF21) signaling,

Integrase-Rna Interactions Underscore The Critical Role Of Integrase In Hiv-1 Virion Morphogenesis, Jennifer L. Elliott, Jenna E. Eschbach, Pratibha C. Koneru, Wen Li, Maritza Puray-Chavez, Dana Townsend, Dana Q. Lawson, Alan N. Engelman, Mamuka Kvaratskhelia, Sebla B. Kutluay

Open Access Publications

A large number of human immunodeficiency virus 1 (HIV-1) integrase (IN) alterations, referred to as class II substitutions, exhibit pleiotropic effects during virus replication. However, the underlying mechanism for the class II phenotype is not known. Here we demonstrate that all tested class II IN substitutions compromised IN-RNA binding in virions by one of the three distinct mechanisms: (i) markedly reducing IN levels thus precluding the formation of IN complexes with viral RNA; (ii) adversely affecting functional IN multimerization and consequently impairing IN binding to viral RNA; and (iii) directly compromising IN-RNA interactions without substantially affecting IN levels or functional …

Interplay Of Rfx Transcription Factors 1, 2 And 3 In Motile Ciliogenesis, Sylvain Lemeille, Marie Paschaki, Dominique Baas, Laurette Morlé, Jean-Luc Duteyrat, Aouatef Ait-Lounis, Emmanuèle Barras, Fabien Soulavie, Julie Jerber, Joëlle Thomas, Yong Zhang, Michael J. Holtzman, W Stephen Kistler, Walter Reith, Bénédicte Durand

Open Access Publications

Cilia assembly is under strict transcriptional control during animal development. In vertebrates, a hierarchy of transcription factors (TFs) are involved in controlling the specification, differentiation and function of multiciliated epithelia. RFX TFs play key functions in the control of ciliogenesis in animals. Whereas only one RFX factor regulates ciliogenesis in C. elegans, several distinct RFX factors have been implicated in this process in vertebrates. However, a clear understanding of the specific and redundant functions of different RFX factors in ciliated cells remains lacking. Using RNA-seq and ChIP-seq approaches we identified genes regulated directly and indirectly by RFX1, RFX2 and RFX3 …