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Huang L, Lv Y, Guan S, Yan H, Han L, Wang Z, Han Q, Dai G, Shi Y. High somatic mutations in circulating tumor DNA predict response of metastatic pancreatic ductal adenocarcinoma to first-line nab-paclitaxel plus S-1: prospective study. J Transl Med 2024; 22:184. [PMID: 38378604 PMCID: PMC10877900 DOI: 10.1186/s12967-024-04989-z] [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: 11/26/2023] [Accepted: 02/12/2024] [Indexed: 02/22/2024] Open
Abstract
AIMS We previously showed that the nab-paclitaxel plus S-1 (NPS) regimen had promising effects against metastatic pancreatic ducal adenocarcinoma (mPDAC), whose efficacy however could not be precisely predicted by routine biomarkers. This prospective study aimed to investigate the values of mutations in circulating tumor DNA (ctDNA) and their dynamic changes in predicting response of mPDAC to NPS chemotherapy. METHODS Paired tumor tissue and blood samples were prospectively collected from patients with mPDAC receiving first-line NPS chemotherapy, and underwent next-generation sequencing with genomic profiling of 425 genes for ctDNA. High mutation allelic frequency (MAF) was defined as ≥ 30% and ≥ 5% in tumor tissue and blood, respectively. Kappa statistics were used to assess agreement between mutant genes in tumor and ctDNA. Associations of mutations in ctDNA and their dynamic changes with tumor response, overall survival (OS), and progression-free survival (PFS) were assessed using the Kaplan-Meier method, multivariable-adjusted Cox proportional hazards regression, and longitudinal data analysis. RESULTS 147 blood samples and 43 paired tumor specimens from 43 patients with mPDAC were sequenced. The most common driver genes with high MAF were KRAS (tumor, 35%; ctDNA, 37%) and TP53 (tumor, 37%; ctDNA, 33%). Mutation rates of KRAS and TP53 in ctDNA were significantly higher in patients with liver metastasis, with baseline CA19-9 ≥ 2000 U/mL, and/or without an early CA19-9 response. κ values for the 5 most commonly mutated genes between tumor and ctDNA ranged from 0.48 to 0.76. MAFs of the genes mostly decreased sequentially during subsequent measurements, which significantly correlated with objective response, with an increase indicating cancer progression. High mutations of KRAS and ARID1A in both tumor and ctDNA, and of TP53, CDKN2A, and SMAD4 in ctDNA but not in tumor were significantly associated with shorter survival. When predicting 6-month OS, AUCs for the 5 most commonly mutated genes in ctDNA ranged from 0.59 to 0.84, larger than for genes in tumor (0.56 to 0.71) and for clinicopathologic characteristics (0.51 to 0.68). Repeated measurements of mutations in ctDNA significantly differentiated survival and tumor response. Among the 31 patients with ≥ 2 ctDNA tests, longitudinal analysis of changes in gene MAF showed that ctDNA progression was 60 and 58 days ahead of radiologic and CA19-9 progression for 48% and 42% of the patients, respectively. CONCLUSIONS High mutations of multiple driving genes in ctDNA and their dynamic changes could effectively predict response of mPDAC to NPS chemotherapy, with promising reliable predictive performance superior to routine clinicopathologic parameters. Inspiringly, longitudinal ctDNA tracking could predict disease progression about 2 months ahead of radiologic or CA19-9 evaluations, with the potential to precisely devise individualized therapeutic strategies for mPDAC.
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Affiliation(s)
- Lei Huang
- Medical Center on Aging of Ruijin Hospital, MCARJH, Shanghai Jiaotong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China.
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Yao Lv
- Department of Medical Oncology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Shasha Guan
- Department of Medical Oncology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Huan Yan
- Department of Medical Oncology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Lu Han
- Department of Medical Oncology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Zhikuan Wang
- Department of Medical Oncology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China.
| | - Quanli Han
- Department of Medical Oncology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China.
| | - Guanghai Dai
- Department of Medical Oncology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China.
| | - Yan Shi
- Department of General Surgery, Shanghai Seventh People's Hospital, Shanghai University of Traditional Chinese Medicine, 358 Datong Road, Gaoqiao Town, Shanghai, 200137, China.
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Huang L, Yuan X, Zhao L, Han Q, Yan H, Yuan J, Guan S, Xu X, Dai G, Wang J, Shi Y. Gene signature developed for predicting early relapse and survival in early-stage pancreatic cancer. BJS Open 2023; 7:7169392. [PMID: 37196196 DOI: 10.1093/bjsopen/zrad031] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 01/23/2023] [Accepted: 02/23/2023] [Indexed: 05/19/2023] Open
Abstract
BACKGROUND The aim of this study was to construct a predictive signature integrating tumour-mutation- and copy-number-variation-associated features using machine learning to precisely predict early relapse and survival in patients with resected stage I-II pancreatic ductal adenocarcinoma. METHODS Patients with microscopically confirmed stage I-II pancreatic ductal adenocarcinoma undergoing R0 resection at the Chinese PLA General Hospital between March 2015 and December 2016 were enrolled. Whole exosome sequencing was performed, and genes with different mutation or copy number variation statuses between patients with and without relapse within 1 year were identified using bioinformatics analysis. A support vector machine was used to evaluate the importance of the differential gene features and to develop a signature. Signature validation was performed in an independent cohort. The associations of the support vector machine signature and single gene features with disease-free survival and overall survival were assessed. Biological functions of integrated genes were further analysed. RESULTS Overall, 30 and 40 patients were included in the training and validation cohorts, respectively. Some 11 genes with differential patterns were first identified; using a support vector machine, four features (mutations of DNAH9, TP53, and TUBGCP6, and copy number variation of TMEM132E) were further selected and integrated to construct a predictive signature (the support vector machine classifier). In the training cohort, the 1-year disease-free survival rates were 88 per cent (95 per cent c.i. 73 to 100) and 7 per cent (95 per cent c.i. 1 to 47) in the low-support vector machine subgroup and the high-support vector machine subgroup respectively (P < 0.001). Multivariable analyses showed that high support vector machine was significantly and independently associated with both worse overall survival (HR 29.20 (95 per cent c.i. 4.48 to 190.21); P < 0.001) and disease-free survival (HR 72.04 (95 per cent c.i. 6.74 to 769.96); P < 0.001). The area under the curve of the support vector machine signature for 1-year disease-free survival (0.900) was significantly larger than the area under the curve values of the mutations of DNAH9 (0.733; P = 0.039), TP53 (0.767; P = 0.024), and TUBGCP6 (0.733; P = 0.023), the copy number variation of TMEM132E (0.700; P = 0.014), TNM stage (0.567; P = 0.002), and differentiation grade (0.633; P = 0.005), suggesting higher predictive accuracy for prognosis. The value of the signature was further validated in the validation cohort. The four genes included in the support vector machine signature (DNAH9, TUBGCP6, and TMEM132E were novel in pancreatic ductal adenocarcinoma) were significantly associated with the tumour immune microenvironment, G protein-coupled receptor binding and signalling, cell-cell adhesion, etc. CONCLUSION The newly constructed support vector machine signature precisely and powerfully predicted relapse and survival in patients with stage I-II pancreatic ductal adenocarcinoma after R0 resection.
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Affiliation(s)
- Lei Huang
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Medical Centre on Ageing of Ruijin Hospital, MCARJH, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiaodong Yuan
- Organ Transplant Center, Department of Hepatobiliary and Transplantation Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Liangchao Zhao
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Quanli Han
- Department of Medical Oncology, Chinese PLA General Hospital, Beijing, China
| | - Huan Yan
- Department of Medical Oncology, Chinese PLA General Hospital, Beijing, China
| | - Jing Yuan
- Department of Pathology, Chinese PLA General Hospital, Beijing, China
| | - Shasha Guan
- Department of Medical Oncology, Chinese PLA General Hospital, Beijing, China
| | - Xiaofeng Xu
- Shanghai Chief Technician Studio (Information & Technology), Shanghai, China
| | - Guanghai Dai
- Department of Medical Oncology, Chinese PLA General Hospital, Beijing, China
| | - Junqing Wang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Shi
- Department of General Surgery, Shanghai Seventh People's Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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Shi Y, Han Q, Yan H, Lv Y, Yuan J, Li J, Guan S, Wang Z, Huang L, Dai G. S-1 Maintenance Therapy After First-Line Treatment With Nab-Paclitaxel Plus S-1 for Advanced Pancreatic Adenocarcinoma: A Real-World Study. Front Oncol 2022; 12:865404. [PMID: 35646689 PMCID: PMC9141286 DOI: 10.3389/fonc.2022.865404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Background In our previous phase II study, nab-paclitaxel plus S-1 (NPS) showed encouraging objective response rate (ORR) as first-line treatment for advanced pancreatic adenocarcinoma (APAC). This study aimed to evaluate the effectiveness and safety of S-1 maintenance after NPS in APAC and to explore factors predicting survival benefits when using S-1 maintenance. Methods Between 2014 and 2018 a total of 182 patients with APAC, who were primarily treated with NPS, were included. For patients without progression or with treatment discontinuation due to any reasons within 4 months during NPS treatment, S-1 monotherapy was administrable as maintenance therapy at the physicians’ discretion based on the patients’ preference and performance status. Efficacy and safety of S-1 maintenance were investigated. Results In 123 patients without progression within 4 months during NPS treatment, 74 received S-1 maintenance and had median progression-free survival of 9.6 months and median overall survival of 16.7 months. Multivariable analysis showed that in patients receiving S-1 maintenance after first-line NPS therapy, an Eastern Cooperative Oncology Group (ECOG) Performance Status score of 0, non-metastatic disease, and complete or partial response as best response to NPS chemotherapy were independently associated with better survival. The most common all-grade hematological and non-hematological adverse events were neutropenia (82.4%) and peripheral neurotoxicity (66.2%), respectively, and the most common ≥Grade 3 hematological and non-hematological adverse events were neutropenia (40.5%) and peripheral neurotoxicity (6.8%), respectively in patients who received S-1 maintenance. Conclusions Our real-world study showed that S-1 maintenance after tumor response or stable disease induced by first-line NPS treatment was effective and well-tolerated for some patients with APAC, which offers a promising alternative treatment strategy with encouraging survival for APAC.
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Affiliation(s)
- Yan Shi
- Department of Oncology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Yan Shi, ; Lei Huang, ; Guanghai Dai,
| | - Quanli Han
- Department of Medical Oncology, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Huan Yan
- Department of Medical Oncology, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Yao Lv
- Department of Medical Oncology, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Jing Yuan
- Department of Pathology, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Jie Li
- Department of Pathology, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Shasha Guan
- Department of Medical Oncology, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Zhikuan Wang
- Department of Medical Oncology, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Lei Huang
- Department of Oncology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Medical Center on Aging of Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Yan Shi, ; Lei Huang, ; Guanghai Dai,
| | - Guanghai Dai
- Department of Medical Oncology, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
- *Correspondence: Yan Shi, ; Lei Huang, ; Guanghai Dai,
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