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Marques A, Cavaco P, Torre C, Sepodes B, Rocha J. Tumor mutational burden in colorectal cancer: Implications for treatment. Crit Rev Oncol Hematol 2024; 197:104342. [PMID: 38614266 DOI: 10.1016/j.critrevonc.2024.104342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/27/2024] [Accepted: 03/29/2024] [Indexed: 04/15/2024] Open
Abstract
Although immune checkpoint inhibitors have revolutionized the treatment of several advanced solid cancers, in colorectal cancer, the transformative benefit of these innovative medicines is currently limited to those with deficient mismatch repair or high microsatellite instability. Tumor mutational burden (TMB) has emerged as a potential predictor of immunotherapy benefit, but the lack of standardization in its assessment and reporting has hindered the introduction of this biomarker in routine clinical practice. Here, we compiled 45 colorectal cancer studies utilizing numerical thresholds for high-TMB. In this group of studies, TMB cut-offs ranged from 6.88 to 41 mut/Mb and were most often set at 10, 17, or 20 mut/Mb. Additionally, we observed divergent TMB definitions and inconsistent disclosure of specific methodological details, which collectively emphasize the substantial lack of harmonization within the field. Ongoing efforts to harmonize TMB assessment will be critical to validate TMB as a predictive marker of immunotherapy response.
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Affiliation(s)
- Adriana Marques
- Research Institute for Medicines (iMed.ULisboa), Lisboa 1649-003, Portugal; Faculdade de Farmácia, Universidade de Lisboa, Lisboa 1649-003, Portugal
| | - Patrícia Cavaco
- Research Institute for Medicines (iMed.ULisboa), Lisboa 1649-003, Portugal; Faculdade de Farmácia, Universidade de Lisboa, Lisboa 1649-003, Portugal; Pharmacy Department, Centro Hospitalar de Lisboa Ocidental, Lisboa 1449-005, Portugal
| | - Carla Torre
- Research Institute for Medicines (iMed.ULisboa), Lisboa 1649-003, Portugal; Faculdade de Farmácia, Universidade de Lisboa, Lisboa 1649-003, Portugal
| | - Bruno Sepodes
- Research Institute for Medicines (iMed.ULisboa), Lisboa 1649-003, Portugal; Faculdade de Farmácia, Universidade de Lisboa, Lisboa 1649-003, Portugal
| | - João Rocha
- Research Institute for Medicines (iMed.ULisboa), Lisboa 1649-003, Portugal; Faculdade de Farmácia, Universidade de Lisboa, Lisboa 1649-003, Portugal.
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Choi Y, Lee J, Shin K, Lee JW, Kim JW, Lee S, Choi YJ, Park KH, Kim JH. Integrated clinical and genomic models using machine-learning methods to predict the efficacy of paclitaxel-based chemotherapy in patients with advanced gastric cancer. BMC Cancer 2024; 24:502. [PMID: 38643078 PMCID: PMC11031899 DOI: 10.1186/s12885-024-12268-9] [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: 01/19/2024] [Accepted: 04/16/2024] [Indexed: 04/22/2024] Open
Abstract
BACKGROUND Paclitaxel is commonly used as a second-line therapy for advanced gastric cancer (AGC). The decision to proceed with second-line chemotherapy and select an appropriate regimen is critical for vulnerable patients with AGC progressing after first-line chemotherapy. However, no predictive biomarkers exist to identify patients with AGC who would benefit from paclitaxel-based chemotherapy. METHODS This study included 288 patients with AGC receiving second-line paclitaxel-based chemotherapy between 2017 and 2022 as part of the K-MASTER project, a nationwide government-funded precision medicine initiative. The data included clinical (age [young-onset vs. others], sex, histology [intestinal vs. diffuse type], prior trastuzumab use, duration of first-line chemotherapy), and genomic factors (pathogenic or likely pathogenic variants). Data were randomly divided into training and validation sets (0.8:0.2). Four machine learning (ML) methods, namely random forest (RF), logistic regression (LR), artificial neural network (ANN), and ANN with genetic embedding (ANN with GE), were used to develop the prediction model and validated in the validation sets. RESULTS The median patient age was 64 years (range 25-91), and 65.6% of those were male. A total of 288 patients were divided into the training (n = 230) and validation (n = 58) sets. No significant differences existed in baseline characteristics between the training and validation sets. In the training set, the areas under the ROC curves (AUROC) for predicting better progression-free survival (PFS) with paclitaxel-based chemotherapy were 0.499, 0.679, 0.618, and 0.732 in the RF, LR, ANN, and ANN with GE models, respectively. The ANN with the GE model that achieved the highest AUROC recorded accuracy, sensitivity, specificity, and F1-score performance of 0.458, 0.912, 0.724, and 0.579, respectively. In the validation set, the ANN with GE model predicted that paclitaxel-sensitive patients had significantly longer PFS (median PFS 7.59 vs. 2.07 months, P = 0.020) and overall survival (OS) (median OS 14.70 vs. 7.50 months, P = 0.008). The LR model predicted that paclitaxel-sensitive patients showed a trend for longer PFS (median PFS 6.48 vs. 2.33 months, P = 0.078) and OS (median OS 12.20 vs. 8.61 months, P = 0.099). CONCLUSIONS These ML models, integrated with clinical and genomic factors, offer the possibility to help identify patients with AGC who may benefit from paclitaxel chemotherapy.
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Grants
- HR22C1302 Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea
- HR22C1302 Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea
- HR22C1302 Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea
- HR22C1302 Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea
- HR22C1302 Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea
- HR22C1302 Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea
- HR22C1302 Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea
- HR22C1302 Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea
- HR22C1302 Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea
- Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea
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Affiliation(s)
- Yonghwa Choi
- Department of Computer Science and Engineering, Korea University, Seoul, Korea
- OncoMASTER Inc., Seoul, Korea
| | - Jangwoo Lee
- Institute of Human Behavior & Genetic, Korea University College of Medicine, Seoul, Korea
- Biomedical Research Center, Korea University Anam Hospital, Seoul, Korea
| | - Keewon Shin
- Biomedical Research Center, Korea University Anam Hospital, Seoul, Korea
| | - Ji Won Lee
- Division of Medical Oncology, Department of Internal Medicine, Korea University College of Medicine, Korea University Anam Hospital, 73, Goryeodae-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Ju Won Kim
- Division of Medical Oncology, Department of Internal Medicine, Korea University College of Medicine, Korea University Anam Hospital, 73, Goryeodae-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Soohyeon Lee
- Division of Medical Oncology, Department of Internal Medicine, Korea University College of Medicine, Korea University Anam Hospital, 73, Goryeodae-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Yoon Ji Choi
- Division of Medical Oncology, Department of Internal Medicine, Korea University College of Medicine, Korea University Anam Hospital, 73, Goryeodae-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Kyong Hwa Park
- Division of Medical Oncology, Department of Internal Medicine, Korea University College of Medicine, Korea University Anam Hospital, 73, Goryeodae-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Jwa Hoon Kim
- Division of Medical Oncology, Department of Internal Medicine, Korea University College of Medicine, Korea University Anam Hospital, 73, Goryeodae-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea.
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Lee K, Lee J, Choi J, Sim SH, Kim JE, Kim MH, Park YH, Kim JH, Koh SJ, Park KH, Kang MJ, Ahn MS, Lee KE, Kim HJ, Ahn HK, Kim HJ, Park KU, Park IH. Genomic analysis of plasma circulating tumor DNA in patients with heavily pretreated HER2 + metastatic breast cancer. Sci Rep 2023; 13:9928. [PMID: 37336919 DOI: 10.1038/s41598-023-35925-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 05/25/2023] [Indexed: 06/21/2023] Open
Abstract
We explored accumulated genomic alterations in patients with heavily treated HER2 + metastatic breast cancer enrolled in the KCSG BR18-14/KM10B trial. Targeted sequencing was performed with circulating tumor DNAs (ctDNAs) collected before the treatment of 92 patients. ctDNAs collected at the time of disease progression from seven patients who had a durable response for > 12 months were also analyzed. Sixty-five genes were identified as pathogenic alterations in 99 samples. The most frequently altered genes were TP53 (n = 48), PIKCA (n = 21) and ERBB3 (n = 19). TP53 and PIK3CA mutations were significantly related with shorter progression free survival (PFS), and patients with a higher ctDNA fraction showed a worse PFS. The frequency of homologous recombination deficiency (HRD)-related gene mutations was higher than that in matched tumor tissues, and these mutations tended to be associated with shorter PFS. New pathogenic variants were found at the end of treatment in all seven patients, including BRCA2, VHL, RAD50, RB1, BRIP1, ATM, FANCA, and PIK3CA mutations. In conclusion, TP53 and PIK3CA mutations, as well as a higher ctDNA fraction, were associated with worse PFS with trastuzumab and cytotoxic chemotherapy. The enrichment of HRD-related gene mutations and newly detected variants in ctDNA may be related to resistance to treatment.
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Affiliation(s)
- Kyoungmin Lee
- Division of Oncology/Hematology, Department of Internal Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Korea
| | - Jongwon Lee
- Brain Korea 21 Plus Project for Biomedical Science, Korea University College of Medicine, Seoul, Korea
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Korea
| | - Jungmin Choi
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Korea
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Sung Hoon Sim
- Center for Breast Cancer, National Cancer Center, Goyang, Korea
| | - Jeong Eun Kim
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Min Hwan Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Yeon Hee Park
- Division of Hematology/Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jee Hyun Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Su-Jin Koh
- Department of Hematology and Oncology, Ulsan University Hospital, Ulsan University College of Medicine, Ulsan, Korea
| | - Kyong Hwa Park
- Division of Oncology/Hematology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Korea
| | - Myoung Joo Kang
- Division of Oncology, Department of Internal Medicine, Haeundae Paik Hospital, Inje University College of Medicine, Busan, Korea
| | - Mi Sun Ahn
- Department of Hematology-Oncology, Ajou University School of Medicine, Suwon, Korea
| | - Kyoung Eun Lee
- Department of Hematology and Oncology, Ewha Womans University Hospital, Seoul, Korea
| | - Hee-Jun Kim
- Division of Hematology/Medical Oncology, Department of Internal Medicine, Chung-Ang University Hospital, Seoul, Korea
| | - Hee Kyung Ahn
- Division of Medical Oncology, Department of Internal Medicine, Gachon University Gil Medical Center, Incheon, Korea
| | - Han Jo Kim
- Division of Oncology and Hematology, Department of Internal Medicine, Soonchunhyang University Cheonan Hospital, Cheonan, Korea
| | - Keon Uk Park
- Division of Hematology/Oncology, Department of Internal Medicine, Keimyung University Dongsan Hospital, Daegu, Korea
| | - In Hae Park
- Division of Oncology/Hematology, Department of Internal Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Korea.
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Kdimati S, Bürtin F, Linnebacher M, Mullins CS. Patient-Derived Organoids for In Vivo Validation of In Vitro Data. Methods Mol Biol 2023; 2589:111-126. [PMID: 36255621 DOI: 10.1007/978-1-0716-2788-4_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Patient-derived organoids are promising tumor models for functional validation of next-generation sequencing-based therapy recommendations. In times of rapidly advancing precision oncology approaches in everyday clinical processes, reliable and valid tumor models are required. Tumor organoids consist of tumor "stem" cells, differentiated (epithelial) tumor, and stroma cells. The cellular architecture and interactions closely mimic the original patient tumor. These organoids can be implanted into immunodeficient mice, generating patient-derived organoid-derived xenografts, thus enabling in vitro to in vivo transfer. Most importantly, the high clinical relevance of PDO models is maintained in this conversion. This protocol describes in detail the methods and techniques as well as the materials necessary to generate in vitro PDO and in vivo PDO-derived xenograft models. The elaborate process description starts with the processing of freshly obtained tumor tissue. The proceedings include tissue processing, organoid culturing, PDO implantation into immunodeficient mice, tumor explantation, and finally tumor preservation. All these proceedings are described in this timely chronological order. This protocol will enable researchers to generate PDO models from freshly received tumor tissue and generate PDO-derived xenografts. Models generated according to these methods are suitable for a very broad research spectrum.
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Affiliation(s)
- Said Kdimati
- Department of General Surgery, Molecular Oncology and Immunotherapy, Rostock, Germany
| | - Florian Bürtin
- Department of General Surgery, Molecular Oncology and Immunotherapy, Rostock, Germany
| | - Michael Linnebacher
- Department of General Surgery, Molecular Oncology and Immunotherapy, Rostock, Germany
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Sim SH, Kim JE, Kim MH, Park YH, Kim JH, Suh KJ, Koh SJ, Park KH, Kang MJ, Ahn MS, Lee KE, Kim HJ, Ahn HK, Kim HJ, Park KU, Byun JH, Park JH, Lee GW, Lee KS, Sohn J, Jung KH, Park IH. Phase II study to investigate the efficacy of trastuzumab biosimilar (Herzuma®) plus treatment of physician's choice (TPC) in patients with heavily pretreated HER-2+ metastatic breast cancer (KCSG BR 18–14/KM10B). Breast 2022; 65:172-178. [PMID: 36029565 PMCID: PMC9429798 DOI: 10.1016/j.breast.2022.08.002] [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: 05/10/2022] [Revised: 08/01/2022] [Accepted: 08/07/2022] [Indexed: 11/29/2022] Open
Abstract
We investigated the efficacy and safety of a trastuzumab biosimilar, Herzuma®, in combination with treatment of physician's choice (TPC) in patients with HER2+ metastatic breast cancer (MBC) who had failed at least two HER2 directed chemotherapies. Treatment of HER2-positive breast cancer is rapidly evolving with the development of new agents. However, treatment options are still limited after progression with proven anti-HER2 therapies. The combination of chemotherapy with a trastuzumab biosimilar, Herzuma®, was effective and safe in patients with heavily pre-treated HER2+ MBC. Duration of response to previous anti-HER2 therapy, PIK3CA and ERBB2 mutations were associated with clinical efficacies of trastuzumab biosimilar plus chemotherapy.
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Ali SM, Adnan Y, Ahmad Z, Farooqui HA, Chawla T, Ali SMA. Genetic landscape of pancreatic adenocarcinoma patients: a pilot study from Pakistan. Mol Biol Rep 2022; 49:1341-1350. [PMID: 34812998 DOI: 10.1007/s11033-021-06964-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: 10/12/2021] [Accepted: 11/16/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Pancreatic adenocarcinoma is one of the most aggressive malignancies with extremely low survival rate. Studies have shown that the exploration of key genes can provide a basis for targeted treatment of these patients. The genomic architecture of the Pakistani pancreatic adenocarcinoma patients remains unexplored. Keeping the scenario in place, the current study aims to analyse 88 cancer related genes in Pakistani pancreatic adenocarcinoma patients in order to elucidate candidate gene(s) for targeted molecular therapy. METHODS AND RESULTS A total 18 patients were included in the study initially and FFPE tumor samples were obtained. After confirmation of diagnosis and appropriate tumor content, DNA was extracted. Based on the quality and quantity of the extracted DNA, six pancreatic adenocarcinoma tumor samples were selected. Following to this, all the samples were subjected to targeted sequencing (Axen Cancer Panel 1). Variant detection was done and clinical significance of identified variants was assessed using ClinVar database. Targeted sequencing of tumor samples revealed a total of 29 alterations in the coding region of various genes. Among these five pathogenic variants were found in KRAS, BRCA1, TP53 and APC genes. CONCLUSION This is the first study that explores genes involved in pancreatic adenocarcinoma from the Pakistani population. Results obtained from the pilot study can guide us about the key genetic players in the Pakistani pancreatic adenocarcinoma population. This can lead to our better understanding of the molecular targeted therapies for these patients and designing future researches on larger sample size.
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Affiliation(s)
| | - Yumna Adnan
- Aga Khan University Hospital, Karachi, Pakistan
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Yoon S, Kim M, Hong YS, Kim HS, Kim ST, Kim J, Yun H, Yoo C, Ahn HK, Kim HS, Lee IH, Kim IH, Park I, Jeong JH, Cheon J, Kim JW, Yun J, Lim SM, Cha Y, Jang SJ, Zang DY, Kim TW, Kang JH, Kim JH. Recommendations for the Use of Next-Generation Sequencing and the Molecular Tumor Board for Patients with Advanced Cancer: A Report from KSMO and KCSG Precision Medicine Networking Group. Cancer Res Treat 2021; 54:1-9. [PMID: 34902959 PMCID: PMC8756119 DOI: 10.4143/crt.2021.1115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/08/2021] [Indexed: 11/21/2022] Open
Abstract
Next-generation sequencing (NGS) is becoming essential in the fields of precision oncology. With implementation of NGS in daily clinic, the needs for continued education, facilitated interpretation of NGS results and optimal treatment delivery based on NGS results have been addressed. Molecular tumor board (MTB) is multidisciplinary approach to keep pace with the growing knowledge of complex molecular alterations in patients with advanced solid cancer. Although guidelines for NGS use and MTB have been developed in western countries, there is limitation for reflection of Korea’s public health environment and daily clinical practice. These recommendations provide a critical guidance from NGS panel testing to final treatment decision based on MTB discussion.
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Affiliation(s)
- Shinkyo Yoon
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Miso Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Yong Sang Hong
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Han Sang Kim
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Seung Tae Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jihun Kim
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Hongseok Yun
- Department of Genomic Medicine, Seoul National University Hospital, College of Medicine, Seoul, Korea
| | - Changhoon Yoo
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Hee Kyung Ahn
- Division of Medical Oncology, Department of Internal Medicine, Gachon University Gil Medical Center, Incheon, Korea
| | - Hyo Song Kim
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - In Hee Lee
- Department of Oncology/Hematology, Kyungpook National University Chilgok Hospital, Daegu, Korea
| | - In-Ho Kim
- Division of Medical Oncology, Department of Internal Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea College of Medicine, Seoul, Korea
| | - Inkeun Park
- Division of Medical Oncology, Department of Internal Medicine, Gachon University Gil Medical Center, Incheon, Korea
| | - Jae Ho Jeong
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jaekyung Cheon
- Department of Medical Oncology, CHA Bundang Medical Center, CHA University School of Medicine, Seongnam, Korea
| | - Jin Won Kim
- Division of Hematology/Medical Oncology, Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Jina Yun
- Division of Medical Oncology, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Korea
| | - Sun Min Lim
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Yongjun Cha
- Center for Colorectal Cancer, National Cancer Center, Research Institute and Hospital, Goyang, Korea
| | - Se Jin Jang
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Dae Young Zang
- Department of Internal Medicine, Hallym University Medical Center, Hallym University, Anyang, Korea
| | - Tae Won Kim
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jin Hyoung Kang
- Division of Medical Oncology, Department of Internal Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea College of Medicine, Seoul, Korea
| | - Jee Hyun Kim
- Division of Hematology/Medical Oncology, Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
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Chowdhury S, Hofree M, Lin K, Maru D, Kopetz S, Shen JP. Implications of Intratumor Heterogeneity on Consensus Molecular Subtype (CMS) in Colorectal Cancer. Cancers (Basel) 2021; 13:4923. [PMID: 34638407 PMCID: PMC8507736 DOI: 10.3390/cancers13194923] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 09/21/2021] [Accepted: 09/25/2021] [Indexed: 01/04/2023] Open
Abstract
The implications of intratumor heterogeneity on the four consensus molecular subtypes (CMS) of colorectal cancer (CRC) are not well known. Here, we use single-cell RNA sequencing (scRNASeq) to build an algorithm to assign CMS classification to individual cells, which we use to explore the distributions of CMSs in tumor and non-tumor cells. A dataset of colorectal tumors with bulk RNAseq (n = 3232) was used to identify CMS specific-marker gene sets. These gene sets were then applied to a discovery dataset of scRNASeq profiles (n = 10) to develop an algorithm for single-cell CMS (scCMS) assignment, which recapitulated the intrinsic biology of all four CMSs. The single-cell CMS assignment algorithm was used to explore the scRNASeq profiles of two prospective CRC tumors with mixed CMS via bulk sequencing. We find that every CRC tumor contains individual cells of each scCMS, as well as many individual cells that have enrichment for features of more than one scCMS (called mixed cells). scCMS4 and scCMS1 cells dominate stroma and immune cell clusters, respectively, but account for less than 3% epithelial cells. These data imply that CMS1 and CMS4 are driven by the transcriptomic contribution of immune and stromal cells, respectively, not tumor cells.
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Affiliation(s)
- Saikat Chowdhury
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Matan Hofree
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Kangyu Lin
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dipen Maru
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John Paul Shen
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Evaluation of a Targeted Next-Generation Sequencing Panel for the Non-Invasive Detection of Variants in Circulating DNA of Colorectal Cancer. J Clin Med 2021; 10:jcm10194487. [PMID: 34640513 PMCID: PMC8509146 DOI: 10.3390/jcm10194487] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/20/2021] [Accepted: 09/24/2021] [Indexed: 12/17/2022] Open
Abstract
Molecular profiling of circulating cell-free DNA (cfDNA) has shown utility for the management of colorectal cancer (CRC). TruSight Tumor 170 (TST170) is a next-generation sequencing (NGS) panel that covers 170 cancer-related genes, including KRAS, which is a key driver gene in CRC. We evaluated the capacity of TST170 to detect gene variants in cfDNA from a retrospective cohort of 20 metastatic CRC patients with known KRAS variants in tumor tissue and in cfDNA previously analyzed by pyrosequencing and BEAMing, respectively. The cfDNA of most of the patients (95%) was successfully sequenced. We frequently detected variants with clinical significance in KRAS (79%, 15/19) and PIK3CA (26%, 5/19) genes. Variants with potential clinical significance were also identified in another 27 cancer genes, such as APC. The type of KRAS variant detected in cfDNA by TST170 showed high concordance with those detected in tumor tissue (77%), and very high concordance with cfDNA analyzed by BEAMing (94%). The variant allele fractions for KRAS obtained in cfDNA by TST170 and BEAMing correlated strongly. This proof-of-principle study indicates that targeted NGS analysis of cfDNA with TST170 could be useful for non-invasive detection of gene variants in metastatic CRC patients, providing an assay that could be easily implemented for detecting somatic alterations in the clinic.
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Park S, Lee C, Ku BM, Kim M, Park WY, Kim NKD, Ahn MJ. Paired analysis of tumor mutation burden calculated by targeted deep sequencing panel and whole exome sequencing in non-small cell lung cancer. BMB Rep 2021. [PMID: 34154699 PMCID: PMC8328823 DOI: 10.5483/bmbrep.2021.54.7.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Owing to rapid advancements in NGS (next generation sequen-cing), genomic alteration is now considered an essential pre-dictive biomarkers that impact the treatment decision in many cases of cancer. Among the various predictive biomarkers, tumor mutation burden (TMB) was identified by NGS and was con-sidered to be useful in predicting a clinical response in cancer cases treated by immunotherapy. In this study, we directly com-pared the lab-developed-test (LDT) results by target sequencing panel, K-MASTER panel v3.0 and whole-exome sequencing (WES) to evaluate the concordance of TMB. As an initial step, the reference materials (n = 3) with known TMB status were used as an exploratory test. To validate and evaluate TMB, we used one hundred samples that were acquired from surgically resected tissues of non-small cell lung cancer (NSCLC) patients. The TMB of each sample was tested by using both LDT and WES methods, which extracted the DNA from samples at the same time. In addition, we evaluated the impact of capture re-gion, which might lead to different values of TMB; the evalu-ation of capture region was based on the size of NGS and target sequencing panels. In this pilot study, TMB was evalu-ated by LDT and WES by using duplicated reference samples; the results of TMB showed high concordance rate (R2 = 0.887). This was also reflected in clinical samples (n = 100), which showed R2 of 0.71. The difference between the coding sequence ratio (3.49%) and the ratio of mutations (4.8%) indicated that the LDT panel identified a relatively higher number of mutations. It was feasible to calculate TMB with LDT panel, which can be useful in clinical practice. Furthermore, a customized approach must be developed for calculating TMB, which differs according to cancer types and specific clinical settings.
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Affiliation(s)
- Sehhoon Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Chung Lee
- Geninus Inc., Seoul 05836, 3Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea
| | - Bo Mi Ku
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Minjae Kim
- Geninus Inc., Seoul 05836, 3Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea
| | - Woong-Yang Park
- Geninus Inc., Seoul 05836, 3Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea
| | - Nayoung K. D. Kim
- Geninus Inc., Seoul 05836, 3Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea
| | - Myung-Ju Ahn
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
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Wang Y, Zheng D. The importance of precision medicine in modern molecular oncology. Clin Genet 2021; 100:248-257. [PMID: 33997970 DOI: 10.1111/cge.13998] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 12/12/2022]
Abstract
With the rapid development of modern medical technology, information data modeling has been gradually applied to clinical diagnosis and treatment. Precision medicine is an important approach that focuses on individual patients in terms of their own characteristics, genomic information, proteomics and even social environments. Genome-wide high-throughput technologies, including DNA-seq, RNA-seq, exosome-seq…, contribute enormous amounts of molecular data to aid in diagnosis and analysis. Here, we review the developmental history of different next-generation sequencing platforms, introduce their applications in different tumor diagnosis and therapy, and further discuss the remaining challenges in precision medicine.
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Affiliation(s)
- Yuanli Wang
- The Precision Medicine Laboratory, The First People's Hospital of Qinzhou, Qinzhou, China
| | - Dawu Zheng
- The Precision Medicine Laboratory, The First People's Hospital of Qinzhou, Qinzhou, China
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12
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Choi YJ, Choi JY, Kim JW, Lim AR, Lee Y, Chang WJ, Lee S, Sung JS, Chung HJ, Lee JW, Kang EJ, Kim JS, Lim T, Kim HS, Kim YJ, Ahn MS, Kim YS, Park JH, Lim S, Cho SS, Cho JH, Shin SW, Park KH, Kim YH. Comparison of the Data of a Next-Generation Sequencing Panel from K-MASTER Project with that of Orthogonal Methods for Detecting Targetable Genetic Alterations. Cancer Res Treat 2021; 54:30-39. [PMID: 34015890 PMCID: PMC8756135 DOI: 10.4143/crt.2021.218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/18/2021] [Indexed: 11/21/2022] Open
Abstract
Purpose K-MASTER project is a Korean national precision medicine platform that screened actionable mutations by analyzing next-generation sequencing (NGS) of solid tumor patients. We compared gene analyses between NGS panel from the K-MASTER project and orthogonal methods. Materials and Methods Colorectal, breast, non–small cell lung, and gastric cancer patients were included. We compared NGS results from K-MASTER projects with those of non-NGS orthogonal methods (KRAS, NRAS, and BRAF mutations in colorectal cancer [CRC]; epidermal growth factor receptor [EGFR], anaplastic lymphoma kinase [ALK] fusion, and reactive oxygen species 1 [ROS1] fusion in non–small cell lung cancer [NSCLC], and Erb-B2 receptor tyrosine kinase 2 (ERBB2) positivity in breast and gastric cancers). Results In the CRC cohort (n=225), the sensitivity and specificity of NGS were 87.4% and 79.3% (KRAS); 88.9% and 98.9% (NRAS); and 77.8% and 100.0% (BRAF), respectively. In the NSCLC cohort (n=109), the sensitivity and specificity of NGS for EGFR were 86.2% and 97.5%, respectively. The concordance rate for ALK fusion was 100%, but ROS1 fusion was positive in only one of three cases that were positive in orthogonal tests. In the breast cancer cohort (n=260), ERBB2 amplification was detected in 45 by NGS. Compared with orthogonal methods that integrated immunohistochemistry and in situ hybridization, sensitivity and specificity were 53.7% and 99.4%, respectively. In the gastric cancer cohort (n=64), ERBB2 amplification was detected in six by NGS. Compared with orthogonal methods, sensitivity and specificity were 62.5% and 98.2%, respectively. Conclusion The results of the K-MASTER NGS panel and orthogonal methods showed a different degree of agreement for each genetic alteration, but generally showed a high agreement rate.
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Affiliation(s)
- Yoon Ji Choi
- Division of Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Korea.,Cancer Precision Medicine Diagnosis and Treatment Enterprise, Korea University Anam Hospital, Seoul, Korea
| | - Jung Yoon Choi
- Division of Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Korea.,Cancer Precision Medicine Diagnosis and Treatment Enterprise, Korea University Anam Hospital, Seoul, Korea
| | - Ju Won Kim
- Division of Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Korea.,Cancer Precision Medicine Diagnosis and Treatment Enterprise, Korea University Anam Hospital, Seoul, Korea
| | - Ah Reum Lim
- Division of Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Korea.,Cancer Precision Medicine Diagnosis and Treatment Enterprise, Korea University Anam Hospital, Seoul, Korea
| | - Youngwoo Lee
- Division of Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Korea
| | - Won Jin Chang
- Division of Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Korea.,Cancer Precision Medicine Diagnosis and Treatment Enterprise, Korea University Anam Hospital, Seoul, Korea
| | - Soohyeon Lee
- Division of Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Korea.,Cancer Precision Medicine Diagnosis and Treatment Enterprise, Korea University Anam Hospital, Seoul, Korea
| | - Jae Sook Sung
- Cancer Precision Medicine Diagnosis and Treatment Enterprise, Korea University Anam Hospital, Seoul, Korea
| | - Hee-Joon Chung
- Cancer Precision Medicine Diagnosis and Treatment Enterprise, Korea University Anam Hospital, Seoul, Korea
| | - Jong Won Lee
- Brain Korea 21 Plus Project for Biomedical Science, Korea University College of Medicine, Seoul, Korea
| | - Eun Joo Kang
- Division of Oncology, Department of Internal Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Korea
| | - Jung Sun Kim
- Division of Oncology, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine, Ansan, Korea
| | - Taekyu Lim
- Division of Hematology-Oncology, Department of Internal Medicine, Veterans Health Service Medical Center, Seoul, Korea
| | - Hye Sook Kim
- Department of Internal Medicine, Inje University Ilsan Hospital, Goyang, Korea
| | - Yu Jung Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Mi Sun Ahn
- Ajou University Medical Center, Suwon, Korea
| | - Young Saing Kim
- Division of Medical Oncology, Department of Internal Medicine, Gil Medical Center, Gachon University College of Medicine, Incheon, Korea
| | - Ji Hyun Park
- Department of Hemato-Oncology, Konkuk Medical Center, University of Konkuk College of Medicine, Seoul, Korea
| | - Seungtaek Lim
- Department of Oncology, Wonju Severance Christianity Hospital, Wonju, Korea
| | - Sung Shim Cho
- Division of Medical Oncology, Department of Internal Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Suwon, Korea
| | - Jang Ho Cho
- Division of Oncology, Department of Internal Medicine, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Incheon, Korea
| | - Sang Won Shin
- Division of Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Korea
| | - Kyong Hwa Park
- Division of Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Korea.,Cancer Precision Medicine Diagnosis and Treatment Enterprise, Korea University Anam Hospital, Seoul, Korea
| | - Yeul Hong Kim
- Division of Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Korea.,Cancer Precision Medicine Diagnosis and Treatment Enterprise, Korea University Anam Hospital, Seoul, Korea
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