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Martins F, Machado AL, Ribeiro A, Oliveira SM, Carvalho J, Matthiesen R, Backman V, Velho S. KRAS silencing alters chromatin physical organization and transcriptional activity in colorectal cancer cells. Res Sq 2024:rs.3.rs-3752760. [PMID: 38410476 PMCID: PMC10896403 DOI: 10.21203/rs.3.rs-3752760/v2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Clinical data revealed that KRAS mutant tumors, while initially sensitive to treatment, rapidly bypass KRAS dependence to acquire a drug-tolerant phenotype. However, the mechanisms underlying the transition from a drug-sensitive to a drug-tolerant state still elude us. Here, we show that global chromatin reorganization is a recurrent and specific feature of KRAS-dependent cells that tolerated KRAS silencing. We show that KRAS-dependent cells undergo G0/G1 cell cycle arrest after KRAS silencing, presenting a transcriptomic signature of quiescence. Proteomic analysis showed upregulated chromatin-associated proteins and transcription-associated biological processes. Accordingly, these cells shifted euchromatin/heterochromatin states, gained topologically associating domains, and altered the nanoscale physical organization of chromatin, more precisely by downregulating chromatin packing domains, a feature associated with the induction of quiescence. In addition, they also accumulated transcriptional alterations over time leading to a diversification of biological processes, linking chromatin alterations to transcriptional performance. Overall, our observations pinpoint a novel molecular mechanism of tolerance to KRAS oncogenic loss driven not by specific gene alterations but by global reorganization of genomic information, in which cells transition chromatin domain structure towards a more quiescent state and gain transcriptional reprogramming capacity.
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Affiliation(s)
| | | | | | | | | | | | | | - Sérgia Velho
- i3S - Institute for Research and Innovation in Health
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2
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Tan YQ, Sun B, Zhang X, Zhang S, Guo H, Basappa B, Zhu T, Sethi G, Lobie PE, Pandey V. Concurrent inhibition of pBADS99 synergistically improves MEK inhibitor efficacy in KRAS G12D-mutant pancreatic ductal adenocarcinoma. Cell Death Dis 2024; 15:173. [PMID: 38409090 PMCID: PMC10897366 DOI: 10.1038/s41419-024-06551-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/28/2024]
Abstract
Therapeutic targeting of KRAS-mutant pancreatic ductal adenocarcinoma (PDAC) has remained a significant challenge in clinical oncology. Direct targeting of KRAS has proven difficult, and inhibition of the KRAS effectors have shown limited success due to compensatory activation of survival pathways. Being a core downstream effector of the KRAS-driven p44/42 MAPK and PI3K/AKT pathways governing intrinsic apoptosis, BAD phosphorylation emerges as a promising therapeutic target. Herein, a positive association of the pBADS99/BAD ratio with higher disease stage and worse overall survival of PDAC was observed. Homology-directed repair of BAD to BADS99A or small molecule inhibition of BADS99 phosphorylation by NCK significantly reduced PDAC cell viability by promoting cell cycle arrest and apoptosis. NCK also abrogated the growth of preformed colonies of PDAC cells in 3D culture. Furthermore, high-throughput screening with an oncology drug library to identify potential combinations revealed a strong synergistic effect between NCK and MEK inhibitors in PDAC cells harboring either wild-type or mutant-KRAS. Mechanistically, both mutant-KRAS and MEK inhibition increased the phosphorylation of BADS99 in PDAC cells, an effect abrogated by NCK. Combined pBADS99-MEK inhibition demonstrated strong synergy in reducing cell viability, enhancing apoptosis, and achieving xenograft stasis in KRAS-mutant PDAC. In conclusion, the inhibition of BADS99 phosphorylation enhances the efficacy of MEK inhibition, and their combined inhibition represents a mechanistically based and potentially effective therapeutic strategy for the treatment of KRAS-mutant PDAC.
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Affiliation(s)
- Yan Qin Tan
- Institute of Biopharmaceutical and Health Engineering and Tsinghua Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, People's Republic of China
- Food Science and Technology Program, Department of Life Sciences, BNU-HKBU United International College, Zhuhai, 519087, Guangdong, People's Republic of China
| | - Bowen Sun
- Institute of Biopharmaceutical and Health Engineering and Tsinghua Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, People's Republic of China
| | - Xi Zhang
- Institute of Biopharmaceutical and Health Engineering and Tsinghua Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, People's Republic of China
- Shenzhen Bay Laboratory, Shenzhen, 518055, Guangdong, People's Republic of China
| | - Shuwei Zhang
- Institute of Biopharmaceutical and Health Engineering and Tsinghua Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, People's Republic of China
| | - Hui Guo
- Institute of Biopharmaceutical and Health Engineering and Tsinghua Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, People's Republic of China
| | - Basappa Basappa
- Laboratory of Chemical Biology, Department of Studies in Organic Chemistry, University of Mysore, Manasagangotri, 570006, Mysore, India
| | - Tao Zhu
- Shenzhen Bay Laboratory, Shenzhen, 518055, Guangdong, People's Republic of China
- Department of Oncology, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, People's Republic of China
- Hefei National Laboratory for Physical Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, People's Republic of China
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117600, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
| | - Peter E Lobie
- Institute of Biopharmaceutical and Health Engineering and Tsinghua Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, People's Republic of China.
- Shenzhen Bay Laboratory, Shenzhen, 518055, Guangdong, People's Republic of China.
| | - Vijay Pandey
- Institute of Biopharmaceutical and Health Engineering and Tsinghua Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, People's Republic of China.
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3
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Weisman CM. The permissive binding theory of cancer. Front Oncol 2023; 13:1272981. [PMID: 38023252 PMCID: PMC10666763 DOI: 10.3389/fonc.2023.1272981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
The later stages of cancer, including the invasion and colonization of new tissues, are actively mysterious compared to earlier stages like primary tumor formation. While we lack many details about both, we do have an apparently successful explanatory framework for the earlier stages: one in which genetic mutations hold ultimate causal and explanatory power. By contrast, on both empirical and conceptual grounds, it is not currently clear that mutations alone can explain the later stages of cancer. Can a different type of molecular change do better? Here, I introduce the "permissive binding theory" of cancer, which proposes that novel protein binding interactions are the key causal and explanatory entity in invasion and metastasis. It posits that binding is more abundant at baseline than we observe because it is restricted in normal physiology; that any large perturbation to physiological state revives this baseline abundance, unleashing many new binding interactions; and that a subset of these cause the cellular functions at the heart of oncogenesis, especially invasion and metastasis. Significant physiological perturbations occur in cancer cells in very early stages, and generally become more extreme with progression, providing interactions that continually fuel invasion and metastasis. The theory is compatible with, but not limited to, causal roles for the diverse molecular changes observed in cancer (e.g. gene expression or epigenetic changes), as these generally act causally upstream of proteins, and so may exert their effects by changing the protein binding interactions that occur in the cell. This admits the possibility that molecular changes that appear quite different may actually converge in creating the same few protein complexes, simplifying our picture of invasion and metastasis. If correct, the theory offers a concrete therapeutic strategy: targeting the key novel complexes. The theory is straightforwardly testable by large-scale identification of protein interactions in different cancers.
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Affiliation(s)
- Caroline M. Weisman
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, United States
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4
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DAL Z, ARU B. The role of curcumin on apoptosis and NLRP3 inflammasome-dependent pyroptosis on colorectal cancer in vitro. Turk J Med Sci 2023; 53:883-893. [PMID: 38031951 PMCID: PMC10760590 DOI: 10.55730/1300-0144.5652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 08/18/2023] [Accepted: 03/27/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the most common cancers worldwide. Many factors such as stress, lifestyle, and dietary habits are known to play a role in the initiation and progression of the disease. Herbal therapeutic agents including curcumin can hold a great potential against cancer treatment; however, their efficacy on CRC is still under investigation. Herein, we evaluated the anticancer mechanism of curcumin on four different CRC cell lines. METHODS Cells were treated with curcumin for 24, 48 and 72 h, and IC50 doses for each cell line were calculated. Mechanistic studies were conducted with the lowest IC50 dose determined for each cell line by evaluating apoptosis and necrosis, cell division, and NLRP3-mediated pyroptosis. RESULTS Curcumin treatment significantly decreased viability while increasing the SubG1 phase in all cell lines tested, indicating apoptosis is the main programmed cell death pathway activated upon curcumin treatment in CRC. In terms of pyroptosis, components of NLRP3 inflammasome were found to be elevated in SW480 and HCT116 cell lines, although to a lesser extent in the latter, and NLRP3 inflammasome activation was not observed in LoVo and HT29 cells. DISCUSSION Our results reveal that while curcumin effectively induces apoptosis, its effects on NLRP3-inflammasome mediated pyroptosis vary. Our results underline the need for further research focusing on the other inflammasome complexes to confirm the differential effects of curcumin on CRC.
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Affiliation(s)
- Zeynep DAL
- 6th Phase Student, Faculty of Medicine, Yeditepe University, İstanbul,
Turkiye
| | - Başak ARU
- Department of Immunology, Faculty of Medicine, Yeditepe University, İstanbul,
Turkiye
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5
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Tam SY, Islam Khan MZ, Chen JY, Yip JHY, Yan HY, Tam TY, Law HKW. Proteomic Profiling of Chemotherapy Responses in FOLFOX-Resistant Colorectal Cancer Cells. Int J Mol Sci 2023; 24:9899. [PMID: 37373047 DOI: 10.3390/ijms24129899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Chemoresistance mechanisms of colorectal cancer remain largely elusive. We aim to compare the difference of chemotherapy responses between FOLFOX-resistant and wild-type colorectal cancer cells by proteomic profiling to suggest novel treatment targets. FOLFOX-resistant colorectal cancer cells DLD1-R and HCT116-R were developed by chronic exposure to progressive FOLFOX doses. Proteomic profiling of FOLFOX-resistant and wild-type cells under FOLFOX exposure were conducted by mass-spectrometry-based protein-analysis technology. Verification of selected KEGG pathways was conducted by Western blot. DLD1-R had significantly higher FOLFOX-chemoresistance (10.81 times) than its wild-type counterpart. A total of 309 and 90 differentially expressed proteins were identified in DLD1-R and HCT116-R, respectively. In terms of gene ontology molecular function, RNA binding and cadherin binding ranked first for DLD1 and HCT116 groups, respectively. For gene set enrichment analysis, ribosome pathway and DNA replication were significantly up-regulated and down-regulated in DLD1-R, respectively. The most significantly up-regulated pathway in HCT116-R was regulation of the actin cytoskeleton. Up-regulations in the ribosome pathway (DLD1-R) and actin cytoskeleton (HCT116-R) were verified by Western blot. There were several significantly altered signaling pathways in FOLFOX-resistant colorectal cancer cells under FOLFOX with notable up-regulations in the ribosomal process and actin cytoskeleton.
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Affiliation(s)
- Shing-Yau Tam
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Md Zahirul Islam Khan
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Ju-Yu Chen
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Jerica Hiu-Yui Yip
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Hong-Yiu Yan
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Tsz-Yan Tam
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Helen Ka-Wai Law
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong
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6
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Sers C, Schäfer R. Silencing effects of mutant RAS signalling on transcriptomes. Adv Biol Regul 2023; 87:100936. [PMID: 36513579 DOI: 10.1016/j.jbior.2022.100936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 11/23/2022] [Indexed: 11/30/2022]
Abstract
Mutated genes of the RAS family encoding small GTP-binding proteins drive numerous cancers, including pancreatic, colon and lung tumors. Besides the numerous effects of mutant RAS gene expression on aberrant proliferation, transformed phenotypes, metabolism, and therapy resistance, the most striking consequences of chronic RAS activation are changes of the genetic program. By performing systematic gene expression studies in cellular models that allow comparisons of pre-neoplastic with RAS-transformed cells, we and others have estimated that 7 percent or more of all transcripts are altered in conjunction with the expression of the oncogene. In this context, the number of up-regulated transcripts approximates that of down-regulated transcripts. While up-regulated transcription factors such as MYC, FOSL1, and HMGA2 have been identified and characterized as RAS-responsive drivers of the altered transcriptome, the suppressed factors have been less well studied as potential regulators of the genetic program and transformed phenotype in the breadth of their occurrence. We therefore have collected information on downregulated RAS-responsive factors and discuss their potential role as tumor suppressors that are likely to antagonize active cancer drivers. To better understand the active mechanisms that entail anti-RAS function and those that lead to loss of tumor suppressor activity, we focus on the tumor suppressor HREV107 (alias PLAAT3 [Phospholipase A and acyltransferase 3], PLA2G16 [Phospholipase A2, group XVI] and HRASLS3 [HRAS-like suppressor 3]). Inactivating HREV107 mutations in tumors are extremely rare, hence epigenetic causes modulated by the RAS pathway are likely to lead to down-regulation and loss of function.
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Affiliation(s)
- Christine Sers
- Laboratory of Molecular Tumor Pathology and systems Biology, Institute of Pathology, Charité Universitätstmedizin Berlin, Charitéplatz 1, D-10117 Berlin, Germany; German Cancer Consortium, German Cancer Research Center, Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany
| | - Reinhold Schäfer
- Comprehensive Cancer Center, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany; German Cancer Consortium, German Cancer Research Center, Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany.
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7
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Costa B, Fernandez LM, Parés O, Rio-Tinto R, Santiago I, Castillo-Martin M, Parvaiz A, Fior R. Zebrafish Avatars of rectal cancer patients validate the radiosensitive effect of metformin. Front Oncol 2022; 12:862889. [PMID: 36249066 PMCID: PMC9554544 DOI: 10.3389/fonc.2022.862889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 08/23/2022] [Indexed: 11/13/2022] Open
Abstract
Neoadjuvant chemoradiation (nCRT) followed by surgery represents the standard of care in patients with locally advanced rectal cancer. Increasing radiotherapy (RT) doses and chemotherapy cycles with 5FU have been associated with increased rates of complete response, however these strategies imply significant toxicity. In the last years, epidemiologic findings have demonstrated that metformin is associated with significantly higher rates of pathological complete response to nCRT. Also, pre-clinical studies using cell lines provide evidence for the radiosensitive effect of metformin. However, no studies have been performed using rectal cancer patient samples to test this radiosensitive effect of metformin and compared it to the standard 5FU. Here, we designed an experimental study to compare both radiosensitizers in the zebrafish xenograft model (zAvatar), using rectal cancer surgical specimens and diagnostic biopsies. Patient zAvatars confirmed that metformin has indeed a powerful in vivo radiosensitizer effect, similar to 5FU. Our work confirms that metformin constitutes a promising less toxic alternative to the standard 5FU, which could be game changing in elderly/frail patients to optimize tumor regression.
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Affiliation(s)
- Bruna Costa
- Champalimaud Research, Champalimaud Foundation, Lisbon, Portugal
- *Correspondence: Bruna Costa, ; Laura M. Fernandez, ; Rita Fior,
| | - Laura M. Fernandez
- Colorectal Surgery Department, Champalimaud Clinical Centre, Champalimaud Foundation, Lisbon, Portugal
- *Correspondence: Bruna Costa, ; Laura M. Fernandez, ; Rita Fior,
| | - Oriol Parés
- Radiation Oncology Department, Champalimaud Clinical Centre, Champalimaud Foundation, Lisbon, Portugal
| | - Ricardo Rio-Tinto
- Gastroenterology Department, Champalimaud Clinical Centre, Champalimaud Foundation, Lisbon, Portugal
| | - Inês Santiago
- Radiology Department, Champalimaud Clinical Centre, Champalimaud Foundation, Lisbon, Portugal
| | - Mireia Castillo-Martin
- Pathology Service, Champalimaud Clinical Centre, Champalimaud Foundation, Lisbon, Portugal
| | - Amjad Parvaiz
- Colorectal Surgery Department, Champalimaud Clinical Centre, Champalimaud Foundation, Lisbon, Portugal
| | - Rita Fior
- Champalimaud Research, Champalimaud Foundation, Lisbon, Portugal
- *Correspondence: Bruna Costa, ; Laura M. Fernandez, ; Rita Fior,
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8
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Kealey J, Düssmann H, Llorente-Folch I, Niewidok N, Salvucci M, Prehn JHM, D’Orsi B. Effect of TP53 deficiency and KRAS signaling on the bioenergetics of colon cancer cells in response to different substrates: A single cell study. Front Cell Dev Biol 2022; 10:893677. [PMID: 36238683 PMCID: PMC9550869 DOI: 10.3389/fcell.2022.893677] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 09/09/2022] [Indexed: 11/16/2022] Open
Abstract
Metabolic reprogramming is a hallmark of cancer. Somatic mutations in genes involved in oncogenic signaling pathways, including KRAS and TP53, rewire the metabolic machinery in cancer cells. We here set out to determine, at the single cell level, metabolic signatures in human colon cancer cells engineered to express combinations of activating KRAS gene mutations and TP53 gene deletions. Specifically, we explored how somatic mutations in these genes and substrate availability (lactate, glucose, substrate deprivation) from the extracellular microenvironment affect bioenergetic parameters, including cellular ATP, NADH and mitochondrial membrane potential dynamics. Employing cytosolic and mitochondrial FRET-based ATP probes, fluorescent NADH sensors, and the membrane-permeant cationic fluorescent probe TMRM in HCT-116 cells as a model system, we observed that TP53 deletion and KRAS mutations drive a shift in metabolic signatures enabling lactate to become an efficient metabolite to replenish both ATP and NADH following nutrient deprivation. Intriguingly, cytosolic, mitochondrial and overall cellular ATP measurements revealed that, in WT KRAS cells, TP53 deficiency leads to an enhanced ATP production in the presence of extracellular lactate and glucose, and to the greatest increase in ATP following a starvation period. On the other hand, oncogenic KRAS in TP53-deficient cells reversed the alterations in cellular ATP levels. Moreover, cell population measurements of mitochondrial and glycolytic metabolism using a Seahorse analyzer demonstrated that WT KRAS TP53-silenced cells display an increase of the basal respiration and tightly-coupled mitochondria, in the presence of glucose as substrate, compared to TP53 competent cells. Furthermore, cells possessing oncogenic KRAS, independently of TP53 status, showed less pronounced mitochondrial membrane potential changes in response to metabolic nutrients. Furthermore, analysis of cytosolic and mitochondrial NADH levels revealed that the simultaneous presence of TP53 deletion and oncogenic KRAS showed the most pronounced alteration in cytosolic and mitochondrial NADH during metabolic stress. In conclusion, our findings demonstrate how activating KRAS mutation and loss of TP53 remodel cancer metabolism and lead to alterations in bioenergetics under metabolic stress conditions by modulating cellular ATP production, NADH oxidation, mitochondrial respiration and function.
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Affiliation(s)
- James Kealey
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Heiko Düssmann
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- RCSI Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Irene Llorente-Folch
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- RCSI Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Department of Basic Sciences of Health, Area of Biochemistry and Molecular Biology, Universidad Rey Juan Carlos, Alcorcon-Madrid, Spain
| | - Natalia Niewidok
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Manuela Salvucci
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- RCSI Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Jochen H. M. Prehn
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- RCSI Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- *Correspondence: Jochen H. M. Prehn, ; Beatrice D’Orsi,
| | - Beatrice D’Orsi
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Institute of Neuroscience, Italian National Research Council, Pisa, Italy
- *Correspondence: Jochen H. M. Prehn, ; Beatrice D’Orsi,
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9
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Lamichhane A, Shahi Thakuri P, Singh S, Rafsanjani Nejad P, Heiss J, Luker GD, Tavana H. Therapeutic Targeting of Cancer Stem Cells Prevents Resistance of Colorectal Cancer Cells to MEK Inhibition. ACS Pharmacol Transl Sci 2022; 5:724-734. [PMID: 36110381 PMCID: PMC9469186 DOI: 10.1021/acsptsci.1c00257] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Indexed: 11/30/2022]
Abstract
Drug resistance is a leading cause for the failure of cancer treatments. Plasticity of cancer cells to acquire stem cell-like properties enables them to escape drug toxicity through different adaptive mechanisms. Eliminating cancer stem cells (CSCs) can potentially improve treatment outcomes for patients. To determine the role of CSCs in resistance of colorectal cancer cells to targeted therapies and identify treatment strategies, we treated spheroids of BRAFmut and KRASmut colorectal cancer cells with inhibitors of the mitogen-activated protein kinase pathway and studied resistance mechanisms through gene and protein expression analyses. We found that treatments activated several oncogenic pathways and expression of CSC markers CD166 and ALDH1A3. We identified a specific combination treatment using trametinib and mithramycin A to simultaneously inhibit the CSC phenotype and activities of several pathways in cancer cells. This study demonstrates the feasibility of therapeutic targeting of CSCs as a strategy to block tumorigenic activities of cancer cells.
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Affiliation(s)
- Astha Lamichhane
- Department
of Biomedical Engineering, The University
of Akron, Akron, Ohio 44325, United States
| | - Pradip Shahi Thakuri
- Department
of Biomedical Engineering, The University
of Akron, Akron, Ohio 44325, United States
| | - Sunil Singh
- Department
of Biomedical Engineering, The University
of Akron, Akron, Ohio 44325, United States
| | - Pouria Rafsanjani Nejad
- Department
of Biomedical Engineering, The University
of Akron, Akron, Ohio 44325, United States
| | - Jacob Heiss
- Department
of Biomedical Engineering, The University
of Akron, Akron, Ohio 44325, United States
| | - Gary D. Luker
- Department
of Radiology, Microbiology and Immunology, Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48105, United States
| | - Hossein Tavana
- Department
of Biomedical Engineering, The University
of Akron, Akron, Ohio 44325, United States
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10
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Kim S, Oh M, Kang M, Ko J. Small leucine zipper protein functions as a modulator for metabolic reprogramming of colorectal cancer cells by inducing nutrient stress-mediated autophagy. Cell Mol Life Sci 2022; 79:505. [PMID: 36057892 DOI: 10.1007/s00018-022-04535-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/01/2022] [Accepted: 08/23/2022] [Indexed: 11/03/2022]
Abstract
In multiple cancers, autophagy promotes tumor development by recycling intracellular components into metabolic pathways. Autophagy-induced metabolic reprogramming and plasticity lead to cancer cell survival and resistance to anticancer therapy. We investigated the role of small leucine zipper protein (sLZIP) in autophagy and cell survival under nutrient-deficient conditions in colorectal cancer (CRC). sLZIP was induced by nutrient stress and increased the transcription of microtubule-associated protein 1A/1B-light chain 3 (LC3), by directly binding to its promoter. Under nutrient stress conditions, sLZIP activated autophagy and promoted the survival of CRC cells. sLZIP induced metabolic reprogramming of CRC cells, to activate glutaminolysis and the tricarboxylic acid cycle. sLZIP also enhanced the autophagic degradation of Keap1 and the nuclear accumulation of Nrf2, leading to NQO1 expression, for maintenance of redox homeostasis. sLZIP-knockout CRC cells exhibited impaired autophagy induction in the glycolytic inhibition state. Xenograft mice lacking sLZIP showed decreased tumor growth, by rendering CRC cells sensitive to glycolysis inhibition. The expression of sLZIP and LC3B was highly elevated in tumors of CRC patients compared to that in normal tissues, and correlated with the progression of CRC. These findings suggest that sLZIP drives autophagy and metabolic reprogramming to promote colorectal tumorigenesis.
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11
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Saliani M, Jalal R, Javadmanesh A. Differential expression analysis of genes and long non-coding RNAs associated with KRAS mutation in colorectal cancer cells. Sci Rep 2022; 12:7965. [PMID: 35562390 PMCID: PMC9106686 DOI: 10.1038/s41598-022-11697-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 04/13/2022] [Indexed: 02/07/2023] Open
Abstract
KRAS mutation is responsible for 40–50% of colorectal cancers (CRCs). RNA-seq data and bioinformatics methods were used to analyze the transcriptional profiles of KRAS mutant (mtKRAS) in comparison with the wild-type (wtKRAS) cell lines, followed by in-silico and quantitative real-time PCR (qPCR) validations. Gene set enrichment analysis showed overrepresentation of KRAS signaling as an oncogenic signature in mtKRAS. Gene ontology and pathway analyses on 600 differentially-expressed genes (DEGs) indicated their major involvement in the cancer-associated signal transduction pathways. Significant hub genes were identified through analyzing PPI network, with the highest node degree for PTPRC. The evaluation of the interaction between co-expressed DEGs and lncRNAs revealed 12 differentially-expressed lncRNAs which potentially regulate the genes majorly enriched in Rap1 and RAS signaling pathways. The results of the qPCR showed the overexpression of PPARG and PTGS2, and downregulation of PTPRC in mtKRAS cells compared to the wtKRAS one, which confirming the outputs of RNA-seq analysis. Further, significant upregualtion of miR-23b was observed in wtKRAS cells. The comparison between the expression level of hub genes and TFs with expression data of CRC tissue samples deposited in TCGA databank confirmed them as distinct biomarkers for the discrimination of normal and tumor patient samples. Survival analysis revealed the significant prognostic value for some of the hub genes, TFs, and lncRNAs. The results of the present study can extend the vision on the molecular mechanisms involved in KRAS-driven CRC pathogenesis.
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Affiliation(s)
- Mahsa Saliani
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, 9177948974, Iran
| | - Razieh Jalal
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, 9177948974, Iran. .,Novel Diagnostics and Therapeutics Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, 9177948974, Iran.
| | - Ali Javadmanesh
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran.,Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, 9177948974, Iran
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12
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Gao X, Guo R, Li Y, Kang G, Wu Y, Cheng J, Jia J, Wang W, Li Z, Wang A, Xu H, Jia Y, Li Y, Qi X, Wei Z, Wei C. Contribution of upregulated aminoacyl-tRNA biosynthesis to metabolic dysregulation in gastric cancer. J Gastroenterol Hepatol 2021; 36:3113-3126. [PMID: 34159625 PMCID: PMC9292402 DOI: 10.1111/jgh.15592] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/04/2021] [Accepted: 06/15/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIM Metabolic reprogramming is characterized by dysregulated levels of metabolites and metabolic enzymes. Integrated metabolomic and transcriptomic data analysis can help to elucidate changes in the levels of metabolites and metabolic enzymes, screen the core metabolic pathways, and develop novel therapeutic strategies for cancer. METHODS Here, the metabolome of gastric cancer tissues was determined using liquid chromatography-mass spectrometry. The transcriptome data from The Cancer Genome Atlas dataset were integrated with the liquid chromatography-mass spectrometry data to identify the common dysregulated gastric cancer-specific metabolic pathways. Additionally, the protein expression and clinical significance of key metabolic enzymes were examined using a gastric cancer tissue array. RESULTS Metabolomic analysis of 16 gastric cancer tissues revealed that among the 15 dysregulated metabolomic pathways, the aminoacyl-tRNA biosynthesis pathway in the gastric tissues was markedly upregulated relative to that in the adjacent noncancerous tissues, which was consistent with the results of transcriptome analysis. Bioinformatic analysis revealed that among the key regulators in the aminoacyl-tRNA biosynthesis pathway, the expression levels of threonyl-tRNA synthetase (TARS) and phenylalanyl-tRNA synthetase (FARSB) were correlated with tumor grade and poor survival, respectively. Additionally, gastric tissue array data analysis indicated that TARS and FARSB were upregulated in gastric cancer tissues and were correlated with poor prognosis and tumor metastasis. CONCLUSIONS This study demonstrated that the aminoacyl-tRNA biosynthesis pathway is upregulated in gastric cancer and both TARS and FARSB play key roles in the progression of gastric cancer. Additionally, a novel therapeutic strategy for gastric cancer was proposed that involves targeting the aminoacyl-tRNA biosynthesis pathway.
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Affiliation(s)
- Xiaoling Gao
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal TumorGansu Provincial HospitalLanzhouChina,The Institute of Clinical Research and Translational MedicineGansu Provincial HospitalLanzhouChina
| | - Rui Guo
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal TumorGansu Provincial HospitalLanzhouChina,The Institute of Clinical Research and Translational MedicineGansu Provincial HospitalLanzhouChina
| | - Yonghong Li
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal TumorGansu Provincial HospitalLanzhouChina,The Institute of Clinical Research and Translational MedicineGansu Provincial HospitalLanzhouChina
| | - Guolan Kang
- Department of Endoscopic Diagnosis and Treatment CenterGansu Provincial HospitalLanzhouChina
| | - Yu Wu
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal TumorGansu Provincial HospitalLanzhouChina
| | - Jia Cheng
- Department of Endoscopic Diagnosis and Treatment CenterGansu Provincial HospitalLanzhouChina
| | - Jing Jia
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal TumorGansu Provincial HospitalLanzhouChina
| | - Wanxia Wang
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal TumorGansu Provincial HospitalLanzhouChina
| | - Zhenhao Li
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal TumorGansu Provincial HospitalLanzhouChina
| | - Anqi Wang
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal TumorGansu Provincial HospitalLanzhouChina
| | - Hui Xu
- The Institute of Clinical Research and Translational MedicineGansu Provincial HospitalLanzhouChina
| | - Yanjuan Jia
- The Institute of Clinical Research and Translational MedicineGansu Provincial HospitalLanzhouChina
| | - Yuanting Li
- The Institute of Clinical Research and Translational MedicineGansu Provincial HospitalLanzhouChina
| | - Xiaoming Qi
- The Institute of Clinical Research and Translational MedicineGansu Provincial HospitalLanzhouChina
| | - Zhenhong Wei
- The Institute of Clinical Research and Translational MedicineGansu Provincial HospitalLanzhouChina
| | - Chaojun Wei
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal TumorGansu Provincial HospitalLanzhouChina,The Institute of Clinical Research and Translational MedicineGansu Provincial HospitalLanzhouChina
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13
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Abstract
Mitogen-activated protein kinase-interacting kinases 1 and 2 (MNK1/2) represent a central class of enzymes that are activated by extracellular signal-regulated kinase (ERK) or p38 mitogen-activated protein (MAP) kinases. MNK1 and MNK2 coordinate cellular signaling, control production of inflammatory chemokines, and regulate cell proliferation and survival. MNK1/2 are referred to as serine/threonine kinases as they phosphorylate serine or threonine residues on their substrates. Upon activation, MNK1/2 phosphorylate eukaryotic translation initiation factor 4E (eIF4E) at Ser209, which in turn initiates ribosome assembly and protein translation. Deleterious overexpression of MNK1/2 and/or eIF4E have been reported in several diseases including cancers, neurological disorders, autism, and inflammation. Recently, there have been intense efforts toward the development of potent and selective inhibitors of MNK1/2 in both academia and industry. Herein, we review the current understanding of the structural and biological aspects of MNK1/2 and provide an update of pharmacological inhibitors of MNK1/2 including candidates in clinical trials.
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Affiliation(s)
- Weijun Xu
- Experimental Drug Development Centre (EDDC), A*STAR, 10 Biopolis Road, Chromos #05-01, 138670, Singapore
| | | | - Chandra S Verma
- Bioinformatics Institute (BII), A*STAR, 30 Biopolis Street, #07-01 Matrix, 138671, Singapore.,Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, 117558, Singapore.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Kassoum Nacro
- Experimental Drug Development Centre (EDDC), A*STAR, 10 Biopolis Road, Chromos #05-01, 138670, Singapore
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14
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Lastraioli E, Ruffinatti FA, Di Costanzo F, Sala C, Munaron L, Arcangeli A. A Transcriptomic Approach Reveals Selective Ribosomal Remodelling in the Tumour Versus the Stromal Compartment of Metastatic Colorectal Cancer. Cancers (Basel) 2021; 13:4188. [PMID: 34439343 DOI: 10.3390/cancers13164188] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/09/2021] [Accepted: 08/18/2021] [Indexed: 12/20/2022] Open
Abstract
Simple Summary In this study, we analyzed a cohort of six colorectal cancer patients harboring KRAS mutations and with wild-type BRAF from a transcriptional perspective, with the aim of elucidating the role of the stromal cells in tumor progression. Specifically, paraffin-embedded specimens were subjected to microdissection and hybridized on Agilent-026652 microarrays to compare the gene expression of tumor samples composed of neoplastic epithelial samples against the neighboring stromal tissue. A paired rank-product test led to the detection of 193 differentially expressed genes. Subsequent functional enrichment analysis pointed to extracellular matrix constituents, angiogenesis, and cell migration as the main biological processes enhanced in stromata, while the tumor compartment was characterized by an overexpression of many ribosomal protein genes. A further gene set enrichment analysis against a comprehensive ribosomal protein gene set finally revealed that only cytosolic ribosomes (80S) were affected by such upregulation, while mitochondrial ribosomes were virtually unaltered. Abstract Because of its high incidence and poor prognosis, colorectal cancer (CRC) represents an important health issue in several countries. As with other carcinomas, the so-called tumour microenvironment (TME) has been shown to play key roles in CRC progression and related therapeutical outcomes, even though a deeper understanding of the underlying molecular mechanisms is needed to devise new treatment strategies. For some years now, omics technologies and consolidated bioinformatics pipelines have allowed scientists to access large amounts of biologically relevant information, even when starting from small tissue samples; thus, in order to shed new light upon the role of the TME in CRC, we compared the gene expression profiles of 6 independent tumour tissues (all progressed towards metastatic disease) to the expression profile of the surrounding stromata. To do this, paraffin-embedded whole tissues were first microdissected to obtain samples enriched with tumour and stromal cells, respectively. Afterwards, RNA was extracted and analysed using a microarray-based approach. A thorough bioinformatics analysis was then carried out to identify transcripts differentially expressed between the two groups and possibly enriched functional terms. Overall, 193 genes were found to be significantly downregulated in tumours compared to the paired stromata. The functional analysis of the downregulated gene list revealed three principal macro areas of interest: the extracellular matrix, cell migration, and angiogenesis. Conversely, among the upregulated genes, the main alterations detected by the functional annotation were related to the ribosomal proteins (rProteins) of both the large (60S) and small (40S) subunits of the cytosolic ribosomes. Subsequent gene set enrichment analysis (GSEA) confirmed the massive overexpression of most cytosolic—but not mitochondrial—ribosome rProteins.
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15
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Cui Y, Bai Y, Yang J, Yao Y, Zhang C, Liu C, Shi J, Li Q, Zhang J, Lu X, Zhang Y. SIRT4 is the molecular switch mediating cellular proliferation in colorectal cancer through GLS mediated activation of AKT/GSK3β/CyclinD1 pathway. Carcinogenesis 2021; 42:481-492. [PMID: 33315089 DOI: 10.1093/carcin/bgaa134] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/30/2020] [Accepted: 12/09/2020] [Indexed: 01/11/2023] Open
Abstract
Mitochondria-localized sirtuin 4 (SIRT4) is associated with malignant phenotypes in colorectal cancer (CRC). However, the molecular mechanisms that drive SIRT4-mediated carcinogenesis are unclear. Initially, we confirmed expression of SIRT4 in CRC through public database and in CRC patient tissues using quantitative real-time reverse transcription PCR. We established HCT116 colorectal cells that overexpressed SIRT4 and HT29 cells were transfected with plasmids bearing a small interfering RNA construct to silence SIRT4. Assays to determine the malignant phenotypes (proliferation, invasion and migration) were performed. Xenograft in vivo models were also constructed. A protein interactome network was built using differentially expressed proteins identified using the liquid chromatography/tandem mass spectrophotometry, the findings of which were confirmed using co-immunoprecipitation, western blotting and phenotype rescue experiments. Decreased SIRT4 expression was associated with malignant phenotypes in vitro and in vivo. The ribosomal biogenesis pathway was enriched in the interactome network. SIRT4 suppression activated glutaminase, thereby initiating AKT activation. Our research provided novel insights into the molecular mechanisms underlying CRC, and identified that SIRT4 exerts its antitumor activity in CRC possibly dependent on glutaminase to inhibit proliferation, migration and invasion via the AKT/GSK3β/CyclinD1 pathway.
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Affiliation(s)
- Ying Cui
- Department of Radiation Oncology, Harbin Medical University Cancer Hospital, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Yibing Bai
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China.,Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jiani Yang
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China.,Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yuanfei Yao
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China.,Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Chunhui Zhang
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China.,Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Chao Liu
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China.,Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jiaqi Shi
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China.,Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - QingWei Li
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China.,Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jingchun Zhang
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China.,Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xiaolin Lu
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China.,Department of Orthopedics, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yanqiao Zhang
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China.,Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
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16
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Meng M, Zhong K, Jiang T, Liu Z, Kwan HY, Su T. The current understanding on the impact of KRAS on colorectal cancer. Biomed Pharmacother 2021; 140:111717. [PMID: 34044280 DOI: 10.1016/j.biopha.2021.111717] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 02/07/2023] Open
Abstract
KRAS (kirsten rat sarcoma viral oncogene) is a member of the RAS family. KRAS mutations are one of most dominant mutations in colorectal cancer (CRC). The impact of KRAS mutations on the prognosis and survival of CRC patients drives many research studies to explore potential therapeutics or target therapy for the KRAS mutant CRC. This review summarizes the current understanding of the pathological consequences of the KRAS mutations in the development of CRC; and the impact of the mutations on the response and the sensitivity to the current front-line chemotherapy. The current therapeutic strategies for treating KRAS mutant CRC, the difficulties and challenges will also be discussed.
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Affiliation(s)
- Mingjing Meng
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Keying Zhong
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Ting Jiang
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Zhongqiu Liu
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China.
| | - Hiu Yee Kwan
- Centre for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
| | - Tao Su
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China.
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17
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Kandasamy P, Zlobec I, Nydegger DT, Pujol-Giménez J, Bhardwaj R, Shirasawa S, Tsunoda T, Hediger MA. Oncogenic KRAS mutations enhance amino acid uptake by colorectal cancer cells via the hippo signaling effector YAP1. Mol Oncol 2021; 15:2782-2800. [PMID: 34003553 PMCID: PMC8486573 DOI: 10.1002/1878-0261.12999] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 04/14/2021] [Accepted: 05/14/2021] [Indexed: 12/28/2022] Open
Abstract
Oncogenic KRAS mutations develop unique metabolic dependencies on nutrients to support tumor metabolism and cell proliferation. In particular, KRAS mutant cancer cells exploit amino acids (AAs) such as glutamine and leucine, to accelerate energy metabolism, redox balance through glutathione synthesis and macromolecule biosynthesis. However, the identities of the amino acid transporters (AATs) that are prominently upregulated in KRAS mutant cancer cells, and the mechanism regulating their expression have not yet been systematically investigated. Here, we report that the majority of the KRAS mutant colorectal cancer (CRC) cells upregulate selected AATs (SLC7A5/LAT1, SLC38A2/SNAT2, and SLC1A5/ASCT2), which correlates with enhanced uptake of AAs such as glutamine and leucine. Consistently, knockdown of oncogenic KRAS downregulated the expression of AATs, thereby decreasing the levels of amino acids taken up by CRC cells. Moreover, overexpression of mutant KRAS upregulated the expression of AATs (SLC7A5/LAT1, SLC38A2/SNAT2, and SLC1A5/ASCT2) in KRAS wild-type CRC cells and mouse embryonic fibroblasts. In addition, we show that the YAP1 (Yes-associated protein 1) transcriptional coactivator accounts for increased expression of AATs and mTOR activation in KRAS mutant CRC cells. Specific knockdown of AATs by shRNAs or pharmacological blockage of AATs effectively inhibited AA uptake, mTOR activation, and cell proliferation. Collectively, we conclude that oncogenic KRAS mutations enhance the expression of AATs via the hippo effector YAP1, leading to mTOR activation and CRC cell proliferation.
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Affiliation(s)
- Palanivel Kandasamy
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension, Inselspital, University of Bern, Switzerland.,Department of Biomedical Research, University of Bern, Switzerland
| | - Inti Zlobec
- Translational Research Unit (TRU), Institute of Pathology, University of Bern, Switzerland
| | - Damian T Nydegger
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension, Inselspital, University of Bern, Switzerland.,Department of Biomedical Research, University of Bern, Switzerland
| | - Jonai Pujol-Giménez
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension, Inselspital, University of Bern, Switzerland.,Department of Biomedical Research, University of Bern, Switzerland
| | - Rajesh Bhardwaj
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension, Inselspital, University of Bern, Switzerland.,Department of Biomedical Research, University of Bern, Switzerland
| | - Senji Shirasawa
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Japan
| | - Toshiyuki Tsunoda
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Japan
| | - Matthias A Hediger
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension, Inselspital, University of Bern, Switzerland.,Department of Biomedical Research, University of Bern, Switzerland
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18
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Cho K, Choi E, Lee SY, Kim J, Moon DW, Son J, Kim E. Screening of important metabolites and KRAS genotypes in colon cancer using secondary ion mass spectrometry. Bioeng Transl Med 2021; 6:e10200. [PMID: 34027089 PMCID: PMC8126813 DOI: 10.1002/btm2.10200] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/06/2020] [Accepted: 10/29/2020] [Indexed: 11/08/2022] Open
Abstract
Time-of-flight secondary ion mass spectrometry (TOF-SIMS) is an imaging-based analytical technique that can characterize the surfaces of biomaterials. We used TOF-SIMS to identify important metabolites and oncogenic KRAS mutation expressed in human colorectal cancer (CRC). We obtained 540 TOF-SIMS spectra from 180 tissue samples by scanning cryo-sections and selected discriminatory molecules using the support vector machine (SVM) algorithm. Each TOF-SIMS spectrum contained nearly 860,000 ion profiles and hundreds of spectra were analyzed; therefore, reducing the dimensionality of the original data was necessary. We performed principal component analysis after preprocessing the spectral data, and the principal components (20) of each spectrum were used as the inputs of the SVM algorithm using the R package. The performance of the algorithm was evaluated using the receiver operating characteristic (ROC) area under the curve (AUC) (0.9297). Spectral peaks (m/z) corresponding to discriminatory molecules used to classify normal and tumor samples were selected according to p-value and were assigned to arginine, α-tocopherol, and fragments of glycerophosphocholine. Pathway analysis using these discriminatory molecules showed that they were involved in gastrointestinal disease and organismal abnormalities. In addition, spectra were classified according to the expression of KRAS somatic mutation, with 0.9921 AUC. Taken together, TOF-SIMS efficiently and simultaneously screened metabolite biomarkers and performed KRAS genotyping. In addition, a machine learning algorithm was provided as a diagnostic tool applied to spectral data acquired from clinical samples prepared as frozen tissue slides, which are commonly used in a variety of biomedical tests.
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Affiliation(s)
- Kookrae Cho
- Division of Electronic Information System ResearchDaegu Gyeongbuk Institute of Science and Technology (DGIST)DaeguRepublic of Korea
| | - Eun‐Sook Choi
- Division of Bio‐Fusion ResearchDaegu Gyeongbuk Institute of Science and Technology (DGIST)DaeguRepublic of Korea
| | - Sung Young Lee
- Division of Technology Business, National Institute for Nanomaterials Technology (NINT)Pohang University of Science and Technology (POSTECH)PohangRepublic of Korea
| | - Jung‐Hee Kim
- Division of Electronic Information System ResearchDaegu Gyeongbuk Institute of Science and Technology (DGIST)DaeguRepublic of Korea
| | - Dae Won Moon
- Department of New BiologyDaegu Gyeongbuk Institute of Science and Technology (DGIST)DaeguRepublic of Korea
| | - Jong‐Wuk Son
- Division of Electronic Information System ResearchDaegu Gyeongbuk Institute of Science and Technology (DGIST)DaeguRepublic of Korea
| | - Eunjoo Kim
- Division of Electronic Information System ResearchDaegu Gyeongbuk Institute of Science and Technology (DGIST)DaeguRepublic of Korea
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19
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Trafalis DT, Sagredou S, Dalezis P, Voura M, Fountoulaki S, Nikoleousakos N, Almpanakis K, Deligiorgi MV, Sarli V. Anticancer Activity of Triazolo-Thiadiazole Derivatives and Inhibition of AKT1 and AKT2 Activation. Pharmaceutics 2021; 13:pharmaceutics13040493. [PMID: 33916378 PMCID: PMC8066331 DOI: 10.3390/pharmaceutics13040493] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/28/2021] [Accepted: 03/29/2021] [Indexed: 12/18/2022] Open
Abstract
The fusion of 1,2,4-triazole and 1,3,4-thiadiazole rings results in a class of heterocycles compounds with an extensive range of pharmacological properties. A series of 1,2,4-triazolo[3,4-b]-1,2,4-thiadiazoles was synthesized and tested for its enzyme inhibition potential and anticancer activity. The results show that 1,2,4-triazolo[3,4-b]-1,2,4-thiadiazoles display potent anticancer properties in vitro against a panel of cancer cells and in vivo efficacy in HT-29 human colon tumor xenograft in CB17 severe combined immunodeficient (SCID) mice. Preliminary mechanistic studies revealed that KA25 and KA39 exhibit time- and concentration-dependent inhibition of Akt Ser-473 phosphorylation. Molecular modeling experiments indicated that 1,2,4-triazolo[3,4-b]-1,2,4-thiadiazoles bind well to the ATP binding site in Akt1 and Akt2. The low acute toxicity combined with in vitro and in vivo anticancer activity render triazolo[3,4-b]thiadiazoles KA25, KA26, and KA39 promising cancer therapeutic agents.
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Affiliation(s)
- Dimitrios T. Trafalis
- Laboratory of Pharmacology, Faculty of Medicine, National and Kapodistrian University of Athens, 115 27 Athens, Greece; (S.S.); (P.D.); (N.N.); (M.V.D.)
- Correspondence: (D.T.T.); (V.S.)
| | - Sofia Sagredou
- Laboratory of Pharmacology, Faculty of Medicine, National and Kapodistrian University of Athens, 115 27 Athens, Greece; (S.S.); (P.D.); (N.N.); (M.V.D.)
| | - Panayiotis Dalezis
- Laboratory of Pharmacology, Faculty of Medicine, National and Kapodistrian University of Athens, 115 27 Athens, Greece; (S.S.); (P.D.); (N.N.); (M.V.D.)
| | - Maria Voura
- Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 541 24 Thessaloniki, Greece; (M.V.); (S.F.); (K.A.)
| | - Stella Fountoulaki
- Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 541 24 Thessaloniki, Greece; (M.V.); (S.F.); (K.A.)
| | - Nikolaos Nikoleousakos
- Laboratory of Pharmacology, Faculty of Medicine, National and Kapodistrian University of Athens, 115 27 Athens, Greece; (S.S.); (P.D.); (N.N.); (M.V.D.)
| | - Konstantinos Almpanakis
- Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 541 24 Thessaloniki, Greece; (M.V.); (S.F.); (K.A.)
| | - Maria V. Deligiorgi
- Laboratory of Pharmacology, Faculty of Medicine, National and Kapodistrian University of Athens, 115 27 Athens, Greece; (S.S.); (P.D.); (N.N.); (M.V.D.)
| | - Vasiliki Sarli
- Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 541 24 Thessaloniki, Greece; (M.V.); (S.F.); (K.A.)
- Correspondence: (D.T.T.); (V.S.)
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20
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Kyriakopoulos G, Katopodi V, Skeparnias I, Kaliatsi EG, Grafanaki K, Stathopoulos C. KRAS G12C Can Either Promote or Impair Cap-Dependent Translation in Two Different Lung Adenocarcinoma Cell Lines. Int J Mol Sci 2021; 22:ijms22042222. [PMID: 33672357 PMCID: PMC7926983 DOI: 10.3390/ijms22042222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 02/19/2021] [Accepted: 02/20/2021] [Indexed: 12/14/2022] Open
Abstract
KRASG12C is among the most common oncogenic mutations in lung adenocarcinoma and a promising target for treatment by small-molecule inhibitors. KRAS oncogenic signaling is responsible for modulation of tumor microenvironment, with translation factors being among the most prominent deregulated targets. In the present study, we used TALENs to edit EGFRWT CL1-5 and A549 cells for integration of a Tet-inducible KRASG12C expression system. Subsequent analysis of both cell lines showed that cap-dependent translation was impaired in CL1-5 cells via involvement of mTORC2 and NF-κB. In contrast, in A549 cells, which additionally harbor the KRASG12S mutation, cap-dependent translation was favored via recruitment of mTORC1, c-MYC and the positive regulation of eIF4F complex. Downregulation of eIF1, eIF5 and eIF5B in the same cell line suggested a stringency loss of start codon selection during scanning of mRNAs. Puromycin staining and polysome profile analysis validated the enhanced translation rates in A549 cells and the impaired cap-dependent translation in CL1-5 cells. Interestingly, elevated translation rates were restored in CL1-5 cells after prolonged induction of KRASG12C through an mTORC1/p70S6K-independent way. Collectively, our results suggest that KRASG12C signaling differentially affects the regulation of the translational machinery. These differences could provide additional insights and facilitate current efforts to effectively target KRAS.
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Affiliation(s)
- George Kyriakopoulos
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (G.K.)
| | - Vicky Katopodi
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (G.K.)
- Laboratory for RNA Cancer Biology, Department of Oncology, KU Leuven, 3001 Leuven, Belgium
| | - Ilias Skeparnias
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (G.K.)
| | - Eleni G Kaliatsi
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (G.K.)
| | - Katerina Grafanaki
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (G.K.)
- Department of Dermatology, School of Medicine, University of Patras, 26504 Patras, Greece
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21
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Abstract
Protein synthesis is one of the most essential processes in every kingdom of life, and its dysregulation is a known driving force in cancer development. Multiple signaling pathways converge on the translation initiation machinery, and this plays a crucial role in regulating differential gene expression. In colorectal cancer, dysregulation of initiation results in translational reprogramming, which promotes the selective translation of mRNAs required for many oncogenic processes. The majority of upstream mutations found in colorectal cancer, including alterations in the WNT, MAPK, and PI3K\AKT pathways, have been demonstrated to play a significant role in translational reprogramming. Many translation initiation factors are also known to be dysregulated, resulting in translational reprogramming during tumor initiation and/or maintenance. In this review, we outline the role of translational reprogramming that occurs during colorectal cancer development and progression and highlight some of the most critical factors affecting the etiology of this disease.
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Affiliation(s)
- Emma Minnee
- Division of Oncogenomics, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - William James Faller
- Division of Oncogenomics, Netherlands Cancer Institute, Amsterdam, The Netherlands
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22
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Nait Slimane S, Marcel V, Fenouil T, Catez F, Saurin JC, Bouvet P, Diaz JJ, Mertani HC. Ribosome Biogenesis Alterations in Colorectal Cancer. Cells 2020; 9:E2361. [PMID: 33120992 PMCID: PMC7693311 DOI: 10.3390/cells9112361] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/23/2020] [Accepted: 10/25/2020] [Indexed: 12/24/2022] Open
Abstract
Many studies have focused on understanding the regulation and functions of aberrant protein synthesis in colorectal cancer (CRC), leaving the ribosome, its main effector, relatively underappreciated in CRC. The production of functional ribosomes is initiated in the nucleolus, requires coordinated ribosomal RNA (rRNA) processing and ribosomal protein (RP) assembly, and is frequently hyperactivated to support the needs in protein synthesis essential to withstand unremitting cancer cell growth. This elevated ribosome production in cancer cells includes a strong alteration of ribosome biogenesis homeostasis that represents one of the hallmarks of cancer cells. None of the ribosome production steps escape this cancer-specific dysregulation. This review summarizes the early and late steps of ribosome biogenesis dysregulations described in CRC cell lines, intestinal organoids, CRC stem cells and mouse models, and their possible clinical implications. We highlight how this cancer-related ribosome biogenesis, both at quantitative and qualitative levels, can lead to the synthesis of ribosomes favoring the translation of mRNAs encoding hyperproliferative and survival factors. We also discuss whether cancer-related ribosome biogenesis is a mere consequence of cancer progression or is a causal factor in CRC, and how altered ribosome biogenesis pathways can represent effective targets to kill CRC cells. The association between exacerbated CRC cell growth and alteration of specific steps of ribosome biogenesis is highlighted as a key driver of tumorigenesis, providing promising perspectives for the implementation of predictive biomarkers and the development of new therapeutic drugs.
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Affiliation(s)
- Sophie Nait Slimane
- Cancer Initiation and Tumor Cell Identity, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286 Centre Léon Bérard, 69008 Lyon, France; (S.N.S.); (V.M.); (F.C.); (P.B.)
| | - Virginie Marcel
- Cancer Initiation and Tumor Cell Identity, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286 Centre Léon Bérard, 69008 Lyon, France; (S.N.S.); (V.M.); (F.C.); (P.B.)
| | - Tanguy Fenouil
- Institute of Pathology EST, Hospices Civils de Lyon, Site-Est Groupement Hospitalier- Est, 69677 Bron, France;
| | - Frédéric Catez
- Cancer Initiation and Tumor Cell Identity, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286 Centre Léon Bérard, 69008 Lyon, France; (S.N.S.); (V.M.); (F.C.); (P.B.)
| | - Jean-Christophe Saurin
- Gastroenterology and Genetic Department, Edouard Herriot Hospital, Hospices Civils de Lyon, 69008 Lyon, France;
| | - Philippe Bouvet
- Cancer Initiation and Tumor Cell Identity, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286 Centre Léon Bérard, 69008 Lyon, France; (S.N.S.); (V.M.); (F.C.); (P.B.)
| | - Jean-Jacques Diaz
- Cancer Initiation and Tumor Cell Identity, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286 Centre Léon Bérard, 69008 Lyon, France; (S.N.S.); (V.M.); (F.C.); (P.B.)
| | - Hichem C. Mertani
- Cancer Initiation and Tumor Cell Identity, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286 Centre Léon Bérard, 69008 Lyon, France; (S.N.S.); (V.M.); (F.C.); (P.B.)
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23
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Ge J, Huang X, Wang P, Lu C. Expression of biogenesis of ribosomes BRX1 is associated with malignant progression and prognosis in colorectal cancer. Transl Cancer Res 2020; 9:5595-5602. [PMID: 35117923 PMCID: PMC8798812 DOI: 10.21037/tcr-20-2564] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/28/2020] [Indexed: 11/06/2022]
Abstract
BACKGROUND Upregulated ribosome synthesis is associated with an increased risk of cancer onset. However, the role of biogenesis of ribosomes BRX1 (BRIX1), which is involved in the synthesis of ribosomal 60S subunits, in the progression and prognosis of colorectal cancer (CRC) is not clear. METHODS Sixty CRC patients requiring surgical treatment were enrolled in the present prospective study. Patient characteristics were collected at admission. The CRC tissue samples and adjacent normal tissue samples from patients were collected for further quantitative reverse transcription-polymerase chain reaction and Western blot. All enrolled patients were followed up for 12 months, and overall patient survival during follow-up was recorded. RESULTS The level of BRIX1 mRNA in CRC tissues was higher compared with that in adjacent normal tissues (1.0±0.5 vs. 5.5±1.7, P<0.01). Similarly, the level of the BRIX1 protein in CRC tissues was significantly higher than that in adjacent normal tissues (1.0±0.6 vs. 6.4±2.1, P<0.01). On further analysis, we found that the levels of BRIX1 mRNA and protein were positively correlated with tumor stage. Patients at stages III-IV had a higher expression of BRIX1 mRNA and protein than at stages I-II. The Kaplan-Meier survival curve indicated that patients with higher level of the BRIX1 protein had a lower overall survival rate. The Cox proportional hazards model was used to identify tumor stage III or IV, poor differentiation, and elevated expression of the BRIX1 protein as risk factors for the overall survival of CRC patients. CONCLUSIONS BRIX1 expression is positively correlated with CRC tumor stage; it also acts as a risk factor for the overall survival of CRC patients.
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Affiliation(s)
- Jianxin Ge
- Department of Gastroenterology, the Affiliated Nanjing Jiangbei Hospital of Nantong University, Nanjing, China
| | - Xiaoli Huang
- Department of Gastroenterology, the Affiliated Nanjing Jiangbei Hospital of Nantong University, Nanjing, China
| | - Ping Wang
- Department of Gastroenterology, the Affiliated Nanjing Jiangbei Hospital of Nantong University, Nanjing, China
| | - Cuihua Lu
- Department of Gastroenterology, the Affiliated Hospital of Nantong University, Nantong, China
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24
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Matadamas-Guzman M, Zazueta C, Rojas E, Resendis-Antonio O. Analysis of Epithelial-Mesenchymal Transition Metabolism Identifies Possible Cancer Biomarkers Useful in Diverse Genetic Backgrounds. Front Oncol 2020; 10:1309. [PMID: 32850411 PMCID: PMC7406688 DOI: 10.3389/fonc.2020.01309] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/23/2020] [Indexed: 12/17/2022] Open
Abstract
Epithelial-to-mesenchymal transition (EMT) relates to many molecular and cellular alterations that occur when epithelial cells undergo a switch in differentiation generating mesenchymal-like cells with newly acquired migratory and invasive properties. In cancer cells, EMT leads to drug resistance and metastasis. Moreover, differences in genetic backgrounds, even between patients with the same type of cancer, also determine resistance to some treatments. Metabolic rewiring is essential to induce EMT, hence it is important to identify key metabolic elements for this process, which can be later used to treat cancer cells with different genetic backgrounds. Here we used a mathematical modeling approach to determine which are the metabolic reactions altered after induction of EMT, based on metabolomic and transcriptional data of three non-small cell lung cancer (NSCLC) cell lines. The model suggested that the most affected pathways were the Krebs cycle, amino acid metabolism, and glutathione metabolism. However, glutathione metabolism had many alterations either on the metabolic reactions or at the transcriptional level in the three cell lines. We identified Glutamate-cysteine ligase (GCL), a key enzyme of glutathione synthesis, as an important common feature that is dysregulated after EMT. Analyzing survival data of men with lung cancer, we observed that patients with mutations in GCL catalytic subunit (GCLC) or Glutathione peroxidase 1 (GPX1) genes survived less time than people without mutations on these genes. Besides, patients with low expression of ANPEP, GPX3 and GLS genes also survived less time than those with high expression. Hence, we propose that glutathione metabolism and glutathione itself could be good targets to delay or potentially prevent EMT induction in NSCLC cell lines.
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Affiliation(s)
- Meztli Matadamas-Guzman
- Programa de Doctorado en Ciencias Biomédicas, UNAM, Mexico City, Mexico.,Human Systems Biology Lab, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Cecilia Zazueta
- Departamento de Biomedicina Cardiovascular, Instituto Nacional de Cardiología-Ignacio Chávez, Mexico City, Mexico
| | - Emilio Rojas
- Department of Genomic Medicine and Environmental Toxicology, Institute of Biomedical Research, UNAM, Mexico City, Mexico
| | - Osbaldo Resendis-Antonio
- Human Systems Biology Lab, National Institute of Genomic Medicine, Mexico City, Mexico.,Coordinación de la Investigación Científica-Red de Apoyo a la Investigación, UNAM, Mexico City, Mexico
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25
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Ghergurovich JM, Esposito M, Chen Z, Wang JZ, Bhatt V, Lan T, White E, Kang Y, Guo JY, Rabinowitz JD. Glucose-6-Phosphate Dehydrogenase Is Not Essential for K-Ras-Driven Tumor Growth or Metastasis. Cancer Res 2020; 80:3820-3829. [PMID: 32661137 DOI: 10.1158/0008-5472.can-19-2486] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 04/30/2020] [Accepted: 07/07/2020] [Indexed: 12/21/2022]
Abstract
The enzyme glucose-6-phosphate dehydrogenase (G6PD) is a major contributor to NADPH production and redox homeostasis and its expression is upregulated and correlated with negative patient outcomes in multiple human cancer types. Despite these associations, whether G6PD is essential for tumor initiation, growth, or metastasis remains unclear. Here, we employ modern genetic tools to evaluate the role of G6PD in lung, breast, and colon cancer driven by oncogenic K-Ras. Human HCT116 colorectal cancer cells lacking G6PD exhibited metabolic indicators of oxidative stress, but developed into subcutaneous xenografts with growth comparable with that of wild-type controls. In a genetically engineered mouse model of non-small cell lung cancer driven by K-Ras G12D and p53 deficiency, G6PD knockout did not block formation or proliferation of primary lung tumors. In MDA-MB-231-derived human triple-negative breast cancer cells implanted as orthotopic xenografts, loss of G6PD modestly decreased primary site growth without ablating spontaneous metastasis to the lung and moderately impaired the ability of breast cancer cells to colonize the lung when delivered via tail vein injection. Thus, in the studied K-Ras tumor models, G6PD was not strictly essential for tumorigenesis and at most modestly promoted disease progression. SIGNIFICANCE: K-Ras-driven tumors can grow and metastasize even in the absence of the oxidative pentose pathway, a main NADPH production route.
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Affiliation(s)
- Jonathan M Ghergurovich
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey.,Department of Molecular Biology, Princeton University, Princeton, New Jersey
| | - Mark Esposito
- Department of Molecular Biology, Princeton University, Princeton, New Jersey
| | - Zihong Chen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey.,Department of Chemistry, Princeton University, Princeton, New Jersey
| | - Joshua Z Wang
- Department of Chemistry, Princeton University, Princeton, New Jersey
| | - Vrushank Bhatt
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Taijin Lan
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Eileen White
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey.,Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey
| | - Yibin Kang
- Department of Molecular Biology, Princeton University, Princeton, New Jersey
| | - Jessie Yanxiang Guo
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey. .,Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey.,Department of Chemical Biology, Rutgers Ernest Mario School of Pharmacy, Piscataway, New Jersey
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey. .,Department of Chemistry, Princeton University, Princeton, New Jersey
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26
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Bao F, Deng Y, Du M, Ren Z, Wan S, Liang KY, Liu S, Wang B, Xin J, Chen F, Christiani DC, Wang M, Dai Q. Explaining the Genetic Causality for Complex Phenotype via Deep Association Kernel Learning. Patterns (N Y) 2020; 1:100057. [PMID: 33205126 PMCID: PMC7660384 DOI: 10.1016/j.patter.2020.100057] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 05/25/2020] [Accepted: 06/01/2020] [Indexed: 02/07/2023]
Abstract
The genetic effect explains the causality from genetic mutations to the development of complex diseases. Existing genome-wide association study (GWAS) approaches are always built under a linear assumption, restricting their generalization in dissecting complicated causality such as the recessive genetic effect. Therefore, a sophisticated and general GWAS model that can work with different types of genetic effects is highly desired. Here, we introduce a deep association kernel learning (DAK) model to enable automatic causal genotype encoding for GWAS at pathway level. DAK can detect both common and rare variants with complicated genetic effects where existing approaches fail. When applied to four real-world GWAS datasets including cancers and schizophrenia, our DAK discovered potential casual pathways, including the association between dilated cardiomyopathy pathway and schizophrenia.
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Affiliation(s)
- Feng Bao
- Department of Automation, Tsinghua University, Beijing 100084, China.,Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China
| | - Yue Deng
- School of Astronautics, Beihang University, Beijing 100191, China.,Beijing Advanced Innovation Center for Big Data and Brain Computing, Beihang University, Beijing 100191, China
| | - Mulong Du
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.,Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Zhiquan Ren
- Department of Automation, Tsinghua University, Beijing 100084, China
| | - Sen Wan
- Department of Automation, Tsinghua University, Beijing 100084, China
| | - Kenny Ye Liang
- Department of Automation, Tsinghua University, Beijing 100084, China
| | - Shaohua Liu
- School of Astronautics, Beihang University, Beijing 100191, China
| | - Bo Wang
- School of Astronautics, Beihang University, Beijing 100191, China
| | - Junyi Xin
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Feng Chen
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - David C Christiani
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.,Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Meilin Wang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing 100084, China.,Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China
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27
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Tabuso M, Christian M, Kimani PK, Gopalakrishnan K, Arasaradnam RP. KRAS Status is Associated with Metabolic Parameters in Metastatic Colorectal Cancer According to Primary Tumour Location. Pathol Oncol Res 2020; 26:2537-2548. [PMID: 32594310 PMCID: PMC7471139 DOI: 10.1007/s12253-020-00850-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 06/11/2020] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) is characterized by complex interplay between macroenvironmental factors and tumour microenvironment, leading to variable outcomes in CRC patients. To date, there is still a need to identify macroenvironment/microenvironment factors that could define subgroup of patients that would benefit from specific anti-cancer treatment in order to improve patient selection for individualized targeted-based therapy. Aim of this study was to evaluate associations between metabolic parameters and KRAS status in metastatic CRC (mCRC) according to a new tumour site classification. Retrospective data were extracted from a total of 201 patients diagnosed with mCRC between 2012 and 2017 extracted from an established CRC database at our tertiary institute. Clinical-pathological data, including age, gender, BMI, hypertension, diabetes, pre-CRC diagnosis serum lipid levels and KRAS status were recorded. Categorical characteristics were compared using chi-squared test. Continuous characteristics were compared using Mann-Whitney U test. Log rank test was used to compare hazards for survival. In all comparisons, a two-sided P value <0.05 was considered statistically significant. Out of 201 patients, 170 patients with complete serum lipid profile were included in the analysis. In recto-sigmoid cancers there was a statistically significant association between high cholesterol:high-density lipoprotein (chol:HDL) ratio and KRAS mutation (OR 2.69, 95% CI 1.1–6.4, p = 0,02). In non recto-sigmoid cancers, high cholesterol was associated with KRAS WT (OR 0.39, CI 0.15–0.97, p = 0.04). In 22 patients with KRAS mutated recto-sigmoid cancer stage IV at diagnosis normal chol:HDL ratio was associated with a trend to better survival (p = 0.06). High chol:HDL ratio was significantly associated with KRAS mutated metastatic recto-sigmoid cancers. A subgroup of mCRC patients with KRAS mutated recto-sigmoid cancer may benefit from optimal lipid lowering treatment.
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Affiliation(s)
- M Tabuso
- Department of Gastroenterology, University Hospital Coventry and Warwickshire, Clifford Bridge Road, Coventry, CV2 2DX, UK. .,Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK.
| | - M Christian
- School of Science and Technology, Nottingham Trent University, Nottingham, NG11 8NS, UK
| | - P K Kimani
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - K Gopalakrishnan
- Department of Pathology, University Hospitals of Coventry and Warwickshire NHS Trust, Clifford Bridge Road, Coventry, CV2 2DX, UK
| | - R P Arasaradnam
- Department of Gastroenterology, University Hospital Coventry and Warwickshire, Clifford Bridge Road, Coventry, CV2 2DX, UK.,The University of Warwick, School of life Sciences, Coventry, CV4 7AL, UK.,Faculty of Health and Life Sciences, University of Coventry, Priory Street, Coventry, CV1 5BF, UK.,University of Leicester, Leicester, LE1 7RH, UK
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28
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Schmidt S, Denk S, Wiegering A. Targeting Protein Synthesis in Colorectal Cancer. Cancers (Basel) 2020; 12:cancers12051298. [PMID: 32455578 PMCID: PMC7281195 DOI: 10.3390/cancers12051298] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/15/2020] [Accepted: 05/19/2020] [Indexed: 12/19/2022] Open
Abstract
Under physiological conditions, protein synthesis controls cell growth and survival and is strictly regulated. Deregulation of protein synthesis is a frequent event in cancer. The majority of mutations found in colorectal cancer (CRC), including alterations in the WNT pathway as well as activation of RAS/MAPK and PI3K/AKT and, subsequently, mTOR signaling, lead to deregulation of the translational machinery. Besides mutations in upstream signaling pathways, deregulation of global protein synthesis occurs through additional mechanisms including altered expression or activity of initiation and elongation factors (e.g., eIF4F, eIF2α/eIF2B, eEF2) as well as upregulation of components involved in ribosome biogenesis and factors that control the adaptation of translation in response to stress (e.g., GCN2). Therefore, influencing mechanisms that control mRNA translation may open a therapeutic window for CRC. Over the last decade, several potential therapeutic strategies targeting these alterations have been investigated and have shown promising results in cell lines, intestinal organoids, and mouse models. Despite these encouraging in vitro results, patients have not clinically benefited from those advances so far. In this review, we outline the mechanisms that lead to deregulated mRNA translation in CRC and highlight recent progress that has been made in developing therapeutic strategies that target these mechanisms for tumor therapy.
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Affiliation(s)
- Stefanie Schmidt
- Department of Biochemistry and Molecular Biology, Theodor Boveri Institute, Biocenter, University of Würzburg, 97074 Würzburg, Germany; (S.S.); (S.D.)
- Department of General, Visceral, Transplant, Vascular and Pediatric Surgery, University Hospital Würzburg, 97074 Würzburg, Germany
| | - Sarah Denk
- Department of Biochemistry and Molecular Biology, Theodor Boveri Institute, Biocenter, University of Würzburg, 97074 Würzburg, Germany; (S.S.); (S.D.)
- Department of General, Visceral, Transplant, Vascular and Pediatric Surgery, University Hospital Würzburg, 97074 Würzburg, Germany
| | - Armin Wiegering
- Department of Biochemistry and Molecular Biology, Theodor Boveri Institute, Biocenter, University of Würzburg, 97074 Würzburg, Germany; (S.S.); (S.D.)
- Department of General, Visceral, Transplant, Vascular and Pediatric Surgery, University Hospital Würzburg, 97074 Würzburg, Germany
- Department of Biochemistry and Molecular Biology, Comprehensive Cancer Center Mainfranken, University of Würzburg, 97074 Würzburg, Germany
- Correspondence: ; Tel.: +49-931-20138714
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29
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Rink AD, Kienle P, Aigner F, Ulrich A. How to reduce anastomotic leakage in colorectal surgery-report from German expert meeting. Langenbecks Arch Surg 2020; 405:223-232. [PMID: 32189067 DOI: 10.1007/s00423-020-01864-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 03/05/2020] [Indexed: 01/16/2023]
Abstract
AIMS Anastomotic leakage is one of the most worrisome complications in colorectal surgery. An expert meeting was organized to discuss and find a consensus on various aspects of the surgical management of colorectal disease with a possible impact on anastomotic leakage. METHODS A three-step Delphi-method was used to find consensus recommendations. RESULTS Strong consensus was achieved for the use of mechanical bowel preparation and oral antibiotics prior to colorectal resections, the abundance of non-selective NSAIDs, the preoperative treatment of severe iron deficiency anemia, and for attempting to improve the patients' general performance in the case of frailty. Concerning technical aspects of rectal resection, there was a strong consensus in regard to routinely mobilizing the splenic flexure, to dividing the inferior mesenteric vein, and to using air leak tests to check anastomotic integrity. There was also a strong consensus on not to oversew the stapled anastomoses routinely, to use protective ileostomies for low rectal and intersphincteric, but not for high-rectal anastomoses. Furthermore, a consensus was reached in regard to using CT-scans with rectal contrast enema to evaluate suspected anastomotic leakage as well as measuring C-reactive protein routinely to monitor the postoperative course after colorectal resections. No consensus was found concerning the indication and technique for testing bowel perfusion, the routine use of endoscopy to check the integrity of the anastomosis, the placement of transanal drains for rectal anastomoses and the management of anastomotic leakage with peritonitis. CONCLUSION Consensus could be found for several practice details in the perioperative management in colorectal surgery that might have an influence on anastomotic leakage.
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Affiliation(s)
- Andreas D Rink
- Klinik für Allgemein-, Viszeral- und Thoraxchirurgie, Klinikum Leverkusen gGmbH, Am Gesundheitspark 11, 51375, Leverkusen, Germany.
- Klinik für Allgemein-, Viszeral- und Transplantationschirurgie, Universitätsmedizin der Johannes Gutenberg-Universität Mainz, Mainz, Germany.
| | - Peter Kienle
- Klinik für Allgemein- und Viszeralchirurgie, Theresienkrankenhaus und St. Hedwig-Klinik GmbH, Mannheim, Germany
| | - Felix Aigner
- Chirurgische Klinik Campus Charité Mitte/Campus Virchow, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Alexis Ulrich
- Chirurgische Klinik I, Rheinland Klinikum GmbH, Lukaskrankenhaus Neuss, Neuss, Germany
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30
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Kennedy SA, Jarboui MA, Srihari S, Raso C, Bryan K, Dernayka L, Charitou T, Bernal-Llinares M, Herrera-Montavez C, Krstic A, Matallanas D, Kotlyar M, Jurisica I, Curak J, Wong V, Stagljar I, LeBihan T, Imrie L, Pillai P, Lynn MA, Fasterius E, Al-Khalili Szigyarto C, Breen J, Kiel C, Serrano L, Rauch N, Rukhlenko O, Kholodenko BN, Iglesias-Martinez LF, Ryan CJ, Pilkington R, Cammareri P, Sansom O, Shave S, Auer M, Horn N, Klose F, Ueffing M, Boldt K, Lynn DJ, Kolch W. Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRAS G13D. Nat Commun 2020; 11:499. [PMID: 31980649 PMCID: PMC6981206 DOI: 10.1038/s41467-019-14224-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023] Open
Abstract
Protein-protein-interaction networks (PPINs) organize fundamental biological processes, but how oncogenic mutations impact these interactions and their functions at a network-level scale is poorly understood. Here, we analyze how a common oncogenic KRAS mutation (KRASG13D) affects PPIN structure and function of the Epidermal Growth Factor Receptor (EGFR) network in colorectal cancer (CRC) cells. Mapping >6000 PPIs shows that this network is extensively rewired in cells expressing transforming levels of KRASG13D (mtKRAS). The factors driving PPIN rewiring are multifactorial including changes in protein expression and phosphorylation. Mathematical modelling also suggests that the binding dynamics of low and high affinity KRAS interactors contribute to rewiring. PPIN rewiring substantially alters the composition of protein complexes, signal flow, transcriptional regulation, and cellular phenotype. These changes are validated by targeted and global experimental analysis. Importantly, genetic alterations in the most extensively rewired PPIN nodes occur frequently in CRC and are prognostic of poor patient outcomes.
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Affiliation(s)
- Susan A Kennedy
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | - Mohamed-Ali Jarboui
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
- Werner Siemens Imaging Center, University of Tübingen, Tübingen, Germany
| | - Sriganesh Srihari
- EMBL Australia Group, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
- QIMR-Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Cinzia Raso
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | - Kenneth Bryan
- EMBL Australia Group, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Layal Dernayka
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Theodosia Charitou
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
- EMBL Australia Group, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Manuel Bernal-Llinares
- EMBL Australia Group, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | | | | | - David Matallanas
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | - Max Kotlyar
- Krembil Research Institute, University Health Network, Toronto, Canada
| | - Igor Jurisica
- Krembil Research Institute, University Health Network, Toronto, Canada
- Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Jasna Curak
- Donnelly Centre, University of Toronto, Toronto, Canada
- Department of Biochemistry, University of Toronto, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Victoria Wong
- Donnelly Centre, University of Toronto, Toronto, Canada
- Department of Biochemistry, University of Toronto, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Igor Stagljar
- Donnelly Centre, University of Toronto, Toronto, Canada
- Department of Biochemistry, University of Toronto, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Mediterranean Institute for Life Sciences, Split, Croatia
| | - Thierry LeBihan
- Synthetic and Systems Biology, University of Edinburgh, Edinburgh, UK
| | - Lisa Imrie
- Synthetic and Systems Biology, University of Edinburgh, Edinburgh, UK
| | - Priyanka Pillai
- EMBL Australia Group, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Miriam A Lynn
- EMBL Australia Group, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Erik Fasterius
- School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Cristina Al-Khalili Szigyarto
- School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - James Breen
- School of Biological Sciences, University of Adelaide Bioinformatics Hub, Adelaide, SA, Australia
- Computational & Systems Biology Program, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Christina Kiel
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Conway Institute, University College Dublin, Dublin, Ireland
| | - Luis Serrano
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Nora Rauch
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | | | - Boris N Kholodenko
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
- Conway Institute, University College Dublin, Dublin, Ireland
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Colm J Ryan
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
- School of Computer Science, University College Dublin, Dublin, Ireland
| | - Ruth Pilkington
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | | | - Owen Sansom
- Cancer Research UK Beatson Institute, Glasgow, UK
- Institute of Cancer Studies, Glasgow University, Glasgow, UK
| | - Steven Shave
- School of Biological Sciences and School of Biomedical Sciences, University of Edinburgh, Edinburgh, UK
| | - Manfred Auer
- School of Biological Sciences and School of Biomedical Sciences, University of Edinburgh, Edinburgh, UK
| | - Nicola Horn
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Franziska Klose
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Marius Ueffing
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Karsten Boldt
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany.
| | - David J Lynn
- EMBL Australia Group, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia.
- College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia.
| | - Walter Kolch
- Systems Biology Ireland, University College Dublin, Dublin, Ireland.
- Conway Institute, University College Dublin, Dublin, Ireland.
- School of Medicine, University College Dublin, Dublin, Ireland.
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31
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Abstract
In human cells, three closely related RAS genes, termed HRAS, KRAS, and NRAS, encode four highly homologous proteins. RAS proteins are small GTPases involved in a broad spectrum of key molecular and cellular activities, including proliferation and survival among others. Gain-of-function missense mutations, mostly located at codons 12, 13, and 61, constitutively activate RAS proteins and can be detected in various types of human cancers. KRAS is the most frequently mutated, followed by NRAS and HRAS. However, each isoform exhibits distinctive mutation frequency at each codon, supporting the hypothesis that different RAS mutants may lead to distinct biologic manifestations. This review is focused on the differences in signaling and phenotype, as well as on transcriptomics, proteomics, and metabolomics profiles related to individual RAS-mutated variants. Additionally, association of these mutants with particular targeted outcomes and rare mutations at additional RAS codons are discussed.
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Affiliation(s)
- Carmen Muñoz-Maldonado
- Department of Radiation Oncology, Inselspital, Bern University Hospital, Bern, Switzerland.,Radiation Oncology, Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Yitzhak Zimmer
- Department of Radiation Oncology, Inselspital, Bern University Hospital, Bern, Switzerland.,Radiation Oncology, Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Michaela Medová
- Department of Radiation Oncology, Inselspital, Bern University Hospital, Bern, Switzerland.,Radiation Oncology, Department for BioMedical Research, University of Bern, Bern, Switzerland
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32
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Magalhaes I, Yogev O, Mattsson J, Schurich A. The Metabolic Profile of Tumor and Virally Infected Cells Shapes Their Microenvironment Counteracting T Cell Immunity. Front Immunol 2019; 10:2309. [PMID: 31636636 PMCID: PMC6788393 DOI: 10.3389/fimmu.2019.02309] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 09/12/2019] [Indexed: 12/11/2022] Open
Abstract
Upon activation naïve T cells undergo metabolic changes to support the differentiation into subsets of effector or regulatory cells, and enable subsequent metabolic adaptations to form memory. Interfering with these metabolic alterations leads to abrogation or reprogramming of T cell differentiation, demonstrating the importance of these pathways in T cell development. It has long been appreciated that the conversion of a healthy cell to a cancerous cell is accompanied by metabolic changes, which support uncontrolled proliferation. Especially in solid tumors these metabolic changes significantly influence the tumor microenvironment (TME) and affect tumor infiltrating immune cells. The TME is often hypoxic and nutrient depleted, additionally tumor cells produce co-inhibitory signals, together suppressing the immune response. Interestingly, viruses can stimulate a metabolism akin to that seen in tumor cells in their host cells and even in neighboring cells (e.g., via transfer of virally modified extracellular vesicles). Thus, viruses create their own niche which favors viral persistence and propagation, while again keeping the immune response at bay. In this review we will focus on the mechanisms employed by tumor cells and viruses influencing T cell metabolic regulation and the impact they have on shaping T cell fate.
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Affiliation(s)
- Isabelle Magalhaes
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Ohad Yogev
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Jonas Mattsson
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Gloria and Seymour Epstein Chair in Cell Therapy and Transplantation, Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
- Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Anna Schurich
- Department of Infectious Diseases, King's College London, London, United Kingdom
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33
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Mottini C, Napolitano F, Li Z, Gao X, Cardone L. Computer-aided drug repurposing for cancer therapy: Approaches and opportunities to challenge anticancer targets. Semin Cancer Biol 2021; 68:59-74. [PMID: 31562957 DOI: 10.1016/j.semcancer.2019.09.023] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/24/2019] [Accepted: 09/24/2019] [Indexed: 12/14/2022]
Abstract
Despite huge efforts made in academic and pharmaceutical worldwide research, current anticancer therapies achieve effective treatment in a limited number of neoplasia cases only. Oncology terms such as big killers - to identify tumours with yet a high mortality rate - or undruggable cancer targets, and chemoresistance, represent the current therapeutic debacle of cancer treatments. In addition, metastases, tumour microenvironments, tumour heterogeneity, metabolic adaptations, and immunotherapy resistance are essential features controlling tumour response to therapies, but still, lack effective therapeutics or modulators. In this scenario, where the pharmaceutical productivity and drug efficacy in oncology seem to have reached a plateau, the so-called drug repurposing - i.e. the use of old drugs, already in clinical use, for a different therapeutic indication - is an appealing strategy to improve cancer therapy. Opportunities for drug repurposing are often based on occasional observations or on time-consuming pre-clinical drug screenings that are often not hypothesis-driven. In contrast, in-silico drug repurposing is an emerging, hypothesis-driven approach that takes advantage of the use of big-data. Indeed, the extensive use of -omics technologies, improved data storage, data meaning, machine learning algorithms, and computational modeling all offer unprecedented knowledge of the biological mechanisms of cancers and drugs' modes of action, providing extensive availability for both disease-related data and drugs-related data. This offers the opportunity to generate, with time and cost-effective approaches, computational drug networks to predict, in-silico, the efficacy of approved drugs against relevant cancer targets, as well as to select better responder patients or disease' biomarkers. Here, we will review selected disease-related data together with computational tools to be exploited for the in-silico repurposing of drugs against validated targets in cancer therapies, focusing on the oncogenic signaling pathways activation in cancer. We will discuss how in-silico drug repurposing has the promise to shortly improve our arsenal of anticancer drugs and, likely, overcome certain limitations of modern cancer therapies against old and new therapeutic targets in oncology.
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