Hedgehog Signaling in the Neural Crest Cells Regulates the Patterning and Growth of Facial Primordia
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Core Transcriptional Regulatory Circuitries in Cancer
Oncogene (2020) 39:6633–6646 https://doi.org/10.1038/s41388-020-01459-w REVIEW ARTICLE Core transcriptional regulatory circuitries in cancer 1 1,2,3 1 2 1,4,5 Ye Chen ● Liang Xu ● Ruby Yu-Tong Lin ● Markus Müschen ● H. Phillip Koeffler Received: 14 June 2020 / Revised: 30 August 2020 / Accepted: 4 September 2020 / Published online: 17 September 2020 © The Author(s) 2020. This article is published with open access Abstract Transcription factors (TFs) coordinate the on-and-off states of gene expression typically in a combinatorial fashion. Studies from embryonic stem cells and other cell types have revealed that a clique of self-regulated core TFs control cell identity and cell state. These core TFs form interconnected feed-forward transcriptional loops to establish and reinforce the cell-type- specific gene-expression program; the ensemble of core TFs and their regulatory loops constitutes core transcriptional regulatory circuitry (CRC). Here, we summarize recent progress in computational reconstitution and biologic exploration of CRCs across various human malignancies, and consolidate the strategy and methodology for CRC discovery. We also discuss the genetic basis and therapeutic vulnerability of CRC, and highlight new frontiers and future efforts for the study of CRC in cancer. Knowledge of CRC in cancer is fundamental to understanding cancer-specific transcriptional addiction, and should provide important insight to both pathobiology and therapeutics. 1234567890();,: 1234567890();,: Introduction genes. Till now, one critical goal in biology remains to understand the composition and hierarchy of transcriptional Transcriptional regulation is one of the fundamental mole- regulatory network in each specified cell type/lineage. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
FOX) Proteins in Osteosarcoma Wentao Zhang1*, Ning Duan1*, Tao Song1, Zhong Li1, Caiguo Zhang2, Xun Chen1
Journal of Cancer 2017, Vol. 8 1619 Ivyspring International Publisher Journal of Cancer 2017; 8(9): 1619-1628. doi: 10.7150/jca.18778 Review The Emerging Roles of Forkhead Box (FOX) Proteins in Osteosarcoma Wentao Zhang1*, Ning Duan1*, Tao Song1, Zhong Li1, Caiguo Zhang2, Xun Chen1 1. Department of Orthopaedics, Xi'an Hong-Hui Hospital affiliated to medical college of Xi'an Jiaotong University, Xi'an, Shaanxi, China, 710054; 2. Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA. * These authors contributed equally to this work. Corresponding authors: [email protected]; [email protected] © Ivyspring International Publisher. This is an open access article distributed under the terms of the Creative Commons Attribution (CC BY-NC) license (https://creativecommons.org/licenses/by-nc/4.0/). See http://ivyspring.com/terms for full terms and conditions. Received: 2016.12.15; Accepted: 2017.02.27; Published: 2017.06.03 Abstract Osteosarcoma is the most common bone cancer primarily occurring in children and young adults. Over the past few years, the deregulation of a superfamily transcription factors, known as forkhead box (FOX) proteins, has been demonstrated to contribute to the pathogenesis of osteosarcoma. Molecular mechanism studies have demonstrated that FOX family proteins participate in a variety of signaling pathways and that their expression can be regulated by multiple factors. The dysfunction of FOX genes can alter osteosarcoma cell differentiation, metastasis and progression. In this review, we summarized the evidence that FOX genes play direct or indirect roles in the development and progression of osteosarcoma, and evaluated the emerging role of FOX proteins as targets for therapeutic intervention. -
The Genetic Network of Forkhead Gene Family in Development of Brown Planthoppers
biology Article The Genetic Network of Forkhead Gene Family in Development of Brown Planthoppers Hai-Yan Lin 1,2, Cheng-Qi Zhu 1,2, Hou-Hong Zhang 2, Zhi-Cheng Shen 2, Chuan-Xi Zhang 2,3 and Yu-Xuan Ye 1,2,* 1 The Rural Development Academy, Zhejiang University, Hangzhou 310058, China; [email protected] (H.-Y.L.); [email protected] (C.-Q.Z.) 2 Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China; [email protected] (H.-H.Z.); [email protected] (Z.-C.S.); [email protected] (C.-X.Z.) 3 State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China * Correspondence: [email protected] Simple Summary: Forkhead (Fox) genes encode a family of transcription factors defined by a ‘winged helix’ DNA-binding domain and play important roles in regulating the expression of genes involved in cell growth, proliferation, differentiation and longevity. However, we still lack a comprehensive understanding of the Fox gene family in animals. Here, we take an integrated study, which combines genomics, transcriptomics and phenomics, to construct the Fox gene genetic network in the brown planthopper, Nilaparvata lugens, a major rice pest. We show that FoxG, FoxQ, FoxA, FoxN1, FoxN2 and their potential target genes are indispensable for embryogenesis; FoxC, FoxJ1 and FoxP have complementary effects on late embryogenesis; FoxA, FoxNl and FoxQ are pleiotropism and also essential for nymph molting; FoxT belongs to a novel insect-specific Fox subfamily; and FoxL2 and FoxO are involved in the development of eggshells and wings, respectively. -
Anti-Carcinogenic Glucosinolates in Cruciferous Vegetables and Their Antagonistic Effects on Prevention of Cancers
molecules Review Anti-Carcinogenic Glucosinolates in Cruciferous Vegetables and Their Antagonistic Effects on Prevention of Cancers Prabhakaran Soundararajan and Jung Sun Kim * Genomics Division, Department of Agricultural Bio-Resources, National Institute of Agricultural Sciences, Rural Development Administration, Wansan-gu, Jeonju 54874, Korea; [email protected] * Correspondence: [email protected] Academic Editor: Gautam Sethi Received: 15 October 2018; Accepted: 13 November 2018; Published: 15 November 2018 Abstract: Glucosinolates (GSL) are naturally occurring β-D-thioglucosides found across the cruciferous vegetables. Core structure formation and side-chain modifications lead to the synthesis of more than 200 types of GSLs in Brassicaceae. Isothiocyanates (ITCs) are chemoprotectives produced as the hydrolyzed product of GSLs by enzyme myrosinase. Benzyl isothiocyanate (BITC), phenethyl isothiocyanate (PEITC) and sulforaphane ([1-isothioyanato-4-(methyl-sulfinyl) butane], SFN) are potential ITCs with efficient therapeutic properties. Beneficial role of BITC, PEITC and SFN was widely studied against various cancers such as breast, brain, blood, bone, colon, gastric, liver, lung, oral, pancreatic, prostate and so forth. Nuclear factor-erythroid 2-related factor-2 (Nrf2) is a key transcription factor limits the tumor progression. Induction of ARE (antioxidant responsive element) and ROS (reactive oxygen species) mediated pathway by Nrf2 controls the activity of nuclear factor-kappaB (NF-κB). NF-κB has a double edged role in the immune system. NF-κB induced during inflammatory is essential for an acute immune process. Meanwhile, hyper activation of NF-κB transcription factors was witnessed in the tumor cells. Antagonistic activity of BITC, PEITC and SFN against cancer was related with the direct/indirect interaction with Nrf2 and NF-κB protein. -
The Forkhead-Box Family of Transcription Factors: Key Molecular Players in Colorectal Cancer Pathogenesis Paul Laissue
Laissue Molecular Cancer (2019) 18:5 https://doi.org/10.1186/s12943-019-0938-x REVIEW Open Access The forkhead-box family of transcription factors: key molecular players in colorectal cancer pathogenesis Paul Laissue Abstract Colorectal cancer (CRC) is the third most commonly occurring cancer worldwide and the fourth most frequent cause of death having an oncological origin. It has been found that transcription factors (TF) dysregulation, leading to the significant expression modifications of genes, is a widely distributed phenomenon regarding human malignant neoplasias. These changes are key determinants regarding tumour’s behaviour as they contribute to cell differentiation/proliferation, migration and metastasis, as well as resistance to chemotherapeutic agents. The forkhead box (FOX) transcription factor family consists of an evolutionarily conserved group of transcriptional regulators engaged in numerous functions during development and adult life. Their dysfunction has been associated with human diseases. Several FOX gene subgroup transcriptional disturbances, affecting numerous complex molecular cascades, have been linked to a wide range of cancer types highlighting their potential usefulness as molecular biomarkers. At least 14 FOX subgroups have been related to CRC pathogenesis, thereby underlining their role for diagnosis, prognosis and treatment purposes. This manuscript aims to provide, for the first time, a comprehensive review of FOX genes’ roles during CRC pathogenesis. The molecular and functional characteristics of most relevant FOX molecules (FOXO, FOXM1, FOXP3) have been described within the context of CRC biology, including their usefulness regarding diagnosis and prognosis. Potential CRC therapeutics (including genome-editing approaches) involving FOX regulation have also been included. Taken together, the information provided here should enable a better understanding of FOX genes’ function in CRC pathogenesis for basic science researchers and clinicians. -
Biophysical Investigation of the Dual Binding Surfaces of Human Transcription Factors FOXO4 and P53
bioRxiv preprint doi: https://doi.org/10.1101/2021.01.11.425814; this version posted January 11, 2021. 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. Biophysical investigation of the dual binding surfaces of human transcription factors FOXO4 and p53 Jinwoo Kim+, Dabin Ahn+, and Chin-Ju Park* Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju, 61005, Korea *Correspondence to: [email protected]. + These authors contributed equally to this work. 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.01.11.425814; this version posted January 11, 2021. 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. Abstract Cellular senescence is protective against external oncogenic stress, but its accumulation causes aging- related diseases. Forkhead box O4 (FOXO4) and p53 are human transcription factors known to promote senescence by interacting in the promyelocytic leukemia bodies. Inhibiting their binding is a strategy for inducing apoptosis of senescent cells, but the binding surfaces that mediate the interaction of FOXO4 and p53 remain elusive. Here, we investigated two binding sites involved in the interaction between FOXO4 and p53 by using NMR spectroscopy. NMR chemical shift perturbation analysis showed that the binding between FOXO4’s forkhead domain (FHD) and p53’s transactivation domain (TAD), and between FOXO4’s C-terminal transactivation domain (CR3) and p53’s DNA binding domain (DBD), mediate the FOXO4-p53 interaction. -
Supplemental Methods Proband and Control Lung Samples Lung Sections from Both the Proband and Age-Matched Controls Were Obtained
Supplementary material J Med Genet Supplemental Methods Proband and Control Lung Samples Lung sections from both the proband and age-matched controls were obtained in the form of fixed formalin paraffin embedded (FFPE) samples. Control lung samples were obtained from the BRINDL biorepository at the University of Rochester(1). RNA expression analyses RNA was obtained for mRNA expression studies using the RNeasy FFPE kit (Qiagen) according to manufacturer’s instructions. cDNA was then generated using iScrpit kit (biorad), and quantitative PCR was done as previously published (2). Primers for qPCR are listed in supplemental table 1. Chromatin Immunoprecipitation of FFPE for Fixed Formalin Paraffin Embedded samples Chromatin immunoprecipitation was done on FFPE sections using a protocol modified from Fanelli and colleagues, Nature Methods, 2011(3) Samples were deparaffinized by incubating 10uM sections in 1ml of Xylene for 10 minutes at room temperature. The tissue was then pelleted at 17,000 x gravity for 3 min at room temperature. This process was repeated 3 times. Samples were then rehydrated by incubating with 1 ml of 100% Ethanol for 10 minutes at RT. Cells were pelleted and resuspended in progressively increasing percentage of water as follows: 95% ethanol, 70% ethanol, 50% ethanol, 20% ethanol. The sample was then resuspended in 1x PBS and the tissue dissociated by sonicating with a Bioruptor (Diagnode, NJ USA) for 30 seconds on the medium setting. Cells then resuspended in Collagenase digestion buffer and treated with collagenase A (Roche 11 088 785 103) to a final concentration of 2mg/ml and digested at 37 C for 45 minutes. -
Daneshshahab.Pdf (3.352Mb)
BMP SIGNALING THROUGH BMPR1A IS REQUIRED FOR ESTABLISHMENT OF PANCREATIC LATERALITY APPROVED BY SUPERVISORY COMMITTEE Ondine Cleaver, Ph.D. Melanie H. Cobb, Ph.D. Raymond J. MacDonald, Ph.D. Eric N. Olson, Ph.D. THIS DISSERTATION IS DEDICATED TO MY FAMILY, PAST, PRESENT AND FUTURE BMP SIGNALING THROUGH BMPR1A IS REQUIRED FOR ESTABLISHMENT OF PANCREATIC LATERALITY by SHAHAB SHAUN MALEKPOUR DANESH DISSERTATION Presented to the Faculty of the Graduate School of Biomedical Sciences The University of Texas Southwestern Medical Center at Dallas In Partial Fulfillment of the Requirements For the Degree of DOCTOR OF PHILOSOPHY The University of Texas Southwestern Medical Center at Dallas Dallas, Texas May, 2009 Copyright by SHAHAB SHAUN MALEKPOUR DANESH, 2009 All Rights Reserved ACKNOWLEDGEMENTS I would like to thank my thesis advisor, Dr. Ondine Cleaver for her guidance and support. Ondine accepted me into her lab as a fifth year graduate student who had already been in three labs and had no background in developmental biology or mouse work. Her undying guidance, motivation and enthusiasm for science have allowed me to grow as a scientist and complete my thesis in two short years. I would like to thank my committee members Dr. Melanie Cobb, Dr. Eric Olson, and especially my thesis chair, Dr. Raymond MacDonald. They have provided invaluable suggestions and guidance that have facilitated my project that has allowed me to complete a substantial amount of work in a short time. I would like to thank the members of the Cleaver lab for providing a collaborative environment for science. Aly Villasenor was a great resource for exchange of valuable scientific ideas. -
Most Variable Genes and Transcription Factors in Acute Lymphoblastic Leukemia Patients
Interdisciplinary Sciences: Computational Life Sciences https://doi.org/10.1007/s12539-019-00325-y ORIGINAL RESEARCH ARTICLE Most Variable Genes and Transcription Factors in Acute Lymphoblastic Leukemia Patients Anil Kumar Tomar1 · Rahul Agarwal2 · Bishwajit Kundu1 Received: 24 September 2018 / Revised: 21 January 2019 / Accepted: 26 February 2019 © International Association of Scientists in the Interdisciplinary Areas 2019 Abstract Acute lymphoblastic leukemia (ALL) is a hematologic tumor caused by cell cycle aberrations due to accumulating genetic disturbances in the expression of transcription factors (TFs), signaling oncogenes and tumor suppressors. Though survival rate in childhood ALL patients is increased up to 80% with recent medical advances, treatment of adults and childhood relapse cases still remains challenging. Here, we have performed bioinformatics analysis of 207 ALL patients’ mRNA expression data retrieved from the ICGC data portal with an objective to mark out the decisive genes and pathways responsible for ALL pathogenesis and aggression. For analysis, 3361 most variable genes, including 276 transcription factors (out of 16,807 genes) were sorted based on the coefcient of variance. Silhouette width analysis classifed 207 ALL patients into 6 subtypes and heat map analysis suggests a need of large and multicenter dataset for non-overlapping subtype classifcation. Overall, 265 GO terms and 32 KEGG pathways were enriched. The lists were dominated by cancer-associated entries and highlight crucial genes and pathways that can be targeted for designing more specifc ALL therapeutics. Diferential gene expression analysis identifed upregulation of two important genes, JCHAIN and CRLF2 in dead patients’ cohort suggesting their pos- sible involvement in diferent clinical outcomes in ALL patients undergoing the same treatment. -
Gene Regulation Is Governed by a Core Network in Hepatocellular Carcinoma Zuguang Gu, Chenyu Zhang* and Jin Wang*
Gu et al. BMC Systems Biology 2012, 6:32 http://www.biomedcentral.com/1752-0509/6/32 RESEARCH ARTICLE Open Access Gene regulation is governed by a core network in hepatocellular carcinoma Zuguang Gu, Chenyu Zhang* and Jin Wang* Abstract Background: Hepatocellular carcinoma (HCC) is one of the most lethal cancers worldwide, and the mechanisms that lead to the disease are still relatively unclear. However, with the development of high-throughput technologies it is possible to gain a systematic view of biological systems to enhance the understanding of the roles of genes associated with HCC. Thus, analysis of the mechanism of molecule interactions in the context of gene regulatory networks can reveal specific sub-networks that lead to the development of HCC. Results: In this study, we aimed to identify the most important gene regulations that are dysfunctional in HCC generation. Our method for constructing gene regulatory network is based on predicted target interactions, experimentally-supported interactions, and co-expression model. Regulators in the network included both transcription factors and microRNAs to provide a complete view of gene regulation. Analysis of gene regulatory network revealed that gene regulation in HCC is highly modular, in which different sets of regulators take charge of specific biological processes. We found that microRNAs mainly control biological functions related to mitochondria and oxidative reduction, while transcription factors control immune responses, extracellular activity and the cell cycle. On the higher level of gene regulation, there exists a core network that organizes regulations between different modules and maintains the robustness of the whole network. There is direct experimental evidence for most of the regulators in the core gene regulatory network relating to HCC. -
Prenatal Testing Requisition Form
BAYLOR MIRACA GENETICS LABORATORIES SHIP TO: Baylor Miraca Genetics Laboratories 2450 Holcombe, Grand Blvd. -Receiving Dock PHONE: 800-411-GENE | FAX: 713-798-2787 | www.bmgl.com Houston, TX 77021-2024 Phone: 713-798-6555 PRENATAL COMPREHENSIVE REQUISITION FORM PATIENT INFORMATION NAME (LAST,FIRST, MI): DATE OF BIRTH (MM/DD/YY): HOSPITAL#: ACCESSION#: REPORTING INFORMATION ADDITIONAL PROFESSIONAL REPORT RECIPIENTS PHYSICIAN: NAME: INSTITUTION: PHONE: FAX: PHONE: FAX: NAME: EMAIL (INTERNATIONAL CLIENT REQUIREMENT): PHONE: FAX: SAMPLE INFORMATION CLINICAL INDICATION FETAL SPECIMEN TYPE Pregnancy at risk for specific genetic disorder DATE OF COLLECTION: (Complete FAMILIAL MUTATION information below) Amniotic Fluid: cc AMA PERFORMING PHYSICIAN: CVS: mg TA TC Abnormal Maternal Screen: Fetal Blood: cc GESTATIONAL AGE (GA) Calculation for AF-AFP* NTD TRI 21 TRI 18 Other: SELECT ONLY ONE: Abnormal NIPT (attach report): POC/Fetal Tissue, Type: TRI 21 TRI 13 TRI 18 Other: Cultured Amniocytes U/S DATE (MM/DD/YY): Abnormal U/S (SPECIFY): Cultured CVS GA ON U/S DATE: WKS DAYS PARENTAL BLOODS - REQUIRED FOR CMA -OR- Maternal Blood Date of Collection: Multiple Pregnancy Losses LMP DATE (MM/DD/YY): Parental Concern Paternal Blood Date of Collection: Other Indication (DETAIL AND ATTACH REPORT): *Important: U/S dating will be used if no selection is made. Name: Note: Results will differ depending on method checked. Last Name First Name U/S dating increases overall screening performance. Date of Birth: KNOWN FAMILIAL MUTATION/DISORDER SPECIFIC PRENATAL TESTING Notice: Prior to ordering testing for any of the disorders listed, you must call the lab and discuss the clinical history and sample requirements with a genetic counselor.