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Venken T, Miller IS, Arijs I, Thomas V, Barat A, Betge J, Zhan T, Gaiser T, Ebert MP, O'Farrell AC, Prehn J, Klinger R, O'Connor DP, Moulton B, Murphy V, Serna G, Nuciforo PG, McDermott R, Bird B, Leonard G, Grogan L, Horgan A, Schulte N, Moehler M, Lambrechts D, Byrne AT. Analysis of cell free DNA to predict outcome to bevacizumab therapy in colorectal cancer patients. NPJ Genom Med 2024; 9:33. [PMID: 38811554 PMCID: PMC11137102 DOI: 10.1038/s41525-024-00415-x] [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: 09/22/2023] [Accepted: 05/02/2024] [Indexed: 05/31/2024] Open
Abstract
To predict outcome to combination bevacizumab (BVZ) therapy, we employed cell-free DNA (cfDNA) to determine chromosomal instability (CIN), nucleosome footprints (NF) and methylation profiles in metastatic colorectal cancer (mCRC) patients. Low-coverage whole-genome sequencing (LC-WGS) was performed on matched tumor and plasma samples, collected from 74 mCRC patients from the AC-ANGIOPREDICT Phase II trial (NCT01822444), and analysed for CIN and NFs. A validation cohort of plasma samples from the University Medical Center Mannheim (UMM) was similarly profiled. 61 AC-ANGIOPREDICT plasma samples collected before and following BVZ treatment were selected for targeted methylation sequencing. Using cfDNA CIN profiles, AC-ANGIOPREDICT samples were subtyped with 92.3% accuracy into low and high CIN clusters, with good concordance observed between matched plasma and tumor. Improved survival was observed in CIN-high patients. Plasma-based CIN clustering was validated in the UMM cohort. Methylation profiling identified differences in CIN-low vs. CIN high (AUC = 0.87). Moreover, significant methylation score decreases following BVZ was associated with improved outcome (p = 0.013). Analysis of CIN, NFs and methylation profiles from cfDNA in plasma samples facilitates stratification into CIN clusters which inform patient response to treatment.
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Affiliation(s)
- Tom Venken
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for Cancer Biology, Leuven, Belgium
| | - Ian S Miller
- Precision Cancer Medicine Group, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Ingrid Arijs
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for Cancer Biology, Leuven, Belgium
| | - Valentina Thomas
- Precision Cancer Medicine Group, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Ana Barat
- Centre for Systems Medicine, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Johannes Betge
- Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Junior Clinical Cooperation Unit Translational Gastrointestinal Oncology and Preclinical Models, German Cancer Research Center (DKFZ), Heidelberg, Germany
- DKFZ-Hector Cancer Institute at University Medical Center Mannheim, Mannheim, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Tianzuo Zhan
- Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Timo Gaiser
- Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Matthias P Ebert
- Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- DKFZ-Hector Cancer Institute at University Medical Center Mannheim, Mannheim, Germany
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Alice C O'Farrell
- Precision Cancer Medicine Group, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Jochen Prehn
- Centre for Systems Medicine, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Rut Klinger
- UCD Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Darran P O'Connor
- Department of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | | | | | - Garazi Serna
- Val d'Hebron Institute of Oncology, Barcelona, Spain
| | | | - Ray McDermott
- Cancer Trials Ireland, Dublin, Ireland
- Department of Medical Oncology, Tallaght University Hospital, Dublin, Ireland
- Department of Medical Oncology, St. Vincent's University Hospital, Dublin, Ireland
| | - Brian Bird
- Bon Secours Cork Cancer Centre, Bon Secours Hospital Cork, Cork, Ireland
| | | | - Liam Grogan
- Medical Oncology Department, Beaumont Hospital, Dublin, Ireland
| | - Anne Horgan
- Department of Medical Oncology, South East Cancer Center, University Hospital Waterford, Waterford, Ireland
| | - Nadine Schulte
- Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Markus Moehler
- Department of Medicine, Johannes-Gutenberg University Clinic, Mainz, Germany
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium.
- VIB Center for Cancer Biology, Leuven, Belgium.
| | - Annette T Byrne
- Precision Cancer Medicine Group, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland.
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Bhatia S, Khanna KK, Duijf PHG. Targeting chromosomal instability and aneuploidy in cancer. Trends Pharmacol Sci 2024; 45:210-224. [PMID: 38355324 DOI: 10.1016/j.tips.2024.01.009] [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: 12/21/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 02/16/2024]
Abstract
Cancer development and therapy resistance are driven by chromosomal instability (CIN), which causes chromosome gains and losses (i.e., aneuploidy) and structural chromosomal alterations. Technical limitations and knowledge gaps have delayed therapeutic targeting of CIN and aneuploidy in cancers. However, our toolbox for creating and studying aneuploidy in cell models has greatly expanded recently. Moreover, accumulating evidence suggests that seven conventional antimitotic chemotherapeutic drugs achieve clinical response by inducing CIN instead of mitotic arrest, although additional anticancer activities may also contribute in vivo. In this review, we discuss these recent developments. We also highlight new discoveries, which together show that 25 chromosome arm aneuploidies (CAAs) may be targetable by 36 drugs across 14 types of cancer. Collectively, these advances offer many new opportunities to improve cancer treatment.
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Affiliation(s)
- Sugandha Bhatia
- Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalised Health and Centre for Biomedical Technologies at the Translational Research Institute, Woolloongabba, QLD 4102, Australia.
| | - Kum Kum Khanna
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD 4006, Australia; Mater Research Institute, The University of Queensland, Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - Pascal H G Duijf
- Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalised Health and Centre for Biomedical Technologies at the Translational Research Institute, Woolloongabba, QLD 4102, Australia; Centre for Cancer Biology, Clinical and Health Sciences, University of South Australia and SA Pathology, Adelaide, SA 5001, Australia; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.
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3
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LIM SUNGHEE, CHO HEEJIN, KIM KYOUNGMEE, LIM HOYEONG, KANG WONKI, LEE JEEYUN, PARK YOUNGSUK, KIM HEECHEOL, KIM SEUNGTAE. Comprehensive molecular analysis to predict the efficacy of chemotherapy containing bevacizumab in patients with metastatic colorectal cancer. Oncol Res 2023; 31:855-866. [PMID: 37744267 PMCID: PMC10513961 DOI: 10.32604/or.2023.030374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/24/2023] [Indexed: 09/26/2023] Open
Abstract
Background Although bevacizumab is an important treatment for metastatic colorectal cancer (CRC), not all patients with CRC benefit from it; in unselected patient populations, only modest survival benefits have been reported. Methods We evaluated clinical outcomes in 110 patients using comprehensive molecular characterization to identify biomarkers for a response to bevacizumab-containing treatment. The molecular analysis comprised whole-exome sequencing, ribonucleic acid sequencing, and a methylation array on patient tissues. Results Genomic and molecular characterization was successfully conducted in 103 patients. Six of 103 CRC samples were hypermutated, and none of the non-hypermutant tumors were microsatellite unstable. Among those 103 patients, 89 had adenocarcinoma (ADC), 15 were diagnosed with mucinous ADC, and six had signet-ring cell carcinoma (SRCC). Consensus molecular subtype (CMS) 2 was unique to ADC. Of the four SRCCs, two were CMS1, one was CMS4, and the other was CMS3. APC mutation status was a significantly enriched factor in responders to bevacizumab treatment. Fibroblast growth factor receptor (FGFR) 1/2 signaling was upregulated in non-responders, whereas cell cycle, transfer ribonucleic acid processing, nucleotide excision repair, and oxidative phosphorylation pathways were enriched in responders. In addition, IGF1 was differentially expressed in non-responders (log2 fold change = -1.43, p = 4.11 × 10-5, false discovery rate = 0.098), and FLT1 was highly methylated in non-responders (p = 7.55 × 10-3). When the molecular pathways were reanalyzed separately according to the backbone chemotherapy (FOLFOX vs. FOLFIRI), the significance of the molecular pathways varied according to the backbone chemotherapy. Conclusions This study sought a subset of CRC patients with a distinct clinical response to chemotherapy containing bevacizumab. Our results need to be validated in a large group of homogenous patient cohort and examined according to the different chemotherapy backbones to create personalized therapeutic opportunities in CRC.
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Affiliation(s)
- SUNG HEE LIM
- Division of Hematology/Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Gangnam-gu, Seoul, 06351, Korea
| | - HEE JIN CHO
- Division of Hematology/Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Gangnam-gu, Seoul, 06351, Korea
- Precision Medicine Research Institute, Samsung Medical Center, Gangnam-gu, Seoul, 06351, Korea
- Department of Biomedical Convergence Science and Technology, Kyungpook National University, Daegu, 41566, Korea
| | - KYOUNG-MEE KIM
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Korea
| | - HO YEONG LIM
- Division of Hematology/Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Gangnam-gu, Seoul, 06351, Korea
| | - WON KI KANG
- Division of Hematology/Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Gangnam-gu, Seoul, 06351, Korea
| | - JEEYUN LEE
- Division of Hematology/Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Gangnam-gu, Seoul, 06351, Korea
| | - YOUNG SUK PARK
- Division of Hematology/Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Gangnam-gu, Seoul, 06351, Korea
| | - HEE CHEOL KIM
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Gangnam-gu, Seoul, 06351, Korea
| | - SEUNG TAE KIM
- Division of Hematology/Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Gangnam-gu, Seoul, 06351, Korea
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Gonzalez RD, Small GW, Green AJ, Akhtari FS, Motsinger-Reif AA, Quintanilha JCF, Havener TM, Reif DM, McLeod HL, Wiltshire T. MKX-AS1 Gene Expression Associated with Variation in Drug Response to Oxaliplatin and Clinical Outcomes in Colorectal Cancer Patients. Pharmaceuticals (Basel) 2023; 16:ph16050757. [PMID: 37242540 DOI: 10.3390/ph16050757] [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: 03/15/2023] [Revised: 05/11/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Oxaliplatin (OXAL) is a commonly used chemotherapy for treating colorectal cancer (CRC). A recent genome wide association study (GWAS) showed that a genetic variant (rs11006706) in the lncRNA gene MKX-AS1 and partnered sense gene MKX could impact the response of genetically varied cell lines to OXAL treatment. This study found that the expression levels of MKX-AS1 and MKX in lymphocytes (LCLs) and CRC cell lines differed between the rs11006706 genotypes, indicating that this gene pair could play a role in OXAL response. Further analysis of patient survival data from the Cancer Genome Atlas (TCGA) and other sources showed that patients with high MKX-AS1 expression status had significantly worse overall survival (HR = 3.2; 95%CI = (1.17-9); p = 0.024) compared to cases with low MKX-AS1 expression status. Alternatively, high MKX expression status had significantly better overall survival (HR = 0.22; 95%CI = (0.07-0.7); p = 0.01) compared to cases with low MKX expression status. These results suggest an association between MKX-AS1 and MKX expression status that could be useful as a prognostic marker of response to OXAL and potential patient outcomes in CRC.
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Affiliation(s)
- Ricardo D Gonzalez
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Center for Pharmacogenomics and Individualized Therapy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - George W Small
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Center for Pharmacogenomics and Individualized Therapy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Adrian J Green
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27606, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27606, USA
| | - Farida S Akhtari
- Biostatistics and Computational Biology Branch, Division of Intramural Research, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Alison A Motsinger-Reif
- Biostatistics and Computational Biology Branch, Division of Intramural Research, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | | | - Tammy M Havener
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David M Reif
- Predictive Toxicology Branch, Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Howard L McLeod
- Center for Precision Medicine and Functional Genomics, Utah Tech University, St. George, UT 84770, USA
| | - Tim Wiltshire
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Center for Pharmacogenomics and Individualized Therapy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Ten Hoorn S, Mol L, Sommeijer DW, Nijman L, van den Bosch T, de Back TR, Ylstra B, van Dijk E, van Noesel CJM, Reinten RJ, Nagtegaal ID, Koopman M, Punt CJA, Vermeulen L. Long-term Survival Update and Extended RAS Mutational Analysis of the CAIRO2 Trial: Addition of Cetuximab to CAPOX/Bevacizumab in Metastatic Colorectal Cancer. Clin Colorectal Cancer 2023; 22:67-75. [PMID: 36564280 DOI: 10.1016/j.clcc.2022.11.006] [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: 06/26/2022] [Revised: 11/16/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND Here we present updated survival of the CAIRO2 trial and assessed whether the addition of anti-EGFR to anti-VEGF therapy could still be an effective treatment option for patients with extended RAS/BRAF wildtype and left-sided metastatic colorectal cancer (mCRC). MATERIALS AND METHODS Retrospective updated survival and extended RAS and BRAF V600E mutational analysis were performed in the CAIRO2 trial, a multicenter, randomized phase III trial on the effect of adding cetuximab to a combination of capecitabine, oxaliplatin (CAPOX), and bevacizumab in mCRC. RESULTS Updated survival analysis confirmed that the addition of cetuximab did not provide a benefit on either progression free (PFS) or overall survival (OS) in the intention-to-treat population. With the extended mutational analyses 31 KRAS, 31 NRAS and 12 BRAF V600E additional mutations were found. No benefit of the addition of cetuximab was observed within the extended wildtype group, even when selecting only left-sided tumors (PFS HR 0.96, p = 0.7775). However, compared to the original trial an increase of 6.5 months was seen for patients with both extended wildtype and left-sided tumors (median OS 28.6 months). CONCLUSION Adding cetuximab to CAPOX and bevacizumab does not provide clinical benefit in patients with mCRC, even in the extended wildtype group with left-sided tumors. However, in the extended wildtype group we did observe clinically relevant higher survival compared to the initial trial report, indicating that it is important to analyze a broader panel of RAS and BRAF variants using more recent sequencing techniques when assessing survival benefit after anti-EGFR therapy.
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Affiliation(s)
- Sanne Ten Hoorn
- Amsterdam UMC location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, The Netherlands; Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands; Oncode Institute, Utrecht, The Netherlands
| | - Linda Mol
- Clinical Research Department, Netherlands Comprehensive Cancer Center (IKNL), Nijmegen, The Netherlands
| | - Dirkje W Sommeijer
- Amsterdam UMC location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, The Netherlands; Amsterdam UMC location University of Amsterdam, Department of Medical Oncology, Amsterdam, The Netherlands; Flevohospital, Department of Internal Medicine, Almere, The Netherlands
| | - Lisanne Nijman
- Amsterdam UMC location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, The Netherlands; Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands; Oncode Institute, Utrecht, The Netherlands
| | - Tom van den Bosch
- Amsterdam UMC location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, The Netherlands; Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands; Oncode Institute, Utrecht, The Netherlands; Amsterdam UMC location University of Amsterdam, Amsterdam Gastroenterology & Metabolism, Amsterdam, The Netherlands
| | - Tim R de Back
- Amsterdam UMC location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, The Netherlands; Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands; Oncode Institute, Utrecht, The Netherlands
| | - Bauke Ylstra
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Erik van Dijk
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Carel J M van Noesel
- Amsterdam UMC location University of Amsterdam, Department of Pathology, Amsterdam, The Netherlands
| | - Roy J Reinten
- Amsterdam UMC location University of Amsterdam, Department of Pathology, Amsterdam, The Netherlands
| | - Iris D Nagtegaal
- Radboud Institute for Molecular Life Sciences, Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Miriam Koopman
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Cornelis J A Punt
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Louis Vermeulen
- Amsterdam UMC location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, The Netherlands; Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands; Oncode Institute, Utrecht, The Netherlands.
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Wang W, Tang X, Duan C, Tian S, Han C, Qian W, Jiang X, Hou X, Lin R. Intestinal epithelium-specific Fut2 deficiency promotes colorectal cancer through down-regulating fucosylation of MCAM. J Transl Med 2023; 21:82. [PMID: 36739428 PMCID: PMC9899399 DOI: 10.1186/s12967-023-03906-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/19/2023] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Our previous study showed that fucosyltransferase 2 (Fut2) deficiency is closely related to colitis. Colitis increases the risk for the development of colorectal cancer (CRC). This study aimed to investigate the effect and underlying mechanism of action of Fut2 in CRC. METHODS Intestinal epithelium-specific Fut2 knockout (Fut2△IEC) mice were used in this study. CRC was induced using azoxymethane (AOM) and dextran sulfate sodium (DSS). Immunofluorescence was used to examine the fucosylation levels. Proteomics and N-glycoproteomics analyses, Ulex Europaeus Agglutinin I (UEA-I) affinity chromatography, immunoprecipitation, and rescue assay were used to investigate the mechanism of Fut2 in CRC. RESULTS The expression of Fut2 and α-1,2-fucosylation was lower in colorectal tumor tissues than in the adjacent normal tissues of AOM/DSS-induced CRC mice. More colorectal tumors were detected in Fut2△IEC mice than in control mice, and significant downregulation of melanoma cell adhesion molecule (MCAM) fucosylation was detected in the colorectal tumor tissues of Fut2△IEC mice. Overexpression of Fut2 inhibited cell proliferation, invasion and tumor metastasis in vivo and in vitro in SW480 and HCT116 cells. Moreover, fucosylation of MCAM may be a mediator of Fut2 in CRC. Peracetylated 2-F-Fuc, a fucosyltransferase inhibitor, repressed fucosylation modification of MCAM and reversed the inhibitory effects of Fut2 overexpression on SW480 cell proliferation, migration, and invasion. Our results indicate that Fut2 deficiency in the intestinal epithelium promotes CRC by downregulating the fucosylation of MCAM. CONCLUSIONS The regulation of fucosylation may be an potential therapy for CRC, especially in patients with Fut2 gene defects.
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Affiliation(s)
- Weijun Wang
- grid.33199.310000 0004 0368 7223Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Xuelian Tang
- grid.33199.310000 0004 0368 7223Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Caihan Duan
- grid.33199.310000 0004 0368 7223Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Shuxin Tian
- grid.33199.310000 0004 0368 7223Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China ,grid.411680.a0000 0001 0514 4044Department of Gastroenterology, The First Affiliated Hospital of Medical College, Shihezi University, Shihezi, 832008 China
| | - Chaoqun Han
- grid.33199.310000 0004 0368 7223Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Wei Qian
- grid.33199.310000 0004 0368 7223Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Xin Jiang
- grid.33199.310000 0004 0368 7223Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Xiaohua Hou
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Rong Lin
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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Yamada S, Osakabe M, Uesugi N, Yanagawa N, Matsumoto T, Suzuki H, Sugai T. Genome-wide analysis of colorectal cancer based on gene-based somatic copy number alterations during neoplastic progression within the same tumor. Cancer Med 2023; 12:4446-4454. [PMID: 35920319 PMCID: PMC9972084 DOI: 10.1002/cam4.5117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND The objective of this study was to elucidate the association between neoplastic progression and somatic copy number alterations (SCNAs) occurring within the same colorectal cancer (CRC) tumor. METHODS We investigated SCNAs to identify the progression from a high-grade intramucosal lesion (HGIL) to an invasive front lesion (IFL), via an invasive submucosal lesion (ISL), within the same tumor using a crypt isolation method combined with a SNP array. Immunohistochemistry was also performed. RESULTS We identified 51 amplified genes that potentially promote progression from HGIL to ISL and 6 amplified genes involved in the progression from ISL to IFL. Of the 51 genes involved in HGIL to ISL progression, TORC1, MSLN, and STUB1, which are closely associated with CRC, were identified as candidate markers of submucosal invasion. However, no candidate genes were identified among the six genes associated with ISL to IFL progression. In addition, the number of total SCNAs and the number of gains were correlated with cancer progression (from HGIL to IFL). Finally, immunohistochemistry revealed higher expression of TORC1, MSLN, and STUB1 in ISL than in HGIL. CONCLUSIONS These results suggest that specific SCNAs are required for acquisition of invasive ability in CRC, and the affected genes are potential markers of invasion.
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Affiliation(s)
- Shun Yamada
- Department of Molecular Diagnostic Pathology, School of MedicineIwate Medical UniversityYahabaJapan
- Division of Gastroenterology, Department of Internal MedicineIwate Medical UniversityYahabaJapan
| | - Mitsumasa Osakabe
- Department of Molecular Diagnostic Pathology, School of MedicineIwate Medical UniversityYahabaJapan
| | - Noriyuki Uesugi
- Department of Molecular Diagnostic Pathology, School of MedicineIwate Medical UniversityYahabaJapan
| | - Naoki Yanagawa
- Department of Molecular Diagnostic Pathology, School of MedicineIwate Medical UniversityYahabaJapan
| | - Takayuki Matsumoto
- Division of Gastroenterology, Department of Internal MedicineIwate Medical UniversityYahabaJapan
| | - Hiromu Suzuki
- Department of Molecular BiologySapporo Medical UniversitySapporoJapan
| | - Tamotsu Sugai
- Department of Molecular Diagnostic Pathology, School of MedicineIwate Medical UniversityYahabaJapan
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Lakbir S, Lahoz S, Cuatrecasas M, Camps J, Glas RA, Heringa J, Meijer GA, Abeln S, Fijneman RJA. Tumour break load is a biologically relevant feature of genomic instability with prognostic value in colorectal cancer. Eur J Cancer 2022; 177:94-102. [PMID: 36334560 DOI: 10.1016/j.ejca.2022.09.034] [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: 07/06/2022] [Revised: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 01/06/2023]
Abstract
BACKGROUND Clinically implemented prognostic biomarkers are lacking for the 80% of colorectal cancers (CRCs) that exhibit chromosomal instability (CIN). CIN is characterised by chromosome segregation errors and double-strand break repair defects that lead to somatic copy number aberrations (SCNAs) and chromosomal rearrangement-associated structural variants (SVs), respectively. We hypothesise that the number of SVs is a distinct feature of genomic instability and defined a new measure to quantify SVs: the tumour break load (TBL). The present study aimed to characterise the biological impact and clinical relevance of TBL in CRC. METHODS Disease-free survival and SCNA data were obtained from The Cancer Genome Atlas and two independent CRC studies. TBL was defined as the sum of SCNA-associated SVs. RNA gene expression data of microsatellite stable (MSS) CRC samples were used to train an RNA-based TBL classifier. Dichotomised DNA-based TBL data were used for survival analysis. RESULTS TBL shows large variation in CRC with poor correlation to tumour mutational burden and fraction of genome altered. TBL impact on tumour biology was illustrated by the high accuracy of classifying cancers in TBL-high and TBL-low (area under the receiver operating characteristic curve [AUC]: 0.88; p < 0.01). High TBL was associated with disease recurrence in 85 stages II-III MSS CRCs from The Cancer Genome Atlas (hazard ratio [HR]: 6.1; p = 0.007) and in two independent validation series of 57 untreated stages II-III (HR: 4.1; p = 0.012) and 74 untreated stage II MSS CRCs (HR: 2.4; p = 0.01). CONCLUSION TBL is a prognostic biomarker in patients with non-metastatic MSS CRC with great potential to be implemented in routine molecular diagnostics.
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Affiliation(s)
- Soufyan Lakbir
- Bioinformatics Group, Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam 1081HV, the Netherlands; Department of Pathology, Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066CX, the Netherlands
| | - Sara Lahoz
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology Team, Institut D'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, 08036, Spain
| | - Miriam Cuatrecasas
- Pathology Department, Biomedical Diagnostic Center (CDB), Hospital Clínic de Barcelona, Institut D'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Universitat de Barcelona (UB), Barcelona, 08036, Spain
| | - Jordi Camps
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology Team, Institut D'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, 08036, Spain; Department of Cell Biology, Physiology and Immunology, Faculty of Medicine, Autonomous University of Barcelona, Bellaterra, 08193, Spain
| | - Roel A Glas
- Bioinformatics Group, Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam 1081HV, the Netherlands; Department of Pathology, Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066CX, the Netherlands
| | - Jaap Heringa
- Bioinformatics Group, Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam 1081HV, the Netherlands; AIMMS - Amsterdam Institute for Molecules Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam 1081HV, the Netherlands
| | - Gerrit A Meijer
- Department of Pathology, Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066CX, the Netherlands
| | - Sanne Abeln
- Bioinformatics Group, Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam 1081HV, the Netherlands; Life Sciences and Health Research Group, Centrum Wiskunde & Informatica (CWI), Science Park 123, Amsterdam 1098 XG, the Netherlands.
| | - Remond J A Fijneman
- Department of Pathology, Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066CX, the Netherlands.
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9
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Russo V, Lallo E, Munnia A, Spedicato M, Messerini L, D’Aurizio R, Ceroni EG, Brunelli G, Galvano A, Russo A, Landini I, Nobili S, Ceppi M, Bruzzone M, Cianchi F, Staderini F, Roselli M, Riondino S, Ferroni P, Guadagni F, Mini E, Peluso M. Artificial Intelligence Predictive Models of Response to Cytotoxic Chemotherapy Alone or Combined to Targeted Therapy for Metastatic Colorectal Cancer Patients: A Systematic Review and Meta-Analysis. Cancers (Basel) 2022; 14:4012. [PMID: 36011003 PMCID: PMC9406544 DOI: 10.3390/cancers14164012] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/26/2022] [Accepted: 08/12/2022] [Indexed: 12/24/2022] Open
Abstract
Tailored treatments for metastatic colorectal cancer (mCRC) have not yet completely evolved due to the variety in response to drugs. Therefore, artificial intelligence has been recently used to develop prognostic and predictive models of treatment response (either activity/efficacy or toxicity) to aid in clinical decision making. In this systematic review, we have examined the ability of learning methods to predict response to chemotherapy alone or combined with targeted therapy in mCRC patients by targeting specific narrative publications in Medline up to April 2022 to identify appropriate original scientific articles. After the literature search, 26 original articles met inclusion and exclusion criteria and were included in the study. Our results show that all investigations conducted on this field have provided generally promising results in predicting the response to therapy or toxic side-effects. By a meta-analytic approach we found that the overall weighted means of the area under the receiver operating characteristic (ROC) curve (AUC) were 0.90, 95% C.I. 0.80-0.95 and 0.83, 95% C.I. 0.74-0.89 in training and validation sets, respectively, indicating a good classification performance in discriminating response vs. non-response. The calculation of overall HR indicates that learning models have strong ability to predict improved survival. Lastly, the delta-radiomics and the 74 gene signatures were able to discriminate response vs. non-response by correctly identifying up to 99% of mCRC patients who were responders and up to 100% of patients who were non-responders. Specifically, when we evaluated the predictive models with tests reaching 80% sensitivity (SE) and 90% specificity (SP), the delta radiomics showed an SE of 99% and an SP of 94% in the training set and an SE of 85% and SP of 92 in the test set, whereas for the 74 gene signatures the SE was 97.6% and the SP 100% in the training set.
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Affiliation(s)
- Valentina Russo
- Research and Development Branch, Regional Cancer Prevention Laboratory, ISPRO-Study, Prevention and Oncology Network Institute, 50139 Florence, Italy
| | - Eleonora Lallo
- Research and Development Branch, Regional Cancer Prevention Laboratory, ISPRO-Study, Prevention and Oncology Network Institute, 50139 Florence, Italy
| | - Armelle Munnia
- Research and Development Branch, Regional Cancer Prevention Laboratory, ISPRO-Study, Prevention and Oncology Network Institute, 50139 Florence, Italy
| | - Miriana Spedicato
- Research and Development Branch, Regional Cancer Prevention Laboratory, ISPRO-Study, Prevention and Oncology Network Institute, 50139 Florence, Italy
| | - Luca Messerini
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
| | - Romina D’Aurizio
- Institute of Informatics and Telematics, National Research Council, 56124 Pisa, Italy
| | - Elia Giuseppe Ceroni
- Institute of Informatics and Telematics, National Research Council, 56124 Pisa, Italy
| | - Giulia Brunelli
- Institute of Informatics and Telematics, National Research Council, 56124 Pisa, Italy
| | - Antonio Galvano
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Antonio Russo
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Ida Landini
- Department of Health Sciences, University of Florence, 50139 Florence, Italy
| | - Stefania Nobili
- Department of Neurosciences, Imaging and Clinical Sciences, “G. D’Annunzio” Chieti-Pescara, 66100 Chieti, Italy
| | - Marcello Ceppi
- Clinical Epidemiology Unit, IRCCS-Ospedale Policlinico San Martino, 16131 Genova, Italy
| | - Marco Bruzzone
- Clinical Epidemiology Unit, IRCCS-Ospedale Policlinico San Martino, 16131 Genova, Italy
| | - Fabio Cianchi
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
| | - Fabio Staderini
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
| | - Mario Roselli
- Medical Oncology Unit, Department of Systems Medicine, Tor Vergata University, 00133 Rome, Italy
| | - Silvia Riondino
- Medical Oncology Unit, Department of Systems Medicine, Tor Vergata University, 00133 Rome, Italy
| | - Patrizia Ferroni
- BioBIM (InterInstitutional Multidisciplinary Biobank), IRCCS San Raffaele Roma, 00166 Rome, Italy
- Department of Human Sciences & Quality of Life Promotion, San Raffaele Roma Open University, 00166 Rome, Italy
| | - Fiorella Guadagni
- BioBIM (InterInstitutional Multidisciplinary Biobank), IRCCS San Raffaele Roma, 00166 Rome, Italy
- Department of Human Sciences & Quality of Life Promotion, San Raffaele Roma Open University, 00166 Rome, Italy
| | - Enrico Mini
- Department of Health Sciences, University of Florence, 50139 Florence, Italy
| | - Marco Peluso
- Research and Development Branch, Regional Cancer Prevention Laboratory, ISPRO-Study, Prevention and Oncology Network Institute, 50139 Florence, Italy
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10
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Xi W, Zhou C, Xu F, Sun D, Wang S, Chen Y, Ji J, Ma T, Wu J, Shangguan C, Zhu Z, Zhang J. Molecular evolutionary process of advanced gastric cancer during sequential chemotherapy detected by circulating tumor DNA. Lab Invest 2022; 20:365. [PMID: 35962408 PMCID: PMC9373478 DOI: 10.1186/s12967-022-03567-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 08/02/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND Efficacy of conventional sequential chemotherapy paradigm for advanced gastric cancer (AGC) patients has largely plateaued. Dynamic molecular changes during and after sequential chemotherapy have not been fully delineated. We aimed to profile the molecular evolutionary process of AGC patients during sequential chemotherapy by next generation sequencing (NGS) of plasma circulating tumor DNA (ctDNA). METHODS A total of 30 chemo-naïve patients who were diagnosed with unresectable advanced or metastatic stomach adenocarcinoma were enrolled. All patients received sequential chemotherapy regimens following the clinical guideline. One hundred and eight serial peripheral blood samples were collected at baseline, radiographical assessment and disease progression. Plasma ctDNA was isolated and a customized NGS panel was used to detect the genomic features of ctDNA including single nucleotide variants (SNVs) and gene-level copy number variations (CNVs). KEGG pathway enrichment analysis was performed. RESULTS Platinum-based combination chemotherapy was administrated as first-line regimen. Objective response rate was 50% (15/30). Patients with higher baseline values of copy number instability (CNI), CNVs and variant allel frequency (VAF) were more sensitive to platinum-based first-line regimens. Tumor mutation burden (TMB), CNI and CNV burden at partial response and stable disease were significantly lower than those at baseline, where at progressive disease they recovered to baseline levels. Dynamic change of TMB (ΔTMB) was correlated with progression-free survival of first-line treatment. Fluctuating changes of SNVs and gene-level CNVs could be observed during sequential chemotherapy. Under the pressure of conventional chemotherapy, the number of novel gene-level CNVs were found to be higher than that of novel SNVs. Such novel molecular alterations could be enriched into multiple common oncologic signaling pathways, including EGFR tyrosine kinase inhibitor resistance and platinum drug resistance pathways, where their distributions were found to be highly heterogenous among patients. The impact of subsequent regimens, including paclitaxel-based and irinotecan-based regimens, on the molecular changes driven by first-line therapy was subtle. CONCLUSION Baseline and dynamic changes of genomic features of ctDNA could be biomarkers for predicting response of platinum-based first-line chemotherapy in AGC patients. After treatment with standard chemotherapy regimens, convergent oncologic pathway enrichment was identified, which is yet characterized by inter-patient heterogenous gene-level CNVs.
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Affiliation(s)
- Wenqi Xi
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, Shanghai, 200025, China
| | - Chenfei Zhou
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, Shanghai, 200025, China.,Department of Oncology, Wuxi Branch of Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No 197 Zhixian Road, Xinwu District, Wuxi, 214028, China
| | - Fei Xu
- Genecast Biotechnology Co., Ltd, Wuxi City, 214104, Jiangsu, China
| | - Debin Sun
- Genecast Biotechnology Co., Ltd, Wuxi City, 214104, Jiangsu, China
| | - Shengzhou Wang
- Genecast Biotechnology Co., Ltd, Wuxi City, 214104, Jiangsu, China
| | - Yawei Chen
- Genecast Biotechnology Co., Ltd, Wuxi City, 214104, Jiangsu, China
| | - Jun Ji
- Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, Shanghai, 200025, China
| | - Tao Ma
- Department of Radiation Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, Shanghai, 200025, China
| | - Junwei Wu
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, Shanghai, 200025, China.,Department of Oncology, Wuxi Branch of Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No 197 Zhixian Road, Xinwu District, Wuxi, 214028, China
| | - Chengfang Shangguan
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, Shanghai, 200025, China
| | - Zhenggang Zhu
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, Shanghai, 200025, China.,Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, Shanghai, 200025, China
| | - Jun Zhang
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, Shanghai, 200025, China. .,Department of Oncology, Wuxi Branch of Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No 197 Zhixian Road, Xinwu District, Wuxi, 214028, China. .,State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai, 200025, China.
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11
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Peña M, Guzmán A, Martínez R, Mesas C, Prados J, Porres JM, Melguizo C. Preventive effects of Brassicaceae family for colon cancer prevention: A focus on in vitro studies. Biomed Pharmacother 2022; 151:113145. [PMID: 35623168 DOI: 10.1016/j.biopha.2022.113145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 05/10/2022] [Accepted: 05/15/2022] [Indexed: 11/02/2022] Open
Abstract
The emergence of adverse effects and resistance to colorectal cancer (CRC) current therapies calls for the development of new strategies aimed at both preventing and treating. In this context, functional extracts from Brassicaceae family contains abundant bioactive compounds directly related to a positive effect on human health including cancer. The main objective of this systematic review is to compile all recent studies that analyzed the in vitro antiproliferative activity of functional extracts or isolated molecules from the Brassicaceae family against CRC. A total of 711 articles published between January 2011 and May 2021 were identified. Of them, 68 met our inclusion criteria. Different standardized protocols using variable parts of plants of the Brassicaceae family resulted in diverse bioactive extracts and/or compounds. Most of them were related to isothiocyanates, which showed significant antitumor activity against CRC. These in vitro studies provide an excellent guide to direct research on the applications of plants of the Brassicaceae family to the prevention of this type of tumor. The extracts and molecules with demonstrated activity against CRC should be tested in vivo and in clinical trials to determine their usefulness in the prevention of this cancer to reduce its global incidence.
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Affiliation(s)
- Mercedes Peña
- Institute of Biopathology and Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, 18100 Granada, Spain; Department of Anatomy and Embryology, Faculty of Medicine, University of Granada, 18071 Granada, Spain; Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18014 Granada, Spain
| | - Ana Guzmán
- Institute of Biopathology and Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, 18100 Granada, Spain; Cellbitec S.L., N.I.F. B04847216, Scientific Headquarters of the Almería Technology Park, Universidad de Almería, 04128 La Cañada, Almería, Spain
| | - Rosario Martínez
- Cellbitec S.L., N.I.F. B04847216, Scientific Headquarters of the Almería Technology Park, Universidad de Almería, 04128 La Cañada, Almería, Spain; Department of Physiology, Institute of Nutrition and Food Technology (INyTA), Center of Biomedical Research (CIBM), University of Granada, 18100 Granada, Spain
| | - Cristina Mesas
- Institute of Biopathology and Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, 18100 Granada, Spain; Department of Anatomy and Embryology, Faculty of Medicine, University of Granada, 18071 Granada, Spain
| | - Jose Prados
- Institute of Biopathology and Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, 18100 Granada, Spain; Department of Anatomy and Embryology, Faculty of Medicine, University of Granada, 18071 Granada, Spain; Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18014 Granada, Spain.
| | - Jesús M Porres
- Department of Physiology, Institute of Nutrition and Food Technology (INyTA), Center of Biomedical Research (CIBM), University of Granada, 18100 Granada, Spain
| | - Consolación Melguizo
- Institute of Biopathology and Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, 18100 Granada, Spain; Department of Anatomy and Embryology, Faculty of Medicine, University of Granada, 18071 Granada, Spain; Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18014 Granada, Spain
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12
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Lalonde E, Ewens K, Richards-Yutz J, Ebrahimzedeh J, Terai M, Gonsalves CF, Sato T, Shields CL, Ganguly A. Improved Uveal Melanoma Copy Number Subtypes Including an Ultra–High-Risk Group. OPHTHALMOLOGY SCIENCE 2022; 2:100121. [PMID: 36249692 PMCID: PMC9559896 DOI: 10.1016/j.xops.2022.100121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 01/08/2022] [Accepted: 01/24/2022] [Indexed: 11/03/2022]
Abstract
Purpose Design Participants Methods Main Outcome Measures Results Conclusions
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13
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Lahoz S, Archilla I, Asensio E, Hernández‐Illán E, Ferrer Q, López‐Prades S, Nadeu F, Del Rey J, Sanz‐Pamplona R, Lozano JJ, Castells A, Cuatrecasas M, Camps J. Copy-number intratumor heterogeneity increases the risk of relapse in chemotherapy-naive stage II colon cancer. J Pathol 2022; 257:68-81. [PMID: 35066875 PMCID: PMC9790656 DOI: 10.1002/path.5870] [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: 07/28/2021] [Revised: 12/17/2021] [Accepted: 01/13/2022] [Indexed: 12/30/2022]
Abstract
Optimal selection of high-risk patients with stage II colon cancer is crucial to ensure clinical benefit of adjuvant chemotherapy. Here, we investigated the prognostic value of genomic intratumor heterogeneity and aneuploidy for disease recurrence. We combined targeted sequencing, SNP arrays, fluorescence in situ hybridization, and immunohistochemistry on a retrospective cohort of 84 untreated stage II colon cancer patients. We assessed the clonality of copy-number alterations (CNAs) and mutations, CD8+ lymphocyte infiltration, and their association with time to recurrence. Prognostic factors were included in machine learning analysis to evaluate their ability to predict individual relapse risk. Tumors from recurrent patients displayed a greater proportion of CNAs compared with non-recurrent (mean 31.3% versus 23%, respectively; p = 0.014). Furthermore, patients with elevated tumor CNA load exhibited a higher risk of recurrence compared with those with low levels [p = 0.038; hazard ratio (HR) 2.46], which was confirmed in an independent cohort (p = 0.004; HR 3.82). Candidate chromosome-specific aberrations frequently observed in recurrent cases included gain of the chromosome arm 13q (p = 0.02; HR 2.67) and loss of heterozygosity at 17q22-q24.3 (p = 0.05; HR 2.69). CNA load positively correlated with intratumor heterogeneity (R = 0.52; p < 0.0001). Consistently, incremental subclonal CNAs were associated with an elevated risk of relapse (p = 0.028; HR 2.20), which we did not observe for subclonal single-nucleotide variants and small insertions and deletions. The clinico-genomic model rated an area under the curve of 0.83, achieving a 10% incremental gain compared with clinicopathological markers (p = 0.047). In conclusion, tumor aneuploidy and copy-number intratumor heterogeneity were predictive of poor outcome and improved discriminative performance in early-stage colon cancer. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Sara Lahoz
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology TeamInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of BarcelonaBarcelonaSpain
| | - Ivan Archilla
- Pathology Department, Biomedical Diagnostic Center, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of BarcelonaBarcelonaSpain
| | - Elena Asensio
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology TeamInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of BarcelonaBarcelonaSpain
| | - Eva Hernández‐Illán
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology TeamInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of BarcelonaBarcelonaSpain
| | - Queralt Ferrer
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology TeamInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of BarcelonaBarcelonaSpain
| | - Sandra López‐Prades
- Pathology Department, Biomedical Diagnostic Center, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of BarcelonaBarcelonaSpain
| | - Ferran Nadeu
- Molecular Pathology of Lymphoid NeoplasmsInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC)BarcelonaSpain
| | - Javier Del Rey
- Department of Cell Biology, Physiology and Immunology, Faculty of MedicineUniversity Autonomous of BarcelonaBellaterraSpain
| | - Rebeca Sanz‐Pamplona
- Unit of Biomarkers and SusceptibilityOncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESPl'Hospitalet de LlobregatSpain
| | - Juan José Lozano
- Bioinformatics PlatformCentro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD)MadridSpain
| | - Antoni Castells
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology TeamInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of BarcelonaBarcelonaSpain
| | - Miriam Cuatrecasas
- Pathology Department, Biomedical Diagnostic Center, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of BarcelonaBarcelonaSpain
| | - Jordi Camps
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology TeamInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of BarcelonaBarcelonaSpain,Department of Cell Biology, Physiology and Immunology, Faculty of MedicineUniversity Autonomous of BarcelonaBellaterraSpain
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14
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van Dijk E, van Werkhoven E, Asher R, Mooi JK, Espinoza D, van Essen HF, van Tinteren H, van Grieken NCT, Punt CJA, Tebbutt NC, Ylstra B. Predictive value of chromosome 18q11.2-q12.1 loss for benefit from bevacizumab in metastatic colorectal cancer; a post-hoc analysis of the randomized phase III-trial AGITG-MAX. Int J Cancer 2022; 151:1166-1174. [PMID: 35489024 PMCID: PMC9545440 DOI: 10.1002/ijc.34061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 03/07/2022] [Accepted: 04/12/2022] [Indexed: 11/24/2022]
Abstract
The VEGF‐A monoclonal antibody bevacizumab is currently recommended for first‐line treatment of all metastatic colorectal cancer (mCRC) patients. Cost‐benefit ratio and side‐effects however necessitate patient selection. A large retrospective yet nonrandomized study showed that patients with loss of chromosome 18q11.2‐q12.1 in the tumor and treated with bevacizumab have 3 months improved median progression‐free (PFS) and overall survival (OS) benefit compared to patients without this loss and/or treatment modality. Implementation for loss of chromosome 18q11.2‐q12.1 as a marker in clinical practice mandates evidence in a randomized controlled trial for bevacizumab. Of the trials with randomization of chemotherapy vs chemotherapy with bevacizumab, the AGITG‐MAX trial was the only one with tumor materials available. Chromosome 18q11.2‐q12.1 copy number status was measured for 256 AGITG‐MAX trial patients and correlated with PFS according to a predefined analysis plan with marker‐treatment interaction as the primary end‐point. Chromosome 18q11.2‐q12.1 losses were detected in 71% of patients (181/256) characteristic for mCRC. Consistent with the nonrandomized study, significant PFS benefit of bevacizumab was observed in patients with chromosome 18q11.2‐q12.1 loss (P = .009), and not in patients without 18q loss (P = .67). Although significance for marker‐treatment interaction was not reached (Pinteraction = .28), hazard ratio and 95% confidence interval of this randomized cohort (HRinteraction = 0.72; 95% CI = 0.39‐1.32) shows striking overlap with the nonrandomized study cohorts (HRinteraction = 0.41; 95% CI = 0.32‐0.8) supported by a nonsignificant Cochrane χ2 test (P = .11) for heterogeneity. We conclude that post hoc analysis of the AGITG‐MAX RCT provides supportive evidence for chromosome 18q11.2‐q12.1 as a predictive marker for bevacizumab in mCRC patients.
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Affiliation(s)
- Erik van Dijk
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands
| | - Erik van Werkhoven
- Biometrics Department, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Rebecca Asher
- Department of Biostatistics, NHMRC Clinical Trials Centre, University of Sydney, Camperdown, Australia
| | - Jennifer K Mooi
- Olivia Newton-John Cancer Research Institute, Heidelberg; Department of Medicine, University of Melbourne, Melbourne, Australia.,Peter MacCallum Cancer Institute, Melbourne, Australia
| | - David Espinoza
- Department of Biostatistics, NHMRC Clinical Trials Centre, University of Sydney, Camperdown, Australia
| | - Hendrik F van Essen
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands
| | - Harm van Tinteren
- Trial and Datacenter, Princess Máxima Center for pedeatric oncology, Utrecht, The Netherlands
| | - Nicole C T van Grieken
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands
| | - Cornelis J A Punt
- Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht University, Utrecht, Netherlands.,Department of Epidemiology, University Medical Centre Utrecht, Utrecht University, Utrecht, Netherlands
| | - Niall C Tebbutt
- Department of Medical Oncology, Austin Health, Heidelberg, Australia.,Department of Surgery, University of Melbourne
| | - Bauke Ylstra
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands
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15
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Frigola J, Carbonell C, Iranzo P, Pardo N, Callejo A, Cedres S, Martinez-Marti A, Navarro A, Soleda M, Jimenez J, Hernandez-Losa J, Vivancos A, Felip E, Amat R. High levels of chromosomal aberrations negatively associate with benefit to checkpoint inhibition in NSCLC. J Immunother Cancer 2022; 10:jitc-2021-004197. [PMID: 35477861 PMCID: PMC9047699 DOI: 10.1136/jitc-2021-004197] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Immune checkpoint inhibitors (ICIs) targeting the programmed cell death 1/programmed death-ligand 1 axis have transformed the management of advanced non-small cell lung cancer (NSCLC). However, many patients do not benefit from this type of treatment, and thus several molecular biomarkers of benefit have been explored. The value of somatic copy number alterations (SCNAs) burden remains elusive. PATIENTS AND METHODS We assembled a cohort of 109 patients with NSCLC treated with ICIs and available tumor samples. We performed shallow whole-genome sequencing on 89 patients to determine genome-wide SCNAs and targeted gene expression analysis on 63 patients to study immune infiltration. We analyzed SCNAs burden in different ways (ie, the fraction of the genome altered or number of events) and studied their association with ICIs benefit based on survival analysis. We correlated SCNAs burden and immune infiltration on 35 patients of our cohort and on patients with lung adenocarcinoma from The Cancer Genome Atlas (TCGA). RESULTS High SCNAs burden, computed in diverse ways, is negatively associated with ICIs progression-free survival (PFS), with the fraction of the genome altered (FGA) by arm and chromosome events showing the strongest association with PFS (p=0.002) (n=77). Nevertheless, we found differences in SCNAs across some clinicopathological features (sample site origin). A multivariate analysis adjusted for relevant characteristics showed that the FGA of arm and chromosome alterations was strongly associated with PFS (HR=2.21, p=3.3 x 10-5). Finally, we confirmed that SCNAs burden negatively correlates with tumor immune infiltration (n=35), although this correlation was not found for the males studied. Similar results were observed in the TCGA cohort. CONCLUSIONS SCNAs burden is a potential biomarker of benefit to ICIs in patients with NSCLC, although there appear to be some nuances worth consideration. Further studies will be needed to establish its role as a biomarker of benefit to ICIs.
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Affiliation(s)
- Joan Frigola
- Thoracic Cancers Translational Genomics Unit, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain,Clinical Research Department, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Caterina Carbonell
- Thoracic Cancers Translational Genomics Unit, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain,Clinical Research Department, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Patricia Iranzo
- Clinical Research Department, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain,Oncology Department, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Nuria Pardo
- Clinical Research Department, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain,Oncology Department, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Ana Callejo
- Clinical Research Department, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain,Oncology Department, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Susana Cedres
- Clinical Research Department, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain,Oncology Department, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Alex Martinez-Marti
- Clinical Research Department, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain,Oncology Department, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Alejandro Navarro
- Clinical Research Department, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain,Oncology Department, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Mireia Soleda
- Thoracic Cancers Translational Genomics Unit, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain,Clinical Research Department, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Jose Jimenez
- Molecular Oncology Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | - Ana Vivancos
- Cancer Genomics Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Enriqueta Felip
- Thoracic Cancers Translational Genomics Unit, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain,Clinical Research Department, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain,Oncology Department, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Ramon Amat
- Thoracic Cancers Translational Genomics Unit, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain,Clinical Research Department, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
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16
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Riedesser JE, Ebert MP, Betge J. Precision medicine for metastatic colorectal cancer in clinical practice. Ther Adv Med Oncol 2022; 14:17588359211072703. [PMID: 35237350 PMCID: PMC8882813 DOI: 10.1177/17588359211072703] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/17/2021] [Indexed: 12/22/2022] Open
Abstract
Globally, metastatic colorectal cancer is one of the leading causes for cancer-related death. Treatment limited to conventional chemotherapeutics extended life for only a few months. However, advances in surgical approaches and medical treatment regimens have greatly increased survival, even leading to long-term remission in selected patients. Advances in multiomics analysis of tumors have built a foundation for molecular-targeted therapies. Furthermore, immunotherapies are on the edge of revolutionizing oncological practice. This review summarizes recent advances in the growing toolbox of personalized treatment for patients with metastatic colorectal cancer. We provide an overview of current multimodal therapy and explain novel immunotherapy and targeted therapy approaches in detail. We emphasize clinically relevant therapies, such as inhibitors of MAPK signaling, and give recommendations for clinical practice. Finally, we describe the potential predictive impact of molecular subtypes and provide an outlook on novel concepts, such as functional precision medicine.
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Affiliation(s)
- Julian E. Riedesser
- Junior Clinical Cooperation Unit Translational
Gastrointestinal Oncology and Preclinical Models, German Cancer Research
Center (DKFZ), Heidelberg, Germany
| | - Matthias P. Ebert
- Department of Medicine II, University Medical
Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim,
GermanyMannheim Cancer Center, University Medical Center Mannheim, Medical
Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Johannes Betge
- Junior Clinical Cooperation Unit Translational
Gastrointestinal Oncology and Preclinical Models, German Cancer Research
Center (DKFZ), Im Neuenheimer Feld 580, Heidelberg 69120, GermanyDKFZ-Hector
Cancer Institute at University Medical Center Mannheim, Mannheim,
Germany.Department of Medicine II, University Medical Center Mannheim,
Medical Faculty Mannheim, Heidelberg University, Mannheim, GermanyMannheim
Cancer Center, University Medical Center Mannheim, Medical Faculty Mannheim,
Heidelberg University, Mannheim, Germany
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17
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Li M, Kaili D, Shi L. Biomarkers for response to immune checkpoint inhibitors in gastrointestinal cancers. World J Gastrointest Oncol 2022; 14:19-37. [PMID: 35116101 PMCID: PMC8790411 DOI: 10.4251/wjgo.v14.i1.19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 09/08/2021] [Accepted: 12/23/2021] [Indexed: 02/06/2023] Open
Abstract
Gastrointestinal (GI) cancers account for a large proportion of cancer deaths worldwide and pose a major public health challenge. Immunotherapy is considered to be one of the prominent and successful approaches in cancer treatment in recent years. Among them, immune checkpoint inhibitor (ICI) therapy, has received widespread attention, and many clinical findings support the feasibility of ICIs, with sustained responses and significantly prolonged lifespan observed in a wide range of tumors. However, patients treated with ICIs have not fully benefited, and therefore, the identification and development of biomarkers for predicting ICI treatment response have received further attention and exploration. From tumor genome to molecular interactions in the tumor microenvironment, and further expanding to circulating biomarkers and patient characteristics, the exploration of biomarkers is evolving with high-throughput sequencing as well as bioinformatics. More large-scale prospective and specific studies are needed to explore biomarkers in GI cancers. In this review, we summarize the known biomarkers used in ICI therapy for GI tumors. In addition, some ICI biomarkers applied to other tumors are included to provide insights and further validation for GI tumors. Moreover, we present single-cell analysis and machine learning approaches that have emerged in recent years. Although there are no clear applications yet, it can be expected that these techniques will play an important role in the application of biomarker prediction.
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Affiliation(s)
- Meng Li
- School of Life Sciences, Chongqing University, Chongqing 400044, China
| | - Denis Kaili
- Department of Surgery, Wexner Medical Center, The Ohio State University, Columbus, OH 43210, United States
| | - Lei Shi
- School of Life Sciences, Chongqing University, Chongqing 400044, China
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18
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Lafferty A, O'Farrell AC, Migliardi G, Khemka N, Lindner AU, Sassi F, Zanella ER, Salvucci M, Vanderheyden E, Modave E, Boeckx B, Halang L, Betge J, Ebert MPA, Dicker P, Argilés G, Tabernero J, Dienstmann R, Medico E, Lambrechts D, Bertotti A, Isella C, Trusolino L, Prehn JHM, Byrne AT. Molecular Subtyping Combined with Biological Pathway Analyses to Study Regorafenib Response in Clinically Relevant Mouse Models of Colorectal Cancer. Clin Cancer Res 2021; 27:5979-5992. [PMID: 34426441 DOI: 10.1158/1078-0432.ccr-21-0818] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 07/05/2021] [Accepted: 08/18/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Regorafenib (REG) is approved for the treatment of metastatic colorectal cancer, but has modest survival benefit and associated toxicities. Robust predictive/early response biomarkers to aid patient stratification are outstanding. We have exploited biological pathway analyses in a patient-derived xenograft (PDX) trial to study REG response mechanisms and elucidate putative biomarkers. EXPERIMENTAL DESIGN Molecularly subtyped PDXs were annotated for REG response. Subtyping was based on gene expression (CMS, consensus molecular subtype) and copy-number alteration (CNA). Baseline tumor vascularization, apoptosis, and proliferation signatures were studied to identify predictive biomarkers within subtypes. Phospho-proteomic analysis was used to identify novel classifiers. Supervised RNA sequencing analysis was performed on PDXs that progressed, or did not progress, following REG treatment. RESULTS Improved REG response was observed in CMS4, although intra-subtype response was variable. Tumor vascularity did not correlate with outcome. In CMS4 tumors, reduced proliferation and higher sensitivity to apoptosis at baseline correlated with response. Reverse phase protein array (RPPA) analysis revealed 4 phospho-proteomic clusters, one of which was enriched with non-progressor models. A classification decision tree trained on RPPA- and CMS-based assignments discriminated non-progressors from progressors with 92% overall accuracy (97% sensitivity, 67% specificity). Supervised RNA sequencing revealed that higher basal EPHA2 expression is associated with REG resistance. CONCLUSIONS Subtype classification systems represent canonical "termini a quo" (starting points) to support REG biomarker identification, and provide a platform to identify resistance mechanisms and novel contexts of vulnerability. Incorporating functional characterization of biological systems may optimize the biomarker identification process for multitargeted kinase inhibitors.
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Affiliation(s)
- Adam Lafferty
- Department of Physiology and Medical Physics, Precision Cancer Medicine Group, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Alice C O'Farrell
- Department of Physiology and Medical Physics, Precision Cancer Medicine Group, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Giorgia Migliardi
- Department of Oncology, University of Torino, Candiolo, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Niraj Khemka
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Center for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Andreas U Lindner
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Center for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | | | | | - Manuela Salvucci
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Center for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Evy Vanderheyden
- Department of Human Genetics, VIB Center for Cancer Biology, Leuven, Belgium, Laboratory for Translational Genetics, KU Leuven, Leuven, Belgium
| | - Elodie Modave
- Department of Human Genetics, VIB Center for Cancer Biology, Leuven, Belgium, Laboratory for Translational Genetics, KU Leuven, Leuven, Belgium
| | - Bram Boeckx
- Department of Human Genetics, VIB Center for Cancer Biology, Leuven, Belgium, Laboratory for Translational Genetics, KU Leuven, Leuven, Belgium
| | - Luise Halang
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Center for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Johannes Betge
- Department of Medicine II, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Junior Clinical Cooperation Unit Translational Gastrointestinal Oncology and Preclinical Models, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias P A Ebert
- Department of Medicine II, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Patrick Dicker
- Department of Epidemiology and Public Health Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Guillem Argilés
- Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, CIBERONC, Barcelona, Spain
| | - Josep Tabernero
- Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, CIBERONC, Barcelona, Spain
| | - Rodrigo Dienstmann
- Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, CIBERONC, Barcelona, Spain
| | - Enzo Medico
- Department of Oncology, University of Torino, Candiolo, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Diether Lambrechts
- Department of Human Genetics, VIB Center for Cancer Biology, Leuven, Belgium, Laboratory for Translational Genetics, KU Leuven, Leuven, Belgium
| | - Andrea Bertotti
- Department of Oncology, University of Torino, Candiolo, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Claudio Isella
- Department of Oncology, University of Torino, Candiolo, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Livio Trusolino
- Department of Oncology, University of Torino, Candiolo, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Jochen H M Prehn
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Center for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Annette T Byrne
- Department of Physiology and Medical Physics, Precision Cancer Medicine Group, Royal College of Surgeons in Ireland, Dublin, Ireland.
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
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19
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Stahler A, Heinemann V, Holch JW, von Einem JC, Westphalen CB, Heinrich K, Schlieker L, Jelas I, Alig AHS, Fischer LE, Weiss L, Modest DP, von Weikersthal LF, Decker T, Kiani A, Moehler M, Kaiser F, Kirchner T, Jung A, Stintzing S. Mutational profiles of metastatic colorectal cancer treated with FOLFIRI plus cetuximab or bevacizumab before and after secondary resection (AIO KRK 0306; FIRE-3). Int J Cancer 2021; 149:1935-1943. [PMID: 34310714 DOI: 10.1002/ijc.33747] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 06/12/2021] [Accepted: 06/28/2021] [Indexed: 12/15/2022]
Abstract
Secondary resection of metastases is recommended in metastatic colorectal cancer (mCRC). Data describing changes in mutational profiles of corresponding primary tumor and metastatic tissue after conversion treatment are limited. Next generation sequencing was performed in formalin-fixed mCRC samples from patients of the FIRE-3 trial (FOLFIRI plus cetuximab or bevacizumab) before treatment start (baseline) and after secondary resection of metastases (post baseline). Changes of mutational profiles and tumor mutational burden (TMB) were assessed within a post-hoc analysis. Median overall survival (OS), progression-free survival (PFS) and objective response rate (ORR) were compared between treatment arms. Paired tumor samples were obtained from 25 patients (19 RAS wild-type, 6 RAS mutant by pyrosequencing). ORR (92.0% vs 58.0%) and OS (60.8 vs 35.4 months, hazard ratio = 0.39 [95% CI 0.14-1.12], P = .08) were higher for patients receiving cetuximab. After conversion therapy, 56 alterations (42 in the cetuximab and 14 in the bevacizumab arm) were newly observed in 18 patients (9 each treated with cetuximab or bevacizumab). Gains (n = 21) and losses (n = 21) of alterations occurred during cetuximab-based treatment, while mainly gains of alterations occurred during bevacizumab (n = 10). Three of nine patients treated with cetuximab that presented a change of mutational profiles, developed resistance to cetuximab. Mutational profiles were largely comparable before and after treatment with anti-VEGF or anti-EGFR directed monoclonal antibodies after secondary resection. Mutations associated with resistance to anti-EGFR antibodies were observed in only one-third of patients.
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Affiliation(s)
- Arndt Stahler
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Medical Department, Division of Hematology, Oncology and Tumor Immunology, Berlin, Germany
| | - Volker Heinemann
- Department of Medicine III, University Hospital, University of Munich, Munich, Germany.,LMU Munich, German Cancer Consortium (DKTK), partner site Munich, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Julian Walter Holch
- Department of Medicine III, University Hospital, University of Munich, Munich, Germany.,LMU Munich, German Cancer Consortium (DKTK), partner site Munich, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Jobst Christian von Einem
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Medical Department, Division of Hematology, Oncology and Tumor Immunology, Berlin, Germany
| | | | - Kathrin Heinrich
- Department of Medicine III, University Hospital, University of Munich, Munich, Germany
| | | | - Ivan Jelas
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Medical Department, Division of Hematology, Oncology and Tumor Immunology, Berlin, Germany
| | - Annabel Helga Sophie Alig
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Medical Department, Division of Hematology, Oncology and Tumor Immunology, Berlin, Germany
| | | | - Lena Weiss
- Department of Medicine III, University Hospital, University of Munich, Munich, Germany
| | - Dominik Paul Modest
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Medical Department, Division of Hematology, Oncology and Tumor Immunology, Berlin, Germany.,German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Centre (DKFZ), Charité-Universitätsmedizin Berlin, Heidelberg, Germany
| | | | | | - Alexander Kiani
- Department of Medicine IV, Klinikum Bayreuth GmbH, Bayreuth, Germany
| | - Markus Moehler
- Department of Internal Medicine I, University Medical Center Mainz, Mainz, Germany
| | | | - Thomas Kirchner
- LMU Munich, German Cancer Consortium (DKTK), partner site Munich, German Cancer Research Centre (DKFZ), Heidelberg, Germany.,Institute of Pathology, University of Munich, Munich, Germany
| | - Andreas Jung
- LMU Munich, German Cancer Consortium (DKTK), partner site Munich, German Cancer Research Centre (DKFZ), Heidelberg, Germany.,Institute of Pathology, University of Munich, Munich, Germany
| | - Sebastian Stintzing
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Medical Department, Division of Hematology, Oncology and Tumor Immunology, Berlin, Germany.,German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Centre (DKFZ), Charité-Universitätsmedizin Berlin, Heidelberg, Germany
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20
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Chromosomal copy number heterogeneity predicts survival rates across cancers. Nat Commun 2021; 12:3188. [PMID: 34045449 PMCID: PMC8160133 DOI: 10.1038/s41467-021-23384-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/14/2021] [Indexed: 12/20/2022] Open
Abstract
Survival rates of cancer patients vary widely within and between malignancies. While genetic aberrations are at the root of all cancers, individual genomic features cannot explain these distinct disease outcomes. In contrast, intra-tumour heterogeneity (ITH) has the potential to elucidate pan-cancer survival rates and the biology that drives cancer prognosis. Unfortunately, a comprehensive and effective framework to measure ITH across cancers is missing. Here, we introduce a scalable measure of chromosomal copy number heterogeneity (CNH) that predicts patient survival across cancers. We show that the level of ITH can be derived from a single-sample copy number profile. Using gene-expression data and live cell imaging we demonstrate that ongoing chromosomal instability underlies the observed heterogeneity. Analysing 11,534 primary cancer samples from 37 different malignancies, we find that copy number heterogeneity can be accurately deduced and predicts cancer survival across tissues of origin and stages of disease. Our results provide a unifying molecular explanation for the different survival rates observed between cancer types.
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21
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Jimenez-Luna C, González-Flores E, Ortiz R, Martínez-González LJ, Antúnez-Rodríguez A, Expósito-Ruiz M, Melguizo C, Caba O, Prados J. Circulating PTGS2, JAG1, GUCY2C and PGF mRNA in Peripheral Blood and Serum as Potential Biomarkers for Patients with Metastatic Colon Cancer. J Clin Med 2021; 10:2248. [PMID: 34067294 PMCID: PMC8196898 DOI: 10.3390/jcm10112248] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/18/2021] [Accepted: 05/20/2021] [Indexed: 12/24/2022] Open
Abstract
Genes involved in the angiogenic process have been proposed for the diagnosis and therapeutic response of metastatic colorectal cancer (CRC). This study aimed to investigate the value of PTGS2, JAG1, GUCY2C and PGF-circulating RNA as biomarkers in metastatic CRC. Blood cells and serum mRNA from 59 patients with metastatic CRC and 47 healthy controls were analyzed by digital PCR. The area under the receiver operating characteristic curve (AUC) was used to estimate the diagnostic value of each mRNA alone or mRNA combinations. A significant upregulation of the JAG1, PTGS2 and GUCY2C genes in blood cells and serum samples from metastatic CRC patients was detected. Circulating mRNA levels in the serum of all genes were significantly more abundant than in blood. The highest discrimination ability between metastatic CRC patients and healthy donors was obtained with PTGS2 (AUC of 0.984) and GUCY2C (AUC of 0.896) in serum samples. Biomarker combinations did not improve the discriminatory capacity of biomarkers separately. Analyzed biomarkers showed no correlation with overall survival or progression-free survival, but GUCY2C and GUCY2C/PTGS2 expression in serum correlated significantly with the response to antiangiogenic agents. These findings demonstrate that assessment of genes involved in the angiogenic process may be a potential non-invasive diagnostic tool for metastatic CRC and its response to antiangiogenic therapy.
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Affiliation(s)
- Cristina Jimenez-Luna
- Institute of Biopathology and Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, 18100 Granada, Spain; (C.J.-L.); (R.O.); (O.C.); (J.P.)
- Department of Anatomy and Embryology, Faculty of Medicine, University of Granada, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria ibs. Granada, 18012 Granada, Spain;
| | - Encarnación González-Flores
- Instituto de Investigación Biosanitaria ibs. Granada, 18012 Granada, Spain;
- Medical Oncology Service, Hospital Virgen de las Nieves, 18014 Granada, Spain
| | - Raul Ortiz
- Institute of Biopathology and Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, 18100 Granada, Spain; (C.J.-L.); (R.O.); (O.C.); (J.P.)
- Department of Anatomy and Embryology, Faculty of Medicine, University of Granada, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria ibs. Granada, 18012 Granada, Spain;
| | - Luis J. Martínez-González
- GENyO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, 18016 Granada, Spain; (L.J.M.-G.); (A.A.-R.)
| | - Alba Antúnez-Rodríguez
- GENyO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, 18016 Granada, Spain; (L.J.M.-G.); (A.A.-R.)
| | - Manuela Expósito-Ruiz
- Unit of Biostatistics, Department of Statistics and Operations Research, School of Medicine, University of Granada, 18071 Granada, Spain;
| | - Consolación Melguizo
- Institute of Biopathology and Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, 18100 Granada, Spain; (C.J.-L.); (R.O.); (O.C.); (J.P.)
- Department of Anatomy and Embryology, Faculty of Medicine, University of Granada, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria ibs. Granada, 18012 Granada, Spain;
| | - Octavio Caba
- Institute of Biopathology and Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, 18100 Granada, Spain; (C.J.-L.); (R.O.); (O.C.); (J.P.)
- Department of Anatomy and Embryology, Faculty of Medicine, University of Granada, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria ibs. Granada, 18012 Granada, Spain;
| | - Jose Prados
- Institute of Biopathology and Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, 18100 Granada, Spain; (C.J.-L.); (R.O.); (O.C.); (J.P.)
- Department of Anatomy and Embryology, Faculty of Medicine, University of Granada, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria ibs. Granada, 18012 Granada, Spain;
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22
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Tang Y, Zong S, Zeng H, Ruan X, Yao L, Han S, Hou F. MicroRNAs and angiogenesis: a new era for the management of colorectal cancer. Cancer Cell Int 2021; 21:221. [PMID: 33865381 PMCID: PMC8052662 DOI: 10.1186/s12935-021-01920-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 04/07/2021] [Indexed: 02/08/2023] Open
Abstract
MicroRNAs (miRNAs) are a class of small noncoding RNA molecules containing only 20–22 nucleotides. MiRNAs play a role in gene silencing and translation suppression by targeting and binding to mRNA. Proper control of miRNA expression is very important for maintaining a normal physiological environment because miRNAs can affect most cellular pathways, including cell cycle checkpoint, cell proliferation, and apoptosis pathways, and have a wide range of target genes. With these properties, miRNAs can modulate multiple signalling pathways involved in cancer development, such as cell proliferation, apoptosis, and migration pathways. MiRNAs that activate or inhibit the molecular pathway related to tumour angiogenesis are common topics of research. Angiogenesis promotes tumorigenesis and metastasis by providing oxygen and diffusible nutrients and releasing proangiogenic factors and is one of the hallmarks of tumour progression. CRC is one of the most common tumours, and metastasis has always been a difficult issue in its treatment. Although comprehensive treatments, such as surgery, radiotherapy, chemotherapy, and targeted therapy, have prolonged the survival of CRC patients, the overall response is not optimistic. Therefore, there is an urgent need to find new therapeutic targets to improve CRC treatment. In a series of recent reports, miRNAs have been shown to bidirectionally regulate angiogenesis in colorectal cancer. Many miRNAs can directly act on VEGF or inhibit angiogenesis through other pathways (HIF-1a, PI3K/AKT, etc.), while some miRNAs, specifically many exosomal miRNAs, are capable of promoting CRC angiogenesis. Understanding the mechanism of action of miRNAs in angiogenesis is of great significance for finding new targets for the treatment of tumour angiogenesis. Deciphering the exact role of specific miRNAs in angiogenesis is a challenge due to the high complexity of their actions. Here, we describe the latest advances in the understanding of miRNAs and their corresponding targets that play a role in CRC angiogenesis and discuss possible miRNA-based therapeutic strategies.
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Affiliation(s)
- Yufei Tang
- Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, China
| | - Shaoqi Zong
- Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, China.,Graduate School of Shanghai, University of Traditional Chinese Medicine, Shanghai, China
| | - Hailun Zeng
- Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, China
| | - Xiaofeng Ruan
- Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, China
| | - Liting Yao
- Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, China
| | - Susu Han
- Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, China
| | - Fenggang Hou
- Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, China.
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23
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Avolio M, Trusolino L. Rational Treatment of Metastatic Colorectal Cancer: A Reverse Tale of Men, Mice, and Culture Dishes. Cancer Discov 2021; 11:1644-1660. [PMID: 33820776 DOI: 10.1158/2159-8290.cd-20-1531] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/04/2021] [Accepted: 02/01/2021] [Indexed: 11/16/2022]
Abstract
Stratification of colorectal cancer into subgroups with different response to therapy was initially guided by descriptive associations between specific biomarkers and treatment outcome. Recently, preclinical models based on propagatable patient-derived tumor samples have yielded an improved understanding of disease biology, which has facilitated the functional validation of correlative information and the discovery of novel response determinants, therapeutic targets, and mechanisms of tumor adaptation and drug resistance. We review the contribution of patient-derived models to advancing colorectal cancer characterization, discuss their influence on clinical decision-making, and highlight emerging challenges in the interpretation and clinical transferability of results obtainable with such approaches. SIGNIFICANCE: Association studies in patients with colorectal cancer have led to the identification of response biomarkers, some of which have been implemented as companion diagnostics for therapeutic decisions. By enabling biological investigation in a clinically relevant experimental context, patient-derived colorectal cancer models have proved useful to examine the causal role of such biomarkers in dictating drug sensitivity and are providing fresh knowledge on new actionable targets, dynamics of tumor evolution and adaptation, and mechanisms of drug resistance.
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Affiliation(s)
- Marco Avolio
- Department of Oncology, University of Torino, Candiolo, Torino, Italy.,Candiolo Cancer Institute - FPO IRCCS, Candiolo, Torino, Italy
| | - Livio Trusolino
- Department of Oncology, University of Torino, Candiolo, Torino, Italy. .,Candiolo Cancer Institute - FPO IRCCS, Candiolo, Torino, Italy
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24
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NSD2 promotes tumor angiogenesis through methylating and activating STAT3 protein. Oncogene 2021; 40:2952-2967. [PMID: 33742125 DOI: 10.1038/s41388-021-01747-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 02/23/2021] [Accepted: 03/03/2021] [Indexed: 01/31/2023]
Abstract
Tumor angiogenesis plays vital roles in tumorigenesis and development; regulatory mechanism of angiogenesis is still not been fully elucidated. NSD2, a histone methyltransferase catalyzing di-methylation of histone H3 at lysine 36, has been proved a critical molecule in proliferation, metastasis, and tumorigenesis. But its role in tumor angiogenesis remains unknown. Here we demonstrated that NSD2 promoted tumor angiogenesis in vitro and in vivo. Furthermore, we confirmed that the angiogenic function of NSD2 was mediated by STAT3. Momentously, we found that NSD2 promoted the methylation and activation of STAT3. In addition, mass spectrometry and site-directed mutagenesis assays revealed that NSD2 methylated STAT3 at lysine 163 (K163). Meanwhile, K to R mutant at K163 of STAT3 attenuated the activation and angiogenic function of STAT3. Taken together, we conclude that methylation of STAT3 catalyzed by NSD2 promotes the activation of STAT3 pathway and enhances the ability of tumor angiogenesis. Our findings investigate a NSD2-dependent methylation-phosphorylation regulation pattern of STAT3 and reveal that NSD2/STAT3/VEGFA axis might be a potential target for tumor therapy.
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25
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Prognostic Cancer Gene Expression Signatures: Current Status and Challenges. Cells 2021; 10:cells10030648. [PMID: 33804045 PMCID: PMC8000474 DOI: 10.3390/cells10030648] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/05/2021] [Accepted: 03/08/2021] [Indexed: 12/27/2022] Open
Abstract
Current staging systems of cancer are mainly based on the anatomical extent of disease. They need refinement by biological parameters to improve stratification of patients for tumor therapy or surveillance strategies. Thanks to developments in genomic, transcriptomic, and big-data technologies, we are now able to explore molecular characteristics of tumors in detail and determine their clinical relevance. This has led to numerous prognostic and predictive gene expression signatures that have the potential to establish a classification of tumor subgroups by biological determinants. However, only a few gene signatures have reached the stage of clinical implementation so far. In this review article, we summarize the current status, and present and future challenges of prognostic gene signatures in three relevant cancer entities: breast cancer, colorectal cancer, and hepatocellular carcinoma.
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26
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Tang D, Huang W, Yang Z, Wu X, Sang X, Wang K, Cao G, Hao M. Two immune-enhanced molecular subtypes differ in inflammation, immune checkpoints, mutations, and prognostic outcome in stage I-II colonic carcinoma. J Biochem Mol Toxicol 2021; 35:e22703. [PMID: 33410236 DOI: 10.1002/jbt.22703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 11/16/2020] [Accepted: 12/17/2020] [Indexed: 11/07/2022]
Abstract
The purpose of this paper is to investigate the immune function of the tumor microenvironment and its clinical correlation with colonic carcinoma. Immune genes were downloaded from the The Cancer Genome Atlas database. Five subtypes are obtained by cluster screening based on immune gene expression data. The C3 and C4 subtypes show stronger immune activity. In addition, the C4 subtype has the largest number of gene mutations and the worst prognosis. Most of the immune signatures are upregulated in the C4 subtype, while most of the immune infiltration-related cells are upregulated in the C3 and C4 subtypes. The different immune microenvironments between these subtypes may provide new ideas for immunotherapy strategies in colon carcinoma.
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Affiliation(s)
- Dongxin Tang
- Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Wei Huang
- College of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Zhu Yang
- Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Xin Wu
- School of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Xianan Sang
- School of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Kuilong Wang
- School of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Gang Cao
- School of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Min Hao
- School of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
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27
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Genetic Alterations of Metastatic Colorectal Cancer. Biomedicines 2020; 8:biomedicines8100414. [PMID: 33066148 PMCID: PMC7601984 DOI: 10.3390/biomedicines8100414] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/05/2020] [Accepted: 10/09/2020] [Indexed: 02/06/2023] Open
Abstract
Genome sequencing studies have characterized the genetic alterations of different tumor types, highlighting the diversity of the molecular processes driving tumor development. Comprehensive sequencing studies have defined molecular subtypes of colorectal cancers (CRCs) through the identification of genetic events associated with microsatellite stability (MSS), microsatellite-instability-high (MSI-H), and hypermutation. Most of these studies characterized primary tumors. Only recent studies have addressed the characterization of the genetic and clinical heterogeneity of metastatic CRC. Metastatic CRC genomes were found to be not fundamentally different from primary CRCs in terms of the mutational landscape or of genes that drive tumorigenesis, and a genomic heterogeneity associated with tumor location of primary tumors helps to define different clinical behaviors of metastatic CRCs. Although CRC metastatic spreading was traditionally seen as a late-occurring event, growing evidence suggests that this process can begin early during tumor development and the clonal architecture of these tumors is consistently influenced by cancer treatment. Although the survival rate of patients with metastatic CRC patients improved in the last years, the response to current treatments and prognosis of many of these patients remain still poor, indicating the need to discover new improvements for therapeutic vulnerabilities and to formulate a rational prospective of personalized therapies.
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28
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You XH, Jiang YH, Fang Z, Sun F, Li Y, Wang W, Xia ZJ, Wang XZ, Ying HQ. Chemotherapy plus bevacizumab as an optimal first-line therapeutic treatment for patients with right-sided metastatic colon cancer: a meta-analysis of first-line clinical trials. ESMO Open 2020; 4:S2059-7029(20)30051-X. [PMID: 32132090 PMCID: PMC7064070 DOI: 10.1136/esmoopen-2019-000605] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/23/2019] [Accepted: 11/27/2019] [Indexed: 02/06/2023] Open
Abstract
Background Monoclonal antibodies of anti-epidermal growth factor receptor (EGFR) have been recommended as first-line therapy for patients with left-sided metastatic colorectal cancer (mCRC) with wild-type RAS. The effect of tumour laterality on antivascular endothelial growth factor antibody and how to optimise targeted therapies for the right-sided cases remain controversial. Patients and methods A comprehensive meta-analysis enrolling 16 first-line clinical trials was performed to evaluate the efficacy of chemotherapy alone and chemotherapy plus targeted therapies for patients with mCRC with right primary tumour site, and we validated the results in metastatic setting (14 trials containing 4306 patients with unresectable mCRC). Results Here, we found that progression-free survival (PFS) (combined HR 1.30, 95% CI 1.17 to 1.44) and overall survival (OS) (combined HR 1.46, 95% CI 1.32 to 1.62) of the right-sided patients were significantly inferior to the left-sided individuals receiving chemotherapy alone in overall population, regardless of race. Similar results were also observed in metastatic setting. OS of patients with left-sided mCRC receiving chemotherapy plus bevacizumab was superior to the right-sided individuals (combined median survival ratio (MSR)=1.23, 95% CI 1.08 to 1.39 for overall population; combined MSR=1.23, 95% CI 1.05 to 1.45 for metastatic setting), especially for wild-type RAS and mixed population. Moreover, the right-sided patients benefited more from chemotherapy plus bevacizumab comparing with chemotherapy alone in both overall population and metastatic setting. Importantly, the RAS-wild right-sided patients achieved longer PFS (combined HR 0.67, 95% CI 0.52 to 0.88) and OS (combined HR 0.74, 95% CI 0.56 to 0.98) from chemotherapy plus bevacizumab comparing with chemotherapy associated with anti-EGFR agents. Conclusions Patients with right-sided mCRC show impaired chemosensitivity, and chemotherapy plus bevacizumab can be an optimal first-line therapeutic regimen for the RAS-wild patients with right-sided mCRC.
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Affiliation(s)
- Xia-Hong You
- Department of Clinical Laboratory, Jiangxi Province Key Laboratory of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Yu-Huan Jiang
- Department of Clinical Laboratory, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Zhou Fang
- Department of Laboratory Medicine, Nanchang University Medical College, Nanchang, Jiangxi, China
| | - Fan Sun
- Department of Clinical Laboratory, Jiangxi Province Key Laboratory of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Yao Li
- Department of Laboratory Medicine, Nanchang University Medical College, Nanchang, Jiangxi, China
| | - Wei Wang
- Department of Laboratory Medicine, Nanchang University Medical College, Nanchang, Jiangxi, China
| | - Zi-Jin Xia
- Department of Laboratory Medicine, Nanchang University Medical College, Nanchang, Jiangxi, China
| | - Xiao-Zhong Wang
- Department of Clinical Laboratory, Jiangxi Province Key Laboratory of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Hou-Qun Ying
- Department of Clinical Laboratory, Jiangxi Province Key Laboratory of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China .,Department of Nuclear Medicine, Jiangxi Province Key Laboratory of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
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29
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Sawayama H, Miyamoto Y, Ogawa K, Yoshida N, Baba H. Investigation of colorectal cancer in accordance with consensus molecular subtype classification. Ann Gastroenterol Surg 2020; 4:528-539. [PMID: 33005848 PMCID: PMC7511559 DOI: 10.1002/ags3.12362] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/06/2020] [Accepted: 05/16/2020] [Indexed: 02/06/2023] Open
Abstract
The classification of colorectal cancer (CRC) plays a pivotal role in predicting a patient's prognosis and determining treatment strategies. The consensus molecular subtype (CMS) classification system was constructed by analyzing genetic information from 18 CRC data sets, containing 4151 CRC samples. CRC was classified into four subtypes with distinct molecular and biological characteristics: CMS1 (microsatellite instability immune), CMS2 (canonical), CMS3 (metabolic), and CMS4 (mesenchymal). Since their designation in 2015, these classifications have been applied to basic and translational research of CRC, with the hope that understanding these subsets will influence a clinician's approach to therapeutic treatment and improve clinical outcomes. We reviewed CRC investigations in accordance with CMSs published in the last 5 years to further explore the clinical significance of these subtypes and identify underlying trends that may direct relevant future research. We determined that CMSs linked common features of CRC cell lines and PDX models in various studies. Furthermore, associations between prognosis and clinicopathological findings, including pathological grade and the stage of carcinogenesis, tumor budding, and tumor location, were correlated with CMS classification. Novel prognostic factors were identified, and the relationship between chemotherapeutic drug resistance and CMS has been fortified by our compilation of research; thus, indicating that this review provides advanced insight into clinical questions and treatment strategies for CRC.
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Affiliation(s)
- Hiroshi Sawayama
- Department of Gastroenterological SurgeryGraduate School of Medical SciencesKumamoto UniversityHonjoJapan
| | - Yuji Miyamoto
- Department of Gastroenterological SurgeryGraduate School of Medical SciencesKumamoto UniversityHonjoJapan
| | - Katsuhiro Ogawa
- Department of Gastroenterological SurgeryGraduate School of Medical SciencesKumamoto UniversityHonjoJapan
| | - Naoya Yoshida
- Department of Gastroenterological SurgeryGraduate School of Medical SciencesKumamoto UniversityHonjoJapan
| | - Hideo Baba
- Department of Gastroenterological SurgeryGraduate School of Medical SciencesKumamoto UniversityHonjoJapan
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30
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Wei T, Zhang J, Li J, Chen Q, Zhi X, Tao W, Ma J, Yang J, Lou Y, Ma T, Li X, Zhang Q, Chen W, Que R, Gao S, Bai X, Liang T. Genome-wide profiling of circulating tumor DNA depicts landscape of copy number alterations in pancreatic cancer with liver metastasis. Mol Oncol 2020; 14:1966-1977. [PMID: 32593194 PMCID: PMC7463305 DOI: 10.1002/1878-0261.12757] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 04/09/2020] [Accepted: 04/14/2020] [Indexed: 12/11/2022] Open
Abstract
Cell‐free DNA (cfDNA) offers an alternative to tissue biopsies for genomic profiling in tumors. Here, we sought to evaluate copy number alterations in PDAC through whole‐genome sequencing (WGS) of cfDNA and determine their clinical significance. Using shallow WGS across 90 plasma samples from 70 pancreatic cancer patients, we detected somatic copy number alterations (CNAs) in 34 subjects (48.6%). Additionally, a higher tumor fraction (TFx) was associated with increased carbohydrate antigen 19‐9 (CA19‐9), metastasis, and a worse prognosis. Serial cfDNA analysis suggested that CNAs were highly concordant even for progressive disease after chemotherapy. TFx dynamics were largely in line with changed CA19‐9 levels and tumor burden following chemotherapy. Notably, patients with more abundant, baseline CNAs exhibited a better response to chemotherapy. In conclusion, shallow WGS for cfDNA enables a high‐throughput characterization of CNAs and an estimation of tumor burden in metastatic pancreatic cancer. These findings reinforce our understanding of the genomic evolution of metastatic PDAC and might have clinical relevance for guiding treatment.
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Affiliation(s)
- Tao Wei
- Department of Hepatobiliary and Pancreatic Surgery, School of Medicine, the First Affiliated Hospital of Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, China.,Innovation Center for the study of Pancreatic Diseases, Hangzhou, China
| | - Jian Zhang
- Department of Hepatobiliary and Pancreatic Surgery, School of Medicine, the First Affiliated Hospital of Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, China.,Innovation Center for the study of Pancreatic Diseases, Hangzhou, China
| | - Jin Li
- Department of Hepatobiliary and Pancreatic Surgery, School of Medicine, the First Affiliated Hospital of Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, China.,Innovation Center for the study of Pancreatic Diseases, Hangzhou, China
| | - Qi Chen
- Department of Hepatobiliary and Pancreatic Surgery, School of Medicine, the First Affiliated Hospital of Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, China.,Innovation Center for the study of Pancreatic Diseases, Hangzhou, China
| | - Xiao Zhi
- Department of Hepatobiliary and Pancreatic Surgery, School of Medicine, the First Affiliated Hospital of Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, China.,Innovation Center for the study of Pancreatic Diseases, Hangzhou, China
| | - Wei Tao
- The Scientific and Technical Department, Novogene Bioinformatics Institute, Beijing, China
| | - Jingjiao Ma
- The Scientific and Technical Department, Novogene Bioinformatics Institute, Beijing, China
| | - Jiaqi Yang
- Department of Hepatobiliary and Pancreatic Surgery, School of Medicine, the First Affiliated Hospital of Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, China.,Innovation Center for the study of Pancreatic Diseases, Hangzhou, China
| | - Yu Lou
- Department of Hepatobiliary and Pancreatic Surgery, School of Medicine, the First Affiliated Hospital of Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, China.,Innovation Center for the study of Pancreatic Diseases, Hangzhou, China
| | - Tao Ma
- Department of Hepatobiliary and Pancreatic Surgery, School of Medicine, the First Affiliated Hospital of Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, China.,Innovation Center for the study of Pancreatic Diseases, Hangzhou, China
| | - Xiang Li
- Department of Hepatobiliary and Pancreatic Surgery, School of Medicine, the First Affiliated Hospital of Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, China.,Innovation Center for the study of Pancreatic Diseases, Hangzhou, China
| | - Qi Zhang
- Department of Hepatobiliary and Pancreatic Surgery, School of Medicine, the First Affiliated Hospital of Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, China.,Innovation Center for the study of Pancreatic Diseases, Hangzhou, China
| | - Wei Chen
- Department of Hepatobiliary and Pancreatic Surgery, School of Medicine, the First Affiliated Hospital of Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, China.,Innovation Center for the study of Pancreatic Diseases, Hangzhou, China
| | - Risheng Que
- Department of Hepatobiliary and Pancreatic Surgery, School of Medicine, the First Affiliated Hospital of Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, China.,Innovation Center for the study of Pancreatic Diseases, Hangzhou, China
| | - Shunliang Gao
- Department of Hepatobiliary and Pancreatic Surgery, School of Medicine, the First Affiliated Hospital of Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, China.,Innovation Center for the study of Pancreatic Diseases, Hangzhou, China
| | - Xueli Bai
- Department of Hepatobiliary and Pancreatic Surgery, School of Medicine, the First Affiliated Hospital of Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, China.,Innovation Center for the study of Pancreatic Diseases, Hangzhou, China
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery, School of Medicine, the First Affiliated Hospital of Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, China.,Innovation Center for the study of Pancreatic Diseases, Hangzhou, China
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31
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Buikhuisen JY, Torang A, Medema JP. Exploring and modelling colon cancer inter-tumour heterogeneity: opportunities and challenges. Oncogenesis 2020; 9:66. [PMID: 32647253 PMCID: PMC7347540 DOI: 10.1038/s41389-020-00250-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 06/10/2020] [Accepted: 06/23/2020] [Indexed: 02/06/2023] Open
Abstract
Colon cancer inter-tumour heterogeneity is installed on multiple levels, ranging from (epi)genetic driver events to signalling pathway rewiring reflected by differential gene expression patterns. Although the existence of heterogeneity in colon cancer has been recognised for a longer period of time, it is sparingly incorporated as a determining factor in current clinical practice. Here we describe how unsupervised gene expression-based classification efforts, amongst which the consensus molecular subtypes (CMS), can stratify patients in biological subgroups associated with distinct disease outcome and responses to therapy. We will discuss what is needed to extend these subtyping efforts to the clinic and we will argue that preclinical models recapitulate CMS subtypes and can be of vital use to increase our understanding of treatment response and resistance and to discover novel targets for therapy.
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Affiliation(s)
- Joyce Y Buikhuisen
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands
| | - Arezo Torang
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands
| | - Jan Paul Medema
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands. .,Oncode Institute, Amsterdam, The Netherlands.
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32
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Personalised mapping of tumour development in synchronous colorectal cancer patients. NPJ Genom Med 2020; 5:27. [PMID: 32655884 PMCID: PMC7335056 DOI: 10.1038/s41525-020-0134-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/15/2020] [Indexed: 12/12/2022] Open
Abstract
Synchronous colorectal cancers (syCRCs) are two or more primary tumours identified simultaneously in a patient. Previous studies report high inter-tumour heterogeneity between syCRCs, suggesting independent origin and different treatment response, making their management particularly challenging, with no specific guidelines currently in place. Here, we performed in-depth bioinformatic analyses of genomic and transcriptomic data of a total of eleven syCRCs and one metachronous CRC collected from three patients. We found mixed microsatellite status between and within patients. Overlap of mutations between synchronous tumours was consistently low (<0.5%) and heterogeneity of driver events across syCRCs was high in all patients. Microbial analysis revealed the presence of Fusobacterium nucleatum species in patients with MSI tumours, while quantification of tumour immune infiltration showed varying immune responses between syCRCs. Our results suggest high heterogeneity of syCRCs within patients but find clinically actionable biomarkers that help predict responses to currently available targeted therapies. Our study highlights the importance of personalised genome and transcriptome sequencing of all synchronous lesions to aid therapy decision and improve management of syCRC patients.
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33
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Barat A, Smeets D, Moran B, Zhang W, Cao S, Das S, Klinger R, Betge J, Murphy V, Bacon O, Kay EW, Van Grieken NCT, Verheul HMW, Gaiser T, Schulte N, Ebert MP, Fender B, Hennessy BT, McNamara DA, O'Connor D, Gallagher WM, Cremolini C, Loupakis F, Parikh A, Mancao C, Ylstra B, Lambrechts D, Lenz HJ, Byrne AT, Prehn JHM. Combination of variations in inflammation- and endoplasmic reticulum-associated genes as putative biomarker for bevacizumab response in KRAS wild-type colorectal cancer. Sci Rep 2020; 10:9778. [PMID: 32555399 PMCID: PMC7299973 DOI: 10.1038/s41598-020-65869-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 05/05/2020] [Indexed: 12/30/2022] Open
Abstract
Chemotherapy combined with the angiogenesis inhibitor bevacizumab (BVZ) is approved as a first-line treatment in metastatic colorectal cancer (mCRC). Limited clinical benefit underpins the need for improved understanding of resistance mechanisms and the elucidation of novel predictive biomarkers. We assessed germline single-nucleotide polymorphisms (SNPs) in 180 mCRC patients (Angiopredict [APD] cohort) treated with combined BVZ + chemotherapy and investigated previously reported predictive SNPs. We further employed a machine learning approach to identify novel associations. In the APD cohort IL8 rs4073 any A carriers, compared to TT carriers, were associated with worse progression-free survival (PFS) (HR = 1.51, 95% CI:1.03-2.22, p-value = 0.037) and TBK1 rs7486100 TT carriers, compared to any A carriers, were associated with worse PFS in KRAS wild-type (wt) patients (HR = 1.94, 95% CI:1.04-3.61, p-value = 0.037), replicating previous findings. Machine learning identified novel associations in genes encoding the inflammasome protein NLRP1 and the ER protein Sarcalumenin (SRL). A negative association between PFS and carriers of any A at NLRP1 rs12150220 and AA for SRL rs13334970 in APD KRAS wild-type patients (HR = 4.44, 95% CI:1.23-16.13, p-value = 0.005), which validated in two independent clinical cohorts involving BVZ, MAVERICC and TRIBE. Our findings highlight a key role for inflammation and ER signalling underpinning BVZ + chemotherapy responsiveness.
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Affiliation(s)
- Ana Barat
- Centre for Systems Medicine and Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland.
| | | | - Bruce Moran
- UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Wu Zhang
- USC Norris Comprehensive Cancer Center, Los Angeles, USA
| | - Shu Cao
- USC Norris Comprehensive Cancer Center, Los Angeles, USA
| | - Sudipto Das
- Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Rut Klinger
- UCD, School of Biomolecular and Biomedical Science, Dublin, Ireland
| | - Johannes Betge
- Department of Medicine II, University Hospital Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics, Heidelberg, Germany
| | | | - Orna Bacon
- Centre for Systems Medicine and Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Elaine W Kay
- Department of Pathology, Beaumont Hospital, Dublin, Ireland
| | | | - Henk M W Verheul
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Timo Gaiser
- Institute of Pathology, University Hospital Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Nadine Schulte
- Department of Medicine II, University Hospital Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Matthias P Ebert
- Department of Medicine II, University Hospital Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Bozena Fender
- OncoMark Ltd., NovaUCD, Belfield Innovation Park, Dublin, Ireland
| | - Bryan T Hennessy
- Department of Medical Oncology, Beaumont Hospital, Dublin, Ireland
| | | | - Darran O'Connor
- Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | | | - Chiara Cremolini
- Unit of Medical Oncology 2, Department of Translational Research and New Technologies in Medicine and Surgery, Azienda Ospedaliera Universitaria Pisana, Pisa, Italy
| | - Fotios Loupakis
- Oncology Unit, Istituto Oncologico Veneto, IOV-IRCCS, Padua, Italy
| | - Aparna Parikh
- Division of Hematology and Oncology, Massachusetts General Hospital, Boston, USA
| | - Christoph Mancao
- Oncology Biomarker Development, Genentech Inc., San Francisco, USA
| | - Bauke Ylstra
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | | | | | - Annette T Byrne
- Centre for Systems Medicine and Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Jochen H M Prehn
- Centre for Systems Medicine and Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland.
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Belardinilli F, Capalbo C, Malapelle U, Pisapia P, Raimondo D, Milanetti E, Yasaman M, Liccardi C, Paci P, Sibilio P, Pepe F, Bonfiglio C, Mezi S, Magri V, Coppa A, Nicolussi A, Gradilone A, Petroni M, Di Giulio S, Fabretti F, Infante P, Coni S, Canettieri G, Troncone G, Giannini G. Clinical Multigene Panel Sequencing Identifies Distinct Mutational Association Patterns in Metastatic Colorectal Cancer. Front Oncol 2020; 10:560. [PMID: 32457828 PMCID: PMC7221020 DOI: 10.3389/fonc.2020.00560] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 03/27/2020] [Indexed: 12/12/2022] Open
Abstract
Extensive molecular characterization of human colorectal cancer (CRC) via Next Generation Sequencing (NGS) indicated that genetic or epigenetic dysregulation of a relevant, but limited, number of molecular pathways typically occurs in this tumor. The molecular picture of the disease is significantly complicated by the frequent occurrence of individually rare genetic aberrations, which expand tumor heterogeneity. Inter- and intratumor molecular heterogeneity is very likely responsible for the remarkable individual variability in the response to conventional and target-driven first-line therapies, in metastatic CRC (mCRC) patients, whose median overall survival remains unsatisfactory. Implementation of an extensive molecular characterization of mCRC in the clinical routine does not yet appear feasible on a large scale, while multigene panel sequencing of most commonly mutated oncogene/oncosuppressor hotspots is more easily achievable. Here, we report that clinical multigene panel sequencing performed for anti-EGFR therapy predictive purposes in 639 formalin-fixed paraffin-embedded (FFPE) mCRC specimens revealed previously unknown pairwise mutation associations and a high proportion of cases carrying actionable gene mutations. Most importantly, a simple principal component analysis directed the delineation of a new molecular stratification of mCRC patients in eight groups characterized by non-random, specific mutational association patterns (MAPs), aggregating samples with similar biology. These data were validated on a The Cancer Genome Atlas (TCGA) CRC dataset. The proposed stratification may provide great opportunities to direct more informed therapeutic decisions in the majority of mCRC cases.
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Affiliation(s)
| | - Carlo Capalbo
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | | | - Pasquale Pisapia
- Department of Public Health, University Federico II, Naples, Italy
| | - Domenico Raimondo
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | | | - Mahdavian Yasaman
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | - Carlotta Liccardi
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | - Paola Paci
- Institute for System Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Pasquale Sibilio
- Institute for System Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Francesco Pepe
- Department of Public Health, University Federico II, Naples, Italy
| | - Caterina Bonfiglio
- National Institute of Gastroenterology-Research Hospital, IRCCS "S. de Bellis", Bari, Italy
| | - Silvia Mezi
- Department of Radiological Oncological and Pathological Sciences, University La Sapienza, Rome, Italy
| | - Valentina Magri
- Department of Surgery Pietro Valdoni, Faculty of Medicine and Dentistry, Sapienza University of Rome, Rome, Italy
| | - Anna Coppa
- Department of Experimental Medicine, University La Sapienza, Rome, Italy
| | - Arianna Nicolussi
- Department of Experimental Medicine, University La Sapienza, Rome, Italy
| | - Angela Gradilone
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | - Marialaura Petroni
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Stefano Di Giulio
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | | | - Paola Infante
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Sonia Coni
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | - Gianluca Canettieri
- Department of Molecular Medicine, University La Sapienza, Rome, Italy.,Pasteur Institute-Cenci Bolognetti Foundation, Rome, Italy
| | | | - Giuseppe Giannini
- Department of Molecular Medicine, University La Sapienza, Rome, Italy.,Pasteur Institute-Cenci Bolognetti Foundation, Rome, Italy
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35
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Yang J, Song K, Guo W, Zheng H, Fu Y, You T, Wang K, Qi L, Zhao W, Guo Z. A Qualitative Transcriptional Signature for Predicting Prognosis and Response to Bevacizumab in Metastatic Colorectal Cancer. Mol Cancer Ther 2020; 19:1497-1505. [PMID: 32371582 DOI: 10.1158/1535-7163.mct-19-0864] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 12/17/2019] [Accepted: 05/01/2020] [Indexed: 11/16/2022]
Abstract
Bevacizumab is the molecular-targeted agent used for the antiangiogenic therapy of metastatic colorectal cancer. But some patients are resistant to bevacizumab, it needs an effective biomarker to predict the prognosis and responses of metastatic colorectal cancer (mCRC) to bevacizumab therapy. In this work, we developed a qualitative transcriptional signature to individually predict the response of bevacizumab in patients with mCRC. First, using mCRC samples treated with bevacizumab, we detected differentially expressed genes between response and nonresponse groups. Then, the gene pairs, consisting of at least one differentially expressed gene, with stable relative expression orderings in the response samples but reversal stable relative expression orderings in the nonresponse samples were identified, denoted as pairs-bevacizumab. Similarly, we screened the gene pairs significantly associated with primary tumor locations, donated as pairs-LR. Among the overlapped gene pairs between the pairs-bevacizumab and pairs-LR, we adopted a feature selection process to extract gene pairs that reached the highest F-score for predicting bevacizumab response status in mCRC as the final gene pair signature (GPS), denoted as 64-GPS. In two independent datasets, the predicted response group showed significantly better overall survival than the nonresponse group (P = 6.00e-4 in GSE72970; P = 0.04 in TCGA). Genomic analyses showed that the predicted response group was characterized by frequent copy number alternations, whereas the nonresponse group was characterized by hypermutation. In conclusion, 64-GPS was an objective and robust predictive signature for patients with mCRC treated with bevacizumab, which could effectively assist in the decision of clinical therapy.
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Affiliation(s)
- Jing Yang
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Kai Song
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Wenbing Guo
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hailong Zheng
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yelin Fu
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Tianyi You
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Kai Wang
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Lishuang Qi
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Wenyuan Zhao
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
| | - Zheng Guo
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
- Key Laboratory of Medical Bioinformatics, Fujian Province, Fuzhou, China
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36
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Lin L, Ding D, Xiao X, Li B, Cao P, Li S. Trametinib potentiates TRAIL-induced apoptosis via FBW7-dependent Mcl-1 degradation in colorectal cancer cells. J Cell Mol Med 2020; 24:6822-6832. [PMID: 32352219 PMCID: PMC7299726 DOI: 10.1111/jcmm.15336] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 04/03/2020] [Accepted: 04/12/2020] [Indexed: 12/14/2022] Open
Abstract
Trametinib is a MEK1/2 inhibitor and exerts anticancer activity against a variety of cancers. However, the effect of Trametinib on colorectal cancer (CRC) is not well understood. In the current study, our results demonstrate the ability of sub-toxic doses of Trametinib to enhance TRAIL-mediated apoptosis in CRC cells. Our findings also indicate that Trametinib and TRAIL activate caspase-dependent apoptosis in CRC cells. Moreover, Mcl-1 overexpression can reduce apoptosis in CRC cells treated with Trametinib with or without TRAIL. We further demonstrate that Trametinib degrades Mcl-1 through the proteasome pathway. In addition, GSK-3β phosphorylates Mcl-1 at S159 and promotes Mcl-1 degradation. The E3 ligase FBW7, known to polyubiquitinate Mcl-1, is involved in Trametinib-induced Mcl-1 degradation. Taken together, these results provide the first evidence that Trametinib enhances TRAIL-mediated apoptosis through FBW7-dependent Mcl-1 ubiquitination and degradation.
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Affiliation(s)
- Lin Lin
- Department of Clinical Laboratory, First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Dapeng Ding
- Department of Clinical Laboratory, First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Xiaoguang Xiao
- Department of Clinical Laboratory, First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Bing Li
- Department of Clinical Laboratory, First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Penglong Cao
- Department of Clinical Laboratory, First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Shijun Li
- Department of Clinical Laboratory, First Affiliated Hospital of Dalian Medical University, Dalian, China
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37
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Pappas-Gogos G, Baltagiannis EG, Kyrochristos ID, Ziogas DE, Goussia A, Mitsis M, Roukos DH. Predictive and patient-monitoring biomarkers: precision in the management of colorectal cancer. Biomark Med 2020; 14:335-339. [PMID: 32250157 DOI: 10.2217/bmm-2020-0025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Georgios Pappas-Gogos
- Centre for Biosystems and Genome Network Medicine, Ioannina University, Ioannina, Greece.,Department of Surgery, University Hospital of Ioannina, Ioannina, Greece
| | - Evangelos G Baltagiannis
- Centre for Biosystems and Genome Network Medicine, Ioannina University, Ioannina, Greece.,Department of Surgery, University Hospital of Ioannina, Ioannina, Greece
| | - Ioannis D Kyrochristos
- Centre for Biosystems and Genome Network Medicine, Ioannina University, Ioannina, Greece.,Department of Surgery, University Hospital of Ioannina, Ioannina, Greece
| | - Demosthenes E Ziogas
- Centre for Biosystems and Genome Network Medicine, Ioannina University, Ioannina, Greece.,Department of Surgery, 'G Hatzikosta' General Hospital, Ioannina, Greece
| | - Anna Goussia
- Department of Pathology, University Hospital of Ioannina, Ioannina, Greece
| | - Michail Mitsis
- Department of Surgery, University Hospital of Ioannina, Ioannina, Greece
| | - Dimitrios H Roukos
- Centre for Biosystems and Genome Network Medicine, Ioannina University, Ioannina, Greece.,Department of Surgery, University Hospital of Ioannina, Ioannina, Greece.,Department of Systems Biology, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece
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38
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Vishwakarma R, McManus KJ. Chromosome Instability; Implications in Cancer Development, Progression, and Clinical Outcomes. Cancers (Basel) 2020; 12:cancers12040824. [PMID: 32235397 PMCID: PMC7226245 DOI: 10.3390/cancers12040824] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 03/27/2020] [Accepted: 03/28/2020] [Indexed: 12/15/2022] Open
Abstract
Chromosome instability (CIN) refers to an ongoing rate of chromosomal changes and is a driver of genetic, cell-to-cell heterogeneity. It is an aberrant phenotype that is intimately associated with cancer development and progression. The presence, extent, and level of CIN has tremendous implications for the clinical management and outcomes of those living with cancer. Despite its relevance in cancer, there is still extensive misuse of the term CIN, and this has adversely impacted our ability to identify and characterize the molecular determinants of CIN. Though several decades of genetic research have provided insight into CIN, the molecular determinants remain largely unknown, which severely limits its clinical potential. In this review, we provide a definition of CIN, describe the two main types, and discuss how it differs from aneuploidy. We subsequently detail its impact on cancer development and progression, and describe how it influences metastatic potential with reference to cancer prognosis and outcomes. Finally, we end with a discussion of how CIN induces genetic heterogeneity to influence the use and efficacy of several precision medicine strategies, including patient and risk stratification, as well as its impact on the acquisition of drug resistance and disease recurrence.
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Affiliation(s)
- Raghvendra Vishwakarma
- Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada;
| | - Kirk J. McManus
- Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada;
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- Correspondence: ; Tel.: +1-204-787-2833
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39
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Dienstmann R, Connor K, Byrne AT. Precision Therapy in RAS Mutant Colorectal Cancer. Gastroenterology 2020; 158:806-811. [PMID: 31972237 DOI: 10.1053/j.gastro.2019.12.051] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/18/2019] [Accepted: 12/29/2019] [Indexed: 12/13/2022]
Affiliation(s)
| | - Kate Connor
- Royal College of Surgeons in Ireland, Dept of Physiology and Medical Physics, RCSI Centre for Systems Medicine, Dublin 2, Ireland
| | - Annette T Byrne
- Royal College of Surgeons in Ireland, Dept of Physiology and Medical Physics, RCSI Centre for Systems Medicine, Dublin 2, Ireland
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40
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Fridman WH, Miller I, Sautès-Fridman C, Byrne AT. Therapeutic Targeting of the Colorectal Tumor Stroma. Gastroenterology 2020; 158:303-321. [PMID: 31622621 DOI: 10.1053/j.gastro.2019.09.045] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 09/05/2019] [Accepted: 09/08/2019] [Indexed: 02/07/2023]
Abstract
Colorectal tumors have been classified based on histologic factors, genetic factors, and consensus molecular subtypes, all of which affect the tumor microenvironment. Elements of the tumor microenvironment serve as therapeutic targets and might be used as prognostic factors. For example, immune checkpoint inhibitors are used to treat tumors with microsatellite instability, and anti-angiogenic agents may be used in combination with other drugs to slow or inhibit tumor growth. We review the features of the colorectal tumor stroma that are associated with patient outcomes and discuss potential therapeutic agents that target these features.
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Affiliation(s)
- Wolf H Fridman
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, Inflammation, Complement and Cancer Team, Paris, France.
| | - Ian Miller
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Catherine Sautès-Fridman
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, Inflammation, Complement and Cancer Team, Paris, France
| | - Annette T Byrne
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
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41
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Kyrochristos ID, Ziogas DE, Goussia A, Glantzounis GK, Roukos DH. Bulk and Single-Cell Next-Generation Sequencing: Individualizing Treatment for Colorectal Cancer. Cancers (Basel) 2019; 11:cancers11111809. [PMID: 31752125 PMCID: PMC6895993 DOI: 10.3390/cancers11111809] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 11/12/2019] [Accepted: 11/14/2019] [Indexed: 12/24/2022] Open
Abstract
The increasing incidence combined with constant rates of early diagnosis and mortality of colorectal cancer (CRC) over the past decade worldwide, as well as minor overall survival improvements in the industrialized world, suggest the need to shift from conventional research and clinical practice to the innovative development of screening, predictive and therapeutic tools. Explosive integration of next-generation sequencing (NGS) systems into basic, translational and, more recently, basket trials is transforming biomedical and cancer research, aiming for substantial clinical implementation as well. Shifting from inter-patient tumor variability to the precise characterization of intra-tumor genetic, genomic and transcriptional heterogeneity (ITH) via multi-regional bulk tissue NGS and emerging single-cell transcriptomics, coupled with NGS of circulating cell-free DNA (cfDNA), unravels novel strategies for therapeutic response prediction and drug development. Remarkably, underway and future genomic/transcriptomic studies and trials exploring spatiotemporal clonal evolution represent most rational expectations to discover novel prognostic, predictive and therapeutic tools. This review describes latest advancements and future perspectives of integrated sequencing systems for genome and transcriptome exploration to overcome unmet research and clinical challenges towards Precision Oncology.
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Affiliation(s)
- Ioannis D. Kyrochristos
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece; (I.D.K.); (D.E.Z.)
- Department of Surgery, Ioannina University Hospital, 45500 Ioannina, Greece;
| | - Demosthenes E. Ziogas
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece; (I.D.K.); (D.E.Z.)
- Department of Surgery, ‘G. Hatzikosta’ General Hospital, 45001 Ioannina, Greece
| | - Anna Goussia
- Department of Pathology, Ioannina University Hospital, 45500 Ioannina, Greece;
| | | | - Dimitrios H. Roukos
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece; (I.D.K.); (D.E.Z.)
- Department of Surgery, Ioannina University Hospital, 45500 Ioannina, Greece;
- Department of Systems Biology, Biomedical Research Foundation of the Academy of Athens (BRFAA), 11527 Athens, Greece
- Correspondence: ; Tel.: +302651005572
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42
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Clinical impact of first-line bevacizumab plus chemotherapy in metastatic colorectal cancer of mucinous histology: a multicenter, retrospective analysis on 685 patients. J Cancer Res Clin Oncol 2019; 146:493-501. [DOI: 10.1007/s00432-019-03077-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 11/02/2019] [Indexed: 01/26/2023]
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43
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SIX4 activates Akt and promotes tumor angiogenesis. Exp Cell Res 2019; 383:111495. [PMID: 31301290 DOI: 10.1016/j.yexcr.2019.111495] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/08/2019] [Accepted: 07/09/2019] [Indexed: 02/06/2023]
Abstract
Angiogenesis plays important roles in solid tumors progression. Growth factors such as vascular endothelial growth factors (VEGFs) can induce angiogenesis and hypoxia promotes the expression of VEGFs through activating hypoxia-inducible factor 1 (HIF-1α). However, the regulation of HIF-1α still not been fully understood. Here, we demonstrate that the Sine Oculis Homeobox Homolog 4 (SIX4) is up-regulated in colorectal cancer (CRC) and high expression of SIX4 predicts a poor prognosis. Overexpression of SIX4 enhances tumor growth and angiogenesis in vitro and in vivo, while knockdown of SIX4 inhibits tumor growth and angiogenesis. Furthermore, we show that SIX4 increases the expression of VEGF-A by coordinating with the HIF-1α. Mechanically, we explore that SIX4 up-regulates the expression of HIF-1α depending on Akt activation. Collectively, we demonstrate that SIX4 is functional in regulating tumor angiogenesis and SIX4 might be used as anti-angiogenic therapy in CRC.
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44
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A Shallow Convolutional Learning Network for Classification of Cancers Based on Copy Number Variations. SENSORS 2019; 19:s19194207. [PMID: 31569801 PMCID: PMC6806227 DOI: 10.3390/s19194207] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/18/2019] [Accepted: 09/25/2019] [Indexed: 12/29/2022]
Abstract
Genomic copy number variations (CNVs) are among the most important structural variations. They are linked to several diseases and cancer types. Cancer is a leading cause of death worldwide. Several studies were conducted to investigate the causes of cancer and its association with genomic changes to enhance its management and improve the treatment opportunities. Classification of cancer types based on the CNVs falls in this category of research. We reviewed the recent, most successful methods that used machine learning algorithms to solve this problem and obtained a dataset that was tested by some of these methods for evaluation and comparison purposes. We propose three deep learning techniques to classify cancer types based on CNVs: a six-layer convolutional net (CNN6), residual six-layer convolutional net (ResCNN6), and transfer learning of pretrained VGG16 net. The results of the experiments performed on the data of six cancer types demonstrated a high accuracy of 86% for ResCNN6 followed by 85% for CNN6 and 77% for VGG16. The results revealed a lower prediction accuracy for one of the classes (uterine corpus endometrial carcinoma (UCEC)). Repeating the experiments after excluding this class reveals improvements in the accuracies: 91% for CNN6 and 92% for Res CNN6. We observed that UCEC and ovarian serous carcinoma (OV) share a considerable subset of their features, which causes a struggle for learning in the classifiers. We repeated the experiment again by balancing the six classes through oversampling of the training dataset and the result was an enhancement in both overall and UCEC classification accuracies.
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45
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Chen Z, Zhang C, Zhang M, Li B, Niu Y, Chen L, Yang J, Lu S, Gao J, Shen L. Chromosomal instability of circulating tumor DNA reflect therapeutic responses in advanced gastric cancer. Cell Death Dis 2019; 10:697. [PMID: 31541076 PMCID: PMC6754425 DOI: 10.1038/s41419-019-1907-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 08/19/2019] [Accepted: 08/26/2019] [Indexed: 12/14/2022]
Abstract
Gastric cancer is characterized by chromosomal instability. In this study, we investigated chromosomal instability quantified by copy number instability (CNI) score of circulating tumor DNA (ctDNA) during the drug treatment in advanced gastric cancer (AGC). A total of 55 pretherapeutic plasmas from 55 AGC patients and 75 plasmas during drug treatment of 26 AGC patients were collected. Plasma ctDNA was extracted and assessed by whole-genome sequencing (WGS) for somatic copy number alteration (SCNA), and according to which we calculated the CNI scores. We next assessed the correlations between chromosomal instability and therapeutic response. The cutoff value of chromosomal instability was defined as the mean + SD of the CNI scores (56.60) in cfDNA of plasmas from 100 healthy people. For 55 enrolled cases, chromosomal instability was observed in 27 (49%) prior to drug treatment, whose response rate (59%, 16/27) was higher than in 28 patients with stable chromosomes (32%, 9/28, P = 0.043). We also observed that CNI scores fluctuated during treatment in 26 patients. Specifically, the CNI scores in 93% (14/15) of patients sensitive to drug treatment reduced to the level of chromosomal stability and the CNI scores in 52% (13/25) of patients resistant to treatment elevated again. For ctDNA with developed resistance, the SCNA patterns were identical to those before treatment, whereas the CNI scores were lower than the pretherapeutic scores. We found that chromosomal instability based on ctDNA could predict and monitor therapeutic response in gastric cancer, although validation in a larger cohort will be necessary.
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Affiliation(s)
- Zuhua Chen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Cheng Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Mengqi Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Beifang Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Yunyun Niu
- Department of Clinical Research, Yikon Genomics Co. Ltd., Shanghai, China
| | - Limeng Chen
- Department of Clinical Research, Yikon Genomics Co. Ltd., Shanghai, China
| | - Jing Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Sijia Lu
- Department of Clinical Research, Yikon Genomics Co. Ltd., Shanghai, China.
| | - Jing Gao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital and Institute, Beijing, China.
| | - Lin Shen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital and Institute, Beijing, China.
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Chen XY, Huang WL, Peng XP, Lv YN, Li JH, Xiong JP. miR-140-5p mediates bevacizumab-induced cytotoxicity to cardiomyocytes by targeting the VEGFA/14-3-3γ signal pathway. Toxicol Res (Camb) 2019; 8:875-884. [PMID: 32190292 DOI: 10.1039/c9tx00100j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 09/03/2019] [Indexed: 12/14/2022] Open
Abstract
Bevacizumab (BVZ) is the first recombinant humanized monoclonal antibody against vascular endothelial growth factor (VEGFA) approved by the FDA for the treatment of different kinds of cancers, especially colorectal cancer. Although the anti-tumor effects have been verified, the side effects of BVZ are also noteworthy, among which, cardiotoxicity may be the most serious side effect of BVZ. However, the exact mechanisms of cardiotoxicity induced by BVZ have been little explored. This study was conducted in vitro in a human cardiac myocyte (HCM) model. MTT assay was conducted to determine BVZ-stimulated cell viability. For testing the function and mechanism, the cells were transfected with miR-140-5p mimics, miR-140-5p inhibitor and/or VEGFA small interfering RNA (si-VEGFA). Then, apoptosis of the cells was detected via annexin V/propidium iodide (AV-PI) staining followed by flow cytometry. qRT-PCR and western blot assays were applied to measure gene expression (i.e. mRNA) and protein levels, respectively. The CK, LDH, SOD, CAT and GSH-Px activities and MDA level were determined using commercial kits. ROS levels were determined by DCFH-DA assay. Mitochondrial membrane potential was measured by JC-1 assay. Dual-luciferase reporter assay was used to detect the interaction between miR-140-5p and VEGFA. BVZ could inhibit HCM proliferation and induce apoptosis. miR-140-5p was upregulated in response to BVZ treatment and miR-140-5p restraint could alleviate HCM damage caused by BVZ treatment. In contrast, VEGFA and 14-3-3γ expressions were down-regulated by BVZ, and miR-140-5p could inhibit the expression of 14-3-3γ by directly targeting VEGFA. Moreover, VEGFA suppression enhanced HCM injury stimulated by BVZ and partially reversed the functional role of the miR-140-5p inhibitor in BVZ-treated cells. Taken together, miR-140-5p promoted BVZ-treated cardiomyocyte toxicity by targeting the VEGFA/14-3-3γ signal pathway. Collectively, miR-140-5p mediated the BVZ-induced cytotoxicity to cardiomyocytes by targeting the VEGFA/14-3-3γ signal pathway, indicating that miR-140-5p may be a novel target for treating BVZ-induced cardiotoxicity.
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Affiliation(s)
- Xuan-Ying Chen
- Department of Pharmacy , The First Affiliated Hospital , Nanchang University , Nanchang 330006 , P.R China
| | - Wei-Lin Huang
- Department of Cardiovascular , The First Affiliated Hospital , Nanchang University , Nanchang 330006 , P.R China
| | - Xiao-Ping Peng
- Department of Cardiovascular , The First Affiliated Hospital , Nanchang University , Nanchang 330006 , P.R China
| | - Yan-Ni Lv
- Department of Pharmacy , The First Affiliated Hospital , Nanchang University , Nanchang 330006 , P.R China
| | - Jun-He Li
- Department of Oncology , The First Affiliated Hospital , Nanchang University , Nanchang 330006 , P.R China . ; Tel: +86-13879109229
| | - Jian-Ping Xiong
- Department of Oncology , The First Affiliated Hospital , Nanchang University , Nanchang 330006 , P.R China . ; Tel: +86-13879109229
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Kyrochristos ID, Roukos DH. Comprehensive intra-individual genomic and transcriptional heterogeneity: Evidence-based Colorectal Cancer Precision Medicine. Cancer Treat Rev 2019; 80:101894. [PMID: 31518831 DOI: 10.1016/j.ctrv.2019.101894] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 08/27/2019] [Accepted: 08/29/2019] [Indexed: 12/14/2022]
Abstract
Despite advances in translating conventional research into multi-modal treatment for colorectal cancer (CRC), therapeutic resistance and relapse remain unresolved in advanced resectable and, particularly, non-resectable disease. Genome and transcriptome sequencing and editing technologies, coupled with interaction mapping and machine learning, are transforming biomedical research, representing the most rational hope to overcome unmet research and clinical challenges. Rapid progress in both bulk and single-cell next-generation sequencing (NGS) analyses in the identification of primary and metastatic intratumor genomic and transcriptional heterogeneity (ITH) and the detection of circulating cell-free DNA (cfDNA) alterations is providing critical insight into the origins and spatiotemporal evolution of genomic clones responsible for early and late therapeutic resistance and relapse. Moreover, DNA and RNA editing pave new avenues towards the discovery of novel drug targets. Breakthrough combinations of sequencing and editing systems with technologies exploring dynamic interaction networks within pioneering studies could delineate how coding and non-coding mutations perturb regulatory networks and gene expression. This review discusses latest data on genomic and transcriptomic landscapes in time and space, as well as early-phase clinical trials on targeted drug combinations, highlighting the transition from research to clinical Colorectal Cancer Precision Medicine, through non-invasive screening, individualized drug response prediction and development of multiple novel drugs. Future studies exploring the potential to target key transcriptional drivers and regulators will contribute to the next-generation pharmaceutical controllability of multi-layered aberrant transcriptional biocircuits.
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Affiliation(s)
- Ioannis D Kyrochristos
- Centre for Biosystems and Genome Network Medicine, Ioannina University, Ioannina, Greece; Department of Surgery, Ioannina University Hospital, Ioannina, Greece
| | - Dimitrios H Roukos
- Centre for Biosystems and Genome Network Medicine, Ioannina University, Ioannina, Greece; Department of Surgery, Ioannina University Hospital, Ioannina, Greece; Department of Systems Biology, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece.
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You XH, Wen C, Xia ZJ, Sun F, Li Y, Wang W, Fang Z, Chen QG, Zhang L, Jiang YH, Wang XZ, Ying HQ, Zong Z. Primary Tumor Sidedness Predicts Bevacizumab Benefit in Metastatic Colorectal Cancer Patients. Front Oncol 2019; 9:723. [PMID: 31475100 PMCID: PMC6702298 DOI: 10.3389/fonc.2019.00723] [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: 04/08/2019] [Accepted: 07/19/2019] [Indexed: 12/17/2022] Open
Abstract
The emerging debate between primary tumor location and clinical outcome of bevacizumab treated metastatic colorectal cancer (mCRC) continues. The aim of the present study is to investigate the association between the primary tumor location and clinical outcome of 115 mCRC patients receiving bevacizumab based treatment. A meta-analysis including 21 studies was carried out to confirm the conclusion. In our prospective study, we found that right-sided mCRC commonly occurred in older cases (p = 0.03) with multiple-site metastasis (p = 0.03). Progression-free survival (PFS) of the left-sided patients undergoing bevacizumab plus a FOLFIRI regimen was superior to the right-sided cases (p = 0.03, crude HR = 0.31, 95%CI = 0.11-0.87; adjusted HR = 0.21, 95%CI = 0.06-0.66). The meta-analysis confirmed that efficacy of bevacizumab-based treatment in left-sided mCRC patients was better than the right-sided cases in the overall population (P h = 0.24, combined OR = 1.36, 95%CI = 1.07-1.72), RAS/BRAF wild-type (P h = 0.19, combined OR = 1.66, 95%CI = 1.17-2.34), clinical trial (P h = 0.23, combined OR = 1.42, 95%CI = 1.07-1.88), Caucasian population (P h = 0.18, combined OR = 1.37, 95%CI = 1.02-1.85) and first-line (P h = 0.19, combined OR = 1.48, 95%CI = 1.13-1.96) subgroups. Improved survival of bevacizumab plus chemotherapy treated left-sided mCRC patients was observed in the overall population [P h < 0.01, combined MSR = 1.09, 95%CI = 1.00-1.18 for PFS; P h < 0.01, combined MSR = 1.24, 95%CI = 1.13-1.36 for overall survival (OS)], especially in the RAS/BRAF wild-type (P h = 0.09, combined MSR = 1.10, 95%CI = 1.03-1.19 for PFS; P h = 0.02, combined MSR = 1.34, 95%CI = 1.21-1.49 for OS). These findings indicate that primary tumor sidedness can predict clinical outcome of bevacizumab-treated RAS/BRAF wild-type mCRC patients and the left-sided patients may benefit more from bevacizumab plus FOLFIRI.
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Affiliation(s)
- Xia-Hong You
- Department of Clinical Laboratory, Jiangxi Province Key Laboratory of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Can Wen
- Department of Clinical Laboratory, Jiangxi Cancer Hospital, Nanchang, China
| | - Zi-Jin Xia
- Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Fan Sun
- Department of Clinical Laboratory, Jiangxi Province Key Laboratory of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yao Li
- Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Wei Wang
- Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Zhou Fang
- Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Qing-Gen Chen
- Department of Clinical Laboratory, Jiangxi Province Key Laboratory of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Lei Zhang
- Department of Clinical Laboratory, Jiangxi Province Key Laboratory of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yu-Huang Jiang
- Department of Clinical Laboratory, Jiangxi Province Key Laboratory of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiao-Zhong Wang
- Department of Clinical Laboratory, Jiangxi Province Key Laboratory of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Hou-Qun Ying
- Department of Clinical Laboratory, Jiangxi Province Key Laboratory of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- Department of Nuclear Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhen Zong
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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Ried T, Meijer GA, Harrison DJ, Grech G, Franch-Expósito S, Briffa R, Carvalho B, Camps J. The landscape of genomic copy number alterations in colorectal cancer and their consequences on gene expression levels and disease outcome. Mol Aspects Med 2019; 69:48-61. [PMID: 31365882 DOI: 10.1016/j.mam.2019.07.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/23/2019] [Accepted: 07/26/2019] [Indexed: 12/18/2022]
Abstract
Aneuploidy, the unbalanced state of the chromosome content, represents a hallmark of most solid tumors, including colorectal cancer. Such aneuploidies result in tumor specific genomic imbalances, which emerge in premalignant precursor lesions. Moreover, increasing levels of chromosomal instability have been observed in adenocarcinomas and are maintained in distant metastases. A number of studies have systematically integrated copy number alterations with gene expression changes in primary carcinomas, cell lines, and experimental models of aneuploidy. In fact, chromosomal aneuploidies target a number of genes conferring a selective advantage for the metabolism of the cancer cell. Copy number alterations not only have a positive correlation with expression changes of the majority of genes on the altered genomic segment, but also have effects on the transcriptional levels of genes genome-wide. Finally, copy number alterations have been associated with disease outcome; nevertheless, the translational applicability in clinical practice requires further studies. Here, we (i) review the spectrum of genetic alterations that lead to colorectal cancer, (ii) describe the most frequent copy number alterations at different stages of colorectal carcinogenesis, (iii) exemplify their positive correlation with gene expression levels, and (iv) discuss copy number alterations that are potentially involved in disease outcome of individual patients.
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Affiliation(s)
- Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute/National Institutes of Health, Bethesda, MD, USA.
| | - Gerrit A Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - David J Harrison
- School of Medicine, University of St Andrews, St Andrews, Scotland, UK
| | - Godfrey Grech
- Laboratory of Molecular Pathology, Department of Pathology, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
| | - Sebastià Franch-Expósito
- Gastrointestinal and Pancreatic Oncology Group, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), CIBEREHD, Barcelona, Spain
| | - Romina Briffa
- School of Medicine, University of St Andrews, St Andrews, Scotland, UK; Laboratory of Molecular Pathology, Department of Pathology, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
| | - Beatriz Carvalho
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Jordi Camps
- Gastrointestinal and Pancreatic Oncology Group, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), CIBEREHD, Barcelona, Spain; Unitat de Biologia Cel·lular i Genètica Mèdica, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain.
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TP53 DNA Binding Domain Mutations Predict Progression-Free Survival of Bevacizumab Therapy in Metastatic Colorectal Cancer. Cancers (Basel) 2019; 11:cancers11081079. [PMID: 31366114 PMCID: PMC6721375 DOI: 10.3390/cancers11081079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 07/22/2019] [Accepted: 07/26/2019] [Indexed: 12/21/2022] Open
Abstract
(1) Background: Bevacizumab-based regimens are a standard treatment for metastatic colorectal cancer (mCRC) patients, however meaningful clinical biomarkers for treatment benefit remain scarce. (2) Methods: Tumor samples from 36 mCRC patients treated with bevacizumab-based chemotherapy underwent comprehensive genomic profiling. Alterations in frequently altered genes and important signaling pathways were correlated with progression-free survival (PFS). (3) Results: Overall genetic alteration analysis of investigated genes and pathways did not identify promising new predictors of PFS. However, when considering mutation subtypes, TP53 DNA binding domain (DBD) missense mutations were associated with prolonged PFS (HR, 0.41; 95% CI, 0.13−0.65; p = 0.005). In contrast, TP53 truncating mutations were associated with short PFS (HR, 2.95; 95% CI, 1.45−27.50; p = 0.017). Importantly, neither TP53 mutation subtype was associated with overall response rate. In multivariate analysis, TP53 DBD missense mutations remained an independent PFS predictor (HR, 0.31; 95% CI, 0.13–0.77; p = 0.011). The other genetic factor independently associated with PFS were PTPRT/PTPRD deleterious alterations, which we previously identified in a screen for biomarkers of bevacizumab response. (4) Conclusions: TP53 DBD missense mutations may predict prolonged PFS in mCRC patients treated with bevacizumab-based therapy. Analyses of TP53 mutations as clinical biomarkers should take the biological impact of different mutation subtypes into consideration to improve patient stratification.
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