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Miranda S, Tonin FS, Pinto-Sousa C, Fortes-Gabriel E, Brito M. Genetic Profile of Rotavirus Type A in Children under 5 Years Old in Africa: A Systematic Review of Prevalence. Viruses 2024; 16:243. [PMID: 38400019 PMCID: PMC10893345 DOI: 10.3390/v16020243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/19/2023] [Accepted: 10/24/2023] [Indexed: 02/25/2024] Open
Abstract
Human type A rotavirus (RV-A) is world-recognized as the major pathogen causing viral gastroenteritis in children under 5 years of age. The literature indicates a substantial increase in the diversity of rotavirus strains across continents, especially in Africa, which can pose significant challenges including an increase of disease burden and a reduction of vaccines' effectiveness. However, few studies have mapped the variety of circulating virus strains in different regions, which may hamper decisions on epidemiological surveillance and preventive public health measures. Thus, our aim was to compile the most updated available evidence on the genetic profile of RV-A among children in Africa and determine the prevalence of different genotypes according to the geographical regions by means of a broad systematic review. Systematic searches were performed in PubMed, Scopus, Web of Science, and Scielo without language, time limits, or geographical restrictions within the African continent. We selected full-text peer-reviewed articles assessing the genetic profile (i.e., genotyping) of RV-A in children up to 5 years old in Africa. Overall, 682 records were retrieved, resulting in 75 studies included for evidence synthesis. These studies were published between 1999 and 2022, were conducted in 28 countries from the five African regions, and 48% of the studies were carried out for 24 months or more. Most studies (n = 55; 73.3%) evaluated RV-A cases before the introduction of the vaccines, while around 20% of studies (n = 13) presented data after the vaccine approval in each country. Only seven (9.3%) studies compared evidence from both periods (pre- and post-vaccine introduction). Genotyping methods to assess RV-A varied between RT-PCR, nested or multiplex RT-PCR, testing only the most common P and G-types. We observed G1 and P[8] to be the most prevalent strains in Africa, with values around 31% and 43%, respectively. Yet if all the genotypes with the following highest prevalence were added ((G1 + G2, G3, G9) and (P[8] + P[6], P[4])), these figures would represent 80% and 99% of the total prevalence. The combination G1P[8] was the most reported in the studies (around 22%). This review study demonstrated an increased strain diversity in the past two decades, which could represent a challenge to the efficacy of the current vaccine.
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Affiliation(s)
- Sandra Miranda
- Faculdade de Medicine, Universidade Agostinho Neto, Luanda, Angola; (S.M.); (C.P.-S.)
- CISA-Centro de Investigação em Saúde de Angola, Caxito, Bengo, Angola;
- Clínica Girassol, Luanda, Angola
| | - Fernanda S. Tonin
- ESTeSL-Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, 1990-096 Lisboa, Portugal;
- Pharmaceutical Sciences Postgraduate Program, Federal University of Paraná, Curitiba 80210-170, Brazil
| | - Carlos Pinto-Sousa
- Faculdade de Medicine, Universidade Agostinho Neto, Luanda, Angola; (S.M.); (C.P.-S.)
- UPRA-Universidade Privada de Angola, Luanda, Angola
| | - Elsa Fortes-Gabriel
- CISA-Centro de Investigação em Saúde de Angola, Caxito, Bengo, Angola;
- ISTM- Instituto Superior Técnico Militar, Luanda, Angola
| | - Miguel Brito
- CISA-Centro de Investigação em Saúde de Angola, Caxito, Bengo, Angola;
- ESTeSL-Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, 1990-096 Lisboa, Portugal;
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Papadakos S, Issa H, Alamri A, Alamri A, Semlali A. Rapamycin as a Potential Alternative Drug for Squamous Cell Gingiva Carcinoma (Ca9-22): A Focus on Cell Cycle, Apoptosis and Autophagy Genetic Profile. Pharmaceuticals (Basel) 2024; 17:131. [PMID: 38276004 PMCID: PMC10818555 DOI: 10.3390/ph17010131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/01/2024] [Accepted: 01/08/2024] [Indexed: 01/27/2024] Open
Abstract
Oral cancer is considered as one of the most common malignancies worldwide. Its conventional treatment primarily involves surgery with or without postoperative adjuvant therapy. The targeting of signaling pathways implicated in tumorigenesis is becoming increasingly prevalent in the development of new anticancer drug candidates. Based on our recently published data, Rapamycin, an inhibitor of the mTOR pathway, exhibits selective antitumor activity in oral cancer by inhibiting cell proliferation and inducing cancer cell apoptosis, autophagy, and cellular stress. In the present study, our focus is on elucidating the genetic determinants of Rapamycin's action and the interaction networks accountable for tumorigenesis suppression. To achieve this, gingival carcinoma cell lines (Ca9-22) were exposed to Rapamycin at IC50 (10 µM) for 24 h. Subsequently, we investigated the genetic profiles related to the cell cycle, apoptosis, and autophagy, as well as gene-gene interactions, using QPCR arrays and the Gene MANIA website. Overall, our results showed that Rapamycin at 10 µM significantly inhibits the growth of Ca9-22 cells after 24 h of treatment by around 50% by suppression of key modulators in the G2/M transition, namely, Survivin and CDK5RAP1. The combination of Rapamycin with Cisplatin potentializes the inhibition of Ca9-22 cell proliferation. A P1/Annexin-V assay was performed to evaluate the effect of Rapamycin on cell apoptosis. The results obtained confirm our previous findings in which Rapamycin at 10 μM induces a strong apoptosis of Ca9-22 cells. The live cells decreased, and the late apoptotic cells increased when the cells were treated by Rapamycin. To identify the genes responsible for cell apoptosis induced by Rapamycin, we performed the RT2 Profiler PCR Arrays for 84 apoptotic genes. The blocked cells were believed to be directed towards cell death, confirmed by the downregulation of apoptosis inhibitors involved in both the extrinsic and intrinsic pathways, including BIRC5, BNIP3, CD40LG, DAPK1, LTA, TNFRSF21 and TP73. The observed effects of Rapamycin on tumor suppression are likely to involve the autophagy process, evidenced by the inhibition of autophagy modulators (TGFβ1, RGS19 and AKT1), autophagosome biogenesis components (AMBRA1, ATG9B and TMEM74) and autophagy byproducts (APP). Identifying gene-gene interaction (GGI) networks provided a comprehensive view of the drug's mechanism and connected the studied tumorigenesis processes to potential functional interactions of various kinds (physical interaction, co-expression, genetic interactions etc.). In conclusion, Rapamycin shows promise as a clinical agent for managing Ca9-22 gingiva carcinoma cells.
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Affiliation(s)
- Sofia Papadakos
- Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec, QC G1V 0A6, Canada; (S.P.); (H.I.)
| | - Hawraa Issa
- Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec, QC G1V 0A6, Canada; (S.P.); (H.I.)
| | - Abdulaziz Alamri
- Biochemistry Department, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (A.A.); (A.A.)
| | - Abdullah Alamri
- Biochemistry Department, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (A.A.); (A.A.)
| | - Abdelhabib Semlali
- Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec, QC G1V 0A6, Canada; (S.P.); (H.I.)
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Saito Y, Kage H, Kobayashi K, Yoshida M, Fukuoka O, Yamamura K, Mukai T, Oda K, Yamasoba T. TERT promoter mutation positive oral cavity carcinomas, a clinically and genetically distinct subgroup of head and neck squamous cell carcinomas. Head Neck 2023; 45:3107-3118. [PMID: 37815002 DOI: 10.1002/hed.27540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 08/14/2023] [Accepted: 09/26/2023] [Indexed: 10/11/2023] Open
Abstract
BACKGROUNDS The importance of TERT promoter (pTERT) mutation of oral cavity squamous cell carcinoma (OCSCC) with clinical features and genetic alterations are not well recognized. METHODS We retrospectively analyzed genetic data from multiple databases, including 260 cases from the C-CAT database, 407 cases from the MSK-MetTropism database, and 40 OCSCC datasets from in-house clinical samples. RESULTS From C-CAT database, TP53 (66%), CDKN2A (51%), and pTERT (29%) were the most frequent mutations observed. pTERT mutations were more prevalent in OCSCC (63%), younger individuals, and women (46%), with lower rates of alcohol abuse and smoking and co-mutated with TP53, HRAS, and CASP8. MSK-MetTroposim data validated with the enrichment of pTERT mutations in OCSCC, among women and Asian individuals. In-house datasets OCSCC with pTERT mutation (50%) characterized by fewer recurrent neck metastases. CONCLUSION The study suggests that OCSCC with pTERT mutation represents a distinct subgroup with unique clinical and genetic characteristics.
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Affiliation(s)
- Yuki Saito
- Departments of Otolaryngology, Head and Neck Surgery, University of Tokyo, Tokyo, Japan
| | - Hidenori Kage
- Department of Integrative Genomics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kenya Kobayashi
- Departments of Otolaryngology, Head and Neck Surgery, University of Tokyo, Tokyo, Japan
| | - Masafumi Yoshida
- Department of Otolaryngology, Showa General Hospital, Tokyo, Japan
| | - Osamu Fukuoka
- Departments of Otolaryngology, Head and Neck Surgery, University of Tokyo, Tokyo, Japan
| | - Koji Yamamura
- Departments of Otolaryngology, Head and Neck Surgery, University of Tokyo, Tokyo, Japan
| | - Toshiyuki Mukai
- Departments of Otolaryngology, Head and Neck Surgery, University of Tokyo, Tokyo, Japan
| | - Katsutoshi Oda
- Department of Integrative Genomics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tatsuya Yamasoba
- Departments of Otolaryngology, Head and Neck Surgery, University of Tokyo, Tokyo, Japan
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Godoy LFDS, Paes VR, Ayres AS, Bandeira GA, Moreno RA, Hirata FDCC, Silva FAB, Nascimento F, Campos Neto GDC, Gentil AF, Lucato LT, Amaro Junior E, Young RJ, Malheiros SMF. Advances in diffuse glial tumors diagnosis. Arq Neuropsiquiatr 2023; 81:1134-1145. [PMID: 38157879 PMCID: PMC10756793 DOI: 10.1055/s-0043-1777729] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 10/27/2023] [Indexed: 01/03/2024]
Abstract
In recent decades, there have been significant advances in the diagnosis of diffuse gliomas, driven by the integration of novel technologies. These advancements have deepened our understanding of tumor oncogenesis, enabling a more refined stratification of the biological behavior of these neoplasms. This progress culminated in the fifth edition of the WHO classification of central nervous system (CNS) tumors in 2021. This comprehensive review article aims to elucidate these advances within a multidisciplinary framework, contextualized within the backdrop of the new classification. This article will explore morphologic pathology and molecular/genetics techniques (immunohistochemistry, genetic sequencing, and methylation profiling), which are pivotal in diagnosis, besides the correlation of structural neuroimaging radiophenotypes to pathology and genetics. It briefly reviews the usefulness of tractography and functional neuroimaging in surgical planning. Additionally, the article addresses the value of other functional imaging techniques such as perfusion MRI, spectroscopy, and nuclear medicine in distinguishing tumor progression from treatment-related changes. Furthermore, it discusses the advantages of evolving diagnostic techniques in classifying these tumors, as well as their limitations in terms of availability and utilization. Moreover, the expanding domains of data processing, artificial intelligence, radiomics, and radiogenomics hold great promise and may soon exert a substantial influence on glioma diagnosis. These innovative technologies have the potential to revolutionize our approach to these tumors. Ultimately, this review underscores the fundamental importance of multidisciplinary collaboration in employing recent diagnostic advancements, thereby hoping to translate them into improved quality of life and extended survival for glioma patients.
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Affiliation(s)
- Luis Filipe de Souza Godoy
- Hospital Israelita Albert Einstein, Departamento de Radiologia, Seção de Neuroradiologia, São Paulo SP, Brazil.
- Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Seção de Neuroradiologia, São Paulo SP, Brazil.
| | - Vitor Ribeiro Paes
- Hospital Israelita Albert Einstein, Laboratório de Patologia Cirúrgica, São Paulo SP, Brazil.
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Patologia, São Paulo SP, Brazil.
| | - Aline Sgnolf Ayres
- Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Seção de Neuroradiologia, São Paulo SP, Brazil.
| | - Gabriela Alencar Bandeira
- Instituto do Câncer do Estado de São Paulo, Departamento de Radiologia, Seção de Neuroradiologia, São Paulo SP, Brazil.
| | - Raquel Andrade Moreno
- Instituto do Câncer do Estado de São Paulo, Departamento de Radiologia, Seção de Neuroradiologia, São Paulo SP, Brazil.
- Rede D'Or São Luiz, Departamento de Radiologia, Seção de Neuroradiologia, São Paulo SP, Brazil.
| | | | | | - Felipe Nascimento
- Hospital Israelita Albert Einstein, Departamento de Radiologia, Seção de Neuroradiologia, São Paulo SP, Brazil.
| | | | - Andre Felix Gentil
- Hospital Israelita Albert Einstein, Departamento de Neurocirurgia, São Paulo SP, Brazil.
| | - Leandro Tavares Lucato
- Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Seção de Neuroradiologia, São Paulo SP, Brazil.
- Grupo Fleury, São Paulo SP, Brazil.
| | - Edson Amaro Junior
- Hospital Israelita Albert Einstein, Departamento de Radiologia, Seção de Neuroradiologia, São Paulo SP, Brazil.
| | - Robert J. Young
- Memorial Sloan-Kettering Cancer Center, Neuroradiology Service, New York, New York, United States.
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Braga VLL, Lima DP, Mariano TC, Lima PLGDSB, Maia ABDA, da Silva Meireles WW, de Oliveira Pessoa KT, de Oliveira CM, Ribeiro EM, Nóbrega PR, Pessoa ALS. Higher Prevalence of Nonsense Pathogenic DMD Variants in a Single-Center Cohort from Brazil: A Genetic Profile Study That May Guide the Choice of Disease-Modifying Treatments. Brain Sci 2023; 13:1521. [PMID: 38002481 PMCID: PMC10669865 DOI: 10.3390/brainsci13111521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
Dystrophinopathies are muscle diseases caused by pathogenic variants in DMD, the largest gene described in humans, representing a spectrum of diseases ranging from asymptomatic creatine phosphokinase elevation to severe Duchenne muscular dystrophy (DMD). Several therapeutic strategies are currently in use or under development, each targeting different pathogenic variants. However, little is known about the genetic profiles of northeast Brazilian patients with dystrophinopathies. We describe the spectrum of pathogenic DMD variants in a single center in northeast Brazil. This is an observational, cross-sectional study carried out through molecular-genetic analysis of male patients diagnosed with dystrophinopathies using Multiplex Ligation-dependent Probe Amplification (MLPA) followed by Next-Generation Sequencing (NGS)-based strategies. A total of 94 male patients were evaluated. Deletions (43.6%) and duplications (10.6%) were the most recurring patterns of pathogenic variants. However, small variants were present in 47.1% of patients, most of them nonsense variants (27.6%). This is the largest South American single-center case series of dystrophinopathies to date. We found a higher frequency of treatment-amenable nonsense single-nucleotide variants than most previous studies. These findings may have implications for diagnostic strategies in less-known populations, as a higher frequency of nonsense variants may mean a higher possibility of treating patients with disease-modifying drugs.
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Affiliation(s)
- Vitor Lucas Lopes Braga
- Division of Pediatry, Hospital Infantil Albert Sabin, Fortaleza 60410-794, CE, Brazil; (V.L.L.B.); (A.B.d.A.M.)
| | - Danielle Pessoa Lima
- Division of Geriatry, Walter Cantidio University Hospital, Federal University of Ceara, Fortaleza 60430-372, CE, Brazil;
| | - Tamiris Carneiro Mariano
- Division of Neurogenetics and Neuromuscular Disorders, Hospital Infantil Albert Sabin, Fortaleza 60410-794, CE, Brazil;
| | | | - Ana Beatriz de Almeida Maia
- Division of Pediatry, Hospital Infantil Albert Sabin, Fortaleza 60410-794, CE, Brazil; (V.L.L.B.); (A.B.d.A.M.)
| | | | | | | | | | - Paulo Ribeiro Nóbrega
- Division of Neurology, Walter Cantidio University Hospital, Federal University of Ceara, Fortaleza 60430-372, CE, Brazil
- Campus Parque Ecológico, Centro Universitário Christus, Fortaleza 60160-230, CE, Brazil
| | - André Luiz Santos Pessoa
- Albert Sabin Children’s Hospital, Fortaleza 60410-794, CE, Brazil;
- Faculty of Medicine, State University of Ceará (UECE), Fortaleza 60714-903, CE, Brazil
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de Sousa Azulay RS, Rodrigues V, França de Abreu JDM, Pereira de Almeida AGF, Lago D, Tavares MDG, Nascimento G, Rocha V, Magalhães M, Facundo A, de Oliveira Neto CP, Guimarães Sá A, Parente CRV, Silva DA, Gomes MB, Faria MDS. Healthy lifestyle and genomic ancestry related to good glycemic control in type 1 diabetes patients from Northeastern Brazil: a hierarchical analysis. Front Endocrinol (Lausanne) 2023; 14:1233050. [PMID: 37900142 PMCID: PMC10611485 DOI: 10.3389/fendo.2023.1233050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/03/2023] [Indexed: 10/31/2023] Open
Abstract
Introduction This study aimed to investigate the sociodemographic factors, dietary adherence, regular physical activity, and genomic ancestry percentage associated with good glycemic control in Brazilian patients with type 1 diabetes (T1D) using a hierarchical approach. Methods A cross-sectional study was conducted in 152 T1D patients. Glycated hemoglobin (HbA1C) levels were measured to evaluate the glycemic control status (good, moderate, or poor). Independent factors included sex, age, self-reported skin color, educational level, family income, dietary patterns, and physical activity. The percentage of genomic ancestry (Native American, European, and African) was influenced by a panel of 46 autosomal insertion/deletion ancestry markers. Statistical analyses included receiver operating characteristic curves, and hierarchical logistic regression analysis. Results The hierarchical analysis, patients who had high dietary adherence showed a positive association with good glycemic control (adjustedOR = 2.56, 95% CI:1.18-5.59, P = 0.016). Thus, age greater than 40 years was associated with good glycemic control compared to the children and adolescents group (adjustedOR = 4.55, 95% CI:1.14-18.1, P = 0.031). Males were associated with good glycemic control (adjustedOR = 2.00, 95% CI:1.01-4.00, P =0.047). Conclusion The study findings suggest that consistent adherence to dietary regimens is associated with good glycemic control after adjusting for sociodemographic and genomic ancestry factors in an admixed population of T1D patients from Northeast Brazil.
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Affiliation(s)
- Rossana Santiago de Sousa Azulay
- Service of Endocrinology, University Hospital of the Federal University of Maranhão (HUUFMA), São Luís, Brazil
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), Federal University of Maranhão, São Luís, Brazil
| | - Vandilson Rodrigues
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), Federal University of Maranhão, São Luís, Brazil
| | - Joana D’Arc Matos França de Abreu
- Service of Endocrinology, University Hospital of the Federal University of Maranhão (HUUFMA), São Luís, Brazil
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), Federal University of Maranhão, São Luís, Brazil
| | | | - Débora Lago
- Service of Endocrinology, University Hospital of the Federal University of Maranhão (HUUFMA), São Luís, Brazil
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), Federal University of Maranhão, São Luís, Brazil
| | - Maria da Glória Tavares
- Service of Endocrinology, University Hospital of the Federal University of Maranhão (HUUFMA), São Luís, Brazil
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), Federal University of Maranhão, São Luís, Brazil
| | - Gilvan Nascimento
- Service of Endocrinology, University Hospital of the Federal University of Maranhão (HUUFMA), São Luís, Brazil
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), Federal University of Maranhão, São Luís, Brazil
| | - Viviane Rocha
- Service of Endocrinology, University Hospital of the Federal University of Maranhão (HUUFMA), São Luís, Brazil
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), Federal University of Maranhão, São Luís, Brazil
| | - Marcelo Magalhães
- Service of Endocrinology, University Hospital of the Federal University of Maranhão (HUUFMA), São Luís, Brazil
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), Federal University of Maranhão, São Luís, Brazil
| | - Alexandre Facundo
- Service of Endocrinology, University Hospital of the Federal University of Maranhão (HUUFMA), São Luís, Brazil
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), Federal University of Maranhão, São Luís, Brazil
| | - Clariano Pires de Oliveira Neto
- Service of Endocrinology, University Hospital of the Federal University of Maranhão (HUUFMA), São Luís, Brazil
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), Federal University of Maranhão, São Luís, Brazil
| | - Adriana Guimarães Sá
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), Federal University of Maranhão, São Luís, Brazil
| | - Conceição Ribeiro Veiga Parente
- Service of Endocrinology, University Hospital of the Federal University of Maranhão (HUUFMA), São Luís, Brazil
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), Federal University of Maranhão, São Luís, Brazil
| | - Dayse Aparecida Silva
- DNA Diagnostic Laboratory (LDD), Rio de Janeiro State University (UERJ), Rio de Janeiro, Brazil
| | - Marília Brito Gomes
- Diabetes Unit, Rio de Janeiro State University (UERJ), Rio de Janeiro, Brazil
| | - Manuel dos Santos Faria
- Service of Endocrinology, University Hospital of the Federal University of Maranhão (HUUFMA), São Luís, Brazil
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), Federal University of Maranhão, São Luís, Brazil
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Budowle B. Unraveling crime scenes strand by strand: the forensic odyssey of Bruce Budowle. Biotechniques 2023; 75:85-89. [PMID: 37622321 DOI: 10.2144/btn-2023-0069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023] Open
Abstract
Bruce Budowle speaks to Ashling Cannon, Journal Development Editor for BioTechniques, about advancements & challenges in forensic science. Budowle completed his doctorate in genetics at Virginia Tech (VA, USA) formally known as Virginia Polytechnic Institute and State University. He then went on to complete a postdoctoral fellowship at the University of Alabama at Birmingham (AL, USA) to study genetic risk factors for acute lymphocytic leukemia, diabetes and melanoma. Budowle was early in his career and hadn't spent much time in forensics at this stage, but in 1982 an advert caught his eye for a job with the FBI to develop genetic marker systems to identify people who have left biological evidence at crime scenes. Budowle spent 26 years with the FBI and helped develop a plethora of genetic analysis methods. In 1985, it became a reality that DNA could be a signature for identifying people, and there were huge developments in DNA forensic analysis. In 2009, Budowle moved into academia and went to the University of North Texas Health Science Center (TX, USA), eventually becoming the Director of the Center for Human Identification, where he oversaw missing person and traditional crime cases, taught students and carried out fundamental and applied research. Budowle feels incredibly lucky to have had the resources, opportunities and academic infrastructure to learn and develop his knowledge. Budowle recently retired from academia and now spends his time building capacity for DNA forensics applications in Africa through the Department of Justice, with a well-established program known as the International Criminal Investigative Training Assistance Program (ICITAP) as well as with the non-government organization (NGO) DNAforAfrica.
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Affiliation(s)
- Bruce Budowle
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
- Radford University Forensic Science Institute, Radford University, Radford, VA, USA
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Peng J, Fang S, Li M, Liu Y, Liang X, Li Z, Chen G, Peng L, Chen N, Liu L, Xu X, Dai W. Genetic alterations of KRAS and TP53 in intrahepatic cholangiocarcinoma associated with poor prognosis. Open Life Sci 2023; 18:20220652. [PMID: 37483430 PMCID: PMC10358752 DOI: 10.1515/biol-2022-0652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/13/2023] [Accepted: 06/05/2023] [Indexed: 07/25/2023] Open
Abstract
The aim of this study is to investigate certain genetic features of intrahepatic cholangiocarcinoma (ICCA). A total of 12 eligible ICCA patients were enrolled, and tumor tissues from the patients were subjected to next-generation sequencing of a multi-genes panel. Tumor mutation burden (TMB), mutated genes, copy number variants (CNVs), and pathway enrichment analysis were performed. The median TMB was 2.76 Mutation/Mb (range, 0-36.62 Mutation/Mb) in ICCA patients. The top two most commonly mutated genes in ICCA were KRAS (33%) and TP53 (25%). The co-mutations of KRAS and TP53 were 16.7% (2/12) in ICCA patients. Notably, patient P6 with the highest TMB did not have KRAS and TP53 mutations. Additionally, TP53 and/or KRAS alterations were significantly associated with poor progression-free survival than those with wild type (1.4 months vs 18 months). DNA damage repair and homologs recombinant repair deficiencies were significantly associated with high TMB in ICCA cases. In conclusion, we found that certain genetic mutations of TP53 and KRAS could predict poor prognosis in ICCA patients.
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Affiliation(s)
- Jianbo Peng
- Foshan Traditional Chinese Medicine Hospital, Guangdong, 518000, China
| | - Shuo Fang
- Department of Oncology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, 518000, China
| | - Meisheng Li
- Foshan First People’s Hospital, Guangdong, 518000, China
| | - Yuxin Liu
- Guangdong Medical University, Zhanjiang, Guangdong, 524000, China
| | - Xiaolu Liang
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, 524000, China
| | - Zuobiao Li
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, 524000, China
| | - Gaohui Chen
- Guangdong Medical University, Zhanjiang, Guangdong, 524000, China
| | - Lijiao Peng
- Department of Oncology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, 524000, China
| | - Nianping Chen
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, 524000, China
| | - Lei Liu
- Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, 524000, China
| | - Xiaohong Xu
- Department of Ultrasound, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, 524000, China
| | - Wei Dai
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, 524000, China
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9
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Yuan Y, Yan D, Skidmore J, Chapagain P, Liu X, He S. Responsiveness of the electrically stimulated cochlear nerve in patients with a missense variant in ACTG1: Preliminary Results. Front Audiol Otol 2023; 1:1213323. [PMID: 38590973 PMCID: PMC11000624 DOI: 10.3389/fauot.2023.1213323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
This preliminary study identified a missense variant in ACTG1 (NM_001614.5) in a family with autosomal dominant non-syndromic hearing loss (ADNSHL). The responsiveness of the electrically-stimulated cochlear nerve (CN) in two implanted participants with this missense change was also evaluated and reported. Genetic testing was done using a custom capture panel (MiamiOtoGenes) and whole exome sequencing. The responsiveness of the electrically-stimulated CN was evaluated in two members of this family (G1 and G4) using the electrically evoked compound action potential (eCAP). eCAP results from these two participants were compared with those measured three implanted patient populations: children with cochlear nerve deficiency, children with idiopathic hearing loss and normal-sized cochlear nerves, and postligually deafened adults. Sequencing of ACTG1 identified a missense c.737A>T (p. Gln246Leu) variant in ACTG1 (NM_001614.5) which is most likely the genetic cause of ADNSHL in this family. eCAP results measured in these two participants showed substantial variations. The results indicated the missense c.737A>T (p. Gln246Leu) variant in ACTG1 (NM_001614.5) co-segregated with hearing loss in this family. The responsiveness of the electrically-stimulated CN can vary among patients with the same genetic variants, which suggests the importance of evaluating the functional status of the CN for individual CI patients.
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Affiliation(s)
- Yi Yuan
- Department of Otolaryngology – Head & Neck Surgery, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Denise Yan
- Department of Otolaryngology – Head & Neck Surgery, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Jeffrey Skidmore
- Department of Otolaryngology – Head & Neck Surgery, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Prem Chapagain
- Department of Physics and Biomolecular Sciences Institute, Florida International University, Miami, Florida, USA
| | - Xuezhong Liu
- Department of Otolaryngology – Head & Neck Surgery, University of Miami Miller School of Medicine, Miami, Florida, USA
- Dr. John T. MacDonald Foundation, Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Shuman He
- Department of Otolaryngology – Head & Neck Surgery, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
- Department of Audiology, Nationwide Children’s Hospital, Columbus, Ohio, USA
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10
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Hu Y, Gao P, Xu G, Sun J, Xin W, Kong S, Ding H, Zhu J, Fang L. Correlation of gene expression profiles to identify pancreatic cancer cell lines that best model primary human tumors. Transl Cancer Res 2023; 12:980-991. [PMID: 37180676 PMCID: PMC10174970 DOI: 10.21037/tcr-23-173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/17/2023] [Indexed: 05/16/2023]
Abstract
Background Cancer cell lines are important research models for studying tumor biology in vivo. The accuracy of such studies is highly dependent on the phenotypic and genetic similarity of cell lines to patient tumors, but this is not always the case, particularly for pancreatic cancer. Methods We compared the gene expression profiles of various pancreatic cancer cell lines and primary human pancreatic tumor tissues to determine which pancreatic cancer cell line best models human primary tumor. Profiles of messenger RNA (mRNA) expression of 33 pancreatic cancer cell lines and 892 patient samples of pancreatic adenocarcinoma (PAAD) were obtained from the Gene Expression Omnibus (GEO) database. Microarray data were normalized using the robust multichip average (RMA) algorithm and batch effect removal was performed using ComBat. The pooled data of each PAAD cell line were compared to patient tumors based on the top 2,000 genes with largest interquartile range (IQR), 134 gene-collections of cancer-related pathways, and 504 gene-collections of cancer-related functions using pairwise Pearson's correlation analysis. Results PAAD cell lines were poorly correlated with patient tumor tissues based on the top 2,000 genes. Up to 50% of cancer-related pathways were not strongly recommended in PAAD cell lines, and a small proportion of cancer-related functions (12-17%) were poorly correlated with PAAD cell lines. In pan-pathway analysis, the cell lines showing the highest genetic correlation to patient tumors were Panc 03.27 for PAAD cell lines from a primary lesion site and CFPAC-1 for PAAD cell lines from a metastatic lesion site. In pan-function analysis, the cell lines showing the highest genetic correlation to patient tumors were Panc 03.27 for PAAD cell lines from a primary lesion site and Capan-1 for PAAD cell lines from a metastatic lesion site. Conclusions The gene expression profiles of PAAD cell lines correlate weakly with those of primary pancreatic tumors. Through comparison of the genetic similarity between PAAD cell lines and human tumor tissue, we have provided a strategy for choosing the appropriate PAAD cell line.
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Affiliation(s)
- Yan Hu
- Department of Pharmacy, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Peng Gao
- Department of Pharmacy, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Gaoqi Xu
- Department of Pharmacy, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Jiao Sun
- Department of Pharmacy, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Wenxiu Xin
- Department of Pharmacy, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Sisi Kong
- Department of Pharmacy, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Haiying Ding
- Department of Pharmacy, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Junfeng Zhu
- Department of Pharmacy, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Luo Fang
- Department of Pharmacy, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
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Shimada M, Taniguchi H, Yamaguchi H, Gyotoku H, Sasaki D, Kaku N, Senju C, Senju H, Imamura E, Takemoto S, Yamamoto K, Sakamoto N, Obase Y, Tsuchiya T, Fukuda M, Soda H, Ashizawa K, Fukuoka J, Nagayasu T, Yanagihara K, Mukae H. Genetic profile of thymic epithelial tumors in the Japanese population: an exploratory study examining potential therapeutic targets. Transl Lung Cancer Res 2023; 12:707-718. [PMID: 37197618 PMCID: PMC10183388 DOI: 10.21037/tlcr-22-794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 03/07/2023] [Indexed: 03/29/2023]
Abstract
Background Thymic epithelial tumors (TETs) are prone to developing in East Asian populations. However, little is known about the genomic profile of TETs in East Asian populations, and the genomic aberrations in TETs have not yet been fully clarified. Thus, molecular targeted therapies for patients with TETs have not been established. This prospective study was conducted to explore the genetic abnormalities of surgically resected TETs in a Japanese cohort and to identify clues for carcinogenesis and potential therapeutic targets in TETs. Methods Genetic profiles of TETs were investigated using fresh-frozen specimens resected from operable cases with TETs. DNA sequencing was performed using a next-generation sequencing (NGS) gene panel test with Ion Reporter™ and CLC Genomics Workbench 11.0. The mutation sites were further confirmed by Sanger sequencing, digital droplet polymerase chain reaction (ddPCR), and TA cloning for validation. Results Among 43 patients diagnosed with anterior mediastinal tumors between January 2013 and March 2019, NGS and validation analyses were performed in 31 patients [29 thymomas and two thymic cancers (TCs)] who met the study criteria. Of these, 12 cases of thymoma types A, AB, B1, and B2 harbored the general transcription factor 2-I (GTF2I) mutation (L424H). Conversely, the mutation was not detected in type B3 thymoma or TC, suggesting that the GTF2I mutation existed in indolent types of TETs. Rat sarcoma viral oncogene (RAS) mutations were detected in three cases [Harvey RAS (HRAS) in two cases of type AB thymoma and neuroblastoma RAS (NRAS)] in one case of type B1 thymoma), and additional sex combs like 1 (ASXL1) mutation was present in one case of TC. All RAS mutations were observed in GTF2I-mutated cases. Conclusions The GTF2I mutation (L424H) is the most frequently occurring mutation in the limited histology of thymoma, consistent with those in the non-Asian population. HRAS and NRAS mutations co-occurred in cases harboring the GTF2I mutation. These findings suggest that the existence of the GTF2I mutation might be related to indolent types of TETs, and RAS mutations could be candidates as therapeutic targets in TETs.
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Affiliation(s)
- Midori Shimada
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
- Clinical Research Center, Nagasaki University Hospital, Nagasaki, Japan
| | - Hirokazu Taniguchi
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hiroyuki Yamaguchi
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
- Clinical Oncology Center, Nagasaki University Hospital, Nagasaki, Japan
| | - Hiroshi Gyotoku
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Daisuke Sasaki
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Norihito Kaku
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Chikako Senju
- Department of Plastic and Reconstructive Surgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
- Senju Hospital, Sasebo, Japan
| | - Hiroaki Senju
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
- Senju Hospital, Sasebo, Japan
| | - Erika Imamura
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Shinnosuke Takemoto
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Kazuko Yamamoto
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
- Division of Infectious, Respiratory, and Digestive Medicine, First Department of Internal Medicine, University of the Ryukyus Graduate School of Medicine, Okinawa, Japan
| | - Noriho Sakamoto
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Yasushi Obase
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Tomoshi Tsuchiya
- Department of Surgical Oncology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
- Department of Thoracic Surgery, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
| | - Minoru Fukuda
- Clinical Oncology Center, Nagasaki University Hospital, Nagasaki, Japan
- Department of Respiratory Medicine, Nagasaki Prefecture Shimabara Hospital, Shimabara, Japan
| | - Hiroshi Soda
- Department of Respiratory Medicine, Sasebo City General Hospital, Sasebo, Japan
| | - Kazuto Ashizawa
- Clinical Oncology Center, Nagasaki University Hospital, Nagasaki, Japan
| | - Junya Fukuoka
- Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Takeshi Nagayasu
- Department of Surgical Oncology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Katsunori Yanagihara
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hiroshi Mukae
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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12
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Kholin SK. Genetic profile of domestic cat (Felis catus L.) population of Aoshima Island (Japan). Vavilovskii Zhurnal Genet Selektsii 2023; 27:169-176. [PMID: 37063514 PMCID: PMC10090102 DOI: 10.18699/vjgb-23-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/25/2022] [Accepted: 12/27/2023] [Indexed: 04/18/2023] Open
Abstract
The paper analyzes the genetic profile of the domestic cat population of the Aoshima Island. The population has been established in the middle of the last century, after a small group of animals was imported for rodent control. Based on three photographs, the genotypes of the cats in three overlapping groups (75, 56, and 70 individuals) were determined. The mutant allele frequencies of the sex-linked O (Orange) locus and the three autosomal loci a, W, and l (Agouti, White, and Long hair) responsible for coat color and length were estimated. The population lacks the mutant alleles d (Dilution locus), W and wg (White), tab (Tabby), Ti A (Ticked) present in other populations of Japan. This is an almost monomorphic population with prevailing red and tortoiseshell individuals. Most cats have interrupted stripes (genotype Ti+Ti+TaM-). The island's population differs from the other populations of the Japanese islands in the frequencies of two mutant alleles, O and a. The frequency of the O allele (q(O) = 0.580) is one of the highest in the region, while the frequency of the a allele (q(a) = 0.276) is two times lower than in the other populations. In both cases, the differences in frequencies between the neighbouring populations are significant (p < 0.0001). An independent study of the same population revealed a similar genetic structure. However, it detected the presence of the d allele, the frequency of the a allele was higher (0.534 versus 0.276, p < 0.020). The genetic profile, frequencies of mutant alleles in the population, and history of its origin indicate a significant influence of the founder effect on the genetic structure of the island's domestic cat population.
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Affiliation(s)
- S K Kholin
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
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13
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Singh S, Singh PK, Sachan K, Garg S, Sharma AN. Recent Progress and Challenges in the Development of Edible Vaccines Produced by Genetically Modified Plants. Curr Protein Pept Sci 2023; 24:711-720. [PMID: 37537938 DOI: 10.2174/1389203724666230804095716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 06/23/2023] [Accepted: 07/03/2023] [Indexed: 08/05/2023]
Abstract
Biotechnologists have pioneered the idea of an edible vaccination in recent years. Subunit vaccines, such as those used to create edible vaccines, involve the introduction of certain genes into transgenic plants, which are subsequently coaxed into producing the corresponding protein. Bananas, potatoes, legumes, lettuce, soybeans, corn, and rice are all examples of foods that fall under this category. They have a low unit cost, can be stored conveniently, and are simple to administer to patients of varying ages. There is great hope that the use of edible vaccinations, particularly in underdeveloped countries, could drastically reduce the prevalence of diseases, including measles, cholera, hepatitis B, and diarrhea. The development of effective and widely applicable edible vaccination, however, faces a number of technological and regulatory hurdles. When compared to traditional immunizations, edible vaccines offer significant cost savings, increased productivity, and reduced risk. It raises the possibility of a more efficient approach to illness prevention. This article includes important uses, production, host plants, benefits, drawbacks, mechanism of action, and many regulatory difficulties related to edible vaccines. In this article, we have discussed the most recent developments and successes with edible and intradermal vaccines in terms of the system used for immunogen production, the molecular properties of these vaccines, and their ability to generate a protective systemic and mucosal response.
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Affiliation(s)
- Smita Singh
- SRM Modinagar College of Pharmacy, SRM Institute of Science and Technology, Delhi NCR Campus, Modinagar, UP, India
| | - Pranjal Kumar Singh
- SRM Modinagar College of Pharmacy, SRM Institute of Science and Technology, Delhi NCR Campus, Modinagar, UP, India
| | - Kapil Sachan
- Department of Pharmaceutics, Dr. Ram Manohar Lohia College of Pharmacy, Modinagar, Ghaziabad, UP, India
| | - Sakshi Garg
- KIET School of Pharmacy, KIET Group of Institutions, Ghaziabad, India
| | - Alok Nath Sharma
- Faculty of Pharmacy, Raja Balwant Singh Engineering Technical Campus, Bichpuri, Agra, India
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14
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Tozzo P, Mazzobel E, Marcante B, Delicati A, Caenazzo L. Touch DNA Sampling Methods: Efficacy Evaluation and Systematic Review. Int J Mol Sci 2022; 23:15541. [PMID: 36555182 PMCID: PMC9779423 DOI: 10.3390/ijms232415541] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/01/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
Collection and interpretation of "touch DNA" from crime scenes represent crucial steps during criminal investigations, with clear consequences in courtrooms. Although the main aspects of this type of evidence have been extensively studied, some controversial issues remain. For instance, there is no conclusive evidence indicating which sampling method results in the highest rate of biological material recovery. Thus, this study aimed to describe the actual considerations on touch DNA and to compare three different sampling procedures, which were "single-swab", "double-swab", and "other methods" (i.e., cutting out, adhesive tape, FTA® paper scraping), based on the experimental results published in the recent literature. The data analysis performed shows the higher efficiency of the single-swab method in DNA recovery in a wide variety of experimental settings. On the contrary, the double-swab technique and other methods do not seem to improve recovery rates. Despite the apparent discrepancy with previous research, these results underline certain limitations inherent to the sampling procedures investigated. The application of this information to forensic investigations and laboratories could improve operative standard procedures and enhance this almost fundamental investigative tool's probative value.
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Affiliation(s)
- Pamela Tozzo
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, Legal Medicine Section, University of Padova, 35121 Padova, Italy
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15
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Liu C, Yan B, Wang Y, Di W, Lou W. Aggressive Gliomatosis Peritonei Arising from Ovarian Mature Teratoma with NF1 Mutation: A Case Report and Literature Review. Cancer Manag Res 2022; 14:2979-2986. [PMID: 36247331 PMCID: PMC9554576 DOI: 10.2147/cmar.s374987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 09/12/2022] [Indexed: 11/23/2022] Open
Abstract
Background GP arising from ovarian mature teratoma is a rare disease, and no confirmed pathogenesis signature genes are reported. The progress of GP is seen as relatively slow. Rare aggressive GP cases with poor prognosis were reported and no guidelines to follow for treatment. Case Presentation Herein, we report a 17-year-old girl with a 3-year-history of GP arising from ovarian mature teratoma. Surgeries and drug therapy were used to treat the aggressively growing tumour. Genetic profiling revealed the pathogenic mutation with potential therapeutic approaches. We firstly reported the NF1 mutations in GP secondary to teratomas and may cause bad prognosis. Conclusion GP arising from ovarian mature teratoma is rare; we found NF1 mutation could be the trigger of GP. The study may provide new insights into a better understanding of this rare disease.
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Affiliation(s)
- Chang Liu
- Department of Obstetrics and Gynecology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China,Shanghai Key Laboratory of Gynecologic Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Bin Yan
- Department of Obstetrics and Gynecology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China,Shanghai Key Laboratory of Gynecologic Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - You Wang
- Department of Obstetrics and Gynecology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China,Shanghai Key Laboratory of Gynecologic Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Wen Di
- Department of Obstetrics and Gynecology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China,Shanghai Key Laboratory of Gynecologic Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China,Correspondence: Wen Di; Weihua Lou, Department of Obstetrics and Gynecology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, No. 160 Pujian Road, Shanghai, 200127, People’s Republic of China, Email ;
| | - Weihua Lou
- Department of Obstetrics and Gynecology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China,Shanghai Key Laboratory of Gynecologic Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
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16
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Goodman MO, Cade BE, Shah NA, Huang T, Dashti HS, Saxena R, Rutter MK, Libby P, Sofer T, Redline S. Pathway-Specific Polygenic Risk Scores Identify Obstructive Sleep Apnea-Related Pathways Differentially Moderating Genetic Susceptibility to Coronary Artery Disease. Circ Genom Precis Med 2022; 15:e003535. [PMID: 36170352 PMCID: PMC9588629 DOI: 10.1161/circgen.121.003535] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 06/02/2022] [Indexed: 01/04/2023]
Abstract
BACKGROUND Obstructive sleep apnea (OSA) and its features, such as chronic intermittent hypoxia, may differentially affect specific molecular pathways and processes in the pathogenesis of coronary artery disease (CAD) and influence the subsequent risk and severity of CAD events. In particular, competing adverse (eg, inflammatory) and protective (eg, increased coronary collateral blood flow) mechanisms may operate, but remain poorly understood. We hypothesize that common genetic variation in selected molecular pathways influences the likelihood of CAD events differently in individuals with and without OSA, in a pathway-dependent manner. METHODS We selected a cross-sectional sample of 471 877 participants from the UK Biobank, with 4974 ascertained to have OSA, 25 988 to have CAD, and 711 to have both. We calculated pathway-specific polygenic risk scores for CAD, based on 6.6 million common variants evaluated in the CARDIoGRAMplusC4D genome-wide association study (Coronary ARtery DIsease Genome wide Replication and Meta-analysis [CARDIoGRAM] plus The Coronary Artery Disease [C4D] Genetics), annotated to specific genes and pathways using functional genomics databases. Based on prior evidence of involvement with intermittent hypoxia and CAD, we tested pathway-specific polygenic risk scores for the HIF1 (hypoxia-inducible factor 1), VEGF (vascular endothelial growth factor), NFκB (nuclear factor kappa-light-chain-enhancer of activated B cells) and TNF (tumor necrosis factor) signaling pathways. RESULTS In a multivariable-adjusted logistic generalized additive model, elevated pathway-specific polygenic risk scores for the Kyoto Encyclopedia of Genes and Genomes VEGF pathway (39 genes) associated with protection for CAD in OSA (interaction odds ratio 0.86, P=6×10-4). By contrast, the genome-wide CAD PRS did not show evidence of statistical interaction with OSA. CONCLUSIONS We find evidence that pathway-specific genetic risk of CAD differs between individuals with and without OSA in a qualitatively pathway-dependent manner. These results provide evidence that gene-by-environment interaction influences CAD risk in certain pathways among people with OSA, an effect that is not well-captured by the genome-wide PRS. This invites further study of how OSA interacts with genetic risk at the molecular level and suggests eventual personalization of OSA treatment to reduce CAD risk according to individual pathway-specific genetic risk profiles.
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Affiliation(s)
- Matthew O Goodman
- Division of Sleep & Circadian Disorders (M.O.G., B.E.C., R.S., T.S., S.R.), Brigham and Women's Hospital & Harvard Medical School
- Division of Sleep Medicine, Harvard Medical School, Boston (M.O.G., B.E.C., T.H., R.S., T.S., S.R.)
- Program in Medical & Population Genetics, Broad Institute, Cambridge, MA (M.O.G., B.E.C., H.S.D., R.S.)
| | - Brian E Cade
- Division of Sleep & Circadian Disorders (M.O.G., B.E.C., R.S., T.S., S.R.), Brigham and Women's Hospital & Harvard Medical School
- Division of Sleep Medicine, Harvard Medical School, Boston (M.O.G., B.E.C., T.H., R.S., T.S., S.R.)
- Program in Medical & Population Genetics, Broad Institute, Cambridge, MA (M.O.G., B.E.C., H.S.D., R.S.)
| | - Neomi A Shah
- Icahn School of Medicine at Mount Sinai, New York, NY (N.A.S.)
| | - Tianyi Huang
- Channing Division of Network Medicine (T.H.), Brigham and Women's Hospital & Harvard Medical School
- Division of Sleep Medicine, Harvard Medical School, Boston (M.O.G., B.E.C., T.H., R.S., T.S., S.R.)
| | - Hassan S Dashti
- Program in Medical & Population Genetics, Broad Institute, Cambridge, MA (M.O.G., B.E.C., H.S.D., R.S.)
- Center for Genomic Medicine, Massachusetts General Hospital (H.S.D., R.S.)
- Department of Anesthesia, Critical Care & Pain Medicine, Massachusetts General Hospital & Harvard Medical School, Boston (H.S.D., R.S.)
| | - Richa Saxena
- Division of Sleep & Circadian Disorders (M.O.G., B.E.C., R.S., T.S., S.R.), Brigham and Women's Hospital & Harvard Medical School
- Division of Sleep Medicine, Harvard Medical School, Boston (M.O.G., B.E.C., T.H., R.S., T.S., S.R.)
- Program in Medical & Population Genetics, Broad Institute, Cambridge, MA (M.O.G., B.E.C., H.S.D., R.S.)
- Center for Genomic Medicine, Massachusetts General Hospital (H.S.D., R.S.)
- Department of Anesthesia, Critical Care & Pain Medicine, Massachusetts General Hospital & Harvard Medical School, Boston (H.S.D., R.S.)
| | - Martin K Rutter
- Division of Diabetes, Endocrinology & Gastroenterology, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester (M.K.R.)
- Diabetes, Endocrinology & Metabolism Centre, Manchester Univ NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom (M.K.R.)
| | - Peter Libby
- Division of Cardiovascular Medicine, Department of Medicine (P.L.), Brigham and Women's Hospital & Harvard Medical School
| | - Tamar Sofer
- Division of Sleep & Circadian Disorders (M.O.G., B.E.C., R.S., T.S., S.R.), Brigham and Women's Hospital & Harvard Medical School
- Division of Sleep Medicine, Harvard Medical School, Boston (M.O.G., B.E.C., T.H., R.S., T.S., S.R.)
| | - Susan Redline
- Division of Sleep & Circadian Disorders (M.O.G., B.E.C., R.S., T.S., S.R.), Brigham and Women's Hospital & Harvard Medical School
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Isoda N, Onuma M, Hiono T, Sobolev I, Lim HY, Nabeshima K, Honjyo H, Yokoyama M, Shestopalov A, Sakoda Y. Detection of New H5N1 High Pathogenicity Avian Influenza Viruses in Winter 2021-2022 in the Far East, Which Are Genetically Close to Those in Europe. Viruses 2022; 14:v14102168. [PMID: 36298722 PMCID: PMC9606862 DOI: 10.3390/v14102168] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 01/06/2023] Open
Abstract
Many high pathogenicity avian influenza (HPAI) cases in wild birds due to H5N1 HPAI virus (HPAIV) infection were reported in northern Japan in the winter of 2021-2022. To investigate the epidemiology of HPAIVs brought to Japan from surrounding areas, a genetic analysis of H5 HPAIVs isolated in northern Japan was performed, and the pathogenicity of the HPAIV in chickens was assessed by experimental infection. Based on the genetic analysis of the hemagglutinin gene, pathogenic viruses detected in northern Japan as well as one in Sakhalin, the eastern part of Russia, were classified into the same subgroup as viruses prevalent in Europe in the same season but distinct from those circulating in Asia in winter 2020-2021. High identities of all eight segment sequences of A/crow/Hokkaido/0103B065/2022 (H5N1) (Crow/Hok), the representative isolates in northern Japan in 2022, to European isolates in the same season could also certify the unlikeliness of causing gene reassortment between H5 HPAIVs and viruses locally circulating in Asia. According to intranasal challenge results in six-week-old chickens, 50% of the chicken-lethal dose of Crow/Hok was calculated as 104.5 times of the 50% egg-infectious dose. These results demonstrated that the currently prevalent H5 HPAIVs could spread widely from certain origins throughout the Eurasian continent, including Europe and the Far East, and implied a possibility that contagious viruses are gathered in lakes in the northern territory via bird migration. Active monitoring of wild birds at the global level is essential to estimate the geographical source and spread dynamics of HPAIVs.
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Affiliation(s)
- Norikazu Isoda
- Laboratory of Microbiology, Faculty of Veterinary Medicine, Hokkaido University, Kita 18, Nishi 9, Kita-ku, Sapporo 060-0818, Hokkaido, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Kita 20, Nishi 11, Kita-ku, Sapporo 001-0020, Hokkaido, Japan
| | - Manabu Onuma
- Ecological Risk Assessment and Control Section for Environmental Biology and Ecosystem, Biology Division, National Institute for Environmental Studies, Onogawa 16-2, Tsukuba 305-8506, Ibaraki, Japan
| | - Takahiro Hiono
- Laboratory of Microbiology, Faculty of Veterinary Medicine, Hokkaido University, Kita 18, Nishi 9, Kita-ku, Sapporo 060-0818, Hokkaido, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Kita 20, Nishi 11, Kita-ku, Sapporo 001-0020, Hokkaido, Japan
| | - Ivan Sobolev
- Institute of Virology of the Federal Research Center of Fundamental and Translational Medicine, Novosibirsk State University, Bild 2, Timakova St., Novosibirsk 630117, Russia
| | - Hew Yik Lim
- Laboratory of Microbiology, Faculty of Veterinary Medicine, Hokkaido University, Kita 18, Nishi 9, Kita-ku, Sapporo 060-0818, Hokkaido, Japan
| | - Kei Nabeshima
- Ecological Risk Assessment and Control Section for Environmental Biology and Ecosystem, Biology Division, National Institute for Environmental Studies, Onogawa 16-2, Tsukuba 305-8506, Ibaraki, Japan
| | - Hisako Honjyo
- Ecological Risk Assessment and Control Section for Environmental Biology and Ecosystem, Biology Division, National Institute for Environmental Studies, Onogawa 16-2, Tsukuba 305-8506, Ibaraki, Japan
| | - Misako Yokoyama
- Ecological Risk Assessment and Control Section for Environmental Biology and Ecosystem, Biology Division, National Institute for Environmental Studies, Onogawa 16-2, Tsukuba 305-8506, Ibaraki, Japan
| | - Alexander Shestopalov
- Institute of Virology of the Federal Research Center of Fundamental and Translational Medicine, Novosibirsk State University, Bild 2, Timakova St., Novosibirsk 630117, Russia
- Correspondence: (A.S.); (Y.S.); Tel./Fax: +7-383-335-9405 (A.S.); Tel.: +81-11-706-5207 (Y.S.); Fax: +81-11-706-5273 (Y.S.)
| | - Yoshihiro Sakoda
- Laboratory of Microbiology, Faculty of Veterinary Medicine, Hokkaido University, Kita 18, Nishi 9, Kita-ku, Sapporo 060-0818, Hokkaido, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Kita 20, Nishi 11, Kita-ku, Sapporo 001-0020, Hokkaido, Japan
- Correspondence: (A.S.); (Y.S.); Tel./Fax: +7-383-335-9405 (A.S.); Tel.: +81-11-706-5207 (Y.S.); Fax: +81-11-706-5273 (Y.S.)
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Li JA, Rong Y, Mao W, Zhang L, Kuang T, Lou W. Gene expression profiling reveals the genomic changes caused by MLN4924 and the sensitizing effects of NAPEPLD knockdown in pancreatic cancer. Cell Cycle 2022; 21:152-171. [PMID: 34874801 PMCID: PMC8837228 DOI: 10.1080/15384101.2021.2014254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/25/2021] [Accepted: 11/22/2021] [Indexed: 10/19/2022] Open
Abstract
MLN4924 inhibits the proteolytic degradation of Cullin-Ring E3 ligase (CRL) substrates and exhibits antitumor activity toward various malignancies, including pancreatic cancer. MLN4924 suppresses tumor growth by altering various key regulator proteins; however, its impact on gene expression in tumors remains unknown. In this study, the genomic changes caused by MLN4924 in pancreatic cancer were examined by gene chip analysis and ingenuity pathway analysis. Eleven pathways were significantly altered (5 activated and 6 inhibited), 45 functions were significantly changed (21 activated and 24 inhibited), and the most activated upstream factor was predicted to be TNF. Of 691 differentially expressed genes, NAPEPLD knockdown showed synergism with MLN4924, as determined by real-time quantitative PCR and high content screening. NAPEPLD knockdown enhanced the effect of MLN4924 on inhibiting proliferation and inducing apoptosis in vitro. In a pancreatic cancer nude mouse model, MLN4924 inhibited tumor growth more significantly in the NAPEPLD knockdown group than in the control group. NAPEPLD expression was higher in pancreatic cancer tissues than in the normal pancreas but was not associated with prognosis. These findings indicate that MLN4924 causes extensive genomic changes in pancreatic cancer cells, and targeting NAPEPLD may increase the efficacy of MLN4924.
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Affiliation(s)
- Jian-Ang Li
- Department of Pancreatic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yefei Rong
- Department of Pancreatic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Weilin Mao
- Department of Pancreatic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lei Zhang
- Department of Pancreatic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Tiantao Kuang
- Department of Pancreatic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wenhui Lou
- Department of Pancreatic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
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Stocker M, Le Nail LR, De Belenet H, Wunder JS, Andrulis IL, Gokgoz N, Levy N, Mattei JC, Olschwang S. Inhibition of P53-mediated cell cycle control as the determinant in dedifferentiated liposarcomas development. Am J Cancer Res 2021; 11:3271-3284. [PMID: 34249461 PMCID: PMC8263664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/28/2021] [Indexed: 06/13/2023] Open
Abstract
Liposarcomas are a heterogeneous group of sarcomas, including well-differentiated and dedifferentiated liposarcoma, myxoid/round cell liposarcoma, and pleomorphic liposarcoma. Complete surgical resection is the key of treatment. Radiotherapy, based on the tumor grade and the vicinity of critical structures with the tumor, can be used to prevent local recurrence. The group of dedifferentiated liposarcomas (DDLS) is poorly sensitive to adjuvant chemotherapy. Improved understanding of the genetic aberrations that lead to liposarcoma initiation is necessary for the development of targeted therapies to improve tumor control and survival. DDLS share genetic abnormalities with other groups, exhibiting high-level amplifications of chromosome 12, including the MDM2 and CDK4 genes, and harbor additional amplifications of chromosomes 6 and 1. Novel therapies targeted at the gene products of chromosome 12 are currently considered in clinical trials. Our work consisted in a genomic characterization of DDLS to draw up a complete picture of alterations, including genomic signatures, tumor mutation burden, gene mutations, copy number variations, translocations, gene fusions and methylation modifications. Analysis of translocations helped to understand the mechanisms underlying the amplification processes. Combination of mutations and loss of heterozygosity or homozygous deletions were detected and led to inactivate tumor suppressor genes (TSG). In contrast, methylation anomalies seemed not linked to any particular genomic profile. All identified anomalies, whether amplifications and/or TSG inactivation, involve genes playing a role in p53 regulation, that appears to be the epicenter of the initiation process in DDLS tumorigenesis, as is also known to be responsible for Li-Fraumeni syndrome, a family cancer syndrome highly predisposing to sarcomas.
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Affiliation(s)
- Mossane Stocker
- INSERM UMR1251 Marseille Medical Genetics GeneticsMarseille, France
- GCS Pour l’Enseignement et la Recherche, Ramsay Santé, Hôpital Privé ClairvalMarseille, France
| | | | - Hubert De Belenet
- GCS Pour l’Enseignement et la Recherche, Ramsay Santé, Hôpital Privé ClairvalMarseille, France
| | - Jay S Wunder
- Lunenfeld_Tanenbaum Research Institute, University of TorontoToronto, Canada
| | - Irene L Andrulis
- Lunenfeld_Tanenbaum Research Institute, University of TorontoToronto, Canada
| | - Nalan Gokgoz
- Lunenfeld_Tanenbaum Research Institute, University of TorontoToronto, Canada
| | - Nicolas Levy
- INSERM UMR1251 Marseille Medical Genetics GeneticsMarseille, France
- AP-HMMarseille, France
| | - Jean-Camille Mattei
- INSERM UMR1251 Marseille Medical Genetics GeneticsMarseille, France
- AP-HMMarseille, France
| | - Sylviane Olschwang
- INSERM UMR1251 Marseille Medical Genetics GeneticsMarseille, France
- GCS Pour l’Enseignement et la Recherche, Ramsay Santé, Hôpital Privé ClairvalMarseille, France
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Ceja Galvez HR, Salazar Flores J, Torres Sanchez ED, Rojas Bravo D, Reyna Villela MZ, Reyes Uribe E. Genetic profile for the detection of susceptibility to poisoning by exposure to pesticides. Ann Agric Environ Med 2021; 28:208-213. [PMID: 34184499 DOI: 10.26444/aaem/136362] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
INTRODUCTION In humans, there are sets of genes that encode enzymes that decrease or increase the risks derived from exposure to pesticides. These include DNA repair genes (XRCC1, OGG1 and XRCC4); pesticide metabolizers (GSTP1 and PON1), and genes that act against oxidative stress (SOD2 and NQO1). OBJECTIVE The aim of this literature review is to provide information about the genes involved in the defence systems against exposure to pesticides, as well as their polymorphisms, functions, and general characteristics of the encoded enzymes. MATERIAL AND METHODS Information was obtained from scientific articles published between 2015-2020 in the PubMed database (https://pubmed.ncbi.nlm.nih.gov). RESULTS Genes related to the defence processes against pesticides present single-nucleotide polymorphisms (SNPs) with allelic variants that affect the expressions or structures of the encoded enzymes, negatively altering their activities. If we knew the genetic profile that includes polymorphisms of DNA-repairing genes, metabolizing genes, and genes against oxidative stress in subjects exposed to pesticides, we would also know about their susceptibility to poisoning caused by these chemicals. CONCLUSIONS The genes could be used to propose a genetic profile in farmers exposed to various pesticides, including 10 gene polymorphisms involved in susceptibility to various pathologies related to DNA repair, xenobiotic metabolism, and oxidative stress. It could also be useful as a preventive measure to identify susceptibility to pesticide poisoning.
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21
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da Silva LV, Ossai S, Chigbu P, Parveen S. Antimicrobial and Genetic Profiles of Vibrio vulnificus and Vibrio parahaemolyticus Isolated From the Maryland Coastal Bays, United States. Front Microbiol 2021; 12:676249. [PMID: 34093499 PMCID: PMC8175909 DOI: 10.3389/fmicb.2021.676249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 04/26/2021] [Indexed: 12/19/2022] Open
Abstract
Vibrio vulnificus and V. parahaemolyticus, found naturally in marine and estuarine environments, are the leading cause of seafood associated gastrointestinal illness and death. Consumption of improperly cooked crabs and handling of live crabs are potential routes of exposure to pathogenic bacteria such as V. vulnificus and V. parahaemolyticus. Little information is available on serotype genetic and antimicrobial profiles of V. vulnificus and V. parahaemolyticus recovered from Maryland estuaries. The aim of the present study was to determine the serotype of V. parahaemolyticus, evaluate antimicrobial susceptibility and genetic profiles of V. vulnificus and V. parahaemolyticus isolated from water and blue crab (Callinectes sapidus) samples collected from the Maryland Coastal Bays. One hundred and fifty (150) PCR confirmed V. parahaemolyticus including 52 tdh+ (pathogenic) and 129 V. vulnificus strains were tested for susceptibility to twenty (20) different antibiotics chosen by clinical usage for Vibrio species. The O serogroups were determined using an agglutination test with V. parahaemolyticus antisera. Pulsed-field gel electrophoresis (PFGE) was used for molecular subtyping to investigate the genetic diversity among tested strains. The most prevalent serotypes were O5 (33.3%), O3 (18.7%) and O1 (14.7%). More than 41% of all tested Vibrio isolates were resistant to three or more antibiotics. Cephalothin showed the highest resistance (42% and 61%), followed by cefoxitin (42% and 31%) and ceftazidime (36% and 29%) for V. vulnificus and V. parahaemolyticus, respectively. Most strains (99–100%) were susceptible to ampicillin/sulbactam, levofloxacin, piperacillin, piperacillin/tazobactam, and tetracycline. Fifty percent (50%) of the cephalothin resistant strains were crab isolates. Vibrio vulnificus and V. parahaemolyticus isolates demonstrated a high genetic diversity and 31% of V. vulnificus and 16% of V. parahaemolyticus strains were PFGE untypeable. No correlations were found between the V. parahaemolyticus serotype, pathogenicity, genetic and antimicrobial resistance profiles of both species of Vibrio. The observed high multiple drug resistance of V. vulnificus and V. parahaemolyticus from blue crab and its environment is of public health concern. Therefore, there is a need for frequent antibiotic sensitivity surveillance for Vibrio spp.
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Affiliation(s)
- Ligia V da Silva
- Department of Natural Sciences, CREST Center for the Integrated Study of Coastal Ecosystem Processes and Dynamics in the Mid-Atlantic Region, NOAA Living Marine Resources Cooperative Science Center, University of Maryland Eastern Shore, Princess Anne, MD, United States
| | - Sylvia Ossai
- Department of Agriculture, Food and Resource Sciences, Food and Agricultural Sciences Program, University of Maryland Eastern Shore, Princess Anne, MD, United States
| | - Paulinus Chigbu
- Department of Natural Sciences, CREST Center for the Integrated Study of Coastal Ecosystem Processes and Dynamics in the Mid-Atlantic Region, NOAA Living Marine Resources Cooperative Science Center, University of Maryland Eastern Shore, Princess Anne, MD, United States
| | - Salina Parveen
- Department of Natural Sciences, CREST Center for the Integrated Study of Coastal Ecosystem Processes and Dynamics in the Mid-Atlantic Region, NOAA Living Marine Resources Cooperative Science Center, University of Maryland Eastern Shore, Princess Anne, MD, United States.,Department of Agriculture, Food and Resource Sciences, Food and Agricultural Sciences Program, University of Maryland Eastern Shore, Princess Anne, MD, United States
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22
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Jin M, Song DE, Ahn J, Song E, Lee YM, Sung TY, Kim TY, Kim WB, Shong YK, Jeon MJ, Kim WG. Genetic Profiles of Aggressive Variants of Papillary Thyroid Carcinomas. Cancers (Basel) 2021; 13:cancers13040892. [PMID: 33672707 PMCID: PMC7924361 DOI: 10.3390/cancers13040892] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Aggressive variants of papillary thyroid carcinoma (PTC) are associated with unfavorable clinical outcomes. However, limited data exist on the genetic profile of these variants of PTC. We performed targeted next-generation sequencing in 36 tissue samples from patients with aggressive variants of PTC. Aggressive variants of PTC had a higher prevalence of the BRAF mutation and a lower prevalence of RAS mutation than other types of thyroid cancer. The prevalence of mutations in the TERT promoter, TP53, and genes encoding histone methyl transferases (HMTs), switch/sucrose non-fermenting (SWI/SNF) chromatin remodeling complex, and the phosphoinositide 3-kinase/protein kinase B (PKB/AKT)/mammalian target of the rapamycin (PI3K/AKT/mTOR) pathway was between the range of PTCs and poorly differentiated/anaplastic carcinoma from The Cancer Genome Atlas (TCGA) and the Memorial Sloan Kettering Cancer Center (MSKCC) data. Abstract Aggressive variants of papillary thyroid carcinoma (PTC) have been described with increasing frequency and are associated with unfavorable clinical outcomes. However, limited data exist on the comprehensive genetic profile of these variants. We performed targeted next-generation sequencing in 36 patients with aggressive variants of PTC and compared it to PTC from The Cancer Genome Atlas (TCGA) project and poorly differentiated thyroid cancers (PDTCs)/anaplastic thyroid cancers (ATCs) from the Memorial Sloan Kettering Cancer Center (MSKCC). BRAF mutation was the most prevalent (89%) in aggressive variants of PTC compared to that in other thyroid cancers. RAS mutation was identified in one patient (3%), which was less frequent than in others. TERT promoter mutation (17%) ranged between that of PTCs (9%) and PDTCs (40%). Tumor suppressor genes, ZFHX3, TP53, and CHEK2, were mutated in 14%, 3%, and 6% of aggressive variants of PTC, respectively. The mutation rate of TP53 (3%) was significantly higher than that of PTCs (0.7%) and lower than that of ATCs (73%). Mutations in three functional groups, histone methyl transferases, SWI/SNF chromatin remodeling complex, and the PI3K/AKT/mTOR pathway, were present in 11%, 14%, and 11% of samples, respectively. In conclusion, aggressive variants of PTC had higher BRAF and lower NRAS mutation prevalence than other thyroid cancers. The prevalence of mutations in the TERT promoter, TP53, and genes encoding three functional groups ranged between that of PTCs and PDTCs/ATCs.
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Affiliation(s)
- Meihua Jin
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul 05505, Korea; (M.J.); (J.A.); (T.Y.K.); (W.B.K.); (Y.K.S.)
| | - Dong Eun Song
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul 05505, Korea;
| | - Jonghwa Ahn
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul 05505, Korea; (M.J.); (J.A.); (T.Y.K.); (W.B.K.); (Y.K.S.)
| | - Eyun Song
- Division of Endocrinology and Metablosim, Department of Internal Medicine, Korea University College of Medicine and School of Medicine, Seoul 08308, Korea;
| | - Yu-Mi Lee
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul 05505, Korea; (Y.-M.L.); (T.-Y.S.)
| | - Tae-Yon Sung
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul 05505, Korea; (Y.-M.L.); (T.-Y.S.)
| | - Tae Yong Kim
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul 05505, Korea; (M.J.); (J.A.); (T.Y.K.); (W.B.K.); (Y.K.S.)
| | - Won Bae Kim
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul 05505, Korea; (M.J.); (J.A.); (T.Y.K.); (W.B.K.); (Y.K.S.)
| | - Young Kee Shong
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul 05505, Korea; (M.J.); (J.A.); (T.Y.K.); (W.B.K.); (Y.K.S.)
| | - Min Ji Jeon
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul 05505, Korea; (M.J.); (J.A.); (T.Y.K.); (W.B.K.); (Y.K.S.)
- Correspondence: (M.J.J.); (W.G.K.); Tel.: +82-230-101-317 (M.J.J.); +82-230-105-883 (W.G.K.)
| | - Won Gu Kim
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul 05505, Korea; (M.J.); (J.A.); (T.Y.K.); (W.B.K.); (Y.K.S.)
- Correspondence: (M.J.J.); (W.G.K.); Tel.: +82-230-101-317 (M.J.J.); +82-230-105-883 (W.G.K.)
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Park HJ, Hong YB, Hong JM, Yun U, Kim SW, Shin HY, Kim SM, Choi YC. Null variants in DYSF result in earlier symptom onset. Clin Genet 2021; 99:396-406. [PMID: 33215690 DOI: 10.1111/cge.13887] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/06/2020] [Accepted: 11/16/2020] [Indexed: 01/11/2023]
Abstract
We investigated the clinical, laboratory, and genetic spectra in Korean patients with dysferlinopathy to clarify its genotype-phenotype correlation. We retrospectively reviewed 101 patients from 96 unrelated families with pathogenic variants of DYSF. The most common initial phenotype was Miyoshi myopathy in 50 patients. Median ages at examination and symptom onset were 23 [interquartile range (IQR): 18-30] and 36 years [IQR: 27-48], respectively. We observed 38 variants, including nine novel variants. Four variants (c.2494C > T, c.1284 + 2 T > C, c.663 + 1G > C, and c.2997G > T) in DYSF accounted for 62% of total allele frequencies of pathogenic variants. To analyze the genotype-phenotype correlation, we compared the clinical phenotype between patients with null/null (N/N; n = 55) and null/missense variants (N/M; n = 35). The N/N group had an earlier symptom onset age (median: 20 years [IQR: 17-25]) than the N/M group (median: 29 years [IQR: 23-35], p < .001). Total manual muscle testing scores in lower extremities were lower in the N/N group (median: 80 [IQR: 56-92]) than in the N/M group (median: 89 [IQR: 78-98], p = .013). Our study is the first to report that null variants in DYSF result in an earlier symptom onset than missense variants.
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Affiliation(s)
- Hyung Jun Park
- Department of Neurology, Rehabilitation Institute of Neuromuscular Disease, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Young Bin Hong
- Department of Biochemistry, College of Medicine, Dong-A University, Busan, South Korea
| | - Ji-Man Hong
- Department of Neurology, Yongin Severance Hospital, Yonsei University College of Medicine, Yongin, South Korea
| | - UnKyu Yun
- Department of Neurology, Rehabilitation Institute of Neuromuscular Disease, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Seung Woo Kim
- Department of Neurology, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Ha Young Shin
- Department of Neurology, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Seung Min Kim
- Department of Neurology, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Young-Chul Choi
- Department of Neurology, Rehabilitation Institute of Neuromuscular Disease, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
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Abstract
Background Autosomal dominant polycystic liver disease (ADPLD) is characterized by multiple cysts in the liver without (or only occasional) renal cysts. At least seven genes are associated with high risk for developing ADPLD; however, clear genetic involvement is undetermined in more than 50% of ADPLD patients. Methods To identify additional ADPLD-associated genes, we collected 18 unrelated Chinese ADPLD cases, and performed whole exome sequencing on all the participants. After filtering the sequencing data against the human gene mutation database (HGMD) professional edition, we identified new mutations. We then sequenced this gene in family members of the patient. Results Among the 18 ADPLD cases analyzed by whole exome sequencing, we found 2 cases with a PRKCSH mutation (~11.1%), 2 cases with a PKD2 mutation (~11.1%), 1 case with both PKHD1 and PKD1 mutations (~5.6%), 1 case with GANAB mutation (~5.6%), 1 case with PKHD1 mutation (~5.6%), and 1 case with PKD1 mutations (~5.6%). We identified a new PKHD1 missense mutation in an ADPLD family, in which both patients showed innumerable small hepatic cysts, as reported previously. Additionally, we found that PRKCSH and SEC63 mutation frequencies were lower in the Chinese population compared with those in European and American populations. Conclusions We report a family with ADPLD associated with a novel PKHD1 mutation (G1210R). The genetic profile of ADPLD in the Chinese population is different from that in European and American populations, suggesting that further genetic research on genetic mutation of ADPLD in the Chinese population is warranted.
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Affiliation(s)
- Jiaru Wang
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Huayu Yang
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Ruohan Guo
- Department of Internal Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Xinting Sang
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Yilei Mao
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
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Yang L, Dong Y, Ma Y, Ni W, Wu ZY. Genetic profile and clinical characteristics of Chinese patients with spinocerebellar ataxia type 2: A multicenter experience over 10 years. Eur J Neurol 2020; 28:955-964. [PMID: 33070405 DOI: 10.1111/ene.14601] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 10/14/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND AND PURPOSE Spinocerebellar ataxia type 2 (SCA2) is the second most common type of spinocerebellar ataxia in China. However, data on the clinical and genetic features of Chinese SCA2 patients are scarce. This study aims to provide a comprehensive description of in the Chinese SCA2 cohort. METHODS A total of 135 patients with SCA2 from 92 families and 104 unrelated normal controls were recruited from three medical centers between 2008 and 2020. Sanger sequencing and TA cloning were used to determine the CAG repeat length and intrinsic structure. The clinical data of patients with SCA2, including electromyography, magnetic resonance imaging, positron-emission tomography, and clinical scale scores, were recorded. RESULTS The mean ± SD age at onset of SCA2 patients was 32.6 ± 11.9 years and the corresponding CAG repeat length was 42.1 ± 3.6. CAG repeat length accounted for 64% of the age-at-onset variance. We observed that patients had a significantly lower proportion of (CAG)8 CAA(CAG)4 CAA(CAG)8 within normal alleles than normal controls (48.8% vs. 64.9%; p = 0.003), while the distribution of the proportion of (CAG)13 CAA (CAG)8 was the opposite. Peripheral neuropathy was frequent, occurring in 75.9% of the patients. Parkinsonism was relatively common, with a frequency of 11.8%. Two patients with parkinsonism had a significantly more severe reduction in dopamine transporter levels in the bilateral striatum than the one patient with pure ataxia. An infant-onset case of SCA2 with more than 180 CAG repeats was characterized by global development delay, hypotonia and hearing impairment. CONCLUSIONS This study describes the genetic profile and clinical characteristics of the largest SCA2 cohort to date in the Chinese population and analyzes inter-population differences. Many aspects of this study population were different from other populations with SCA2.
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Affiliation(s)
- Lu Yang
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Yi Dong
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China.,Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yin Ma
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Wang Ni
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China.,Department of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Zhi-Ying Wu
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China.,CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai, China
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Proietti PC, Stefanetti V, Musa L, Zicavo A, Dionisi AM, Bellucci S, Mensa AL, Menchetti L, Branciari R, Ortenzi R, Franciosini MP. Genetic Profiles and Antimicrobial Resistance Patterns of Salmonella Infantis Strains Isolated in Italy in the Food Chain of Broiler Meat Production. Antibiotics (Basel) 2020; 9:antibiotics9110814. [PMID: 33207568 PMCID: PMC7696838 DOI: 10.3390/antibiotics9110814] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/13/2020] [Accepted: 11/14/2020] [Indexed: 01/30/2023] Open
Abstract
This work aimed to evaluate the antimicrobial susceptibility of 87 Salmonella Infantis strains isolated in Italy from 2016 to 2019 along the food chain of broiler meat production and in humans and to determine the genetic profiles of the strains in order to establish a possible correlation with the antimicrobial pattern. All isolates were tested by the disk diffusion method to evaluate antimicrobial susceptibility toward sixteen antimicrobials, and the broth microdilution method was used to confirm extended spectrum β-lactamase (ESBL) production. PCR and pulsed field gel electrophoresis (PFGE) were applied to characterize ESBL-encoding and AmpC β-lactamase genes and to analyze the S. Infantis strains genetic profiles respectively. S. Infantis isolates showed high prevalence of resistance, in particular toward nalidixic acid (97.7%), tetracycline (96.5%), sulphamethoxazole/trimethoprim (91%) and cefepime (72.4%). The 80.5% of isolates were ESBL, cefotaxime-resistant, carrying the blaCTX-M1 gene. The most prevalent PFGE profile was XbaI.0126 (35.6%). The remaining strains had a genetic homology from 81% to 97% with the XbaI.0126 profile. The strains belonging to these profiles were isolated from different matrices collected along the broiler food chain independently on the year and from the region and there was no correlation between the PFGE profiles and resistance patterns. We found two ESBL-producing S. Infantis strains with the same XbaI.2621 profile isolated from humans and from poultry feces, not yet reported in Italy. Our findings confirmed the diffusion of ESBL-multi drug resistant (MDR) S. Infantis along the broiler food chain and in humans and underlined the importance of continuous monitoring to control and to reduce the prevalence of this bacterium, applying a global One Health approach.
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Affiliation(s)
- Patrizia Casagrande Proietti
- Department of Veterinary Medicine, Via S. Costanzo 4, 06126 Perugia, Italy; (V.S.); (L.M.); (S.B.); (A.L.M.); (R.B.); (M.P.F.)
- Correspondence:
| | - Valentina Stefanetti
- Department of Veterinary Medicine, Via S. Costanzo 4, 06126 Perugia, Italy; (V.S.); (L.M.); (S.B.); (A.L.M.); (R.B.); (M.P.F.)
| | - Laura Musa
- Department of Veterinary Medicine, Via S. Costanzo 4, 06126 Perugia, Italy; (V.S.); (L.M.); (S.B.); (A.L.M.); (R.B.); (M.P.F.)
| | - Alessia Zicavo
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, Via G. Salvemini, 1, 06126 Perugia, Italy; (A.Z.); (R.O.)
| | - Anna Maria Dionisi
- Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161 Roma, Italy;
| | - Sara Bellucci
- Department of Veterinary Medicine, Via S. Costanzo 4, 06126 Perugia, Italy; (V.S.); (L.M.); (S.B.); (A.L.M.); (R.B.); (M.P.F.)
| | - Agnese La Mensa
- Department of Veterinary Medicine, Via S. Costanzo 4, 06126 Perugia, Italy; (V.S.); (L.M.); (S.B.); (A.L.M.); (R.B.); (M.P.F.)
| | - Laura Menchetti
- Department of Agricultural and Food Sciences, Viale Fanin 42, 40127 Bologna, Italy;
| | - Raffaella Branciari
- Department of Veterinary Medicine, Via S. Costanzo 4, 06126 Perugia, Italy; (V.S.); (L.M.); (S.B.); (A.L.M.); (R.B.); (M.P.F.)
| | - Roberta Ortenzi
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, Via G. Salvemini, 1, 06126 Perugia, Italy; (A.Z.); (R.O.)
| | - Maria Pia Franciosini
- Department of Veterinary Medicine, Via S. Costanzo 4, 06126 Perugia, Italy; (V.S.); (L.M.); (S.B.); (A.L.M.); (R.B.); (M.P.F.)
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Chen X, Xu B, Li Q, Xu X, Li X, You X, Yu Z. Genetic profile of non-small cell lung cancer (NSCLC): A hospital-based survey in Jinhua. Mol Genet Genomic Med 2020; 8:e1398. [PMID: 32657049 PMCID: PMC7507563 DOI: 10.1002/mgg3.1398] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 05/18/2020] [Accepted: 06/15/2020] [Indexed: 01/06/2023] Open
Abstract
Background We describe the clinical features, genetic profile, and their correlation in NSCLC patients. Methods A total of 256 Chinese patients with NSCLC were enrolled in this study. NGS‐based genomic profiling of major lung cancer‐related genes was performed on formalin‐fixed paraffin‐embedded tumor samples. Results Of 256 patients with NSCLC, 219 were adenocarcinoma and most of them were in the early stage. Among patients, 63.3% patients have more than two gene mutations. By analyzing variant allele frequency (VAF), we found that the median VAF has significant differences between squamous cell carcinoma and adenocarcinoma, as well as early stage and advanced stage. The frequency of mutations in EGFR, MET, and RET were significantly higher in nonsmokers than in smokers. Besides, Pearson correlation analysis found that ALK, BRAF, and MET mutations had a strong correlation with age. Notably, higher frequencies of ALK and BRAF alterations were associated with younger age, while more frequent MET mutations appear in the patients at age 55 or older. Conclusion More unique features of cancer driver genes in Chinese NSCLC were identified by next‐generation sequencing. These findings highlighted that it is necessary to carry out targeted detection according to different clinical features for NSCLC.
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Affiliation(s)
- Xianguo Chen
- Department of Thoracic SurgeryJinhua Municipal Central HospitalJinhua Hospital of Zhejiang UniversityJinhuaChina
| | - Bo Xu
- Department of Thoracic SurgeryJinhua Municipal Central HospitalJinhua Hospital of Zhejiang UniversityJinhuaChina
| | - Qiang Li
- Hangzhou D.A. Medical LaboratoryHangzhouChina
| | - Xiaoyi Xu
- Department of Thoracic SurgeryJinhua Municipal Central HospitalJinhua Hospital of Zhejiang UniversityJinhuaChina
| | - Xianshuai Li
- Department of Thoracic SurgeryJinhua Municipal Central HospitalJinhua Hospital of Zhejiang UniversityJinhuaChina
| | - Xia You
- Hangzhou D.A. Medical LaboratoryHangzhouChina
| | - Zhaonan Yu
- Hangzhou D.A. Medical LaboratoryHangzhouChina
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Cavalcante FS, Alvarenga CVDCG, Saintive S, Dios Abad ED, Carvalho Ferreira DD, Netto Dos Santos KR. Staphylococcus aureus nasal isolates may have the same genetic profile in atopic dermatitis paediatric patients and their close contacts. J Med Microbiol 2020; 69:850-853. [PMID: 32430095 DOI: 10.1099/jmm.0.001197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Atopic dermatitis (AD) is a chronic skin disease that affects up to 20 % of the paediatric population worldwide. Staphylococcus aureus colonizes anterior nares and can be transmitted in the home environment, aggravating AD. This study aimed to detect S. aureus from nares of AD patients and their family contacts, as well as to evaluate the antimicrobial resistance, virulence and clonality of these isolates. Among the 48 family groups investigated, 30 groups were selected, as both the child and his/her respective contact had methicillin-sensitive S. aureus (MSSA) (24 cases; 54 MSSA isolates) or methicillin-resistant S. aureus (MRSA) isolates (6 cases; 13 MRSA isolates). All MRSA isolates carried SCCmec IV. S. aureus carrying PVL genes were detected in 60 % of patients. Pulsed-field gel electrophoresis (PFGE) analysis was performed for 31 isolates from 15 family groups: all 6 with MRSA and 9 with MSSA isolates. Similar genotypic profiles between isolates from patients and their family contacts were noted in 10 (66.6 %) family groups, 5 (83.3 %) of the MRSA family groups and 5 (55.5 %) of the MSSA family groups, indicating that the pathogen was transmitted through family contacts.
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Affiliation(s)
| | - Celina Vieira da Cunha Guedes Alvarenga
- Laboratório de Infecção Hospitalar, Departamento de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Simone Saintive
- Instituto de Puericultura e Pediatria Martagão Gesteira, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Eliane de Dios Abad
- Instituto de Puericultura e Pediatria Martagão Gesteira, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Kátia Regina Netto Dos Santos
- Laboratório de Infecção Hospitalar, Departamento de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Hu Y, Ren S, Liu Y, Han W, Liu W. Pulmonary Lymphoepithelioma-Like Carcinoma: A Mini-Review. Onco Targets Ther 2020; 13:3921-3929. [PMID: 32494151 PMCID: PMC7227818 DOI: 10.2147/ott.s241337] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/30/2020] [Indexed: 12/13/2022] Open
Abstract
Pulmonary lymphoepithelioma-like carcinoma (PLELC) is a rare and distinct subtype of non-small-cell lung carcinoma associated with Epstein–Barr virus (EBV) infection. We systematically reviewed the recent research that expands our knowledge about PLELC, with main focus on its genetic profile, tumor-infiltrating environment, PD-L1 expression, circulating EBV-DNA, clinical utility of 18F-FDG PET/CT, and treatment strategy. A low frequency of typical driver mutations and widespread existence of copy number variations was detected in PLELC. Persistent EBV infection may trigger intense infiltration of lymphocytes, representing enhanced tumor immunity and possibly resulting in a better prognosis. Circulating EBV-DNA in the plasma of patients with PLELC may predict disease progression and response to therapy. PLELC is 18F-FDG avid, and 18F-FDG PET may help refine palliation strategies and subsequently improve the prognosis. Most of the reported patients present at early and resectable stage, and surgical resection with curative intent is the preferred approach. There is currently no consensus on the regimen of chemotherapy for patients with advanced stages. EGFR-targeted therapies seem to have no therapeutic effect, and the clinical impact of PD-1/PD-L1 therapy is uncertain but worthy of further research.
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Affiliation(s)
- Yan Hu
- Department of Thoracic Surgery, Second Xiangya Hospital of Central South University, Changsha 410011, People's Republic of China
| | - Siying Ren
- Department of Respiratory and Critical Care Medicine, Second Xiangya Hospital of Central South University, Changsha 410011, People's Republic of China
| | - Yukang Liu
- Department of Thoracic Surgery, Second Xiangya Hospital of Central South University, Changsha 410011, People's Republic of China
| | - Wei Han
- Department of Thoracic Surgery, Second Xiangya Hospital of Central South University, Changsha 410011, People's Republic of China
| | - Wenliang Liu
- Department of Thoracic Surgery, Second Xiangya Hospital of Central South University, Changsha 410011, People's Republic of China
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30
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Varillas Delgado D, Tellería Orriols JJ, Monge Martín D, Del Coso J. Genotype scores in energy and iron-metabolising genes are higher in elite endurance athletes than in nonathlete controls. Appl Physiol Nutr Metab 2020; 45:1225-1231. [PMID: 32379996 DOI: 10.1139/apnm-2020-0174] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Information about the association of energy and iron-metabolising genes with endurance performance is scarce. The objective of this investigation was to compare the frequencies of polymorphic variations of genes involved in energy generation and iron metabolism in elite endurance athletes versus nonathlete controls. Genotype frequencies in 123 male elite endurance athletes (75 professional road cyclists and 48 elite endurance runners) and 122 male nonathlete participants were compared by assessing 4 genetic polymorphisms: AMPD1 c.34C/T (rs17602729), PPARGC1A c.1444G/A (rs8192678) HFEH63D c.187C/G (rs1799945) and HFEC282Y c.845G/A (rs1800562). A weighted genotype score (w-TGS; from 0 to 100 arbitrary units (a.u.)) was calculated by assigning a corresponding weight to each polymorphism. In the nonathlete population, the mean w-TGS value was lower (39.962 ± 14.654 a.u.) than in the group of elite endurance athletes (53.344 ± 17.053 a.u). The binary logistic regression analysis showed that participants with a w-TGS > 38.975 a.u had an odds ratio of 1.481 (95% confidence interval: 1.244-1.762; p < 0.001) for achieving elite athlete status. The genotypic distribution of polymorphic variations involved in energy generation and iron metabolism was different in elite endurance athletes vs. controls. Thus, an optimal genetic profile in these genes might contribute to physical endurance in athlete status. Novelty Genetic profile in energy generation and iron-metabolising genes in elite endurance athletes is different than that of nonathletes. There is an implication of an "optimal" genetic profile in the selected genes favouring endurance sporting performance.
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Affiliation(s)
- David Varillas Delgado
- Universidad Francisco de Vitoria, Faculty of Medicine, Research Unit, Pozuelo de Alarcón, Madrid 28223, Spain
| | | | - Diana Monge Martín
- Universidad Francisco de Vitoria, Faculty of Medicine, Pozuelo de Alarcón, Madrid 28223, Spain
| | - Juan Del Coso
- Rey Juan Carlos University, Centre for Sport Studies, Fuenlabrada, Madrid 28933, Spain
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Korula S, Danda S, Paul PG, Mathai S, Simon A. Hepatic Glycogenoses Among Children-Clinical and Biochemical Characterization: Single-Center Study. J Clin Exp Hepatol 2020; 10:222-227. [PMID: 32405178 PMCID: PMC7212290 DOI: 10.1016/j.jceh.2019.07.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/17/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Glycogen storage disease (GSD) is typified by early morning seizures. Absence of this results in delayed diagnosis, especially the non-GSD 1 group. Data are limited to few patients with unclear outcome. OBJECTIVES 1. Study the common presentation and types of GSD. 2. Study the clinical and biochemical outcome. 3. Review genetic mutations. METHODS Observational study from May 2016-April 2019 at metabolic clinic at our center. RESULTS Total of 30 patients were diagnosed with GSD. Ten were excluded-Fanconi-Bickel (3) and <4 months follow-up (7). Data were analyzed for 20 patients (16 males). Mean age at presentation was 4.3 yrs. All had hepatomegaly, 90% had short stature, and 40% had early morning seizures. Mean follow-up was 22 months. There was a statistically significant improvement in metabolic parameters on treatment (mean)-fasting glucose from 50.4 to 79.5 mg/dl, SGPT from 416 to 199 U/L. Lipid profile showed reduction in triglycerides (318-225 mg/dl) but minimal increase in cholesterol (178-188 mg/dl). Mean weight centile improved from 14.1 to 20.3 and height centile from 2.3 to 7.9. Genetic testing confirmed types VI (3), III (3), IXa (1), IXc (1), and Ia (1). Liver biopsy confirmed GSD in 15/20. All were managed with uncooked corn starch. In addition, omega-3 fatty acid was used in 8/20 and high protein diet in 2 with GSD type III. CONCLUSION Awareness of GSD needs to improve among pediatricians and hepatologists. The most common symptoms are asymptomatic hepatomegaly and short stature. Dietary therapy with uncooked corn starch remains mainstay of treatment. Mixed hyperlipidemia is difficult to control despite good metabolic improvement. Role of omega-3 fatty acid needs to be explored further. Genetic mutation analysis can assist with tailoring treatment and should get precedence over liver biopsy.
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Affiliation(s)
- Sophy Korula
- Paediatric Endocrinology and Metabolism Unit, Christian Medical College and Hospital, Vellore, India
| | - Sumita Danda
- Clinical Genetics Department, Christian Medical College and Hospital, Vellore, India
| | - Praveen G. Paul
- Paediatric Endocrinology and Metabolism Unit, Christian Medical College and Hospital, Vellore, India
| | - Sarah Mathai
- Paediatric Endocrinology and Metabolism Unit, Christian Medical College and Hospital, Vellore, India
| | - Anna Simon
- Paediatric Endocrinology and Metabolism Unit, Christian Medical College and Hospital, Vellore, India
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Song E, Song DE, Ahn J, Kim TY, Kim WB, Shong YK, Jeon MJ, Kim WG. Genetic profile of advanced thyroid cancers in relation to distant metastasis. Endocr Relat Cancer 2020; 27:285-293. [PMID: 32163911 DOI: 10.1530/erc-19-0452] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 03/09/2020] [Indexed: 11/08/2022]
Abstract
Major clinical challenges exist with differentiated thyroid cancers with distant metastases or rare but aggressive types, such as poorly differentiated thyroid carcinomas and anaplastic thyroid carcinomas. The precise characterization of the mutational profile in these advanced thyroid cancers is crucial. Samples were collected from primary tumors and distant metastases of 64 patients with distant metastases from differentiated thyroid cancer, poorly differentiated thyroid carcinoma, or anaplastic thyroid carcinoma. Targeted next-generation sequencing was performed with 50 known thyroid-cancer-related genes. Of the 82 tissues, 63 were from primary tumors and 19 from distant metastases. The most prevalent mutation observed from the primary tumors was TERT promoter mutation (56%), followed by BRAF (41%) and RAS (24%) mutations. TP3 was altered by 11%. Mutations in histone methyltransferases, SWI/SNF subunit-related genes, and PI3K/AKT/mTOR pathway-related genes were present in 42%, 12%, and 22%, respectively. When the mutational status was analyzed in 15 matched pairs of thyroid tumors and their matched distant metastases and one pair of distant metastases with two distinct sites, the concordance was high. A similar frequency of mutations in TERT promoter (58%) and BRAF (42%) as well as histone methyltransferases (37%), SWI/SNF subunits (10%), and PI3K/AKT/mTOR pathway (26%) were noted. The same main, early and late mutations were practically always present in individual primary tumor-metastasis pairs. Enrichment of TERT promoter, BRAF, and RAS mutations were detected in highly advanced thyroid cancers with distant metastasis. The genetic profiles of primary thyroid tumors and their corresponding distant metastases showed a high concordance.
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Affiliation(s)
- Eyun Song
- Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Songpa-gu, Seoul, Republic of Korea
| | - Dong Eun Song
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Songpa-gu, Seoul, Republic of Korea
| | - Jonghwa Ahn
- Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Songpa-gu, Seoul, Republic of Korea
| | - Tae Yong Kim
- Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Songpa-gu, Seoul, Republic of Korea
| | - Won Bae Kim
- Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Songpa-gu, Seoul, Republic of Korea
| | - Young Kee Shong
- Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Songpa-gu, Seoul, Republic of Korea
| | - Min Ji Jeon
- Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Songpa-gu, Seoul, Republic of Korea
| | - Won Gu Kim
- Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Songpa-gu, Seoul, Republic of Korea
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Selivanova LS, Roslyakova AA, Bogolyubova AV, Tertychnyi AS, Beltsevich DG, Abrosimov AY, Melnichenko GA. [Molecular genetic markers and criteria for the prediction of adrenocortical carcinoma]. Arkh Patol 2019; 81:92-96. [PMID: 31626211 DOI: 10.17116/patol20198105192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Studies of the last decade have demonstrated that the morphological and immunophenotypic patterns of adrenocortical carcinoma (ACC) have a high heterogeneity in both the occurrence of various tumors and the development of a solitary tumor. Carcinogenesis of ACC, like most neoplastic processes, is associated with mutations in at least 15 driver genes, with a wide range of chromosomal aberrations, epigenomic changes, and alterations of the microRNA profile. According to the literature, isolated genetic damage is also insufficient for the manifestation of the malignant phenotype of adrenocortical cells. Knudson's two-hit hypothesis is implemented in at least germline mutations: the development of ACC requires a second genetic event occurring in somatic cells, which leads to inactivation of the second allele of the gene. ACC is an extremely heterogeneous disease, which determines the complexity of differential diagnosis with benign adrenocortical tumors and that of prediction of the clinical course. Another no less important issue is the lack of valid predictors for the efficacy of mitotane, the use of which may be associated with severe adverse effects.
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Affiliation(s)
- L S Selivanova
- National Medical Research Center of Endocrinology, Ministry of Health of Russia, Moscow, Russia
| | - A A Roslyakova
- National Medical Research Center of Endocrinology, Ministry of Health of Russia, Moscow, Russia
| | - A V Bogolyubova
- V.A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia; Center for Genetics and Life Sciences, Talent and Success Educational Fund, Sirius Educational Center, Sochi, Russia
| | - A S Tertychnyi
- I.M. Sechenov First Moscow State Medical University, Ministry of Health of Russia, Moscow, Russia
| | - D G Beltsevich
- National Medical Research Center of Endocrinology, Ministry of Health of Russia, Moscow, Russia
| | - A Yu Abrosimov
- National Medical Research Center of Endocrinology, Ministry of Health of Russia, Moscow, Russia
| | - G A Melnichenko
- National Medical Research Center of Endocrinology, Ministry of Health of Russia, Moscow, Russia
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Young K, Friedman E. Lung Carcinoma Presenting as a Superior Vena Cava Syndrome, Burnt and Twice Reborn as Adrenal and Facial Tumors. Cureus 2019; 11:e5746. [PMID: 31723507 PMCID: PMC6825460 DOI: 10.7759/cureus.5746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Eighty-five percent of all lung cancers are Non-Small-Cell Lung Carcinoma (NSCLC) with common sites of metastasis to the adrenal glands and liver. Onset is insidious, and seventy-five percent of patients have either regional or distant metastases at initial presentation. The five-year relative survival rate is four and a half percent with a distantly spread disease based on recent studies. Here we present a unique case of a ten-year survival with NSCLC initially presenting as a Superior Vena Cava Syndrome and reoccurring with adrenal gland, bone, and CNS lesions. The patient presented with SVC caused by lung cancer and underwent chemo and radiotherapy with complete response in 2010. Five years later, the same cancer returned disguised as an adrenal tumor. In 2017, the patient came in with facial neuropathy, shooting pains, sinus headaches, eyelid concerns, and active tumoral activity was detected in the middle cranial fossa, involving parotid glands and the vertebral column. Craniotomy revealed a metastatic poorly differentiated adenocarcinoma that extended through foramen ovale and rotundum to the infratemporal fossa and caused left-sided facial paralysis, hearing loss and numbness in CN V2 - V3 distribution. Considering that the patient has experienced several recurrences of disease on standard protocols and is not a candidate for targeted molecular therapies, an immunotherapy trial was suggested as the next step. The natural history of this disease is remarkable in terms of metastatic sites, paraneoplastic manifestations, and a substantially prolonged lifespan. Thus, more studies of similar cases will advance our understanding of tumor genetics and immunotherapy allowing the greater benefit to future patients.
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Affiliation(s)
- Kate Young
- Internal Medicine, Ross University School of Medicine, Tampa, USA
| | - Eitan Friedman
- Oncology/hematology, United Oncology Medical Associates, Miami, USA
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Montesanto A, Bonfigli AR, Crocco P, Garagnani P, De Luca M, Boemi M, Marasco E, Pirazzini C, Giuliani C, Franceschi C, Passarino G, Testa R, Olivieri F, Rose G. Genes associated with Type 2 Diabetes and vascular complications. Aging (Albany NY) 2018; 10:178-96. [PMID: 29410390 DOI: 10.18632/aging.101375] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 01/30/2018] [Indexed: 12/20/2022]
Abstract
Type 2 Diabetes (T2D) is a chronic disease associated with a number of micro- and macrovascular complications that increase the morbidity and mortality of patients. The risk of diabetic complications has a strong genetic component. To this end, we sought to evaluate the association of 40 single nucleotide polymorphisms (SNPs) in 21 candidate genes with T2D and its vascular complications in 503 T2D patients and 580 healthy controls. The genes were chosen because previously reported to be associated with T2D complications and/or with the aging process. We replicated the association of T2D risk with IGF2BP rs4402960 and detected novel associations with TERT rs2735940 and rs2736098. The addition of these SNPs to a model including traditional risk factors slightly improved risk prediction. After stratification of patients according to the presence/absence of vascular complications, we found significant associations of variants in the CAT, FTO, and UCP1 genes with diabetic retinopathy and nephropathy. Additionally, a variant in the ADIPOQ gene was found associated with macrovascular complications. Notably, these genes are involved in some way in mitochondrial biology and reactive oxygen species regulation. Hence, our findings strongly suggest a potential link between mitochondrial oxidative homeostasis and individual predisposition to diabetic vascular complications.
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Ahangari Cohan R, Nouri Inanlou D, Samiee Aref MH, Zeinali S, Farhoudi R. Microsatellite Marker Analysis for Laboratory Mice Profiling. Adv Biomed Res 2019; 8:40. [PMID: 31360681 PMCID: PMC6621418 DOI: 10.4103/abr.abr_53_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background: The key point in the production procedure of inbred animals is checking the genetic purity. Skin grafting and coat color test are used traditionally to prove genetic purity, but they have some disadvantages. Recent advances in DNA profiling have enabled scientists to check easily the genetic purity of laboratory animals. In the current study, a set of microsatellite markers was designed to check the purity of inbred laboratory mice. Materials and Methods: Twenty microsatellites located on 20 chromosomes were employed to create a distinctive genetic profile for parentage analysis. Each individual primer was designed based on distinguishable colors and separable sizes. Results: Twenty specific microsatellite markers were used in the polymerase chain reaction mixture to identify inbred BALB/cJ strains. Our results confirmed that the designed microsatellites are excellent genetic markers for testing inbred BALB/cJ strain in laboratories. Conclusion: Our study showed that genetic profiling using microsatellite markers allows us to detect the genetic differences of laboratory mouse species in quality control tests and validation steps.
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Affiliation(s)
- Reza Ahangari Cohan
- Department of Nanobiotechnology, New Technologies Research Group, Pasteur Institute of Iran, Tehran, Iran
| | | | | | - Sirous Zeinali
- Department of Molecular Medicine, Pasteur Institute of Iran, Tehran, Iran
| | - Ramin Farhoudi
- Department of Quality Control, Pasteur Institute of Iran, Tehran, Iran
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Melguizo-Rodríguez L, Manzano-Moreno FJ, Illescas-Montes R, Ramos-Torrecillas J, Luna-Bertos E, Ruiz C, García-Martínez O. Bone Protective Effect of Extra-Virgin Olive Oil Phenolic Compounds by Modulating Osteoblast Gene Expression. Nutrients 2019; 11:E1722. [PMID: 31349732 DOI: 10.3390/nu11081722] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/18/2019] [Accepted: 07/23/2019] [Indexed: 02/07/2023] Open
Abstract
The phenolic compounds of extra-virgin olive oil can act at various levels to protect individuals against cardiovascular and neurodegenerative diseases, cancer, and osteoporosis, among others. Polyphenols in extra-virgin olive oil can stimulate the proliferation of osteoblasts, modify their antigen profile, and promote alkaline phosphatase synthesis. The objective of this work was to determine the effect of different extra-virgin olive oil phenolic compounds on the gene expression of osteoblast-related markers. The cells of the MG63 osteoblast line were cultured for 24 h with 10−6 M of the phenolic compounds ferulic acid, caffeic acid, coumaric acid, apigenin, or luteolin. The expression of studied markers was quantified using quantitative real-time polymerase chain reaction (q-RT-PCR). The expression by MG63 osteoblasts of growth and differentiation/maturation markers was modified after 24 h of treatment with 10−6 M of the phenolic compounds under study, most of which increased the gene expression of the transforming growth factor β1 (TGF-β1), TGF-β receptor 1,2 and 3 (TGF-βR1, TGF-βR2, TGF-βR3), bone morphogenetic protein 2 and 7 (BMP2, BMP7), run-related transcription factor 2 (RUNX-2), Alkaline phosphatase (ALP), Osteocalcin (OSC), Osterix (OSX), Collagen type I (Col-I) and osteoprotegerin (OPN). The extra-virgin olive oil phenolic compounds may have a beneficial effect on bone by modulating osteoblast physiology, which would support their protective effect against bone pathologies.
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Abstract
RATIONALE Primary splenic angiosarcoma (PSA) is a rare mesenchymal malignancy of the splenic vascular origin often with a dismal prognosis. Genomic profile may provide evidence for the solution of therapy. PATIENT CONCERNS We reported a case of a 51-year-old woman with splenectomy 4 years ago and the postoperative histopathology diagnosis revealed "splenic hemangioma" with spontaneous rupture. Two years after the operation, the patient's rechecked abdominal computed tomography (CT) showed multiple hepatic occupations. DIAGNOSES Pathological test suggested PSA hepatic metastasis. INTERVENTIONS The patient was treated with trans-catheter arterial chemoembolization (TACE) and a pathological diagnosis of PSA was highly suspected in the hepatic biopsy. Four somatic alterations, phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA), Fos proto-oncogene, AP-1 transcription factor subunit (FOS), MCL1 apoptosis regulator (MCL1), and phosphoinositide-3-kinase regulatory subunit 1 (PIK3R1) were detected in the tumor tissue using a Next generation sequencing (NGS) technology. The results prompted that the patient may get clinical benefit from using some agents for targeted therapy, Everolimus, Temsirolimus, or Copanlisib. OUTCOMES The patient refused targeted therapy. As a result, the patient passed away within 51 months after splenectomy. LESSONS PSA is an aggressive disease that often presented with a high propensity for metastasis and rupture hemorrhage. Some of these mutations were first discovered in PSA and these findings added new contents to the genomic mutation profile of PSA.
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Affiliation(s)
- Linping Cao
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery
| | - Jiawei Hong
- Key Lab of Combined Multi-Organ Transplantation, Ministry of Public Health
| | - Yacong Wang
- Department of Gerontology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou
| | - Jun Yu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery
| | | | - Jia Li
- OrigiMed, Shanghai, China
| | - Jian Wu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery
| | - Shusen Zheng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery
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Ida K, Miyamoto T, Takatsu A, Ando H, Asaka R, Takeuchi H, Ono M, Yamada S, Asaka S, Shiozawa T. Whole-exome sequencing of lobular endocervical glandular hyperplasia. Oncol Lett 2019; 18:2592-2597. [PMID: 31452744 DOI: 10.3892/ol.2019.10549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 06/04/2019] [Indexed: 12/13/2022] Open
Abstract
Lobular endocervical glandular hyperplasia (LEGH) was first reported as a benign proliferative disorder of the uterine cervix. However, it currently remains unclear whether it has the biological characteristics of pyloric metaplasia or precursor of minimal deviation adenocarcinoma (MDA)/gastric-type mucinous cervical adenocarcinoma (GAS). Therefore, in the present study we performed whole-exome sequencing on three cases of LEGH collected by laser-microdissection from the frozen tissue sections of surgically removed uteri. Analysis of the results identified 50 somatic variants. After several filtering processes, we identified 13 functional variants, including 12 missense and one insertion-deletion variants. Of these mutations, keratinocyte proline-rich protein, olfactory receptor M4 and zinc finger protein 645 mutations were found in the Catalogue Of Somatic Mutations In Cancer but were not related to carcinogenic diseases. We did not detect any significant copy number alterations or signatures. Although this was a limited case series, we did not identify any variants relevant to the tumorigenesis of LEGH to MDA/GAS, suggesting a metaplastic aspect of LEGH.
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Affiliation(s)
- Koichi Ida
- Department of Obstetrics and Gynecology, Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan
| | - Tsutomu Miyamoto
- Department of Obstetrics and Gynecology, Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan
| | - Akiko Takatsu
- Department of Obstetrics and Gynecology, Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan
| | - Hirofumi Ando
- Department of Obstetrics and Gynecology, Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan
| | - Ryoichi Asaka
- Department of Obstetrics and Gynecology, Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan
| | - Hodaka Takeuchi
- Department of Obstetrics and Gynecology, Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan
| | - Motoki Ono
- Department of Obstetrics and Gynecology, Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan
| | - Satoshi Yamada
- Department of Obstetrics and Gynecology, Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan
| | - Shiho Asaka
- Department of Laboratory Medicine, Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan
| | - Tanri Shiozawa
- Department of Obstetrics and Gynecology, Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan
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Abstract
Background Small cell lung cancer (SCLC) has unique biology and chromosomal modifications; however, only a few studies have investigated the molecular map of SCLC. The present study aimed to evaluate the genomic aberrations in patients with SCLC in a Chinese cohort. Methods Tumor samples of SCLC were prospectively collected from Zhejiang Cancer Hospital. A total of 5 genes [EGFR (epidermal growth factor receptor) E18, EGFR E19, EGFR E20, EGFR E21, KRAS (Kirsten rat sarcoma viral oncogene homolog) E2, BRAF E15, PTEN (phosphatase and tensin homolog deleted on chromosome ten) E5, PTEN E6, PTEN E8, PIK3CA (phosphatidylinositol 3-kinase/protein kinase B) E9, PIK3CA E20] were evaluated using direct sequencing. Results Between November 2012 and November 2016, 30 SCLC patients were prospectively enrolled in the study. A total of 10 genomic aberrations were detected in 30 cases (33.3%): an EGFR mutation (n=6, E19, E21), a KRAS mutation (n=1, E2), PIK3CA mutations (n=1, E20), a PTEN mutation (n=2, E5, E8). No significant differences were detected in the characteristics of patients with and without genomic aberrations or patients with and without EGFR mutation. Conclusions The genomic aberrations of SCLC occur, offering mutational data to clinicians might be helpful for assigning patients to appropriate clinical studies, especially the anti-EFGR and PIK3CA treatment. Moreover, whether the molecular genetic profile of the SCLC patients is correlated with the effect of anti-tumor treatment, necessitating further investigation.
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Affiliation(s)
- Zeng Wang
- Department of Pharmacy, Zhejiang Cancer Hospital, Hangzhou 310022, China
| | - Zhiming Jiang
- Zhejiang Key Laboratory of Diagnosis & Treatment Technology on Thoracic Oncology (Lung and Esophagus), Zhejiang Cancer Hospital, Hangzhou 310022, China
| | - Hongyang Lu
- Zhejiang Key Laboratory of Diagnosis & Treatment Technology on Thoracic Oncology (Lung and Esophagus), Zhejiang Cancer Hospital, Hangzhou 310022, China.,Deparment of Thoracic Medical Oncology, Zhejiang Cancer Hospital, Hangzhou 310022, China
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de Biase D, Torricelli F, Ragazzi M, Donati B, Kuhn E, Visani M, Acquaviva G, Pession A, Tallini G, Piana S, Ciarrocchi A. Not the same thing: metastatic PTCs have a different background than ATCs. Endocr Connect 2018; 7:1370-1379. [PMID: 30400028 PMCID: PMC6280609 DOI: 10.1530/ec-18-0386] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 10/30/2018] [Indexed: 02/05/2023]
Abstract
Anaplastic thyroid cancer (ATC) is a rare but highly aggressive form of thyroid cancer. By contrast, differentiated papillary thyroid cancer (PTC) only rarely behave aggressively and develop distant metastasis. Whether distantly metastatic PTC (DM-PTC) and ATC share a common genetic background is still to be defined. We used next-generation sequencing (NGS) to explore the genetic background of a cohort of ATC and DM-PTC and a group of well-differentiated PTCs that did not developed distant metastasis as control (ctrl-PTC). A panel of 128 amplicons within 21 thyroid cancer-related genes was analyzed in a set of 151 thyroid cancer samples including 66 ATCs and DM-PTCs. We showed that the ATC/DM-PTC group had an overall mutational load higher than ctrl-PTCs and that ATCs and DM-PTCs are characterized by a different genetic background, with the exception of mutations in the TERT promoter that were overrepresented in both ATCs (61.1%) and DM-PTCs (48.2%) vs non-aggressive ctrl-PTCs (7.6%). In ATCs, TERT promoter mutations were frequently associated with TP53 mutations, while in the DM-PTCs no significant co-occurrence was observed. No significant association of MED12 mutations with aggressiveness of thyroid cancer was observed in our analysis. Finally, correlation analysis showed that increasing number of mutations negatively impact on patient overall survival also within the ATC and DM-PTC group. In conclusions, overall our analysis further highlights the relevance of TERT promoter mutations in driving aggressiveness and provides new pieces of information in the definition of aggressiveness evolution of thyroid cancer lesions.
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Affiliation(s)
- Dario de Biase
- Department of Pharmacy and Biotechnology (Dipartimento di Farmacia e Biotecnologie) – Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna, Bologna, Italy
- Correspondence should be addressed to A Ciarrocchi or D de Biase: or
| | - Federica Torricelli
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale AUSL-IRCCS, Reggio Emilia, Italy
| | - Moira Ragazzi
- Pathology Unit, Azienda Unità Sanitaria Locale AUSL-IRCCS, Reggio Emilia, Italy
| | - Benedetta Donati
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale AUSL-IRCCS, Reggio Emilia, Italy
| | - Elisabetta Kuhn
- Pathology Unit, Azienda Unità Sanitaria Locale AUSL-IRCCS, Reggio Emilia, Italy
| | - Michela Visani
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale) – Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna School of Medicine, Bologna, Italy
| | - Giorgia Acquaviva
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale) – Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna School of Medicine, Bologna, Italy
| | - Annalisa Pession
- Department of Pharmacy and Biotechnology (Dipartimento di Farmacia e Biotecnologie) – Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna, Bologna, Italy
| | - Giovanni Tallini
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale) – Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna School of Medicine, Bologna, Italy
| | - Simonetta Piana
- Pathology Unit, Azienda Unità Sanitaria Locale AUSL-IRCCS, Reggio Emilia, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale AUSL-IRCCS, Reggio Emilia, Italy
- Correspondence should be addressed to A Ciarrocchi or D de Biase: or
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Sprugnoli G, Vatti G, Rossi S, Cerase A, Renieri A, Mencarelli MA, Zara F, Rossi A, Santarnecchi E. Functional Connectivity and Genetic Profile of a "Double-Cortex"-Like Malformation. Front Integr Neurosci 2018; 12:22. [PMID: 29946244 PMCID: PMC6005822 DOI: 10.3389/fnint.2018.00022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/22/2018] [Indexed: 11/13/2022] Open
Abstract
Laminar heterotopia is a rare condition consisting in an extra layer of gray matter under properly migrated cortex; it configures an atypical presentation of periventricular nodular heterotopia (PNH) or a double cortex (DC) syndrome. We conducted an original functional MRI (fMRI) analysis in a drug-resistant epilepsy patient with “double-cortex”-like malformation to reveal her functional connectivity (FC) as well as a wide genetic analysis to identify possible genetic substrates. Heterotopias were segmented into region of interests (ROIs), whose voxel-wise FC was compared to that of (i) its normally migrated counterpart, (ii) its contralateral homologous, and (iii) those of 30 age-matched healthy controls. Extensive genetic analysis was conducted to screen cortical malformations-associated genes. Compared to healthy controls, both laminar heterotopias and the overlying cortex showed significant reduction of FC with the contralateral hemisphere. Two heterozygous variants of uncertain clinical significance were found, involving autosomal recessive disease-causing genes, FAT4 and COL18A1. This first FC analysis of a unique case of “double-cortex”-like malformation revealed a hemispheric connectivity segregation both in the laminar cortex as in the correctly migrated one, with a new pattern of genes’ mutations. Our study suggests the altered FC could have an electrophysiological and functional impact on large-scale brain networks, and the involvement of not yet identified genes in “double-cortex”-like malformation with a possible role of rare variants in recessive genes as pathogenic cofactors.
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Affiliation(s)
- Giulia Sprugnoli
- Department of Medicine, Surgery and Neuroscience, Brain Investigation & Neuromodulation Laboratory, University of Siena, Siena, Italy.,Department of Medicine, Surgery and Neuroscience, Neurology and Clinical Neurophysiology Section, University of Siena, Siena, Italy
| | - Giampaolo Vatti
- Department of Medicine, Surgery and Neuroscience, Neurology and Clinical Neurophysiology Section, University of Siena, Siena, Italy
| | - Simone Rossi
- Department of Medicine, Surgery and Neuroscience, Brain Investigation & Neuromodulation Laboratory, University of Siena, Siena, Italy.,Department of Medicine, Surgery and Neuroscience, Neurology and Clinical Neurophysiology Section, University of Siena, Siena, Italy
| | - Alfonso Cerase
- Department of Medicine, Surgery and Neuroscience, Section of Neuroradiology, University of Siena, Siena, Italy
| | - Alessandra Renieri
- Department of Medicine, Surgery and Neuroscience, Section of Medical Genetics, University of Siena, Siena, Italy
| | - Maria A Mencarelli
- Department of Medicine, Surgery and Neuroscience, Section of Medical Genetics, University of Siena, Siena, Italy
| | - Federico Zara
- Laboratory of Neurogenetics and Neuroscience, Istituto Giannina Gaslini, Genoa, Italy
| | - Alessandro Rossi
- Department of Medicine, Surgery and Neuroscience, Brain Investigation & Neuromodulation Laboratory, University of Siena, Siena, Italy.,Department of Medicine, Surgery and Neuroscience, Neurology and Clinical Neurophysiology Section, University of Siena, Siena, Italy
| | - Emiliano Santarnecchi
- Department of Medicine, Surgery and Neuroscience, Brain Investigation & Neuromodulation Laboratory, University of Siena, Siena, Italy.,Department of Medicine, Surgery and Neuroscience, Neurology and Clinical Neurophysiology Section, University of Siena, Siena, Italy.,Department of Cognitive Neurology, Beth Israel Deaconess Medical Center, Berenson-Allen Center for Noninvasive Brain Stimulation, Harvard Medical School, Boston, MA, United States
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Coricovac D, Dehelean C, Moaca EA, Pinzaru I, Bratu T, Navolan D, Boruga O. Cutaneous Melanoma-A Long Road from Experimental Models to Clinical Outcome: A Review. Int J Mol Sci 2018; 19:E1566. [PMID: 29795011 DOI: 10.3390/ijms19061566] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 05/21/2018] [Accepted: 05/22/2018] [Indexed: 02/07/2023] Open
Abstract
Cutaneous melanoma is a complex disorder characterized by an elevated degree of heterogeneity, features that place it among the most aggressive types of cancer. Although significant progress was recorded in both the understanding of melanoma biology and genetics, and in therapeutic approaches, this malignancy still represents a major problem worldwide due to its high incidence and the lack of a curative treatment for advanced stages. This review offers a survey of the most recent information available regarding the melanoma epidemiology, etiology, and genetic profile. Also discussed was the topic of cutaneous melanoma murine models outlining the role of these models in understanding the molecular pathways involved in melanoma initiation, progression, and metastasis.
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Pérez-Alea M, Vivancos A, Caratú G, Matito J, Ferrer B, Hernandez-Losa J, Cortés J, Muñoz E, Garcia-Patos V, Recio JA. Genetic profile of GNAQ-mutated blue melanocytic neoplasms reveals mutations in genes linked to genomic instability and the PI3K pathway. Oncotarget 2018; 7:28086-95. [PMID: 27057633 PMCID: PMC5053711 DOI: 10.18632/oncotarget.8578] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 03/28/2016] [Indexed: 12/20/2022] Open
Abstract
Melanomas arising in association with a common or cellular blue nevus (MABN) comprise a relatively rare and heterogeneous group of lethal melanomas. Although GNAQ is known to be frequently mutated in common blue nevus, cellular blue nevus (CBN) and MABN and these malignant lesions present gross chromosome alterations harboring BAP1 mutations, little is known about other mutations that contribute to the development and progression of these neoplasms. Thus, the genetic profile of these tumors is important to increase the number of intervention and treatment modalities. Here, we characterized and genetically profiled two different sections of a rare MABN and two CBNs from three different patients. All of the samples harbored a GNAQ mutation, exhibited RAS pathway activation, and harbored additional mutations in genes associated with genomic instability and epigenetic regulation (KMT2C, FANCD2, ATR, ATRX, NBN, ERCC2, SETD2, and WHSC1). In addition, all neoplasms harbored mutations that directly or indirectly affected either the regulation or activation of the PI3K pathway (PIK3CA, NF1, INPP5B and GSK3B). Our results not only help understand the genetic complexity of these blue melanocytic lesions but provide a rationale to use the combination of PI3K/MTOR and MEK1/2 inhibitors against these types of tumors.
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Affiliation(s)
- Mileidys Pérez-Alea
- Biomedical Research in Melanoma-Animal Models and Cancer Laboratory, Oncology Program, Vall d'Hebron Research institute, VHIR-Vall d'Hebron Hospital, Barcelona-UAB 08035, Barcelona, Spain
| | - Ana Vivancos
- Cancer Genomics Group Translational Research Program, Vall d'Hebron Institute of Oncology-VHIO, Vall d'Hebron Hospital, Barcelona-UAB, Barcelona 08035, Spain
| | - Ginevra Caratú
- Cancer Genomics Group Translational Research Program, Vall d'Hebron Institute of Oncology-VHIO, Vall d'Hebron Hospital, Barcelona-UAB, Barcelona 08035, Spain
| | - Judit Matito
- Cancer Genomics Group Translational Research Program, Vall d'Hebron Institute of Oncology-VHIO, Vall d'Hebron Hospital, Barcelona-UAB, Barcelona 08035, Spain
| | - Berta Ferrer
- Biomedical Research in Melanoma-Animal Models and Cancer Laboratory, Oncology Program, Vall d'Hebron Research institute, VHIR-Vall d'Hebron Hospital, Barcelona-UAB 08035, Barcelona, Spain.,Anatomy Pathology Department, Vall d'Hebron Hospital, Barcelona-UAB, Barcelona 08035, Spain
| | - Javier Hernandez-Losa
- Anatomy Pathology Department, Vall d'Hebron Hospital, Barcelona-UAB, Barcelona 08035, Spain
| | - Javier Cortés
- Clinical Oncology Program, Vall d'Hebron Institute of Oncology-VHIO, Vall d'Hebron Hospital, Barcelona-UAB, Barcelona 08035, Spain
| | - Eva Muñoz
- Biomedical Research in Melanoma-Animal Models and Cancer Laboratory, Oncology Program, Vall d'Hebron Research institute, VHIR-Vall d'Hebron Hospital, Barcelona-UAB 08035, Barcelona, Spain.,Clinical Oncology Program, Vall d'Hebron Institute of Oncology-VHIO, Vall d'Hebron Hospital, Barcelona-UAB, Barcelona 08035, Spain
| | - Vicente Garcia-Patos
- Biomedical Research in Melanoma-Animal Models and Cancer Laboratory, Oncology Program, Vall d'Hebron Research institute, VHIR-Vall d'Hebron Hospital, Barcelona-UAB 08035, Barcelona, Spain.,Dermatology Department, Vall d'Hebron Hospital, Barcelona-UAB, Barcelona 08035, Spain
| | - Juan A Recio
- Biomedical Research in Melanoma-Animal Models and Cancer Laboratory, Oncology Program, Vall d'Hebron Research institute, VHIR-Vall d'Hebron Hospital, Barcelona-UAB 08035, Barcelona, Spain
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Shaik RS, Zhu X, Clements DR, Weston LA. Understanding invasion history and predicting invasive niches using genetic sequencing technology in Australia: case studies from Cucurbitaceae and Boraginaceae. Conserv Physiol 2016; 4:cow030. [PMID: 27766152 PMCID: PMC5069847 DOI: 10.1093/conphys/cow030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 06/20/2016] [Accepted: 06/27/2016] [Indexed: 05/07/2023]
Abstract
Part of the challenge in dealing with invasive plant species is that they seldom represent a uniform, static entity. Often, an accurate understanding of the history of plant introduction and knowledge of the real levels of genetic diversity present in species and populations of importance is lacking. Currently, the role of genetic diversity in promoting the successful establishment of invasive plants is not well defined. Genetic profiling of invasive plants should enhance our understanding of the dynamics of colonization in the invaded range. Recent advances in DNA sequencing technology have greatly facilitated the rapid and complete assessment of plant population genetics. Here, we apply our current understanding of the genetics and ecophysiology of plant invasions to recent work on Australian plant invaders from the Cucurbitaceae and Boraginaceae. The Cucurbitaceae study showed that both prickly paddy melon (Cucumis myriocarpus) and camel melon (Citrullus lanatus) were represented by only a single genotype in Australia, implying that each was probably introduced as a single introduction event. In contrast, a third invasive melon, Citrullus colocynthis, possessed a moderate level of genetic diversity in Australia and was potentially introduced to the continent at least twice. The Boraginaceae study demonstrated the value of comparing two similar congeneric species; one, Echium plantagineum, is highly invasive and genetically diverse, whereas the other, Echium vulgare, exhibits less genetic diversity and occupies a more limited ecological niche. Sequence analysis provided precise identification of invasive plant species, as well as information on genetic diversity and phylogeographic history. Improved sequencing technologies will continue to allow greater resolution of genetic relationships among invasive plant populations, thereby potentially improving our ability to predict the impact of these relationships upon future spread and better manage invaders possessing potentially diverse biotypes and exhibiting diverse breeding systems, life histories and invasion histories.
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Affiliation(s)
- Razia S. Shaik
- Graham Centre for Agricultural Innovation (Charles Sturt University and NSW Department of Primary Industries), Locked Bag 588, Wagga Wagga, NSW 2678, Australia
| | - Xiaocheng Zhu
- Graham Centre for Agricultural Innovation (Charles Sturt University and NSW Department of Primary Industries), Locked Bag 588, Wagga Wagga, NSW 2678, Australia
| | - David R. Clements
- Department of Biology, Trinity Western University, Langley, BC, CanadaV2Y 1Y1
| | - Leslie A. Weston
- Graham Centre for Agricultural Innovation (Charles Sturt University and NSW Department of Primary Industries), Locked Bag 588, Wagga Wagga, NSW 2678, Australia
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Brito AF, Abrantes AM, Ribeiro M, Oliveira R, Casalta-Lopes J, Gonçalves AC, Sarmento-Ribeiro AB, Tralhão JG, Botelho MF. Fluorine-18 Fluorodeoxyglucose Uptake in Hepatocellular Carcinoma: Correlation with Glucose Transporters and p53 Expression. J Clin Exp Hepatol 2015; 5:183-9. [PMID: 26628835 PMCID: PMC4632095 DOI: 10.1016/j.jceh.2015.05.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 05/25/2015] [Indexed: 02/07/2023] Open
Abstract
INTRODUCTION Hepatocellular Carcinoma (HCC) is one of most lethal cancers worldwide. The prognosis is very poor and therapeutic options are limited. The aim of this study was to determine the correlation of the [(18)F]FDG uptake profile of three HCC cell lines with p53 and glucose transporters (GLUTs) 1, 2, 3, 5 and 12 expression and with the glucose level present in the cell culture medium. METHODS Cell lines used are HepG2 (wp53), HuH7 (overexpress p53) and Hep3B2.1-7 (p53null). An immunocytochemical analysis was performed to evaluate p53 expression. Through uptake studies were analyzed the [(18)F]FDG uptake profiles of all cell lines under study. The expression of GLUTs were quantified by flow cytometry. The [(18)F]FDG uptake studies GLUTs expression analysis were performed on cells that grew in a high and low glucose medium in order to determine the effect of glucose concentration on GLUTs expression and on [(18)F]FDG uptake. RESULTS Immunocytochemical analysis confirmed the p53 expression profiles of all cell lines. It was found out that for all cell lines, [(18)F]FDG uptake is higher when cells grow in low glucose medium, however, the glucose level doesn't affect mostly the GLUTs expression. The Hep3B2.1-7 (p53null) is always the one that have higher [(18)F]FDG uptake. It was found that not always GLUT1 and GLUT3 are the most expressed by these cell lines. CONCLUSIONS Our results shown that the p53 expression influences [(18)F]FDG uptake. This suggests that [(18)F]FDG may be used in HCC diagnosis, and may even provide some information about the genetic profile of the tumor.
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Affiliation(s)
- Ana F. Brito
- Biophysics Unit, Faculty of Medicine of University of Coimbra, Coimbra, Portugal,Center of Investigation on Environmental, Genetics and Oncobiology (CIMAGO), Faculty of Medicine of University of Coimbra, Coimbra, Portugal,CNC.IBILI, University of Coimbra, Coimbra, Portugal,Address for correspondence: Ana F. Brito, Biophysics Unit, Faculty of Medicine of University of Coimbra, Pólo III – Pólo das Ciências da Saúde, Azinhaga de Santa Comba, Celas. 3000-548 Coimbra, Portugal. Tel.: +351 239480200; fax: +351 239480217.
| | - Ana M. Abrantes
- Biophysics Unit, Faculty of Medicine of University of Coimbra, Coimbra, Portugal,Center of Investigation on Environmental, Genetics and Oncobiology (CIMAGO), Faculty of Medicine of University of Coimbra, Coimbra, Portugal
| | - Marina Ribeiro
- Biophysics Unit, Faculty of Medicine of University of Coimbra, Coimbra, Portugal,Faculty of Sciences and Technology of University of Coimbra, Coimbra, Portugal
| | - Rui Oliveira
- Biophysics Unit, Faculty of Medicine of University of Coimbra, Coimbra, Portugal,Center of Investigation on Environmental, Genetics and Oncobiology (CIMAGO), Faculty of Medicine of University of Coimbra, Coimbra, Portugal,Anatomical Pathology Department, CHUC, Coimbra, Portugal
| | - João Casalta-Lopes
- Biophysics Unit, Faculty of Medicine of University of Coimbra, Coimbra, Portugal,Center of Investigation on Environmental, Genetics and Oncobiology (CIMAGO), Faculty of Medicine of University of Coimbra, Coimbra, Portugal
| | - Ana C. Gonçalves
- Center of Investigation on Environmental, Genetics and Oncobiology (CIMAGO), Faculty of Medicine of University of Coimbra, Coimbra, Portugal,CNC.IBILI, University of Coimbra, Coimbra, Portugal,Applied Molecular Biology and Hematology Group, Faculty of Medicine of University of Coimbra, Coimbra, Portugal
| | - Ana B. Sarmento-Ribeiro
- Center of Investigation on Environmental, Genetics and Oncobiology (CIMAGO), Faculty of Medicine of University of Coimbra, Coimbra, Portugal,CNC.IBILI, University of Coimbra, Coimbra, Portugal,Applied Molecular Biology and Hematology Group, Faculty of Medicine of University of Coimbra, Coimbra, Portugal
| | - José G. Tralhão
- Biophysics Unit, Faculty of Medicine of University of Coimbra, Coimbra, Portugal,Center of Investigation on Environmental, Genetics and Oncobiology (CIMAGO), Faculty of Medicine of University of Coimbra, Coimbra, Portugal,Surgical Department A, CHUC, Coimbra, Portugal
| | - Maria F. Botelho
- Biophysics Unit, Faculty of Medicine of University of Coimbra, Coimbra, Portugal,Center of Investigation on Environmental, Genetics and Oncobiology (CIMAGO), Faculty of Medicine of University of Coimbra, Coimbra, Portugal,CNC.IBILI, University of Coimbra, Coimbra, Portugal
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47
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Abstract
Bone repair following a fracture is a complex, well orchestrated, physiological process in response to injury. Even though the exact number of the genes and expressed proteins involved in fracture healing remains unknown, the molecular complexity of the repair process has been demonstrated, and it involves numerous genes and molecules, such as extracellular matrix genes, growth and differentiation factors, matrix metalloproteinases, angiogenic factors and others. Discrepancies in fracture healing responses and final outcome seen in the clinical practice may be attributed among other factors to biological variations between patients and different genetic "profiles", resulting in "altered" signalling pathways that regulate the bone repair process. Preliminary human studies support a "genetic" component in the pathophysiology of impaired bone repair seen in atrophic non-unions by correlating genetic variations of specific molecules regulating fracture healing with non-union. However, the role of the genetic "profile" of each individual in fracture healing and final outcome, and its possible interaction with other exogenous factors remains a topic of extensive research.
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Affiliation(s)
- Rozalia Dimitriou
- Academic Department of Trauma and Orthopaedics, Leeds General Infirmary, Leeds, UK
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48
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Abstract
Research integrating neuroimaging and molecular genetics has yielded important insights into how variability in brain chemistry predicts individual differences in brain function, behavior and related risk for psychopathology. However, existing studies have been limited by their focus on the independent effects of single polymorphisms with modest impact on brain chemistry. Here, we explored the effects of five functional polymorphisms affecting dopamine (DA) signaling on reward-related ventral striatum (VS) reactivity, measured with BOLD fMRI, in a sample of 69 Caucasians. We also compiled individual multilocus genetic profile scores reflecting the additive effects of alleles conferring relatively increased DA signaling across the five polymorphic loci: DAT1 9-repeat, DRD4 7-repeat, DRD2 -141C Del, DRD2 Taq1A C (A2), and COMT (158)Met. These multilocus DA profile scores accounted for 10.9% of the inter-individual variability in reward-related VS reactivity. In contrast, none of the individual polymorphisms accounted for significant variability. Our results show that biologically informed multilocus genetic profiles have unique promise as indices of variability in brain chemistry that may yield advances in mapping individual differences in behaviorally relevant brain function. In turn, such genetic profiles may fuel gene-environment interactions research establishing trajectories of risk for psychopathology.
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Affiliation(s)
- Yuliya S Nikolova
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
| | - Robert E Ferrell
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Stephen B Manuck
- Department of Psychology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ahmad R Hariri
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA,Institute for Genome Sciences and Policy, Duke University, Durham, NC, USA,Department of Psychology and Neuroscience, Box 90086, 417 Chapel Drive, Durham, NC 27708-0086, USA. Tel: +1 91 9681 1039; Fax: +1 91 9660 5726; E-mail:
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49
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Cardoso S, Valverde L, Odriozola A, Elcoroaristizabal X, de Pancorbo MM. Quality standards in Biobanking: authentication by genetic profiling of blood spots from donor's original sample. Eur J Hum Genet 2010; 18:848-51. [PMID: 20234395 PMCID: PMC2987351 DOI: 10.1038/ejhg.2010.16] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Revised: 12/22/2009] [Accepted: 01/08/2010] [Indexed: 11/09/2022] Open
Abstract
The field of Biobanking requires extensive work to maintain traceability of samples. However, sometimes the necessity to authenticate a sample may arise. To address these circumstances, we herein present a method for authenticating derivatives by using a blood spot from each donor, attached to a sample authentication form, by means of genetic profiling. Blood spots are collected at the time a blood sample is donated at a health centre and before processing the blood sample at the biobank. To test the validity of our approach over time, we analyzed 26 blood spots stored at room temperature in our facilities for more than 15 years. DNA was successfully extracted from the three storage materials tested in this study and 15 STR markers plus amelogenin were subsequently analyzed. The storage of a small blood spot attached to a sample authentication form proved to be efficient for genetic profiling and, therefore, may constitute a long-lasting (at least 15 years), cost-effective and effortless approach for genetic authentication of samples in biobanks.
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Affiliation(s)
- Sergio Cardoso
- BIOMICs Research Group, Centro de Investigación y Estudios Avanzados ‘Lucio Lascaray', University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Laura Valverde
- BIOMICs Research Group, Centro de Investigación y Estudios Avanzados ‘Lucio Lascaray', University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Adrian Odriozola
- BIOMICs Research Group, Centro de Investigación y Estudios Avanzados ‘Lucio Lascaray', University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Xabier Elcoroaristizabal
- BIOMICs Research Group, Centro de Investigación y Estudios Avanzados ‘Lucio Lascaray', University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Marian M de Pancorbo
- BIOMICs Research Group, Centro de Investigación y Estudios Avanzados ‘Lucio Lascaray', University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
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Vanhoutte K, de Asmundis C, Francesconi A, Figysl J, Steurs G, Boussy T, Roos M, Mueller A, Massimo L, Paparella G, Van Caelenberg K, Chierchia GB, Sarkozy A, Terradellas PBY, Zizi M. Leaving out control groups: an internal contrast analysis of gene expression profiles in atrial fibrillation patients--a systems biology approach to clinical categorization. Bioinformation 2009; 3:275-8. [PMID: 19255648 PMCID: PMC2649423 DOI: 10.6026/97320630003275] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2008] [Accepted: 09/14/2008] [Indexed: 12/25/2022] Open
Abstract
Atrial fibrillation (AF) is a frequent chronic dysrythmia with an incidence that increases with age (>40). Because of its medical and socio-economic impacts it is expected to become an increasing burden on most health care systems. AF is a multi-factorial disease for which the identification of subtypes is warranted. Novel approaches based on the broad concepts of systems biology may overcome the blurred notion of normal and pathological phenotype, which is inherent to high throughput molecular arrays analysis. Here we apply an internal contrast algorithm on AF patient data with an analytical focus on potential entry pathways into the disease. We used a RMA (Robust Multichip Average) normalized Affymetrix micro-array data set from 10 AF patients (geo_accession #GSE2240). Four series of probes were selected based on physiopathogenic links with AF entryways: apoptosis (remodeling), MAP kinase (cell remodeling), OXPHOS (ability to sustain hemodynamic workload) and glycolysis (ischemia). Annotated probe lists were polled with Bioconductor packages in R (version 2.7.1). Genetic profile contrasts were analysed with hierarchical clustering and principal component analysis. The analysis revealed distinct patient groups for all probe sets. A substantial part (54% till 67%) of the variance is explained in the first 2 principal components. Genes in PC1/2 with high discriminatory value were selected and analyzed in detail. We aim for reliable molecular stratification of AF. We show that stratification is possible based on physiologically relevant gene sets. Genes with high contrast value are likely to give pathophysiological insight into permanent AF subtypes.
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Affiliation(s)
- Kurt Vanhoutte
- Faculty of Medicine and Pharmacy, Dept of Physiology, Vrije Universiteit Brussel.
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