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Savel H, Meyer-Losic F, Proust-Lima C, Richert L. Statistical classification of treatment responses in mouse clinical trials for stratified medicine in oncology drug discovery. Sci Rep 2024; 14:934. [PMID: 38195626 PMCID: PMC10776864 DOI: 10.1038/s41598-023-51055-7] [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: 08/08/2023] [Accepted: 12/29/2023] [Indexed: 01/11/2024] Open
Abstract
Translational oncology research strives to explore a new aspect: identifying subgroups that exhibit treatment response even during pre-clinical phases. In this study, we focus on PDX models and their implementation in mouse clinical trials (MCT). Our primary objective was to identify subgroups with different treatment responses using Latent Class Mixed Model (LCMM).We used a public dataset and focused on one treatment, encorafenib, and two indications, melanoma and colorectal cancer, for which efficacy depends on a specific mutation BRAF V600E. One LCMM per indication was implemented to classify treatment responses at the PDX level, analyzing the growth kinetics of treated tumors and matched controls within the PDX models. A simulation study was carried out to explore the performance of LCMM in this context. For both applications, LCMM identified classes for which the higher the proportion of mutated BRAF V600E PDX models the greater the treatment effect, which is aligned with encorafenib use recommendations. The simulation study showed that LCMM could identify classes with large differences in treatment effects. LCMM is a suitable tool for MCT to explore treatment response subgroups of PDX. Once these subgroups are defined, characterization of their phenotypes/genotypes could be performed to explore treatment response predictors.
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Affiliation(s)
- Hélène Savel
- U1219, Inserm Bordeaux Population Health Research Centre, Department of Public Health, Université de Bordeaux, 33000, Bordeaux, France
- Ipsen Innovation, 5 Avenue du Canada, 91940, Les Ulis, France
- Inria, SISTM, 33400, Talence, France
| | | | - Cécile Proust-Lima
- U1219, Inserm Bordeaux Population Health Research Centre, Department of Public Health, Université de Bordeaux, 33000, Bordeaux, France
- Institut Bergonié, CHU de Bordeaux, INSERM, Université de Bordeaux, CIC-EC 1401, 33000, Bordeaux, France
| | - Laura Richert
- U1219, Inserm Bordeaux Population Health Research Centre, Department of Public Health, Université de Bordeaux, 33000, Bordeaux, France.
- Institut Bergonié, CHU de Bordeaux, INSERM, Université de Bordeaux, CIC-EC 1401, 33000, Bordeaux, France.
- Inria, SISTM, 33400, Talence, France.
- Université de Bordeaux, 146 Rue Léo Saignat, 33076, Bordeaux Cedex, France.
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4
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Wang J, Li R, Li J, Yi Y, Liu X, Chen J, Zhang H, Lu J, Li C, Wu H, Liang Z. Comprehensive analysis of oncogenic fusions in mismatch repair deficient colorectal carcinomas by sequential DNA and RNA next generation sequencing. J Transl Med 2021; 19:433. [PMID: 34657620 PMCID: PMC8522100 DOI: 10.1186/s12967-021-03108-6] [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: 05/22/2021] [Accepted: 10/06/2021] [Indexed: 11/26/2022] Open
Abstract
Background Colorectal carcinoma (CRC) harboring oncogenic fusions has been reported to be highly enriched in mismatch repair deficient (dMMR) tumors with MLH1 hypermethylation (MLH1me+) and wild-type BRAF and RAS. In this study, dMMR CRCs were screened for oncogene fusions using sequential DNA and RNA next generation sequencing (NGS). Results Comprehensive analysis of fusion variants, genetic profiles and clinicopathological features in fusion-positive dMMR CRCs was performed. Among 193 consecutive dMMR CRCs, 39 cases were identified as MLH1me+BRAF/RAS wild-type. Eighteen fusion-positive cases were detected by DNA NGS, all of which were MLH1me+ and BRAF/RAS wild-type. RNA NGS was sequentially conducted in the remaining 21 MLH1me+BRAF/RAS wild-type cases lacking oncogenic fusions by DNA NGS, and revealed four additional fusions, increasing the proportion of fusion-positive tumors from 46% (18/39) to 56% (22/39) in MLH1me+BRAF/RAS wild-type dMMR cases. All 22 fusions were found to involve RTK-RAS pathway. Most fusions affected targetable receptor tyrosine kinases, including NTRK1(9/22, 41%), NTRK3(5/22, 23%), ALK(3/22, 14%), RET(2/22, 9%) and MET(1/22, 5%), whilst only two fusions affected mitogen-activated protein kinase cascade components BRAF and MAPK1, respectively. RNF43 was identified as the most frequently mutated genes, followed by APC, TGFBR2, ATM, BRCA2 and FBXW7. The vast majority (19/22, 86%) displayed alterations in key WNT pathway components, whereas none harbored additional mutations in RTK-RAS pathway. In addition, fusion-positive tumors were typically diagnosed in elder patients and predominantly right-sided, and showed a significantly higher preponderance of hepatic flexure localization (P < 0.001) and poor differentiation (P = 0.019), compared to fusion-negative MLH1me+ CRCs. Conclusions We proved that sequential DNA and RNA NGS was highly effective for fusion detection in dMMR CRCs, and proposed an optimized practical fusion screening strategy. We further revealed that dMMR CRCs harboring oncogenic fusion was a genetically and clinicopathologically distinctive subgroup, and justified more precise molecular subtyping for personalized therapy. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-03108-6.
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Affiliation(s)
- Jing Wang
- Department of Pathology, Peking Union Medical College Hospital, and Molecular Pathology Research Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Ruiyu Li
- Department of Pathology, Peking Union Medical College Hospital, and Molecular Pathology Research Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Junjie Li
- Department of Pathology, Peking Union Medical College Hospital, and Molecular Pathology Research Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Yuting Yi
- Geneplus-Beijing Institute, Beijing, China
| | - Xiaoding Liu
- Department of Pathology, Peking Union Medical College Hospital, and Molecular Pathology Research Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Jingci Chen
- Department of Pathology, Peking Union Medical College Hospital, and Molecular Pathology Research Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Hui Zhang
- Department of Pathology, Peking Union Medical College Hospital, and Molecular Pathology Research Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Junliang Lu
- Department of Pathology, Peking Union Medical College Hospital, and Molecular Pathology Research Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Cami Li
- Department of Pathology, Peking Union Medical College Hospital, and Molecular Pathology Research Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Huanwen Wu
- Department of Pathology, Peking Union Medical College Hospital, and Molecular Pathology Research Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| | - Zhiyong Liang
- Department of Pathology, Peking Union Medical College Hospital, and Molecular Pathology Research Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
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5
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Hsu HC, Huang KC, Chen WS, Jiang JK, Yang SH, Wang HS, Chang SC, Lan YT, Lin CC, Lin HH, Huang SC, Cheng HH, Yang TS, Chen CC, Chao Y, Teng HW. Preference criteria for regorafenib in treating refractory metastatic colorectal cancer are the small tumor burden, slow growth and poor/scanty spread. Sci Rep 2021; 11:15370. [PMID: 34321583 PMCID: PMC8319410 DOI: 10.1038/s41598-021-94968-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 07/19/2021] [Indexed: 02/08/2023] Open
Abstract
Given the unclear preference criteria for regorafenib in treating refractory metastatic colorectal cancer (mCRC), this study aimed to construct an algorithm in selecting right patients for regorafenib. This was a multicenter retrospective cohort study. Patients with pathology confirmed mCRC and administered with regorafenib for > 3 weeks were enrolled. Patients with good response were defined to have progression-free survival (PFS) of ≥ 4 months. The Kaplan–Meier plot was used to analyze survival. A Cox proportional hazards model was used to analyze univariate and multivariate prognostic factors and was visualized using forest plot. A clustering heatmap was used to classify patients according to responses. The decision tree and nomogram were used to construct the approaching algorithm. A total of 613 patients was analyzed. The median PFS and overall survival (OS) were 2.7 and 10.6 months, respectively. The partial response and stable disease rate are 2.4% and 36.4%. The interval between metastasis (M1) and regorafenib, metastatic status (number, liver, and brain), and CEA level were independent prognostics factors of PFS that classifies patients into three groups: good, bad and modest-1/modest-2 group with PFS > = 4 months rates of 51%, 20%, 39% and 30%, respectively. Results were used to develop the decision tree and nomogram for approaching patients indicated with regorafenib. The preference criteria for regorafenib in treating patients with refractory mCRC are small tumor burden (CEA), slow growth (interval between metastasis and regorafenib) and poor/scanty spread (metastatic status: number and sites of metastasis): The 3S rules. TRIAL registration ClinicalTrials.gov Identifier: NCT03829852; Date of first registration (February 11, 2019).
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Affiliation(s)
- Hung-Chih Hsu
- Division of Hematology-Oncology, Chang Gung Memorial Hospital at Linkou, Tao-Yuan City, Taiwan.,College of Medicine, Chang Gung University, Tao-Yuan City, Taiwan
| | - Kuo-Cheng Huang
- Department of Hematology and Medical Oncology, Koo Foundation Sun Yat-Sen Cancer Center, Taipei, Taiwan
| | - Wei-Shone Chen
- School of Medicine, National Yang-Ming University, Taipei, 112, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Li-Nong Street, Taipei, 112, Taiwan.,Department of Surgery, Division of Colon and Rectal Surgery, Taipei Veterans General Hospital, Taipei, 112, Taiwan
| | - Jeng-Kai Jiang
- School of Medicine, National Yang-Ming University, Taipei, 112, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Li-Nong Street, Taipei, 112, Taiwan.,Department of Surgery, Division of Colon and Rectal Surgery, Taipei Veterans General Hospital, Taipei, 112, Taiwan
| | - Shung-Haur Yang
- School of Medicine, National Yang-Ming University, Taipei, 112, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Li-Nong Street, Taipei, 112, Taiwan.,Department of Surgery, Division of Colon and Rectal Surgery, Taipei Veterans General Hospital, Taipei, 112, Taiwan.,Department of Surgery, National Yang Ming Chiao Tung University Hospital, Yilan, Taiwan
| | - Huann-Sheng Wang
- School of Medicine, National Yang-Ming University, Taipei, 112, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Li-Nong Street, Taipei, 112, Taiwan.,Department of Surgery, Division of Colon and Rectal Surgery, Taipei Veterans General Hospital, Taipei, 112, Taiwan
| | - Shih-Ching Chang
- School of Medicine, National Yang-Ming University, Taipei, 112, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Li-Nong Street, Taipei, 112, Taiwan.,Department of Surgery, Division of Colon and Rectal Surgery, Taipei Veterans General Hospital, Taipei, 112, Taiwan
| | - Yuan-Tzu Lan
- School of Medicine, National Yang-Ming University, Taipei, 112, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Li-Nong Street, Taipei, 112, Taiwan.,Department of Surgery, Division of Colon and Rectal Surgery, Taipei Veterans General Hospital, Taipei, 112, Taiwan
| | - Chun-Chi Lin
- School of Medicine, National Yang-Ming University, Taipei, 112, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Li-Nong Street, Taipei, 112, Taiwan.,Department of Surgery, Division of Colon and Rectal Surgery, Taipei Veterans General Hospital, Taipei, 112, Taiwan
| | - Hung-Hsin Lin
- School of Medicine, National Yang-Ming University, Taipei, 112, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Li-Nong Street, Taipei, 112, Taiwan.,Department of Surgery, Division of Colon and Rectal Surgery, Taipei Veterans General Hospital, Taipei, 112, Taiwan
| | - Sheng-Chieh Huang
- School of Medicine, National Yang-Ming University, Taipei, 112, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Li-Nong Street, Taipei, 112, Taiwan.,Department of Surgery, Division of Colon and Rectal Surgery, Taipei Veterans General Hospital, Taipei, 112, Taiwan
| | - Hou-Hsuan Cheng
- School of Medicine, National Yang-Ming University, Taipei, 112, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Li-Nong Street, Taipei, 112, Taiwan.,Department of Surgery, Division of Colon and Rectal Surgery, Taipei Veterans General Hospital, Taipei, 112, Taiwan
| | - Tsai-Sheng Yang
- Division of Hematology-Oncology, Chang Gung Memorial Hospital at Linkou, Tao-Yuan City, Taiwan.,College of Medicine, Chang Gung University, Tao-Yuan City, Taiwan
| | - Chien-Chih Chen
- Department of Surgery, Koo Foundation Sun Yat-Sen Cancer Center, Taipei, Taiwan
| | - Yee Chao
- School of Medicine, National Yang-Ming University, Taipei, 112, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Li-Nong Street, Taipei, 112, Taiwan.,Department of Oncology, Division of Medical Oncology, Taipei Veterans General Hospital, No. 201, Sec. 2, Shih-Pai Road, Taipei, 112, Taiwan
| | - Hao-Wei Teng
- School of Medicine, National Yang-Ming University, Taipei, 112, Taiwan. .,School of Medicine, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Li-Nong Street, Taipei, 112, Taiwan. .,Department of Oncology, Division of Medical Oncology, Taipei Veterans General Hospital, No. 201, Sec. 2, Shih-Pai Road, Taipei, 112, Taiwan.
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6
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Gornowicz A, Szymanowska A, Mojzych M, Czarnomysy R, Bielawski K, Bielawska A. The Anticancer Action of a Novel 1,2,4-Triazine Sulfonamide Derivative in Colon Cancer Cells. Molecules 2021; 26:molecules26072045. [PMID: 33918514 PMCID: PMC8038278 DOI: 10.3390/molecules26072045] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/01/2021] [Accepted: 04/01/2021] [Indexed: 11/16/2022] Open
Abstract
Cancer therapy is one of the most important challenges of modern medical and chemical sciences. Among the many methods of combating cancer, chemotherapy plays a special role. Imperfect modern chemotherapy justifies continuing the search for new, more effective, and safe drugs. Sulfonamides are the classic group of chemotherapeutic drugs with a broad spectrum of pharmacological activity. Recent literature reports show that sulfonamide derivatives have anti-tumor activity in vitro and in vivo. The aim of the study was to synthesize a novel 1,2,4-triazine sulfonamide derivative and check its anticancer potential in DLD-1 and HT-29 colon cancer cells. The biological studies included MTT assay, DNA biosynthesis, cell cycle analysis, Annexin V binding assay, ethidium bromide/acridine orange staining, and caspase-8, -9, and -3/7 activity. The concentrations of important molecules (sICAM-1, mTOR, Beclin-1, cathepsin B) involved in the pathogenesis and poor prognosis of colorectal cancer were also evaluated by ELISA. We demonstrated that the novel compound was able to induce apoptosis through intrinsic and extrinsic pathways and was capable of decreasing sICAM-1, mTOR, cathepsin B concentrations, whereas increased Beclin-1 concentration was detected in both colon cancer cell lines. The novel compound represents promising multi-targeted potential in colorectal cancer, but further in vivo examinations are needed to confirm the claim.
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Affiliation(s)
- Agnieszka Gornowicz
- Department of Biotechnology, Medical University of Bialystok, 15-222 Bialystok, Poland; (A.S.); (A.B.)
- Correspondence:
| | - Anna Szymanowska
- Department of Biotechnology, Medical University of Bialystok, 15-222 Bialystok, Poland; (A.S.); (A.B.)
| | - Mariusz Mojzych
- Department of Chemistry, Siedlce University of Natural Sciences and Humanities, 08-110 Siedlce, Poland;
| | - Robert Czarnomysy
- Department of Synthesis and Technology of Drugs, Medical University of Bialystok, 15-222 Bialystok, Poland; (R.C.); (K.B.)
| | - Krzysztof Bielawski
- Department of Synthesis and Technology of Drugs, Medical University of Bialystok, 15-222 Bialystok, Poland; (R.C.); (K.B.)
| | - Anna Bielawska
- Department of Biotechnology, Medical University of Bialystok, 15-222 Bialystok, Poland; (A.S.); (A.B.)
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