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Abondio P, Bruno F, Passarino G, Montesanto A, Luiselli D. Pangenomics: A new era in the field of neurodegenerative diseases. Ageing Res Rev 2024; 94:102180. [PMID: 38163518 DOI: 10.1016/j.arr.2023.102180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/14/2023] [Accepted: 12/28/2023] [Indexed: 01/03/2024]
Abstract
A pangenome is composed of all the genetic variability of a group of individuals, and its application to the study of neurodegenerative diseases may provide valuable insights into the underlying aspects of genetic heterogenetiy for these complex ailments, including gene expression, epigenetics, and translation mechanisms. Furthermore, a reference pangenome allows for the identification of previously undetected structural commonalities and differences among individuals, which may help in the diagnosis of a disease, support the prediction of what will happen over time (prognosis) and aid in developing novel treatments in the perspective of personalized medicine. Therefore, in the present review, the application of the pangenome concept to the study of neurodegenerative diseases will be discussed and analyzed for its potential to enable an improvement in diagnosis and prognosis for these illnesses, leading to the development of tailored treatments for individual patients from the knowledge of the genomic composition of a whole population.
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Affiliation(s)
- Paolo Abondio
- Laboratory of Ancient DNA, Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121 Ravenna, Italy.
| | - Francesco Bruno
- Academy of Cognitive Behavioral Sciences of Calabria (ASCoC), Lamezia Terme, Italy; Regional Neurogenetic Centre (CRN), Department of Primary Care, Azienda Sanitaria Provinciale Di Catanzaro, Viale A. Perugini, 88046 Lamezia Terme, CZ, Italy; Association for Neurogenetic Research (ARN), Lamezia Terme, CZ, Italy
| | - Giuseppe Passarino
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende 87036, Italy
| | - Alberto Montesanto
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende 87036, Italy
| | - Donata Luiselli
- Laboratory of Ancient DNA, Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121 Ravenna, Italy
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2
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de Sousa MSA, Nunes IN, Christiano YP, Sisdelli L, Cerutti JM. Genetic alterations landscape in paediatric thyroid tumours and/or differentiated thyroid cancer: Systematic review. Rev Endocr Metab Disord 2024; 25:35-51. [PMID: 37874477 DOI: 10.1007/s11154-023-09840-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/27/2023] [Indexed: 10/25/2023]
Abstract
Differentiated thyroid cancer (DTC) is a rare disease in the paediatric population (≤ 18 years old. at diagnosis). Increasing incidence is reflected by increases in incidence for papillary thyroid carcinoma (PTC) subtypes. Compared to those of adults, despite aggressive presentation, paediatric DTC has an excellent prognosis. As for adult DTC, European and American guidelines recommend individualised management, based on the differences in clinical presentation and genetic findings. Therefore, we conducted a systematic review to identify the epidemiological landscape of all genetic alterations so far investigated in paediatric populations at diagnosis affected by thyroid tumours and/or DTC that have improved and/or informed preventive and/or curative diagnostic and prognostic clinical conduct globally. Fusions involving the gene RET followed by NTRK, ALK and BRAF, were the most prevalent rearrangements found in paediatric PTC. BRAF V600E was found at lower prevalence in paediatric (especially ≤ 10 years old) than in adults PTC. We identified TERT and RAS mutations at very low prevalence in most countries. DICER1 SNVs, while found at higher prevalence in few countries, they were found in both benign and DTC. Although the precise role of DICER1 is not fully understood, it has been hypothesised that additional genetic alterations, similar to that observed for RAS gene, might be required for the malignant transformation of these nodules. Regarding aggressiveness, fusion oncogenes may have a higher growth impact compared with BRAF V600E. We reported the shortcomings of the systematized research and outlined three key recommendations for global authors to improve and inform precision health approaches, glocally.
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Affiliation(s)
- Maria Sharmila Alina de Sousa
- Genetic Bases of Thyroid Tumours Laboratory, Division of Genetics, Department of Morphology and Genetics and Division of Endocrinology, Department of Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Pedro de Toledo 669, 11 andar, São Paulo, SP, 04039-032, Brazil
| | - Isabela Nogueira Nunes
- Genetic Bases of Thyroid Tumours Laboratory, Division of Genetics, Department of Morphology and Genetics and Division of Endocrinology, Department of Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Pedro de Toledo 669, 11 andar, São Paulo, SP, 04039-032, Brazil
| | - Yasmin Paz Christiano
- Genetic Bases of Thyroid Tumours Laboratory, Division of Genetics, Department of Morphology and Genetics and Division of Endocrinology, Department of Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Pedro de Toledo 669, 11 andar, São Paulo, SP, 04039-032, Brazil
| | - Luiza Sisdelli
- Genetic Bases of Thyroid Tumours Laboratory, Division of Genetics, Department of Morphology and Genetics and Division of Endocrinology, Department of Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Pedro de Toledo 669, 11 andar, São Paulo, SP, 04039-032, Brazil
- PreScouter Inc., 29 E Madison St #500, Chicago, IL, 60602, USA
| | - Janete Maria Cerutti
- Genetic Bases of Thyroid Tumours Laboratory, Division of Genetics, Department of Morphology and Genetics and Division of Endocrinology, Department of Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Pedro de Toledo 669, 11 andar, São Paulo, SP, 04039-032, Brazil.
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Luo G, Zhang L, Wu W, Zhang L, Lin J, Shi H, Wu X, Yu Y, Qiu W, Chen J, Ding H, Chen X. Upregulation of ubiquitin carboxy‑terminal hydrolase 47 (USP47) in papillary thyroid carcinoma ex vivo and reduction of tumor cell malignant behaviors after USP47 knockdown by stabilizing SATB1 expression in vitro. Oncol Lett 2023; 26:370. [PMID: 37564825 PMCID: PMC10410197 DOI: 10.3892/ol.2023.13956] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 06/19/2023] [Indexed: 08/12/2023] Open
Abstract
Aberrant ubiquitination contributes to cancer development, including thyroid carcinoma. The present study assessed the expression of ubiquitin carboxy-terminal hydrolase 47 (USP47) and underlying molecular events in the development of papillary thyroid carcinoma (PTC). The effects of USP47 on PTC cell invasion and migration were analyzed by Transwell assays, while. the effects of USP47 and SATB1on PTC cell gene expression and changes in tumor cell metabolism were assayed by reverse transcription-quantitative PCR, western bolt, or ELISA, respectively. The expression of USP47 mRNA and protein was upregulated in PTC tissue and associated with the PTC tumor size. Knockdown of USP47 expression in PTC cell lines (TPC-1 and K1), decreased the cell proliferation mobility and invasion capacities, whereas USP47 overexpression in these cell lines showed an inverse effect and promoted cell glycolysis and glutamine metabolism. Moreover, expression of special AT-rich sequence-binding protein-1 (SATB1) was high in PTC tissue and was associated with USP47 expression. SATB1 expression promoted tumor cell glycolysis and glutamine metabolism, while USP47 protein bound to and deubiquitinated SATB1 to increase its intracellular levels, thus promoting glycolysis and glutamine metabolism. USP47 promotion of PTC development may be due to its stabilization of SATB1 protein, suggesting that targeting the USP47/SATB1 signaling axis may serve as a therapeutic intervention for PTC.
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Affiliation(s)
- Guirong Luo
- Department of Thyroid and Breast Surgery, The Second Affiliated Clinical School of Medicine, Fujian Medical University, Quanzhou, Fujian 362000, P.R. China
| | - Liting Zhang
- Department of Endocrinology, The Number 910 Hospital, The Joint Logistics Support Force, Quanzhou, Fujian 362000, P.R. China
| | - Wenyi Wu
- Department of Thyroid and Breast Surgery, The Second Affiliated Clinical School of Medicine, Fujian Medical University, Quanzhou, Fujian 362000, P.R. China
| | - Lihong Zhang
- Jinshang Town Health Center, Shishi, Fujian 362000, P.R. China
| | - Jianqing Lin
- Department of Thyroid and Breast Surgery, The Second Affiliated Clinical School of Medicine, Fujian Medical University, Quanzhou, Fujian 362000, P.R. China
| | - Haihong Shi
- Department of Thyroid and Breast Surgery, The Second Affiliated Clinical School of Medicine, Fujian Medical University, Quanzhou, Fujian 362000, P.R. China
| | - Xinquan Wu
- Department of Thyroid and Breast Surgery, The Second Affiliated Clinical School of Medicine, Fujian Medical University, Quanzhou, Fujian 362000, P.R. China
| | - Yihuang Yu
- Department of Thyroid and Breast Surgery, The Second Affiliated Clinical School of Medicine, Fujian Medical University, Quanzhou, Fujian 362000, P.R. China
| | - Weigang Qiu
- Department of Thyroid and Breast Surgery, The Second Affiliated Clinical School of Medicine, Fujian Medical University, Quanzhou, Fujian 362000, P.R. China
| | - Jinyan Chen
- Department of Thyroid and Breast Surgery, The Second Affiliated Clinical School of Medicine, Fujian Medical University, Quanzhou, Fujian 362000, P.R. China
| | - Hansen Ding
- Department of Thyroid and Breast Surgery, The Second Affiliated Clinical School of Medicine, Fujian Medical University, Quanzhou, Fujian 362000, P.R. China
| | - Xinyao Chen
- Department of Thyroid and Breast Surgery, The Second Affiliated Clinical School of Medicine, Fujian Medical University, Quanzhou, Fujian 362000, P.R. China
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Abondio P, Cilli E, Luiselli D. Human Pangenomics: Promises and Challenges of a Distributed Genomic Reference. Life (Basel) 2023; 13:1360. [PMID: 37374141 DOI: 10.3390/life13061360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/02/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
A pangenome is a collection of the common and unique genomes that are present in a given species. It combines the genetic information of all the genomes sampled, resulting in a large and diverse range of genetic material. Pangenomic analysis offers several advantages compared to traditional genomic research. For example, a pangenome is not bound by the physical constraints of a single genome, so it can capture more genetic variability. Thanks to the introduction of the concept of pangenome, it is possible to use exceedingly detailed sequence data to study the evolutionary history of two different species, or how populations within a species differ genetically. In the wake of the Human Pangenome Project, this review aims at discussing the advantages of the pangenome around human genetic variation, which are then framed around how pangenomic data can inform population genetics, phylogenetics, and public health policy by providing insights into the genetic basis of diseases or determining personalized treatments, targeting the specific genetic profile of an individual. Moreover, technical limitations, ethical concerns, and legal considerations are discussed.
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Affiliation(s)
- Paolo Abondio
- Laboratory of Ancient DNA, Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121 Ravenna, Italy
| | - Elisabetta Cilli
- Laboratory of Ancient DNA, Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121 Ravenna, Italy
| | - Donata Luiselli
- Laboratory of Ancient DNA, Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121 Ravenna, Italy
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Kotanidou EP, Giza S, Tsinopoulou VR, Margaritis K, Papadopoulou A, Sakellari E, Kolanis S, Litou E, Serbis A, Galli-Tsinopoulou A. The Prognostic Significance of BRAF Gene Analysis in Children and Adolescents with Papillary Thyroid Carcinoma: A Systematic Review and Meta-Analysis. Diagnostics (Basel) 2023; 13:diagnostics13061187. [PMID: 36980495 PMCID: PMC10047331 DOI: 10.3390/diagnostics13061187] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/08/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Thyroid cancer represents the prominent endocrine cancer in children. Papillary thyroid cancer (PTC) constitutes its most frequent (>90%) pediatric histological type. Mutations energizing the mitogen-activated-protein kinase (MAPK) pathway are definitely related to PTC. Its most common genetic alteration is in proto-oncogene B-Raf (BRAF). Mutated BRAF is proposed as a prognostic tool in adult PTC. We conducted a systematic review and meta-analysis evaluating the association of mutated BRAF gene and prognostic clinicopathological characteristics of PTC in children/adolescents. Systematic search for relevant studies included PubMed, MEDLINE, Scopus, clinicaltrials.gov and Cochrane Library. Pooled estimates of odds ratios for categorical data and mean difference for continuous outcomes were calculated using random/fixed-effect meta-analytic models. BRAFV600E mutation presents a pooled pediatric/adolescent prevalence of 33.12%. Distant metastasis is significantly associated with mutated BRAF gene (OR = 0.32, 95% CI = 0.16-0.61, p = 0.001). Tumor size (MD = -0.24, 95% CI = -0.62-0.135, p = 0.21), multifocality (OR = 1.13, 95% CI = 0.65-2.34, p = 0.74), vascular invasion (OR = 1.17, 95% CI = 0.67-2.05, p = 0.57), lymph node metastasis (OR = 0.92, 95% CI = 0.63-1.33, p = 0.66), extra-thyroid extension (OR = 0.78, 95% CI = 0.53-1.13, p = 0.19) and tumor recurrence (OR = 1.66, 95% CI = 0.68-4.21, p = 0.376) presented no association or risk with BRAF mutation among pediatric/adolescent PTC. Mutated BRAF gene in children and adolescents is less common than in adults. Mutation in BRAF relates significantly to distant metastasis among children/adolescents with PTC.
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Affiliation(s)
- Eleni P Kotanidou
- Unit of Pediatric Endocrinology and Metabolism, 2nd Department of Pediatrics, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, AHEPA University Hospital, Stilponos Kyriakidi 1, 54636 Thessaloniki, Greece
| | - Styliani Giza
- Unit of Pediatric Endocrinology and Metabolism, 2nd Department of Pediatrics, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, AHEPA University Hospital, Stilponos Kyriakidi 1, 54636 Thessaloniki, Greece
| | - Vasiliki Rengina Tsinopoulou
- Unit of Pediatric Endocrinology and Metabolism, 2nd Department of Pediatrics, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, AHEPA University Hospital, Stilponos Kyriakidi 1, 54636 Thessaloniki, Greece
| | - Kosmas Margaritis
- Unit of Pediatric Endocrinology and Metabolism, 2nd Department of Pediatrics, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, AHEPA University Hospital, Stilponos Kyriakidi 1, 54636 Thessaloniki, Greece
| | - Anastasia Papadopoulou
- Unit of Pediatric Endocrinology and Metabolism, 2nd Department of Pediatrics, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, AHEPA University Hospital, Stilponos Kyriakidi 1, 54636 Thessaloniki, Greece
| | - Eleni Sakellari
- Unit of Pediatric Endocrinology and Metabolism, 2nd Department of Pediatrics, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, AHEPA University Hospital, Stilponos Kyriakidi 1, 54636 Thessaloniki, Greece
| | - Savvas Kolanis
- Unit of Pediatric Endocrinology and Metabolism, 2nd Department of Pediatrics, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, AHEPA University Hospital, Stilponos Kyriakidi 1, 54636 Thessaloniki, Greece
| | - Eleni Litou
- Unit of Pediatric Endocrinology and Metabolism, 2nd Department of Pediatrics, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, AHEPA University Hospital, Stilponos Kyriakidi 1, 54636 Thessaloniki, Greece
| | - Anastasios Serbis
- Department of Pediatrics, School of Medicine, Faculty of Health Sciences, University of Ioannina, 45500 Ioannina, Greece
| | - Assimina Galli-Tsinopoulou
- Unit of Pediatric Endocrinology and Metabolism, 2nd Department of Pediatrics, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, AHEPA University Hospital, Stilponos Kyriakidi 1, 54636 Thessaloniki, Greece
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CHEK2 Alterations in Pediatric Malignancy: A Single-Institution Experience. Cancers (Basel) 2023; 15:cancers15061649. [PMID: 36980535 PMCID: PMC10046043 DOI: 10.3390/cancers15061649] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/03/2023] [Indexed: 03/11/2023] Open
Abstract
Background: Approximately 10% of pediatric malignancies are secondary to germline alterations in cancer-predisposing genes. Checkpoint kinase 2 (CHEK2) germline loss-of-function variants have been reported in pediatric cancer patients, but clinical phenotypes and outcomes are poorly described. We present our single-institution experience of pediatric oncology patients with CHEK2 germline alterations, including clinical presentations and outcomes. Methods: Pediatric oncology patients with CHEK2 germline alterations were identified among those assessed by clinical or translational research at the Institute for Genomic Medicine at Nationwide Children’s Hospital. A chart review of disease course was conducted on identified patients. Results: We identified 6 patients with germline CHEK2 variants from a cohort of 300 individuals, including 1 patient with concurrent presentation of Burkitt lymphoma and neuroblastoma, 3 patients with brain tumors, 1 patient with Ewing sarcoma, and 1 patient with myelodysplastic syndrome. Three patients had a family history of malignancies. Four patients were in remission; one was undergoing treatment; one patient had developed treatment-related meningiomas. We review prior data regarding CHEK2 variants in this population, challenges associated with variant interpretation, and genetic counseling for individuals with CHEK2 variants. Conclusions: CHEK2 germline loss-of-function alterations occur in patients with a variety of pediatric tumors. Larger multicenter studies will improve our understanding of the incidence, phenotype, and molecular biology of CHEK2 germline variants in pediatric cancers.
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Lebbink CA, Links TP, Czarniecka A, Dias RP, Elisei R, Izatt L, Krude H, Lorenz K, Luster M, Newbold K, Piccardo A, Sobrinho-Simões M, Takano T, Paul van Trotsenburg AS, Verburg FA, van Santen HM. 2022 European Thyroid Association Guidelines for the management of pediatric thyroid nodules and differentiated thyroid carcinoma. Eur Thyroid J 2022; 11:e220146. [PMID: 36228315 PMCID: PMC9716393 DOI: 10.1530/etj-22-0146] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 10/13/2022] [Indexed: 11/08/2022] Open
Abstract
At present, no European recommendations for the management of pediatric thyroid nodules and differentiated thyroid carcinoma (DTC) exist. Differences in clinical, molecular, and pathological characteristics between pediatric and adult DTC emphasize the need for specific recommendations for the pediatric population. An expert panel was instituted by the executive committee of the European Thyroid Association including an international community of experts from a variety of disciplines including pediatric and adult endocrinology, pathology, endocrine surgery, nuclear medicine, clinical genetics, and oncology. The 2015 American Thyroid Association Pediatric Guideline was used as framework for the present guideline. Areas of discordance were identified, and clinical questions were formulated. The expert panel members discussed the evidence and formulated recommendations based on the latest evidence and expert opinion. Children with a thyroid nodule or DTC require expert care in an experienced center. The present guideline provides guidance for healthcare professionals to make well-considered decisions together with patients and parents regarding diagnosis, treatment, and follow-up of pediatric thyroid nodules and DTC.
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Affiliation(s)
- Chantal A Lebbink
- Wilhelmina Children’s Hospital and Princess Máxima Center, Utrecht, The Netherlands
| | - Thera P Links
- Department of Endocrinology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Agnieszka Czarniecka
- The Oncologic and Reconstructive Surgery Clinic, M. Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, Gliwice, Poland
| | - Renuka P Dias
- Department of Paediatric Endocrinology and Diabetes, Birmingham Children's Hospital NHS Foundation Trust, Birmingham, United Kingdom
| | - Rossella Elisei
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Louise Izatt
- Department of Clinical Genetics, Guy's and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Heiko Krude
- Institute of Experimental Pediatric Endocrinology, Charité - Universitätsmedizin, Berlin, Germany
| | - Kerstin Lorenz
- Department of Visceral, Vascular and Endocrine Surgery, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Markus Luster
- Department of Nuclear Medicine, University Hospital Marburg, Marburg, Germany
| | - Kate Newbold
- Thyroid Therapy Unit, The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Arnoldo Piccardo
- Department of Nuclear Medicine, EO Ospedali Galliera, Genoa, Italy
| | - Manuel Sobrinho-Simões
- University Hospital of São João, Medical Faculty and Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Toru Takano
- Thyroid Center, Rinku General Medical Center, Osaka, Japan
| | - A S Paul van Trotsenburg
- Department of Pediatric Endocrinology, Emma Children's Hospital, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Frederik A Verburg
- Department of Radiology and Nuclear Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Hanneke M van Santen
- Wilhelmina Children’s Hospital and Princess Máxima Center, Utrecht, The Netherlands
- Correspondence should be addressed to H M van Santen;
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Ge W, Ma J, Mao T, Xu H, Zhang X, Li S, Wang Y, Yao J, Yue M, Jiao F, Wang Y, Zhuo M, Han T, Hu J, Zhang X, Cui J, Wang L. Distinguishable Prognostic Signatures and Tumor Immunogenicity Between Pancreatic Head Cancer and Pancreatic Body/Tail Cancer. Front Oncol 2022; 12:890715. [PMID: 35756644 PMCID: PMC9213676 DOI: 10.3389/fonc.2022.890715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 05/09/2022] [Indexed: 11/13/2022] Open
Abstract
Background Pancreatic head cancer and pancreatic body/tail cancer are considered to have different clinical presentations and to have altered outcomes. Methods Ninety cases of pancreatic adenocarcinoma (PDAC) from our institution were used as a discovery set and 166 cases of PDAC from the TCGA cohort were used as a validation set. According to the anatomical location, the cases of PDAC were divided into the pancreatic head cancer group and the pancreatic body/tail cancer group. Firstly, the different biological functions of the two groups were assessed by ssGSEA. Meanwhile, ESTIMATE and CIBERSORT were conducted to estimate immune infiltration. Then, a novel anatomical site-related risk score (SRS) model was constructed by LASSO and Cox regression. Survival and time-dependent ROC analysis was used to prove the predictive ability of our model in two cohorts. Subsequently, an integrated survival decision tree and a scoring nomogram were constructed to improve prognostic stratification and predictive accuracy for individual patients. In addition, gseaGO and gseaKEGG pathway analyses were performed on genes in the key module by the R package. Results Overall survival and the objective response rate (ORR) of patients with pancreatic body/tail cancer were markedly superior to those with pancreatic head cancer. In addition, distinct immune characteristics and gene patterns were observed between the two groups. Then, we screened 5 biomarkers related to the prognosis of pancreatic cancer and constructed a more powerful novel SRS model to predict prognosis. Conclusions Our research shed some light on the revelation of gene patterns, immune and mutational landscape characterizations, and their relationships in different PDAC locations.
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Affiliation(s)
- Weiyu Ge
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Department of Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jingyu Ma
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Department of Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Tiebo Mao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Department of Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Haiyan Xu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Department of Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaofei Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Department of Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shumin Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Department of Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yongchao Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Department of Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jiayu Yao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Department of Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ming Yue
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Department of Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Feng Jiao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Department of Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Department of Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Meng Zhuo
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Department of Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ting Han
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Department of Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jiong Hu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Department of Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiao Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Department of Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jiujie Cui
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Department of Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Liwei Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Department of Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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9
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Jin A, Zhou J, Yu P, Zhou S, Chang C. High Expression of THBS1 Leads to a Poor Prognosis in Papillary Thyroid Cancer and Suppresses the Anti-Tumor Immune Microenvironment. Technol Cancer Res Treat 2022; 21:15330338221085360. [PMID: 35315710 PMCID: PMC8943644 DOI: 10.1177/15330338221085360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Objectives: To study the role of thrombospondin-1 (THBS1) in
papillary thyroid cancer (PTC) prognosis and the immune microenvironment.
Methods: A retrospective cohort study was designed, and data
from The Cancer Genome Atlas database and PTC tissues from Fudan University
Shanghai Cancer Center were used. Weighted gene co-expression network analysis
was performed to build a THBS1-immune-related gene prognostic
index (T-I index). Results: High THBS1 expression
was correlated with advanced TNM stage, higher recurrence risk, and shorter
progression-free interval. High THBS1 expression correlated
with MAPK and PD1 pathways indicating a tumor promoting and immunity-inhibiting
tendency. The T-I index showed a powerful capacity to predict progression-free
survival and immunotherapy benefit. Conclusion: High expression of
THBS1 leads to a poor prognosis in PTCs and suppresses the
anti-tumor immune microenvironment.
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Affiliation(s)
- Anqi Jin
- 89667Fudan University Shanghai Cancer Center, Shanghai, China
| | - Jin Zhou
- 89667Fudan University Shanghai Cancer Center, Shanghai, China
| | - Pengcheng Yu
- 89667Fudan University Shanghai Cancer Center, Shanghai, China
| | - Shichong Zhou
- 89667Fudan University Shanghai Cancer Center, Shanghai, China
| | - Cai Chang
- 89667Fudan University Shanghai Cancer Center, Shanghai, China
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10
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Hescheler DA, Riemann B, Hartmann MJM, Michel M, Faust M, Bruns CJ, Alakus H, Chiapponi C. Targeted Therapy of Papillary Thyroid Cancer: A Comprehensive Genomic Analysis. Front Endocrinol (Lausanne) 2021; 12:748941. [PMID: 34630336 PMCID: PMC8498581 DOI: 10.3389/fendo.2021.748941] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 08/27/2021] [Indexed: 12/15/2022] Open
Abstract
Background A limited number of targeted therapy options exist for papillary thyroid cancer (PTC) to date. Based on genetic alterations reported by the "The Cancer Genome Atlas (TCGA)", we explored whether PTC shows alterations that may be targetable by drugs approved by the FDA for other solid cancers. Methods Databases of the National Cancer Institute and MyCancerGenome were screened to identify FDA-approved drugs for targeted therapy. Target genes were identified using Drugbank. Genetic alterations were classified into conferring drug sensitivity or resistance using MyCancerGenome, CiViC, TARGET, and OncoKB. Genomic data for PTC were extracted from TCGA and mined for alterations predicting drug response. Results A total of 129 FDA-approved drugs with 128 targetable genes were identified. One hundred ninety-six (70%) of 282 classic, 21 (25%) of 84 follicular, and all 30 tall-cell variant PTCs harbored druggable alterations: 259 occurred in 29, 39 in 19, and 31 in 2 targetable genes, respectively. The BRAF V600 mutation was seen in 68% of classic, 16% of follicular variant, and 93% of tall-cell variant PTCs. The RET gene fusion was seen in 8% of classic PTCs, NTRK1 and 3 gene fusions in 3%, and other alterations in <2% of classic variant PTCs. Ninety-nine of 128 (77%) FDA-approved targetable genes did not show any genetic alteration in PTC. Beside selective and non-selective BRAF-inhibitors, no other FDA-approved drug showed any frequent predicted drug sensitivity (<10%). Conclusion Treatment strategies need to focus on resistance mechanisms to BRAF inhibition and on genetic alteration-independent alternatives rather than on current targeted drugs.
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Affiliation(s)
- Daniel A. Hescheler
- Department of Nuclear Medicine, University Hospital Münster, Münster, Germany
- European Institute for Molecular Imaging (EIMI), University of Münster, Münster, Germany
| | - Burkhard Riemann
- Department of Nuclear Medicine, University Hospital Münster, Münster, Germany
| | - Milan J. M. Hartmann
- Department of General, Visceral, Tumor and Transplant Surgery, University Hospital Cologne, Cologne, Germany
| | - Maximilian Michel
- Institute of Zoology, University of Cologne Germany, Cologne, Germany
| | - Michael Faust
- Policlinic for Prevention, Diabetes and Endocrinology, University of Cologne, Cologne, Germany
| | - Christiane J. Bruns
- Department of General, Visceral, Tumor and Transplant Surgery, University Hospital Cologne, Cologne, Germany
| | - Hakan Alakus
- Department of General, Visceral, Tumor and Transplant Surgery, University Hospital Cologne, Cologne, Germany
| | - Costanza Chiapponi
- Department of General, Visceral, Tumor and Transplant Surgery, University Hospital Cologne, Cologne, Germany
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11
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Sun J, Shi R, Zhang X, Fang D, Rauch J, Lu S, Wang X, Käsmann L, Ma J, Belka C, Su C, Li M. Characterization of immune landscape in papillary thyroid cancer reveals distinct tumor immunogenicity and implications for immunotherapy. Oncoimmunology 2021; 10:e1964189. [PMID: 34513318 PMCID: PMC8425706 DOI: 10.1080/2162402x.2021.1964189] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Although the vast majority of patients with papillary thyroid cancer (PTC) have a favorable prognosis when conventional treatments are implemented, local recurrence and distant metastasis of advanced PTCs still hamper the survival and clinical management in certain patients. As immune checkpoint blockade (ICB) therapy achieves a great success in some advanced cancers, we aimed to investigate the immune landscape in PTC and its potential implications for prognosis and immunotherapy. In this study, different algorithms were conducted to estimate immune infiltration in PTC samples. A series of bioinformatic and machine learning approaches were performed to identify PTC-specific immune-related genes (IRGs) and distinct immune clusters. Differences in intrinsic tumor immunogenicity and potential immunotherapy response were observed between distinct immune clusters. A prognostic immune-related signature (IRS) was established to predict progression-free survival (PFS). IRS exhibited more powerful prognostic capacity and accurate survival prediction compared to conventional clinicopathological features. Furthermore, an integrated survival decision tree and a scoring nomogram were constructed to improve prognostic stratification and predictive accuracy for individual patients. In addition, altered pathways, mutational patterns, and potential applicable drugs were analyzed in different immune-related risk groups. Our study gained some insight into the immune landscape of PTC, and provided some useful clues for introducing immune-based molecular classification into risk stratification and guiding ICB decision-making.
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Affiliation(s)
- Jing Sun
- Department of Endocrinology, Drum Tower Hospital Affiliated to Nanjing University Medical School, Nanjing, China.,Department of Radiation Oncology, University Hospital, LMU Munich, Germany
| | - Run Shi
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Xiaowen Zhang
- Department of Endocrinology, Drum Tower Hospital Affiliated to Nanjing University Medical School, Nanjing, China
| | - Da Fang
- Department of Endocrinology, Drum Tower Hospital Affiliated to Nanjing University Medical School, Nanjing, China
| | - Josefine Rauch
- Department of Radiation Oncology, University Hospital, LMU Munich, Germany
| | - Shun Lu
- Department of Radiotherapy, Sichuan Cancer Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Xuanbin Wang
- Laboratory of Chinese Herbal Pharmacology, Oncology Center, Renmin Hospital, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan, China
| | - Lukas Käsmann
- Department of Radiation Oncology, University Hospital, LMU Munich, Germany
| | - Jing Ma
- Department of Radiation Oncology, University Hospital, LMU Munich, Germany
| | - Claus Belka
- Department of Radiation Oncology, University Hospital, LMU Munich, Germany.,German Cancer Consortium (DKTK), Munich, Germany
| | - Chuan Su
- Department of Pathogen Biology and Immunology, Jiangsu Province Key Laboratory of Pathogen Biology, Center for Global Health, Nanjing Medical University, Nanjing, China
| | - Minglun Li
- Department of Radiation Oncology, University Hospital, LMU Munich, Germany
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12
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Zeng X, Wang Z, Gui Z, Xiang J, Cao M, Sun W, He L, Dong W, Huang J, Zhang D, Lv C, Zhang T, Shao L, Zhang P, Zhang H. High Incidence of Distant Metastasis Is Associated With Histopathological Subtype of Pediatric Papillary Thyroid Cancer - a Retrospective Analysis Based on SEER. Front Endocrinol (Lausanne) 2021; 12:760901. [PMID: 34858334 PMCID: PMC8632520 DOI: 10.3389/fendo.2021.760901] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/20/2021] [Indexed: 01/07/2023] Open
Abstract
OBJECTIVE Children with papillary thyroid cancer (PTC) have a higher invasive rate and distant metastasis rate, but the mortality rate is lower with unknown reasons. The majority of PTC cases comprise classical papillary thyroid carcinoma (CPTC) and follicular variant papillary thyroid carcinoma (FVPTC). This study aimed to determine the relationship between histopathological subtype and rate of distant metastasis and investigate factors influencing distant metastasis in pediatric PTC. METHODS A total of 102,981 PTC patients were recruited from SEER registry, 2004-2015. Proportion of distant metastasis between children (≤18 years) and adults with different histopathological subtypes was compared by propensity score matching. The cut-off age for distant metastasis in children was calculated by receiver operating characteristic (ROC) curve, and the risk factors for distant metastasis in pediatric patients were analyzed by logistic regression models. RESULTS Among the 1,484 children and 101,497 adults included in the study, the incidence of CPTC patients with distant metastasis in children was higher than that in adults (p<0.001). The ROC curve was calculated, which yielded a cut-off age for distant metastasis in CPTC children as 16 years old. In CPTC, the proportion of young children (2-16 years) with distant metastasis was higher than that of adolescents (17-18 years) and adults (>18 years) (both p<0.001). While there was no such trend in FVPTC. In young children (2-16 years), the incidence of CPTC with distant metastasis was higher than FVPTC (p=0.006). There was no difference between the proportion of CPTC and FVPTC with distant metastasis in adolescents (17-18 years) and adults. Logistic regression models revealed that extrathyroidal extension, lymph node metastasis and CPTC histopathological subtype were risk factors for distant metastasis in young children aged 2 -16 years. CONCLUSIONS In CPTC, the incidence of distant metastasis in young children (2-16 years) was significantly higher than that in adolescents (17-18 years) and adults (>18 years). In patients with distant metastasis aged 2-16 years, the proportion of CPTC was higer than that of FVPTC. Extrathyroidal extension, lymph node metastasis, and CPTC histopathological subtype were risk factors for distant metastasis in young children aged 2-16 years.
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