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Zarlenga DS, Hoberg EP, Thompson P, Rosenthal B. Trichinella: Becoming a parasite. Vet Parasitol 2024:110220. [PMID: 38910035 DOI: 10.1016/j.vetpar.2024.110220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/25/2024]
Abstract
Phylogenetic evidence indicates that free-living nematodes gave rise to parasitic nematodes where parasitism evolved independently at least 15 times. The high level of genetic and biological diversity among parasites dictates an equally high level of diversity in the transition to parasitism. We previously hypothesized that horizontal gene transfer (HGT) played an important role in the evolution of parasitism among early ancestors of Trichinella, mediated by an interplay of ecological and evolutionary pathways that contributed to persistence and diversification. We propose that host selection may have been associated with the metabolism of ammonia and engender a new paradigm whereby the reprogrammed nurse cell is capable of generating cyanate thereby enabling the importance of the Trichinella cyanase in the longevity of the cell. Parasites and parasitism have revealed considerable resilience against a backdrop of climate change and environmental perturbation. Here we provide a putative link between key periods in the evolution of Trichinella and major geological and climatological events dating back 500 million years. A useful lens for exploring such ideas, the Stockholm Paradigm, integrates Ecological Fitting (a foundation for host colonization and diversification), the Oscillation Hypothesis (recurring shifts between trends in generalization and specialization relative to host range), the Geographic Mosaic Theory of Coevolution (microevolutionary co-adaptive processes), and the Taxon Pulse Hypothesis (alternating events of biotic expansion i.e., exploitation in evolutionary and ecological time). Here we examine how one or more of these interactive theories, in a phylogenetic-historical context and in conjunction with HGT, may help explain the scope and depth of diversity among Trichinella genotypes.
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Affiliation(s)
- Dante S Zarlenga
- USDA-Agricultural Research Service, Animal Parasitic Diseases Lab, Beltsville, MD, USA.
| | - Eric P Hoberg
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA; Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, WI, USA
| | - Peter Thompson
- USDA-Agricultural Research Service, Animal Parasitic Diseases Lab, Beltsville, MD, USA
| | - Benjamin Rosenthal
- USDA-Agricultural Research Service, Animal Parasitic Diseases Lab, Beltsville, MD, USA
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2
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Maekawa M, Tanaka A, Ogawa M, Roehrl MH. Propensity score matching as an effective strategy for biomarker cohort design and omics data analysis. PLoS One 2024; 19:e0302109. [PMID: 38696425 PMCID: PMC11065211 DOI: 10.1371/journal.pone.0302109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/27/2024] [Indexed: 05/04/2024] Open
Abstract
BACKGROUND Analysis of omics data that contain multidimensional biological and clinical information can be complex and make it difficult to deduce significance of specific biomarker factors. METHODS We explored the utility of propensity score matching (PSM), a statistical technique for minimizing confounding factors and simplifying the examination of specific factors. We tested two datasets generated from cohorts of colorectal cancer (CRC) patients, one comprised of immunohistochemical analysis of 12 protein markers in 544 CRC tissues and another consisting of RNA-seq profiles of 163 CRC cases. We examined the efficiency of PSM by comparing pre- and post-PSM analytical results. RESULTS Unlike conventional analysis which typically compares randomized cohorts of cancer and normal tissues, PSM enabled direct comparison between patient characteristics uncovering new prognostic biomarkers. By creating optimally matched groups to minimize confounding effects, our study demonstrates that PSM enables robust extraction of significant biomarkers while requiring fewer cancer cases and smaller overall patient cohorts. CONCLUSION PSM may emerge as an efficient and cost-effective strategy for multiomic data analysis and clinical trial design for biomarker discovery.
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Affiliation(s)
- Masaki Maekawa
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, United States of America
- Harvard Medical School, Boston, MA, United States of America
- Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
| | - Atsushi Tanaka
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, United States of America
- Harvard Medical School, Boston, MA, United States of America
- Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
| | - Makiko Ogawa
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, United States of America
- Harvard Medical School, Boston, MA, United States of America
- Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
| | - Michael H. Roehrl
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, United States of America
- Harvard Medical School, Boston, MA, United States of America
- Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
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3
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Hajaj E, Pozzi S, Erez A. From the Inside Out: Exposing the Roles of Urea Cycle Enzymes in Tumors and Their Micro and Macro Environments. Cold Spring Harb Perspect Med 2024; 14:a041538. [PMID: 37696657 PMCID: PMC10982720 DOI: 10.1101/cshperspect.a041538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
Catabolic pathways change in anabolic diseases such as cancer to maintain metabolic homeostasis. The liver urea cycle (UC) is the main catabolic pathway for disposing excess nitrogen. Outside the liver, the UC enzymes are differentially expressed based on each tissue's needs for UC intermediates. In tumors, there are changes in the expression of UC enzymes selected for promoting tumorigenesis by increasing the availability of essential UC substrates and products. Consequently, there are compensatory changes in the expression of UC enzymes in the cells that compose the tumor microenvironment. Moreover, extrahepatic tumors induce changes in the expression of the liver UC, which contribute to the systemic manifestations of cancer, such as weight loss. Here, we review the multilayer changes in the expression of UC enzymes throughout carcinogenesis. Understanding the changes in UC expression in the tumor and its micro and macro environment can help identify biomarkers for early cancer diagnosis and vulnerabilities that can be targeted for therapy.
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Affiliation(s)
- Emma Hajaj
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sabina Pozzi
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ayelet Erez
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
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Mahé M, Rios-Fuller TJ, Karolin A, Schneider RJ. Genetics of enzymatic dysfunctions in metabolic disorders and cancer. Front Oncol 2023; 13:1230934. [PMID: 37601653 PMCID: PMC10433910 DOI: 10.3389/fonc.2023.1230934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 07/19/2023] [Indexed: 08/22/2023] Open
Abstract
Inherited metabolic disorders arise from mutations in genes involved in the biogenesis, assembly, or activity of metabolic enzymes, leading to enzymatic deficiency and severe metabolic impairments. Metabolic enzymes are essential for the normal functioning of cells and are involved in the production of amino acids, fatty acids and nucleotides, which are essential for cell growth, division and survival. When the activity of metabolic enzymes is disrupted due to mutations or changes in expression levels, it can result in various metabolic disorders that have also been linked to cancer development. However, there remains much to learn regarding the relationship between the dysregulation of metabolic enzymes and metabolic adaptations in cancer cells. In this review, we explore how dysregulated metabolism due to the alteration or change of metabolic enzymes in cancer cells plays a crucial role in tumor development, progression, metastasis and drug resistance. In addition, these changes in metabolism provide cancer cells with a number of advantages, including increased proliferation, resistance to apoptosis and the ability to evade the immune system. The tumor microenvironment, genetic context, and different signaling pathways further influence this interplay between cancer and metabolism. This review aims to explore how the dysregulation of metabolic enzymes in specific pathways, including the urea cycle, glycogen storage, lysosome storage, fatty acid oxidation, and mitochondrial respiration, contributes to the development of metabolic disorders and cancer. Additionally, the review seeks to shed light on why these enzymes represent crucial potential therapeutic targets and biomarkers in various cancer types.
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Affiliation(s)
| | | | | | - Robert J. Schneider
- Department of Microbiology, Grossman NYU School of Medicine, New York, NY, United States
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5
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Unraveling the therapeutic potential of carbamoyl phosphate synthetase 1 (CPS1) in human disease. Bioorg Chem 2022; 130:106253. [DOI: 10.1016/j.bioorg.2022.106253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/23/2022] [Accepted: 11/01/2022] [Indexed: 11/07/2022]
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6
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Qi Q, Zhong R, Liu YN, Zhao C, Huang Y, Lu Y, Ma Z, Zheng HD, Wu LY. Mechanism of electroacupuncture and herb-partitioned moxibustion on ulcerative colitis animal model: A study based on proteomics. World J Gastroenterol 2022; 28:3644-3665. [PMID: 36161055 PMCID: PMC9372807 DOI: 10.3748/wjg.v28.i28.3644] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 11/19/2021] [Accepted: 06/26/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Ulcerative colitis (UC) is a chronic, nonspecific intestinal inflammatory disease. Acupuncture and moxibustion is proved effective in treating UC, but the mechanism has not been clarified. Proteomic technology has revealed a variety of biological markers related to immunity and inflammation in UC, which provide new insights and directions for the study of mechanism of acupuncture and moxibustion treatment of UC.
AIM To investigate the mechanism of electroacupuncture (EA) and herb-partitioned moxibustion (HM) on UC rats by using proteomics technology.
METHODS Male Sprague-Dawley rats were randomly divided into the normal (N) group, the dextran sulfate sodium (DSS)-induced UC model (M) group, the HM group, and the EA group. UC rat model was prepared with 3% DSS, and HM and EA interventions at the bilateral Tianshu and Qihai acupoints were performed in HM or EA group. Haematoxylin and eosin staining was used for morphological evaluation of colon tissues. Isotope-labeled relative and absolute quantification (iTRAQ) and liquid chromatography-tandem mass spectrometry were performed for proteome analysis of the colon tissues, followed by bioinformatics analysis and protein-protein interaction networks establishment of differentially expressed proteins (DEPs) between groups. Then western blot was used for verification of selected DEPs.
RESULTS The macroscopic colon injury scores and histopathology scores in the HM and EA groups were significantly decreased compared to the rats in the M group (P < 0.01). Compared with the N group, a total of 202 DEPs were identified in the M group, including 111 up-regulated proteins and 91 down-regulated proteins, of which 25 and 15 proteins were reversed after HM and EA interventions, respectively. The DEPs were involved in various biological processes such as biological regulation, immune system progression and in multiple pathways including natural killer cell mediated cytotoxicity, intestinal immune network for immunoglobulin A (IgA) production, and FcγR-mediated phagocytosis. The Kyoto Encyclopedia of Genes and Genomes pathways of DEPs between HM and M groups, EA and M groups both included immune-associated and oxidative phosphorylation. Network analysis revealed that multiple pathways for the DEPs of each group were involved in protein-protein interactions, and the expression of oxidative phosphorylation pathway-related proteins, including ATP synthase subunit g (ATP5L), ATP synthase beta subunit precursor (Atp5f), cytochrome c oxidase subunit 4 isoform 1 (Cox4i1) were down-regulated after HM and EA interventions. Subsequent verification of selected DEPs (Synaptic vesicle glycoprotein 2A; nuclear cap binding protein subunit 1; carbamoyl phosphate synthetase 1; Cox4i1; ATP synthase subunit b, Atp5f1; doublecortin like kinase 3) by western blot confirmed the reliability of the iTRAQ data, HM and EA interventions can significantly down-regulate the expression of oxidative phosphorylation-associated proteins (Cox4i1, Atp5f1) (P < 0.01).
CONCLUSION EA and HM could regulate the expression of ATP5L, Atp5f1, Cox4i1 that associated with oxidative phosphorylation, then might regulate immune-related pathways of intestinal immune network for IgA production, FcγR-mediated phagocytosis, thereby alleviating colonic inflammation of DSS-induced UC rats.
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Affiliation(s)
- Qin Qi
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, China
| | - Rui Zhong
- Shanghai QiGong Research Institute, Shanghai University of Traditional Chinese Medicine, Shanghai 200030, China
| | - Ya-Nan Liu
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, China
| | - Chen Zhao
- School of Acupuncture, Moxibustion and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yan Huang
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, China
| | - Yuan Lu
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, China
| | - Zhe Ma
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, China
| | - Han-Dan Zheng
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, China
| | - Lu-Yi Wu
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, China
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Caruntu A, Moraru L, Ciubotaru DA, Tanase C, Scheau C, Caruntu C. Assessment of Serum Urea, Creatinine and Uric Acid in Oral Cancer. J Clin Med 2022; 11:jcm11123459. [PMID: 35743528 PMCID: PMC9225481 DOI: 10.3390/jcm11123459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/12/2022] [Accepted: 06/14/2022] [Indexed: 02/01/2023] Open
Abstract
Background: Oral squamous cell carcinoma (OSCC) is a common malignancy worldwide, leading to significant disease-associated social and financial burdens. The investigation of underlying mechanisms involved in carcinogenesis and tumor progression in OSCC might provide new therapeutic perspectives with an impact on disease control and patient survival. Our study aims to investigate the interrelation between metabolic processes, expressed through final catabolism products and clinicopathological characteristics in OSCC. Materials and methods: This is a single cancer comparative retrospective study investigating metabolic byproducts, namely serum urea, creatinine and uric acid, detected at the moment of diagnosis in patients with OSCC, in comparison to healthy controls. Clinical and paraclinical data regarding exposure to risk factors, disease staging and pathological characteristics were collected for all patients. Subjects with co-existing systemic or metabolic diseases, or with a history of malignancy, were excluded from the study. Subsequently, the metabolic byproducts revealing significant changes in OSCC patients were considered for a correlation analysis with the disease clinico-pathological characteristics. Results: Blood levels for urea, creatinine and uric acid were determined in a total of 225 subjects: 145 patients diagnosed with OSCC and 80 healthy control subjects admitted to our hospital between 2016 and 2021. The comparative analysis between groups revealed that the serum urea level was significantly lower in OSCC patients (p = 0.0344). Serum creatinine and uric acid did not reveal significant differences between groups. Furthermore, in advanced stages of the disease (stages III and IV), the blood level of urea was significantly lower compared to incipient OSCC (stages I and II) (p = 0.003). We found a negative correlation of serum urea levels with smoking (p = 0.0004) and cervical lymph node metastasis (p = 0.0070), and a positive correlation with aging (p = 0.0000). We found no significant correlation of serum urea with primary tumor size (p = 0.5061) and patient survival (p = 0.2932). Conclusions: Decreased serum urea levels are detected in patients with advanced OSCC, in correlation with lymph node metastasis. The invasive features of tumor cells in OSCC might be promoted in association with dysregulation of protein catabolism processes, facilitating aggressive behavior in OSCC.
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Affiliation(s)
- Ana Caruntu
- Department of Oral and Maxillofacial Surgery, “Carol Davila” Central Military Emergency Hospital, 010825 Bucharest, Romania; (A.C.); (L.M.); (D.A.C.)
- Department of Oral and Maxillofacial Surgery, Faculty of Dental Medicine, “Titu Maiorescu” University, 031593 Bucharest, Romania
| | - Liliana Moraru
- Department of Oral and Maxillofacial Surgery, “Carol Davila” Central Military Emergency Hospital, 010825 Bucharest, Romania; (A.C.); (L.M.); (D.A.C.)
- Department of Oral and Maxillofacial Surgery, Faculty of Dental Medicine, “Titu Maiorescu” University, 031593 Bucharest, Romania
| | - Diana Alina Ciubotaru
- Department of Oral and Maxillofacial Surgery, “Carol Davila” Central Military Emergency Hospital, 010825 Bucharest, Romania; (A.C.); (L.M.); (D.A.C.)
| | - Cristiana Tanase
- Proteomics Department, Cajal Institute, Faculty of Medicine, “Titu Maiorescu” University, 031593 Bucharest, Romania;
- Department of Biochemistry-Proteomics, “Victor Babes” National Institute of Pathology, 050096 Bucharest, Romania
| | - Cristian Scheau
- Department of Physiology, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania;
- Correspondence:
| | - Constantin Caruntu
- Department of Physiology, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania;
- Department of Dermatology, “Prof. N.C. Paulescu” National Institute of Diabetes, Nutrition and Metabolic Diseases, 011233 Bucharest, Romania
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The Role of TRIP6, ABCC3 and CPS1 Expression in Resistance of Ovarian Cancer to Taxanes. Int J Mol Sci 2021; 23:ijms23010073. [PMID: 35008510 PMCID: PMC8744980 DOI: 10.3390/ijms23010073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/18/2021] [Accepted: 12/19/2021] [Indexed: 02/07/2023] Open
Abstract
The main problem precluding successful therapy with conventional taxanes is de novo or acquired resistance to taxanes. Therefore, novel experimental taxane derivatives (Stony Brook taxanes; SB-Ts) are synthesized and tested as potential drugs against resistant solid tumors. Recently, we reported alterations in ABCC3, CPS1, and TRIP6 gene expression in a breast cancer cell line resistant to paclitaxel. The present study aimed to investigate gene expression changes of these three candidate molecules in the highly resistant ovarian carcinoma cells in vitro and corresponding in vivo models treated with paclitaxel and new experimental Stony Brook taxanes of the third generation (SB-T-121605 and SB-T-121606). We also addressed their prognostic meaning in ovarian carcinoma patients treated with taxanes. We estimated and observed changes in mRNA and protein profiles of ABCC3, CPS1, and TRIP6 in resistant and sensitive ovarian cancer cells and after the treatment of resistant ovarian cancer models with paclitaxel and Stony Brook taxanes in vitro and in vivo. Combining Stony Brook taxanes with paclitaxel caused downregulation of CPS1 in the paclitaxel-resistant mouse xenograft tumor model in vivo. Moreover, CPS1 overexpression seems to play a role of a prognostic biomarker of epithelial ovarian carcinoma patients’ poor survival. ABCC3 was overexpressed in EOC tumors, but after the treatment with taxanes, its up-regulation disappeared. Based on our results, we can suggest ABCC3 and CPS1 for further investigations as potential therapeutic targets in human cancers.
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Peng W, Lin C, Jing S, Su G, Jin X, Di G, Shao Z. A Novel Seven Gene Signature-Based Prognostic Model to Predict Distant Metastasis of Lymph Node-Negative Triple-Negative Breast Cancer. Front Oncol 2021; 11:746763. [PMID: 34604089 PMCID: PMC8481824 DOI: 10.3389/fonc.2021.746763] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 09/02/2021] [Indexed: 12/26/2022] Open
Abstract
Background The prognosis of lymph node-negative triple-negative breast cancer (TNBC) is still worse than that of other subtypes despite adjuvant chemotherapy. Reliable prognostic biomarkers are required to identify lymph node-negative TNBC patients at a high risk of distant metastasis and optimize individual treatment. Methods We analyzed the RNA sequencing data of primary tumor tissue and the clinicopathological data of 202 lymph node-negative TNBC patients. The cohort was randomly divided into training and validation sets. Least absolute shrinkage and selection operator Cox regression and multivariate Cox regression were used to construct the prognostic model. Results A clinical prognostic model, seven-gene signature, and combined model were constructed using the training set and validated using the validation set. The seven-gene signature was established based on the genomic variables associated with distant metastasis after shrinkage correction. The difference in the risk of distant metastasis between the low- and high-risk groups was statistically significant using the seven-gene signature (training set: P < 0.001; validation set: P = 0.039). The combined model showed significance in the training set (P < 0.001) and trended toward significance in the validation set (P = 0.071). The seven-gene signature showed improved prognostic accuracy relative to the clinical signature in the training data (AUC value of 4-year ROC, 0.879 vs. 0.699, P = 0.046). Moreover, the composite clinical and gene signature also showed improved prognostic accuracy relative to the clinical signature (AUC value of 4-year ROC: 0.888 vs. 0.699, P = 0.029; AUC value of 5-year ROC: 0.882 vs. 0.693, P = 0.038). A nomogram model was constructed with the seven-gene signature, patient age, and tumor size. Conclusions The proposed signature may improve the risk stratification of lymph node-negative TNBC patients. High-risk lymph node-negative TNBC patients may benefit from treatment escalation.
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Affiliation(s)
- Wenting Peng
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Breast Surgery, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Caijin Lin
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shanshan Jing
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Nursing Administration, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Guanhua Su
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xi Jin
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Genhong Di
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhiming Shao
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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Salahshouri P, Emadi-Baygi M, Jalili M, Khan FM, Wolkenhauer O, Salehzadeh-Yazdi A. A Metabolic Model of Intestinal Secretions: The Link between Human Microbiota and Colorectal Cancer Progression. Metabolites 2021; 11:metabo11070456. [PMID: 34357350 PMCID: PMC8303431 DOI: 10.3390/metabo11070456] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 12/22/2022] Open
Abstract
The human gut microbiota plays a dual key role in maintaining human health or inducing disorders, for example, obesity, type 2 diabetes, and cancers such as colorectal cancer (CRC). High-throughput data analysis, such as metagenomics and metabolomics, have shown the diverse effects of alterations in dynamic bacterial populations on the initiation and progression of colorectal cancer. However, it is well established that microbiome and human cells constantly influence each other, so it is not appropriate to study them independently. Genome-scale metabolic modeling is a well-established mathematical framework that describes the dynamic behavior of these two axes at the system level. In this study, we created community microbiome models of three conditions during colorectal cancer progression, including carcinoma, adenoma and health status, and showed how changes in the microbial population influence intestinal secretions. Conclusively, our findings showed that alterations in the gut microbiome might provoke mutations and transform adenomas into carcinomas. These alterations include the secretion of mutagenic metabolites such as H2S, NO compounds, spermidine and TMA (trimethylamine), as well as the reduction of butyrate. Furthermore, we found that the colorectal cancer microbiome can promote inflammation, cancer progression (e.g., angiogenesis) and cancer prevention (e.g., apoptosis) by increasing and decreasing certain metabolites such as histamine, glutamine and pyruvate. Thus, modulating the gut microbiome could be a promising strategy for the prevention and treatment of CRC.
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Affiliation(s)
- Pejman Salahshouri
- Department of Genetics, Faculty of Basic Sciences, Shahrekord University, Shahrekord 8818634141, Iran; (P.S.); (M.E.-B.)
| | - Modjtaba Emadi-Baygi
- Department of Genetics, Faculty of Basic Sciences, Shahrekord University, Shahrekord 8818634141, Iran; (P.S.); (M.E.-B.)
- Biotechnology Research Institute, Shahrekord University, Shahrekord 8818634141, Iran
| | - Mahdi Jalili
- Hematology, Oncology and SCT Research Center, Tehran University of Medical Sciences, Tehran 14114, Iran;
| | - Faiz M. Khan
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany; (F.M.K.); (O.W.)
| | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany; (F.M.K.); (O.W.)
| | - Ali Salehzadeh-Yazdi
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany; (F.M.K.); (O.W.)
- Correspondence:
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11
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Fang X, Wu X, Xiang E, Luo F, Li Q, Ma Q, Yuan F, Chen P. Expression profiling of CPS1 in Correa's cascade and its association with gastric cancer prognosis. Oncol Lett 2021; 21:441. [PMID: 33868479 PMCID: PMC8045184 DOI: 10.3892/ol.2021.12702] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 02/26/2021] [Indexed: 12/13/2022] Open
Abstract
Carbamoyl phosphate synthetase 1 (CPS1), which is the antigen for the hepatocyte paraffin 1 antibody, exhibits focal immunoreactivity in adenocarcinoma from the gastrointestinal tract, but its expression profiles and roles in gastric cancer (GC) remain largely unknown. The present study aimed to determine the expression pattern and prognostic value of CPS1 in Correa's cascade using tissues from 32 patients with chronic atrophic gastritis with intestinal metaplasia (IM), 62 patients with low- or high-grade intraepithelial neoplasia (IN) and 401 patients with GC. The expression of CPS1 was diffuse and strongly positive in 32 cases (100%) of IM of the glandular epithelium, and gradually downregulated in Correa's cascade, with a strongly positive ratio of 21 (70%) in low-grade IN and 4 (12.5%) in high-grade IN. The levels of CPS1 expression were significantly higher in diffuse-type GC, with 37 (26%) cases strongly positive for CPS1, compared with 14 (8%) in intestinal-type and 11 (13%) cases in mixed-type GC. In intestinal-type GC, CPS1 expression was completely lost in 107 (62%) of cases, which was associated with an advanced Tumor-Node-Metastasis stage (P=0.031) and depth of invasion (P=0.037). Kaplan-Meier analysis suggested that low CPS1 expression levels were independently associated with a short overall survival (OS) time in the three types of GC (P<0.001 in intestinal-type, P=0.003 in diffuse-type and P=0.018 in mixed-type GC). Furthermore, low levels of CPS1 mRNA and high methylation levels in the CPS1 promoter were associated with a short OS time in patients with GC. These results suggested that the expression of CPS1 was progressively downregulated in Correa's cascade, and that CPS1 may serve as a prognostic marker for patients with GC, regardless of tumor type.
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Affiliation(s)
- Xuqian Fang
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201821, P.R. China
| | - Xiaoqiong Wu
- Department of Clinical Laboratory, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201821, P.R. China
| | - Enfei Xiang
- Clinical Research Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201821, P.R. China
| | - Fangxiu Luo
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201821, P.R. China
| | - Qinqin Li
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201821, P.R. China
| | - Qianchen Ma
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201821, P.R. China
| | - Fei Yuan
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201821, P.R. China
| | - Peizhan Chen
- Clinical Research Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201821, P.R. China
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12
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Zhang T, Hu L, Tang JF, Xu H, Tian K, Wu MN, Huang SY, Du YM, Zhou P, Lu RJ, He S, Xu JM, Si JJ, Li J, Chen DL, Ran JH. Metformin Inhibits the Urea Cycle and Reduces Putrescine Generation in Colorectal Cancer Cell Lines. Molecules 2021; 26:molecules26071990. [PMID: 33915902 PMCID: PMC8038129 DOI: 10.3390/molecules26071990] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/24/2021] [Accepted: 03/28/2021] [Indexed: 12/20/2022] Open
Abstract
The urea cycle (UC) removes the excess nitrogen and ammonia generated by nitrogen-containing compound composites or protein breakdown in the human body. Research has shown that changes in UC enzymes are not only related to tumorigenesis and tumor development but also associated with poor survival in hepatocellular, breast, and colorectal cancers (CRC), etc. Cytoplasmic ornithine, the intermediate product of the urea cycle, is a specific substrate for ornithine decarboxylase (ODC, also known as ODC1) for the production of putrescine and is required for tumor growth. Polyamines (spermidine, spermine, and their precursor putrescine) play central roles in more than half of the steps of colorectal tumorigenesis. Given the close connection between polyamines and cancer, the regulation of polyamine metabolic pathways has attracted attention regarding the mechanisms of action of chemical drugs used to prevent CRC, as the drug most widely used for treating type 2 diabetes (T2D), metformin (Met) exhibits antitumor activity against a variety of cancer cells, with a vaguely defined mechanism. In addition, the influence of metformin on the UC and putrescine generation in colorectal cancer has remained unclear. In our study, we investigated the effect of metformin on the UC and putrescine generation of CRC in vivo and in vitro and elucidated the underlying mechanisms. In nude mice bearing HCT116 tumor xenografts, the administration of metformin inhibited tumor growth without affecting body weight. In addition, metformin treatment increased the expression of monophosphate (AMP)-activated protein kinase (AMPK) and p53 in both HCT116 xenografts and colorectal cancer cell lines and decreased the expression of the urea cycle enzymes, including carbamoyl phosphate synthase 1 (CPS1), arginase 1 (ARG1), ornithine trans-carbamylase (OTC), and ODC. The putrescine levels in both HCT116 xenografts and HCT116 cells decreased after metformin treatment. These results demonstrate that metformin inhibited CRC cell proliferation via activating AMPK/p53 and that there was an association between metformin, urea cycle inhibition and a reduction in putrescine generation.
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Affiliation(s)
- Tao Zhang
- Department of Anatomy, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China; (T.Z.); (L.H.); (H.X.); (K.T.); (M.-N.W.); (J.-M.X.); (J.-J.S.)
- Lab of Stem Cell and Tissue Engineering, Department of Histology and Embryology, Chongqing Medical University, Chongqing 400016, China; (J.-F.T.); (S.-Y.H.); (Y.-M.D.); (P.Z.); (R.-J.L.); (S.H.); (J.L.); (D.-L.C.)
- Chongqing Three Gorges Medical College, Chongqing Engineering Research Center of Antitumor Natural Drugs, Chongqing 404120, China
| | - Ling Hu
- Department of Anatomy, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China; (T.Z.); (L.H.); (H.X.); (K.T.); (M.-N.W.); (J.-M.X.); (J.-J.S.)
- Lab of Stem Cell and Tissue Engineering, Department of Histology and Embryology, Chongqing Medical University, Chongqing 400016, China; (J.-F.T.); (S.-Y.H.); (Y.-M.D.); (P.Z.); (R.-J.L.); (S.H.); (J.L.); (D.-L.C.)
| | - Jia-Feng Tang
- Lab of Stem Cell and Tissue Engineering, Department of Histology and Embryology, Chongqing Medical University, Chongqing 400016, China; (J.-F.T.); (S.-Y.H.); (Y.-M.D.); (P.Z.); (R.-J.L.); (S.H.); (J.L.); (D.-L.C.)
- Chongqing Three Gorges Medical College, Chongqing Engineering Research Center of Antitumor Natural Drugs, Chongqing 404120, China
| | - Hang Xu
- Department of Anatomy, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China; (T.Z.); (L.H.); (H.X.); (K.T.); (M.-N.W.); (J.-M.X.); (J.-J.S.)
- Lab of Stem Cell and Tissue Engineering, Department of Histology and Embryology, Chongqing Medical University, Chongqing 400016, China; (J.-F.T.); (S.-Y.H.); (Y.-M.D.); (P.Z.); (R.-J.L.); (S.H.); (J.L.); (D.-L.C.)
| | - Kuan Tian
- Department of Anatomy, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China; (T.Z.); (L.H.); (H.X.); (K.T.); (M.-N.W.); (J.-M.X.); (J.-J.S.)
| | - Meng-Na Wu
- Department of Anatomy, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China; (T.Z.); (L.H.); (H.X.); (K.T.); (M.-N.W.); (J.-M.X.); (J.-J.S.)
- Lab of Stem Cell and Tissue Engineering, Department of Histology and Embryology, Chongqing Medical University, Chongqing 400016, China; (J.-F.T.); (S.-Y.H.); (Y.-M.D.); (P.Z.); (R.-J.L.); (S.H.); (J.L.); (D.-L.C.)
| | - Shi-Ying Huang
- Lab of Stem Cell and Tissue Engineering, Department of Histology and Embryology, Chongqing Medical University, Chongqing 400016, China; (J.-F.T.); (S.-Y.H.); (Y.-M.D.); (P.Z.); (R.-J.L.); (S.H.); (J.L.); (D.-L.C.)
| | - Yu-Mei Du
- Lab of Stem Cell and Tissue Engineering, Department of Histology and Embryology, Chongqing Medical University, Chongqing 400016, China; (J.-F.T.); (S.-Y.H.); (Y.-M.D.); (P.Z.); (R.-J.L.); (S.H.); (J.L.); (D.-L.C.)
| | - Peng Zhou
- Lab of Stem Cell and Tissue Engineering, Department of Histology and Embryology, Chongqing Medical University, Chongqing 400016, China; (J.-F.T.); (S.-Y.H.); (Y.-M.D.); (P.Z.); (R.-J.L.); (S.H.); (J.L.); (D.-L.C.)
| | - Rui-Jin Lu
- Lab of Stem Cell and Tissue Engineering, Department of Histology and Embryology, Chongqing Medical University, Chongqing 400016, China; (J.-F.T.); (S.-Y.H.); (Y.-M.D.); (P.Z.); (R.-J.L.); (S.H.); (J.L.); (D.-L.C.)
| | - Shuang He
- Lab of Stem Cell and Tissue Engineering, Department of Histology and Embryology, Chongqing Medical University, Chongqing 400016, China; (J.-F.T.); (S.-Y.H.); (Y.-M.D.); (P.Z.); (R.-J.L.); (S.H.); (J.L.); (D.-L.C.)
| | - Jia-Mei Xu
- Department of Anatomy, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China; (T.Z.); (L.H.); (H.X.); (K.T.); (M.-N.W.); (J.-M.X.); (J.-J.S.)
| | - Jian-Jun Si
- Department of Anatomy, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China; (T.Z.); (L.H.); (H.X.); (K.T.); (M.-N.W.); (J.-M.X.); (J.-J.S.)
| | - Jing Li
- Lab of Stem Cell and Tissue Engineering, Department of Histology and Embryology, Chongqing Medical University, Chongqing 400016, China; (J.-F.T.); (S.-Y.H.); (Y.-M.D.); (P.Z.); (R.-J.L.); (S.H.); (J.L.); (D.-L.C.)
| | - Di-Long Chen
- Lab of Stem Cell and Tissue Engineering, Department of Histology and Embryology, Chongqing Medical University, Chongqing 400016, China; (J.-F.T.); (S.-Y.H.); (Y.-M.D.); (P.Z.); (R.-J.L.); (S.H.); (J.L.); (D.-L.C.)
- Chongqing Three Gorges Medical College, Chongqing Engineering Research Center of Antitumor Natural Drugs, Chongqing 404120, China
| | - Jian-Hua Ran
- Department of Anatomy, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China; (T.Z.); (L.H.); (H.X.); (K.T.); (M.-N.W.); (J.-M.X.); (J.-J.S.)
- Lab of Stem Cell and Tissue Engineering, Department of Histology and Embryology, Chongqing Medical University, Chongqing 400016, China; (J.-F.T.); (S.-Y.H.); (Y.-M.D.); (P.Z.); (R.-J.L.); (S.H.); (J.L.); (D.-L.C.)
- Correspondence: ; Tel.: +86-150-8681-4824
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13
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Ben Kridis-Rejeb W, Ben Ayed-Guerfali D, Ammous-Boukhris N, Ayadi W, Kifagi C, Charfi S, Saguem I, Sellami-Boudawara T, Daoud J, Khanfir A, Mokdad-Gargouri R. Identification of novel candidate genes by exome sequencing in Tunisian familial male breast cancer patients. Mol Biol Rep 2020; 47:6507-6516. [PMID: 32901360 DOI: 10.1007/s11033-020-05703-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/01/2020] [Indexed: 12/11/2022]
Abstract
Male Breast Cancer (MBC) is a rare and aggressive disease that is associated with genetic factors. Mutations in BRCA1 and BRCA2 account for 10% of all MBC cases suggesting that other genetic factors are involved. The aim of the present study is to screen whole BRCA1 and BRCA2 exons using the Ampliseq BRCA panel in Tunisian MBC patients with family history. Furthermore, we performed exome sequencing using the TruSight One sequencing panel on an early onset BRCA negative patient. We showed that among the 6 MBC patients, only one (MBC-F1) harbored a novel frameshift mutation in exon 2 of the BRCA2 gene (c.17-20delAAGA, p.Lys6Xfs) resulting in a short BRCA2 protein of only 6 amino-acids. We selected 9 rare variants after applying several filter steps on the exome sequencing data. Among these variants, and based on their role in breast carcinogenesis, we retained 6 candidate genes (MSH5, DCC, ERBB3, NOTCH3, DIAPH1, and DNAH11). Further studies are needed to confirm the association of the selected genes with family MBC.
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Affiliation(s)
| | - Dorra Ben Ayed-Guerfali
- Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Street Km 6, BP 1177, 3038, Sfax, Tunisia
| | - Nihel Ammous-Boukhris
- Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Street Km 6, BP 1177, 3038, Sfax, Tunisia
| | - Wajdi Ayadi
- Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Street Km 6, BP 1177, 3038, Sfax, Tunisia
| | - Chamseddine Kifagi
- Division of Immunology & Vaccinology, DTU Nanotech, Department of Micro-and Nanotechnology, Kemitorvet, Buildings 202 and 204, Lyngby Campus, 2800, Kgs. Lyngby, Denmark
| | - Slim Charfi
- Department of Anatomo-Pathology, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
| | - Ines Saguem
- Department of Anatomo-Pathology, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
| | - Tahia Sellami-Boudawara
- Department of Anatomo-Pathology, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
| | - Jamel Daoud
- Department of Radiotherapy, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
| | - Afef Khanfir
- Department of Oncology, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
| | - Raja Mokdad-Gargouri
- Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Street Km 6, BP 1177, 3038, Sfax, Tunisia.
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14
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Rolfe A, Yao S, Nguyen TV, Omoto K, Colombo F, Virrankoski M, Vaillancourt FH, Yu L, Cook A, Reynolds D, Ioannidis S, Zhu P, Larsen NA, Bolduc DM. Discovery of 2,6-Dimethylpiperazines as Allosteric Inhibitors of CPS1. ACS Med Chem Lett 2020; 11:1305-1309. [PMID: 32551016 DOI: 10.1021/acsmedchemlett.0c00145] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 05/21/2020] [Indexed: 12/24/2022] Open
Abstract
Carbamoyl phosphate synthetase 1 (CPS1) is a potential synthetic lethal target in LKB1-deficient nonsmall cell lung cancer, where its overexpression supports the production of pyrimidine synthesis. In other cancer types, CPS1 overexpression and activity may prevent the accumulation of toxic levels of intratumoral ammonia to support tumor growth. Herein we report the discovery of a novel series of potent and selective small-molecule inhibitors of CPS1. Piperazine 2 was initially identified as a promising CPS1 inhibitor through a high-throughput screening effort. Subsequent structure-activity relationship optimization and structure-based drug design led to the discovery of piperazine H3B-616 (25), a potent allosteric inhibitor of CPS1 (IC50 = 66 nM).
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Affiliation(s)
- Alan Rolfe
- H3 Biomedicine Inc., 300 Technology Square, Fifth Floor, Cambridge, Massachusetts 02139, United States
| | - Shihua Yao
- H3 Biomedicine Inc., 300 Technology Square, Fifth Floor, Cambridge, Massachusetts 02139, United States
| | - Toung-Vi Nguyen
- H3 Biomedicine Inc., 300 Technology Square, Fifth Floor, Cambridge, Massachusetts 02139, United States
| | - Kiyoyuki Omoto
- H3 Biomedicine Inc., 300 Technology Square, Fifth Floor, Cambridge, Massachusetts 02139, United States
| | - Federico Colombo
- H3 Biomedicine Inc., 300 Technology Square, Fifth Floor, Cambridge, Massachusetts 02139, United States
| | - Milena Virrankoski
- H3 Biomedicine Inc., 300 Technology Square, Fifth Floor, Cambridge, Massachusetts 02139, United States
| | - Frédéric H. Vaillancourt
- H3 Biomedicine Inc., 300 Technology Square, Fifth Floor, Cambridge, Massachusetts 02139, United States
| | - Lihua Yu
- H3 Biomedicine Inc., 300 Technology Square, Fifth Floor, Cambridge, Massachusetts 02139, United States
| | - Andrew Cook
- H3 Biomedicine Inc., 300 Technology Square, Fifth Floor, Cambridge, Massachusetts 02139, United States
| | - Dominic Reynolds
- H3 Biomedicine Inc., 300 Technology Square, Fifth Floor, Cambridge, Massachusetts 02139, United States
| | - Stephanos Ioannidis
- H3 Biomedicine Inc., 300 Technology Square, Fifth Floor, Cambridge, Massachusetts 02139, United States
| | - Ping Zhu
- H3 Biomedicine Inc., 300 Technology Square, Fifth Floor, Cambridge, Massachusetts 02139, United States
| | - Nicholas A. Larsen
- H3 Biomedicine Inc., 300 Technology Square, Fifth Floor, Cambridge, Massachusetts 02139, United States
| | - David M. Bolduc
- H3 Biomedicine Inc., 300 Technology Square, Fifth Floor, Cambridge, Massachusetts 02139, United States
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15
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Wu G, Zhao Z, Yan Y, Zhou Y, Wei J, Chen X, Lin W, Ou C, Li J, Wang X, Xiong K, Zhou J, Xu Z. CPS1 expression and its prognostic significance in lung adenocarcinoma. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:341. [PMID: 32355785 PMCID: PMC7186668 DOI: 10.21037/atm.2020.02.146] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Background Studies have increasingly shown that carbamoyl phosphate synthetase 1 (CPS1) plays a vital role in the occurrence and development of human malignant disease. Unfortunately, the detailed function of CPS1 in the development and prognosis of lung cancer, especially lung adenocarcinoma (LADC), is still not fully understood. In this research, we performed a comprehensive bioinformatics analysis with respect to the function of CPS1 in human LADC. Methods Several biological databases including UALCAN, GEPIA and Oncomine were used to analyze the expression of CPS1 in LADC. Meanwhile, TCGA and GEO databases were utilized to analyze relevant clinical data. In addition, databases including Methsurv, etc., were used to analyze CPS1 methylation levels in LADC. Results The Oncomine platform, UALCAN and gene expression profiling interactive analysis (GEPIA) were used and revealed that the expression levels of CPS1 were significantly increased in LADC tissues. Furthermore, we analyzed the methylation level of CPS1 in LADC and found that cases with high levels of CPS1 showed hypomethylated CPS1. The clinical data from the Wanderer database, which is linked to The Cancer Genome Atlas (TCGA) database, demonstrated that the expression and methylation values of CPS1 were both significantly related to the clinical characteristics and prognosis of LADC. Through analysis of the dataset from the Gene Expression Omnibus (GEO) database, we found that the expression level of CPS1 was markedly downregulated in human A549 lung cancer cells treated with the chemotherapeutic drug motexafin gadolinium (MGd) in a time-dependent manner. Conclusions Our work indicated that CPS1 is upregulated in LADC samples and that CPS1 might be used as a potential biomarker for the diagnostic and prognostic evaluation of LADC. Determining the detailed biological function of CPS1 in LADC tissues will provide promising and insightful information for our further study.
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Affiliation(s)
- Geting Wu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Zijin Zhao
- Department of Neurosurgery, Xiangya Hospital, Central South University, Institute of Skull Base Surgery and Neuro-oncology at Hunan, Changsha 410008, China
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yangying Zhou
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Jie Wei
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Xi Chen
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Wei Lin
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Chunlin Ou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Jia Li
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Xiang Wang
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Kun Xiong
- Department of Anatomy and Neurobiology, School of Basic Medical Sciences, Central South University, Changsha 410013, China
| | - Jianhua Zhou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
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16
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Yao S, Nguyen TV, Rolfe A, Agrawal AA, Ke J, Peng S, Colombo F, Yu S, Bouchard P, Wu J, Huang KC, Bao X, Omoto K, Selvaraj A, Yu L, Ioannidis S, Vaillancourt FH, Zhu P, Larsen NA, Bolduc DM. Small Molecule Inhibition of CPS1 Activity through an Allosteric Pocket. Cell Chem Biol 2020; 27:259-268.e5. [PMID: 32017919 DOI: 10.1016/j.chembiol.2020.01.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/09/2019] [Accepted: 01/13/2020] [Indexed: 02/06/2023]
Abstract
Carbamoyl phosphate synthetase 1 (CPS1) catalyzes the first step in the ammonia-detoxifying urea cycle, converting ammonia to carbamoyl phosphate under physiologic conditions. In cancer, CPS1 overexpression supports pyrimidine synthesis to promote tumor growth in some cancer types, while in others CPS1 activity prevents the buildup of toxic levels of intratumoral ammonia to allow for sustained tumor growth. Targeted CPS1 inhibitors may, therefore, provide a therapeutic benefit for cancer patients with tumors overexpressing CPS1. Herein, we describe the discovery of small-molecule CPS1 inhibitors that bind to a previously unknown allosteric pocket to block ATP hydrolysis in the first step of carbamoyl phosphate synthesis. CPS1 inhibitors are active in cellular assays, blocking both urea synthesis and CPS1 support of the pyrimidine biosynthetic pathway, while having no activity against CPS2. These newly discovered CPS1 inhibitors are a first step toward providing researchers with valuable tools for probing CPS1 cancer biology.
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Affiliation(s)
- Shihua Yao
- H3 Biomedicine Inc., 300 Technology Square, Cambridge, MA 02139, USA
| | - Tuong-Vi Nguyen
- H3 Biomedicine Inc., 300 Technology Square, Cambridge, MA 02139, USA
| | - Alan Rolfe
- H3 Biomedicine Inc., 300 Technology Square, Cambridge, MA 02139, USA
| | - Anant A Agrawal
- H3 Biomedicine Inc., 300 Technology Square, Cambridge, MA 02139, USA
| | - Jiyuan Ke
- H3 Biomedicine Inc., 300 Technology Square, Cambridge, MA 02139, USA
| | - Shouyong Peng
- H3 Biomedicine Inc., 300 Technology Square, Cambridge, MA 02139, USA
| | - Federico Colombo
- H3 Biomedicine Inc., 300 Technology Square, Cambridge, MA 02139, USA
| | - Sean Yu
- RMI Laboratories LLC, 418 Industrial Drive, North Wales, PA 19454, USA
| | - Patricia Bouchard
- NMX Research and Solutions, Inc., 500 Cartier Boulevard W., Laval, Quebec H7V 5B7, Canada
| | - Jiayi Wu
- H3 Biomedicine Inc., 300 Technology Square, Cambridge, MA 02139, USA
| | - Kuan-Chun Huang
- H3 Biomedicine Inc., 300 Technology Square, Cambridge, MA 02139, USA
| | - Xingfeng Bao
- H3 Biomedicine Inc., 300 Technology Square, Cambridge, MA 02139, USA
| | - Kiyoyuki Omoto
- H3 Biomedicine Inc., 300 Technology Square, Cambridge, MA 02139, USA
| | - Anand Selvaraj
- H3 Biomedicine Inc., 300 Technology Square, Cambridge, MA 02139, USA
| | - Lihua Yu
- H3 Biomedicine Inc., 300 Technology Square, Cambridge, MA 02139, USA
| | | | | | - Ping Zhu
- H3 Biomedicine Inc., 300 Technology Square, Cambridge, MA 02139, USA
| | - Nicholas A Larsen
- H3 Biomedicine Inc., 300 Technology Square, Cambridge, MA 02139, USA
| | - David M Bolduc
- H3 Biomedicine Inc., 300 Technology Square, Cambridge, MA 02139, USA.
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17
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Wu G, Yan Y, Zhou Y, Wang X, Wei J, Chen X, Lin W, Ou C, Zhou J, Xu Z. Expression and clinical significance of CPS1 in glioblastoma multiforme. Curr Res Transl Med 2019; 67:123-128. [PMID: 31492588 DOI: 10.1016/j.retram.2019.08.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/27/2019] [Accepted: 08/27/2019] [Indexed: 02/08/2023]
Abstract
Carbamoyl phosphate synthetase-1 (CPS1), the first rate-limiting mitochondrial enzyme in the urea cycle, regulates proliferation and differentiation during tumor progression. However, the detailed function of CPS1 in glioblastoma Multiforme (GBM) is still unclear. Here, we highlight mechanisms for CPS1 upregulation and the effects of upregulated CPS1 on GBM tumorigenesis. The transcriptome data from several public databases, such as Oncomine and GEPIA, revealed that CPS1 transcriptional level was significantly upregulated in GBM tissues and cells. Moreover, CPS1 was hypomethylated in GBM tissues. The Wanderer database, linked to the Cancer Genome Atlas (TCGA), showed the association between CPS1 expression or its methylation values and the clinicopathological parameters in GBM patients. Our work fully demonstrated that CPS1 expression was upregulated in GBM and this gene could be used as a potential diagnostic and prognosis indicator for GBM.
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Affiliation(s)
- Geting Wu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Yangying Zhou
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Xiang Wang
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Jie Wei
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Xi Chen
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Wei Lin
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Chunlin Ou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Jianhua Zhou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.
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18
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Wang HC, Chou CL, Yang CC, Huang WL, Hsu YC, Luo CW, Chen TJ, Li CF, Pan MR. Over-Expression of CHD4 Is an Independent Biomarker of Poor Prognosis in Patients with Rectal Cancers Receiving Concurrent Chemoradiotherapy. Int J Mol Sci 2019; 20:ijms20174087. [PMID: 31438571 PMCID: PMC6747537 DOI: 10.3390/ijms20174087] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/19/2019] [Accepted: 08/19/2019] [Indexed: 12/18/2022] Open
Abstract
Neoadjuvant concurrent chemoradiotherapy (CCRT), followed by radical proctectomy, is the standard treatment for locally advanced rectal cancer. However, a poor response and therapeutic resistance continue to occur despite this treatment. In this study, we analyzed the microarray datasets (GSE68204) of rectal cancer from the Gene Expression Omnibus database, and identified CHD4 as one of the most significantly up-regulated genes among all subunits of the nucleosome remodeling and histone deacetylation (NuRD) complex, in non-responders to CCRT, among locally advanced rectal cancer (LARC) patients. We confirmed the predictive and prognostic significance of CHD4 expression in CCRT treatment, and its correlation with other clinicopathological features, such as tumor regression grade (TRG), therapeutic response, and patient survival. This was carried out by immunohistochemical studies on endoscopic biopsy tissues from 172 rectal cancer patients, receiving neoadjuvant concurrent chemoradiotherapy (CCRT). A high expression of CHD4 was significantly associated with pre-treatment tumor status (p < 0.001) and lymph node metastasis (p < 0.001), post-treatment tumor status (p < 0.001), and lymph node metastasis (p < 0.001), vascular invasion (p = 0.042), and tumor regression grade (p = 0.001). A high expression of CHD4 could also predict poor disease-specific survival and metastasis-free survival (log-rank test, p = 0.0373 and p < 0.0001, respectively). In multivariate Cox proportional-hazards regression analysis, CHD4 overexpression was an independent factor of poor prognosis for metastasis-free survival (HR, 4.575; 95% CI, 1.717–12.192; p = 0.002). By in vitro studies, based on cell line models, we also demonstrated that, the overexpression of CHD4 induced radio-resistance in microsatellite instability-high (MSI-H) colorectal cells (CRCs). On the contrary, the knockdown of CHD4 enhanced radiosensitivity in microsatellite stable (MSS) CRCs. Altogether, we have identified CHD4 as an important regulator of radio-resistance in both MSI-H and MSS CRC cell lines.
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Affiliation(s)
- Hui-Ching Wang
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Division of Hematology and Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Chia-Lin Chou
- Division of Colon & Rectal Surgery, Department of Surgery, Chi Mei Medical Center, Tainan 710, Taiwan
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan
| | - Ching-Chieh Yang
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan
- Department of Radiation Oncology, Chi-Mei Medical Center, Tainan 710, Taiwan
- Department of Pharmacy, Chia-Nan University of Pharmacy and Science, Tainan 71745, Taiwan
| | - Wei-Lun Huang
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Radiation Oncology, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan
| | - Yin-Chou Hsu
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Emergency Medicine, E-Da Hospital, I-Shou University, Kaohsiung 824, Taiwan
| | - Chi-Wen Luo
- Division of Breast Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Tzu-Ju Chen
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan
- Department of Pathology, Chi Mei Medical Center, Tainan 710, Taiwan
- Department of Optometry, Chung Hwa University of Medical Technology, Tainan 717, Taiwan
| | - Chien-Feng Li
- Department of Pathology, Chi Mei Medical Center, Tainan 710, Taiwan
- Department of Medical Research, Chi Mei Medical Center, Tainan 710, Taiwan
- National Institute of Cancer Research, National Health Research Institute, Tainan 704, Taiwan
| | - Mei-Ren Pan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
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19
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Differentially Expressed Mitochondrial Proteins in Human MCF7 Breast Cancer Cells Resistant to Paclitaxel. Int J Mol Sci 2019; 20:ijms20122986. [PMID: 31248089 PMCID: PMC6628585 DOI: 10.3390/ijms20122986] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/08/2019] [Accepted: 06/17/2019] [Indexed: 12/12/2022] Open
Abstract
Identification of novel proteins with changed expression in resistant cancer cells could be helpful in elucidation mechanisms involved in the development of acquired resistance to paclitaxel. In this study, we carried out a 2D-PAGE using the mitochondrial-enriched fraction from paclitaxel-resistant MCF7/PacR cells compared to original paclitaxel-sensitive MCF7 breast cancer cells. Differentially expressed proteins were identified employing mass spectrometry. We found that lysosomal cathepsin D and mitochondrial abhydrolase-domain containing protein 11 (ABHD11) had decreased expression in MCF7/PacR cells. On the other hand, mitochondrial carbamoyl-phosphate synthetase 1 (CPS1) and ATPase family AAA-domain containing protein 3A and 3B (ATAD3A, ATAD3B) were overexpressed in MCF7/PacR cells. Further, we showed that there was no difference in localization of CPS1 in MCF7 and MCF7/PacR cells. We demonstrated a significant increase in the number of CPS1 positive MCF7/PacR cells, using FACS analysis, compared to the number of CPS1 positive MCF7 cells. Silencing of CPS1 expression by specific siRNA had no significant effect on the resistance of MCF7/PacR cells to paclitaxel. To summarize, we identified several novel proteins of a mitochondrial fraction whose role in acquired resistance to paclitaxel in breast cancer cells should be further assessed.
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20
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Snezhkina AV, Lukyanova EN, Zaretsky AR, Kalinin DV, Pokrovsky AV, Golovyuk AL, Krasnov GS, Fedorova MS, Pudova EA, Kharitonov SL, Melnikova NV, Alekseev BY, Kiseleva MV, Kaprin AD, Dmitriev AA, Kudryavtseva AV. Novel potential causative genes in carotid paragangliomas. BMC MEDICAL GENETICS 2019; 20:48. [PMID: 30967136 PMCID: PMC6454587 DOI: 10.1186/s12881-019-0770-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Background Carotid paragangliomas (CPGLs) are rare neuroendocrine tumors that arise from the paraganglion at the bifurcation of the carotid artery and are responsible for approximately 65% of all head and neck paragangliomas. CPGLs can occur sporadically or along with different hereditary tumor syndromes. Approximately 30 genes are known to be associated with CPGLs. However, the genetic basis behind the development of these tumors is not fully elucidated, and the molecular mechanisms underlying CPGL pathogenesis remain unclear. Methods Whole exome and transcriptome high-throughput sequencing of CPGLs was performed on an Illumina platform. Exome libraries were prepared using a Nextera Rapid Capture Exome Kit (Illumina) and were sequenced under 75 bp paired-end model. For cDNA library preparation, a TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina) was used; transcriptome sequencing was carried out with 100 bp paired-end read length. Obtained data were analyzed using xseq which estimates the influence of mutations on gene expression profiles allowing to identify potential causative genes. Results We identified a total of 16 candidate genes (MYH15, CSP1, MYH3, PTGES3L, CSGALNACT2, NMD3, IFI44, GMCL1, LSP1, PPFIBP2, RBL2, MAGED1, CNIH3, STRA6, SLC6A13, and ATM) whose variants potentially influence their expression (cis-effect). The strongest cis-effect of loss-of-function variants was found in MYH15, CSP1, and MYH3, and several likely pathogenic variants in these genes associated with CPGLs were predicted. Conclusions Using the xseq probabilistic model, three novel potential causative genes, namely MYH15, CSP1, and MYH3, were identified in carotid paragangliomas.
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Affiliation(s)
| | - Elena N Lukyanova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Andrew R Zaretsky
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry V Kalinin
- Vishnevsky Institute of Surgery, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Anatoly V Pokrovsky
- Vishnevsky Institute of Surgery, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Alexander L Golovyuk
- Vishnevsky Institute of Surgery, Ministry of Health of the Russian Federation, Moscow, Russia
| | - George S Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Maria S Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elena A Pudova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Sergey L Kharitonov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nataliya V Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Boris Y Alekseev
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Marina V Kiseleva
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Andrey D Kaprin
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Alexey A Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
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21
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Pham-Danis C, Gehrke S, Danis E, Rozhok AI, Daniels MW, Gao D, Collins C, Paola JTD, D'Alessandro A, DeGregori J. Urea Cycle Sustains Cellular Energetics upon EGFR Inhibition in EGFR-Mutant NSCLC. Mol Cancer Res 2019; 17:1351-1364. [PMID: 30808730 DOI: 10.1158/1541-7786.mcr-18-1068] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 02/06/2019] [Accepted: 02/22/2019] [Indexed: 12/21/2022]
Abstract
Mutations in oncogenes and tumor suppressor genes engender unique metabolic phenotypes crucial to the survival of tumor cells. EGFR signaling has been linked to the rewiring of tumor metabolism in non-small cell lung cancer (NSCLC). We have integrated the use of a functional genomics screen and metabolomics to identify metabolic vulnerabilities induced by EGFR inhibition. These studies reveal that following EGFR inhibition, EGFR-driven NSCLC cells become dependent on the urea cycle and, in particular, the urea cycle enzyme CPS1. Combining knockdown of CPS1 with EGFR inhibition further reduces cell proliferation and impedes cell-cycle progression. Profiling of the metabolome demonstrates that suppression of CPS1 potentiates the effects of EGFR inhibition on central carbon metabolism, pyrimidine biosynthesis, and arginine metabolism, coinciding with reduced glycolysis and mitochondrial respiration. We show that EGFR inhibition and CPS1 knockdown lead to a decrease in arginine levels and pyrimidine derivatives, and the addition of exogenous pyrimidines partially rescues the impairment in cell growth. Finally, we show that high expression of CPS1 in lung adenocarcinomas correlated with worse patient prognosis in publicly available databases. These data collectively reveal that NSCLC cells have a greater dependency on the urea cycle to sustain central carbon metabolism, pyrimidine biosynthesis, and arginine metabolism to meet cellular energetics upon inhibition of EGFR. IMPLICATIONS: Our results reveal that the urea cycle may be a novel metabolic vulnerability in the context of EGFR inhibition, providing an opportunity to develop rational combination therapies with EGFR inhibitors for the treatment of EGFR-driven NSCLC.
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Affiliation(s)
- Catherine Pham-Danis
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Sarah Gehrke
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Etienne Danis
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Andrii I Rozhok
- Department of Dermatology, Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Michael W Daniels
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Dexiang Gao
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Christina Collins
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - José T Di Paola
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - James DeGregori
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado. .,Department of Dermatology, Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
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22
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Poynter L, Galea D, Veselkov K, Mirnezami A, Kinross J, Nicholson J, Takáts Z, Darzi A, Mirnezami R. Network Mapping of Molecular Biomarkers Influencing Radiation Response in Rectal Cancer. Clin Colorectal Cancer 2019; 18:e210-e222. [PMID: 30928329 DOI: 10.1016/j.clcc.2019.01.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 11/12/2018] [Accepted: 01/23/2019] [Indexed: 02/07/2023]
Abstract
Preoperative radiotherapy (RT) plays an important role in the management of locally advanced rectal cancer (RC). Tumor regression after RT shows marked variability, and robust molecular methods are needed to help predict likely response. The aim of this study was to review the current published literature and use Gene Ontology (GO) analysis to define key molecular biomarkers governing radiation response in RC. A systematic review of electronic bibliographic databases (Medline, Embase) was performed for original articles published between 2000 and 2015. Biomarkers were then classified according to biological function and incorporated into a hierarchical GO tree. Both significant and nonsignificant results were included in the analysis. Significance was binarized on the basis of univariate and multivariate statistics. Significance scores were calculated for each biological domain (or node), and a direct acyclic graph was generated for intuitive mapping of biological pathways and markers involved in RC radiation response. Seventy-two individual biomarkers across 74 studies were identified. On highest-order classification, molecular biomarkers falling within the domains of response to stress, cellular metabolism, and pathways inhibiting apoptosis were found to be the most influential in predicting radiosensitivity. Homogenizing biomarker data from original articles using controlled GO terminology demonstrated that cellular mechanisms of response to RT in RC-in particular the metabolic response to RT-may hold promise in developing radiotherapeutic biomarkers to help predict, and in the future modulate, radiation response.
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Affiliation(s)
- Liam Poynter
- Department of Surgery & Cancer, Imperial College London, London, UK
| | - Dieter Galea
- Computational & Systems Medicine, Imperial College London, London, UK
| | - Kirill Veselkov
- Computational & Systems Medicine, Imperial College London, London, UK
| | | | - James Kinross
- Department of Surgery & Cancer, Imperial College London, London, UK
| | - Jeremy Nicholson
- Computational & Systems Medicine, Imperial College London, London, UK
| | - Zoltán Takáts
- Computational & Systems Medicine, Imperial College London, London, UK
| | - Ara Darzi
- Department of Surgery & Cancer, Imperial College London, London, UK
| | - Reza Mirnezami
- Department of Surgery & Cancer, Imperial College London, London, UK; St Mark's Hospital and Academic Institute, Harrow, London, UK.
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23
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Abstract
Cancer cells reprogramme metabolism to maximize the use of nitrogen and carbon for the anabolic synthesis of macromolecules that are required during tumour proliferation and growth. To achieve this aim, one strategy is to reduce catabolism and nitrogen disposal. The urea cycle (UC) in the liver is the main metabolic pathway to convert excess nitrogen into disposable urea. Outside the liver, UC enzymes are differentially expressed, enabling the use of nitrogen for the synthesis of UC intermediates that are required to accommodate cellular needs. Interestingly, the expression of UC enzymes is altered in cancer, revealing a revolutionary mechanism to maximize nitrogen incorporation into biomass. In this Review, we discuss the metabolic benefits underlying UC deregulation in cancer and the relevance of these alterations for cancer diagnosis and therapy.
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Affiliation(s)
- Rom Keshet
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Peter Szlosarek
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, UK
- Barts Health NHS Trust, St Bartholomew's Hospital, London, UK
| | - Arkaitz Carracedo
- CIC bioGUNE, Bizkaia, Spain
- CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- Biochemistry and Molecular Biology Department, University of the Basque Country, Bilbao, Spain
| | - Ayelet Erez
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel.
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24
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Lee JS, Adler L, Karathia H, Carmel N, Rabinovich S, Auslander N, Keshet R, Stettner N, Silberman A, Agemy L, Helbling D, Eilam R, Sun Q, Brandis A, Malitsky S, Itkin M, Weiss H, Pinto S, Kalaora S, Levy R, Barnea E, Admon A, Dimmock D, Stern-Ginossar N, Scherz A, Nagamani SCS, Unda M, Wilson DM, Elhasid R, Carracedo A, Samuels Y, Hannenhalli S, Ruppin E, Erez A. Urea Cycle Dysregulation Generates Clinically Relevant Genomic and Biochemical Signatures. Cell 2018; 174:1559-1570.e22. [PMID: 30100185 PMCID: PMC6225773 DOI: 10.1016/j.cell.2018.07.019] [Citation(s) in RCA: 182] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 05/21/2018] [Accepted: 07/12/2018] [Indexed: 01/02/2023]
Abstract
The urea cycle (UC) is the main pathway by which mammals dispose of waste nitrogen. We find that specific alterations in the expression of most UC enzymes occur in many tumors, leading to a general metabolic hallmark termed "UC dysregulation" (UCD). UCD elicits nitrogen diversion toward carbamoyl-phosphate synthetase2, aspartate transcarbamylase, and dihydrooratase (CAD) activation and enhances pyrimidine synthesis, resulting in detectable changes in nitrogen metabolites in both patient tumors and their bio-fluids. The accompanying excess of pyrimidine versus purine nucleotides results in a genomic signature consisting of transversion mutations at the DNA, RNA, and protein levels. This mutational bias is associated with increased numbers of hydrophobic tumor antigens and a better response to immune checkpoint inhibitors independent of mutational load. Taken together, our findings demonstrate that UCD is a common feature of tumors that profoundly affects carcinogenesis, mutagenesis, and immunotherapy response.
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Affiliation(s)
- Joo Sang Lee
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Center for Bioinformatics and Computational Biology, University of Maryland Institute for Advanced Computer Studies, Department of Computer Science, University of Maryland, College Park, MD 20742, USA
| | - Lital Adler
- Department of Biological Regulation, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Hiren Karathia
- Center for Bioinformatics and Computational Biology, University of Maryland Institute for Advanced Computer Studies, Department of Computer Science, University of Maryland, College Park, MD 20742, USA
| | - Narin Carmel
- Department of Biological Regulation, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Shiran Rabinovich
- Department of Biological Regulation, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Noam Auslander
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Center for Bioinformatics and Computational Biology, University of Maryland Institute for Advanced Computer Studies, Department of Computer Science, University of Maryland, College Park, MD 20742, USA
| | - Rom Keshet
- Department of Biological Regulation, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Noa Stettner
- Department of Biological Regulation, Weizmann Institute of Science, 7610001 Rehovot, Israel; Department of Veterinary Resources, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Alon Silberman
- Department of Biological Regulation, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Lilach Agemy
- Department of Plant and Environmental Science, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | | | - Raya Eilam
- Department of Veterinary Resources, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Qin Sun
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alexander Brandis
- Life Sciences Core Facilities, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Sergey Malitsky
- Life Sciences Core Facilities, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Maxim Itkin
- Life Sciences Core Facilities, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Hila Weiss
- Department of Biological Regulation, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Sivan Pinto
- Department of Biological Regulation, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Shelly Kalaora
- Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Ronen Levy
- Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Eilon Barnea
- Faculty of Biology, Technion - Israel Institute of Technology, 3200003 Haifa, Israel
| | - Arie Admon
- Faculty of Biology, Technion - Israel Institute of Technology, 3200003 Haifa, Israel
| | - David Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Noam Stern-Ginossar
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Avigdor Scherz
- Department of Veterinary Resources, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Sandesh C S Nagamani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Miguel Unda
- Department of Urology, Basurto University Hospital, 48013 Bilbao, Spain; CIBERONC, Madrid, Spain
| | - David M Wilson
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, NIH, 251 Bayview Blvd., Baltimore, MD 21224, USA
| | - Ronit Elhasid
- Sackler Faculty of Medicine, Department of Pediatric Hemato Oncology, Sourasky Medical Center, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Arkaitz Carracedo
- CIBERONC, Madrid, Spain; CIC bioGUNE, Bizkaia Technology Park, 801 Building, 48160 Derio, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain; Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Yardena Samuels
- Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Sridhar Hannenhalli
- Center for Bioinformatics and Computational Biology, University of Maryland Institute for Advanced Computer Studies, Department of Computer Science, University of Maryland, College Park, MD 20742, USA
| | - Eytan Ruppin
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Center for Bioinformatics and Computational Biology, University of Maryland Institute for Advanced Computer Studies, Department of Computer Science, University of Maryland, College Park, MD 20742, USA; Schools of Medicine and Computer Science, Tel Aviv University, 6997801 Tel Aviv, Israel.
| | - Ayelet Erez
- Department of Biological Regulation, Weizmann Institute of Science, 7610001 Rehovot, Israel.
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25
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Yu L, Li K, Xu Z, Cui G, Zhang X. Integrated omics and gene expression analysis identifies the loss of metabolite-metabolite correlations in small cell lung cancer. Onco Targets Ther 2018; 11:3919-3929. [PMID: 30013371 PMCID: PMC6039056 DOI: 10.2147/ott.s166149] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND AND OBJECTIVE Small cell lung cancer (SCLC) is the most aggressive type of lung carcinoma with high metastatic potential and chemoresistance upon relapse. Cancer cells remodel the existing metabolic pathways for their benefits and the perturbations in cellular metabolism are the hallmark of cancer. However, the extent of these changes remains largely unknown for SCLC. MATERIALS AND METHODS We characterized the metabolic perturbations in SCLC cells (SCLCC) by metabolomics. Large-scale correlation analysis was performed between metabolites. Targeted proteomics and gene expression analysis were employed to investigate the changes of key enzymes and genes in the disturbed pathways. RESULTS We found dramatic decrease of metabolite-metabolite correlations in SCLCC compared with normal control cells and non-small cell lung cancer cells. Pathway analysis revealed that the loss of correlations was associated with the alternations of fatty acid oxidation, urea cycle, and purine salvage pathway in SCLCC. Targeted proteomics and gene expression analysis confirmed significant changes of the expression for the key enzymes and genes in the pathways in SCLCC including the upregulation of carbamoyl phosphate synthase 1 (urea cycle) and carnitine palmitoyltransferase 1A (fatty acid oxidation), and the downregulation of hypoxanthine-guanine phosphoribosyltransferase and adenine phosphoribosyltransferase in purine salvage pathway. CONCLUSION We demonstrated the loss of metabolite-metabolite correlations in SCLCC associated with the upregulation of fatty acid oxidation and urea cycle and the downregulation of purine salvage pathways. Our findings provide insights into the metabolic reprogramming in SCLCC and highlight the potential therapeutic targets for the treatment of SCLC.
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Affiliation(s)
- Li Yu
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China,
| | - Kefeng Li
- School of Medicine, University of California-San Diego, San Diego, CA, USA
| | - Zhaoguo Xu
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China,
| | - Guoyuan Cui
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China,
| | - Xiaoye Zhang
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China,
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26
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Çeliktas M, Tanaka I, Tripathi SC, Fahrmann JF, Aguilar-Bonavides C, Villalobos P, Delgado O, Dhillon D, Dennison JB, Ostrin EJ, Wang H, Behrens C, Do KA, Gazdar AF, Hanash SM, Taguchi A. Role of CPS1 in Cell Growth, Metabolism and Prognosis in LKB1-Inactivated Lung Adenocarcinoma. J Natl Cancer Inst 2017; 109:1-9. [PMID: 28376202 DOI: 10.1093/jnci/djw231] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 09/09/2016] [Indexed: 02/06/2023] Open
Abstract
Background Liver kinase B1 ( LKB1 ) is a tumor suppressor in lung adenocarcinoma (LADC). We investigated the proteomic profiles of 45 LADC cell lines with and without LKB1 inactivation. Carbamoyl phosphate synthetase 1 (CPS1), the first rate-limiting mitochondrial enzyme in the urea cycle, was distinctively overexpressed in LKB1-inactivated LADC cell lines. We therefore assessed the role of CPS1 and its clinical relevance in LKB1-inactivated LADC. Methods Mass spectrometric profiling of proteome and metabolome and function of CPS1 were analyzed in LADC cell lines. CPS1 and LKB1 expression in tumors from 305 LADC and 160 lung squamous cell carcinoma patients was evaluated by immunohistochemistry. Kaplan-Meier and Cox regression analyses were applied to assess the association between overall survival and CPS1 and LKB1 expression. All statistical tests were two-sided. Results CPS1 knockdown reduced cell growth, decreased metabolite levels associated with nucleic acid biosynthesis pathway, and contributed an additive effect when combined with gemcitabine, pemetrexed, or CHK1 inhibitor AZD7762. Tissue microarray analysis revealed that CPS1 was expressed in 65.7% of LKB1-negative LADC, and only 5.0% of LKB1-positive LADC. CPS1 expression showed statistically significant association with poor overall survival in LADC (hazard ratio = 3.03, 95% confidence interval = 1.74 to 5.25, P < .001). Conclusions Our findings suggest functional relevance of CPS1 in LKB1-inactivated LADC and association with worse outcome of LADC. CPS1 is a promising therapeutic target in combination with other chemotherapy agents, as well as a prognostic biomarker, enabling a personalized approach to treatment of LADC.
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Affiliation(s)
- Müge Çeliktas
- Departments of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ichidai Tanaka
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Satyendra Chandra Tripathi
- Departments of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Johannes F Fahrmann
- Departments of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Pamela Villalobos
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Oliver Delgado
- Departments of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dilsher Dhillon
- Departments of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer B Dennison
- Departments of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Edwin J Ostrin
- Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hong Wang
- Departments of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carmen Behrens
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kim-Anh Do
- Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Adi F Gazdar
- Hamon Center for Therapeutic Oncology Research and Department of Pathology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
| | - Samir M Hanash
- Departments of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ayumu Taguchi
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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27
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Lee YY, Wei YC, Tian YF, Sun DP, Sheu MJ, Yang CC, Lin LC, Lin CY, Hsing CH, Li WS, Li CF, Hsieh PL, Lin CY. Overexpression of Transcobalamin 1 is an Independent Negative Prognosticator in Rectal Cancers Receiving Concurrent Chemoradiotherapy. J Cancer 2017; 8:1330-1337. [PMID: 28638446 PMCID: PMC5479237 DOI: 10.7150/jca.18274] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 03/06/2017] [Indexed: 12/27/2022] Open
Abstract
Objective: Neoadjuvant concurrent chemoradiotherapy (CCRT) is an increasingly common therapeutic strategy for locally advanced rectal cancer, but stratification of risk and final outcomes remain a major challenge. Transcobalamin 1 (TCN1), a vitamin B12 (cobalamin)-binding protein, regulates cobalamin homeostasis. High expression of TCN1 have been reported in neoplasms such as breast cancer and hepatocellular carcinoma. However, little is known about the relevance of TCN1 to rectal cancer receiving CCRT. This study examined the predictive and prognostic impact of TCN1 expression in patients with rectal cancer following neoadjuvant CCRT. Methods: Through data mining from a published transcriptome of rectal cancers (GSE35452), we identified upregulation of TCN1 gene as the most significantly predicted poor response to CCRT among ion transport-related genes (GO:0006811). We evaluated TCN1 immunohistochemistry and performed an H-score analysis on endoscopic biopsy specimens from 172 rectal cancer patients receiving neoadjuvant CCRT followed by curative surgery. Expression levels of TCN1 were further correlated with clinicopathologic features, therapeutic response, tumor regression grade (TRG) and survivals including metastasis-free survival (MeFS), disease-specific survival (DSS) and recurrent-free survival (LRFS). Results: TCN1 overexpression was significantly related to advanced post-treatment tumor (T3, T4; p<0.001) and nodal status (N1, N2; p<0.001), vascular invasion (p=0.003) and inferior tumor regression grade (p < 0.001). In survival analyses, TCN1 overexpression was significantly associated with shorter DSS (p<0.0001), MeFS (p=0.0002) and LRFS (p=0.0001). Furthermore, it remained an independent prognosticator of worse DSS (p=0.002, hazard ratio=3.344), MeFS (p=0.021, hazard ratio=3.015) and LRFS (p=0.037, hazard ratio=3.037) in the multivariate comparison. Conclusion: Overexpression of TCN1 is associated with poor therapeutic response and adverse outcomes in rectal cancer patients receiving CCRT, justifying the potential prognostic value of TCN1 in rectal cancer receiving CCRT.
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Affiliation(s)
- Yi-Ying Lee
- Department of Pathology, Chi Mei Medical Center, Liouying, Tainan, Taiwan
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Yu-Ching Wei
- Department of Pathology, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung, Taiwan
| | - Yu-Feng Tian
- Division of General Surgery, Department of Surgery, Chi Mei Medical Center, Tainan, Taiwan
- Department of Health & Nutrition, Chia Nan University of Pharmacy and Science, Tainan, Taiwan
| | - Ding-Ping Sun
- Division of General Surgery, Department of Surgery, Chi Mei Medical Center, Tainan, Taiwan
- Department of Pharmacy, Chia Nan University of Pharmacy and Science, Tainan, Taiwan
| | - Ming-Jen Sheu
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Chi Mei Medical Center, Tainan, Taiwan
| | - Ching-Chieh Yang
- Department of Radiation Oncology, Chi Mei Medical Center, Tainan, Taiwan
| | - Li-Ching Lin
- Department of Radiation Oncology, Chi Mei Medical Center, Tainan, Taiwan
| | - Chen-Yi Lin
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Chi Mei Medical Center, Tainan, Taiwan
| | - Chung-Hsi Hsing
- Department of Anesthesiology, Chi Mei Medical Center, Tainan, Taiwan
| | - Wan-Shan Li
- Department of Pathology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chien-Feng Li
- Department of Pathology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Pathology, Chi Mei Medical Center, Tainan, Taiwan
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
- Department of Biotechnology, Southern Taiwan University of Science and Technology, Tainan, Taiwan
| | - Pei-Ling Hsieh
- Department of Medical Image, Chi Mei Medical Center, Tainan, Taiwan
| | - Ching-Yih Lin
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Chi Mei Medical Center, Tainan, Taiwan
- Department of Leisure, Recreation, and Tourism Management, Southern Taiwan
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28
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Palaniappan A, Ramar K, Ramalingam S. Computational Identification of Novel Stage-Specific Biomarkers in Colorectal Cancer Progression. PLoS One 2016; 11:e0156665. [PMID: 27243824 PMCID: PMC4887059 DOI: 10.1371/journal.pone.0156665] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/17/2016] [Indexed: 12/19/2022] Open
Abstract
It is well-known that the conversion of normal colon epithelium to adenoma and then to carcinoma stems from acquired molecular changes in the genome. The genetic basis of colorectal cancer has been elucidated to a certain extent, and much remains to be known about the identity of specific cancer genes that are associated with the advancement of colorectal cancer from one stage to the next. Here in this study we attempted to identify novel cancer genes that could underlie the stage-specific progression and metastasis of colorectal cancer. We conducted a stage-based meta-analysis of the voluminous tumor genome-sequencing data and mined using multiple approaches for novel genes driving the progression to stage-II, stage-III and stage-IV colorectal cancer. The consensus of these driver genes seeded the construction of stage-specific networks, which were then analyzed for the centrality of genes, clustering of subnetworks, and enrichment of gene-ontology processes. Our study identified three novel driver genes as hubs for stage-II progression: DYNC1H1, GRIN2A, GRM1. Four novel driver genes were identified as hubs for stage-III progression: IGF1R, CPS1, SPTA1, DSP. Three novel driver genes were identified as hubs for stage-IV progression: GSK3B, GGT1, EIF2B5. We also identified several non-driver genes that appeared to underscore the progression of colorectal cancer. Our study yielded potential diagnostic biomarkers for colorectal cancer as well as novel stage-specific drug targets for rational intervention. Our methodology is extendable to the analysis of other types of cancer to fill the gaps in our knowledge.
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Affiliation(s)
- Ashok Palaniappan
- Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Kelambakkam, Tamil Nadu 603103, India
- * E-mail:
| | - Karthick Ramar
- Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Kelambakkam, Tamil Nadu 603103, India
| | - Satish Ramalingam
- Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Kelambakkam, Tamil Nadu 603103, India
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