The Transcription Factor Sox7 Modulates Endocardiac Cushion
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Heart and Circulatory System I
Heart and Circulatory System I Daphne T. Hsu, MD Professor of Clinical Pediatrics [email protected] Outline • Vasculogenesis • Embryonic Folding • Formation of the Primary Heart Tube • Looping • Atrial Septation • Primitive Ventricular Septum • Atrioventricular Canal/Endocardial Cushions • Conotruncal Septation • Ventricular septation • Congenital Heart Defects CARDIOVASCULAR SYSTEM: EARLY DEVELOPMENT: WEEK 3 EMBRYONIC FOLDING: WEEK 4 Formation of Heart Tube (17-22 days) Heart Development: 26 days PRIMITIVE HEART TUBE: WEEK 4 Cardiac Loop (8-16 somites) VENTRICULAR LOOPING END WEEK 4 NORMAL : Loop to the RIGHT: Levocardia! ABNORMAL: Loop to the LEFT: Dextrocardia! FROM TUBE TO FOUR CHAMBERS INTERNAL VIEW Formation of Primitive Ventricles Atrial Septation: 3 Septums Primum, Secundum, Intermedium Endocardial Cushion: 80 days Endocardial Cushions • Atrioventricular Canal: Divide between the atria and ventricles • Endocardial Cushions: Four tissue expansions found in periphery of AV canal – Atrial septation – Atrioventricular valve formation: Mitral and Tricuspid Valves – Ventricular septation Endocardial Cushions • Superior-Inferior cushions – Septum Intermedium – Inferior atrial septum – Posterior/superior ventricular septum • Right and Left Cushions – Ventricular myocardium – Mitral valve – Tricuspid valve Atrioventricular Valve Formation • Left and Right Endocardial Cushions FOUR CHAMBERS- ULTRASOUND VIEW @ 20 wks Congenital Heart Defect: Endocardial Cushion Defect Normal Endocardial Cushion Defect Ventricular Outflow Tracts and Great -
Integrative Differential Expression and Gene Set Enrichment Analysis Using Summary Statistics for Scrna-Seq Studies
ARTICLE https://doi.org/10.1038/s41467-020-15298-6 OPEN Integrative differential expression and gene set enrichment analysis using summary statistics for scRNA-seq studies ✉ Ying Ma 1,7, Shiquan Sun 1,7, Xuequn Shang2, Evan T. Keller 3, Mengjie Chen 4,5 & Xiang Zhou 1,6 Differential expression (DE) analysis and gene set enrichment (GSE) analysis are commonly applied in single cell RNA sequencing (scRNA-seq) studies. Here, we develop an integrative 1234567890():,; and scalable computational method, iDEA, to perform joint DE and GSE analysis through a hierarchical Bayesian framework. By integrating DE and GSE analyses, iDEA can improve the power and consistency of DE analysis and the accuracy of GSE analysis. Importantly, iDEA uses only DE summary statistics as input, enabling effective data modeling through com- plementing and pairing with various existing DE methods. We illustrate the benefits of iDEA with extensive simulations. We also apply iDEA to analyze three scRNA-seq data sets, where iDEA achieves up to five-fold power gain over existing GSE methods and up to 64% power gain over existing DE methods. The power gain brought by iDEA allows us to identify many pathways that would not be identified by existing approaches in these data. 1 Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA. 2 School of Computer Science, Northwestern Polytechnical University, Xi’an, Shaanxi 710072, P.R. China. 3 Department of Urology, University of Michigan, Ann Arbor, MI 48109, USA. 4 Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA. 5 Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA. -
Supplementary Materials
Supplementary Materials + - NUMB E2F2 PCBP2 CDKN1B MTOR AKT3 HOXA9 HNRNPA1 HNRNPA2B1 HNRNPA2B1 HNRNPK HNRNPA3 PCBP2 AICDA FLT3 SLAMF1 BIC CD34 TAL1 SPI1 GATA1 CD48 PIK3CG RUNX1 PIK3CD SLAMF1 CDKN2B CDKN2A CD34 RUNX1 E2F3 KMT2A RUNX1 T MIXL1 +++ +++ ++++ ++++ +++ 0 0 0 0 hematopoietic potential H1 H1 PB7 PB6 PB6 PB6.1 PB6.1 PB12.1 PB12.1 Figure S1. Unsupervised hierarchical clustering of hPSC-derived EBs according to the mRNA expression of hematopoietic lineage genes (microarray analysis). Hematopoietic-competent cells (H1, PB6.1, PB7) were separated from hematopoietic-deficient ones (PB6, PB12.1). In this experiment, all hPSCs were tested in duplicate, except PB7. Genes under-expressed or over-expressed in blood-deficient hPSCs are indicated in blue and red respectively (related to Table S1). 1 C) Mesoderm B) Endoderm + - KDR HAND1 GATA6 MEF2C DKK1 MSX1 GATA4 WNT3A GATA4 COL2A1 HNF1B ZFPM2 A) Ectoderm GATA4 GATA4 GSC GATA4 T ISL1 NCAM1 FOXH1 NCAM1 MESP1 CER1 WNT3A MIXL1 GATA4 PAX6 CDX2 T PAX6 SOX17 HBB NES GATA6 WT1 SOX1 FN1 ACTC1 ZIC1 FOXA2 MYF5 ZIC1 CXCR4 TBX5 PAX6 NCAM1 TBX20 PAX6 KRT18 DDX4 TUBB3 EPCAM TBX5 SOX2 KRT18 NKX2-5 NES AFP COL1A1 +++ +++ 0 0 0 0 ++++ +++ ++++ +++ +++ ++++ +++ ++++ 0 0 0 0 +++ +++ ++++ +++ ++++ 0 0 0 0 hematopoietic potential H1 H1 H1 H1 H1 H1 PB6 PB6 PB7 PB7 PB6 PB6 PB7 PB6 PB6 PB6.1 PB6.1 PB6.1 PB6.1 PB6.1 PB6.1 PB12.1 PB12.1 PB12.1 PB12.1 PB12.1 PB12.1 Figure S2. Unsupervised hierarchical clustering of hPSC-derived EBs according to the mRNA expression of germ layer differentiation genes (microarray analysis) Selected ectoderm (A), endoderm (B) and mesoderm (C) related genes differentially expressed between hematopoietic-competent (H1, PB6.1, PB7) and -deficient cells (PB6, PB12.1) are shown (related to Table S1). -
The Zebrafish Cardiac Endothelial Cell—Roles in Development And
Journal of Cardiovascular Development and Disease Review The Zebrafish Cardiac Endothelial Cell—Roles in Development and Regeneration Vanessa Lowe 1, Laura Wisniewski 2 and Caroline Pellet-Many 3,* 1 Heart Centre, Barts & The London School of Medicine, William Harvey Research Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; [email protected] 2 Centre for Tumour Microenvironment, Barts Cancer Institute, Queen Mary University London, Charterhouse Square, London EC1M 6BQ, UK; [email protected] 3 Department of Comparative Biomedical Sciences, Royal Veterinary College, 4 Royal College Street, London NW1 0TU, UK * Correspondence: [email protected] Abstract: In zebrafish, the spatiotemporal development of the vascular system is well described due to its stereotypical nature. However, the cellular and molecular mechanisms orchestrating post-embryonic vascular development, the maintenance of vascular homeostasis, or how coronary vessels integrate into the growing heart are less well studied. In the context of cardiac regeneration, the central cellular mechanism by which the heart regenerates a fully functional myocardium relies on the proliferation of pre-existing cardiomyocytes; the epicardium and the endocardium are also known to play key roles in the regenerative process. Remarkably, revascularisation of the injured tissue occurs within a few hours after cardiac damage, thus generating a vascular network acting as a scaffold for the regenerating myocardium. The activation of the endocardium leads to the secretion of cytokines, further supporting the proliferation of the cardiomyocytes. Although epicardium, Citation: Lowe, V.; Wisniewski, L.; endocardium, and myocardium interact with each other to orchestrate heart development and Pellet-Many, C. The Zebrafish Cardiac regeneration, in this review, we focus on recent advances in the understanding of the development of Endothelial Cell—Roles in the endocardium and the coronary vasculature in zebrafish as well as their pivotal roles in the heart Development and Regeneration. -
LEFTY2 Inhibits Endometrial Receptivity by Downregulating Orai1 Expression and Store-Operated Ca2+ Entry
J Mol Med (2018) 96:173–182 https://doi.org/10.1007/s00109-017-1610-9 ORIGINAL ARTICLE LEFTY2 inhibits endometrial receptivity by downregulating Orai1 expression and store-operated Ca2+ entry Madhuri S. Salker 1 & Yogesh Singh 2 & Ruban R. Peter Durairaj3 & Jing Yan4 & Md Alauddin1 & Ni Zeng4 & Jennifer H. Steel5,6 & Shaqiu Zhang4 & Jaya Nautiyal5 & Zoe Webster6 & Sara Y. Brucker1 & Diethelm Wallwiener1 & B. Anne Croy7 & Jan J. Brosens3,8 & Florian Lang4,9 Received: 3 May 2017 /Revised: 16 October 2017 /Accepted: 2 November 2017 /Published online: 11 December 2017 # The Author(s) 2017. This article is an open access publication Abstract Furthermore, LEFTY2 and the Orai1 blockers 2-APB, Early embryo development and endometrial differentiation MRS-1845, as well as YM-58483, inhibited, whereas the are initially independent processes, and synchronization, im- Ca2+ ionophore, ionomycin, strongly upregulated COX2, posed by a limited window of implantation, is critical for BMP2 and WNT4 expression in decidualizing HESCs. These reproductive success. A putative negative regulator of endo- findings suggest that LEFTY2 closes the implantation win- metrial receptivity is LEFTY2, a member of the transforming dow, at least in part, by downregulating Orai1, which in turn growth factor (TGF)-β family. LEFTY2 is highly expressed in limits SOCE and antagonizes expression of Ca2+-sensitive decidualizing human endometrial stromal cells (HESCs) dur- receptivity genes. ing the late luteal phase of the menstrual cycle, coinciding with the closure of the window of implantation. Here, we Key messages show that flushing of the uterine lumen in mice with recom- • Endometrial receptivity is negatively regulated by binant LEFTY2 inhibits the expression of key receptivity LEFTY2. -
Down-Regulated Hsa Circ 0067934 Facilitated the Progression of Gastric Cancer by Sponging Hsa-Mir-4705 to Downgrade the Expression of BMPR1B
2703 Original Article Down-regulated hsa_circ_0067934 facilitated the progression of gastric cancer by sponging hsa-mir-4705 to downgrade the expression of BMPR1B Shen-Nan He1, Shi-Hua Guan1, Meng-Yao Wu1, Wei Li1,2,3, Meng-Dan Xu1, Min Tao1,2 1Department of Oncology, the First Affiliated Hospital of Soochow University, Suzhou 215006, China; 2PREMED Key Laboratory for Precision Medicine, Soochow University, Suzhou 215021, China; 3Comprehensive Cancer Center, Suzhou Xiangcheng People’s Hospital, Suzhou 215000, China Contributions: (I) Conception and design: SN He, M Tao, MD Xu; (II) Administrative support: W Li, M Tao; (III) Provision of study materials or patients: None; (IV) Collection and assembly of data: SN He; (V) Data analysis and interpretation: SN He, SH Guan; (VI) Manuscript writing: All authors; (VII) Final approval of manuscript: All authors. Correspondence to: Min Tao, MD, PhD; Meng-Dan Xu, MD. Department of Oncology, the First Affiliated Hospital of Soochow University, Suzhou, China. Email: [email protected]; [email protected]. Background: Gastric cancer is the third most lethal cancer worldwide. Finding a novel marker is essential to targeted therapy and the diagnosis of gastric cancer. As newly discovered markers, circRNAs have aroused widespread attention on a global scale. Our research aims to understand the role of circRNAs in gastric cancer and to explore the underlying pathogenesis. Methods: Raw expression data of circRNAs were obtained from the GEO database. Integrated bioinformatics analysis was used to screen differentially expressed circRNAs (DECs) by RobustRankAggreg package. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed to predict the functions of DECs. -
SOX7 Is Down-Regulated in Lung Cancer
Hayano et al. Journal of Experimental & Clinical Cancer Research 2013, 32:17 http://www.jeccr.com/content/32/1/17 RESEARCH Open Access SOX7 is down-regulated in lung cancer Takahide Hayano1, Manoj Garg1*, Dong Yin2, Makoto Sudo1, Norihiko Kawamata2, Shuo Shi3, Wenwen Chien1, Ling-wen Ding1, Geraldine Leong1, Seiichi Mori4, Dong Xie3, Patrick Tan1,5 and H Phillip Koeffler1,2,6 Abstract Background: SOX7 is a transcription factor belonging to the SOX family. Its role in lung cancer is unknown. Methods: In this study, whole genomic copy number analysis was performed on a series of non-small cell lung cancer (NSCLC) cell lines and samples from individuals with epidermal growth factor receptor (EGFR) mutations using a SNP-Chip platform. SOX7 was measured in NSCLC samples and cell lines, and forced expressed in one of these lines. Results: A notable surprise was that the numerous copy number (CN) changes observed in samples of Asian, non-smoking EGFR mutant NSCLC were nearly the same as those CN alterations seen in a large collection of NSCLC from The Cancer Genome Atlas which is presumably composed of predominantly Caucasians who often smoked. However, four regions had CN changes fairly unique to the Asian EGFR mutant group. We also examined CN changes in NSCLC lines. The SOX7 gene was homozygously deleted in one (HCC2935) of 10 NSCLC cell lines and heterozygously deleted in two other NSCLC lines. Expression of SOX7 was significantly downregulated in NSCLC cell lines (8/10, 80%) and a large collection of NSCLC samples compared to matched normal lung (57/62, 92%, p= 0.0006). -
Twelve-Year Changes in Protein Profiles in Patients with and Without Gastric Bypass Surgery
medRxiv preprint doi: https://doi.org/10.1101/2020.08.13.20173666; this version posted August 14, 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. Twelve-year changes in protein profiles in patients with and without gastric bypass surgery. Noha A. Yousri1,2,*, Rudolf Engelke3, Hina Sarwath3, Rodrick D. McKinlay4, Steven C. Simper4, Ted D. Adams5,6, Frank Schmidt3,7, Karsten Suhre8, Steven C. Hunt1,6 1 Department of Genetic Medicine, Weill Cornell Medicine, Doha, Qatar 2 Computer and Systems Engineering, Alexandria University, Egypt 3 Proteomics core, Weill Cornell Medicine, Doha, Qatar 4 Rocky Mountain Associated Physicians, Salt Lake City, Utah 5 Intermountain Live Well Center, Intermountain Healthcare, Salt Lake City, Utah 6 Department of Internal Medicine, University of Utah, Salt Lake City, Utah 7 Department of Biochemistry, Weill Cornell Medicine, Doha, Qatar 8 Department of Physiology and Biophysics, Weill Cornell Medicine, Doha, Qatar Short title: Proteomic changes after gastric bypass surgery Key words: obesity, bariatric surgery, longitudinal study, proteomics *Corresponding author: Noha A. Yousri, PhD, Department of Genetic Medicine, Weill Cornell Medicine, PO Box 24144, Education City, Doha, Qatar Email: [email protected] Phone: +974 4492 8425 Funding: Supported by a grant (DK-55006) from the National Institute of Diabetes and Digestive and Kidney Diseases of the National Institutes of Health, a U.S. Public Health Service research grant (MO1-RR00064) from the National Center for Research Resources, Biomedical Research Program funds from Intermountain Healthcare, and from Qatar Foundation to Weill Cornell Medicine. -
The First Scube3 Mutant Mouse Line with Pleiotropic Phenotypic Alterations
INVESTIGATION The First Scube3 Mutant Mouse Line with Pleiotropic Phenotypic Alterations Helmut Fuchs,*,†,1 Sibylle Sabrautzki,*,‡,1 Gerhard K. H. Przemeck,*,†,1 Stefanie Leuchtenberger,* Bettina Lorenz-Depiereux,§ Lore Becker,* Birgit Rathkolb,*,†,** Marion Horsch,* Lillian Garrett,*,†† Manuela A. Östereicher,* Wolfgang Hans,* Koichiro Abe,‡‡ Nobuho Sagawa,‡‡ Jan Rozman,*,† Ingrid L. Vargas-Panesso,*,§§,*** Michael Sandholzer,* Thomas S. Lisse,*,2 Thure Adler,*,††† Juan Antonio Aguilar-Pimentel,* Julia Calzada-Wack,*,‡‡‡ Nicole Ehrhard,*,§§§,3 Ralf Elvert,*,4 Christine Gau,* Sabine M. Hölter,*,†† Katja Micklich,*,** Kristin Moreth,* Cornelia Prehn,* Oliver Puk,*,††,5 Ildiko Racz,**** Claudia Stoeger,* Alexandra Vernaleken,*,§§,*** Dian Michel,*,6 Susanne Diener,§ Thomas Wieland,§ Jerzy Adamski,*,† Raffi Bekeredjian,†††† Dirk H. Busch,‡‡‡‡ John Favor,§ Jochen Graw,†† Martin Klingenspor,§§§§,***** Christoph Lengger,* Holger Maier,* Frauke Neff,*,‡‡‡ Markus Ollert,†††††,‡‡‡‡‡,§§§§§ Tobias Stoeger,****** Ali Önder Yildirim,****** Tim M. Strom,§ Andreas Zimmer,**** Eckhard Wolf,** Wolfgang Wurst,††,††††††,‡‡‡‡‡‡,§§§§§§ Thomas Klopstock,§§,***,††††††,§§§§§§ Johannes Beckers,*,†,******* Valerie Gailus-Durner,*,† and Martin Hrabé de Angelis*,†,***,*******,7 ORCID IDs: 0000-0002-5143-2677 (H.F.); 0000-0002-3435-921X (S.S.); 0000-0003-3730-3454 (G.K.H.P.); 0000-0003-3730-3454 (S.L.); 0000-0002-6890-4984 (L.B.); 0000-0003-1239-0547 (B.R.); 0000-0003-4333-2366 (M.A.Ö.); 0000-0002-1221-4108 (W.H.); 0000-0002-8035-8904 (J.R.); 0000-0001-5682-8454 (I.L.V.-P.); -
Genetics of Atrioventricular Canal Defects Flaminia Pugnaloni1, Maria Cristina Digilio2, Carolina Putotto1, Enrica De Luca1, Bruno Marino1 and Paolo Versacci1*
Pugnaloni et al. Italian Journal of Pediatrics (2020) 46:61 https://doi.org/10.1186/s13052-020-00825-4 REVIEW Open Access Genetics of atrioventricular canal defects Flaminia Pugnaloni1, Maria Cristina Digilio2, Carolina Putotto1, Enrica De Luca1, Bruno Marino1 and Paolo Versacci1* Abstract Atrioventricular canal defect (AVCD) represents a quite common congenital heart defect (CHD) accounting for 7.4% of all cardiac malformations. AVCD is a very heterogeneous malformation that can occur as a phenotypical cardiac aspect in the context of different genetic syndromes but also as an isolated, non-syndromic cardiac defect. AVCD has also been described in several pedigrees suggesting a pattern of familiar recurrence. Targeted Next Generation Sequencing (NGS) techniques are proved to be a powerful tool to establish the molecular heterogeneity of AVCD. Given the complexity of cardiac embryology, it is not surprising that multiple genes deeply implicated in cardiogenesis have been described mutated in patients with AVCD. This review attempts to examine the recent advances in understanding the molecular basis of this complex CHD in the setting of genetic syndromes or in non- syndromic patients. Keywords: Congenital heart disease, Atrioventricular canal defect, Genetics Introduction extracellular matrix, leading to absent or incomplete fu- The atrioventricular canal defect (AVCD), also called sion of ventral (antero-superior) and dorsal (postero-in- atrioventricular septal defect, is a quite common con- ferior) atrioventricular cushions [2–4]. Nevertheless, the genital heart defect (CHD), accounting for 7.4% of all hypothesis that extracardiac progenitor cells contribute cardiac malformations. It can be anatomically classified also to the growth of the inlet part of the heart has been in complete, partial and intermediate types. -
Contribution of Copy-Number Variation to Down Syndrome–Associated Atrioventricular Septal Defects
Original Research Article © American College of Medical Genetics and Genomics © American College of Medical Genetics and Genomics ORIGINAL RESEARCH ARTICLE Contribution of copy-number variation to Down syndrome–associated atrioventricular septal defects Dhanya Ramachandran, PhD1, Jennifer G. Mulle, MPH, PhD1,2, Adam E. Locke, PhD3,9, Lora J.H. Bean, PhD1, Tracie C. Rosser, PhD1, Promita Bose, MS1, Kenneth J. Dooley, MD4, Clifford L. Cua, MD5, George T. Capone, MD6, Roger H. Reeves, PhD7, Cheryl L. Maslen, PhD8, David J. Cutler, PhD1, Stephanie L. Sherman, PhD1 and Michael E. Zwick, PhD1 Purpose: The goal of this study was to identify the contribution of contrast, cases had a greater burden of large, rare deletions (P < 0.01) large copy-number variants to Down syndrome–associated atrioven- and intersected more genes (P < 0.007) as compared with controls. tricular septal defects, the risk for which in the trisomic population is We also observed a suggestive enrichment of deletions intersecting 2,000-fold more as compared with that of the general disomic popu- ciliome genes in cases as compared with controls. lation. Conclusion: Our data provide strong evidence that large, rare dele- Methods: Genome-wide copy-number variant analysis was per- tions increase the risk of Down syndrome–associated atrioventricu- formed on 452 individuals with Down syndrome (210 cases with lar septal defects, whereas large, common copy-number variants do complete atrioventricular septal defects; 242 controls with structur- not appear to increase the risk of Down syndrome–associated atrio- ally normal hearts) using Affymetrix SNP 6.0 arrays, making this the ventricular septal defects. -
Identification of Prognostic and Metastasis-Related Alternative
Bioscience Reports (2020) 40 BSR20201001 https://doi.org/10.1042/BSR20201001 Research Article Identification of prognostic and metastasis-related alternative splicing signatures in hepatocellular carcinoma 1,2,3,* 1,* 1,* 3 4 5 1 1 Runzhi Huang , Gaili Yan , Hanlin Sun , Jie Zhang , Dianwen Song , Rui Kong , Penghui Yan , Peng Hu , Downloaded from http://portlandpress.com/bioscirep/article-pdf/40/7/BSR20201001/888290/bsr-2020-1001.pdf by guest on 25 September 2021 Aiqing Xie6, Siqiao Wang3, Juanwei Zhuang1, Huabin Yin4, Tong Meng2,4 and Zongqiang Huang1 1Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, 1 East Jianshe Road, Zhengzhou, China; 2Division of Spine, Department of Orthopedics, Tongji Hospital Affiliated to Tongji University School of Medicine, 389 Xincun Road, Shanghai, China; 3Tongji University School of Medicine, Tongji University, 1239 Siping Road, Shanghai 200092, China; 4Department of Orthopedics, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, 100 Haining Road, Shanghai, China; 5Department of Gastroenterology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai 200072, China; 6School of Ocean and Earth Science, Tongji University, 1239 Siping Road, Shanghai 200092, China Correspondence: Zongqiang Huang ([email protected]) or Huabin Yin ([email protected]) or Tong Meng ([email protected]) As the most common neoplasm in digestive system, hepatocellular carcinoma (HCC) is one of the most important leading cause of cancer deaths worldwide. Its high-frequency metas- tasis and relapse rate lead to the poor survival of HCC patients. However, the mechanism of HCC metastasis is still unclear. Alternative splicing events (ASEs) have a great effect in cancer development, progression and metastasis.