1
|
Formanti Alonso L, Atienza Cuevas L, Romero García R, Mohigefer Barrera J, Del Río Ignacio JJ, Santisteban Espejo A, Bernal Florindo I, Catalina Fernández I, García Rojo M. [Study of genetic variants in 169 non-small cell lung cancer patients]. REVISTA ESPANOLA DE PATOLOGIA : PUBLICACION OFICIAL DE LA SOCIEDAD ESPANOLA DE ANATOMIA PATOLOGICA Y DE LA SOCIEDAD ESPANOLA DE CITOLOGIA 2023; 56:233-242. [PMID: 37879820 DOI: 10.1016/j.patol.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/15/2023] [Accepted: 06/01/2023] [Indexed: 10/27/2023]
Abstract
INTRODUCTION Lung cancer is the leading cause of cancer death in our country. Non-small cell lung cancer (NSCLC) represents the paradigm of personalized medicine. The main objective of this study is analysing the distribution of the most frequently described clinically significant variants in NSCLC, in our environment. MATERIAL AND METHODS We studied the immunohistochemical expression of TTF1, p40 and PD-L1 and the genetic variants frequency using Next-Generation Sequencing (NGS) with a panel of 52 genes, in 174 NSCLC paraffin-embedded samples in 169 patients (111 men and 52 women) from the province of Cádiz. RESULTS The immunohistochemical expression of TTF1, p40 and PD-L1 was positive in 87%, 0% and 46% in adenocarcinoma, and 0%, 100% and 41% in squamous cell carcinoma. In NGS, the most common single nucleotide variants (SNVs) were KRAS (36%), EGFR (14%), BRAF (10%), PIK3CA (8%), and MET (3%). The most frequent copy number variants (CNVs) were amplifications in NF1 (30%), EGFR (18%), CCND1 (9%), MYC (9%) and KRAS (7%). In women, SNV in EGFR are more frequent than in men (P<.0001). Adenocarcinoma is the most frequent histological type with SNV in KRAS (P=.007361) or in EGFR (P<.0001). Gene fusions were detected in 16 patients (9.47%), in 9 cases in the MET gene. CONCLUSIONS We detected associations, not described so far, between immunohistochemical expression and specific gene variants, which could have an impact on the treatment of NSCLC patients.
Collapse
Affiliation(s)
- Lydia Formanti Alonso
- Unidad de Gestión Clínica Anatomía Patológica, Hospital Universitario de Jerez de la Frontera, Jerez de la Frontera, Cádiz, España; Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Cádiz, España.
| | - Lidia Atienza Cuevas
- Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Cádiz, España; Unidad de Gestión Clínica Anatomía Patológica, Hospital Universitario Puerta del Mar, Cádiz, España
| | - Raquel Romero García
- Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Cádiz, España; Unidad de Gestión Clínica Anatomía Patológica, Hospital Universitario Puerta del Mar, Cádiz, España
| | - Javier Mohigefer Barrera
- Unidad de Gestión Clínica Anatomía Patológica, Hospital Universitario de Jerez de la Frontera, Jerez de la Frontera, Cádiz, España; Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Cádiz, España
| | - Juan Jesús Del Río Ignacio
- Unidad de Gestión Clínica Anatomía Patológica, Hospital Universitario de Jerez de la Frontera, Jerez de la Frontera, Cádiz, España; Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Cádiz, España
| | - Antonio Santisteban Espejo
- Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Cádiz, España; Unidad de Gestión Clínica Anatomía Patológica, Hospital Universitario Puerta del Mar, Cádiz, España
| | - Irene Bernal Florindo
- Unidad de Gestión Clínica Anatomía Patológica, Hospital Universitario de Jerez de la Frontera, Jerez de la Frontera, Cádiz, España; Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Cádiz, España
| | - Inmaculada Catalina Fernández
- Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Cádiz, España; Unidad de Gestión Clínica Anatomía Patológica, Hospital Universitario Puerta del Mar, Cádiz, España
| | - Marcial García Rojo
- Unidad de Gestión Clínica Anatomía Patológica, Hospital Universitario de Jerez de la Frontera, Jerez de la Frontera, Cádiz, España; Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Cádiz, España
| |
Collapse
|
2
|
Liu W, Xu Y, Bai S, Liao L. Bioinformatics analysis of key biomarkers for bladder cancer. Biomed Rep 2022; 18:14. [PMID: 36643693 PMCID: PMC9813473 DOI: 10.3892/br.2022.1596] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/09/2022] [Indexed: 12/23/2022] Open
Abstract
Bladder cancer (BC) is one of the most prevalent genitourinary cancers. Despite the growing research interest in BC, the molecular mechanisms underlying its carcinogenesis remain poorly understood. The microarray datasets GSE38264 and GSE61615 obtained from the Gene Expression Omnibus (GEO) database were analyzed and differentially expressed genes (DEGs) were identified, which were then verified using a dataset from The Cancer Genome Atlas (TCGA). By taking the intersection of the two microarray datasets, the common DEGs were identified and these were selected as candidate genes associated with BC. The DEGs were further subjected to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis, and the protein-protein interaction network was constructed. Further module analysis was performed using STRING and Cytoscape. A total of 362 DEGs were identified, including 13 hub genes, and the GO analysis revealed that these genes were mainly enriched in extracellular matrix organization, positive regulation of cell proliferation, angiogenesis and peptidyl-tyrosine phosphorylation. The expression changes of PTPRC, PDGFRA, CASQ2, TGFBI, KLRD1 and MT1X in the different datasets indicated that these genes were involved in the development of BC. Next, the differential expression of these genes was verified in the TCGA dataset, and ultimately, these 13 genes were determined to be related to the occurrence and development of BC. Finally, the cancer tissues and adjacent tissues of patients with BC were collected and subjected to reverse transcription-quantitative PCR, the results of which were consistent with the bioinformatics prediction. The present findings provide several vital genes for the clinical diagnosis and treatment of BC.
Collapse
Affiliation(s)
- Wentao Liu
- Department of Histology and Embryology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region 830011, P.R. China
| | - Yuxin Xu
- Disease Surveillance Department, Center for Disease Control and Prevention, Western Theater Command, Lanzhou, Gansu 730020, P.R. China
| | - Shengbin Bai
- Department of Histology and Embryology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region 830011, P.R. China,Correspondence to: Professor Shengbin Bai or Professor Libin Liao, Department of Histology and Embryology, School of Basic Medical Sciences, Xinjiang Medical University, 393 Xinyi Road, High Tech Zone, Urumqi, Xinjiang Uygur Autonomous Region 830011, P.R. China NULL
| | - Libin Liao
- Department of Histology and Embryology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region 830011, P.R. China,Correspondence to: Professor Shengbin Bai or Professor Libin Liao, Department of Histology and Embryology, School of Basic Medical Sciences, Xinjiang Medical University, 393 Xinyi Road, High Tech Zone, Urumqi, Xinjiang Uygur Autonomous Region 830011, P.R. China NULL
| |
Collapse
|
3
|
Santisteban-Espejo A, Bernal-Florindo I, Perez-Requena J, Atienza-Cuevas L, Catalina-Fernandez I, Fernandez-Valle MDC, Romero-Garcia R, Garcia-Rojo M. Identification of prognostic factors in classic Hodgkin lymphoma by integrating whole slide imaging and next generation sequencing. Mol Omics 2022; 18:1015-1028. [PMID: 36382626 DOI: 10.1039/d2mo00195k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Digital pathology and genomics are increasingly used to improve our understanding of lymphoid neoplasms. Algorithms for quantifying cell populations in the lymph node and genetics can be integrated to identify new biomarkers with prognostic impact in classic Hodgkin lymphoma (cHL). In 16 cHL patients, we have performed whole slide imaging (WSI) analysis and quantification of CD30+, CD20+, CD3+ and MUM1+ cells in whole tissue slides, and Next Generation Sequencing (NGS) in formalin fixed paraffin-embedded (FFPE) tissue, using a widely used NSG panel (Oncomine® Focus Assay) to define genetic variants underlying tumor development. The different cell populations could be successfully identified in scanned slides of cHL, supporting the inclusion of WSI in the histopathological evaluation of cHL as an adequate method for the quantification of different cell populations. We also performed genetic profiling in FFPE samples of cHL leading to the identification of copy number variations in the Neurofibromin 1 gene (17q11.2) and the Androgen Receptor gene (Xq12) accompanied by chromosomal gains and losses in CDK4, KRAS and FGFR2 genes. Progression-free survival (PFS) was statistically significantly higher in cHL patients with amplification in the NF1 gene combined with CD3+ cells above 28.6% (p = 0.006) and MUM1+ cells above 21.8% (p < 0.001). Moreover, patients with MUM1+ cells above 21.8% showed a statistically significantly higher PFS when combined with amplification of the AR gene (p < 0.001) and wild-type KRAS (p < 0.001). The integration of WSI analysis and DNA sequencing could be useful to improve our understanding of the biology of cHL and define risk subgroups.
Collapse
Affiliation(s)
- Antonio Santisteban-Espejo
- Pathology Department, Puerta del Mar University Hospital, Av. Ana de Viya, 21. 11009, Cadiz, Spain. .,Institute of Research and Innovation in Biomedical Sciences of the Province of Cadiz (INiBICA), Cadiz, Spain.,Department of Medicine, University of Cadiz, Cadiz, Spain
| | - Irene Bernal-Florindo
- Institute of Research and Innovation in Biomedical Sciences of the Province of Cadiz (INiBICA), Cadiz, Spain.,Pathology Department, Jerez de la Frontera University Hospital, Cadiz, Spain
| | - Jose Perez-Requena
- Pathology Department, Puerta del Mar University Hospital, Av. Ana de Viya, 21. 11009, Cadiz, Spain.
| | - Lidia Atienza-Cuevas
- Pathology Department, Puerta del Mar University Hospital, Av. Ana de Viya, 21. 11009, Cadiz, Spain.
| | | | | | - Raquel Romero-Garcia
- Institute of Research and Innovation in Biomedical Sciences of the Province of Cadiz (INiBICA), Cadiz, Spain
| | - Marcial Garcia-Rojo
- Institute of Research and Innovation in Biomedical Sciences of the Province of Cadiz (INiBICA), Cadiz, Spain.,Pathology Department, Jerez de la Frontera University Hospital, Cadiz, Spain
| |
Collapse
|
4
|
Prognostic Impact of TP53 Mutations and Tumor Mutational Load in Colorectal Cancer. GASTROINTESTINAL DISORDERS 2022. [DOI: 10.3390/gidisord4030016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The DNA damage response (DDR) is critical for maintaining genome stability, and abnormal DDR—resulting from mutations in DNA damage-sensing and repair proteins—is a hallmark of cancer. Here, we aimed to investigate the predictive power of DDR gene mutations and the tumor mutational load (TML) for survival outcomes in a cohort of 22 rectal cancer patients who received pre-operative neoadjuvant therapy. Univariate analysis revealed that TML-high and TP53 mutations were significantly associated with worse overall survival (OS) with TML-high retaining significance in multivariate analyses. Kaplan–Meier survival analyses further showed TML-high was associated with worse disease-free (p = 0.036) and OS (p = 0.024) results in our patient cohort. A total of 53 somatic mutations were identified in 22 samples with eight (36%) containing mutations in DDR genes, including ATM, ATR, CHEK2, MRE11A, RAD50, NBN, ERCC2 and TP53. TP53 was the most frequently mutated gene, and TP53 mutations were significantly associated with worse OS (p = 0.023) in Kaplan–Meier survival analyses. Thus, our data indicate that TML and TP53 mutations have prognostic value for rectal cancer patients and may be important independent biomarkers for patient management. This suggests that prognostic determination for rectal cancer patients receiving pre-operative neoadjuvant therapy should include consideration of the initial TML and tumor genetic status.
Collapse
|
5
|
Li M, Wu S, Luo H, Niu J, Yan Y, Fang Y, Ke L, Chen W, Xu H, Li H, Hu X, Cao L, Chen Y, Tu H, He Y. Serological and Molecular Characterization of Hepatitis B Virus Infection in Gastric Cancer. Front Cell Infect Microbiol 2022; 12:894836. [PMID: 35592651 PMCID: PMC9113707 DOI: 10.3389/fcimb.2022.894836] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 04/06/2022] [Indexed: 11/17/2022] Open
Abstract
Hepatitis B virus (HBV) infection has been reported to be associated with gastric cancer (GC). Nonetheless, no study has revealed the role of HBV infection in the survival of patients with GC, and the mutation profiles of HBV-infected patients with GC have never been documented. Here, we performed an updated meta-analysis and found a significantly increased risk of GC in HBV-infected individuals (sOR, 1.29; 95% CI, 1.22-1.37). Furthermore, we observed that in the Anhui area, the rate of serum HBsAg positivity (OR, 1.62; 95% CI, 1.03-2.55) was significantly higher in GC patients than in controls. Moreover, our results showed that HBV-positive patients had significantly worse disease-free survival (HR, 1.98; 95% CI, 1.39-2.82) and overall survival (HR, 1.84; 95% CI, 1.19-2.85) than HBV-negative patients. The results of Cox proportional hazards regression proved that HBV infection was an independent adverse prognostic factor in GC. Furthermore, by performing targeted-NGS, we found unique mutation profiles in HBV-infected GC samples, including five frequently mutated protein-coding genes (KMT2B, KMT2D, SOX1, FGF12, and TUBB2B). Expression and survival analyses of these genes identified three novel candidate genes that may have potential roles in GC development. Gene Ontology enrichment analysis showed that the recurrent mutations in HBV-positive GC samples were related to cell proliferation, cell migration, and transcription. Taking together, our study proved that HBV infection is an independent prognostic factor in GC patients. The unique mutation profiles of HBV-infected patients with GC open a new research direction toward the underling mechanism between HBV infection and GC.
Collapse
Affiliation(s)
- Mengge Li
- Department of Medical Oncology, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Shusheng Wu
- Department of Medical Oncology, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Huiqin Luo
- Department of Medical Oncology, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Jiayu Niu
- Department of Medical Oncology, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Ying Yan
- Department of Medical Oncology, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yuan Fang
- Organ Transplantation Center, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Lihong Ke
- Department of Medical Oncology, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Wenju Chen
- Department of Medical Oncology, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Huijun Xu
- Department of Medical Oncology, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Huimin Li
- Department of Medical Oncology, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Xiaoxiu Hu
- Department of Medical Oncology, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Lulu Cao
- Department of Medical Oncology, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yaolin Chen
- Department of Medical Oncology, Anhui Provincial Hospital Affiliated to Wannan Medical University, Wuhu, China
| | - Hong Tu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Hong Tu, ; Yifu He,
| | - Yifu He
- Department of Medical Oncology, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- *Correspondence: Hong Tu, ; Yifu He,
| |
Collapse
|
6
|
Park J, Sul HJ, Kim JG. Rare Occurrence of Microsatellite Instability in Gastrointestinal Stromal Tumors. ACTA ACUST UNITED AC 2021; 57:medicina57020174. [PMID: 33670651 PMCID: PMC7931009 DOI: 10.3390/medicina57020174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/10/2021] [Accepted: 02/15/2021] [Indexed: 12/20/2022]
Abstract
Background and Objectives: This study aimed to objectively determine microsatellite instability (MSI) status using a next-generation sequencing (NGS)-based MSI panel and to resolve the discrepancy regarding whether or not MSI is a rare phenomenon, irrespective of diverse genomic alterations in gastrointestinal stromal tumors (GISTs). Materials and Methods: Genomic DNA was subjected to MSI panel sequencing using an Ion AmpliSeq Microsatellite Instability Assay, as well as to cancer gene panel sequencing using an Oncomine Focus DNA Assay. Results: All of our GIST patients showed microsatellite-stable (MSS) status, which confirmed that MSI status did not affect the molecular pathogenesis of GIST. The KIT gene (79%, 38/48) was the most frequently mutated gene, followed by the PDGFRA (8%, 4/48), PIK3CA (8%, 4/48), and ERBB2 (4%, 2/48) mutations. KIT exon 11 mutant patients were more favorable in responding to imatinib than those with exon 9 mutant or wild-type GISTs, and compared to non-KIT exon 11 mutant GISTs (p = 0.041). The NGS-based MSI panel with MSICall confirmed a rare phenomenon of microsatellite instability in GISTs irrespective of diverse genomic alterations. Conclusion: Massively parallel sequencing can simultaneously provide the MSI status as well as the somatic mutation profile in a single test. This combined approach may help us to understand the molecular pathogenesis of GIST carcinogenesis and malignant progression.
Collapse
Affiliation(s)
- Joonhong Park
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Korea;
- Clinical Medicine-Biomedical Research Institute, Jeonbuk National University Hospital, Jeonju 54907, Korea
| | - Hae Jung Sul
- Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea;
| | - Jeong Goo Kim
- Department of Surgery, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- Correspondence: ; Tel.: +82-42-220-9319
| |
Collapse
|