First-Positive Surveillance Screening in an Asymptomatic SDHA Germline Mutation Carrier
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SUPPLEMENTARY FIGURES and TABLES Genetic Hallmarks of Recurrent/Metastatic Adenoid Cystic Carcinoma
SUPPLEMENTARY FIGURES AND TABLES Genetic Hallmarks Of Recurrent/Metastatic Adenoid Cystic Carcinoma SUPPLEMENTARY FIGURES Figure S1. Flow diagram of study design. Figure S2. Primary and recurrent/metastatic adenoid cystic carcinoma distribution by anatomic site. Figure S3. Variant allelic frequency (VAF) density histogram for NOTCH1 mutations observed in recurrent/metastatic adenoid cystic carcinoma (R/M ACC). Figure S4. Downsampling analysis of R/M MSK-IMPACT cohort (n=94) to simulate mutation detection at 100x coverage. Figure S5. Representative PyClone plots demonstrating intratumoral heterogeneity quantified as number of genomically distinct subclonal populations in adenoid cystic carcinoma. Figure S6. MRI of the neck with contrast of adenoid cystic carcinoma of right parotid gland involving masseter muscle and ascending ramus. Figure S7. Histologic confirmation of 6 representative distant metastatic sites of a single case with parotid adenoid cystic carcinoma. Figure S8. Fluorescence in situ hybridization (FISH) of distant lung metastatic lesions in a single case of parotid adenoid cystic carcinoma. Figure S9. Two-way plots of cancer cell fraction in a single case of parotid adenoid cystic carcinoma, comparing primary tumor with eight metastatic lesions. Figure S10. Multiregion clonal evolution heatmap analysis of two breast adenoid cystic carcinoma cases with transformation to high grade triple-negative breast cancer (TNBC) histology. SUPPLEMENTARY TABLES Table S1. Study distribution of primary and recurrent/metastatic (R/M) adenoid cystic carcinoma (ACC) cases. Mixed entails head and neck, lung, and breast disease sites. Table S2. Top gene alteration incidence by tumor site (includes primary and recurrent/metastatic cases). Table S3. Top gene alteration incidence of recurrent/metastatic adenoid cystic carcinoma (R/M ACC) cases comparing primary site with distant metastatic site. -
Genomic and Transcriptomic Alterations Associated with Drug Vulnerabilities and Prognosis in Adenocarcinoma at the Gastroesophageal Junction
ARTICLE https://doi.org/10.1038/s41467-020-19949-6 OPEN Genomic and transcriptomic alterations associated with drug vulnerabilities and prognosis in adenocarcinoma at the gastroesophageal junction Yuan Lin1,8, Yingying Luo 2,8, Yanxia Sun 2,8, Wenjia Guo 2,3,8, Xuan Zhao2,8, Yiyi Xi2, Yuling Ma 2, ✉ ✉ Mingming Shao2, Wen Tan2, Ge Gao 1,4 , Chen Wu 2,5,6 & Dongxin Lin2,5,7 1234567890():,; Adenocarcinoma at the gastroesophageal junction (ACGEJ) has dismal clinical outcomes, and there are currently few specific effective therapies because of limited knowledge on its genomic and transcriptomic alterations. The present study investigates genomic and tran- scriptomic changes in ACGEJ from Chinese patients and analyzes their drug vulnerabilities and associations with the survival time. Here we show that the major genomic changes of Chinese ACGEJ patients are chromosome instability promoted tumorigenic focal copy- number variations and COSMIC Signature 17-featured single nucleotide variations. We provide a comprehensive profile of genetic changes that are potentially vulnerable to existing therapeutic agents and identify Signature 17-correlated IFN-α response pathway as a prog- nostic marker that might have practical value for clinical prognosis of ACGEJ. These findings further our understanding on the molecular biology of ACGEJ and may help develop more effective therapeutic strategies. 1 Beijing Advanced Innovation Center for Genomics (ICG), Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, China. 2 Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China. 3 Cancer Institute, Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, China. -
Paraganglioma (PGL) Tumors in Patients with Succinate Dehydrogenase-Related PCC–PGL Syndromes: a Clinicopathological and Molecular Analysis
T G Papathomas and others Non-PCC/PGL tumors in the SDH 170:1 1–12 Clinical Study deficiency Non-pheochromocytoma (PCC)/paraganglioma (PGL) tumors in patients with succinate dehydrogenase-related PCC–PGL syndromes: a clinicopathological and molecular analysis Thomas G Papathomas1, Jose Gaal1, Eleonora P M Corssmit2, Lindsey Oudijk1, Esther Korpershoek1, Ketil Heimdal3, Jean-Pierre Bayley4, Hans Morreau5, Marieke van Dooren6, Konstantinos Papaspyrou7, Thomas Schreiner8, Torsten Hansen9, Per Arne Andresen10, David F Restuccia1, Ingrid van Kessel6, Geert J L H van Leenders1, Johan M Kros1, Leendert H J Looijenga1, Leo J Hofland11, Wolf Mann7, Francien H van Nederveen12, Ozgur Mete13,14, Sylvia L Asa13,14, Ronald R de Krijger1,15 and Winand N M Dinjens1 1Department of Pathology, Josephine Nefkens Institute, Erasmus MC, University Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands, 2Department of Endocrinology, Leiden University Medical Center, Leiden,The Netherlands, 3Section for Clinical Genetics, Department of Medical Genetics, Oslo University Hospital, Oslo, Norway, 4Department of Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands, 5Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands, 6Department of Clinical Genetics, Erasmus MC, University Medical Center, Rotterdam, The Netherlands, 7Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany, 8Section for Specialized Endocrinology, -
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. -
Download Via Github on RNA-Seq and Chip-Seq Data Analysis and the University of And/Or Bioconductor [33–35, 38–40]
Kumka and Bauer BMC Genomics (2015) 16:895 DOI 10.1186/s12864-015-2162-4 RESEARCH ARTICLE Open Access Analysis of the FnrL regulon in Rhodobacter capsulatus reveals limited regulon overlap with orthologues from Rhodobacter sphaeroides and Escherichia coli Joseph E. Kumka and Carl E. Bauer* Abstract Background: FNR homologues constitute an important class of transcription factors that control a wide range of anaerobic physiological functions in a number of bacterial species. Since FNR homologues are some of the most pervasive transcription factors, an understanding of their involvement in regulating anaerobic gene expression in different species sheds light on evolutionary similarity and differences. To address this question, we used a combination of high throughput RNA-Seq and ChIP-Seq analysis to define the extent of the FnrL regulon in Rhodobacter capsulatus and related our results to that of FnrL in Rhodobacter sphaeroides and FNR in Escherichia coli. Results: Our RNA-seq results show that FnrL affects the expression of 807 genes, which accounts for over 20 % of the Rba. capsulatus genome. ChIP-seq results indicate that 42 of these genes are directly regulated by FnrL. Importantly, this includes genes involved in the synthesis of the anoxygenic photosystem. Similarly, FnrL in Rba. sphaeroides affects 24 % of its genome, however, only 171 genes are differentially expressed in common between two Rhodobacter species, suggesting significant divergence in regulation. Conclusions: We show that FnrL in Rba. capsulatus activates photosynthesis while in Rba. sphaeroides FnrL regulation reported to involve repression of the photosystem. This analysis highlights important differences in transcriptional control of photosynthetic events and other metabolic processes controlled by FnrL orthologues in closely related Rhodobacter species. -
About SDHD Gene Mutations
About SDHD Gene Mutations About Genes Recommendations Genes are in every cell in our bodies. Genes are made Knowing if you have an SDHD mutation can help you of DNA, which gives instructions to cells about how to grow manage your medical care. and work together. We have two copies of each gene in each cell—one from our mother and one from our father. When MEN AND WOMEN genes work right, they help stop cancer cells from developing. If you know you have an SDHD mutation, it is important If one copy of a gene has a mutation, it cannot function as it to find tumors early. It is also important to tell your doctor should. This increases the risk for certain cancers. that you have this mutation before any medical procedures. TheSDH genes have instructions for turning food into energy Recommendations may vary according to your age. and helping fix mistakes in DNA. The four genes involved are Ages 8-18: SDHA, SDHB, SDHC, and SDHD. If there is a mutation in one • MRI of the whole body every 2-3 years of these genes, it can cause cells to grow and divide too much. This • Neck MRI every 2-3 years can lead to tumors called paragangliomas and pheochromocytomas. These tumors are often benign (non-cancerous) but can be Adults: cancer and spread in some cases. This condition is called • PET/CT scan as your doctor recommends hereditary paraganglioma/pheochromocytoma syndrome. All ages: Paragangliomas and Pheochromocytomas • Physical exam every year with blood pressure check Paragangliomas (PGLs) are slow-growing tumors that develop • Blood test every year along nerves or blood vessels. -
Heme Oxygenase-1 Regulates Mitochondrial Quality Control in the Heart
RESEARCH ARTICLE Heme oxygenase-1 regulates mitochondrial quality control in the heart Travis D. Hull,1,2 Ravindra Boddu,1,3 Lingling Guo,2,3 Cornelia C. Tisher,1,3 Amie M. Traylor,1,3 Bindiya Patel,1,4 Reny Joseph,1,3 Sumanth D. Prabhu,1,4,5 Hagir B. Suliman,6 Claude A. Piantadosi,7 Anupam Agarwal,1,3,5 and James F. George2,3,4 1Department of Medicine, 2Department of Surgery, 3Nephrology Research and Training Center, and 4Comprehensive Cardiovascular Center, University of Alabama at Birmingham, Birmingham, Alabama, USA. 5Department of Veterans Affairs, Birmingham, Alabama, USA. 6Department of Anesthesiology and 7Department of Pulmonary, Allergy and Critical Care, Duke University School of Medicine, Durham, North Carolina, USA. The cardioprotective inducible enzyme heme oxygenase-1 (HO-1) degrades prooxidant heme into equimolar quantities of carbon monoxide, biliverdin, and iron. We hypothesized that HO-1 mediates cardiac protection, at least in part, by regulating mitochondrial quality control. We treated WT and HO-1 transgenic mice with the known mitochondrial toxin, doxorubicin (DOX). Relative to WT mice, mice globally overexpressing human HO-1 were protected from DOX-induced dilated cardiomyopathy, cardiac cytoarchitectural derangement, and infiltration of CD11b+ mononuclear phagocytes. Cardiac-specific overexpression of HO-1 ameliorated DOX-mediated dilation of the sarcoplasmic reticulum as well as mitochondrial disorganization in the form of mitochondrial fragmentation and increased numbers of damaged mitochondria in autophagic vacuoles. HO-1 overexpression promotes mitochondrial biogenesis by upregulating protein expression of NRF1, PGC1α, and TFAM, which was inhibited in WT animals treated with DOX. Concomitantly, HO-1 overexpression inhibited the upregulation of the mitochondrial fission mediator Fis1 and resulted in increased expression of the fusion mediators, Mfn1 and Mfn2. -
Crystal Structure of Bacterial Succinate:Quinone Oxidoreductase Flavoprotein Sdha in Complex with Its Assembly Factor Sdhe
Crystal structure of bacterial succinate:quinone oxidoreductase flavoprotein SdhA in complex with its assembly factor SdhE Megan J. Mahera,1, Anuradha S. Heratha, Saumya R. Udagedaraa, David A. Dougana, and Kaye N. Truscotta,1 aDepartment of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia Edited by Amy C. Rosenzweig, Northwestern University, Evanston, IL, and approved February 14, 2018 (received for review January 4, 2018) Succinate:quinone oxidoreductase (SQR) functions in energy me- quinol:FRD), respectively (13, 15). The importance of this protein tabolism, coupling the tricarboxylic acid cycle and electron transport family, in normal cellular metabolism, is manifested by the iden- chain in bacteria and mitochondria. The biogenesis of flavinylated tification of a mutation in human SDHAF2 (Gly78Arg), which is SdhA, the catalytic subunit of SQR, is assisted by a highly conserved linked to an inherited neuroendocrine disorder, PGL2 (10). Cur- assembly factor termed SdhE in bacteria via an unknown mecha- rently, however, the role of SdhE in flavinylation remains poorly nism. By using X-ray crystallography, we have solved the structure understood. To date, three different modes of action for SdhE/ of Escherichia coli SdhE in complex with SdhA to 2.15-Å resolution. Sdh5 have been proposed, suggesting that SdhE facilitates the Our structure shows that SdhE makes a direct interaction with the binding and delivery of FAD (13), acts as a chaperone for SdhA flavin adenine dinucleotide-linked residue His45 in SdhA and main- (10), or catalyzes the attachment of FAD (10). Moreover, the re- tains the capping domain of SdhA in an “open” conformation. -
Inhibition of Mitochondrial Complex II in Neuronal Cells Triggers Unique
www.nature.com/scientificreports OPEN Inhibition of mitochondrial complex II in neuronal cells triggers unique pathways culminating in autophagy with implications for neurodegeneration Sathyanarayanan Ranganayaki1, Neema Jamshidi2, Mohamad Aiyaz3, Santhosh‑Kumar Rashmi4, Narayanappa Gayathri4, Pulleri Kandi Harsha5, Balasundaram Padmanabhan6 & Muchukunte Mukunda Srinivas Bharath7* Mitochondrial dysfunction and neurodegeneration underlie movement disorders such as Parkinson’s disease, Huntington’s disease and Manganism among others. As a corollary, inhibition of mitochondrial complex I (CI) and complex II (CII) by toxins 1‑methyl‑4‑phenylpyridinium (MPP+) and 3‑nitropropionic acid (3‑NPA) respectively, induced degenerative changes noted in such neurodegenerative diseases. We aimed to unravel the down‑stream pathways associated with CII inhibition and compared with CI inhibition and the Manganese (Mn) neurotoxicity. Genome‑wide transcriptomics of N27 neuronal cells exposed to 3‑NPA, compared with MPP+ and Mn revealed varied transcriptomic profle. Along with mitochondrial and synaptic pathways, Autophagy was the predominant pathway diferentially regulated in the 3‑NPA model with implications for neuronal survival. This pathway was unique to 3‑NPA, as substantiated by in silico modelling of the three toxins. Morphological and biochemical validation of autophagy markers in the cell model of 3‑NPA revealed incomplete autophagy mediated by mechanistic Target of Rapamycin Complex 2 (mTORC2) pathway. Interestingly, Brain Derived Neurotrophic Factor -
Updates on the Genetics of Neuroendocrine Tumors
Updates on the Genetics of Neuroendocrine Tumors NET Patient Conference March 8, 2019 Anna Raper, MS, CGC Division of Translational Medicine and Human Genetics No disclosures 2 3 Overview 1. Cancer/tumor genetics 2. Genetics of neuroendocrine tumors sciencemag.org 4 The Genetics of Cancers and Tumors Hereditary v. Familial v. Sporadic Germline v. somatic genetics Risk When to suspect hereditary susceptibility 5 Cancer Distribution - General Hereditary (5-10%) • Specific gene variant is inherited in family • Associated with increased tumor/cancer risk Familial (10-20%) • Multiple genes and environmental factors may be involved • Some increased tumor/cancer risk Sporadic • Occurs by chance, or related to environmental factors • General population tumor/cancer risk 6 What are genes again? 7 Normal gene Pathogenic gene variant (“mutation”) kintalk.org 8 Cancer is a genetic disease kintalk.org 9 Germline v. Somatic gene mutations 10 Hereditary susceptibility to cancer Germline mutations Depending on the gene, increased risk for certain tumor/cancer types Does not mean an individual WILL develop cancer, but could change screening and management recommendations National Cancer Institute 11 Features that raise suspicion for hereditary condition Specific tumor types Early ages of diagnosis compared to the general population Multiple or bilateral (affecting both sides) tumors Family history • Clustering of certain tumor types • Multiple generations affected • Multiple siblings affected 12 When is genetic testing offered? A hereditary -
The Microbiota-Produced N-Formyl Peptide Fmlf Promotes Obesity-Induced Glucose
Page 1 of 230 Diabetes Title: The microbiota-produced N-formyl peptide fMLF promotes obesity-induced glucose intolerance Joshua Wollam1, Matthew Riopel1, Yong-Jiang Xu1,2, Andrew M. F. Johnson1, Jachelle M. Ofrecio1, Wei Ying1, Dalila El Ouarrat1, Luisa S. Chan3, Andrew W. Han3, Nadir A. Mahmood3, Caitlin N. Ryan3, Yun Sok Lee1, Jeramie D. Watrous1,2, Mahendra D. Chordia4, Dongfeng Pan4, Mohit Jain1,2, Jerrold M. Olefsky1 * Affiliations: 1 Division of Endocrinology & Metabolism, Department of Medicine, University of California, San Diego, La Jolla, California, USA. 2 Department of Pharmacology, University of California, San Diego, La Jolla, California, USA. 3 Second Genome, Inc., South San Francisco, California, USA. 4 Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA, USA. * Correspondence to: 858-534-2230, [email protected] Word Count: 4749 Figures: 6 Supplemental Figures: 11 Supplemental Tables: 5 1 Diabetes Publish Ahead of Print, published online April 22, 2019 Diabetes Page 2 of 230 ABSTRACT The composition of the gastrointestinal (GI) microbiota and associated metabolites changes dramatically with diet and the development of obesity. Although many correlations have been described, specific mechanistic links between these changes and glucose homeostasis remain to be defined. Here we show that blood and intestinal levels of the microbiota-produced N-formyl peptide, formyl-methionyl-leucyl-phenylalanine (fMLF), are elevated in high fat diet (HFD)- induced obese mice. Genetic or pharmacological inhibition of the N-formyl peptide receptor Fpr1 leads to increased insulin levels and improved glucose tolerance, dependent upon glucagon- like peptide-1 (GLP-1). Obese Fpr1-knockout (Fpr1-KO) mice also display an altered microbiome, exemplifying the dynamic relationship between host metabolism and microbiota. -
One in Three Highly Selected Greek Patients with Breast Cancer Carries A
Cancer genetics J Med Genet: first published as 10.1136/jmedgenet-2019-106189 on 12 July 2019. Downloaded from ORIGINAL ARTICLE One in three highly selected Greek patients with breast cancer carries a loss-of-function variant in a cancer susceptibility gene Florentia Fostira, 1 Irene Kostantopoulou,1 Paraskevi Apostolou,1 Myrto S Papamentzelopoulou,1 Christos Papadimitriou,2 Eleni Faliakou,3 Christos Christodoulou,4 Ioannis Boukovinas,5 Evangelia Razis,6 Dimitrios Tryfonopoulos,7 Vasileios Barbounis,8 Andromache Vagena,1 Ioannis S Vlachos,9 Despoina Kalfakakou, 1 George Fountzilas,10 Drakoulis Yannoukakos1 ► Additional material is ABSTRact individuals carrying such pathogenic variants (PVs) published online only. To view Background Gene panel testing has become the norm face an increased lifetime risk for cancer diagnoses.1 please visit the journal online (http:// dx. doi. org/ 10. 1136/ for assessing breast cancer (BC) susceptibility, but actual The implementation of BRCA1 and BRCA2 genetic jmedgenet- 2019- 106189). cancer risks conferred by genes included in panels are testing into clinical practice has enabled the identifi- not established. Contrarily, deciphering the missing cation of individuals at high risk and the application For numbered affiliations see hereditability on BC, through identification of novel of tailored management guidelines, significantly end of article. candidates, remains a challenge. We aimed to investigate improving both cancer prevention and survival.2 the mutation prevalence and spectra in a highly Mutations