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Kinney N, Kang L, Bains H, Lawson E, Husain M, Husain K, Sandhu I, Shin Y, Carter JK, Anandakrishnan R, Michalak P, Garner H. Ethnically biased microsatellites contribute to differential gene expression and glutathione metabolism in Africans and Europeans. PLoS One 2021; 16:e0249148. [PMID: 33765058 PMCID: PMC7993785 DOI: 10.1371/journal.pone.0249148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 03/11/2021] [Indexed: 12/28/2022] Open
Abstract
Approximately three percent of the human genome is occupied by microsatellites: a type of short tandem repeat (STR). Microsatellites have well established effects on (a) the genetic structure of diverse human populations and (b) expression of nearby genes. These lines of inquiry have uncovered 3,984 ethnically biased microsatellite loci (EBML) and 28,375 expression STRs (eSTRs), respectively. We hypothesize that a combination of EBML, eSTRs, and gene expression data (RNA-seq) can be used to show that microsatellites contribute to differential gene expression and phenotype in human populations. In fact, our previous study demonstrated a degree of mutual overlap between EBML and eSTRs but fell short of quantifying effects on gene expression. The present work aims to narrow the gap. First, we identify 313 overlapping EBML/eSTRs and recapitulate their mutual overlap. The 313 EBML/eSTRs are then characterized across ethnicity and tissue type. We use RNA-seq data to pursue validation of 49 regions that affect whole blood gene expression; 32 out of 54 affected genes are differentially expressed in Africans and Europeans. We quantify the relative contribution of these 32 genes to differential expression; fold change tends to be less than other differentially expressed genes. Repeat length correlates with expression for 15 of the 32 genes; two are conspicuously involved in glutathione metabolism. Finally, we repurpose a mathematical model of glutathione metabolism to investigate how a single polymorphic microsatellite affects phenotype. We conclude with a testable prediction that microsatellite polymorphisms affect GPX7 expression and oxidative stress in Africans and Europeans.
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Affiliation(s)
- Nick Kinney
- Edward Via College of Osteopathic Medicine, Blacksburg, Virginia, United States of America
- Gibbs Cancer Center & Research Institute, Spartanburg, South Carolina, United States of America
- * E-mail:
| | - Lin Kang
- Edward Via College of Osteopathic Medicine, Blacksburg, Virginia, United States of America
- Gibbs Cancer Center & Research Institute, Spartanburg, South Carolina, United States of America
| | - Harpal Bains
- Edward Via College of Osteopathic Medicine, Blacksburg, Virginia, United States of America
| | - Elizabeth Lawson
- Edward Via College of Osteopathic Medicine, Blacksburg, Virginia, United States of America
| | - Mesam Husain
- Edward Via College of Osteopathic Medicine, Blacksburg, Virginia, United States of America
| | - Kumayl Husain
- Edward Via College of Osteopathic Medicine, Blacksburg, Virginia, United States of America
| | - Inderjit Sandhu
- Edward Via College of Osteopathic Medicine, Blacksburg, Virginia, United States of America
| | - Yongdeok Shin
- Edward Via College of Osteopathic Medicine, Blacksburg, Virginia, United States of America
| | - Javan K. Carter
- University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Ramu Anandakrishnan
- Edward Via College of Osteopathic Medicine, Blacksburg, Virginia, United States of America
- Gibbs Cancer Center & Research Institute, Spartanburg, South Carolina, United States of America
| | - Pawel Michalak
- Edward Via College of Osteopathic Medicine, Blacksburg, Virginia, United States of America
- Gibbs Cancer Center & Research Institute, Spartanburg, South Carolina, United States of America
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Harold Garner
- Edward Via College of Osteopathic Medicine, Blacksburg, Virginia, United States of America
- Gibbs Cancer Center & Research Institute, Spartanburg, South Carolina, United States of America
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Capasso M, Montella A, Tirelli M, Maiorino T, Cantalupo S, Iolascon A. Genetic Predisposition to Solid Pediatric Cancers. Front Oncol 2020; 10:590033. [PMID: 33194750 PMCID: PMC7656777 DOI: 10.3389/fonc.2020.590033] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/08/2020] [Indexed: 12/15/2022] Open
Abstract
Progresses over the past years have extensively improved our capacity to use genome-scale analyses—including high-density genotyping and exome and genome sequencing—to identify the genetic basis of pediatric tumors. In particular, exome sequencing has contributed to the evidence that about 10% of children and adolescents with tumors have germline genetic variants associated with cancer predisposition. In this review, we provide an overview of genetic variations predisposing to solid pediatric tumors (medulloblastoma, ependymoma, astrocytoma, neuroblastoma, retinoblastoma, Wilms tumor, osteosarcoma, rhabdomyosarcoma, and Ewing sarcoma) and outline the biological processes affected by the involved mutated genes. A careful description of the genetic basis underlying a large number of syndromes associated with an increased risk of pediatric cancer is also reported. We place particular emphasis on the emerging view that interactions between germline and somatic alterations are a key determinant of cancer development. We propose future research directions, which focus on the biological function of pediatric risk alleles and on the potential links between the germline genome and somatic changes. Finally, the importance of developing new molecular diagnostic tests including all the identified risk germline mutations and of considering the genetic predisposition in screening tests and novel therapies is emphasized.
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Affiliation(s)
- Mario Capasso
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy.,CEINGE Biotecnologie Avanzate, Naples, Italy
| | | | - Matilde Tirelli
- CEINGE Biotecnologie Avanzate, Naples, Italy.,European School of Molecular Medicine, Università Degli Studi di Milano, Milan, Italy
| | - Teresa Maiorino
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy.,CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Sueva Cantalupo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy.,CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Achille Iolascon
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy.,CEINGE Biotecnologie Avanzate, Naples, Italy
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