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Yoshihama K, Mutai H, Sekimizu M, Ito F, Saito S, Nakamura S, Mikoshiba T, Nagai R, Takebayashi A, Miya F, Kosaki K, Ozawa H, Matsunaga T. Molecular basis of carotid body tumor and associated clinical features in Japan identified by genomic, immunohistochemical, and clinical analyses. Clin Genet 2023; 103:466-471. [PMID: 36597280 DOI: 10.1111/cge.14294] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/29/2022] [Accepted: 01/01/2023] [Indexed: 01/05/2023]
Abstract
Carotid body tumor (CBT) is classified as a paraganglioma (PGL). Here, we report the genetic background, protein expression pattern, and clinical findings of 30 Japanese CBT cases. Germline pathogenic or likely pathogenic (P/LP) variants of genes encoding succinate dehydrogenase subunits (SDHs) were detected in 15 of 30 cases (50%). The SDHB variants were the most frequently detected, followed by SDHA and SDHD variants. One case with SDHAF2 variant was bilateral CBT, and other two multiple PGL cases were not detected P/LP variants. The three cases with germline variants that could be tested did not have somatic P/LP variants of the same genes. Immunohistochemical analysis showed negative SDHB signals in CBT tissues in five cases with germline P/LP variants of SDHB, SDHD, or SDHA. In addition, SDHB signals in CBT tissues were negative in four of nine cases without germline P/LP variants of SDHs. These findings suggest the involvement of unidentified molecular mechanisms affecting SDHs.
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Affiliation(s)
- Keisuke Yoshihama
- Department of Otolaryngology, Head and Neck Surgery, Keio University School of Medicine, Tokyo, Japan
- Division of Hearing and Balance Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Hideki Mutai
- Division of Hearing and Balance Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Mariko Sekimizu
- Department of Otolaryngology, Head and Neck Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Fumihiro Ito
- Department of Otolaryngology, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Shin Saito
- Department of Otolaryngology, Head and Neck Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Shintaro Nakamura
- Department of Otolaryngology, Head and Neck Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Takuya Mikoshiba
- Department of Otolaryngology, Head and Neck Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Ryoto Nagai
- Department of Otolaryngology, Head and Neck Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Akiko Takebayashi
- Department of Otolaryngology, Head and Neck Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Fuyuki Miya
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Hiroyuki Ozawa
- Department of Otolaryngology, Head and Neck Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Tatsuo Matsunaga
- Division of Hearing and Balance Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
- Department of Otolaryngology, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
- Medical Genetics Center, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
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Schuler BA, Nelson ET, Koziura M, Cogan JD, Hamid R, Phillips JA. Lessons learned: next-generation sequencing applied to undiagnosed genetic diseases. J Clin Invest 2022; 132:e154942. [PMID: 35362483 PMCID: PMC8970663 DOI: 10.1172/jci154942] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Rare genetic disorders, when considered together, are relatively common. Despite advancements in genetics and genomics technologies as well as increased understanding of genomic function and dysfunction, many genetic diseases continue to be difficult to diagnose. The goal of this Review is to increase the familiarity of genetic testing strategies for non-genetics providers. As genetic testing is increasingly used in primary care, many subspecialty clinics, and various inpatient settings, it is important that non-genetics providers have a fundamental understanding of the strengths and weaknesses of various genetic testing strategies as well as develop an ability to interpret genetic testing results. We provide background on commonly used genetic testing approaches, give examples of phenotypes in which the various genetic testing approaches are used, describe types of genetic and genomic variations, cover challenges in variant identification, provide examples in which next-generation sequencing (NGS) failed to uncover the variant responsible for a disease, and discuss opportunities for continued improvement in the application of NGS clinically. As genetic testing becomes increasingly a part of all areas of medicine, familiarity with genetic testing approaches and result interpretation is vital to decrease the burden of undiagnosed disease.
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Affiliation(s)
- Bryce A. Schuler
- Division of Medical Genetics and Genomics and
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Erica T. Nelson
- Division of Medical Genetics and Genomics and
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Mary Koziura
- Division of Medical Genetics and Genomics and
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Joy D. Cogan
- Division of Medical Genetics and Genomics and
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Rizwan Hamid
- Division of Medical Genetics and Genomics and
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - John A. Phillips
- Division of Medical Genetics and Genomics and
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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Gómez de Segura I, Ahechu P, Gómez-Ambrosi J, Rodríguez A, Ramírez B, Becerril S, Unamuno X, Mentxaka A, Baixauli J, Valentí V, Moncada R, Silva C, Frühbeck G, Catalán V. Decreased Levels of Microfibril-Associated Glycoprotein (MAGP)-1 in Patients with Colon Cancer and Obesity Are Associated with Changes in Extracellular Matrix Remodelling. Int J Mol Sci 2021; 22:ijms22168485. [PMID: 34445187 PMCID: PMC8395192 DOI: 10.3390/ijms22168485] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/28/2021] [Accepted: 08/03/2021] [Indexed: 01/22/2023] Open
Abstract
OBJECTIVE The protein microfibril-associated glycoprotein (MAGP)-1 constitutes a crucial extracellular matrix protein. We aimed to determine its impact on visceral adipose tissue (VAT) remodelling during obesity-associated colon cancer (CC). METHODS Samples obtained from 79 subjects (29 normoponderal (NP) (17 with CC) and 50 patients with obesity (OB) (19 with CC)) were used in the study. Circulating concentrations of MAGP-1 and its gene expression levels (MFAP2) in VAT were analysed. The impact of inflammation-related factors and adipocyte-conditioned media (ACM) on MFAP2 mRNA levels in colon adenocarcinoma HT-29 cells were further analysed. The effects of MAGP-1 in the expression of genes involved in the extracellular matrix (ECM) remodelling and tumorigenesis in HT-29 cells was also explored. RESULTS Obesity (p < 0.01) and CC (p < 0.001) significantly decreased MFAP2 gene expression levels in VAT whereas an opposite trend in TGFB1 mRNA levels was observed. Increased mRNA levels of MFAP2 after the stimulation of HT-29 cells with lipopolysaccharide (LPS) (p < 0.01) and interleukin (IL)-4 (p < 0.01) together with a downregulation (p < 0.05) after hypoxia mimicked by CoCl2 treatment was observed. MAGP-1 treatment significantly enhanced the mRNA levels of the ECM-remodelling genes collagen type 6 α3 chain (COL6A3) (p < 0.05), decorin (DCN) (p < 0.01), osteopontin (SPP1) (p < 0.05) and TGFB1 (p < 0.05). Furthermore, MAGP-1 significantly reduced (p < 0.05) the gene expression levels of prostaglandin-endoperoxide synthase 2 (COX2/PTGS2), a key gene controlling cell proliferation, growth and adhesion in CC. Interestingly, a significant decrease (p < 0.01) in the mRNA levels of MFAP2 in HT-29 cells preincubated with ACM from volunteers with obesity compared with control media was observed. Conclusion: The decreased levels of MAGP-1 in patients with obesity and CC together with its capacity to modulate key genes involved in ECM remodelling and tumorigenesis suggest MAGP-1 as a link between AT excess and obesity-associated CC development.
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Affiliation(s)
- Iranzu Gómez de Segura
- Metabolic Research Laboratory, Clínica Universidad de Navarra, 31008 Pamplona, Spain; (I.G.d.S.); (J.G.-A.); (A.R.); (B.R.); (S.B.); (X.U.); (A.M.)
| | - Patricia Ahechu
- Department of Surgery, Clínica Universidad de Navarra, 31008 Pamplona, Spain; (P.A.); (J.B.); (V.V.)
| | - Javier Gómez-Ambrosi
- Metabolic Research Laboratory, Clínica Universidad de Navarra, 31008 Pamplona, Spain; (I.G.d.S.); (J.G.-A.); (A.R.); (B.R.); (S.B.); (X.U.); (A.M.)
- CIBEROBN, Instituto de Salud Carlos III, 31008 Pamplona, Spain; (R.M.); (C.S.)
- Obesity and Adipobiology Group, IdiSNA, 31008 Pamplona, Spain
| | - Amaia Rodríguez
- Metabolic Research Laboratory, Clínica Universidad de Navarra, 31008 Pamplona, Spain; (I.G.d.S.); (J.G.-A.); (A.R.); (B.R.); (S.B.); (X.U.); (A.M.)
- CIBEROBN, Instituto de Salud Carlos III, 31008 Pamplona, Spain; (R.M.); (C.S.)
- Obesity and Adipobiology Group, IdiSNA, 31008 Pamplona, Spain
| | - Beatriz Ramírez
- Metabolic Research Laboratory, Clínica Universidad de Navarra, 31008 Pamplona, Spain; (I.G.d.S.); (J.G.-A.); (A.R.); (B.R.); (S.B.); (X.U.); (A.M.)
- CIBEROBN, Instituto de Salud Carlos III, 31008 Pamplona, Spain; (R.M.); (C.S.)
- Obesity and Adipobiology Group, IdiSNA, 31008 Pamplona, Spain
| | - Sara Becerril
- Metabolic Research Laboratory, Clínica Universidad de Navarra, 31008 Pamplona, Spain; (I.G.d.S.); (J.G.-A.); (A.R.); (B.R.); (S.B.); (X.U.); (A.M.)
- CIBEROBN, Instituto de Salud Carlos III, 31008 Pamplona, Spain; (R.M.); (C.S.)
- Obesity and Adipobiology Group, IdiSNA, 31008 Pamplona, Spain
| | - Xabier Unamuno
- Metabolic Research Laboratory, Clínica Universidad de Navarra, 31008 Pamplona, Spain; (I.G.d.S.); (J.G.-A.); (A.R.); (B.R.); (S.B.); (X.U.); (A.M.)
- CIBEROBN, Instituto de Salud Carlos III, 31008 Pamplona, Spain; (R.M.); (C.S.)
| | - Amaia Mentxaka
- Metabolic Research Laboratory, Clínica Universidad de Navarra, 31008 Pamplona, Spain; (I.G.d.S.); (J.G.-A.); (A.R.); (B.R.); (S.B.); (X.U.); (A.M.)
- CIBEROBN, Instituto de Salud Carlos III, 31008 Pamplona, Spain; (R.M.); (C.S.)
| | - Jorge Baixauli
- Department of Surgery, Clínica Universidad de Navarra, 31008 Pamplona, Spain; (P.A.); (J.B.); (V.V.)
| | - Víctor Valentí
- Department of Surgery, Clínica Universidad de Navarra, 31008 Pamplona, Spain; (P.A.); (J.B.); (V.V.)
- CIBEROBN, Instituto de Salud Carlos III, 31008 Pamplona, Spain; (R.M.); (C.S.)
- Obesity and Adipobiology Group, IdiSNA, 31008 Pamplona, Spain
| | - Rafael Moncada
- CIBEROBN, Instituto de Salud Carlos III, 31008 Pamplona, Spain; (R.M.); (C.S.)
- Department of Anesthesia, Clínica Universidad de Navarra, 31008 Pamplona, Spain
| | - Camilo Silva
- CIBEROBN, Instituto de Salud Carlos III, 31008 Pamplona, Spain; (R.M.); (C.S.)
- Obesity and Adipobiology Group, IdiSNA, 31008 Pamplona, Spain
- Department of Endocrinology & Nutrition, Clínica Universidad de Navarra, 31008 Pamplona, Spain
| | - Gema Frühbeck
- Metabolic Research Laboratory, Clínica Universidad de Navarra, 31008 Pamplona, Spain; (I.G.d.S.); (J.G.-A.); (A.R.); (B.R.); (S.B.); (X.U.); (A.M.)
- CIBEROBN, Instituto de Salud Carlos III, 31008 Pamplona, Spain; (R.M.); (C.S.)
- Obesity and Adipobiology Group, IdiSNA, 31008 Pamplona, Spain
- Department of Endocrinology & Nutrition, Clínica Universidad de Navarra, 31008 Pamplona, Spain
- Correspondence: (G.F.); (V.C.); Tel.: +34-9-4825-5400 (ext. 4484) (G.F.); +34-9-4825-5400 (ext. 5133) (V.C.)
| | - Victoria Catalán
- Metabolic Research Laboratory, Clínica Universidad de Navarra, 31008 Pamplona, Spain; (I.G.d.S.); (J.G.-A.); (A.R.); (B.R.); (S.B.); (X.U.); (A.M.)
- CIBEROBN, Instituto de Salud Carlos III, 31008 Pamplona, Spain; (R.M.); (C.S.)
- Obesity and Adipobiology Group, IdiSNA, 31008 Pamplona, Spain
- Correspondence: (G.F.); (V.C.); Tel.: +34-9-4825-5400 (ext. 4484) (G.F.); +34-9-4825-5400 (ext. 5133) (V.C.)
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Cope H, Spillmann R, Rosenfeld JA, Brokamp E, Signer R, Schoch K, Kelley EG, Sullivan JA, Macnamara E, Lincoln S, Golden‐Grant K, Orengo JP, Clark G, Burrage LC, Posey JE, Punetha J, Robertson A, Cogan J, Phillips JA, Martinez‐Agosto J, Shashi V. Missed diagnoses: Clinically relevant lessons learned through medical mysteries solved by the Undiagnosed Diseases Network. Mol Genet Genomic Med 2020; 8:e1397. [PMID: 32730690 PMCID: PMC7549585 DOI: 10.1002/mgg3.1397] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/04/2020] [Accepted: 06/08/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Resources within the Undiagnosed Diseases Network (UDN), such as genome sequencing (GS) and model organisms aid in diagnosis and identification of new disease genes, but are currently difficult to access by clinical providers. While these resources do contribute to diagnoses in many cases, they are not always necessary to reach diagnostic resolution. The UDN experience has been that participants can also receive diagnoses through the thoughtful and customized application of approaches and resources that are readily available in clinical settings. METHODS The UDN Genetic Counseling and Testing Working Group collected case vignettes that illustrated how clinically available methods resulted in diagnoses. The case vignettes were classified into three themes; phenotypic considerations, selection of genetic testing, and evaluating exome/GS variants and data. RESULTS We present 12 participants that illustrate how clinical practices such as phenotype-driven genomic investigations, consideration of variable expressivity, selecting the relevant tissue of interest for testing, utilizing updated testing platforms, and recognition of alternate transcript nomenclature resulted in diagnoses. CONCLUSION These examples demonstrate that when a diagnosis is elusive, an iterative patient-specific approach utilizing assessment options available to clinical providers may solve a portion of cases. However, this does require increased provider time commitment, a particular challenge in the current practice of genomics.
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Affiliation(s)
- Heidi Cope
- Division of Medical GeneticsDepartment of PediatricsDuke University Medical CenterDurhamNCUSA
| | - Rebecca Spillmann
- Division of Medical GeneticsDepartment of PediatricsDuke University Medical CenterDurhamNCUSA
| | - Jill A. Rosenfeld
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTXUSA
| | - Elly Brokamp
- Division of Medical Genetics and Genomic MedicineVanderbilt University Medical CenterNashvilleTNUSA
| | - Rebecca Signer
- Department of Human GeneticsUniversity of CaliforniaLos AngelesCAUSA
| | - Kelly Schoch
- Division of Medical GeneticsDepartment of PediatricsDuke University Medical CenterDurhamNCUSA
| | - Emily G. Kelley
- Department of Biomedical InformaticsHarvard Medical SchoolBostonMAUSA
| | - Jennifer A. Sullivan
- Division of Medical GeneticsDepartment of PediatricsDuke University Medical CenterDurhamNCUSA
| | - Ellen Macnamara
- Undiagnosed Diseases ProgramCommon FundOffice of the DirectorNational Institutes of HealthNIHBethesdaMDUSA
| | - Sharyn Lincoln
- Division of Genetics and GenomicsDepartment of PediatricsBoston Children’s HospitalBostonMAUSA
| | | | | | - James P. Orengo
- Department of NeurologyBaylor College of MedicineHoustonTXUSA
| | - Gary Clark
- Department of NeurologyBaylor College of MedicineHoustonTXUSA
| | - Lindsay C. Burrage
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTXUSA
| | - Jennifer E. Posey
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTXUSA
| | - Jaya Punetha
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTXUSA
| | - Amy Robertson
- Division of Medical Genetics and Genomic MedicineVanderbilt University Medical CenterNashvilleTNUSA
| | - Joy Cogan
- Division of Medical Genetics and Genomic MedicineVanderbilt University Medical CenterNashvilleTNUSA
| | - John A. Phillips
- Division of Medical Genetics and Genomic MedicineVanderbilt University Medical CenterNashvilleTNUSA
| | | | - Vandana Shashi
- Division of Medical GeneticsDepartment of PediatricsDuke University Medical CenterDurhamNCUSA
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