1
|
Li J, Zhang X, Wang Y, Jin Y, Song Y, Wang T. Clinicopathological characteristics and prognosis of synchronous brain metastases from non-small cell lung cancer compared with metachronous brain metastases. Front Oncol 2024; 14:1400792. [PMID: 38841157 PMCID: PMC11150626 DOI: 10.3389/fonc.2024.1400792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 05/03/2024] [Indexed: 06/07/2024] Open
Abstract
Purpose Brain metastasis (BM) from non-small cell lung cancer (NSCLC) is a serious complication severely affecting patients' prognoses. We aimed to compare the clinicopathological features and prognosis of synchronous and metachronous BM from NSCLC. Methods Clinical data of 461 patients with brain metastases from NSCLC who visited the Cancer Hospital of China Medical University from 2005 to 2017 were retrospectively collected. We analyzed the pathophysiological characteristics of synchronous and metachronous BM from NSCLC and survival rates of the patients. Propensity score matching analysis was used to reduce bias between groups. In addition, we used the Kaplan-Meier method for survival analysis, log-rank test to compare survival rates, and Cox proportional hazards regression model for multivariate prognosis analysis. Results Among 461 patients with BM, the number of people who met the inclusion criteria was 400 cases, and after 1:2 propensity score matching,130 had synchronous BM and 260 had metachronous BM. The survival time was longer for metachronous BM in driver mutation-negative patients with squamous cell carcinoma than synchronous BM. Conversely, metachronous and synchronous BM with gene mutations and adenocarcinoma showed no differences in survival time. Multivariate analysis showed that metachronous BM was an independent prognostic factor for overall survival. Furthermore, the pathological type squamous cell carcinoma and Karnofsky Performance Status score <80 were independent risk factors affecting overall survival. Conclusion BM status is an independent factor influencing patient outcome. Moreover, synchronous and metachronous BM from NSCLC differ in gene mutation profile, pathological type, and disease progression and hence require different treatments.
Collapse
Affiliation(s)
- Jing Li
- School of Graduate, Dalian Medical University, Dalian, Liaoning, China
- Department of Radiotherapy, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, Liaoning, China
| | - Xiaofang Zhang
- Department of Radiotherapy, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, Liaoning, China
- School of Graduate, China Medical University, Shengyang, Liaoning, China
| | - Ye Wang
- School of Graduate, Dalian Medical University, Dalian, Liaoning, China
- Department of Radiotherapy, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, Liaoning, China
| | - Yi Jin
- Department of Breast Surgery, Liaoning Cancer Hospital and Institute, Shenyang, Liaoning, China
| | - Yingqiu Song
- Department of Radiotherapy, Cancer Hospital of China Medical University, Shenyang, Liaoning, China
| | - Tianlu Wang
- Department of Radiotherapy, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, Liaoning, China
- Department of Radiotherapy, Cancer Hospital of China Medical University, Shenyang, Liaoning, China
- Department of Radiotherapy, Cancer Hospital of Dalian University of Technology, Shenyang, Liaoning, China
- Faculty of Medicine, Dalian University of Technology, Shenyang, Liaoning, China
| |
Collapse
|
2
|
Mao G, Yang D, Liu B, Zhang Y, Ma S, Dai S, Wang G, Tang W, Lu H, Cai S, Zhu J, Yang H. Deciphering a cell death-associated signature for predicting prognosis and response to immunotherapy in lung squamous cell carcinoma. Respir Res 2023; 24:176. [PMID: 37415224 DOI: 10.1186/s12931-023-02402-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 03/18/2023] [Indexed: 07/08/2023] Open
Abstract
BACKGROUND Lung squamous cell carcinoma (LUSC) is a subtype of non-small cell carcinoma, accounting for about 30% of all lung cancers. Yet, the evaluation of prognostic outcome and therapy response of patients with LUSC remains to be resolved. This study aimed to explore the prognostic value of cell death pathways and develop a cell death-associated signature for predicting prognosis and guiding treatment in LUSC. METHODS Transcriptome profiles and corresponding clinical information of LUSC patients were gathered from The Cancer Genome Atlas (TCGA-LUSC, n = 493) and Gene Expression Omnibus database (GSE74777, n = 107). The cell death-related genes including autophagy (n = 348), apoptosis (n = 163), and necrosis (n = 166) were retrieved from the Kyoto Encyclopedia of Genes and Genomes and Gene Ontology databases. In the training cohort (TCGA-LUSC), LASSO Cox regression was used to construct four prognostic signatures of respective autophagy, apoptosis, and necrosis pathway and genes of three pathways. After comparing the four signatures, the cell death index (CDI), the signature of combined genes, was further validated in the GSE74777 dataset. We also investigated the clinical significance of the CDI signature in predicting the immunotherapeutic response of LUSC patients. RESULTS The CDI signature was significantly associated with the overall survival of LUSC patients in the training cohort (HR, 2.13; 95% CI, 1.62‒2.82; P < 0.001) and in the validation cohort (HR, 1.94; 95% CI, 1.01‒3.72; P = 0.04). The differentially expressed genes between the high- and low-risk groups contained cell death-associated cytokines and were enriched in immune-associated pathways. We also found a higher infiltration of naive CD4+ T cells, monocytes, activated dendritic cells, neutrophils, and lower infiltration of plasma cells and resting memory CD4+ T cells in the high-risk group. Tumor stemness indices, mRNAsi and mDNAsi, were both negatively correlated with the risk score of the CDI. Moreover, LUSC patients in the low-risk group are more likely to respond to immunotherapy than those in the high-risk group (P = 0.002). CONCLUSIONS This study revealed a reliable cell death-associated signature (CDI) that closely correlated with prognosis and the tumor microenvironment in LUSC, which may assist in predicting the prognosis and response to immunotherapy for patients with LUSC.
Collapse
Affiliation(s)
- Guangxian Mao
- Department of Thoracic Surgery, Peking University Shenzhen Hospital, Shenzhen, 518036, China
| | - Dongyong Yang
- Department of Pulmonary and Critical Care Medicine, Respiratory Medicine Center of Fujian Province, Second Affiliated Hospital of Fujian Medical University, Guangzhou, 362000, China
| | - Bin Liu
- First Division, Department of Respiratory and Critical Care Medicine, Affiliated to Xiangya School of Medicine, Zhuzhou Hospital, Central South University, Zhuzhou Central Hospital, Zhuzhou, 412007, China
| | - Yu Zhang
- Burning Rock Biotech, Guangzhou, 510300, China
| | - Sijia Ma
- Burning Rock Biotech, Guangzhou, 510300, China
| | - Shang Dai
- Burning Rock Biotech, Guangzhou, 510300, China
| | | | - Wenxiang Tang
- Department of General Practice, the Third Xiangya Hospital of Central South University, Changsha, 410013, China
| | - Huafei Lu
- Burning Rock Biotech, Guangzhou, 510300, China
| | - Shangli Cai
- Burning Rock Biotech, Guangzhou, 510300, China
| | - Jialiang Zhu
- Department of Cardiothoracic Surgery, the Third Xiangya Hospital of Central South University, 138 Tongzipo Road, Yuelu District, Changsha, 410013, China.
| | - Huaping Yang
- Department of Respiratory Medicine, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, China.
| |
Collapse
|
3
|
Lee TH, Jang B, Chang JH, Kim E, Park JH, Chie EK. Genomic landscape of locally advanced rectal adenocarcinoma: Comparison between before and after neoadjuvant chemoradiation and effects of genetic biomarkers on clinical outcomes and tumor response. Cancer Med 2023; 12:15664-15675. [PMID: 37260182 PMCID: PMC10417181 DOI: 10.1002/cam4.6169] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 03/05/2023] [Accepted: 05/18/2023] [Indexed: 06/02/2023] Open
Abstract
PURPOSE To explore genomic biomarkers in rectal cancer by performing whole-exome sequencing. MATERIALS AND METHODS Pre-chemoradiation (CRT) biopsy and post-CRT surgical specimens were obtained from 27 patients undergoing neoadjuvant CRT followed by definitive resection. Exomes were sequenced to a mean coverage of 30×. Somatic single-nucleotide variants (SNVs) and insertions/deletions (indels) were identified. Tumor mutational burden was defined as the number of SNVs or indels. Mutational signatures were extracted and fitted to COSMIC reference signatures. Tumor heterogeneity was quantified with a mutant-allele tumor heterogeneity (MATH) score. Genetic biomarkers and frequently occurred copy number alterations (CNAs) were compared between pre- and post-CRT specimens. Their associations with tumor regression grade (TRG) and clinical outcomes were explored. RESULTS Top five mutated genes were APC, TP53, NF1, KRAS, and NOTCH1 for pre-CRT samples and APC, TP53, NF1, CREBBP, and ATM for post-CRT samples. Several gene mutations including RUNX1, EGFR, and TP53 in pre-CRT samples showed significant association with clinical outcomes, but not with TRG. However, no such association was found in post-CRT samples. Discordance of driver mutation status was found between pre- and post-CRT samples. In tumor mutational burden analysis, higher number of SNVs or indels was associated with worse treatment outcomes. Six single-base substitution (SBS) signatures identified were SBS1, SBS30, SBS29, SBS49, SBS3, and SBS44. The MATH score decreased after CRT on paired analysis. Less than half of CNAs frequent in post-CRT samples were present in pre-CRT samples. CONCLUSION Pre- and post-CRT samples showed different genomic landscape. Potential genetic biomarkers of pre-CRT samples found in the current analysis call for external validation.
Collapse
Affiliation(s)
- Tae Hoon Lee
- Department of Radiation OncologySeoul National University HospitalSeoulRepublic of Korea
- Department of Clinical Medical ScienceSeoul National University College of MedicineSeoulRepublic of Korea
| | - Bum‐Sup Jang
- Department of Radiation OncologySeoul National University HospitalSeoulRepublic of Korea
| | - Ji Hyun Chang
- Department of Radiation OncologySeoul National University HospitalSeoulRepublic of Korea
| | - Eunji Kim
- Department of Radiation OncologySeoul Metropolitan Government‐Seoul National University Boramae Medical CenterSeoulRepublic of Korea
| | - Jeong Hwan Park
- Department of PathologySeoul Metropolitan Government‐Seoul National University Boramae Medical CenterSeoulRepublic of Korea
| | - Eui Kyu Chie
- Department of Radiation OncologySeoul National University HospitalSeoulRepublic of Korea
- Department of Clinical Medical ScienceSeoul National University College of MedicineSeoulRepublic of Korea
- Department of Radiation OncologySeoul National University College of MedicineSeoulRepublic of Korea
- Medical Research Center, Institute of Radiation MedicineSeoul National UniversitySeoulRepublic of Korea
| |
Collapse
|
4
|
Butler K, Banday AR. APOBEC3-mediated mutagenesis in cancer: causes, clinical significance and therapeutic potential. J Hematol Oncol 2023; 16:31. [PMID: 36978147 PMCID: PMC10044795 DOI: 10.1186/s13045-023-01425-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
Apolipoprotein B mRNA-editing enzyme, catalytic polypeptides (APOBECs) are cytosine deaminases involved in innate and adaptive immunity. However, some APOBEC family members can also deaminate host genomes to generate oncogenic mutations. The resulting mutations, primarily signatures 2 and 13, occur in many tumor types and are among the most common mutational signatures in cancer. This review summarizes the current evidence implicating APOBEC3s as major mutators and outlines the exogenous and endogenous triggers of APOBEC3 expression and mutational activity. The review also discusses how APOBEC3-mediated mutagenesis impacts tumor evolution through both mutagenic and non-mutagenic pathways, including by inducing driver mutations and modulating the tumor immune microenvironment. Moving from molecular biology to clinical outcomes, the review concludes by summarizing the divergent prognostic significance of APOBEC3s across cancer types and their therapeutic potential in the current and future clinical landscapes.
Collapse
Affiliation(s)
- Kelly Butler
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - A Rouf Banday
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| |
Collapse
|
5
|
Argyris PP, Naumann J, Jarvis MC, Wilkinson PE, Ho DP, Islam MN, Bhattacharyya I, Gopalakrishnan R, Li F, Koutlas IG, Giubellino A, Harris RS. Primary mucosal melanomas of the head and neck are characterised by overexpression of the DNA mutating enzyme APOBEC3B. Histopathology 2023; 82:608-621. [PMID: 36416305 PMCID: PMC10107945 DOI: 10.1111/his.14843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 09/12/2022] [Accepted: 09/23/2022] [Indexed: 11/24/2022]
Abstract
AIMS Primary head/neck mucosal melanomas (MMs) are rare and exhibit aggressive biologic behaviour and elevated mutational loads. The molecular mechanisms responsible for high genomic instability observed in head/neck MMs remain elusive. The DNA cytosine deaminase APOBEC3B (A3B) constitutes a major endogenous source of mutation in human cancer. A3B-related mutations are identified through C-to-T/-G base substitutions in 5'-TCA/T motifs. Herein, we present immunohistochemical and genomic data supportive of a role for A3B in head/neck MMs. METHODS AND RESULTS A3B protein levels were assessed in oral (n = 13) and sinonasal (n = 13) melanomas, and oral melanocytic nevi (n = 13) by immunohistochemistry using a custom rabbit α-A3B mAb (5210-87-13). Heterogeneous, selective-to-diffuse, nuclear only, A3B immunopositivity was observed in 12 of 13 (92.3%) oral melanomas (H-score range = 9-72, median = 40) and 8 of 13 (62%) sinonasal melanomas (H-score range = 1-110, median = 24). Two cases negative for A3B showed prominent cytoplasmic staining consistent with A3G. A3B protein levels were significantly higher in oral and sinonasal MMs than intraoral melanocytic nevi (P < 0.0001 and P = 0.0022, respectively), which were A3B-negative (H-score range = 1-8, median = 4). A3B levels, however, did not differ significantly between oral and sinonasal tumours (P > 0.99). NGS performed in 10 sinonasal MMs revealed missense NRAS mutations in 50% of the studied cases and one each KIT and HRAS mutations. Publicly available whole-genome sequencing (WGS) data disclosed that the number of C-to-T mutations and APOBEC3 enrichment score were markedly elevated in head/neck MMs (n = 2). CONCLUSION The above data strongly indicate a possible role for the mutagenic enzyme A3B in head/neck melanomagenesis, but not benign melanocytic neoplasms.
Collapse
Affiliation(s)
- Prokopios P Argyris
- Department of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMNUSA
- Masonic Cancer CenterUniversity of MinnesotaMinneapolisMNUSA
- Institute for Molecular VirologyUniversity of MinnesotaMinneapolisMNUSA
- Center for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
- Howard Hughes Medical InstituteUniversity of MinnesotaMinneapolisMNUSA
- Division of Oral and Maxillofacial PathologySchool of Dentistry, University of MinnesotaMinneapolisMNUSA
| | - Jordan Naumann
- Department of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMNUSA
- Masonic Cancer CenterUniversity of MinnesotaMinneapolisMNUSA
- Institute for Molecular VirologyUniversity of MinnesotaMinneapolisMNUSA
- Center for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
| | - Matthew C Jarvis
- Department of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMNUSA
- Masonic Cancer CenterUniversity of MinnesotaMinneapolisMNUSA
- Institute for Molecular VirologyUniversity of MinnesotaMinneapolisMNUSA
- Center for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
| | - Peter E Wilkinson
- Department of Diagnostic and Biological SciencesSchool of Dentistry, University of MinnesotaMinneapolisMNUSA
| | - Dan P Ho
- Department of Diagnostic and Biological SciencesSchool of Dentistry, University of MinnesotaMinneapolisMNUSA
| | - Mohammed N Islam
- Department of Oral and Maxillofacial Diagnostic SciencesUniversity of Florida College of DentistryGainesvilleFLUSA
| | - Indraneel Bhattacharyya
- Department of Oral and Maxillofacial Diagnostic SciencesUniversity of Florida College of DentistryGainesvilleFLUSA
| | - Rajaram Gopalakrishnan
- Division of Oral and Maxillofacial PathologySchool of Dentistry, University of MinnesotaMinneapolisMNUSA
| | - Faqian Li
- Department of Laboratory Medicine and PathologyMedical School, University of MinnesotaMinneapolisMNUSA
| | - Ioannis G Koutlas
- Division of Oral and Maxillofacial PathologySchool of Dentistry, University of MinnesotaMinneapolisMNUSA
| | - Alessio Giubellino
- Department of Laboratory Medicine and PathologyMedical School, University of MinnesotaMinneapolisMNUSA
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMNUSA
- Masonic Cancer CenterUniversity of MinnesotaMinneapolisMNUSA
- Institute for Molecular VirologyUniversity of MinnesotaMinneapolisMNUSA
- Center for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
- Howard Hughes Medical InstituteUniversity of MinnesotaMinneapolisMNUSA
| |
Collapse
|
6
|
Li P, Li H, Wan Z, Lu Y. Effect of sample size on prognostic genes analysis in non-small cell lung cancer. Mol Genet Genomics 2023; 298:549-554. [PMID: 36853413 DOI: 10.1007/s00438-023-01999-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 02/15/2023] [Indexed: 03/01/2023]
Abstract
The identification of prognostic genes can help in the clinical management of non-small cell lung cancer (NSCLC). However, there is little overlap in the prognostic genes identified in different NSCLC studies. One reason for this may be the inadequate sample size. Here, the effect of sample size on prognostic genes analysis was investigated based on 515 stage II/III NSCLC cases from two cohorts detected by whole-exome sequencing. Prognostic genes analysis was repeatedly performed 100 times for each sample size level using random resampling methods. In stage II lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) cases from the TCGA Pan-Lung Cancer cohort, the number of statistically significant prognostic genes first increased with sample size in a power law, then fluctuated steadily, and finally decreased slightly. The power law growth curves were also observed in stage III LUAD and LUSC cases from the TCGA Pan-Lung Cancer cohort and stage III Chinese LUAD cases from the OncoSG cohort. The correlation R2 of the fitted power law growth curves were all greater than 0.99. In addition, at the sample size level where the number of prognostic genes peaked, the mean proportion of true prognostic genes in patients with stage II LUAD and LUSC was 28.32% and 23.12%, which could partly explain the little overlap in prognostic genes between reports. In conclusion, the number of prognostic genes takes a power law growth with the sample size in NSCLC, independent of histopathological subtype, race, and stage. These results also show how sample size affects the reliability of prognostic genes and will aid trial design for genomic mutation-based prognostic studies in NSCLC.
Collapse
Affiliation(s)
- Pingdong Li
- Department of Otolaryngology, Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Haiyang Li
- Department of Otolaryngology, People's Hospital of Beijing Daxing District, Beijing, China
| | - Zhiyi Wan
- School of Biomedicine, Beijing City University, Beijing, China
| | - Yanan Lu
- School of Biomedicine, Beijing City University, Beijing, China.
| |
Collapse
|
7
|
Intrinsic and Extrinsic Transcriptional Profiles That Affect the Clinical Response to PD-1 Inhibitors in Patients with Non-Small Cell Lung Cancer. Cancers (Basel) 2022; 15:cancers15010197. [PMID: 36612193 PMCID: PMC9818269 DOI: 10.3390/cancers15010197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/13/2022] [Accepted: 12/26/2022] [Indexed: 12/30/2022] Open
Abstract
Using a machine learning method, we investigated the intrinsic and extrinsic transcriptional profiles that affect the clinical response to PD-1 inhibitors in 57 patients with non-small cell lung cancer (NSCLC). Among the top 100 genes associated with the responsiveness to PD-1 inhibitors, the proportion of intrinsic genes in lung adenocarcinoma (LUAD) (69%) was higher than in NSCLC overall (36%) and lung squamous cell carcinoma (LUSC) (33%). The intrinsic gene signature of LUAD (mean area under the ROC curve (AUC) = 0.957 and mean accuracy = 0.9) had higher predictive power than either the intrinsic gene signature of NSCLC or LUSC or the extrinsic gene signature of NSCLC, LUAD, or LUSC. The high intrinsic gene signature group had a high overall survival rate in LUAD (p = 0.034). When we performed a pathway enrichment analysis, the cell cycle and cellular senescence pathways were related to the upregulation of intrinsic genes in LUAD. The intrinsic signature of LUAD also showed a positive correlation with other immune checkpoint targets, including CD274, LAG3, and PDCD1LG2 (Spearman correlation coefficient > 0.25). PD-1 inhibitor-related intrinsic gene patterns differed significantly between LUAD and LUSC and may be a particularly useful biomarker in LUAD.
Collapse
|
8
|
Dixit R, Pandey M, Rajput M, Shukla VK. Unravelling of the comparative Transcriptomic Profile of Gallbladder Cancer using mRNA sequencing. Mol Biol Rep 2022; 49:6395-6403. [PMID: 35469389 DOI: 10.1007/s11033-022-07448-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/29/2022] [Accepted: 04/01/2022] [Indexed: 12/29/2022]
Abstract
BACKGROUND Gallbladder cancer (GBC) represents a wide geographical diversity as well as heterogeneity in clinical and genomic landscape. There seems to be little progress in the development of diagnostic biomarkers, targeted therapies or individualized approaches to GBC management. In this study, we investigated the whole transcriptome profile of GBC patients using RNA sequencing and identified key genes and pathways associated with gallbladder cancer using bioinformatics. METHODOLOGY A total of 10 cases of GBC were collected and sequenced. The raw reads of the gallbladder sample was compared with the gallbladder normal control (SRA Database ID: ERX288537: HPA RNA-seq normal tissues gallbladder). Using Gene ontology analysis the differentially expressed genes were categorized into the biological pathway, cellular component, and molecular function. Pathway enrichment analyses, protein-protein interaction, transcription factor and miRNA interaction that regulate the expression of hub genes were conducted using bioinformatics tool. RESULTS A total of 954 differentially expressed mRNA transcripts were identified, including overexpression of REG4, TMEM238, S100A2, LYPD2, and KRT17, as well as underexpressed genes like CCKAR, IGSF10, CHRM2, CRISP3, and FGF19. Enrichment analysis showed the metabolic pathways to be the top five cancer pathways in gallbladder carcinogenesis besides PI3k-Akt signalling pathway, cAMP signalling pathway, miRNAs in cancer, and cell adhesion profile of GBC. CONCLUSIONS CCKAR, CDKN2A and LRRK2 were found to be most involved genes in its progression and development through different regulatory pathways. Further, most of the genes were significantly involved in PI3k-Akt, Wnt and hedgehog signaling pathways which have a key role in gallbladder cancer development.
Collapse
Affiliation(s)
- Ruhi Dixit
- Department of General Surgery, Institute of Medical Sciences, Banaras Hindu University, 221 005, Varanasi, India
| | - Manoj Pandey
- Department of Surgical Oncology, Institute of Medical Sciences, Banaras Hindu University, 221005, Varanasi, India
| | - Monika Rajput
- Department of Surgical Oncology, Institute of Medical Sciences, Banaras Hindu University, 221005, Varanasi, India
| | - Vijay Kumar Shukla
- Department of General Surgery, Institute of Medical Sciences, Banaras Hindu University, 221 005, Varanasi, India.
| |
Collapse
|
9
|
Erkin ÖC, Cömertpay B, Göv E. Integrative Analysis for Identification of Therapeutic Targets and Prognostic Signatures in Non-Small Cell Lung Cancer. Bioinform Biol Insights 2022; 16:11779322221088796. [PMID: 35422618 PMCID: PMC9003654 DOI: 10.1177/11779322221088796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/27/2022] [Indexed: 01/12/2023] Open
Abstract
Differential expressions of certain genes during tumorigenesis may serve to identify novel manageable targets in the clinic. In this work with an integrated bioinformatics approach, we analyzed public microarray datasets from Gene Expression Omnibus (GEO) to explore the key differentially expressed genes (DEGs) in non-small cell lung cancer (NSCLC). We identified a total of 984 common DEGs in 252 healthy and 254 NSCLC gene expression samples. The top 10 DEGs as a result of pathway enrichment and protein–protein interaction analysis were further investigated for their prognostic performances. Among these, we identified high expressions of CDC20, AURKA, CDK1, EZH2, and CDKN2A genes that were associated with significantly poorer overall survival in NSCLC patients. On the contrary, high mRNA expressions of CBL, FYN, LRKK2, and SOCS2 were associated with a significantly better prognosis. Furthermore, our drug target analysis for these hub genes suggests a potential use of Trichostatin A, Pracinostat, TGX-221, PHA-793887, AG-879, and IMD0354 antineoplastic agents to reverse the expression of these DEGs in NSCLC patients.
Collapse
Affiliation(s)
| | | | - Esra Göv
- Esra Göv, Department of Bioengineering, Faculty of Engineering, Adana Alparslan Türkeş Science and Technology University, Balcalı Mah., Çatalan Caddesi No: 201/1, Sarıçam, 01250 Adana, Turkey.
| |
Collapse
|
10
|
Crane J, Shi Q, Xi Y, Lai J, Pham K, Wang H. Emerging Trends in the Pathological Research of Human Papillomavirus-positive Oropharyngeal Squamous Cell Carcinoma. JOURNAL OF CLINICAL AND TRANSLATIONAL PATHOLOGY 2022; 2:31-36. [PMID: 36275841 PMCID: PMC9585478 DOI: 10.14218/jctp.2022.00004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Oropharyngeal squamous cell carcinomas (OPSCCs) have shown an alarming rate of increase in incidence over the past several decades, markedly in men. In the United States, transcriptionally-active human papillomavirus (HPV), particularly HPV 16, has become the highest contributive agent of OPSCCs, affecting approximately 16,000 people a year. Compared to patients with HPV-negative OPSCCs, patients with HPV-positive OPSCCs exhibit better health responses to chemoradiotherapy and an overall increase in long-term survival. Despite promising treatment options, many OPSCCs are discovered at an advanced stage, and ~20% of cases will recur after definitive treatment. Therefore, extensive research is ongoing to identify new targets for precision treatment and to stratify tumor prognosis. The aim of this review is to capture the most updated research on HPV-positive OPSCCs, emphasizing their relevance as potential new targets for precision medicine and survival prognosis.
Collapse
Affiliation(s)
- Joshua Crane
- Department of Laboratory Medicine and Pathology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Yibo Xi
- Department of Laboratory Medicine and Pathology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Kien Pham
- Department of Laboratory Medicine and Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - He Wang
- Department of Laboratory Medicine and Pathology, Yale University School of Medicine, New Haven, CT, USA
- Correspondence to: He Wang, Department of Laboratory Medicine and Pathology, Yale University School of Medicine, 310 Cedar Street, New Haven, CT 06510, USA. Tel: +1-203-214-2786, Fax: +1-203-214-2764,
| |
Collapse
|
11
|
Wang W, Liu H, Li G. What's the difference between lung adenocarcinoma and lung squamous cell carcinoma? Evidence from a retrospective analysis in a cohort of Chinese patients. Front Endocrinol (Lausanne) 2022; 13:947443. [PMID: 36105402 PMCID: PMC9465444 DOI: 10.3389/fendo.2022.947443] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) are the two most common subtypes of lung cancer. Previously, they were categorized into one histological subtype known as non-small cell lung cancer (NSCLC) and often treated similarly. However, increasing evidence suggested that LUAD and LUSC should be classified and treated as different cancers. But yet, detailed differences in clinical features between LUAD and LUSC have not been well described. METHODS A cohort of 142 Chinese patients with 111 LUAD and 31 LUSC cases were consecutively enrolled from April 2019 to October 2020 in Hunan Provincial People's Hospital. The clinical features of the patients were retrospectively analyzed and compared in the terms of general information, clinicopathologic characteristics, imaging findings and laboratory data. RESULTS In comparison with LUAD, LUSC patients had a significantly higher proportion of males, smokers, drinkers, higher-stage cases. The mean tumor size in LUSC patients was significantly larger than that in LUAD patients. Compared with LUAD patients, more of patients with LUSC had cough, fever and abundant sputum symptoms. Besides that, more bacterial infections and fungal infections were found in LUSC patients than that in LUAD patients. Imaging data shows that ground-glass opacity and patchy shadows in radiological films were more frequent in LUAD patients than that in LUSC patients. In addition to initial laboratory data, LUSC patients had higher levels of leukocytes, platelets, and creatinine that of LUAD patients. CONCLUSIONS Together, these results suggested that there exist distinct differences between LUAD and LUSC subtypes; LUSC may be a more malignant type in comparison with LUAD. Our findings may have potential implications in clinical settings. However, further multicenter studies are needed to validate these findings in a larger sample size.
Collapse
Affiliation(s)
- Wen Wang
- Department of Cardio-Thoracic Surgery, Hunan Provincial People’s Hospital (The First-Affiliated Hospital of Hunan Normal University), Changsha, China
| | - Hui Liu
- Department of Cardio-Thoracic Surgery, Hunan Provincial People’s Hospital (The First-Affiliated Hospital of Hunan Normal University), Changsha, China
| | - Guoli Li
- Department of Nephrology and Laboratory of Kidney Disease, Hunan Provincial People’s Hospital (The First-Affiliated Hospital of Hunan Normal University), Changsha, China
- Changsha Clinical Research Center for Kidney Disease, Changsha, China
- Hunan Clinical Research Center for Chronic Kidney Disease, Changsha, China
- *Correspondence: Guoli Li,
| |
Collapse
|
12
|
Zhang K, Chen J, Li C, Yuan Y, Fang S, Liu W, Qian Y, Ma J, Chang L, Chen F, Yang Z, Gu W. Exosome-mediated transfer of SNHG7 enhances docetaxel resistance in lung adenocarcinoma. Cancer Lett 2021; 526:142-154. [PMID: 34715254 DOI: 10.1016/j.canlet.2021.10.029] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 09/29/2021] [Accepted: 10/19/2021] [Indexed: 12/25/2022]
Abstract
Long noncoding RNA (lncRNA) small nucleolar RNA host gene 7 (SNHG7) has been widely reported in various cancers, including lung adenocarcinoma (LUAD). However, it is largely unknown whether SNHG7 is involved in docetaxel resistance of LUAD. In the current study, we identified the high expression of SNHG7 in docetaxel-resistant cells. Through functional assays, we determined that silencing of SNHG7 decreased IC50 value of LUAD cells to docetaxel and suppressed proliferation and autophagy in LUAD cells, and reversed M2 polarization in macrophages. Mechanistically, we uncovered that SNHG7 promoted autophagy via recruiting human antigen R (HuR) to stabilize autophagy-related genes autophagy related 5 (ATG5) and autophagy related 12 (ATG12). Moreover, exosomal SNHG7 was transmitted from docetaxel-resistant LUAD cells to parental LUAD cells and thus facilitated docetaxel resistance. Additionally, exosomal SNHG7 activated the phosphatidylinositol 3-kinase (PI3K)/AKT pathway to promote M2 polarization in macrophages via recruiting cullin 4A (CUL4A) to induce ubiquitination and degradation of phosphatase and tensin homolog (PTEN). Taken together, we concluded that exosomal SNHG7 enhances docetaxel resistance of LUAD cells through inducing autophagy and macrophage M2 polarization. All findings in the study suggested that SNHG7 may be a promising target for relieving docetaxel resistance in LUAD.
Collapse
Affiliation(s)
- Kai Zhang
- Department of Respiratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, Jiangsu, China
| | - Jing Chen
- Department of Biochemistry and Molecular Biology, School of Medicine& Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Chen Li
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, 215002, Jiangsu, China
| | - Yuan Yuan
- Department of Respiratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, Jiangsu, China
| | - Surong Fang
- Department of Respiratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, Jiangsu, China
| | - Wenfei Liu
- Department of Respiratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, Jiangsu, China
| | - Yingying Qian
- Department of Respiratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, Jiangsu, China
| | - Jiyong Ma
- Department of Respiratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, Jiangsu, China
| | - Ligong Chang
- Department of Respiratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, Jiangsu, China
| | - Feifei Chen
- Department of Respiratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, Jiangsu, China
| | - Zhenhua Yang
- Department of Respiratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, Jiangsu, China.
| | - Wei Gu
- Department of Respiratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, Jiangsu, China.
| |
Collapse
|
13
|
Chai H, Xia L, Zhang L, Yang J, Zhang Z, Qian X, Yang Y, Pan W. An Adaptive Transfer-Learning-Based Deep Cox Neural Network for Hepatocellular Carcinoma Prognosis Prediction. Front Oncol 2021; 11:692774. [PMID: 34646759 PMCID: PMC8504135 DOI: 10.3389/fonc.2021.692774] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 09/01/2021] [Indexed: 12/24/2022] Open
Abstract
Background Predicting hepatocellular carcinoma (HCC) prognosis is important for treatment selection, and it is increasingly interesting to predict prognosis through gene expression data. Currently, the prognosis remains of low accuracy due to the high dimension but small sample size of liver cancer omics data. In previous studies, a transfer learning strategy has been developed by pre-training models on similar cancer types and then fine-tuning the pre-trained models on the target dataset. However, transfer learning has limited performance since other cancer types are similar at different levels, and it is not trivial to balance the relations with different cancer types. Methods Here, we propose an adaptive transfer-learning-based deep Cox neural network (ATRCN), where cancers are represented by 12 phenotype and 10 genotype features, and suitable cancers were adaptively selected for model pre-training. In this way, the pre-trained model can learn valuable prior knowledge from other cancer types while reducing the biases. Results ATRCN chose pancreatic and stomach adenocarcinomas as the pre-training cancers, and the experiments indicated that our method improved the C-index of 3.8% by comparing with traditional transfer learning methods. The independent tests on three additional HCC datasets proved the robustness of our model. Based on the divided risk subgroups, we identified 10 HCC prognostic markers, including one new prognostic marker, TTC36. Further wet experiments indicated that TTC36 is associated with the progression of liver cancer cells. Conclusion These results proved that our proposed deep-learning-based method for HCC prognosis prediction is robust, accurate, and biologically meaningful.
Collapse
Affiliation(s)
- Hua Chai
- School of Mathematics and Big Data, Foshan University, Foshan, China.,Department of Pancreatic-Hepato-Biliary-Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Long Xia
- Department of Hepatobiliary-Pancreatic-Splenic Surgery, Inner Mongolia Autonomous Region People's Hospital, Hohhot, China
| | - Lei Zhang
- Department of Pancreatic-Hepato-Biliary-Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jiarui Yang
- Department of Pancreatic-Hepato-Biliary-Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhongyue Zhang
- School of Computer Science, Sun Yat-sen University, Guangzhou, China
| | - Xiangjun Qian
- Department of Pancreatic-Hepato-Biliary-Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yuedong Yang
- School of Computer Science, Sun Yat-sen University, Guangzhou, China
| | - Weidong Pan
- Department of Pancreatic-Hepato-Biliary-Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
14
|
Wang S, Yu Y, Xu W, Lv X, Zhang Y, Liu M. Dynamic nomograms combining N classification with ratio-based nodal classifications to predict long-term survival for patients with lung adenocarcinoma after surgery: a SEER population-based study. BMC Cancer 2021; 21:653. [PMID: 34344326 PMCID: PMC8336099 DOI: 10.1186/s12885-021-08410-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/24/2021] [Indexed: 12/20/2022] Open
Abstract
Background The prognostic roles of three lymph node classifications, number of positive lymph nodes (NPLN), log odds of positive lymph nodes (LODDS), and lymph node ratio (LNR) in lung adenocarcinoma are unclear. We aim to find the classification with the strongest predictive power and combine it with the American Joint Committee on Cancer (AJCC) 8th TNM stage to establish an optimal prognostic nomogram. Methods 25,005 patients with T1-4N0–2M0 lung adenocarcinoma after surgery between 2004 to 2016 from the Surveillance, Epidemiology, and End Results database were included. The study cohort was divided into training cohort (13,551 patients) and external validation cohort (11,454 patients) according to different geographic region. Univariate and multivariate Cox regression analyses were performed on the training cohort to evaluate the predictive performance of NPLN (Model 1), LODDS (Model 2), LNR (Model 3) or LODDS+LNR (Model 4) respectively for cancer-specific survival and overall survival. Likelihood-ratio χ2 test, Akaike Information Criterion, Harrell concordance index, integrated discrimination improvement (IDI) and net reclassification improvement (NRI) were used to evaluate the predictive performance of the models. Nomograms were established according to the optimal models. They’re put into internal validation using bootstrapping technique and external validation using calibration curves. Nomograms were compared with AJCC 8th TNM stage using decision curve analysis. Results NPLN, LODDS and LNR were independent prognostic factors for cancer-specific survival and overall survival. LODDS+LNR (Model 4) demonstrated the highest Likelihood-ratio χ2 test, highest Harrell concordance index, and lowest Akaike Information Criterion, and IDI and NRI values suggested Model 4 had better prediction accuracy than other models. Internal and external validations showed that the nomograms combining TNM stage with LODDS+LNR were convincingly precise. Decision curve analysis suggested the nomograms performed better than AJCC 8th TNM stage in clinical practicability. Conclusions We constructed online nomograms for cancer-specific survival and overall survival of lung adenocarcinoma patients after surgery, which may facilitate doctors to provide highly individualized therapy. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08410-6.
Collapse
Affiliation(s)
- Suyu Wang
- Department of Cardiothoracic Surgery, Changzheng Hospital, Naval Medical University, 415 Fengyang Road, Shanghai, 200003, China
| | - Yue Yu
- Department of Cardiothoracic Surgery, Changzheng Hospital, Naval Medical University, 415 Fengyang Road, Shanghai, 200003, China
| | - Wenting Xu
- Fuyang Hospital of Anhui Medical University, 99 Huangshan Road, Fuyang, China.,Department of Anesthesiology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, 507 Zhengmin Road, Shanghai, 200433, China
| | - Xin Lv
- Department of Anesthesiology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, 507 Zhengmin Road, Shanghai, 200433, China
| | - Yufeng Zhang
- Department of Cardiothoracic Surgery, Changzheng Hospital, Naval Medical University, 415 Fengyang Road, Shanghai, 200003, China.
| | - Meiyun Liu
- Department of Anesthesiology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, 507 Zhengmin Road, Shanghai, 200433, China.
| |
Collapse
|
15
|
Lin SY, Zhang A, Lian J, Wang J, Chang TT, Lin YJ, Song W, Su YH. Recurrent HBV Integration Targets as Potential Drivers in Hepatocellular Carcinoma. Cells 2021; 10:cells10061294. [PMID: 34071075 PMCID: PMC8224658 DOI: 10.3390/cells10061294] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/15/2021] [Accepted: 05/20/2021] [Indexed: 02/07/2023] Open
Abstract
Chronic hepatitis B virus (HBV) infection is the major etiology of hepatocellular carcinoma (HCC), frequently with HBV integrating into the host genome. HBV integration, found in 85% of HBV-associated HCC (HBV–HCC) tissue samples, has been suggested to be oncogenic. Here, we investigated the potential of HBV–HCC driver identification via the characterization of recurrently targeted genes (RTGs). A total of 18,596 HBV integration sites from our in-house study and others were analyzed. RTGs were identified by applying three criteria: at least two HCC subjects, reported by at least two studies, and the number of reporting studies. A total of 396 RTGs were identified. Among the 28 most frequent RTGs, defined as affected in at least 10 HCC patients, 23 (82%) were associated with carcinogenesis and 5 (18%) had no known function. Available breakpoint positions from the three most frequent RTGs, TERT, MLL4/KMT2B, and PLEKHG4B, were analyzed. Mutual exclusivity of TERT promoter mutation and HBV integration into TERT was observed. We present an RTG consensus through comprehensive analysis to enable the potential identification and discovery of HCC drivers for drug development and disease management.
Collapse
Affiliation(s)
- Selena Y. Lin
- JBS Science, Inc., Doylestown, PA 18902, USA; (S.Y.L.); (J.W.); (W.S.)
| | - Adam Zhang
- The Baruch S. Blumberg Research Institute, Doylestown, PA 18902, USA; (A.Z.); (J.L.)
| | - Jessica Lian
- The Baruch S. Blumberg Research Institute, Doylestown, PA 18902, USA; (A.Z.); (J.L.)
| | - Jeremy Wang
- JBS Science, Inc., Doylestown, PA 18902, USA; (S.Y.L.); (J.W.); (W.S.)
| | - Ting-Tsung Chang
- Department of Internal Medicine, National Cheng Kung University Medical College, Tainan 704, Taiwan;
| | - Yih-Jyh Lin
- Department of Surgery, National Cheng Kung University Medical College, Tainan 704, Taiwan;
| | - Wei Song
- JBS Science, Inc., Doylestown, PA 18902, USA; (S.Y.L.); (J.W.); (W.S.)
| | - Ying-Hsiu Su
- The Baruch S. Blumberg Research Institute, Doylestown, PA 18902, USA; (A.Z.); (J.L.)
- Correspondence: ; Tel.: +215-489-4907
| |
Collapse
|
16
|
Endogenous APOBEC3B overexpression characterizes HPV-positive and HPV-negative oral epithelial dysplasias and head and neck cancers. Mod Pathol 2021; 34:280-290. [PMID: 32632179 PMCID: PMC8261524 DOI: 10.1038/s41379-020-0617-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/10/2020] [Accepted: 06/23/2020] [Indexed: 12/17/2022]
Abstract
The DNA cytosine deaminase APOBEC3B (A3B) is a newly recognized endogenous source of mutations in a range of human tumors, including head/neck cancer. A3B inflicts C-to-T and C-to-G base substitutions in 5'-TCA/T trinucleotide motifs, contributes to accelerated rates of tumor development, and affects clinical outcomes in a variety of cancer types. High-risk human papillomavirus (HPV) infection causes A3B overexpression, and HPV-positive cervical and head/neck cancers are among tumor types with the highest degree of APOBEC signature mutations. A3B overexpression in HPV-positive tumor types is caused by the viral E6/E7 oncoproteins and may be an early off-to-on switch in tumorigenesis. In comparison, less is known about the molecular mechanisms responsible for A3B overexpression in HPV-negative head/neck cancers. Here, we utilize an immunohistochemical approach to determine whether A3B is turned from off-to-on or if it undergoes a more gradual transition to overexpression in HPV-negative head/neck cancers. As positive controls, almost all HPV-positive oral epithelial dysplasias and oropharyngeal cancers showed high levels of nuclear A3B staining regardless of diagnosis. As negative controls, A3B levels were low in phenotypically normal epithelium adjacent to cancer and oral epithelial hyperplasias. Interestingly, HPV-negative and low-grade oral epithelial dysplasias showed intermediate A3B levels, while high-grade oral dysplasias showed high A3B levels similar to oral squamous cell carcinomas. A3B levels were highest in grade 2 and grade 3 oral squamous cell carcinomas. In addition, a strong positive association was found between nuclear A3B and Ki67 scores suggesting a linkage to the cell cycle. Overall, these results support a model in which gradual activation of A3B expression occurs during HPV-negative tumor development and suggest that A3B overexpression may provide a marker for advanced grade oral dysplasia and cancer.
Collapse
|
17
|
Liu Y, Liu F, Hu X, He J, Jiang Y. Combining Genetic Mutation and Expression Profiles Identifies Novel Prognostic Biomarkers of Lung Adenocarcinoma. Clin Med Insights Oncol 2020; 14:1179554920966260. [PMID: 35153523 PMCID: PMC8826273 DOI: 10.1177/1179554920966260] [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: 03/10/2020] [Accepted: 09/17/2020] [Indexed: 11/17/2022] Open
Abstract
Motivation: Although several prognostic signatures for lung adenocarcinoma (LUAD) have
been developed, they are mainly based on a single-omics data set. This
article aims to develop a novel set of prognostic signatures by combining
genetic mutation and expression profiles of LUAD patients. Methods: The genetic mutation and expression profiles, together with the clinical
profiles of a cohort of LUAD patients from The Cancer Genome Atlas (TCGA),
were downloaded. Patients were separated into 2 groups, namely, the
high-risk and low-risk groups, according to their overall survivals. Then,
differential analysis was performed to determine differentially expressed
genes (DEGs) and mutated genes (DMGs) in the expression and mutation
profiles, respectively, between the 2 groups. Finally, a prognostic model
based on the support vector machine (SVM) algorithm was developed by
combining the expression values of the DEGs and the mutation times of the
DMGs. Results: A total of 13 DEGs and 7 DMGs were recognized between the 2 groups. Their
prognostic values were validated using independent cohorts. Compared with
several existing signatures, the proposed prognostic signatures exhibited
better prediction performance in the testing set. In addition, it is found
that 1 of the 7 DMGs, GRIN2B, is mutated much more
frequently in the high-risk group, showing a potential value as a therapy
target. Conclusions: Combining multi-omics data sets is an applicable manner to identify novel
prognostic signatures and to improve the prognostic prediction for LUAD,
which will be heuristic to other types of cancers.
Collapse
Affiliation(s)
- Yun Liu
- Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China.,College of Communication Engineering, Jilin University, Changchun, China
| | - Fu Liu
- College of Communication Engineering, Jilin University, Changchun, China
| | - Xintong Hu
- Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Jiaxue He
- Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Yanfang Jiang
- Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| |
Collapse
|
18
|
Lathwal A, Kumar R, Arora C, Raghava GPS. Identification of prognostic biomarkers for major subtypes of non-small-cell lung cancer using genomic and clinical data. J Cancer Res Clin Oncol 2020; 146:2743-2752. [PMID: 32661603 DOI: 10.1007/s00432-020-03318-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 07/08/2020] [Indexed: 12/19/2022]
Abstract
PURPOSE Intra-tumor heterogeneity and high mortality among patients with non-small-cell lung carcinoma (NSCLC) emphasize the need to identify reliable prognostic markers unique to each subtype. METHODS In this study, univariate cox regression and prognostic index (PI)-based approaches were used to develop models for predicting NSCLC patients' subtype-specific survival. RESULTS Prognostic analysis of TCGA dataset identified 1334 and 2129 survival-specific genes for LUSC (488 samples) and LUAD (497 samples), respectively. Individually, 32 and 271 prognostic genes were found and validated in GSE study exclusively for LUSC and LUAD. Nearly, 9-10% of the validated genes in each subtype were already reported in multiple studies thus highlighting their importance as prognostic biomarkers. Strong literature evidence against these prognostic genes like "ELANE" (LUSC) and "AHSG" (LUAD) instigates further investigation for their therapeutic and diagnostic roles in the corresponding cohorts. Prognostic models built on five and four genes were validated for LUSC [HR = 2.10, p value = 1.86 × 10-5] and LUAD [HR = 2.70, p value = 3.31 × 10-7], respectively. The model based on the combination of age and tumor stage performed well in both NSCLC subtypes, suggesting that despite having distinctive histological features and treatment paradigms, some clinical features can be good prognostic predictors in both. CONCLUSION This study advocates that investigating the survival-specific biomarkers restricted to respective cohorts can advance subtype-specific prognosis, diagnosis, and treatment for NSCLC patients. Prognostic models and markers described for each subtype may provide insight into the heterogeneity of disease etiology and help in the development of new therapeutic approaches for the treatment of NSCLC patients.
Collapse
Affiliation(s)
- Anjali Lathwal
- Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi, Okhla Industrial Estate, Phase III (Near Govind Puri Metro Station), A-302 (R&D Block), New Delhi, 110020, India
| | - Rajesh Kumar
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Chakit Arora
- Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi, Okhla Industrial Estate, Phase III (Near Govind Puri Metro Station), A-302 (R&D Block), New Delhi, 110020, India
| | - Gajendra Pal Singh Raghava
- Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi, Okhla Industrial Estate, Phase III (Near Govind Puri Metro Station), A-302 (R&D Block), New Delhi, 110020, India.
| |
Collapse
|
19
|
Li J, Liu X, Cui Z, Han G. Comprehensive Analysis of Candidate Diagnostic and Prognostic Biomarkers Associated with Lung Adenocarcinoma. Med Sci Monit 2020; 26:e922070. [PMID: 32578582 PMCID: PMC7331474 DOI: 10.12659/msm.922070] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background We aimed to screen and identify central genetic and molecular targets involved in advancement of lung adenocarcinoma (LUAD) and to perform an integrated analysis and clinical validation. Material/Methods The GEO2R technique was utilized to assess differentially expressed genes (DEGs) among the gene sets GSE75037, GSE85716, and GSE118370. Subsequently, gene Ontology (GO) analyses and Kyoto Encyclopedia of Genes and Genomes (KEGG) analytical methods were executed to determine related biofunctions and signaling pathways, which were annotated with tools from the Database for Annotation, Visualization and Integrated Discovery (DAVID) resource. Then, a protein-protein interaction (PPI) network complex consisting of all detected DEGs was built with the STRING web interface. Cytohubba and MCODE plug-ins for Cytoscape software and Gene Expression Profiling Interactive Analysis (GEPIA) were employed to identify the hub genes. Finally, the mRNA expression of the identified hub genes was quantitatively validated by The Cancer Genome Atlas (TCGA) database analysis and real-time quantitative polymerase chain reaction (RT-qPCR). Results We screened 146 upregulated DEGs and 431 downregulated DEGs with the criteria of |logFC| >1 and P<0.05, and the GO analysis indicated that DEGs were implicated in mitotic nuclear division (biological process, BP), the nucleus (cellular component, CC), and protein binding (molecular function, MF) and were associated with multiple KEGG pathways, such as the p53 signaling pathway in cancer. Then, the top 8 genes that predicted significantly different outcomes in LUAD patients were filtered from the DEGs and selected as hub genes. The TCGA database analysis and RT-qPCR results demonstrated that these genes were differentially expressed with the same trends in LUAD tissues compared with normal tissues. Conclusions Overall, we propose that 8 genes (PECAM1, CDK1, MKI67, SPP1, TOP2A, CHEK1, CCNB1, and RRM2) might be novel hub genes strongly associated with the progression and prognosis of LUAD.
Collapse
Affiliation(s)
- Jingyuan Li
- Faculty of Pharmaceutical Sciences, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China (mainland)
| | - Xingyuan Liu
- Pathology Department, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China (mainland).,Pathology Department, Jinzhou Medical University, Jinzhou, Liaoning, China (mainland)
| | - Zan Cui
- Faculty of Pharmaceutical Sciences, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China (mainland)
| | - Guanying Han
- Faculty of Pharmaceutical Sciences, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China (mainland)
| |
Collapse
|
20
|
Peng Y, Yuan C, Tao X, Zhao Y, Yao X, Zhuge L, Huang J, Zheng Q, Zhang Y, Hong H, Chen H, Sun Y. Integrated analysis of optical mapping and whole-genome sequencing reveals intratumoral genetic heterogeneity in metastatic lung squamous cell carcinoma. Transl Lung Cancer Res 2020; 9:670-681. [PMID: 32676329 PMCID: PMC7354123 DOI: 10.21037/tlcr-19-401] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Background Intratumoral heterogeneity is a crucial factor to the outcome of patients and resistance to therapies, in which structural variants play an indispensable but undiscovered role. Methods We performed an integrated analysis of optical mapping and whole-genome sequencing on a primary tumor (PT) and matched metastases including lymph node metastasis (LNM) and tumor thrombus in the pulmonary vein (TPV). Single nucleotide variants, indels and structural variants were analyzed to reveal intratumoral genetic heterogeneity among tumor cells in different sites. Results Our results demonstrated there were less nonsynonymous somatic variants shared with PT in LNM than in TPV, while there were more structural variants shared with PT in LNM than in TPV. More private variants and its affected genes associated with tumorigenesis and progression were identified in TPV than in LNM. It should be noticed that optical mapping detected an average of 77.1% (74.5-78.5%) large structural variants (>5,000 bp) not detected by whole-genome sequencing and identified several structural variants private to metastases. Conclusions Our study does demonstrate structural variants, especially large structural variants play a crucial role in intratumoral genetic heterogeneity and optical mapping could make up for the deficiency of whole-genome sequencing to identify structural variants.
Collapse
Affiliation(s)
- Yizhou Peng
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Chongze Yuan
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xiaoting Tao
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yue Zhao
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xingxin Yao
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Lingdun Zhuge
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | | | - Qiang Zheng
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.,Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Yue Zhang
- Berry Genomics Corporation, Beijing 100015, China
| | - Hui Hong
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Haiquan Chen
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yihua Sun
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| |
Collapse
|
21
|
Liao Y, Wang X, Zhong P, Yin G, Fan X, Huang C. A nomogram for the prediction of overall survival in patients with stage II and III non-small cell lung cancer using a population-based study. Oncol Lett 2019; 18:5905-5916. [PMID: 31788064 PMCID: PMC6865638 DOI: 10.3892/ol.2019.10977] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 09/17/2019] [Indexed: 12/24/2022] Open
Abstract
As a malignant tumor with poor prognosis, accurate and effective treatment of non-small cell lung cancer (NSCLC) is crucial. To predict overall survival in patients with stage II and III NSCLC, a nomogram was constructed using data from the Surveillance, Epidemiology and End Results database. Eligible patients with NSCLC with available clinical information diagnosed between January 1, 2010 and November 31, 2015 were selected from the database, and the data were randomly divided into a training set and a validation set. Univariate and multivariate Cox regression analyses were used to identify prognostic factors with a threshold of P<0.05, and a nomogram was constructed. Harrell's concordance indexes and calibration plots were used to verify the predictive power of the model. Risk group stratification by stage was also performed. A total of 15,344 patients with stage II and III NSCLC were included in the study. The 3- and 5-year survival rates were 0.382 and 0.278, respectively. The training and validation sets comprised 10,744 and 4,600 patients, respectively. Age, sex, race, marital status, histology, grade, Tumor-Node-Metastasis T and N stage, surgery type, extent of lymph node dissection, radiation therapy and chemotherapy were identified as prognostic factors for the construction of the nomogram. The nomogram exhibited a clinical predictive ability of 0.719 (95% CI, 0.718–0.719) in the training set and 0.721 (95% CI, 0.720–0.722) in the validation set. The predicted calibration curve was similar to the standard curve. In addition, the nomogram was able to divide the patients into groups according to stage IIA, IIB, IIIA, and IIIB NSCLC. Thus, the nomogram provided predictive results for stage II and III NSCLC patients and accurately determined the 3- and 5-year overall survival of patients.
Collapse
Affiliation(s)
- Yi Liao
- Department of Respiratory and Critical Care Medicine II, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Xue Wang
- Department of Respiratory and Critical Care Medicine II, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Ping Zhong
- Department of Respiratory and Critical Care Medicine II, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Guofang Yin
- Department of Respiratory and Critical Care Medicine II, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Xianming Fan
- Department of Respiratory and Critical Care Medicine II, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Chengliang Huang
- Department of Respiratory and Critical Care Medicine II, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| |
Collapse
|
22
|
Wang J, Wang Y, Kong F, Han R, Song W, Chen D, Bu L, Wang S, Yue J, Ma L. Identification of a six‐gene prognostic signature for oral squamous cell carcinoma. J Cell Physiol 2019; 235:3056-3068. [PMID: 31538341 DOI: 10.1002/jcp.29210] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 09/03/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Jiaying Wang
- Department of Stomatology Affiliated Hospital of Qingdao University Qingdao Shandong China
| | - Yuanyong Wang
- Department of Thoracic Surgery Affiliated Hospital of Qingdao University Qingdao China
| | - Fanzhi Kong
- Department of Stomatology Affiliated Hospital of Qingdao University Qingdao Shandong China
| | - Rui Han
- Department of Stomatology Affiliated Hospital of Qingdao University Qingdao Shandong China
| | - Wenbin Song
- Department of Stomatology Affiliated Hospital of Qingdao University Qingdao Shandong China
| | - Di Chen
- Department of Gastroenterology Affiliated Hospital of Qingdao University Qingdao China
| | - Lingxue Bu
- Department of Stomatology Affiliated Hospital of Qingdao University Qingdao Shandong China
| | - Shuangyi Wang
- Department of Stomatology Affiliated Hospital of Qingdao University Qingdao Shandong China
| | - Jin Yue
- Department of Stomatology Affiliated Hospital of Qingdao University Qingdao Shandong China
| | - Lei Ma
- Department of Stomatology Affiliated Hospital of Qingdao University Qingdao Shandong China
| |
Collapse
|
23
|
Ma Q, Xu Y, Liao H, Cai Y, Xu L, Xiao D, Liu C, Pu W, Zhong X, Guo X. Identification and validation of key genes associated with non-small-cell lung cancer. J Cell Physiol 2019; 234:22742-22752. [PMID: 31127628 DOI: 10.1002/jcp.28839] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/30/2019] [Accepted: 05/01/2019] [Indexed: 12/24/2022]
Abstract
Non-small-cell lung cancer (NSCLC) is one of the main causes of death induced by cancer globally. However, the molecular aberrations in NSCLC patients remain unclearly. In the present study, four messenger RNA microarray datasets (GSE18842, GSE40275, GSE43458, and GSE102287) were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between NSCLC tissues and adjacent lung tissues were obtained from GEO2R and the overlapping DEGs were identified. Moreover, functional and pathway enrichment were performed by Funrich, while the protein-protein interaction (PPI) network construction were obtained from STRING and hub genes were visualized and identified by Cytoscape software. Furthermore, validation, overall survival (OS) and tumor staging analysis of selected hub genes were performed by GEPIA. A total of 367 DEGs (95 upregulated and 272 downregulated) were obtained through gene integration analysis. The PPI network consisted of 94 nodes and 1036 edges in the upregulated DEGs and 272 nodes and 464 edges in the downregulated DEGs, respectively. The PPI network identified 46 upregulated and 27 downregulated hub genes among the DEGs, and six (such as CENPE, NCAPH, MYH11, LRRK2, HSD17B6, and A2M) of that have not been identified to be associated with NSCLC so far. Moreover, the expression differences of the mentioned hub genes were consistent with that in lung adenocarcinoma and lung squamous cell carcinoma in the TCGA database. Further analysis showed that all the six hub genes were associated with tumor staging except MYH11, while only the upregulated DEG CENPE was associated with the worse OS of patients with NSCLC. In conclusion, the current study showed that CENPE, NCAPH, MYH11, LRRK2, HSD17B6, and A2M might be the key genes contributed to tumorigenesis or tumor progression in NSCLC, further functional study is needed to explore the involved mechanisms.
Collapse
Affiliation(s)
- Qiang Ma
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China.,Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Yuan Xu
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China.,Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Hebin Liao
- Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China
| | - Yan Cai
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China.,Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Lei Xu
- Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China
| | - Dan Xiao
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China.,Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Chang Liu
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China.,Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Wenjie Pu
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China.,Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Xiaowu Zhong
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China.,Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Xiaolan Guo
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.,Translational Medicine Research Center, North Sichuan Medical College, Nanchong, China.,Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| |
Collapse
|
24
|
Prognostic Role of Circulating miRNAs in Early-Stage Non-Small Cell Lung Cancer. J Clin Med 2019; 8:jcm8020131. [PMID: 30678026 PMCID: PMC6407000 DOI: 10.3390/jcm8020131] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 01/17/2019] [Accepted: 01/20/2019] [Indexed: 12/28/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) is the primary cause of cancer-related death worldwide, with a low 5-year survival rate even in fully resected early-stage disease. Novel biomarkers to identify patients at higher risk of relapse are needed. We studied the prognostic value of 84 circulating microRNAs (miRNAs) in 182 patients with resected early-stage NSCLC (99 adenocarcinoma (ADC), 83 squamous cell carcinoma (SCC)) from whom peripheral blood samples were collected pre-surgery. miRNA expression was analyzed in relation to disease-free survival (DFS) and overall survival (OS). In univariable analyses, five miRNAs (miR-26a-5p, miR-126-3p, miR-130b-3p, miR-205-5p, and miR-21-5p) were significantly associated with DFS in SCC, and four (miR-130b-3p, miR-26a-5p, miR-126-3p, and miR-205-5p) remained significantly associated with OS. In ADC, miR-222-3p, miR-22-3p, and mir-93-5p were significantly associated with DFS, miR-22-3p remaining significant for OS. Given the high-dimensionality of the dataset, multivariable models were obtained using a regularized Cox regression including all miRNAs and clinical covariates. After adjustment for disease stage, only miR-126-3p showed an independent prognostic role, with higher values associated with longer DFS in SCC patients. With regard to ADC and OS, no miRNA remained significant in multivariable analysis. Further investigation into the role of miR-126 as a prognostic marker in early-stage NSCLC is warranted.
Collapse
|