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Komarova AD, Sinyushkina SD, Shchechkin ID, Druzhkova IN, Smirnova SA, Terekhov VM, Mozherov AM, Ignatova NI, Nikonova EE, Shirshin EA, Shimolina LE, Gamayunov SV, Shcheslavskiy VI, Shirmanova MV. Insights into metabolic heterogeneity of colorectal cancer gained from fluorescence lifetime imaging. eLife 2024; 13:RP94438. [PMID: 39197048 PMCID: PMC11357354 DOI: 10.7554/elife.94438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2024] Open
Abstract
Heterogeneity of tumor metabolism is an important, but still poorly understood aspect of tumor biology. Present work is focused on the visualization and quantification of cellular metabolic heterogeneity of colorectal cancer using fluorescence lifetime imaging (FLIM) of redox cofactor NAD(P)H. FLIM-microscopy of NAD(P)H was performed in vitro in four cancer cell lines (HT29, HCT116, CaCo2 and CT26), in vivo in the four types of colorectal tumors in mice and ex vivo in patients' tumor samples. The dispersion and bimodality of the decay parameters were evaluated to quantify the intercellular metabolic heterogeneity. Our results demonstrate that patients' colorectal tumors have significantly higher heterogeneity of energy metabolism compared with cultured cells and tumor xenografts, which was displayed as a wider and frequently bimodal distribution of a contribution of a free (glycolytic) fraction of NAD(P)H within a sample. Among patients' tumors, the dispersion was larger in the high-grade and early stage ones, without, however, any association with bimodality. These results indicate that cell-level metabolic heterogeneity assessed from NAD(P)H FLIM has a potential to become a clinical prognostic factor.
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Affiliation(s)
- Anastasia D Komarova
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical UniversityNizhny NovgorodRussian Federation
- Institute of Biology and Biomedicine, Lobachevsky State University of Nizhny NovgorodNizhny NovgorodRussian Federation
| | - Snezhana D Sinyushkina
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical UniversityNizhny NovgorodRussian Federation
| | - Ilia D Shchechkin
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical UniversityNizhny NovgorodRussian Federation
- Institute of Biology and Biomedicine, Lobachevsky State University of Nizhny NovgorodNizhny NovgorodRussian Federation
| | - Irina N Druzhkova
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical UniversityNizhny NovgorodRussian Federation
| | - Sofia A Smirnova
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical UniversityNizhny NovgorodRussian Federation
| | - Vitaliy M Terekhov
- Nizhny Novgorod Regional Oncologic HospitalNizhny NovgorodRussian Federation
| | - Artem M Mozherov
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical UniversityNizhny NovgorodRussian Federation
| | - Nadezhda I Ignatova
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical UniversityNizhny NovgorodRussian Federation
| | - Elena E Nikonova
- Laboratory of Clinical Biophotonics, Sechenov First Moscow State Medical UniversityMoscowRussian Federation
| | - Evgeny A Shirshin
- Laboratory of Clinical Biophotonics, Sechenov First Moscow State Medical UniversityMoscowRussian Federation
- Faculty of Physics, Lomonosov Moscow State UniversityMoscowRussian Federation
| | - Liubov E Shimolina
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical UniversityNizhny NovgorodRussian Federation
| | - Sergey V Gamayunov
- Nizhny Novgorod Regional Oncologic HospitalNizhny NovgorodRussian Federation
| | - Vladislav I Shcheslavskiy
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical UniversityNizhny NovgorodRussian Federation
- Becker&Hickl GmbHBerlinGermany
| | - Marina V Shirmanova
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical UniversityNizhny NovgorodRussian Federation
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Liu S, Liu F, Hou X, Zhang Q, Ren Y, Zhu H, Yang Z, Xu X. KRAS Mutation Detection with (2 S,4 R)-4-[ 18F]FGln for Noninvasive PDAC Diagnosis. Mol Pharm 2024; 21:2034-2042. [PMID: 38456403 PMCID: PMC10989612 DOI: 10.1021/acs.molpharmaceut.4c00082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 03/09/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC), which has a poor prognosis and nonspecific symptoms and progresses rapidly, is the most common pancreatic cancer type. Inhibitors targeting KRAS G12D and G12C mutations have been pivotal in PDAC treatment. Cancer cells with different KRAS mutations exhibit various degrees of glutamine dependency; in particular, cells with KRAS G12D mutations exhibit increased glutamine uptake. (2S,4R)-4-[18F]FGln has recently been developed for clinical cancer diagnosis and tumor cell metabolism analysis. Thus, we verified the heterogeneity of glutamine dependency in PDAC models with different KRAS mutations by a visual and noninvasive method with (2S,4R)-4-[18F]FGln. Two tumor-bearing mouse models (bearing the KRAS G12D or G12C mutation) were injected with (2S,4R)-4-[18F]FGln, and positron emission tomography (PET) imaging features and biodistribution were observed and analyzed. The SUVmax in the regions of interest (ROI) was significantly higher in PANC-1 (G12D) tumors than in MIA PaCa-2 (G12C) tumors. Biodistribution analysis revealed higher tumor accumulation of (2S,4R)-4-[18F]FGln and other metrics, such as T/M and T/B, in the PANC-1 mouse models compared to those in the MIAPaCa-2 mouse models. In conclusion, PDAC cells with the KRAS G12D and G12C mutations exhibit various degrees of (2S,4R)-4-[18F]FGln uptake, indicating that (2S,4R)-4-[18F]FGln might be applied to detect KRAS G12C and G12D mutations and provide treatment guidance.
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Affiliation(s)
| | | | - Xingguo Hou
- State Key Laboratory
of Holistic
Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory
of Carcinogenesis and Translational Research, NMPA Key Laboratory
for Research and Evaluation of Radiopharmaceuticals (National Medical
Products Administration), Department of Nuclear Medicine, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Qian Zhang
- State Key Laboratory
of Holistic
Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory
of Carcinogenesis and Translational Research, NMPA Key Laboratory
for Research and Evaluation of Radiopharmaceuticals (National Medical
Products Administration), Department of Nuclear Medicine, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Ya’nan Ren
- State Key Laboratory
of Holistic
Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory
of Carcinogenesis and Translational Research, NMPA Key Laboratory
for Research and Evaluation of Radiopharmaceuticals (National Medical
Products Administration), Department of Nuclear Medicine, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Hua Zhu
- State Key Laboratory
of Holistic
Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory
of Carcinogenesis and Translational Research, NMPA Key Laboratory
for Research and Evaluation of Radiopharmaceuticals (National Medical
Products Administration), Department of Nuclear Medicine, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Zhi Yang
- State Key Laboratory
of Holistic
Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory
of Carcinogenesis and Translational Research, NMPA Key Laboratory
for Research and Evaluation of Radiopharmaceuticals (National Medical
Products Administration), Department of Nuclear Medicine, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Xiaoxia Xu
- State Key Laboratory
of Holistic
Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory
of Carcinogenesis and Translational Research, NMPA Key Laboratory
for Research and Evaluation of Radiopharmaceuticals (National Medical
Products Administration), Department of Nuclear Medicine, Peking University Cancer Hospital & Institute, Beijing 100142, China
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Lee G, Lee SM, Lee S, Jeong CW, Song H, Lee SY, Yun H, Koh Y, Kim HU. Prediction of metabolites associated with somatic mutations in cancers by using genome-scale metabolic models and mutation data. Genome Biol 2024; 25:66. [PMID: 38468344 PMCID: PMC11290261 DOI: 10.1186/s13059-024-03208-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 02/28/2024] [Indexed: 03/13/2024] Open
Abstract
BACKGROUND Oncometabolites, often generated as a result of a gene mutation, show pro-oncogenic function when abnormally accumulated in cancer cells. Identification of such mutation-associated metabolites will facilitate developing treatment strategies for cancers, but is challenging due to the large number of metabolites in a cell and the presence of multiple genes associated with cancer development. RESULTS Here we report the development of a computational workflow that predicts metabolite-gene-pathway sets. Metabolite-gene-pathway sets present metabolites and metabolic pathways significantly associated with specific somatic mutations in cancers. The computational workflow uses both cancer patient-specific genome-scale metabolic models (GEMs) and mutation data to generate metabolite-gene-pathway sets. A GEM is a computational model that predicts reaction fluxes at a genome scale and can be constructed in a cell-specific manner by using omics data. The computational workflow is first validated by comparing the resulting metabolite-gene pairs with multi-omics data (i.e., mutation data, RNA-seq data, and metabolome data) from acute myeloid leukemia and renal cell carcinoma samples collected in this study. The computational workflow is further validated by evaluating the metabolite-gene-pathway sets predicted for 18 cancer types, by using RNA-seq data publicly available, in comparison with the reported studies. Therapeutic potential of the resulting metabolite-gene-pathway sets is also discussed. CONCLUSIONS Validation of the metabolite-gene-pathway set-predicting computational workflow indicates that a decent number of metabolites and metabolic pathways appear to be significantly associated with specific somatic mutations. The computational workflow and the resulting metabolite-gene-pathway sets will help identify novel oncometabolites and also suggest cancer treatment strategies.
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Affiliation(s)
- GaRyoung Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon, 34141, Republic of Korea
| | - Sang Mi Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon, 34141, Republic of Korea
| | - Sungyoung Lee
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, 03080, Republic of Korea
| | - Chang Wook Jeong
- Department of Urology, Seoul National University College of Medicine, and Seoul National University Hospital, Seoul, 03080, Republic of Korea
| | - Hyojin Song
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, 03080, Republic of Korea
| | - Sang Yup Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon, 34141, Republic of Korea
- Graduate School of Engineering Biology, BioProcess Engineering Research Center, and BioInformatics Research Center, KAIST, Daejeon, 34141, Republic of Korea
| | - Hongseok Yun
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, 03080, Republic of Korea.
| | - Youngil Koh
- Department of Internal Medicine, Seoul National University Hospital, Seoul, 03080, Republic of Korea.
| | - Hyun Uk Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon, 34141, Republic of Korea.
- Graduate School of Engineering Biology, BioProcess Engineering Research Center, and BioInformatics Research Center, KAIST, Daejeon, 34141, Republic of Korea.
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Zeissig MN, Ashwood LM, Kondrashova O, Sutherland KD. Next batter up! Targeting cancers with KRAS-G12D mutations. Trends Cancer 2023; 9:955-967. [PMID: 37591766 DOI: 10.1016/j.trecan.2023.07.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/12/2023] [Accepted: 07/18/2023] [Indexed: 08/19/2023]
Abstract
KRAS is the most frequently mutated oncogene in cancer. Activating mutations in codon 12, especially G12D, have the highest prevalence across a range of carcinomas and adenocarcinomas. With inhibitors to KRAS-G12D now entering clinical trials, understanding the biology of KRAS-G12D cancers, and identifying biomarkers that predict therapeutic response is crucial. In this Review, we discuss the genomics and biology of KRAS-G12D adenocarcinomas, including histological features, transcriptional landscape, the immune microenvironment, and how these factors influence response to therapy. Moreover, we explore potential therapeutic strategies using novel G12D inhibitors, leveraging knowledge gained from clinical trials using G12C inhibitors.
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Affiliation(s)
- Mara N Zeissig
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, 3052, Australia
| | - Lauren M Ashwood
- QIMR Berghofer Medical Research Institute, Herston, 4006, Australia; The University of Queensland, Brisbane, 4072, Australia
| | - Olga Kondrashova
- QIMR Berghofer Medical Research Institute, Herston, 4006, Australia; The University of Queensland, Brisbane, 4072, Australia
| | - Kate D Sutherland
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, 3052, Australia.
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Yang S, Yang H, Huang Y, Chen G, Shen C, Zheng S. Serum Metabolomic Signatures of Hirschsprung's Disease Based on GC-MS and LC-MS. J Proteome Res 2023. [PMID: 37235583 DOI: 10.1021/acs.jproteome.3c00008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Hirschsprung's disease (HSCR) is a congenital digestive tract malformation characterized by the absence of intramural ganglion cells in the myenteric and submucosal plexuses along variable lengths of the gastrointestinal tract. Although the improvement of surgical methods has allowed great progress in the treatment of HSCR, its incidence and postoperative prognosis are still not ideal. The pathogenesis of HSCR remains unclear to date. In this study, metabolomic profiling of HSCR serum samples was performed by an integrated analysis of gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-high-resolution tandem mass spectrometry (LC-HRMS/MS) as well as multivariate statistical analyses. Based on the random forest algorithm and receiver operator characteristic analysis, 21 biomarkers related to HSCR were optimized. Several amino acid metabolism pathways were identified as important disordered pathways of HSCR, among which tryptophan metabolism was crucial. To our knowledge, this is the first serum metabolomics study focusing on HSCR, and it provides a new perspective for explaining the mechanism of HSCR.
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Affiliation(s)
- Shaobo Yang
- Department of Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Hong Yang
- Department of Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Yanlei Huang
- Department of Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Gong Chen
- Department of Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Chun Shen
- Department of Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Shan Zheng
- Department of Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
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Burska AN, Ilyassova B, Dildabek A, Khamijan M, Begimbetova D, Molnár F, Sarbassov DD. Enhancing an Oxidative "Trojan Horse" Action of Vitamin C with Arsenic Trioxide for Effective Suppression of KRAS-Mutant Cancers: A Promising Path at the Bedside. Cells 2022; 11:3454. [PMID: 36359850 PMCID: PMC9657932 DOI: 10.3390/cells11213454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/19/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
The turn-on mutations of the KRAS gene, coding a small GTPase coupling growth factor signaling, are contributing to nearly 25% of all human cancers, leading to highly malignant tumors with poor outcomes. Targeting of oncogenic KRAS remains a most challenging task in oncology. Recently, the specific G12C mutant KRAS inhibitors have been developed but with a limited clinical outcome because they acquire drug resistance. Alternatively, exploiting a metabolic breach of KRAS-mutant cancer cells related to a glucose-dependent sensitivity to oxidative stress is becoming a promising indirect cancer targeting approach. Here, we discuss the use of a vitamin C (VC) acting in high dose as an oxidative "Trojan horse" agent for KRAS-mutant cancer cells that can be potentiated with another oxidizing drug arsenic trioxide (ATO) to obtain a potent and selective cytotoxic impact. Moreover, we outline the advantages of VC's non-natural enantiomer, D-VC, because of its distinctive pharmacokinetics and lower toxicity. Thus, the D-VC and ATO combination shows a promising path to treat KRAS-mutant cancers in clinical settings.
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Affiliation(s)
- Agata N. Burska
- Department of Biology, Nazarbayev University, Astana 010000, Kazakhstan
| | | | - Aruzhan Dildabek
- Department of Biology, Nazarbayev University, Astana 010000, Kazakhstan
| | - Medina Khamijan
- Department of Biology, Nazarbayev University, Astana 010000, Kazakhstan
| | - Dinara Begimbetova
- National Laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
| | - Ferdinand Molnár
- Department of Biology, Nazarbayev University, Astana 010000, Kazakhstan
| | - Dos D. Sarbassov
- Department of Biology, Nazarbayev University, Astana 010000, Kazakhstan
- National Laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
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Veeravalli S, Varshavi D, Scott FH, Varshavi D, Pullen FS, Veselkov K, Phillips IR, Everett JR, Shephard EA. Treatment of wild-type mice with 2,3-butanediol, a urinary biomarker of Fmo5 -/- mice, decreases plasma cholesterol and epididymal fat deposition. Front Physiol 2022; 13:859681. [PMID: 36003643 PMCID: PMC9393927 DOI: 10.3389/fphys.2022.859681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/11/2022] [Indexed: 11/25/2022] Open
Abstract
We previously showed that Fmo5 -/- mice exhibit a lean phenotype and slower metabolic ageing. Their characteristics include lower plasma glucose and cholesterol, greater glucose tolerance and insulin sensitivity, and a reduction in age-related weight gain and whole-body fat deposition. In this paper, nuclear magnetic resonance (NMR) spectroscopy-based metabolite analyses of the urine of Fmo5 -/- and wild-type mice identified two isomers of 2,3-butanediol as discriminating urinary biomarkers of Fmo5 -/- mice. Antibiotic-treatment of Fmo5 -/- mice increased plasma cholesterol concentration and substantially reduced urinary excretion of 2,3-butanediol isomers, indicating that the gut microbiome contributed to the lower plasma cholesterol of Fmo5 -/- mice, and that 2,3-butanediol is microbially derived. Short- and long-term treatment of wild-type mice with a 2,3-butanediol isomer mix decreased plasma cholesterol and epididymal fat deposition but had no effect on plasma concentrations of glucose or insulin, or on body weight. In the case of long-term treatment, the effects were maintained after withdrawal of 2,3-butanediol. Short-, but not long-term treatment, also decreased plasma concentrations of triglycerides and non-esterified fatty acids. Fecal transplant from Fmo5 -/- to wild-type mice had no effect on plasma cholesterol, and 2,3-butanediol was not detected in the urine of recipient mice, suggesting that the microbiota of the large intestine was not the source of 2,3-butanediol. However, 2,3-butanediol was detected in the stomach of Fmo5 -/- mice, which was enriched for Lactobacillus genera, known to produce 2,3-butanediol. Our results indicate a microbial contribution to the phenotypic characteristic of Fmo5 -/- mice of decreased plasma cholesterol and identify 2,3-butanediol as a potential agent for lowering plasma cholesterol.
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Affiliation(s)
- Sunil Veeravalli
- Department of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Dorsa Varshavi
- Medway Metabonomics Research Group, University of Greenwich, Chatham Maritime, United Kingdom
| | - Flora H. Scott
- Department of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Dorna Varshavi
- Medway Metabonomics Research Group, University of Greenwich, Chatham Maritime, United Kingdom
| | - Frank S. Pullen
- Medway Metabonomics Research Group, University of Greenwich, Chatham Maritime, United Kingdom
| | - Kirill Veselkov
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Ian R. Phillips
- Department of Structural and Molecular Biology, University College London, London, United Kingdom
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Jeremy R. Everett
- Medway Metabonomics Research Group, University of Greenwich, Chatham Maritime, United Kingdom
| | - Elizabeth A. Shephard
- Department of Structural and Molecular Biology, University College London, London, United Kingdom
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Fakih M, Tu H, Hsu H, Aggarwal S, Chan E, Rehn M, Chia V, Kopetz S. Real-World Study of Characteristics and Treatment Outcomes Among Patients with KRAS p.G12C-Mutated or Other KRAS Mutated Metastatic Colorectal Cancer. Oncologist 2022; 27:663-674. [PMID: 35472176 PMCID: PMC9355827 DOI: 10.1093/oncolo/oyac077] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 03/10/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The KRAS p.G12C mutation has recently become an actionable drug target. To further understand KRAS p.G12C disease, we describe clinicopathologic characteristics, treatment patterns, overall survival (OS), and real-world progression-free survival (rwPFS) in patients with metastatic colorectal cancer (mCRC), KRAS p.G12C mutations (KRAS G12C), and other KRAS mutations (KRAS non-G12C) using a de-identified database. PATIENTS AND METHODS Clinical and tumor characteristics, including treatments received, genomic profile, and clinical outcomes were assessed for patients from a US clinical genomic database with mCRC diagnosed between January 1, 2011, and March 31, 2020, with genomic sequencing data available. RESULTS Of 6477 patients with mCRC (mCRC cohort), 238 (3.7%) had KRAS G12C and 2947 (45.5%) had KRAS non-G12C mutations. Treatment patterns were generally comparable across lines of therapy (LOT) in KRAS G12C versus KRAS non-G12C cohorts. Median (95% CI) OS after the first LOT was 16.1 (13.0-19.0) months for the KRAS G12C cohort versus 18.3 (17.2-19.3) months for the KRAS non-G12C cohort, and 19.2 (18.5-19.8) months for the mCRC overall cohort; median (95% CI) rwPFS was 7.4 (6.3-9.5), 9.0 (8.2-9.7), and 9.2 (8.6-9.7) months, respectively. The different KRAS non-G12C mutations examined did not affect clinical outcomes. Median OS and rwPFS for all cohorts declined with each subsequent LOT. CONCLUSIONS Patients with KRAS p.G12C-mutant mCRC have poor treatment outcomes, and outcomes appear numerically worse than for those without this mutation, indicating potential prognostic implications for KRAS p.G12C mutations and an unmet medical need in this population.
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Affiliation(s)
- Marwan Fakih
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | | | - Hil Hsu
- Amgen Inc., Thousand Oaks, CA, USA
| | | | | | | | | | - Scott Kopetz
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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9
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He SY, Li YC, Wang Y, Peng HL, Zhou CL, Zhang CM, Chen SL, Yin JF, Lin M. Fecal gene detection based on next generation sequencing for colorectal cancer diagnosis. World J Gastroenterol 2022; 28:2920-2936. [PMID: 35978873 PMCID: PMC9280739 DOI: 10.3748/wjg.v28.i25.2920] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 03/18/2022] [Accepted: 05/27/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the most common malignancies worldwide. Given its insidious onset, the condition often already progresses to advanced stage when symptoms occur. Thus, early diagnosis is of great significance for timely clinical intervention, efficacy enhancement, and prognostic improvement. Featuring high throughput, fastness, and rich information, next generation sequencing (NGS) can greatly shorten the detection time, which is a widely used detection technique at present. AIM To screen specific genes or gene combinations in fecal DNA that are suitable for diagnosis and prognostic prediction of CRC, and to establish a technological platform for CRC screening, diagnosis, and efficacy monitoring through fecal DNA detection. METHODS NGS was used to sequence the stool DNA of patients with CRC, which were then compared with the genetic testing results of the stool samples of normal controls and patients with benign intestinal disease, as well as the tumor tissues of CRC patients. Specific genes or gene combinations in fecal DNA suitable for diagnosis and prognostic prediction of CRC were screened, and their significances in diagnosing CRC and predicting patients' prognosis were comprehensively evaluated. RESULTS High mutation frequencies of TP53, APC, and KRAS were detected in the stools and tumor tissues of CRC patients prior to surgery. Contrastively, no pathogenic mutations of the above three genes were noted in the postoperative stools, the normal controls, or the benign intestinal disease group. This indicates that tumor-specific DNA was detectable in the preoperative stools of CRC patients. The preoperative fecal expression of tumor-associated genes can reflect the gene mutations in tumor tissues to some extent. Compared to the postoperative stools and the stools in the two control groups, the pathogenic mutation frequencies of TP53 and KRAS were significantly higher for the preoperative stools (χ 2 = 7.328, P < 0.05; χ 2 = 4.219, P < 0.05), suggesting that fecal TP53 and KRAS genes can be used for CRC screening, diagnosis, and prognostic prediction. No significant difference in the pathogenic mutation frequency of the APC gene was found from the postoperative stools or the two control groups (χ 2 = 0.878, P > 0.05), so further analysis with larger sample size is required. Among CRC patients, the pathogenic mutation sites of TP53 occurred in 16 of 27 preoperative stools, with a true positive rate of 59.26%, while the pathogenic mutation sites of KRAS occurred in 10 stools, with a true positive rate of 37.04%. The sensitivity and negative predictive values of the combined genetic testing of TP53 and KRAS were 66.67% (18/27) and 68.97%, respectively, both of which were higher than those of TP53 or KRAS mutation detection alone, suggesting that the combined genetic testing can improve the CRC detection rate. The mutation sites TP53 exon 4 A84G and EGFR exon 20 I821T (mutation start and stop positions were both 7579436 for the former, while 55249164 for the latter) were found in the preoperative stools and tumor tissues. These "undetected" mutation sites may be new types of mutations occurring during the CRC carcinogenesis and progression, which needs to be confirmed through further research. Some mutations of "unknown clinical significance" were found in such genes as TP53, PTEN, KRAS, BRAF, AKT1, and PIK3CA, whose clinical values is worthy of further exploration. CONCLUSION NGS-based fecal genetic testing can be used as a complementary technique for the CRC diagnosis. Fecal TP53 and KRAS can be used as specific genes for the screening, diagnosis, prognostic prediction, and recurrence monitoring of CRC. Moreover, the combined testing of TP53 and KRAS genes can improve the CRC detection rate.
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Affiliation(s)
- Si-Yu He
- Department of Clinical Laboratory, Taizhou People's Hospital (Postgraduate Training Base of Dalian Medical University), Taizhou 225300, Jiangsu Province, China
- Department of Clinical Laboratory, The First People's Hospital of Tianmen City, Tianmen 431700, Hubei Province, China
| | - Ying-Chun Li
- Department of General Surgery, Taizhou People's Hospital (Postgraduate Training Base of Dalian Medical University), Taizhou 225300, Jiangsu Province, China
| | - Yong Wang
- Department of General Surgery, Taizhou People's Hospital (Postgraduate Training Base of Dalian Medical University), Taizhou 225300, Jiangsu Province, China
| | - Hai-Lin Peng
- Department of Clinical Laboratory, Taizhou People's Hospital (Postgraduate Training Base of Dalian Medical University), Taizhou 225300, Jiangsu Province, China
| | - Cheng-Lin Zhou
- Department of Clinical Laboratory, Taizhou People's Hospital (Postgraduate Training Base of Dalian Medical University), Taizhou 225300, Jiangsu Province, China
| | - Chuan-Meng Zhang
- Central Laboratory, Taizhou People's Hospital (Postgraduate training base of Dalian Medical University), Taizhou 225300, Jiangsu Province, China
| | - Sheng-Lan Chen
- Department of Laboratory, Taizhou Genewill Medical Laboratory Company Limited, Taizhou 225300, Jiangsu Province, China
| | - Jian-Feng Yin
- Department of Laboratory, Jiangsu CoWin Biotech Co., Ltd., Taizhou 225300, Jiangsu Province, China
| | - Mei Lin
- Department of Clinical Laboratory, Taizhou People's Hospital (Postgraduate Training Base of Dalian Medical University), Taizhou 225300, Jiangsu Province, China
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10
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Daily Practice Assessment of KRAS Status in NSCLC Patients: A New Challenge for the Thoracic Pathologist Is Right around the Corner. Cancers (Basel) 2022; 14:cancers14071628. [PMID: 35406400 PMCID: PMC8996900 DOI: 10.3390/cancers14071628] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 12/16/2022] Open
Abstract
Simple Summary RAS mutation is the most frequent oncogenic alteration in human cancers and KRAS is the most frequently mutated, notably in non-small cell lung carcinomas (NSCLC). Various attempts to inhibit KRAS in the past were unsuccessful in these latter tumors. However, recently, several small molecules (AMG510, MRTX849, JNJ-74699157, and LY3499446) have been developed to specifically target KRAS G12C-mutated tumors, which seems promising for patient treatment and should soon be administered in daily practice for non-squamous (NS)-NSCLC. In this context, it will be mandatory to systematically assess the KRAS status in routine clinical practice, at least in advanced NS-NSCLC, leading to new challenges for thoracic oncologists. Abstract KRAS mutations are among the most frequent genomic alterations identified in non-squamous non-small cell lung carcinomas (NS-NSCLC), notably in lung adenocarcinomas. In most cases, these mutations are mutually exclusive, with different genomic alterations currently known to be sensitive to therapies targeting EGFR, ALK, BRAF, ROS1, and NTRK. Recently, several promising clinical trials targeting KRAS mutations, particularly for KRAS G12C-mutated NSCLC, have established new hope for better treatment of patients. In parallel, other studies have shown that NSCLC harboring co-mutations in KRAS and STK11 or KEAP1 have demonstrated primary resistance to immune checkpoint inhibitors. Thus, the assessment of the KRAS status in advanced-stage NS-NSCLC has become essential to setting up an optimal therapeutic strategy in these patients. This stimulated the development of new algorithms for the management of NSCLC samples in pathology laboratories and conditioned reorganization of optimal health care of lung cancer patients by the thoracic pathologists. This review addresses the recent data concerning the detection of KRAS mutations in NSCLC and focuses on the new challenges facing pathologists in daily practice for KRAS status assessment.
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van 't Erve I, Wesdorp NJ, Medina JE, Ferreira L, Leal A, Huiskens J, Bolhuis K, van Waesberghe JHTM, Swijnenburg RJ, van den Broek D, Velculescu VE, Kazemier G, Punt CJA, Meijer GA, Fijneman RJA. KRAS A146 Mutations Are Associated With Distinct Clinical Behavior in Patients With Colorectal Liver Metastases. JCO Precis Oncol 2021; 5:PO.21.00223. [PMID: 34820593 PMCID: PMC8608264 DOI: 10.1200/po.21.00223] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/23/2021] [Accepted: 10/13/2021] [Indexed: 12/11/2022] Open
Abstract
Somatic KRAS mutations occur in approximately half of the patients with metastatic colorectal cancer (mCRC). Biologic tumor characteristics differ on the basis of the KRAS mutation variant. KRAS mutations are known to influence patient prognosis and are used as predictive biomarker for treatment decisions. This study examined clinical features of patients with mCRC with a somatic mutation in KRAS G12, G13, Q61, K117, or A146. Patients with mCRC and a KRAS A146 mutation are characterized by high tumor burden and poor prognosis![]()
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Affiliation(s)
- Iris van 't Erve
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Nina J Wesdorp
- Deparment of Surgery, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University, Amsterdam, the Netherlands
| | - Jamie E Medina
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Leonardo Ferreira
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Alessandro Leal
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD.,Center for Personalized Medicine, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | | | - Karen Bolhuis
- Department of Medical Oncology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
| | - Jan-Hein T M van Waesberghe
- Deparment of Radiology and Molecular Imaging, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University, Amsterdam, the Netherlands
| | - Rutger-Jan Swijnenburg
- Deparment of Surgery, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University, Amsterdam, the Netherlands
| | - Daan van den Broek
- Department for Laboratory Medicine, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Victor E Velculescu
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Geert Kazemier
- Deparment of Surgery, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University, Amsterdam, the Netherlands
| | - Cornelis J A Punt
- Department of Medical Oncology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands.,Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Gerrit A Meijer
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Remond J A Fijneman
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
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12
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Varshavi D, Varshavi D, McCarthy N, Veselkov K, Keun HC, Everett JR. Metabonomics study of the effects of single copy mutant KRAS in the presence or absence of WT allele using human HCT116 isogenic cell lines. Metabolomics 2021; 17:104. [PMID: 34822010 PMCID: PMC8616861 DOI: 10.1007/s11306-021-01852-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/31/2021] [Indexed: 12/02/2022]
Abstract
INTRODUCTION KRAS was one of the earliest human oncogenes to be described and is one of the most commonly mutated genes in different human cancers, including colorectal cancer. Despite KRAS mutants being known driver mutations, KRAS has proved difficult to target therapeutically, necessitating a comprehensive understanding of the molecular mechanisms underlying KRAS-driven cellular transformation. OBJECTIVES To investigate the metabolic signatures associated with single copy mutant KRAS in isogenic human colorectal cancer cells and to determine what metabolic pathways are affected. METHODS Using NMR-based metabonomics, we compared wildtype (WT)-KRAS and mutant KRAS effects on cancer cell metabolism using metabolic profiling of the parental KRAS G13D/+ HCT116 cell line and its isogenic, derivative cell lines KRAS +/- and KRAS G13D/-. RESULTS Mutation in the KRAS oncogene leads to a general metabolic remodelling to sustain growth and counter stress, including alterations in the metabolism of amino acids and enhanced glutathione biosynthesis. Additionally, we show that KRASG13D/+ and KRASG13D/- cells have a distinct metabolic profile characterized by dysregulation of TCA cycle, up-regulation of glycolysis and glutathione metabolism pathway as well as increased glutamine uptake and acetate utilization. CONCLUSIONS Our study showed the effect of a single point mutation in one KRAS allele and KRAS allele loss in an isogenic genetic background, hence avoiding confounding genetic factors. Metabolic differences among different KRAS mutations might play a role in their different responses to anticancer treatments and hence could be exploited as novel metabolic vulnerabilities to develop more effective therapies against oncogenic KRAS.
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Affiliation(s)
- Dorna Varshavi
- Medway Metabonomics Research Group, University of Greenwich, Chatham Maritime, ME4 4TB, Kent, UK
- Department of Biological Sciences, University of Alberta, 116 Street & 85 Ave, Edmonton, AB, T6G 2R3, Canada
| | - Dorsa Varshavi
- Medway Metabonomics Research Group, University of Greenwich, Chatham Maritime, ME4 4TB, Kent, UK
- Department of Biological Sciences, University of Alberta, 116 Street & 85 Ave, Edmonton, AB, T6G 2R3, Canada
| | - Nicola McCarthy
- Horizon Discovery Ltd., Cambridge Research Park, 8100 Beach Dr, Waterbeach, Cambridge, CB25 9TL, UK
- Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Kirill Veselkov
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College, London, SW7 2AZ, UK
| | - Hector C Keun
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, W12 ONN, UK
| | - Jeremy R Everett
- Medway Metabonomics Research Group, University of Greenwich, Chatham Maritime, ME4 4TB, Kent, UK.
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13
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Giampieri R, Lupi A, Ziranu P, Bittoni A, Pretta A, Pecci F, Persano M, Giglio E, Copparoni C, Crocetti S, Mandolesi A, Faa G, Coni P, Scartozzi M, Berardi R. Retrospective Comparative Analysis of KRAS G12C vs. Other KRAS Mutations in mCRC Patients Treated With First-Line Chemotherapy Doublet + Bevacizumab. Front Oncol 2021; 11:736104. [PMID: 34660299 PMCID: PMC8514824 DOI: 10.3389/fonc.2021.736104] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 09/09/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND KRAS mutations in metastatic colorectal cancer (mCRC) define a subset of tumors that have primary resistance to anti-EGFR-based therapy. Data concerning whether different KRAS mutations may also have a prognostic value are lacking. Furthermore, novel KRAS G12C inhibitors are currently in development. The aim of our analysis was to compare response rates in patients treated with first-line chemotherapy doublet + Bevacizumab among different KRAS variants. Secondary end-points were progression free survival (PFS) and overall survival (OS). METHODS Patients with KRAS mutated mCRC treated with either FOLFIRI/FOLFOX/XELOX + Bevacizumab were eligible for enrollment. Patients whose tumor harbored NRAS mutations or that coexpressed also BRAF mutations were excluded from this retrospective analysis. Patients' individual data were collected from patients' records. Propensity score matching (nearest method, 1:2 ratio) was used to define the two different groups of patients for comparison (KRAS G12C mutated vs other KRAS variants). Eastern Cooperative Oncology Group Performance Status (ECOG PS), sex, metastatic site of involvement, synchronous vs metachronous metastatic disease, tumor sidedness, mucinous histology, primary tumor surgery, more than two lines of treatment for metastatic disease, and radical surgery of metastases were used as matching factors. Response rate (RR) was calculated by RECIST 1.1 criteria. Both progression free-survival and overall survival were calculated by Kaplan-Meier method. Categorical variables were compared by Fisher exact test for binomial variables and by chi-square test for all other instances. The level of statistical significance p was set at 0.05 for all tests. RESULTS A total of 120 patients were assessed in the final analysis. Out of the 120 patients, 15 (12%) were KRAS G12C mutated. In the whole cohort of patients, 59/120 (49%) had partial response (PR), 42/120 (35%) had stable disease (SD), and 19/120 (16%) had progressive disease (PD) as the best response. In KRAS G12C patients, 4/15 (27%) had PR, 6/15 (40%) had SD, and the remaining 5/15 (33%) had PD as the best response. In patients with other KRAS mutations, 55/105 (52%) had PR, 37/105 (35%) had SD, and the remaining 13/105 (12%) had PD as the best response. The difference in RR between the two groups of patients was statistically significant (p=0.017). On the other hand, no difference in PFS (p=0.76) and OS (p=0.56) was observed. After matching procedures, the difference in response rates between KRAS G12C mutated patients vs the matched cohort of patients with other KRAS mutations remained statistically significant (p=0.016). KRAS G12C mutations were not associated with differences in sites of metastatic involvement, sex, and ECOG PS. On the other hand, synchronous vs metachronous metastatic disease (p=0.039), age > 75 years (p=0.043), and mucinous histology (p=0.008) were more frequent in G12C mutated tumors. CONCLUSIONS In our cohort of patients, it was observed that KRAS G12C mutations are associated with worse response rates compared to other KRAS variants when treated with standard chemotherapy doublet + Bevacizumab. On the other hand, both PFS and OS were not significantly different. Based on these findings, we believe that new treatment options focused on KRAS G12C inhibition should be tested mainly in first-line setting and in addition to standard chemotherapy doublet + Bevacizumab for mCRC patients, as they might "fill the gap" in response rates that was seen in our study.
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Affiliation(s)
- Riccardo Giampieri
- Clinica Oncologica—Dipartimento Scienze Cliniche e Molecolari—Università Politecnica delle Marche, Ancona, Italy
- Clinica Oncologica—Azienda Ospedaliera Universitaria Ospedali Riuniti di Ancona, Ancona, Italy
| | - Alessio Lupi
- Clinica Oncologica—Dipartimento Scienze Cliniche e Molecolari—Università Politecnica delle Marche, Ancona, Italy
| | - Pina Ziranu
- Oncologia, Università ed Azienda Ospedaliera Universitaria di Cagliari, Cagliari, Italy
| | - Alessandro Bittoni
- Clinica Oncologica—Azienda Ospedaliera Universitaria Ospedali Riuniti di Ancona, Ancona, Italy
| | - Andrea Pretta
- Oncologia, Università ed Azienda Ospedaliera Universitaria di Cagliari, Cagliari, Italy
- Oncologia Medica, Università “la Sapienza” di Roma, Rome, Italy
| | - Federica Pecci
- Clinica Oncologica—Dipartimento Scienze Cliniche e Molecolari—Università Politecnica delle Marche, Ancona, Italy
| | - Mara Persano
- Oncologia, Università ed Azienda Ospedaliera Universitaria di Cagliari, Cagliari, Italy
| | - Enrica Giglio
- Clinica Oncologica—Dipartimento Scienze Cliniche e Molecolari—Università Politecnica delle Marche, Ancona, Italy
| | - Cecilia Copparoni
- Clinica Oncologica—Dipartimento Scienze Cliniche e Molecolari—Università Politecnica delle Marche, Ancona, Italy
| | - Sonia Crocetti
- Clinica Oncologica—Dipartimento Scienze Cliniche e Molecolari—Università Politecnica delle Marche, Ancona, Italy
| | - Alessandra Mandolesi
- Anatomia Patologica—Azienda Ospedaliera Universitaria Ospedali Riuniti di Ancona, Ancona, Italy
| | - Gavino Faa
- Anatomia Patologica—Dipartimento di Scienze Mediche e Sanità Pubblica—Università di Cagliari, Cagliari, Italy
| | - Pierpaolo Coni
- Anatomia Patologica—Dipartimento di Scienze Mediche e Sanità Pubblica—Università di Cagliari, Cagliari, Italy
| | - Mario Scartozzi
- Oncologia, Università ed Azienda Ospedaliera Universitaria di Cagliari, Cagliari, Italy
| | - Rossana Berardi
- Clinica Oncologica—Dipartimento Scienze Cliniche e Molecolari—Università Politecnica delle Marche, Ancona, Italy
- Clinica Oncologica—Azienda Ospedaliera Universitaria Ospedali Riuniti di Ancona, Ancona, Italy
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14
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Plekhova V, De Paepe E, Van Renterghem K, Van Winckel M, Hemeryck LY, Vanhaecke L. Disparities in the gut metabolome of post-operative Hirschsprung's disease patients. Sci Rep 2021; 11:16167. [PMID: 34373532 PMCID: PMC8352975 DOI: 10.1038/s41598-021-95589-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/19/2021] [Indexed: 10/26/2022] Open
Abstract
Hirschsprung's disease (HD) is a congenital structural abnormality of the colon seen in approximately 1 to 5000 live births. Despite surgical correction shortly after presentation, up to 60% of patients will express long-term gastrointestinal complaints, including potentially life-threatening Hirschsprung-associated enterocolitis (HAEC). In this study fecal samples from postoperative HD patients (n = 38) and their healthy siblings (n = 21) were analysed using high-resolution liquid chromatography-mass spectrometry aiming to further unravel the nature of the chronic gastrointestinal disturbances. Furthermore, within the patient group, we compared the faecal metabolome between patients with and without a history of HAEC as well as those diagnosed with short or long aganglionic segment. Targeted analysis identified several individual metabolites characteristic for all HD patients as well as those with a history of HAEC and long segment HD. Moreover, multivariate models based on untargeted data established statistically significant (p < 0.05) differences in comprehensive faecal metabolome in the patients' cohort as a whole and in patients with a history of HAEC. Pathway analysis revealed the most impact on amino sugar, lysine, sialic acid, hyaluronan and heparan sulphate metabolism in HD, as well as impaired tyrosine metabolism in HAEC group. Those changes imply disruption of intestinal mucosal barrier due to glycosaminoglycan breakdown and dysbiosis as major metabolic changes in patients' group and should be further explored for potential diagnostic or treatment targets.
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Affiliation(s)
- Vera Plekhova
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Ellen De Paepe
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Katrien Van Renterghem
- Department of Pediatric Surgery, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Myriam Van Winckel
- Department of Pediatrics and Medical Genetics, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Lieselot Y Hemeryck
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Lynn Vanhaecke
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium.
- School of Biological Sciences, Queen's University Belfast, Belfast, UK.
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15
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Common and mutation specific phenotypes of KRAS and BRAF mutations in colorectal cancer cells revealed by integrative -omics analysis. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:225. [PMID: 34233735 PMCID: PMC8265010 DOI: 10.1186/s13046-021-02025-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/18/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Genes in the Ras pathway have somatic mutations in at least 60 % of colorectal cancers. Despite activating the same pathway, the BRAF V600E mutation and the prevalent mutations in codon 12 and 13 of KRAS have all been linked to different clinical outcomes, but the molecular mechanisms behind these differences largely remain to be clarified. METHODS To characterize the similarities and differences between common activating KRAS mutations and between KRAS and BRAF mutations, we used genome editing to engineer KRAS G12C/D/V and G13D mutations in colorectal cancer cells that had their mutant BRAF V600E allele removed and subjected them to transcriptome sequencing, global proteomics and metabolomics analyses. RESULTS By intersecting differentially expressed genes, proteins and metabolites, we uncovered (i) two-fold more regulated genes and proteins when comparing KRAS to BRAF mutant cells to those lacking Ras pathway mutation, (ii) five differentially expressed proteins in KRAS mutants compared to cells lacking Ras pathway mutation (IFI16, S100A10, CD44, GLRX and AHNAK2) and 6 (CRABP2, FLNA, NXN, LCP1, S100A10 and S100A2) compared to BRAF mutant cells, (iii) 19 proteins expressed differentially in a KRAS mutation specific manner versus BRAF V600E cells, (iv) regulation of the Integrin Linked Kinase pathway by KRAS but not BRAF mutation, (v) regulation of amino acid metabolism, particularly of the tyrosine, histidine, arginine and proline pathways, the urea cycle and purine metabolism by Ras pathway mutations, (vi) increased free carnitine in KRAS and BRAF mutant RKO cells. CONCLUSIONS This comprehensive integrative -omics analysis confirms known and adds novel genes, proteins and metabolic pathways regulated by mutant KRAS and BRAF signaling in colorectal cancer. The results from the new model systems presented here can inform future development of diagnostic and therapeutic approaches targeting tumors with KRAS and BRAF mutations.
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16
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László L, Kurilla A, Takács T, Kudlik G, Koprivanacz K, Buday L, Vas V. Recent Updates on the Significance of KRAS Mutations in Colorectal Cancer Biology. Cells 2021; 10:667. [PMID: 33802849 PMCID: PMC8002639 DOI: 10.3390/cells10030667] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/03/2021] [Accepted: 03/10/2021] [Indexed: 12/17/2022] Open
Abstract
The most commonly mutated isoform of RAS among all cancer subtypes is KRAS. In this review, we focus on the special role of KRAS mutations in colorectal cancer (CRC), aiming to collect recent data on KRAS-driven enhanced cell signalling, in vitro and in vivo research models, and CRC development-related processes such as metastasis and cancer stem cell formation. We attempt to cover the diverse nature of the effects of KRAS mutations on age-related CRC development. As the incidence of CRC is rising in young adults, we have reviewed the driving forces of ageing-dependent CRC.
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Affiliation(s)
- Loretta László
- Research Centre for Natural Sciences, Institute of Enzymology, 1051 Budapest, Hungary; (L.L.); (A.K.); (T.T.); (G.K.); (K.K.); (L.B.)
| | - Anita Kurilla
- Research Centre for Natural Sciences, Institute of Enzymology, 1051 Budapest, Hungary; (L.L.); (A.K.); (T.T.); (G.K.); (K.K.); (L.B.)
| | - Tamás Takács
- Research Centre for Natural Sciences, Institute of Enzymology, 1051 Budapest, Hungary; (L.L.); (A.K.); (T.T.); (G.K.); (K.K.); (L.B.)
| | - Gyöngyi Kudlik
- Research Centre for Natural Sciences, Institute of Enzymology, 1051 Budapest, Hungary; (L.L.); (A.K.); (T.T.); (G.K.); (K.K.); (L.B.)
| | - Kitti Koprivanacz
- Research Centre for Natural Sciences, Institute of Enzymology, 1051 Budapest, Hungary; (L.L.); (A.K.); (T.T.); (G.K.); (K.K.); (L.B.)
| | - László Buday
- Research Centre for Natural Sciences, Institute of Enzymology, 1051 Budapest, Hungary; (L.L.); (A.K.); (T.T.); (G.K.); (K.K.); (L.B.)
- Department of Medical Chemistry, Semmelweis University Medical School, 1071 Budapest, Hungary
| | - Virag Vas
- Research Centre for Natural Sciences, Institute of Enzymology, 1051 Budapest, Hungary; (L.L.); (A.K.); (T.T.); (G.K.); (K.K.); (L.B.)
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17
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Ricciardiello F, Bergamaschi L, De Vitto H, Gang Y, Zhang T, Palorini R, Chiaradonna F. Suppression of the HBP Function Increases Pancreatic Cancer Cell Sensitivity to a Pan-RAS Inhibitor. Cells 2021; 10:cells10020431. [PMID: 33670598 PMCID: PMC7923121 DOI: 10.3390/cells10020431] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/05/2021] [Accepted: 02/14/2021] [Indexed: 12/13/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a leading cause of cancer-related death and the search for a resolutive therapy is still a challenge. Since KRAS is commonly mutated in PDAC and is one of the main drivers of PDAC progression, its inhibition should be a key strategy for treatment, especially considering the recent development of specific KRAS inhibitors. Nevertheless, the effects of KRAS inhibition can be increased through the co-inhibition of other nodes important for cancer development. One of them could be the hexosamine biosynthetic pathway (HBP), whose enhancement is considered fundamental for PDAC. Here, we demonstrate that PDAC cells expressing oncogenic KRAS, owing to an increase in the HBP flux, become strongly reliant on HBP for both proliferation and survival. In particular, upon treatment with two different compounds, 2-deoxyglucose and FR054, inhibiting both HBP and protein N-glycosylation, these cells undergo apoptosis significantly more than PDAC cells expressing wild-type KRAS. Importantly, we also show that the combined treatment between FR054 and the pan-RAS inhibitor BI-2852 has an additive negative effect on cell proliferation and survival by means of the suppression of both Akt activity and cyclin D1 expression. Thus, co-inhibition of HBP and oncogenic RAS may represent a novel therapy for PDAC patients.
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Affiliation(s)
- Francesca Ricciardiello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy; (F.R.); (L.B.); (H.D.V.)
| | - Laura Bergamaschi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy; (F.R.); (L.B.); (H.D.V.)
| | - Humberto De Vitto
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy; (F.R.); (L.B.); (H.D.V.)
| | - Yang Gang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China; (Y.G.); (T.Z.)
| | - Taiping Zhang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China; (Y.G.); (T.Z.)
| | - Roberta Palorini
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy; (F.R.); (L.B.); (H.D.V.)
- Correspondence: (R.P.); (F.C.)
| | - Ferdinando Chiaradonna
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy; (F.R.); (L.B.); (H.D.V.)
- Correspondence: (R.P.); (F.C.)
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