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Ramzy GM, Norkin M, Koessler T, Voirol L, Tihy M, Hany D, McKee T, Ris F, Buchs N, Docquier M, Toso C, Rubbia-Brandt L, Bakalli G, Guerrier S, Huelsken J, Nowak-Sliwinska P. Platform combining statistical modeling and patient-derived organoids to facilitate personalized treatment of colorectal carcinoma. J Exp Clin Cancer Res 2023; 42:79. [PMID: 37013646 PMCID: PMC10069117 DOI: 10.1186/s13046-023-02650-z] [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: 01/17/2023] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND We propose a new approach for designing personalized treatment for colorectal cancer (CRC) patients, by combining ex vivo organoid efficacy testing with mathematical modeling of the results. METHODS The validated phenotypic approach called Therapeutically Guided Multidrug Optimization (TGMO) was used to identify four low-dose synergistic optimized drug combinations (ODC) in 3D human CRC models of cells that are either sensitive or resistant to first-line CRC chemotherapy (FOLFOXIRI). Our findings were obtained using second order linear regression and adaptive lasso. RESULTS The activity of all ODCs was validated on patient-derived organoids (PDO) from cases with either primary or metastatic CRC. The CRC material was molecularly characterized using whole-exome sequencing and RNAseq. In PDO from patients with liver metastases (stage IV) identified as CMS4/CRIS-A, our ODCs consisting of regorafenib [1 mM], vemurafenib [11 mM], palbociclib [1 mM] and lapatinib [0.5 mM] inhibited cell viability up to 88%, which significantly outperforms FOLFOXIRI administered at clinical doses. Furthermore, we identified patient-specific TGMO-based ODCs that outperform the efficacy of the current chemotherapy standard of care, FOLFOXIRI. CONCLUSIONS Our approach allows the optimization of patient-tailored synergistic multi-drug combinations within a clinically relevant timeframe.
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Affiliation(s)
- George M Ramzy
- Molecular Pharmacology Group, School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, CMU, 1211, Geneva 4, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211, Geneva, Switzerland
- Translational Research Center in Oncohaematology, 1211, Geneva, Switzerland
| | - Maxim Norkin
- Swiss Institute for Experimental Cancer Research (ISREC), Ecole Polytechnique Fédérale de Lausanne-(EPFL-SV), 1015, Lausanne, Switzerland
| | - Thibaud Koessler
- Department of Oncology, Geneva University Hospitals, 1205, Geneva, Switzerland
| | - Lionel Voirol
- Research Center for Statistics, Geneva School of Economics and Management, University of Geneva, 1205, Geneva, Switzerland
| | - Mathieu Tihy
- Division of Clinical Pathology, Diagnostic Department, University Hospitals of Geneva (HUG), 1205, Geneva, Switzerland
| | - Dina Hany
- Molecular Pharmacology Group, School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, CMU, 1211, Geneva 4, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211, Geneva, Switzerland
- Translational Research Center in Oncohaematology, 1211, Geneva, Switzerland
| | - Thomas McKee
- Division of Clinical Pathology, Diagnostic Department, University Hospitals of Geneva (HUG), 1205, Geneva, Switzerland
| | - Frédéric Ris
- Translational Department of Digestive and Transplant Surgery, Geneva University Hospitals and Faculty of Medicine, 1205, Geneva, Switzerland
| | - Nicolas Buchs
- Translational Department of Digestive and Transplant Surgery, Geneva University Hospitals and Faculty of Medicine, 1205, Geneva, Switzerland
| | - Mylène Docquier
- iGE3 Genomics Platform, University of Geneva, 1211, Geneva, Switzerland
- Department of Genetics & Evolution, University of Geneva, 1211, Geneva, Switzerland
| | - Christian Toso
- Department of Visceral Surgery, Geneva University Hospital, 1211, Geneva, Switzerland
| | - Laura Rubbia-Brandt
- Division of Clinical Pathology, Diagnostic Department, University Hospitals of Geneva (HUG), 1205, Geneva, Switzerland
| | - Gaetan Bakalli
- EMLYON Business School, Artificial Intelligence in Management Institute, Ecully, France
| | - Stéphane Guerrier
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211, Geneva, Switzerland
- Research Center for Statistics, Geneva School of Economics and Management, University of Geneva, 1205, Geneva, Switzerland
| | - Joerg Huelsken
- Swiss Institute for Experimental Cancer Research (ISREC), Ecole Polytechnique Fédérale de Lausanne-(EPFL-SV), 1015, Lausanne, Switzerland
| | - Patrycja Nowak-Sliwinska
- Molecular Pharmacology Group, School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, CMU, 1211, Geneva 4, Switzerland.
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211, Geneva, Switzerland.
- Translational Research Center in Oncohaematology, 1211, Geneva, Switzerland.
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2
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Argilés G, Mulet N, Valladares-Ayerbes M, Viéitez JM, Grávalos C, García-Alfonso P, Santos C, Tobeña M, García-Paredes B, Benavides M, Cano MT, Loupakis F, Rodríguez-Garrote M, Rivera F, Goldberg RM, Cremolini C, Bennouna J, Ciardiello F, Tabernero JM, Aranda E, Argilés G, Tabernero J. A randomised phase 2 study comparing different dose approaches of induction treatment of regorafenib in previously treated metastatic colorectal cancer patients (REARRANGE trial). Eur J Cancer 2022; 177:154-163. [PMID: 36335783 DOI: 10.1016/j.ejca.2022.09.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 02/08/2023]
Abstract
PURPOSE The purpose of this article is to evaluate the safety of two regorafenib dose-escalation approaches in refractory metastatic colorectal cancer (mCRC) patients. PATIENTS AND METHODS Patients with mCRC and progression during or within 3 months following their last standard chemotherapy regimen were randomised to receive the approved dose of regorafenib of 160 mg QD (arm A) or 120 mg QD (arm B) administered as 3 weeks of treatment followed by 1 week off, or 160 mg QD 1 week on/1 week off (arm C). The primary end-point was the percentage of patients with G3/G4 treatment-related adverse events (AEs) in each arm. RESULTS There were 299 patients randomly assigned to arm A (n = 101), arm B (n = 99), or arm C (n = 99); 297 initiated treatments (arm A n = 100, arm B n = 98, arm C n = 99: population for safety analyses). G3/4 treatment-related AEs occurred in 60%, 55%, and 54% of patients in arms A, B, and C, respectively. The most common G3/4 AEs were hypertension (19, 12, and 20 patients), fatigue (20, 14, and 15 patients), hypokalemia (11, 7, and 10 patients), and hand-foot skin reaction (8, 7, and 3 patients). Median overall survival was 7.4 (IQR 4.0-13.7) months in arm A, 8.6 (IQR 3.8-13.4) in arm B, and 7.1 (IQR 4.4-12.4) in arm C. CONCLUSIONS The alternative regorafenib dosing schedules were feasible and safe in patients with mCRC who had been previously treated with standard therapy. There was a higher numerical improvement on the most clinically relevant AEs in the intermittent dosing arm, particularly during the relevant first two cycles. GOV IDENTIFIER NCT02835924.
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Affiliation(s)
- Guillem Argilés
- Vall d'Hebron University Hospital and Institute of Oncology (VHIO), CIBERONC, Barcelona, Spain; Universitat Autònoma de Barcelona, Barcelona, Spain; Memorial Sloan Kettering Cancer Center, New York, USA.
| | - Nuria Mulet
- Vall d'Hebron University Hospital and Institute of Oncology (VHIO), CIBERONC, Barcelona, Spain
| | | | - José M Viéitez
- Hospital Universitario Central de Asturias, Oviedo, Spain
| | | | | | - Cristina Santos
- Institute Català d'Oncologia (ICO), Duran i Reynals Hospital - ONCOBELL, CIBERONC, Barcelona, Spain
| | - María Tobeña
- Santa Creu i Sant Pau Hospital, Barcelona, Spain
| | - Beatriz García-Paredes
- Clínico San Carlos Hospital, Instituto de Investigación Hospital Clinico San Carlos (IdISSC) CIBERONC, Madrid, Spain
| | | | - María T Cano
- IMIBIC, Reina Sofía Hospital, University of Córdoba, CIBERONC, Instituto de Salud Carlos III, Spain
| | | | | | - Fernando Rivera
- University Hospital Marqués de Valdecilla (IDIVAL) Santander, Spain
| | | | - Chiara Cremolini
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Jaafar Bennouna
- University Hospital of Nantes, Digestive Oncology, Nantes, France
| | | | - Josep M Tabernero
- Vall d'Hebron University Hospital and Institute of Oncology (VHIO), CIBERONC, Barcelona, Spain
| | | | - Guillem Argilés
- Vall d'Hebron University Hospital and Institute of Oncology (VHIO), CIBERONC, Barcelona, Spain
| | - Josep Tabernero
- Vall d'Hebron University Hospital and Institute of Oncology (VHIO), CIBERONC, Barcelona, Spain
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3
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Shimozaki K, Hirata K, Sato T, Nakamura M, Kato K, Hirano H, Kumekawa Y, Hino K, Kawakami K, Kito Y, Matsumoto T, Kawakami T, Komoda M, Nagashima K, Sato Y, Yamazaki K, Hironaka S, Takaishi H, Hamamoto Y, Muro K. WJOG13219G: The Efficacy and Safety of FOLFOXIRI or Doublet plus Anti-VEGF Therapy in Previously Untreated BRAF V600E Mutant Metastatic Colorectal Cancer: A Multi-Institutional Registry-Based Study (BRACELET Study). Clin Colorectal Cancer 2022; 21:339-346. [PMID: 36117091 DOI: 10.1016/j.clcc.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/06/2022] [Accepted: 08/09/2022] [Indexed: 01/26/2023]
Abstract
BACKGROUND The real-world survival benefit of FOLFOXIRI (fluorouracil, leucovorin, oxaliplatin, and irinotecan) plus anti-VEGF therapy (Triplet) over doublet chemotherapy (Doublet) remains controversial in patients with BRAFV600E mutant metastatic colorectal cancer (mCRC). PATIENTS AND METHODS WJOG13219G was a multicenter, retrospective, registry-based study of patients with BRAFV600E mutant mCRC who received first-line triplet or doublet chemotherapy from January 2014 to December 2019 in Japan. Inverse probability of treatment weighting (IPTW) was used to adjust for patient background. RESULTS The analysis included 79 and 91 patients in the Triplet and Doublet groups, respectively. The Triplet group was significantly younger and had better performance status. No statistical difference was noted in progression-free survival (PFS; HR, 0.82; 95% CI, 0.60-1.13; P = .22) and overall survival (OS; HR, 0.88; 95% CI, 0.62-1.25; P = .48) between both groups. IPTW analysis also showed no difference between the 2 groups in PFS (HR, 0.86; 95% CI, 0.69-1.08; P = .20) and OS (HR, 0.93; 95% CI, 0.73-1.20; P = .59). The Triplet and Doublet groups had an objective response rate of 53% and 41%, respectively (P = .10). At least one grade 3 or 4 adverse event was seen in 51 (65%) and 43 (47%) patients in the Triplet and Doublet groups, respectively, with the incidence of neutropenia being significantly higher in the former. CONCLUSION Triplet therapy had no survival benefit versus doublet therapy in the overall and IPTW cohorts or specific subgroups for real-world patients with BRAFV600E mutant mCRC.
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Affiliation(s)
- Keitaro Shimozaki
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Kenro Hirata
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan.
| | - Taro Sato
- Gastroenterology Center, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Maho Nakamura
- Department of Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Kyoko Kato
- Department of Clinical Oncology, Aichi Cancer Center Hospital, Aichi, Japan
| | - Hidekazu Hirano
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Yosuke Kumekawa
- Department of Gastroenterology, Saitama Cancer Center, Saitama, Japan
| | - Kaori Hino
- Department of Gastrointestinal Medical Oncology, National Hospital Organization Shikoku Cancer Center, Ehime, Japan
| | - Kentaro Kawakami
- Department of Medical Oncology, Keiyukai Sapporo Hospital, Hokkaido, Japan
| | - Yosuke Kito
- Ishikawa Prefectural Central Hospital Department of Medical Oncology, Ishikawa, Japan
| | | | - Takeshi Kawakami
- Division of Gastrointestinal Oncology, Shizuoka Cancer Center, Shizuoka, Japan
| | - Masato Komoda
- National Hospital Organization Kyushu Cancer Center, Department of Gastrointestinal and Medical Oncology, Fukuoka, Japan
| | - Kengo Nagashima
- Biostatistics Unit, Clinical and Translational Research Center, Keio University Hospital, Tokyo, Japan
| | - Yasunori Sato
- Department of Preventive Medicine and Public Health, Keio University, Tokyo, Japan
| | - Kentaro Yamazaki
- Division of Gastrointestinal Oncology, Shizuoka Cancer Center, Shizuoka, Japan
| | - Shuichi Hironaka
- Department of Medical Oncology, Gastroenterological Oncology, Saitama Medical University International Medical Center, Saitama, Japan
| | - Hiromasa Takaishi
- Center for Preventive Medicine, Keio University Hospital, Tokyo, Japan
| | - Yasuo Hamamoto
- Keio Cancer Center, Keio University Hospital, Tokyo, Japan
| | - Kei Muro
- Division of Gastrointestinal Oncology, Shizuoka Cancer Center, Shizuoka, Japan
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4
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Emerging Role of ERBB2 in Targeted Therapy for Metastatic Colorectal Cancer: Signaling Pathways to Therapeutic Strategies. Cancers (Basel) 2022; 14:cancers14205160. [PMID: 36291943 PMCID: PMC9600272 DOI: 10.3390/cancers14205160] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/16/2022] [Accepted: 10/18/2022] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Colorectal cancer (CRC) is the third most commonly diagnosed malignancy and the second most common cause of cancer-related mortality worldwide. Currently available targeted therapies for metastatic CRC mainly target vascular endothelial growth factor and epidermal growth factor receptor in RAS wild-type tumors. Although Erb-B2 receptor tyrosine kinase 2 (ERBB2/human epidermal growth factor receptor 2) plays a significant therapeutic role in breast and gastric cancers, there are no licensed ERBB2-targeted therapies for metastatic CRC. This review aims to outline the molecular biology of ERBB2-positive metastatic CRC and potential targeted therapeutic strategies. Abstract Despite recent improvements in the comprehensive therapy of malignancy, metastatic colorectal cancer (mCRC) continues to have a poor prognosis. Notably, 5% of mCRC cases harbor Erb-B2 receptor tyrosine kinase 2 (ERBB2) alterations. ERBB2, commonly referred to as human epidermal growth factor receptor 2, is a member of the human epidermal growth factor receptor family of protein tyrosine kinases. In addition to being a recognized therapeutic target in the treatment of gastric and breast malignancies, it is considered crucial in the management of CRC. In this review, we describe the molecular biology of ERBB2 from the perspective of biomarkers for mCRC-targeted therapy, including receptor structures, signaling pathways, gene alterations, and their detection methods. We also discuss the relationship between ERBB2 aberrations and the underlying mechanisms of resistance to anti-EGFR therapy and immunotherapy tolerance in these patients with a focus on novel targeted therapeutics and ongoing clinical trials. This may aid the development of a new standard of care in patients with ERBB2-positive mCRC.
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5
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Conn CW, Jin J. The value of companion diagnostics in oncology drug development. Expert Rev Mol Diagn 2022; 22:591-593. [DOI: 10.1080/14737159.2022.2100697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
| | - Janet Jin
- Department of Precision Medicine, AbbVie Inc, South San Francisco, CA, USA
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6
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Chaudhari VS, Hole KC, Issa AM. Evaluating the quality of the economic evidence in colorectal cancer genomics studies. Per Med 2022; 19:361-375. [PMID: 35786999 DOI: 10.2217/pme-2021-0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The increase in the use of genome-based screening and diagnostic tests adds to the overall costs of oncologic care for colorectal cancer. This, in turn, has resulted in an increase in published economic analyses. Aim: To perform a systematic literature review of the available economic evidence evaluating the value of genomic testing for colorectal cancer and appraise the quality of the economic studies conducted to date. Methods: A systematic review of the literature for economic studies of colorectal cancer genomics from January 2006 through October 2020, and evaluation of study quality using the Quality of Health Economic Studies (QHES) instrument was conducted. The validated QHES was then applied to a final set of articles that met eligibility criteria. Results: Our search of the literature initially yielded 12,859 records. A final set of 49 articles met our inclusion criteria. The QHES score ranged from 24 to 100, with an average score of 82. Most of the studies (n = 40, 82%) scored above 75 and were considered of good quality. Conclusion: Our analysis revealed that most of the economic analyses of colorectal cancer genomic molecular diagnostics in the literature may be of good quality. There is, however, some variation in methodological rigor between the articles.
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Affiliation(s)
- Vivek S Chaudhari
- Personalized Precision Medicine & Targeted Therapeutics, Springfield, PA 19064, USA.,Health Policy, University of the Sciences, Philadelphia, PA 19104, USA
| | - Kanchan C Hole
- Personalized Precision Medicine & Targeted Therapeutics, Springfield, PA 19064, USA
| | - Amalia M Issa
- Personalized Precision Medicine & Targeted Therapeutics, Springfield, PA 19064, USA.,Health Policy, University of the Sciences, Philadelphia, PA 19104, USA.,Pharmaceutical Sciences, University of the Sciences, Philadelphia, PA 19104, USA.,Family Medicine, McGill University, Montreal, QC, H3S 1Z1, Canada
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7
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Ward TM, Cauley CE, Stafford CE, Goldstone RN, Bordeianou LG, Kunitake H, Berger DL, Ricciardi R. Tumour genotypes account for survival differences in right- and left-sided colon cancers. Colorectal Dis 2022; 24:601-610. [PMID: 35142008 DOI: 10.1111/codi.16060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 12/11/2021] [Accepted: 12/14/2021] [Indexed: 02/08/2023]
Abstract
AIM We sought to identify genetic differences between right- and left-sided colon cancers and using these differences explain lower survival in right-sided cancers. METHOD A retrospective review of patients diagnosed with colon cancer was performed using The Cancer Genome Atlas, a cancer genetics registry with patient and tumour data from 20 North American institutions. The primary outcome was 5-year overall survival. Predictors for survival were identified using directed acyclic graphs and Cox proportional hazards models. RESULTS A total of 206 right- and 214 left-sided colon cancer patients with 84 recorded deaths were identified. The frequency of mutated alleles differed significantly in 12 of 25 genes between right- and left-sided tumours. Right-sided tumours had worse survival with a hazard ratio of 1.71 (95% confidence interval 1.10-2.64, P = 0.017). The total effect of the genetic loci on survival showed five genes had a sizeable effect on survival: DNAH5, MUC16, NEB, SMAD4, and USH2A. Lasso-penalized Cox regression selected 13 variables for the highest-performing model, which included cancer stage, positive resection margin, and mutated alleles at nine genes: MUC16, USH2A, SMAD4, SYNE1, FLG, NEB, TTN, OBSCN, and DNAH5. Post-selection inference demonstrated that mutations in MUC16 (P = 0.01) and DNAH5 (P = 0.02) were particularly predictive of 5-year overall survival. CONCLUSIONS Our study showed that genetic mutations may explain survival differences between tumour sites. Further studies on larger patient populations may identify other genes, which could form the foundation for more precise prognostication and treatment decisions beyond current rudimentary TNM staging.
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Affiliation(s)
- Thomas M Ward
- Section of Colon and Rectal Surgery, Division of General and Gastrointestinal Surgery, Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Christy E Cauley
- Section of Colon and Rectal Surgery, Division of General and Gastrointestinal Surgery, Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Caitlin E Stafford
- Section of Colon and Rectal Surgery, Division of General and Gastrointestinal Surgery, Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Robert N Goldstone
- Section of Colon and Rectal Surgery, Division of General and Gastrointestinal Surgery, Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Liliana G Bordeianou
- Section of Colon and Rectal Surgery, Division of General and Gastrointestinal Surgery, Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Hiroko Kunitake
- Section of Colon and Rectal Surgery, Division of General and Gastrointestinal Surgery, Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - David L Berger
- Section of Colon and Rectal Surgery, Division of General and Gastrointestinal Surgery, Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Rocco Ricciardi
- Section of Colon and Rectal Surgery, Division of General and Gastrointestinal Surgery, Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
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8
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Tachibana A, Fujimura N, Takeuchi M, Watanabe K, Teruuchi Y, Uchiki T. Cationic copolymers that enhance wild-type-specific suppression in BNA-clamp PCR and preferentially increase the Tm of fully matched complementary DNA and BNA strands. BIOLOGY METHODS AND PROTOCOLS 2022; 7:bpac009. [PMID: 35664806 PMCID: PMC9154250 DOI: 10.1093/biomethods/bpac009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/17/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022]
Abstract
Abstract
Mutation detection is of major interest in molecular diagnostics, especially in the field of oncology. However, detection can be challenging as mutant alleles often coexists with excess copies of wild-type alleles. Bridged nucleic acid (BNA)-clamp PCR circumvents this challenge by preferentially suppressing the amplification of wild-type alleles and enriching rare mutant alleles. In this study, we screened cationic copolymers containing nonionic and anionic repeat units for their ability to 1) increase the Tm of double-stranded DNA, 2) avoid PCR inhibition, and 3) enhance the suppression of wild-type amplification in BNA-clamp PCR to detect the KRAS G13D mutation. The selected copolymers that met these criteria consisted of four types of amines and anionic and/or nonionic units. In BNA-clamp PCR, these copolymers increased the threshold cycle (Ct) of the wild-type allele only and enabled mutation detection from templates with a 0.01% mutant-to-wild-type ratio. Melting curve analysis with 11-mer DNA-DNA or BNA-DNA complementary strands showed that these copolymers preferentially increased the Tm of perfectly matched strands over strands containing 1-bp mismatches. These results suggested that these copolymers preferentially stabilize perfectly matched DNA and BNA strands and thereby enhance rare mutant detection in BNA-clamp PCR.
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Affiliation(s)
- Ami Tachibana
- Nitto Boseki Co. Ltd., Kawasaki, Kanagawa, 210-0821, Japan
| | | | | | - Koji Watanabe
- Nittobo Medical Co. Ltd., Koriyama, Fukushima, 963-8061, Japan
| | - Yoko Teruuchi
- Nittobo Medical Co. Ltd., Koriyama, Fukushima, 963-8061, Japan
| | - Tomoaki Uchiki
- Nitto Boseki Co. Ltd., Kawasaki, Kanagawa, 210-0821, Japan
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9
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Cho K, Choi E, Lee SY, Kim J, Moon DW, Son J, Kim E. Screening of important metabolites and KRAS genotypes in colon cancer using secondary ion mass spectrometry. Bioeng Transl Med 2021; 6:e10200. [PMID: 34027089 PMCID: PMC8126813 DOI: 10.1002/btm2.10200] [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: 08/18/2020] [Revised: 10/06/2020] [Accepted: 10/29/2020] [Indexed: 11/08/2022] Open
Abstract
Time-of-flight secondary ion mass spectrometry (TOF-SIMS) is an imaging-based analytical technique that can characterize the surfaces of biomaterials. We used TOF-SIMS to identify important metabolites and oncogenic KRAS mutation expressed in human colorectal cancer (CRC). We obtained 540 TOF-SIMS spectra from 180 tissue samples by scanning cryo-sections and selected discriminatory molecules using the support vector machine (SVM) algorithm. Each TOF-SIMS spectrum contained nearly 860,000 ion profiles and hundreds of spectra were analyzed; therefore, reducing the dimensionality of the original data was necessary. We performed principal component analysis after preprocessing the spectral data, and the principal components (20) of each spectrum were used as the inputs of the SVM algorithm using the R package. The performance of the algorithm was evaluated using the receiver operating characteristic (ROC) area under the curve (AUC) (0.9297). Spectral peaks (m/z) corresponding to discriminatory molecules used to classify normal and tumor samples were selected according to p-value and were assigned to arginine, α-tocopherol, and fragments of glycerophosphocholine. Pathway analysis using these discriminatory molecules showed that they were involved in gastrointestinal disease and organismal abnormalities. In addition, spectra were classified according to the expression of KRAS somatic mutation, with 0.9921 AUC. Taken together, TOF-SIMS efficiently and simultaneously screened metabolite biomarkers and performed KRAS genotyping. In addition, a machine learning algorithm was provided as a diagnostic tool applied to spectral data acquired from clinical samples prepared as frozen tissue slides, which are commonly used in a variety of biomedical tests.
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Affiliation(s)
- Kookrae Cho
- Division of Electronic Information System ResearchDaegu Gyeongbuk Institute of Science and Technology (DGIST)DaeguRepublic of Korea
| | - Eun‐Sook Choi
- Division of Bio‐Fusion ResearchDaegu Gyeongbuk Institute of Science and Technology (DGIST)DaeguRepublic of Korea
| | - Sung Young Lee
- Division of Technology Business, National Institute for Nanomaterials Technology (NINT)Pohang University of Science and Technology (POSTECH)PohangRepublic of Korea
| | - Jung‐Hee Kim
- Division of Electronic Information System ResearchDaegu Gyeongbuk Institute of Science and Technology (DGIST)DaeguRepublic of Korea
| | - Dae Won Moon
- Department of New BiologyDaegu Gyeongbuk Institute of Science and Technology (DGIST)DaeguRepublic of Korea
| | - Jong‐Wuk Son
- Division of Electronic Information System ResearchDaegu Gyeongbuk Institute of Science and Technology (DGIST)DaeguRepublic of Korea
| | - Eunjoo Kim
- Division of Electronic Information System ResearchDaegu Gyeongbuk Institute of Science and Technology (DGIST)DaeguRepublic of Korea
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10
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Steele JL, Stevens RC, Cabrera OA, Bassill GJ, Cramer SM, Guzman F, Shuber AP. Novel CRISPR-based sequence specific enrichment methods for target loci and single base mutations. PLoS One 2020; 15:e0243781. [PMID: 33362267 PMCID: PMC7757808 DOI: 10.1371/journal.pone.0243781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/25/2020] [Indexed: 01/10/2023] Open
Abstract
The programmable sequence specificity of CRISPR has found uses in gene editing and diagnostics. This manuscript describes an additional application of CRISPR through a family of novel DNA enrichment technologies. CAMP (CRISPR Associated Multiplexed PCR) and cCAMP (chimeric CRISPR Associated Multiplexed PCR) utilize the sequence specificity of the Cas9/sgRNA complex to target loci for the ligation of a universal adapter that is used for subsequent amplification. cTRACE (chimeric Targeting Rare Alleles with CRISPR-based Enrichment) also applies this method to use Cas9/sgRNA to target loci for the addition of universal adapters, however it has an additional selection for specific mutations through the use of an allele-specific primer. These three methods can produce multiplex PCR that significantly reduces the optimization required for every target. The methods are also not specific to any downstream analytical platform. We additionally will present a mutation specific enrichment technology that is non-amplification based and leaves the DNA in its native state: TRACE (Targeting Rare Alleles with CRISPR-based Enrichment). TRACE utilizes the Cas9/sgRNA complex to sterically protect the ends of targeted sequences from exonuclease activity which digests both the normal variant as well as any off-target sequences.
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Affiliation(s)
| | | | - Oscar A. Cabrera
- Genetics Research LLC, Waltham, Massachusetts, United States of America
| | - Gary J. Bassill
- Genetics Research LLC, Waltham, Massachusetts, United States of America
| | - Sabrina M. Cramer
- Genetics Research LLC, Waltham, Massachusetts, United States of America
| | - Felipe Guzman
- Genetics Research LLC, Waltham, Massachusetts, United States of America
| | - Anthony P. Shuber
- Genetics Research LLC, Waltham, Massachusetts, United States of America
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11
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Loree JM, Dowers A, Tu D, Jonker DJ, Edelstein DL, Quinn H, Holtrup F, Price T, Zalcberg JR, Moore MJ, Karapetis CS, O'Callaghan CJ, Waring P, Kennecke HF, Hamilton SR, Kopetz S. Expanded Low Allele Frequency RAS and BRAF V600E Testing in Metastatic Colorectal Cancer as Predictive Biomarkers for Cetuximab in the Randomized CO.17 Trial. Clin Cancer Res 2020; 27:52-59. [PMID: 33087330 DOI: 10.1158/1078-0432.ccr-20-2710] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/31/2020] [Accepted: 10/16/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Expanded RAS/BRAF mutations have not been assessed as predictive for single-agent cetuximab in metastatic colorectal cancer (mCRC), and low mutant allele frequency (MAF) mutations are of unclear significance. We aimed to establish cetuximab efficacy in optimally selected patients using highly sensitive beads, emulsion, amplification, and magnetics (BEAMing) analysis, capable of detecting alterations below standard clinical assays. PATIENTS AND METHODS CO.17 trial compared cetuximab versus best supportive care (BSC) in RAS/BRAF-unselected mCRC. We performed RAS/BRAF analysis on microdissected tissue of 242 patients in CO.17 trial using BEAMing for KRAS/NRAS (codons 12/13/59/61/117/146) and BRAF V600E. Patients without BEAMing but with previous Sanger sequencing-detected mutations were included. RESULTS KRAS, NRAS, and BRAF mutations were present in 53%, 4%, and 3% of tumors, respectively. Cetuximab improved overall survival [OS; HR, 0.51; 95% confidence interval (CI), 0.32-0.81; P = 0.004] and progression-free survival (PFS; HR, 0.25; 95% CI, 0.15-0.41; P < 0.0001) compared with BSC in RAS/BRAF wild-type patients. Cetuximab did not improve OS/PFS for KRAS-, NRAS-, or BRAF-mutated tumors, and tests of interaction confirmed expanded KRAS (P = 0.0002) and NRAS (P = 0.006) as predictive, while BRAF mutations were not (P = 0.089). BEAMing identified 14% more tumors as RAS mutant than Sanger sequencing, and cetuximab lacked activity in these patients. Mutations at MAF < 5% were noted in 6 of 242 patients (2%). One patient with a KRAS A59T mutation (MAF = 2%) responded to cetuximab. More NRAS than KRAS mutations were low MAF (OR, 20.50; 95% CI, 3.88-96.85; P = 0.0038). CONCLUSIONS We establish single-agent cetuximab efficacy in optimally selected patients and show that subclonal RAS/BRAF alterations are uncommon and remain of indeterminate significance.
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Affiliation(s)
- Jonathan M Loree
- BC Cancer, University of British Columbia, Vancouver, British Columbia, Canada
| | - Anthony Dowers
- The University of Melbourne, Melbourne, Victoria, Australia
| | - Dongsheng Tu
- Canadian Cancer Trials Group, Kingston, Ontario, Canada
| | - Derek J Jonker
- The Ottawa Hospital, University of Ottawa, Ottawa, Ontario, Canada
| | | | | | | | - Timothy Price
- Queen Elizabeth Hospital, Adelaide, South Australia, Australia
| | | | - Malcolm J Moore
- BC Cancer, University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | - Paul Waring
- The University of Melbourne, Melbourne, Victoria, Australia
| | | | | | - Scott Kopetz
- University of Texas, MD Anderson Cancer Center, Houston, Texas.
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12
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Chu JE, Johnson B, Kugathasan L, Morris VK, Raghav K, Swanson L, Lim HJ, Renouf DJ, Gill S, Wolber R, Karsan A, Kopetz S, Schaeffer DF, Loree JM. Population-based Screening for BRAF V600E in Metastatic Colorectal Cancer Reveals Increased Prevalence and Poor Prognosis. Clin Cancer Res 2020; 26:4599-4605. [PMID: 32571791 DOI: 10.1158/1078-0432.ccr-20-1024] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/22/2020] [Accepted: 06/17/2020] [Indexed: 12/23/2022]
Abstract
PURPOSE BRAF V600E mutations portend poor prognosis in metastatic colorectal cancer (mCRC); however, the true prevalence and prognosis are unknown, as unwell patients may not undergo BRAF sequencing. EXPERIMENTAL DESIGN We reviewed a population-based cohort of 1,898 patients with colorectal cancer that underwent reflexive IHC mismatch repair (MMR) and BRAF V600E testing. Outcomes among IHC-detected BRAF V600E mCRC (BRAF IHC) were compared with patients with next-generation sequencing (NGS)-identified BRAF V600E-mutated mCRC from two institutions (BRAF NGS) with patients spanning from 2004 to 2018. RESULTS All-stage population prevalence of BRAF V600E was 12.5% (238/1,898) and did not differ between early and metastatic stages (P = 0.094). Prevalence among mCRC was 10.6% (61/575), of whom 51 (83.6%) were referred to oncology and 26 (42.6%) had NGS testing. BRAF IHC had worse median overall survival (mOS) than BRAF NGS [5.5 vs. 20.4 months; HR, 2.90; 95% confidence interval (CI), 1.89-4.45; P < 0.0001], which persisted in multivariate analysis (P < 0.0001). Across a combined NGS and IHC cohort, BRAF V600E tumors with deficient MMR showed worse mOS compared with MMR proficient tumors (8.9 vs. 17.2 months; HR, 1.46; 95% CI, 0.96-2.27; P = 0.043). In this combined cohort, first-line progression-free survival was 5.9 months, with minimal differences between regimens. Within the population-based cohort, attrition between treatment lines was high with only 60.7% receiving first-line chemotherapy and 26.2% receiving second line. CONCLUSIONS Patients with BRAF V600E-mutated mCRC have a worse prognosis than previously suggested, potentially arising from referral bias for testing. High attrition between lines of therapy suggests efficacious therapies need to be prioritized early for patients to benefit.
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Affiliation(s)
- Jenny E Chu
- Department of Pathology and Laboratory Medicine, Vancouver Coastal Health Authority, Vancouver, British Columbia, Canada
| | - Benny Johnson
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Van K Morris
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kanwal Raghav
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lucas Swanson
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | | | - Robert Wolber
- Department of Pathology and Laboratory Medicine, Vancouver Coastal Health Authority, Vancouver, British Columbia, Canada
| | - Aly Karsan
- Department of Pathology and Laboratory Medicine, Vancouver Coastal Health Authority, Vancouver, British Columbia, Canada.,BC Cancer, Vancouver, British Columbia, Canada
| | - Scott Kopetz
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David F Schaeffer
- Department of Pathology and Laboratory Medicine, Vancouver Coastal Health Authority, Vancouver, British Columbia, Canada
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13
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The Prospect of Identifying Resistance Mechanisms for Castrate-Resistant Prostate Cancer Using Circulating Tumor Cells: Is Epithelial-to-Mesenchymal Transition a Key Player? Prostate Cancer 2020; 2020:7938280. [PMID: 32292603 PMCID: PMC7149487 DOI: 10.1155/2020/7938280] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/19/2019] [Accepted: 02/14/2020] [Indexed: 12/18/2022] Open
Abstract
Prostate cancer (PCa) is initially driven by excessive androgen receptor (AR) signaling with androgen deprivation therapy (ADT) being a major therapeutic approach to its treatment. However, the development of drug resistance is a significant limitation on the effectiveness of both first-line and more recently developed second-line ADTs. There is a need then to study AR signaling within the context of other oncogenic signaling pathways that likely mediate this resistance. This review focuses on interactions between AR signaling, the well-known phosphatidylinositol-3-kinase/AKT pathway, and an emerging mediator of these pathways, the Hippo/YAP1 axis in metastatic castrate-resistant PCa, and their involvement in the regulation of epithelial-mesenchymal transition (EMT), a feature of disease progression and ADT resistance. Analysis of these pathways in circulating tumor cells (CTCs) may provide an opportunity to evaluate their utility as biomarkers and address their importance in the development of resistance to current ADT with potential to guide future therapies.
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14
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Le DM, Ahmed S, Ahmed S, Brunet B, Davies J, Doll C, Ferguson M, Ginther N, Gordon V, Hamilton T, Hebbard P, Helewa R, Kim CA, Lee-Ying R, Lim H, Loree JM, McGhie JP, Mulder K, Park J, Renouf D, Wong RPW, Zaidi A, Asif T. Report from the 20th annual Western Canadian Gastrointestinal Cancer Consensus Conference; Saskatoon, Saskatchewan; 28-29 September 2018. Curr Oncol 2019; 26:e773-e784. [PMID: 31896948 PMCID: PMC6927778 DOI: 10.3747/co.26.5517] [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] [Indexed: 11/15/2022] Open
Abstract
The 20th annual Western Canadian Gastrointestinal Cancer Consensus Conference was held in Saskatoon, Saskatchewan, 28-29 September 2018. This interactive multidisciplinary conference is attended by health care professionals from across Western Canada (British Columbia, Alberta, Saskatchewan, and Manitoba) who are involved in the care of patients with gastrointestinal cancers. In addition, invited speakers from other provinces participate. Surgical, medical, and radiation oncologists, and allied health care professionals participated in presentations and discussion sessions for the purpose of developing the recommendations presented here. This consensus statement addresses current issues in the management of colorectal cancers.
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Affiliation(s)
- D M Le
- Saskatoon Cancer Centre, Saskatchewan Cancer Agency, Saskatoon, SK
| | - S Ahmed
- Saskatoon Cancer Centre, Saskatchewan Cancer Agency, Saskatoon, SK
| | - S Ahmed
- CancerCare Manitoba, Winnipeg, MB
| | - B Brunet
- Saskatoon Cancer Centre, Saskatchewan Cancer Agency, Saskatoon, SK
| | | | - C Doll
- Tom Baker Cancer Centre, Alberta Health Services, AB
| | - M Ferguson
- Allan Blair Cancer Centre, Saskatchewan Cancer Agency, Regina, SK
| | - N Ginther
- University of Saskatchewan, Saskatoon, SK
| | - V Gordon
- CancerCare Manitoba, Winnipeg, MB
| | - T Hamilton
- University of British Columbia, Vancouver, BC
| | | | - R Helewa
- University of Manitoba, Winnipeg, MB
| | - C A Kim
- CancerCare Manitoba, Winnipeg, MB
| | - R Lee-Ying
- Tom Baker Cancer Centre, Alberta Health Services, AB
| | | | | | | | - K Mulder
- Cross Cancer Institute, Edmonton, AB
| | - J Park
- CancerCare Manitoba, Winnipeg, MB
| | | | | | - A Zaidi
- Saskatoon Cancer Centre, Saskatchewan Cancer Agency, Saskatoon, SK
| | - T Asif
- Saskatoon Cancer Centre, Saskatchewan Cancer Agency, Saskatoon, SK
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15
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Abstract
Background The incorporation of novel biomarkers into therapy selection for patients with metastatic colorectal cancer (mcrc) has significantly improved outcomes. Optimal treatment planning now takes into account diverse characteristics of patients and their tumours to create personalized therapeutic plans. Discussion This review is split into two sections. In the first section, we review the prognostic and predictive significance of expanded RAS mutation testing, BRAF mutations, ERBB2 (her2) amplification, microsatellite instability (msi) and deficient mismatch repair (dmmr) protein, NTRK fusions, PIK3CA mutations, and met amplifications. The therapeutic implication of each of those biomarkers for personalizing therapies for each patient with mcrc is discussed. In the second section, we touch on testing methods and considerations of relevance to clinicians when they interpret companion diagnostics meant to guide therapy selection. The advantages and pitfalls of various methods are evaluated, and we also look at the potential of liquid biopsies and circulating tumour dna (ctdna) to change the landscape of therapeutic choice and biologic understanding of the disease. Summary Routine testing for extended RAS, BRAF, dmmr or high msi, and NTRK fusions is necessary to determine the best sequencing of chemotherapy and biologic agents for patients with mcrc. Although next-generation sequencing and ctdna are increasingly being adopted, other techniques such as immunohistochemistry retain their relevance in detection of her2 amplification, NTRK fusions, and dmmr.
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16
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Chen CL, Chen CK, Ho CL, Chi WM, Yeh CH, Hu SP, Friebe P, Palmer S, Huang CS. Clinical Evaluation of IntelliPlex™ KRAS G12/13 Mutation Kit for Detection of KRAS Mutations in Codon 12 and 13: A Novel Multiplex Approach. Mol Diagn Ther 2019; 23:645-656. [DOI: 10.1007/s40291-019-00418-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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17
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Dufraing K, van Krieken JH, De Hertogh G, Hoefler G, Oniscu A, Kuhlmann TP, Weichert W, Marchiò C, Ristimäki A, Ryška A, Scoazec JY, Dequeker E. Neoplastic cell percentage estimation in tissue samples for molecular oncology: recommendations from a modified Delphi study. Histopathology 2019; 75:312-319. [PMID: 31054167 PMCID: PMC6851675 DOI: 10.1111/his.13891] [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: 01/10/2019] [Revised: 04/12/2019] [Accepted: 04/28/2019] [Indexed: 02/07/2023]
Abstract
AIMS Results from external quality assessment revealed considerable variation in neoplastic cell percentages (NCP) estimation in samples for biomarker testing. As molecular biology tests require a minimal NCP, overestimations may lead to false negative test results. We aimed to develop recommendations to improve the NCP determination in a prototypical entity - colorectal carcinoma - that can be adapted for other cancer types. METHODS AND RESULTS A modified Delphi study was conducted to reach consensus by 10 pathologists from 10 countries with experience in determining the NCP for colorectal adenocarcinoma. This study included two online surveys and a decision-making meeting. Consensus was defined a priori as an agreement of > 80%. All pathologists completed both surveys. Consensus was reached for 8 out of 19 and 2 out of 13 questions in the first and second surveys, respectively. Remaining issues were resolved during the meeting. Twenty-four recommendations were formulated. Major recommendations resulted as follows: only pathologists should conduct the morphological evaluation; nevertheless molecular biologists/technicians may estimate the NCP, if specific training has been performed and a pathologist is available for feedback. The estimation should be determined in the area with the highest density of viable neoplastic cells and lowest density of inflammatory cells. Other recommendations concerned: the determination protocol itself, needs for micro- and macro-dissection, reporting and interpreting, referral practices and applicability to other cancer types. CONCLUSION We believe these recommendations may lead to more accurate NCP estimates, ensuring the correct interpretation of test results, and might help in validating digital algorithms in the future.
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Affiliation(s)
- Kelly Dufraing
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium.,Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Gert De Hertogh
- Department of Pathology, University Hospital Leuven, Leuven, Belgium
| | - Gerald Hoefler
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Anca Oniscu
- Department of Molecular Pathology, Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Tine P Kuhlmann
- Department of Pathology, Herlev Hospital, Copenhagen, Denmark
| | - Wilko Weichert
- Department of Pathology, Technical University Munich, Munich, Germany
| | - Caterina Marchiò
- Department of Medical Sciences, University of Turin and Pathology Unit, Torino, Italy.,FPO-IRCCS Candiolo Cancer Institute, Candiolo, Italy
| | - Ari Ristimäki
- Department of Pathology, Research Programs Unit and HUSLAB, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Aleš Ryška
- The Fingerland Department of Pathology, Faculty of Medicine and University Hospital, Hradec Kralove, Czech Republic
| | | | - Elisabeth Dequeker
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
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18
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Abstract
Survival of patients with metastatic colorectal cancer (mCRC) has significantly improved in the last decade. Survival gains are not driven by advances in first-line therapy but by incremental additional effects of subsequent treatment lines. To maximize outcomes, patients should receive all active agents. Identification of patient subgroups is increasing individualization of treatment. Novel oral agents, such as regorafenib and TAS-102, as well as promising immunotherapeutic agents have offered salvage treatment options for refractory mCRC. Although most therapeutic developments for mCRC in the chemorefractory setting focuses on new targets and/or more potent agents, reconsideration of established targets has gained importance with the growth of a rational pharmacogenomic approach to drug development, such as HER2. The authors describe treatment options for patients with refractory colon cancer following first- and second-line therapy.
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Affiliation(s)
- Margaret Byrne
- Northwell Health Cancer Institute, Donald and Barbara Zucker School of Medicine at Hofstra, Lake Success, NY, USA,
| | - Muhammad Wasif Saif
- Northwell Health Cancer Institute, Donald and Barbara Zucker School of Medicine at Hofstra, Lake Success, NY, USA,
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19
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Loree JM, Bailey AM, Johnson AM, Yu Y, Wu W, Bristow CA, Davis JS, Shaw KR, Broaddus R, Banks KC, Lanman RB, Meric-Bernstam F, Overman MJ, Kopetz S, Raghav K. Molecular Landscape of ERBB2/ERBB3 Mutated Colorectal Cancer. J Natl Cancer Inst 2018; 110:1409-1417. [PMID: 29718453 PMCID: PMC6292791 DOI: 10.1093/jnci/djy067] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 02/10/2018] [Accepted: 03/16/2018] [Indexed: 01/14/2023] Open
Abstract
Background Despite growing therapeutic relevance of ERBB2 amplifications in colorectal cancer (CRC), little is known about ERBB2/ERBB3 mutations. We aimed to characterize these subsets of CRC. Methods We performed a retrospective analysis of 419 CRC patients from MD Anderson (MDACC) and 619 patients from the Nurses' Health Study (NHS)/Health Professionals Follow-Up Study (HPFS) with tissue sequencing, clinicopathologic, mutational, and consensus molecular subtype (CMS) profiles of ERBB2/ERBB3 mutant patients. A third cohort of 1623 CRC patients with ctDNA assays characterized the ctDNA profile of ERBB2 mutants. All statistical tests were two-sided. Results ERBB2 mutations occurred in 4.1% (95% confidence interval [CI] = 2.4% to 6.4%), 5.8% (95% CI = 4.1% to 8.0%), and 5.1% (95% CI = 4.0% to 6.2%) of MDACC, NHS/HPFS, and ctDNA patients, respectively. ERBB3 mutations occurred in 5.7% (95% CI = 3.7% to 8.4%, 95% CI = 4.0% to 7.8%) of patients in both tissue cohorts. Age, stage, and tumor location were not associated with either mutation. Microsatellite instability (MSI) was associated with ERBB2 (odds ratio [OR] = 5.98, 95% CI = 2.47 to 14.49, P < .001; OR = 5.13, 95% CI = 2.38 to 11.05, P < .001) and ERBB3 mutations (OR = 3.48, 95% CI = 1.51 to 8.02, P = .002; OR = 3.40, 95% CI = 1.05 to 10.96, P = .03) in both tissue cohorts. Neither gene was associated with TP53, APC, KRAS, NRAS, or BRAF mutations in tissue. However, PIK3CA mutations were strongly associated with ERBB2 mutations in all three cohorts (OR = 3.68, 95% CI = 1.83 to 7.41, P = .001; OR = 2.25, 95% CI = 1.11 to 4.58, P = .02; OR = 2.11, 95% CI = 1.25 to 3.58, P = .004) and ERBB3 mutations in the MDACC cohort (OR = 13.26, 95% CI = 5.27 to 33.33, P < .001). ERBB2 (P = 0.08) and ERBB3 (P = .008) mutations were associated with CMS1 subtype. ERBB2 (hazard ratio [HR] = 1.82, 95% CI = 1.23 to 4.03, P = .009), but not ERBB3 (HR = 0.88, 95% CI = 0.45 to 1.73, P = .73), mutations were associated with worse overall survival. Conclusions MSI and PIK3CA mutations are associated with ERBB2/ERBB3 mutations. Co-occurring PIK3CA mutations may represent a second hit to oncogenic signaling that needs consideration when targeting ERBB2/ERBB3.
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Affiliation(s)
- Jonathan M Loree
- Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ann M Bailey
- Sheikh Khalifa Bin Zayed Al Nahyan Institute of Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Amber M Johnson
- Sheikh Khalifa Bin Zayed Al Nahyan Institute of Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Yao Yu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Wenhui Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Christopher A Bristow
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jennifer S Davis
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Kenna R Shaw
- Sheikh Khalifa Bin Zayed Al Nahyan Institute of Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Russell Broaddus
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Funda Meric-Bernstam
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Michael J Overman
- Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Scott Kopetz
- Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Kanwal Raghav
- Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
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20
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Dufraing K, De Hertogh G, Tack V, Keppens C, Dequeker EMC, van Krieken JH. External Quality Assessment Identifies Training Needs to Determine the Neoplastic Cell Content for Biomarker Testing. J Mol Diagn 2018; 20:455-464. [PMID: 29625250 DOI: 10.1016/j.jmoldx.2018.03.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/14/2018] [Accepted: 03/05/2018] [Indexed: 10/17/2022] Open
Abstract
Neoplastic cell content determination is crucial for biomarker testing. It is known that interobserver variation exists, but largescale data are missing about variation in tumor delineation and cell content determination. Results were obtained from the external quality assessment program for metastatic colorectal cancer from the European Society of Pathology (N = 5776 observations). The study included three parts: current practices were surveyed, neoplastic cell content estimations and delineations were retrieved from stained slides, and clinical reports were analyzed. Seventeen of 43 pathologists determined the neoplastic cell content in a tumor-rich area for DNA extraction and took immune cells (n = 37), tumor cell distribution (n = 33), desmoplastic stroma (n = 30), necrosis (n = 29), and mucus (n = 23) into account. The selected area was highly variable, and the average difference between the highest and lowest estimation ranged between 51% and 78% (2011 to 2017). The number of overestimations was alarmingly high in samples containing <30% tumor cells. Of concern is that 33 of 105 laboratories reported a wild-type result in a sample without tumor in 2017. Standardization of neoplastic cell content determination is needed for test outcome interpretation. The authors' data show variation in estimation practices, tumor delineations and estimations, and interpretation problems (n = 226 reports). Further training for selecting the most suitable block and creating clear reports is urgently needed.
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Affiliation(s)
- Kelly Dufraing
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium; Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Gert De Hertogh
- Department of Pathology, University Hospital Leuven, Leuven, Belgium
| | - Véronique Tack
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| | - Cleo Keppens
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| | - Elisabeth M C Dequeker
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium.
| | - J Han van Krieken
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
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21
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FOCUS4: a new trial design for evaluation of targeted drugs in colorectal cancer? Lancet Gastroenterol Hepatol 2018; 3:143-145. [DOI: 10.1016/s2468-1253(17)30402-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 12/13/2017] [Indexed: 01/18/2023]
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22
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Yan XL, Zhang XB, Ao R, Guan L. Effects of shRNA-Mediated Silencing of PKM2 Gene on Aerobic Glycolysis, Cell Migration, Cell Invasion, and Apoptosis in Colorectal Cancer Cells. J Cell Biochem 2017; 118:4792-4803. [PMID: 28543190 DOI: 10.1002/jcb.26148] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 05/18/2017] [Indexed: 01/06/2023]
Abstract
This study aims to explore the effects of shRNA-mediated silencing on Pyruvate kinase type M2 (PKM2) gene during aerobic glycolysis in colorectal cancer (CRC) cells. CRC tissues and adjacent normal tissues were obtained from 136 patients diagnosed with qRT-PCR, Western blotting, and immunohistochemistry (IHC) were performed to detect mRNA and protein expressions of PKM2. CRC cells were divided into a blank, vector, and PKM2-shRNA groups. Hexokinase (HK) and PKM2 activity were both determined by glucose-6-phosphate dehydrogenase (G-6-PD) coupled colorimetric assay and enzyme coupling rate method. The extracellular lactate concentration was measured by ultraviolet spectrophotometer and caspase activity was measured using spectrophotometry. The proliferation, cell cycle, apoptosis, invasion, and migration of CRC cells were detected by cell counting kit-8 (CCK-8) assay, flow cytometry, transwell assay, and scratch test. Three groups of nude mice were injected with 0.2 mL single-cell suspension from the blank, vector, and PKM2-shRNA groups, respectively. PKM2 protein content in CRC tissues was higher than that in adjacent normal tissues. Results showed that the PKM2-shRNA group exhibited significantly lower mRNA and protein expressions of PKM2, decreased PKM2 activity, reduced lactate metabolism level, increased cell apoptosis rate, elevated caspase-3 and caspase-9 activity, weakened proliferation, and a reduction in cell invasion and migration ability compared to the vector and blank groups. The optical density (OD) value was lower in the PKM2-shRNA group than in the blank and vector groups. These findings indicate that shRNA-mediated silencing of PKM2 gene promotes apoptosis and inhibits aerobic glycolysis, proliferation, migration, and invasion in CRC cells. J. Cell. Biochem. 118: 4792-4803, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Xiao-Ling Yan
- Department of Pathology, Tianjin Huanhu Hospital, Tianjin 300350, P. R. China
- Tianjin Key Laboratory of Cerebral Vascular and Neurodegenerative Diseases, Tianjin 300350, P. R. China
| | - Xue-Bin Zhang
- Department of Pathology, Tianjin Huanhu Hospital, Tianjin 300350, P. R. China
| | - Ran Ao
- Department of Gastroenterology, The First Hospital of China Medical University, Shenyang 110001, P. R. China
| | - Lin Guan
- Department of Gastroenterology, The First Hospital of China Medical University, Shenyang 110001, P. R. China
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23
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Loree JM, Kopetz S. Recent developments in the treatment of metastatic colorectal cancer. Ther Adv Med Oncol 2017; 9:551-564. [PMID: 28794806 PMCID: PMC5524248 DOI: 10.1177/1758834017714997] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/23/2017] [Indexed: 12/11/2022] Open
Abstract
Over the past decade there have been significant advances in the molecular characterization of colorectal cancer (CRC) that are driving treatment decisions. Expanded RAS testing beyond KRAS exon 2 was established as crucial for identifying patients who will respond to anti-epidermal growth factor receptor (EGFR) therapies and low-frequency mutations in RAS/tumor heterogeneity are gaining recognition as potential mechanisms of resistance. Despite this progress, the fact that we do not understand why left-sided but not right-sided tumors have improved outcomes following anti-EGFR therapy highlights our superficial understanding of this disease. Even with few new targeted agents receiving approval in CRC, the incorporation of next-generation sequencing into clinical decision making represents an important step forward. Biomarkers such as BRAF mutations, microsatellite instability, and HER2 amplification represent promising molecular aberrations with therapies in various stages of development, and highlight the importance of companion diagnostics in supporting targeted agents. In this review, we will discuss the importance of incorporating biomarkers into clinical decision making and regimen selection in CRC. We will particularly focus on the recent evidence suggesting an important role for tumor location in selecting first-line therapy, the importance of recent advances in biomarker development and molecular subtyping, as well as recently approved agents (regorafenib and TAS-102) and promising targeted agents that have the potential to change the standard of care.
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Affiliation(s)
- Jonathan M. Loree
- Division of Gastrointestinal Medical Oncology, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Scott Kopetz
- Division of Gastrointestinal Medical Oncology, The University of Texas, MD Anderson Cancer Center, Unit 426, 1515 Holcombe Blvd, Houston, TX 77030, USA
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