|
1
|
Cheng B, Xu L, Zhang Y, Yang H, Liu S, Ding S, Zhao H, Sui Y, Wang C, Quan L, Liu J, Liu Y, Wang H, Zheng Z, Wu X, Guo J, Wen Z, Zhang R, Wang F, Liu H, Sun S. Correlation between NGS panel-based mutation results and clinical information in colorectal cancer patients. Heliyon 2024; 10:e29299. [PMID: 38623252 PMCID: PMC11016705 DOI: 10.1016/j.heliyon.2024.e29299] [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: 12/15/2023] [Revised: 04/04/2024] [Accepted: 04/04/2024] [Indexed: 04/17/2024] Open
Abstract
Early mutation identification guides patients with colorectal cancer (CRC) toward targeted therapies. In the present study, 414 patients with CRC were enrolled, and amplicon-based targeted next-generation sequencing (NGS) was then performed to detect genomic alterations within the 73 cancer-related genes in the OncoAim panel. The overall mutation rate was 91.5 % (379/414). Gene mutations were detected in 38/73 genes tested. The most frequently mutated genes were TP53 (60.9 %), KRAS (46.6 %), APC (30.4 %), PIK3CA (15.9 %), FBXW7 (8.2 %), SMAD4 (6.8 %), BRAF (6.5 %), and NRAS (3.9 %). Compared with the wild type, TP53 mutations were associated with low microsatellite instability/microsatellite stability (MSI-L/MSS) (P = 0.007), tumor location (P = 0.043), and histological grade (P = 0.0009); KRAS mutations were associated with female gender (P = 0.026), distant metastasis (P = 0.023), TNM stage (P = 0.013), and histological grade (P = 0.004); APC mutations were associated with patients <64 years of age at diagnosis (P = 0.04); PIK3CA mutations were associated with tumor location (P = 4.97e-06) and female gender (P = 0.018); SMAD4 mutations were associated with tumor location (P = 0.033); BRAF mutations were associated with high MSI (MSI-H; P = 6.968e-07), tumor location (P = 1.58e-06), and histological grade (P = 0.04). Mutations in 164 individuals were found to be pathogenic or likely pathogenic. A total of 26 patients harbored MSI-H tumors and they all had at least one detected gene mutation. Mutated genes were enriched in signaling pathways associated with CRC. The present findings have important implications for improving the personalized treatment of patients with CRC in China.
Collapse
Affiliation(s)
- Bo Cheng
- Department of Pathology, Chinese People's Liberation Army Rocket Force Characteristic Medical Center, Beijing 100037, China
| | - Lin Xu
- Department of Pathology, Chinese People's Liberation Army Rocket Force Characteristic Medical Center, Beijing 100037, China
| | - Yunzhi Zhang
- Singlera Genomics (Shanghai) Ltd., Shanghai 201318, China
- School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Huimin Yang
- Singlera Genomics (Shanghai) Ltd., Shanghai 201318, China
| | - Shan Liu
- Department of Pathology, Chinese People's Liberation Army Rocket Force Characteristic Medical Center, Beijing 100037, China
| | - Shanshan Ding
- Department of Pathology, Chinese People's Liberation Army Rocket Force Characteristic Medical Center, Beijing 100037, China
| | - Huan Zhao
- Department of Pathology, Chinese People's Liberation Army Rocket Force Characteristic Medical Center, Beijing 100037, China
| | - Yi Sui
- Singlera Genomics (Shanghai) Ltd., Shanghai 201318, China
| | - Chan Wang
- Singlera Genomics (Shanghai) Ltd., Shanghai 201318, China
| | - Lanju Quan
- Department of Pathology, Chinese People's Liberation Army Rocket Force Characteristic Medical Center, Beijing 100037, China
| | - Jinhong Liu
- Department of Pathology, Chinese People's Liberation Army Rocket Force Characteristic Medical Center, Beijing 100037, China
| | - Ye Liu
- Department of Pathology, Chinese People's Liberation Army Rocket Force Characteristic Medical Center, Beijing 100037, China
| | - Hongming Wang
- Singlera Genomics (Shanghai) Ltd., Shanghai 201318, China
| | - Zhaoqing Zheng
- Singlera Genomics (Shanghai) Ltd., Shanghai 201318, China
| | - Xizhao Wu
- Department of Pathology, Chinese People's Liberation Army Rocket Force Characteristic Medical Center, Beijing 100037, China
| | - Jing Guo
- Department of Pathology, Chinese People's Liberation Army Rocket Force Characteristic Medical Center, Beijing 100037, China
| | - Zhaohong Wen
- Singlera Genomics (Shanghai) Ltd., Shanghai 201318, China
| | - Ruya Zhang
- Department of Pathology, Chinese People's Liberation Army Rocket Force Characteristic Medical Center, Beijing 100037, China
| | - Fei Wang
- Department of Pathology, Chinese People's Liberation Army Rocket Force Characteristic Medical Center, Beijing 100037, China
| | - Hongmei Liu
- Singlera Genomics (Shanghai) Ltd., Shanghai 201318, China
| | - Suozhu Sun
- Department of Pathology, Chinese People's Liberation Army Rocket Force Characteristic Medical Center, Beijing 100037, China
| |
Collapse
|
|
2
|
Zhao D, Li H, Mambetsariev I, Chen C, Pharaon R, Fricke J, Baroz AR, Kulkarni P, Xing Y, Massarelli E, Koczywas M, Reckamp KL, Margolin K, Salgia R. Molecular and Clinical Features of Hospital Admissions in Patients with Thoracic Malignancies on Immune Checkpoint Inhibitors. Cancers (Basel) 2021; 13:cancers13112653. [PMID: 34071259 PMCID: PMC8198372 DOI: 10.3390/cancers13112653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/22/2021] [Accepted: 05/25/2021] [Indexed: 11/16/2022] Open
Abstract
Lung cancer patients undergoing systemic treatment with immune checkpoint inhibitors (ICIs) can lead to severe immune-related adverse events (irAEs) that may warrant immediate hospitalization. Patients with thoracic malignancies hospitalized at City of Hope while undergoing treatment with ICIs were identified. Pathology and available next-generation sequencing (NGS) data, including the programmed death-ligand 1 (PD-L1) status and clinical information, including hospitalizations, invasive procedures, and the occurrence of irAEs, were collected. Unpaired T-tests, Chi-square/Fisher's exact test, and logistic regression were used to analyze our cohort. The overall survival (OS) was calculated and compared using univariate and multivariate COX models. Ninety patients with stage IV lung cancer were admitted after ICI treatment. Of those patients, 28 (31.1%) had documented irAEs. Genomic analyses showed an enrichment of LRP1B mutations (n = 5/6 vs. n = 7/26, 83.3% vs. 26.9%; odds ratio (OR) (95% confidence interval (CI): 13.5 (1.7-166.1); p < 0.05) and MLL3 mutations (n = 4/6, 66.7% vs. n = 5/26, 19.2%; OR (95% CI): 8.4 (1.3-49.3), p < 0.05) in patients with irAE occurrences. Patients with somatic genomic alterations (GAs) in MET (median OS of 2.7 vs. 7.2 months; HR (95% CI): 3.1 (0.57-17.1); p < 0.05) or FANCA (median OS of 3.0 vs. 12.4 months; HR (95% CI): 3.1 (0.70-13.8); p < 0.05) demonstrated a significantly shorter OS. Patients with irAEs showed a trend toward improved OS (median OS 16.4 vs. 6.8 months, p = 0.19) compared to hospitalized patients without documented irAEs. Lung cancer patients who required treatment discontinuance or interruption due to irAEs (n = 19) had significantly longer OS (median OS 18.5 vs. 6.2 months; HR (95% CI): 0.47 (0.28-0.79); p < 0.05). Our results showed a significant survival benefit in lung cancer patients hospitalized due to irAEs that necessitated a treatment interruption. Patients with positive somatic GAs in MET and FANCA were associated with significantly worse OS compared to patients with negative GAs.
Collapse
Affiliation(s)
- Dan Zhao
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010-3000, USA; (D.Z.); (I.M.); (R.P.); (J.F.); (A.R.B.); (P.K.); (Y.X.); (E.M.); (M.K.); (K.L.R.); (K.M.)
| | - Haiqing Li
- Integrative Genomics Core, Beckman Research Institute, City of Hope Medical Center, Duarte, CA 91010-3000, USA;
- Department of Computational & Quantitative Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010-3000, USA
| | - Isa Mambetsariev
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010-3000, USA; (D.Z.); (I.M.); (R.P.); (J.F.); (A.R.B.); (P.K.); (Y.X.); (E.M.); (M.K.); (K.L.R.); (K.M.)
| | - Chen Chen
- Applied AI and Data Science, City of Hope National Medical Center, Duarte, CA 91010-3000, USA;
| | - Rebecca Pharaon
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010-3000, USA; (D.Z.); (I.M.); (R.P.); (J.F.); (A.R.B.); (P.K.); (Y.X.); (E.M.); (M.K.); (K.L.R.); (K.M.)
| | - Jeremy Fricke
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010-3000, USA; (D.Z.); (I.M.); (R.P.); (J.F.); (A.R.B.); (P.K.); (Y.X.); (E.M.); (M.K.); (K.L.R.); (K.M.)
| | - Angel R. Baroz
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010-3000, USA; (D.Z.); (I.M.); (R.P.); (J.F.); (A.R.B.); (P.K.); (Y.X.); (E.M.); (M.K.); (K.L.R.); (K.M.)
| | - Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010-3000, USA; (D.Z.); (I.M.); (R.P.); (J.F.); (A.R.B.); (P.K.); (Y.X.); (E.M.); (M.K.); (K.L.R.); (K.M.)
| | - Yan Xing
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010-3000, USA; (D.Z.); (I.M.); (R.P.); (J.F.); (A.R.B.); (P.K.); (Y.X.); (E.M.); (M.K.); (K.L.R.); (K.M.)
| | - Erminia Massarelli
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010-3000, USA; (D.Z.); (I.M.); (R.P.); (J.F.); (A.R.B.); (P.K.); (Y.X.); (E.M.); (M.K.); (K.L.R.); (K.M.)
| | - Marianna Koczywas
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010-3000, USA; (D.Z.); (I.M.); (R.P.); (J.F.); (A.R.B.); (P.K.); (Y.X.); (E.M.); (M.K.); (K.L.R.); (K.M.)
| | - Karen L. Reckamp
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010-3000, USA; (D.Z.); (I.M.); (R.P.); (J.F.); (A.R.B.); (P.K.); (Y.X.); (E.M.); (M.K.); (K.L.R.); (K.M.)
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 91010-3000, USA
| | - Kim Margolin
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010-3000, USA; (D.Z.); (I.M.); (R.P.); (J.F.); (A.R.B.); (P.K.); (Y.X.); (E.M.); (M.K.); (K.L.R.); (K.M.)
| | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010-3000, USA; (D.Z.); (I.M.); (R.P.); (J.F.); (A.R.B.); (P.K.); (Y.X.); (E.M.); (M.K.); (K.L.R.); (K.M.)
- Correspondence: ; Tel.: +1-626-218-3712; Fax: +1-626-471-7322
| |
Collapse
|