Gastrointestinal Pathology
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Resolving Transcriptional States and Predicting Lineages in the Annelid Capitella Teleta Using 1 Single-Cell Rnaseq 2 3 Abhinav
bioRxiv preprint doi: https://doi.org/10.1101/2020.10.16.342709; this version posted October 16, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Resolving transcriptional states and predicting lineages in the annelid Capitella teleta using 2 single-cell RNAseq 3 4 Abhinav Sur1 and Néva P. Meyer2* 5 6 1Unit on Cell Specification and Differentiation, National Institute of Child Health and Human 7 Development (NICHD), Bethesda, Maryland, USA, 20814 8 9 2Department of Biology, Clark University, 950 Main Street, Worcester, Massachusetts, USA, 10 01610. 11 12 13 [email protected] 14 [email protected] 15 16 *Corresponding author 17 18 19 20 21 Keywords: neurogenesis, single-cell RNAseq, annelid, cell type, differentiation trajectory, 22 pseudotime, RNA velocity, gene regulatory network. 23 bioRxiv preprint doi: https://doi.org/10.1101/2020.10.16.342709; this version posted October 16, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 24 Abstract 25 Evolution and diversification of cell types has contributed to animal evolution. However, gene 26 regulatory mechanisms underlying cell fate acquisition during development remains largely 27 uncharacterized in spiralians. Here we use a whole-organism, single-cell transcriptomic approach 28 to map larval cell types in the annelid Capitella teleta at 24- and 48-hours post gastrulation 29 (stages 4 and 5). -
Downloaded from the National Database for Autism Research (NDAR)
International Journal of Molecular Sciences Article Phenotypic Subtyping and Re-Analysis of Existing Methylation Data from Autistic Probands in Simplex Families Reveal ASD Subtype-Associated Differentially Methylated Genes and Biological Functions Elizabeth C. Lee y and Valerie W. Hu * Department of Biochemistry and Molecular Medicine, The George Washington University, School of Medicine and Health Sciences, Washington, DC 20037, USA; [email protected] * Correspondence: [email protected]; Tel.: +1-202-994-8431 Current address: W. Harry Feinstone Department of Molecular Microbiology and Immunology, y Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA. Received: 25 August 2020; Accepted: 17 September 2020; Published: 19 September 2020 Abstract: Autism spectrum disorder (ASD) describes a group of neurodevelopmental disorders with core deficits in social communication and manifestation of restricted, repetitive, and stereotyped behaviors. Despite the core symptomatology, ASD is extremely heterogeneous with respect to the severity of symptoms and behaviors. This heterogeneity presents an inherent challenge to all large-scale genome-wide omics analyses. In the present study, we address this heterogeneity by stratifying ASD probands from simplex families according to the severity of behavioral scores on the Autism Diagnostic Interview-Revised diagnostic instrument, followed by re-analysis of existing DNA methylation data from individuals in three ASD subphenotypes in comparison to that of their respective unaffected siblings. We demonstrate that subphenotyping of cases enables the identification of over 1.6 times the number of statistically significant differentially methylated regions (DMR) and DMR-associated genes (DAGs) between cases and controls, compared to that identified when all cases are combined. Our analyses also reveal ASD-related neurological functions and comorbidities that are enriched among DAGs in each phenotypic subgroup but not in the combined case group. -
Practice Parameters for the Treatment of Patients with Dominantly Inherited Colorectal Cancer
Practice Parameters For The Treatment Of Patients With Dominantly Inherited Colorectal Cancer Diseases of the Colon & Rectum 2003;46(8):1001-1012 Prepared by: The Standards Task Force The American Society of Colon and Rectal Surgeons James Church, MD; Clifford Simmang, MD; On Behalf of the Collaborative Group of the Americas on Inherited Colorectal Cancer and the Standards Committee of the American Society of Colon and Rectal Surgeons. The American Society of Colon and Rectal Surgeons is dedicated to assuring high quality patient care by advancing the science, prevention, and management of disorders and diseases of the colon, rectum, and anus. The standards committee is composed of Society members who are chosen because they have demonstrated expertise in the specialty of colon and rectal surgery. This Committee was created in order to lead international efforts in defining quality care for conditions related to the colon, rectum, and anus. This is accompanied by developing Clinical Practice Guidelines based on the best available evidence. These guidelines are inclusive, and not prescriptive. Their purpose is to provide information on which decisions can be made, rather than dictate a specific form of treatment. These guidelines are intended for the use of all practitioners, health care workers, and patients who desire information about the management of the conditions addressed by the topics covered in these guidelines. Practice Parameters for the Treatment of Patients With Dominantly Inherited Colorectal Cancer Inherited colorectal cancer includes two main syndromes in which predisposition to the disease is based on a germline mutation that may be transmitted from parent to child. -
Genetic/Familial High-Risk Assessment: Colorectal
NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines®) Genetic/Familial High-Risk Assessment: Colorectal Version 2.2019 — August 8, 2019 NCCN.org Continue Version 2.2019, 08/08/19 © 2019 National Comprehensive Cancer Network® (NCCN®), All rights reserved. NCCN Guidelines® and this illustration may not be reproduced in any form without the express written permission of NCCN. Printed by PEDRO ANTONIO PARRA BAOS on 11/18/2019 12:12:24 PM. For personal use only. Not approved for distribution. Copyright © 2019 National Comprehensive Cancer Network, Inc., All Rights Reserved. NCCN Guidelines Index NCCN Guidelines Version 2.2019 Table of Contents Genetic/Familial High-Risk Assessment: Colorectal Discussion *Dawn Provenzale, MD, MS/Chair ¤ Þ Michael J. Hall, MD, MS † ∆ Arnold J. Markowitz, MD ¤ Duke Cancer Institute Fox Chase Cancer Center Memorial Sloan Kettering Cancer Center *Samir Gupta, MD/Vice-chair ¤ Amy L. Halverson, MD ¶ Robert J. Mayer, MD † Þ UC San Diego Moores Cancer Center Robert H. Lurie Comprehensive Cancer Dana-Farber/Brigham and Women’s Center of Northwestern University Cancer Center Dennis J. Ahnen, MD ¤ University of Colorado Cancer Center Stanley R. Hamilton, MD ≠ June Mikkelson, MS, CGC ∆ The University of Texas Roswell Park Cancer Institute Lee-May Chen, MD ¶ MD Anderson Cancer Center UCSF Helen Diller Family Reid M. Ness, MD, MPH ¤ Comprehensive Cancer Center Heather Hampel, MS, CGC ∆ Vanderbilt-Ingram Cancer Center The Ohio State University Comprehensive Daniel C. Chung, MD ¤ ∆ Cancer Center - James Cancer Hospital Shajan Peter, MD ¤ Massachusetts General Hospital and Solove Research Institute O'Neal Comprehensive Cancer Center Cancer Center at UAB Sigurdis Haraldsdottir, MD, PhD † Gregory Cooper, MD ¤ Stanford Cancer Institute Scott E. -
Comparing Right Colon Adenoma and Hyperplastic Polyp
Title: Comparing right colon adenoma and hyperplastic polyp miss rate in colonoscopy using water exchange and carbon dioxide insufflation: A prospective multicenter randomized controlled trial NCT Number: 03845933 Unique Protocol ID: EGH-2019 Date: Feb 16, 2019 頁 1 / 10 INTRODUCTION Colonoscopy is currently regarded as the gold standard to detect and prevent colorectal cancer (CRC) [1]. It estimated to prevent about 76%-90% of CRC [2], but post-colonoscopy CRCs (PCCRCs) still occur. Recent case-control studies consistently demonstrated that protection by colonoscopy against right-sided colon cancer, ranging from 40% to 60%, was lower than the 80% protection attained in the left colon [3-5]. Of all PCCRCs, 58% were attributed to lesions missed during examination [6]. In a systematic review of tandem colonoscopy studies, a 22% pooled miss-rate for all polyps was reported [7]. Colonoscopy maneuvers helping to reduce miss-rate for all polyps, particularly in the right colon, have the potential to decrease the incidence of PCCRCs. Water exchange (WE) colonoscopy is characterized by the gasless insertion to the cecum in clear water and maximizing cleanliness during insertion. WE colonoscopy has been shown to improve the overall adenoma detection rate (ADR), compared to air insufflation colonoscopy, in many prospective randomized controlled trials (RCTs) [8-13]. WE colonoscopy also has been shown to improve right colon ADR in RCTs [10-12] and meta-analyses [14,15]. In a pooled data from two multisite RCTs, WE also significantly increases right colon combined advanced and sessile serrated ADR as compared to air insufflation colonoscopy [16]. Decreased multitasking-related distraction from cleaning maneuvers has been the most recently identified explanation for the increase in ADR by WE [17]. -
Combined Endo-Laparoscopic Surgery for Difficult Benign Colorectal Polyps
485 Review Article (Current Strategies in Colon Cancer Management) Combined endo-laparoscopic surgery for difficult benign colorectal polyps Zhong-Hui Liu1, Li Jiang1, Fion Siu-Yin Chan1,2, Michael Ka-Wah Li3, Joe King-Man Fan1,2,3 1Department of Surgery, The University of Hong Kong-Shenzhen Hospital, Shenzhen 518053, China; 2Department of Surgery, The University of Hong Kong, Hong Kong, China; 3Asia-Pacific Endo-Lap Surgery Group (APELS), Hong Kong, China Contributions: (I) Conception and design: JKM Fan, MKW Li; (II) Administrative support: MKW Li; (III) Provision of study materials or patients: FSY Chan; (IV) Collection and assembly of data: ZH Liu, L Jiang; (V) Data analysis and interpretation: ZH Liu; FSY Chan; JKM Fan; (VI) Manuscript writing: All authors; (VII) Final approval of manuscript: All authors. Correspondence to: Joe King-Man Fan, MBBS (HK), MS (HKU), FRCSEd, FACS. Department of Surgery, The University of Hong Kong-Shenzhen Hospital, Shenzhen 518053, China. Email: [email protected]. Abstract: Prevention of colorectal cancer (CRC) depends largely on the detection and removal of colorectal polyps. Despite the advances in endoscopic techniques, there are still a subgroup of polyps that cannot be treated purely by endoscopic approach, which comprise of about 10–15% of all the polyps. These so-called “difficult colorectal polyps” are polyps with large size, morphology, at difficult location, scarring or due to recurrence, which have historically been managed by surgical segmental resection. In treating benign difficult colorectal polyps, we have to balance the operative risks and morbidities associated with surgical segmental resection. Therefore, combined endoscopic and laparoscopic surgery (CELS) has been developed to remove this subgroup of difficult benign polyps. -
Familial Adenomatous Polyposis Polymnia Galiatsatos, M.D., F.R.C.P.(C),1 and William D
American Journal of Gastroenterology ISSN 0002-9270 C 2006 by Am. Coll. of Gastroenterology doi: 10.1111/j.1572-0241.2006.00375.x Published by Blackwell Publishing CME Familial Adenomatous Polyposis Polymnia Galiatsatos, M.D., F.R.C.P.(C),1 and William D. Foulkes, M.B., Ph.D.2 1Division of Gastroenterology, Department of Medicine, The Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montreal, Quebec, Canada, and 2Program in Cancer Genetics, Departments of Oncology and Human Genetics, McGill University, Montreal, Quebec, Canada Familial adenomatous polyposis (FAP) is an autosomal-dominant colorectal cancer syndrome, caused by a germline mutation in the adenomatous polyposis coli (APC) gene, on chromosome 5q21. It is characterized by hundreds of adenomatous colorectal polyps, with an almost inevitable progression to colorectal cancer at an average age of 35 to 40 yr. Associated features include upper gastrointestinal tract polyps, congenital hypertrophy of the retinal pigment epithelium, desmoid tumors, and other extracolonic malignancies. Gardner syndrome is more of a historical subdivision of FAP, characterized by osteomas, dental anomalies, epidermal cysts, and soft tissue tumors. Other specified variants include Turcot syndrome (associated with central nervous system malignancies) and hereditary desmoid disease. Several genotype–phenotype correlations have been observed. Attenuated FAP is a phenotypically distinct entity, presenting with fewer than 100 adenomas. Multiple colorectal adenomas can also be caused by mutations in the human MutY homologue (MYH) gene, in an autosomal recessive condition referred to as MYH associated polyposis (MAP). Endoscopic screening of FAP probands and relatives is advocated as early as the ages of 10–12 yr, with the objective of reducing the occurrence of colorectal cancer. -
3. Studies of Colorectal Cancer Screening
IARC HANDBOOKS COLORECTAL CANCER SCREENING VOLUME 17 This publication represents the views and expert opinions of an IARC Working Group on the Evaluation of Cancer-Preventive Strategies, which met in Lyon, 14–21 November 2017 LYON, FRANCE - 2019 IARC HANDBOOKS OF CANCER PREVENTION 3. STUDIES OF COLORECTAL CANCER SCREENING 3.1 Methodological considerations end-point of the RCT can be the incidence of the cancer of interest. Methods for colorectal cancer (CRC) screen- The observed effect of screening in RCTs is ing include endoscopic methods and stool-based dependent on, among other things, the partic- tests for blood. The two primary end-points for ipation in the intervention group and the limi- endoscopic CRC screening are (i) finding cancer tation of contamination of the control group. at an early stage (secondary prevention) and Low participation biases the estimate of effect (ii) finding and removing precancerous lesions towards its no-effect value, and therefore it must (adenomatous polyps), to reduce the incidence be evaluated and reported. Screening of controls of CRC (primary prevention). The primary by services outside of the RCT also dilutes the end-point for stool-based tests is finding cancer effect of screening on CRC incidence and/or at an early stage. Stool-based tests also have some mortality. If the screening modality being eval- ability to detect adenomatous polyps; therefore, a uated is widely used in clinical practice in secondary end-point of these tests is reducing the the region or regions where the RCT is being incidence of CRC. conducted, then contamination may be consid- erable, although it may be difficult and/or costly 3.1.1 Randomized controlled trials of to estimate its extent. -
Molecular Classification of Patients with Unexplained Hamartomatous and Hyperplastic Polyposis
ORIGINAL CONTRIBUTION Molecular Classification of Patients With Unexplained Hamartomatous and Hyperplastic Polyposis Kevin Sweet, MS, CGC Context Significant proportions of patients with hamartomatous polyposis or with Joseph Willis, MD hyperplastic/mixed polyposis remain without specific clinical and molecular diagnosis Xiao-Ping Zhou, MD, PhD or present atypically. Assigning a syndromic diagnosis is important because it guides management, especially surveillance and prophylactic surgery. Carol Gallione, PhD Objective To systematically classify patients with unexplained hamartomatous or hy- Takeshi Sawada, MD, PhD perplastic/mixed polyposis by extensive molecular analysis in the context of central Pia Alhopuro, MD rereview of histopathology results. Sok Kean Khoo, PhD Design, Setting, and Patients Prospective, referral-based study of 49 unrelated patients from outside institutions (n=28) and at a comprehensive cancer center (n=21), Attila Patocs, MD, PhD conducted from May 2, 2002, until December 15, 2004. Germline analysis of PTEN, Cossette Martin, PhD BMPR1A, STK11 (sequence, deletion), SMAD4, and ENG (sequence), specific exon screen- Scott Bridgeman, BSc ing of BRAF, MYH, and BHD, and rereview of polyp histology results were performed. John Heinz, PhD Main Outcome Measures Molecular, clinical, and histopathological findings in pa- tients with unexplained polyposis. Robert Pilarski, MS, CGC Results Of the 49 patients, 11 (22%) had germline mutations. Of 14 patients with Rainer Lehtonen, BSc juvenile polyposis, 2 with early-onset disease had mutations in ENG, encoding endo- Thomas W. Prior, PhD glin, previously only associated with hereditary hemorrhagic telangiectasia; 1 had hemi- zygous deletion encompassing PTEN and BMPR1A; and 1 had an SMAD4 mutation. Thierry Frebourg, MD, PhD One individual previously classified with Peutz-Jeghers syndrome had a PTEN dele- Bin Tean Teh, MD, PhD tion. -
Identification of Potential Key Genes and Pathway Linked with Sporadic Creutzfeldt-Jakob Disease Based on Integrated Bioinformatics Analyses
medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Identification of potential key genes and pathway linked with sporadic Creutzfeldt-Jakob disease based on integrated bioinformatics analyses Basavaraj Vastrad1, Chanabasayya Vastrad*2 , Iranna Kotturshetti 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. 3. Department of Ayurveda, Rajiv Gandhi Education Society`s Ayurvedic Medical College, Ron, Karnataka 562209, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Abstract Sporadic Creutzfeldt-Jakob disease (sCJD) is neurodegenerative disease also called prion disease linked with poor prognosis. The aim of the current study was to illuminate the underlying molecular mechanisms of sCJD. The mRNA microarray dataset GSE124571 was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened. -
Neuroscience Recombinant Proteins & Monoclonal Antibodies
www.atgenglobal.com Neuroscience Recombinant Proteins & Monoclonal Antibodies Global Bio Frontier Global Bio Frontier Neurodegenerative Disease Neurodegeneration is the progressive loss of Prion disease structure or function of neurons, including death of Frontotemporal dementia Alzheimer's disease neurons. Many neurodegenerative diseases – including amyotrophic lateral sclerosis, Parkinson's disease, Alzheimer's disease, and Huntington's disease – occur as a result of neurodegenerative processes. Such diseases are incurable, resulting in progres- Lewy body dementia sive degeneration and/or death of neuron cells. As Parkinson's disease research progresses, many similarities appear that relate these diseases to one another on a sub-cellular Huntington's disease level. Neurodegeneration can be found in many different levels of neuronal circuitry ranging from molecular to systemic. Amyotrophic Lateral Sclerosis Related Monoclonal Antibodies Product name Clone No. Applications Host Cat No. AT1E10 ELISA, WB, ICC/IF M ATGA0244 alpha-Synuclein 5C2 ELISA, WB, ICC/IF M ANC0603 alpha/beta-Synuclein 3B6 ELISA, WB, FACS, ICC/IF M ASC0632 HMGB1/HMG-1 J2E1 ELISA, WB, IHC M AHM0915 AT1E12 ELISA, WB, FACS, ICC/IF M ATGA0292 Park7/DJ-1 1B11 ELISA, WB M ADJ0618 UCH-L1/PGP9.5 3D9 ELISA, WB, ICC/IF, IHC M APG0714 AT3F9 ELISA, WB, ICC/IF M ATGA0342 HTRA2/Omi 1B3 ELISA, WB M AOH0607 APP/Protease Nexin II J4H9 ELISA, WB, FACS, ICC/IF M AAP0836 GSK-3 beta 1F7 ELISA, WB, FACS, ICC/IF M AGK0601 SOD1/Cu-Zn SOD AT6F1 ELISA, WB, FACS, ICC/IF M ATGA0405 14-3-3 gamma AT4B9 ELISA, WB, ICC/IF M ATGA0312 14-3-3 epsilon AT4F8 ELISA, WB, ICC/IF M ATGA0124 14-3-3 theta AT1A1 ELISA, WB, ICC/IF M ATGA0132 CAPNS1 AT1D11 ELISA, WB, ICC/IF M ATGA0367 TDP-43/TARDBP k1B8 ELISA, WB, IHC M ATA0834 Alpha-Synuclein antibody (AT1E10) UCH-L1/PGP9.5 antibody (3D9) HMGB1/HMG-1 antibody (J2E1) (Cat No. -
Proteome Dynamics During Homeostatic Scaling in Cultured
RESEARCH ADVANCE Proteome dynamics during homeostatic scaling in cultured neurons Aline Ricarda Do¨ rrbaum1,2, Beatriz Alvarez-Castelao1, Belquis Nassim-Assir1, Julian D Langer1,3*, Erin M Schuman1* 1Max Planck Institute for Brain Research, Frankfurt, Germany; 2Goethe University Frankfurt, Faculty of Biological Sciences, Frankfurt, Germany; 3Max Planck Institute of Biophysics, Frankfurt, Germany Abstract Protein turnover, the net result of protein synthesis and degradation, enables cells to remodel their proteomes in response to internal and external cues. Previously, we analyzed protein turnover rates in cultured brain cells under basal neuronal activity and found that protein turnover is influenced by subcellular localization, protein function, complex association, cell type of origin, and by the cellular environment (Do¨ rrbaum et al., 2018). Here, we advanced our experimental approach to quantify changes in protein synthesis and degradation, as well as the resulting changes in protein turnover or abundance in rat primary hippocampal cultures during homeostatic scaling. Our data demonstrate that a large fraction of the neuronal proteome shows changes in protein synthesis and/or degradation during homeostatic up- and down-scaling. More than half of the quantified synaptic proteins were regulated, including pre- as well as postsynaptic proteins with diverse molecular functions. Introduction *For correspondence: Long-lasting changes in synaptic strength, which are a basis for learning and memory formation, [email protected] (JDL); require de-novo protein synthesis as well as the degradation of existing proteins (Cajigas et al., [email protected] (EMS) 2010; Hegde, 2017; Jarome and Helmstetter, 2013; Tai and Schuman, 2008). For example, injec- tions of the protein synthesis inhibitor puromycin (Flexner et al., 1963) or of the proteasome inhibi- Competing interests: The tor lactacystin (Lopez-Salon et al., 2001) into rodent brains during specific time windows after authors declare that no training blocked long-term memory formation.