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Tian J, Luo B. Identification of Three Prognosis-Related Differentially Expressed lncRNAs Driven by Copy Number Variation in Thyroid Cancer. J Immunol Res 2022; 2022:9203796. [PMID: 35642209 PMCID: PMC9148411 DOI: 10.1155/2022/9203796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/01/2022] [Accepted: 04/11/2022] [Indexed: 02/07/2023] Open
Abstract
Thyroid cancer as the malignant tumor with the highest incidence in the endocrine system also shows a fast growth and development. In this work, we developed a new method to identify copy number variation- (CNV-) driven differentially expressed lncRNAs in thyroid cancer for predicting cancer prognosis. The data of RNA sequencing, CNV, methylation, mutation, and clinical details of thyroid cancer were obtained from the Cancer Genome Atlas database (TCGA). Molecular subtypes were clustered by iClusterPlus. Weighted gene co-expression network analysis (WGCNA) was employed to show co-expression modules. DEseq2 was conducted to identify protein coding genes (PCGs) and differentially expressed lncRNAs. CNV was detected using GISTIC 2.0. Three molecular subtypes were identified, and 68 differentially expressed lncRNAs (DElncRNAs) related to cancer were found among different molecular subtypes. CNV of FOXD2-AS1, FAM181A-AS1, and RNF157-AS1 was associated with overall survival and was involved in cancer-related pathways. These three DElncRNAs discovered based on CNV could serve as prognostic biomarkers to predict prognosis for thyroid cancer and new targets to explore molecular drugs.
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Affiliation(s)
- Jinyi Tian
- Department of General Surgery, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, 168 Litang Road, Changping District, Beijing, China
| | - Bin Luo
- Department of General Surgery, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, 168 Litang Road, Changping District, Beijing, China
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2
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Multiple endocrine neoplasia type 2: A reveiw. Semin Cancer Biol 2021; 79:163-179. [PMID: 33812987 DOI: 10.1016/j.semcancer.2021.03.035] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 03/13/2021] [Accepted: 03/27/2021] [Indexed: 12/16/2022]
Abstract
Multiple endocrine neoplasias are rare hereditary syndromes some of them with malignant potential. Multiple endocrine neoplasia type 2 (MEN 2) is an autosomal dominant hereditary cancer syndrome due to germline variants in the REarranged during Transfection (RET) proto-oncogene. There are two distinct clinical entities: MEN 2A and MEN 2B. MEN 2A is associated with medullary thyroid carcinoma (MTC), phaeochromocytoma, primary hyperparathyroidism, cutaneous lichen amyloidosis and Hirschprung's disease and MEN 2B with MTC, phaeochromocytoma, ganglioneuromatosis of the aerodigestive tract, musculoskeletal and ophthalmologic abnormalities. Germline RET variants causing MEN 2 result in gain-of-function; since the discovery of the genetic variants a thorough search for genotype-phenotype associations began in order to understand the high variability both between families and within family members. These studies have successfully led to improved risk classification of prognosis in relation to the genotype, thus improving the management of the patients by thorough genetic counseling. The present review summarizes the recent developments in the knowledge of these hereditary syndromes as well as the impact on clinical management, including genetic counseling, of both individual patients and families. It furthermore points to future directions of research for better clarification of timing of treatments of the various manifestations of the syndromes in order to improve survival and morbidity in these patients.
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Ahmed P H, V V, More RP, Viswanath B, Jain S, Rao MS, Mukherjee O. INDEX-db: The Indian Exome Reference Database (Phase I). J Comput Biol 2019; 26:225-234. [PMID: 30615482 PMCID: PMC6441288 DOI: 10.1089/cmb.2018.0199] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Deep sequencing-based genetic mapping has greatly enhanced the ability to catalog variants with plausible disease association. Confirming how these identified variants contribute to specific disease conditions, across human populations, poses the next challenge. Differential selection pressure may impact the frequency of genetic variations, and thus detection of association with disease conditions, across populations. To understand genotype to phenotype correlations, it thus becomes important to first understand the spectrum of genetic variation within a population by creating a reference map. In this study, we report the development of phase I of a new database of genetic variations called INDian EXome database (INDEX-db), from the Indian population, with an aim to establish a centralized database of integrated information. This could be useful for researchers involved in studying disease mechanisms at clinical, genetic, and cellular levels.
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Affiliation(s)
- Husayn Ahmed P
- Accelerator Program for Discovery in Brain Disorders Using Stem Cells (ADBS), National Centre for Biological Sciences, Tata Institute of Fundamental Research (NCBS-TIFR), Bengaluru, India
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, India
| | - Vidhya V
- Accelerator Program for Discovery in Brain Disorders Using Stem Cells (ADBS), Centre for Brain Development and Repair (CBDR), Institute for Stem Cell Biology and Regenerative Medicine (InStem), Bengaluru, India
| | - Ravi Prabhakar More
- Accelerator Program for Discovery in Brain Disorders Using Stem Cells (ADBS), National Centre for Biological Sciences, Tata Institute of Fundamental Research (NCBS-TIFR), Bengaluru, India
| | - Biju Viswanath
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India
| | - Sanjeev Jain
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India
| | - Mahendra S. Rao
- Accelerator Program for Discovery in Brain Disorders Using Stem Cells (ADBS), Centre for Brain Development and Repair (CBDR), Institute for Stem Cell Biology and Regenerative Medicine (InStem), Bengaluru, India
| | - Odity Mukherjee
- Address correspondence to: Dr. Odity Mukherjee, Investigator & Chief Technologist, Accelerator Program for Discovery in Brain Disorders Using Stem Cells (ADBS), Centre for Brain Development and Repair (CBDR), Institute for Stem Cell Biology and Regenerative Medicine (InStem), Bellary Road, Bengaluru–560065, Karnataka, India
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A cancer-testis non-coding RNA LIN28B-AS1 activates driver gene LIN28B by interacting with IGF2BP1 in lung adenocarcinoma. Oncogene 2018; 38:1611-1624. [DOI: 10.1038/s41388-018-0548-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 09/11/2018] [Accepted: 09/14/2018] [Indexed: 12/19/2022]
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Genetic diagnosis of a Chinese multiple endocrine neoplasia type 2A family through whole genome sequencing. J Biosci 2018; 42:209-218. [PMID: 28569245 DOI: 10.1007/s12038-017-9686-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Approximately 98% of patients with multiple endocrine neoplasia type 2A (MEN 2A) have an identifiable RET mutation. Prophylactic or early total thyroidectomy or pheochromocytoma/parathyroid removal in patients can be preventative or curative and has become standard management. The general strategy for RET screening on family members at risk is to sequence the most commonly affected exons and, if negative, to extend sequencing to additional exons. However, different families with MEN 2A due to the same RET mutation often have significant variability in the clinical exhibition of disease and aggressiveness of the MTC, which implies additional genetic loci exsit beyond RET coding region. Whole genome sequencing (WGS) greatly expands the breadth of screening from genes associated with a particular disease to the whole genome and, potentially, all the information that the genome contains about diseases or traits. This is presumably due to additive effect of disease modifying factors. In this study, we performed WGS on a typical Chinese MEN 2A proband and identified the pathogenic RET p.C634R mutation. We also identified several neutral variants within RET and pheochromocytoma-related genes. Moreover, we found several interesting structural variants including genetic deletions (RSPO1, OVCH2 and AP3S1, etc.) and fusion transcripts (FSIP1-BAZ2A, etc.).
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Skau CT, Fischer RS, Gurel P, Thiam HR, Tubbs A, Baird MA, Davidson MW, Piel M, Alushin GM, Nussenzweig A, Steeg PS, Waterman CM. FMN2 Makes Perinuclear Actin to Protect Nuclei during Confined Migration and Promote Metastasis. Cell 2016; 167:1571-1585.e18. [PMID: 27839864 DOI: 10.1016/j.cell.2016.10.023] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 07/28/2016] [Accepted: 10/13/2016] [Indexed: 01/14/2023]
Abstract
Cell migration in confined 3D tissue microenvironments is critical for both normal physiological functions and dissemination of tumor cells. We discovered a cytoskeletal structure that prevents damage to the nucleus during migration in confined microenvironments. The formin-family actin filament nucleator FMN2 associates with and generates a perinuclear actin/focal adhesion (FA) system that is distinct from previously characterized actin/FA structures. This system controls nuclear shape and positioning in cells migrating on 2D surfaces. In confined 3D microenvironments, FMN2 promotes cell survival by limiting nuclear envelope damage and DNA double-strand breaks. We found that FMN2 is upregulated in human melanomas and showed that disruption of FMN2 in mouse melanoma cells inhibits their extravasation and metastasis to the lung. Our results indicate a critical role for FMN2 in generating a perinuclear actin/FA system that protects the nucleus and DNA from damage to promote cell survival during confined migration and thus promote cancer metastasis.
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Affiliation(s)
- Colleen T Skau
- Cell Biology and Physiology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert S Fischer
- Cell Biology and Physiology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pinar Gurel
- Cell Biology and Physiology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hawa Racine Thiam
- Cell Biology and Physiology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; Institut Curie, CNRS UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Anthony Tubbs
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michelle A Baird
- Cell Biology and Physiology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; Magnet Lab, Florida State University, Tallahassee, FL 32306, USA
| | | | - Matthieu Piel
- Institut Curie, CNRS UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Gregory M Alushin
- Cell Biology and Physiology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andre Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Patricia S Steeg
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Clare M Waterman
- Cell Biology and Physiology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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