Distinct Populations Within Isl1 Lineages Contribute to Appendicular and Facial Skeletogenesis Through the Β-Catenin Pathway
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Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model
Downloaded from http://www.jimmunol.org/ by guest on September 25, 2021 T + is online at: average * The Journal of Immunology , 34 of which you can access for free at: 2016; 197:1477-1488; Prepublished online 1 July from submission to initial decision 4 weeks from acceptance to publication 2016; doi: 10.4049/jimmunol.1600589 http://www.jimmunol.org/content/197/4/1477 Molecular Profile of Tumor-Specific CD8 Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A. Waugh, Sonia M. Leach, Brandon L. Moore, Tullia C. Bruno, Jonathan D. Buhrman and Jill E. Slansky J Immunol cites 95 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html http://www.jimmunol.org/content/suppl/2016/07/01/jimmunol.160058 9.DCSupplemental This article http://www.jimmunol.org/content/197/4/1477.full#ref-list-1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material References Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2016 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of September 25, 2021. The Journal of Immunology Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A. -
Abstracts from the 9Th Biennial Scientific Meeting of The
International Journal of Pediatric Endocrinology 2017, 2017(Suppl 1):15 DOI 10.1186/s13633-017-0054-x MEETING ABSTRACTS Open Access Abstracts from the 9th Biennial Scientific Meeting of the Asia Pacific Paediatric Endocrine Society (APPES) and the 50th Annual Meeting of the Japanese Society for Pediatric Endocrinology (JSPE) Tokyo, Japan. 17-20 November 2016 Published: 28 Dec 2017 PS1 Heritable forms of primary bone fragility in children typically lead to Fat fate and disease - from science to global policy a clinical diagnosis of either osteogenesis imperfecta (OI) or juvenile Peter Gluckman osteoporosis (JO). OI is usually caused by dominant mutations affect- Office of Chief Science Advsor to the Prime Minister ing one of the two genes that code for two collagen type I, but a re- International Journal of Pediatric Endocrinology 2017, 2017(Suppl 1):PS1 cessive form of OI is present in 5-10% of individuals with a clinical diagnosis of OI. Most of the involved genes code for proteins that Attempts to deal with the obesity epidemic based solely on adult be- play a role in the processing of collagen type I protein (BMP1, havioural change have been rather disappointing. Indeed the evidence CREB3L1, CRTAP, LEPRE1, P4HB, PPIB, FKBP10, PLOD2, SERPINF1, that biological, developmental and contextual factors are operating SERPINH1, SEC24D, SPARC, from the earliest stages in development and indeed across generations TMEM38B), or interfere with osteoblast function (SP7, WNT1). Specific is compelling. The marked individual differences in the sensitivity to the phenotypes are caused by mutations in SERPINF1 (recessive OI type obesogenic environment need to be understood at both the individual VI), P4HB (Cole-Carpenter syndrome) and SEC24D (‘Cole-Carpenter and population level. -
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. -
Single-Cell RNA Sequencing Demonstrates the Molecular and Cellular Reprogramming of Metastatic Lung Adenocarcinoma
ARTICLE https://doi.org/10.1038/s41467-020-16164-1 OPEN Single-cell RNA sequencing demonstrates the molecular and cellular reprogramming of metastatic lung adenocarcinoma Nayoung Kim 1,2,3,13, Hong Kwan Kim4,13, Kyungjong Lee 5,13, Yourae Hong 1,6, Jong Ho Cho4, Jung Won Choi7, Jung-Il Lee7, Yeon-Lim Suh8,BoMiKu9, Hye Hyeon Eum 1,2,3, Soyean Choi 1, Yoon-La Choi6,10,11, Je-Gun Joung1, Woong-Yang Park 1,2,6, Hyun Ae Jung12, Jong-Mu Sun12, Se-Hoon Lee12, ✉ ✉ Jin Seok Ahn12, Keunchil Park12, Myung-Ju Ahn 12 & Hae-Ock Lee 1,2,3,6 1234567890():,; Advanced metastatic cancer poses utmost clinical challenges and may present molecular and cellular features distinct from an early-stage cancer. Herein, we present single-cell tran- scriptome profiling of metastatic lung adenocarcinoma, the most prevalent histological lung cancer type diagnosed at stage IV in over 40% of all cases. From 208,506 cells populating the normal tissues or early to metastatic stage cancer in 44 patients, we identify a cancer cell subtype deviating from the normal differentiation trajectory and dominating the metastatic stage. In all stages, the stromal and immune cell dynamics reveal ontological and functional changes that create a pro-tumoral and immunosuppressive microenvironment. Normal resident myeloid cell populations are gradually replaced with monocyte-derived macrophages and dendritic cells, along with T-cell exhaustion. This extensive single-cell analysis enhances our understanding of molecular and cellular dynamics in metastatic lung cancer and reveals potential diagnostic and therapeutic targets in cancer-microenvironment interactions. 1 Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea. -
The Role of Prrx1 and Snai2 As Master Regulators of Fibroblast Identity Huda A
Eastern Illinois University The Keep Masters Theses Student Theses & Publications 2018 The Role of Prrx1 and Snai2 as Master Regulators of Fibroblast Identity Huda A. Alzahrani Eastern Illinois University This research is a product of the graduate program in Biological Sciences at Eastern Illinois University. Find out more about the program. Recommended Citation Alzahrani, Huda A., "The Role of Prrx1 and Snai2 as Master Regulators of Fibroblast Identity" (2018). Masters Theses. 4290. https://thekeep.eiu.edu/theses/4290 This is brought to you for free and open access by the Student Theses & Publications at The Keep. It has been accepted for inclusion in Masters Theses by an authorized administrator of The Keep. For more information, please contact [email protected]. TheGraduate School� EAmRJ-1IWNOIS UNMJ\SITY· Thesis Maintenance and Reproduction Certificate FOR: Graduate Candidates Completing Theses in Partial Fulfillmentof the Degree Graduate Faculty Advisors Directing the Theses RE: Preservation, Reproduction, and Distribution ofThesis Research Preserving, reproducing, and distributing thesis research is an important part of Booth Library's responsibility to provide access to scholarship. In order to further this goal, Booth Library makes all graduate theses completed as part of a degree program at Eastern Illinois University available for personal study, research, and other not-for· profit educational purposes. Under 17 U.S.C. § 108, the library may reproduce and distribute a copy without infringing on copyright; however, professional courtesy dictates that permission be requested from the author before doing so. Your signatures affirm the following: •The graduate candidate is the author of this thesis. •The graduate candidate retains the copyright and intellectual property rights associated with the original research, creative activity, and intellectual or artistic content of the thesis. -
The Prrx1 Limb Enhancer Marks an Adult Population of Injury-Responsive, Multipotent Dermal Fibroblasts
bioRxiv preprint doi: https://doi.org/10.1101/524124; this version posted January 18, 2019. 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. Currie et al. The Prrx1 limb enhancer marks an adult population of injury- responsive, multipotent dermal fibroblasts Joshua D. Currie1,2, Lidia Grosser1,3, Prayag Murawala1,3, Maritta Schuez1, Martin Michel1, Elly M. Tanaka1,3, Tatiana Sandoval-Guzmán1* 1. CRTD - Center for Regenerative Therapies Dresden, Technische Universität Dresden, Fetscherstrasse 105, 01307 Dresden, Germany 2. Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, M5S 3G5 Toronto, Canada 3. Research Institute for Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus- Vienna-Biocenter 1, 1030 Vienna, Austria * Author to whom correspondence should be addressed: tatiana.sandoval_guzman@tu- dresden.de Running Title: Prrx1-enhancer labels injury-responsive fibroblasts Keywords: Lineage tracing, dermal fibroblast, wound healing, limb progenitor. Competing Interests: The authors declare no competing financial interests. 1 bioRxiv preprint doi: https://doi.org/10.1101/524124; this version posted January 18, 2019. 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. Currie et al. Summary The heterogeneity of adult tissues has been posited to contribute toward the loss of regenerative potential in mammals. -
Core Circadian Clock Transcription Factor BMAL1 Regulates Mammary Epithelial Cell
bioRxiv preprint doi: https://doi.org/10.1101/2021.02.23.432439; this version posted February 23, 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 4.0 International license. 1 Title: Core circadian clock transcription factor BMAL1 regulates mammary epithelial cell 2 growth, differentiation, and milk component synthesis. 3 Authors: Theresa Casey1ǂ, Aridany Suarez-Trujillo1, Shelby Cummings1, Katelyn Huff1, 4 Jennifer Crodian1, Ketaki Bhide2, Clare Aduwari1, Kelsey Teeple1, Avi Shamay3, Sameer J. 5 Mabjeesh4, Phillip San Miguel5, Jyothi Thimmapuram2, and Karen Plaut1 6 Affiliations: 1. Department of Animal Science, Purdue University, West Lafayette, IN, USA; 2. 7 Bioinformatics Core, Purdue University; 3. Animal Science Institute, Agriculture Research 8 Origination, The Volcani Center, Rishon Letsiyon, Israel. 4. Department of Animal Sciences, 9 The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of 10 Jerusalem, Rehovot, Israel. 5. Genomics Core, Purdue University 11 Grant support: Binational Agricultural Research Development (BARD) Research Project US- 12 4715-14; Photoperiod effects on milk production in goats: Are they mediated by the molecular 13 clock in the mammary gland? 14 ǂAddress for correspondence. 15 Theresa M. Casey 16 BCHM Room 326 17 175 South University St. 18 West Lafayette, IN 47907 19 Email: [email protected] 20 Phone: 802-373-1319 21 22 bioRxiv preprint doi: https://doi.org/10.1101/2021.02.23.432439; this version posted February 23, 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. -
Hypermethylation in the Promoter of PRDM16 Is Associated with Decreased Survival in AML Patients
2019 Hypermethylation in the promoter of PRDM16 is associated with decreased survival in AML patients CONNOR SMITH, BS School of Medicine Oregon Health & Science University Certificate of Approval This is to certify that the Master’s Thesis of Connor J. Smith “Hypermethylation in the promoter of PRDM16 is associated with decreased survival in AML patients” Has been approved _________________________________________ Ted G. Laderas, Ph.D. _________________________________________ Lucia Carbone, Ph.D. _________________________________________ Michael A. Mooney, Ph.D. Abstract Acute Myeloid Leukemia (AML) is the most common acute adult leukemia, accounting for approximately 1% of all new cancers in 2018. DNA methylation is an epigenetic modification that has been shown to play a strong role in the development and progression of AML. Disruption of DNA methylation in patients is often due to somatic mutations of epigenetic modifier genes (e.g. (DNMT3A, TET2, IDH1/2, WT1, EZH2, ASXL1). Typically, studies of DNA methylation in AML and other cancers focus on regions of differential methylation (DMRs) between cancer patients and their healthy counterparts. Using the data from The Cancer Genome Atlas study on 194 AML patients, we investigated differential methylation between patients with and without mutations of the epigenetic modification genes commonly mutated in AML. We identified 20,567 differentially methylated probes within 2,893 DMRs and analyzed the affected regions for involvement in AML. In particular, we identified a region within the promoter of PRDM16 which, when hypermethylated, is associated with decreased survival (p = 0.017). In conclusion, we find DMRs between AML patients with and without somatic mutations of epigenetic modification genes that affect biologically relevant pathway and show association with the development and progression of AML. -
Genome-Wide DNA Methylation Analysis Reveals Molecular Subtypes of Pancreatic Cancer
www.impactjournals.com/oncotarget/ Oncotarget, 2017, Vol. 8, (No. 17), pp: 28990-29012 Research Paper Genome-wide DNA methylation analysis reveals molecular subtypes of pancreatic cancer Nitish Kumar Mishra1 and Chittibabu Guda1,2,3,4 1Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA 2Bioinformatics and Systems Biology Core, University of Nebraska Medical Center, Omaha, NE, 68198, USA 3Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198, USA 4Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA Correspondence to: Chittibabu Guda, email: [email protected] Keywords: TCGA, pancreatic cancer, differential methylation, integrative analysis, molecular subtypes Received: October 20, 2016 Accepted: February 12, 2017 Published: March 07, 2017 Copyright: Mishra et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC-BY), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT Pancreatic cancer (PC) is the fourth leading cause of cancer deaths in the United States with a five-year patient survival rate of only 6%. Early detection and treatment of this disease is hampered due to lack of reliable diagnostic and prognostic markers. Recent studies have shown that dynamic changes in the global DNA methylation and gene expression patterns play key roles in the PC development; hence, provide valuable insights for better understanding the initiation and progression of PC. In the current study, we used DNA methylation, gene expression, copy number, mutational and clinical data from pancreatic patients. -
Identification of Paired-Related Homeobox Protein 1 As a Key Mesenchymal Transcription Factor in Idiopathic Pulmonary Fibrosis
bioRxiv preprint doi: https://doi.org/10.1101/2021.01.15.425870; this version posted January 15, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Identification of Paired-related Homeobox Protein 1 as a key mesenchymal transcription factor in Idiopathic Pulmonary Fibrosis E. Marchal-Duval1,*, M. Homps-Legrand1,*, A. Froidure1,2, M. Jaillet1, M. Ghanem3, L. Deneuville1,3, A. Justet1,3, A. Maurac1., A. Vadel1, E. Fortas1, A. Cazes 1,4, A. Joannes1,5, L. Giersch1, H. Mal6, P. Mordant1,7, C.M. Mounier8,9, K. Schirduan10, M. Korfei11, A. Gunther11, B. Mari8, F. Jaschinski10, B. Crestani1,3, A.A. Mailleux1,$ 1 Institut National de la Santé et de la Recherche Médical, UMR1152, Labex Inflamex, DHU FIRE, Université de Paris, Faculté de médecine Xavier Bichat, 75018 Paris, France; 2 Institut de Recherche Expérimentale et Clinique, Pôle de Pneumologie, Université catholique de Louvain, Belgium Service de pneumologie, Cliniques Universitaires Saint-Luc, Brussels, Belgium; 3 Assistance Publique des Hôpitaux de Paris, Hôpital Bichat, Service de Pneumologie A, DHU FIRE, Paris, France ; 4 Assistance Publique des Hôpitaux de Paris, Hôpital Bichat, Département d’Anatomopathologie, DHU FIRE, Paris, France ; 5 Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France 6 Assistance Publique des Hôpitaux de Paris, Hôpital Bichat, Service de Pneumologie et Transplantation, DHU FIRE, Paris, France ; 7 Assistance Publique des Hôpitaux de Paris, Hôpital Bichat, Service de Chirurgie Thoracique et Vasculaire, DHU FIRE, Paris, France ; 8 Université Côte d'Azur, CNRS, IPMC, FHU-OncoAge, Valbonne, France 9 CYU Université, ERRMECe(EA1391), NEUVILLE SUR OISE, France 10 Secarna Pharmaceuticals GmbH & Co. -
The Genetic Factors of Bilaterian Evolution Peter Heger1*, Wen Zheng1†, Anna Rottmann1, Kristen a Panfilio2,3, Thomas Wiehe1
RESEARCH ARTICLE The genetic factors of bilaterian evolution Peter Heger1*, Wen Zheng1†, Anna Rottmann1, Kristen A Panfilio2,3, Thomas Wiehe1 1Institute for Genetics, Cologne Biocenter, University of Cologne, Cologne, Germany; 2Institute for Zoology: Developmental Biology, Cologne Biocenter, University of Cologne, Cologne, Germany; 3School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry, United Kingdom Abstract The Cambrian explosion was a unique animal radiation ~540 million years ago that produced the full range of body plans across bilaterians. The genetic mechanisms underlying these events are unknown, leaving a fundamental question in evolutionary biology unanswered. Using large-scale comparative genomics and advanced orthology evaluation techniques, we identified 157 bilaterian-specific genes. They include the entire Nodal pathway, a key regulator of mesoderm development and left-right axis specification; components for nervous system development, including a suite of G-protein-coupled receptors that control physiology and behaviour, the Robo- Slit midline repulsion system, and the neurotrophin signalling system; a high number of zinc finger transcription factors; and novel factors that previously escaped attention. Contradicting the current view, our study reveals that genes with bilaterian origin are robustly associated with key features in extant bilaterians, suggesting a causal relationship. *For correspondence: [email protected] Introduction The taxon Bilateria consists of multicellular animals -
Pan-Cancer Transcriptome Analysis Reveals a Gene Expression
Modern Pathology (2016) 29, 546–556 546 © 2016 USCAP, Inc All rights reserved 0893-3952/16 $32.00 Pan-cancer transcriptome analysis reveals a gene expression signature for the identification of tumor tissue origin Qinghua Xu1,6, Jinying Chen1,6, Shujuan Ni2,3,4,6, Cong Tan2,3,4,6, Midie Xu2,3,4, Lei Dong2,3,4, Lin Yuan5, Qifeng Wang2,3,4 and Xiang Du2,3,4 1Canhelp Genomics, Hangzhou, Zhejiang, China; 2Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; 3Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China; 4Institute of Pathology, Fudan University, Shanghai, China and 5Pathology Center, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China Carcinoma of unknown primary, wherein metastatic disease is present without an identifiable primary site, accounts for ~ 3–5% of all cancer diagnoses. Despite the development of multiple diagnostic workups, the success rate of primary site identification remains low. Determining the origin of tumor tissue is, thus, an important clinical application of molecular diagnostics. Previous studies have paved the way for gene expression-based tumor type classification. In this study, we have established a comprehensive database integrating microarray- and sequencing-based gene expression profiles of 16 674 tumor samples covering 22 common human tumor types. From this pan-cancer transcriptome database, we identified a 154-gene expression signature that discriminated the origin of tumor tissue with an overall leave-one-out cross-validation accuracy of 96.5%. The 154-gene expression signature was first validated on an independent test set consisting of 9626 primary tumors, of which 97.1% of cases were correctly classified.