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Abdel-Mohsen HT, Nageeb AM, Ghannam IAY. Diphenyl urea-benzylidene acetohydrazide hybrids as fibroblast growth factor receptor 1 inhibitors and anticancer agents. Drug Dev Res 2024; 85:e22249. [PMID: 39180323 DOI: 10.1002/ddr.22249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 07/29/2024] [Accepted: 08/04/2024] [Indexed: 08/26/2024]
Abstract
Molecular hybridization between diphenyl urea and benzylidene acetohydrazide was adopted for the design of a new series of FGFR-1 targeting cancer. The designed series was synthesized and submitted to NCI-USA to be screened for their growth inhibitory activity on NCI cancer cell lines. Some of the synthesized hybrids displayed promising growth inhibitory activity on NCI cancer cell lines with a mean GI% between 70.39% and a lethal effect. Compounds 9a, 9i, 9j, and 9n-p were further selected for a five-dose assay and all the tested candidates showed promising antiproliferative activity with GI50 reaching the submicromolar range. Encouraged by the potent activity of 9a on colon cancer on the one hand and the well-known overexpression of FGFR-1 in it on the other hand, it was further selected as a representative example to be evaluated for its mechanism on the cell cycle and apoptosis of HCT116 cell line. Interestingly, 9a was found to pause the cell cycle of the HCT116 cell line at the G1 phase and induced late apoptosis. In parallel, all the synthesized hybrids 9a-p were examined for their potential to inhibit FGFR-1 at 10 µM. Compounds 9a, 9g, 9h, and 9p were found to have potent inhibitory activity with % inhibition = 63.04%, 58.31%, 60.87% and 79.84%, respectively. Molecular docking simulation of 9a in the binding pocket of FGFR-1 confirms its capability to achieve the characteristic interactions of the type II FGFR-1 inhibitors. Exploration of the ADME properties of 9a-p by SwissADME web tool proved their satisfactory physicochemical properties for the discovery of new anticancer hits.
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Affiliation(s)
- Heba T Abdel-Mohsen
- Chemistry of Natural and Microbial Products Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Cairo, Egypt
| | - Amira M Nageeb
- High Throughput Molecular and Genetic Technology Lab, Center of Excellence for Advanced Sciences, Biochemistry Department, Biotechnology Research Institute, National Research Centre, Cairo, Egypt
| | - Iman A Y Ghannam
- Chemistry of Natural and Microbial Products Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Cairo, Egypt
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Gutiérrez Pérez C, Lastra Aras E, Saiz López P, García Toro E, Blanco Abad C, Rodríguez Ledesma I, Pumares González M, Vela Domínguez M, Espinosa Cabria N, Crespo Herrero G. Single-center analysis of a real-world cohort of patients with metastatic urothelial carcinoma evaluated by NGS: molecular landscape and efficacy of targeted therapies. Clin Transl Oncol 2024:10.1007/s12094-024-03651-w. [PMID: 39147936 DOI: 10.1007/s12094-024-03651-w] [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: 06/12/2024] [Accepted: 07/29/2024] [Indexed: 08/17/2024]
Abstract
PURPOSE To describe the molecular profile of a real-world cohort of patients with metastatic urothelial carcinoma (mUC) and to evaluate the benefit of next-generation sequencing (NGS) panels in guiding therapy in patients with mUC and the outcomes of DNA-matched treatments recommended by a multidisciplinary molecular tumor board (MMTB). METHODS This was a single-center analysis of a real-world cohort of adult patients with mUC included in an ongoing trial that aimed to evaluate the clinical utility of NGS for solid tumors. Genomic analysis was performed for each patient, most of them using the Ion Torrent Oncomine Focus Assay. Genomic results were discussed during MMTB meetings. RESULTS We included 43 patients with mUC treated with platinum-based combinations and immunotherapy. Twenty-five patients (58.1%; 95% CI 43.4-72.9) had at least one tumor pathogenic alteration. The MMTB classified 16 (48.5%) of the 33 tumor pathogenic alterations found in our real-world cohort of mUC patients as ESCAT I, which is the maximum grade of actionability. After excluding patients who were not candidates for targeted therapies, the MMTB provided guidance on matched therapy for seven patients. Among these patients, three achieved a partial response for an overall response rate of 42.9%, a median progression-free survival of 7.3 months (95% CI 6.7-7.9) and a median overall survival of 10.9 months (95% CI 2.4-19.5). CONCLUSIONS We recommend that all patients with mUC undergo NGS at diagnosis given the high percentage of patients with pathogenic alterations in our real-world cohort and the efficacy data of patients treated with targeted therapies.
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Affiliation(s)
- César Gutiérrez Pérez
- Department of Medical Oncology, Hospital Universitario de Burgos (HUBU), Av. Islas Baleares, 3, 09006, Burgos, Spain.
| | - Enrique Lastra Aras
- Department of Medical Oncology, Hospital Universitario de Burgos (HUBU), Av. Islas Baleares, 3, 09006, Burgos, Spain
| | - Patricia Saiz López
- Department of Anatomic Pathology, Hospital Universitario de Burgos (HUBU), Burgos, Spain
| | - Enrique García Toro
- Department of Anatomic Pathology, Hospital Universitario de Burgos (HUBU), Burgos, Spain
| | - Carmen Blanco Abad
- Department of Medical Oncology, Hospital Universitario de Burgos (HUBU), Av. Islas Baleares, 3, 09006, Burgos, Spain
| | - Inmaculada Rodríguez Ledesma
- Department of Medical Oncology, Hospital Universitario de Burgos (HUBU), Av. Islas Baleares, 3, 09006, Burgos, Spain
| | - María Pumares González
- Department of Medical Oncology, Hospital Universitario de Burgos (HUBU), Av. Islas Baleares, 3, 09006, Burgos, Spain
| | - Miriam Vela Domínguez
- Department of Medical Oncology, Hospital Universitario de Burgos (HUBU), Av. Islas Baleares, 3, 09006, Burgos, Spain
| | - Noelia Espinosa Cabria
- Department of Medical Oncology, Hospital Universitario de Burgos (HUBU), Av. Islas Baleares, 3, 09006, Burgos, Spain
| | - Guillermo Crespo Herrero
- Department of Medical Oncology, Hospital Universitario de Burgos (HUBU), Av. Islas Baleares, 3, 09006, Burgos, Spain
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Zhao R, Yin F, Fredimoses M, Zhao J, Fu X, Xu B, Liang M, Chen H, Liu K, Lei M, Laster KV, Li Z, Kundu JK, Dong Z, Lee MH. Targeting FGFR1 by β,β-dimethylacrylalkannin suppresses the proliferation of colorectal cancer in cellular and xenograft models. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 129:155612. [PMID: 38669968 DOI: 10.1016/j.phymed.2024.155612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/05/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024]
Abstract
BACKGROUND Colorectal cancer (CRC) continues to be a major global health challenge, ranking as a top cause of cancer-related mortality. Alarmingly, the five-year survival rate for CRC patients hovers around a mere 10-30 %. The disruption of fibroblast growth factor receptor (FGFRs) signaling pathways is significantly implicated in the onset and advancement of CRC, presenting a promising target for therapeutic intervention in CRC management. Further investigation is essential to comprehensively elucidate FGFR1's function in CRC and to create potent therapies that specifically target FGFR1. PURPOSE This study aims to demonstrate the oncogenic role of FGFR1 in colorectal cancer and to explore the potential of β,β-dimethylacrylalkannin (β,β-DMAA) as a therapeutic option to inhibit FGFR1. METHODS In this research, we employed a comprehensive suite of techniques including tissue array, kinase profiling, computational docking, knockdown assay to predict and explore the inhibitor of FGFR1. Furthermore, we utilized kinase assay, pull-down, cell proliferation tests, and Patient derived xenograft (PDX) mouse models to further investigate a novel FGFR1 inhibitor and its impact on the growth of CRC. RESULTS In our research, we discovered that FGFR1 protein is markedly upregulated in colorectal cancer tissues, suggesting a significant role in regulating cellular proliferation, particularly in patients with colorectal cancer. Furthermore, we conducted a computational docking, kinase profiling analysis, simulation and identified that β,β-DMAA could directly bind with FGFR1 within ATP binding pocket domain. Cell-based assays confirmed that β,β-DMAA effectively inhibited the proliferation of colon cancer cells and also triggered cell cycle arrest, apoptosis, and altered FGFR1-mediated signaling pathways. Moreover, β,β-DMAA effectively attenuated the development of PDX tumors in mice that were FGFR1-positive, with no notable toxicity observed. In summary, our study highlights the pivotal role of FGFR1 in colorectal cancer, suggesting that inhibiting FGFR1 activity could be a promising strategy for therapeutic intervention. We present strong evidence that targeting FGFR1 with β,β-DMAA is a viable approach for the management of colorectal cancer. Given its low toxicity and high efficacy, β,β-DMAA, as an FGFR1 inhibitor, warrants further investigation in clinical settings for the treatment of FGFR1-positive tumors.
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Affiliation(s)
- Ran Zhao
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China; China-US (Henan) Hormel Cancer Institute, Zhengzhou 450000, China; Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou 450000, China
| | - Fanxiang Yin
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China; China-US (Henan) Hormel Cancer Institute, Zhengzhou 450000, China; Translational Medical Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | | | - Jianhua Zhao
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China; China-US (Henan) Hormel Cancer Institute, Zhengzhou 450000, China
| | - Xiaorong Fu
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China; China-US (Henan) Hormel Cancer Institute, Zhengzhou 450000, China
| | - Beibei Xu
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China; China-US (Henan) Hormel Cancer Institute, Zhengzhou 450000, China
| | - Mengrui Liang
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China; China-US (Henan) Hormel Cancer Institute, Zhengzhou 450000, China
| | - Hanyong Chen
- The Hormel Institute, University of Minnesota, Austin, MN55912, USA
| | - Kangdong Liu
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China; The Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou 450000, China
| | - Mingjuan Lei
- China-US (Henan) Hormel Cancer Institute, Zhengzhou 450000, China
| | | | - Zhi Li
- Department of General Surgery, the Affiliated Tumor Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Joydeb Kumar Kundu
- Li Ka Shing Applied Virology Institute, University of Alberta, Edmonton AB T6G 2R3, Canada
| | - Zigang Dong
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China; China-US (Henan) Hormel Cancer Institute, Zhengzhou 450000, China; Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou 450000, China.
| | - Mee-Hyun Lee
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China; China-US (Henan) Hormel Cancer Institute, Zhengzhou 450000, China; The Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou 450000, China; College of Korean Medicine, Dongshin University, Naju 58245, Republic of Korea.
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Rendina D, Abate V, Cacace G, D'Elia L, De Filippo G, Del Vecchio S, Galletti F, Cuocolo A, Strazzullo P. Tumor-induced Osteomalacia: A Systematic Review and Individual Patient's Data Analysis. J Clin Endocrinol Metab 2022; 107:e3428-e3436. [PMID: 35468192 DOI: 10.1210/clinem/dgac253] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Indexed: 01/10/2023]
Abstract
CONTEXT Tumor-induced osteomalacia (TIO) is a rare paraneoplastic syndrome, usually caused by small, benign, and slow-growing phosphaturic mesenchymal tumors. Clinically, TIO is characterized by renal phosphate leak, causing hypophosphatemia and osteomalacia. This review was performed to assess the clinical characteristics of TIO patients described worldwide so far. EVIDENCE ACQUISITION On June 26, 2021, a systematic search was performed in Medline, Google Scholar, Google book, and Cochrane Library using the terms: "tumor induced osteomalacia," "oncogenic osteomalacia," "hypophosphatemia." There were no language restrictions. This review was performed according to Preferred Reporting Items for Systematic reviews and Meta-Analyses criteria. EVIDENCE RESULTS Overall, 1725 TIO cases were collected. TIO was more frequent in adult men, who showed a higher incidence of fractures compared with TIO women. The TIO-causing neoplasms were identified in 1493 patients. The somatostatin receptor-based imaging modalities have the highest sensitivity for the identification of TIO-causing neoplasms. TIO-causing neoplasms were equally located in bone and soft tissues; the latter showed a higher prevalence of fractures and deformities. The surgery is the preferred TIO definitive treatment (successful in > 90% of patients). Promising nonsurgical therapies are treatments with burosumab in TIO patients with elevated fibroblast growth factor-23 levels, and with radiolabeled somatostatin analogs in patients with TIO-causing neoplasm identified by somatostatin receptor-based imaging techniques. CONCLUSION TIO occurs preferentially in adult men. The TIO clinical expressiveness is more severe in men as well as in patients with TIO-causing neoplasms located in soft tissues. Treatments with burosumab and with radiolabeled somatostatin analogs are the most promising nonsurgical therapies.
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Affiliation(s)
- Domenico Rendina
- Department of Clinical Medicine and Surgery, Federico II University, Naples 80131, Italy
| | - Veronica Abate
- Department of Clinical Medicine and Surgery, Federico II University, Naples 80131, Italy
| | - Giuseppe Cacace
- Department of Clinical Medicine and Surgery, Federico II University, Naples 80131, Italy
| | - Lanfranco D'Elia
- Department of Clinical Medicine and Surgery, Federico II University, Naples 80131, Italy
| | - Gianpaolo De Filippo
- Assistance Publique - Hôpitaux de Paris, Hôpital Robert Debré, Service d'Endocrinologie et DiabétologiePédiatrique, Paris 75015, France
| | - Silvana Del Vecchio
- Department of Advanced Biomedical Sciences, Federico II University, Naples 80131, Italy
| | - Ferruccio Galletti
- Department of Clinical Medicine and Surgery, Federico II University, Naples 80131, Italy
| | - Alberto Cuocolo
- Department of Advanced Biomedical Sciences, Federico II University, Naples 80131, Italy
| | - Pasquale Strazzullo
- Department of Clinical Medicine and Surgery, Federico II University, Naples 80131, Italy
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Chang GQ, Yasmin N, Collier AD, Karatayev O, Khalizova N, Onoichenco A, Fam M, Albeg AS, Campbell S, Leibowitz SF. Fibroblast growth factor 2: Role in prenatal alcohol-induced stimulation of hypothalamic peptide neurons. Prog Neuropsychopharmacol Biol Psychiatry 2022; 116:110536. [PMID: 35176416 PMCID: PMC8920779 DOI: 10.1016/j.pnpbp.2022.110536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 12/13/2022]
Abstract
Prenatal alcohol exposure (PAE) increases alcohol consumption and risk for alcohol use disorder. This phenomenon in rodents is suggested to involve a stimulatory effect of PAE, in female more than male offspring, on neurogenesis and density of neurons expressing neuropeptides in lateral hypothalamus (LH), including melanin-concentrating hormone (MCH), known to promote alcohol intake. With evidence suggesting a role for fibroblast growth factor 2 (FGF2) and its receptor FGFR1 in stimulating neurogenesis and alcohol drinking, we investigated here whether the FGF2-FGFR1 system is involved in the PAE-induced increase in MCH neurons, in postnatal offspring of pregnant rats given ethanol orally (embryonic day 10-15) at a low-moderate (2 g/kg/day) or high (5 g/kg/day) dose. Our results demonstrate that PAE at the low-moderate but not high dose stimulates FGF2 and FGFR1 gene expression and increases the density of MCH neurons co-expressing FGF2, only in females, but FGFR1 in both sexes. PAE induces this effect in the dorsal but not ventral area of the LH. Further analysis of FGF2 and FGFR1 transcripts within individual MCH neurons reveals an intracellular, sex-dependent effect, with PAE increasing FGF2 transcripts positively related to FGFR1 in the nucleus as well as cytoplasm of females but transcripts only in the cytoplasm of males. Peripheral injection of FGF2 itself (80 μg/kg, s.c.) in pregnant rats mimics these effects of PAE. Together, these results support the involvement of the FGF2-FGFR1 system in mediating the PAE-induced, sex dependent increase in density of MCH neurons, possibly contributing to increased alcohol consumption in the offspring.
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Affiliation(s)
- Guo-Qing Chang
- Laboratory of Behavioral Neurobiology, The Rockefeller University, New York, NY 10065, United States of America
| | - Nushrat Yasmin
- Laboratory of Behavioral Neurobiology, The Rockefeller University, New York, NY 10065, United States of America
| | - Adam D Collier
- Laboratory of Behavioral Neurobiology, The Rockefeller University, New York, NY 10065, United States of America
| | - Olga Karatayev
- Laboratory of Behavioral Neurobiology, The Rockefeller University, New York, NY 10065, United States of America
| | - Nailya Khalizova
- Laboratory of Behavioral Neurobiology, The Rockefeller University, New York, NY 10065, United States of America
| | - Amanda Onoichenco
- Laboratory of Behavioral Neurobiology, The Rockefeller University, New York, NY 10065, United States of America
| | - Milisia Fam
- Laboratory of Behavioral Neurobiology, The Rockefeller University, New York, NY 10065, United States of America
| | - Avi S Albeg
- Laboratory of Behavioral Neurobiology, The Rockefeller University, New York, NY 10065, United States of America
| | - Samantha Campbell
- Laboratory of Behavioral Neurobiology, The Rockefeller University, New York, NY 10065, United States of America
| | - Sarah F Leibowitz
- Laboratory of Behavioral Neurobiology, The Rockefeller University, New York, NY 10065, United States of America.
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Tan ES, Knepper TC, Wang X, Permuth JB, Wang L, Fleming JB, Xie H. Copy Number Alterations as Novel Biomarkers and Therapeutic Targets in Colorectal Cancer. Cancers (Basel) 2022; 14:2223. [PMID: 35565354 PMCID: PMC9101426 DOI: 10.3390/cancers14092223] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 04/21/2022] [Accepted: 04/24/2022] [Indexed: 12/10/2022] Open
Abstract
In colorectal cancer, somatic mutations have played an important role as prognostic and predictive biomarkers, with some also functioning as therapeutic targets. Another genetic aberration that has shown significance in colorectal cancer is copy number alterations (CNAs). CNAs occur when a change to the DNA structure propagates gain/amplification or loss/deletion in sections of DNA, which can often lead to changes in protein expression. Multiple techniques have been developed to detect CNAs, including comparative genomic hybridization with microarray, low pass whole genome sequencing, and digital droplet PCR. In this review, we summarize key findings in the literature regarding the role of CNAs in the pathogenesis of colorectal cancer, from adenoma to carcinoma to distant metastasis, and discuss the roles of CNAs as prognostic and predictive biomarkers in colorectal cancer.
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Affiliation(s)
- Elaine S. Tan
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA; (E.S.T.); (J.B.P.); (J.B.F.)
| | - Todd C. Knepper
- Department of Individualized Cancer Management, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA;
| | - Xuefeng Wang
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA;
| | - Jennifer B. Permuth
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA; (E.S.T.); (J.B.P.); (J.B.F.)
| | - Liang Wang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, 12901 USF Magnolia Drive Tampa, Tampa, FL 33612, USA;
| | - Jason B. Fleming
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA; (E.S.T.); (J.B.P.); (J.B.F.)
| | - Hao Xie
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA; (E.S.T.); (J.B.P.); (J.B.F.)
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Murolo S, Moumni M, Mancini V, Allagui MB, Landi L, Romanazzi G. Detection and Quantification of Stagonosporopsis cucurbitacearum in Seeds of Cucurbita maxima Using Droplet Digital Polymerase Chain Reaction. Front Microbiol 2022; 12:764447. [PMID: 35087483 PMCID: PMC8788924 DOI: 10.3389/fmicb.2021.764447] [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: 08/25/2021] [Accepted: 12/15/2021] [Indexed: 11/27/2022] Open
Abstract
Stagonosporopsis cucurbitacearum is an important seedborne pathogen of squash (Cucurbita maxima). The aim of our work was to develop a rapid and sensitive diagnostic tool for detection and quantification of S. cucurbitacearum in squash seed samples, to be compared with blotter analysis, that is the current official seed test. In blotter analysis, 29 of 31 seed samples were identified as infected, with contamination from 1.5 to 65.4%. A new set of primers (DB1F/R) was validated in silico and in conventional, quantitative real-time PCR (qPCR) and droplet digital (dd) PCR. The limit of detection of S. cucurbitacearum DNA for conventional PCR was ∼1.82 × 10–2 ng, with 17 of 19 seed samples positive. The limit of detection for ddPCR was 3.6 × 10–3 ng, which corresponded to 0.2 copies/μl. Detection carried out with artificial samples revealed no interference in the absolute quantification when the seed samples were diluted to 20 ng. All seed samples that showed S. cucurbitacearum contamination in the blotter analysis were highly correlated with the absolute quantification of S. cucurbitacearum DNA (copies/μl) in ddPCR (R2 = 0.986; p ≤ 0.01). Our ddPCR protocol provided rapid detection and absolute quantification of S. cucurbitacearum, offering a useful support to the standard procedure.
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Affiliation(s)
- Sergio Murolo
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - Marwa Moumni
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy.,Laboratory of Plant Protection, National Institute for Agronomic Research of Tunisia, University of Carthage, Ariana, Tunisia
| | - Valeria Mancini
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - Mohamed Bechir Allagui
- Laboratory of Plant Protection, National Institute for Agronomic Research of Tunisia, University of Carthage, Ariana, Tunisia
| | - Lucia Landi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - Gianfranco Romanazzi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
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8
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Kim G, Lee SK, Suh DH, Kim K, No JH, Kim YB, Kim H. Clinical evaluation of a droplet digital PCR assay for detecting POLE mutations and molecular classification of endometrial cancer. J Gynecol Oncol 2021; 33:e15. [PMID: 34910396 PMCID: PMC8899877 DOI: 10.3802/jgo.2022.33.e15] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 10/21/2021] [Accepted: 11/15/2021] [Indexed: 11/30/2022] Open
Abstract
Objective We evaluated droplet digital polymerase chain reaction (ddPCR) method for detecting POLE mutations in endometrial cancer (EC) and guiding its molecular classification. Methods We reviewed 240 EC specimens from our hospital database. A ddPCR assay was used to identify POLE mutations at 5 known hotspots (P286R, S297F, V411L, A456P, and S459F). Expressions of p53 and mismatch repair proteins were identified using immunohistochemistry. Results The ddPCR assay identified POLE mutations in 10.8% of patients. The most common mutation was V411L (61.54%), followed by P286R (23.07%), S459F (7.69%), S297F (3.85%), and A456P (3.85%). Eight/one cases had positive ddPCR but negative Sanger sequencing/next-generation sequencing, respectively. Molecular classification revealed p53-mutated subtype as significantly more common for tumors with a high International Federation of Gynecology and Obstetrics (FIGO) grade, deep myometrial invasion, lymphovascular space invasion, advanced stage, and high/advanced risk groups; the POLE mutated group was more frequent in the low stage and low/intermediate risk group. Survival analyses revealed the poorest outcomes for p53-mutated EC, while mismatch repair-deficient and no specific molecular profile ECs had similar progression-free survival (PFS) outcomes, and POLE-mutated ECs had the best PFS outcome (p<0.001). When only intermediate, high-intermediate, and high-risk groups were analyzed for subgroups, molecular classification still showed differences both in PFS (p=0.003) and overall survival (p=0.017). Conclusion Hotspot POLE mutations can be detected using the ddPCR assay. We suggest simultaneously evaluating POLE mutation status using ddPCR and p53/mismatch repair protein expressions using immunohistochemistry, which can rapidly and accurately determine the molecular subtype of EC. Using droplet digital polymerase chain reaction (ddPCR), we successfully detected the 5 most frequent pathogenic hotspot mutations in the POLE gene in samples from endometrial cancer patients, thus confirming the utility of ddPCR in their identification.
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Affiliation(s)
- Gilhyang Kim
- Department of Pathology, Hallym University Kangnam Sacred Heart Hospital, Seoul, Korea
| | - Song Kook Lee
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Dong Hoon Suh
- Department of Obstetrics and Gynecology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Kidong Kim
- Department of Obstetrics and Gynecology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Jae Hong No
- Department of Obstetrics and Gynecology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Yong Beom Kim
- Department of Obstetrics and Gynecology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Hyojin Kim
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, Korea.
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9
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Ferguson HR, Smith MP, Francavilla C. Fibroblast Growth Factor Receptors (FGFRs) and Noncanonical Partners in Cancer Signaling. Cells 2021; 10:1201. [PMID: 34068954 PMCID: PMC8156822 DOI: 10.3390/cells10051201] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/06/2021] [Accepted: 05/09/2021] [Indexed: 02/07/2023] Open
Abstract
Increasing evidence indicates that success of targeted therapies in the treatment of cancer is context-dependent and is influenced by a complex crosstalk between signaling pathways and between cell types in the tumor. The Fibroblast Growth Factor (FGF)/FGF receptor (FGFR) signaling axis highlights the importance of such context-dependent signaling in cancer. Aberrant FGFR signaling has been characterized in almost all cancer types, most commonly non-small cell lung cancer (NSCLC), breast cancer, glioblastoma, prostate cancer and gastrointestinal cancer. This occurs primarily through amplification and over-expression of FGFR1 and FGFR2 resulting in ligand-independent activation. Mutations and translocations of FGFR1-4 are also identified in cancer. Canonical FGF-FGFR signaling is tightly regulated by ligand-receptor combinations as well as direct interactions with the FGFR coreceptors heparan sulfate proteoglycans (HSPGs) and Klotho. Noncanonical FGFR signaling partners have been implicated in differential regulation of FGFR signaling. FGFR directly interacts with cell adhesion molecules (CAMs) and extracellular matrix (ECM) proteins, contributing to invasive and migratory properties of cancer cells, whereas interactions with other receptor tyrosine kinases (RTKs) regulate angiogenic, resistance to therapy, and metastatic potential of cancer cells. The diversity in FGFR signaling partners supports a role for FGFR signaling in cancer, independent of genetic aberration.
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Affiliation(s)
- Harriet R. Ferguson
- Division of Molecular and Cellular Function, School of Biological Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, Manchester M13 9PT, UK;
| | - Michael P. Smith
- Division of Molecular and Cellular Function, School of Biological Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, Manchester M13 9PT, UK;
| | - Chiara Francavilla
- Division of Molecular and Cellular Function, School of Biological Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, Manchester M13 9PT, UK;
- Manchester Breast Centre, Manchester Cancer Research Centre, The University of Manchester, Manchester M20 4GJ, UK
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10
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Liu G, Chen T, Ding Z, Wang Y, Wei Y, Wei X. Inhibition of FGF-FGFR and VEGF-VEGFR signalling in cancer treatment. Cell Prolif 2021; 54:e13009. [PMID: 33655556 PMCID: PMC8016646 DOI: 10.1111/cpr.13009] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 01/18/2021] [Accepted: 01/29/2021] [Indexed: 02/05/2023] Open
Abstract
The sites of targeted therapy are limited and need to be expanded. The FGF‐FGFR signalling plays pivotal roles in the oncogenic process, and FGF/FGFR inhibitors are a promising method to treat FGFR‐altered tumours. The VEGF‐VEGFR signalling is the most crucial pathway to induce angiogenesis, and inhibiting this cascade has already got success in treating tumours. While both their efficacy and antitumour spectrum are limited, combining FGF/FGFR inhibitors with VEGF/VEGFR inhibitors are an excellent way to optimize the curative effect and expand the antitumour range because their combination can target both tumour cells and the tumour microenvironment. In addition, biomarkers need to be developed to predict the efficacy, and combination with immune checkpoint inhibitors is a promising direction in the future. The article will discuss the FGF‐FGFR signalling pathway, the VEGF‐VEGFR signalling pathway, the rationale of combining these two signalling pathways and recent small‐molecule FGFR/VEGFR inhibitors based on clinical trials.
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Affiliation(s)
- Guihong Liu
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Tao Chen
- Cardiology Department, Chengdu NO.7 People's Hospital, Chengdu Tumor Hospital, Chengdu, China
| | - Zhenyu Ding
- Department of Biotherapy, State Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yang Wang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Yuquan Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
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11
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Du Y, Fan K, Lu X, Wu C. Integrating Multi–Omics Data for Gene-Environment Interactions. BIOTECH 2021; 10:biotech10010003. [PMID: 35822775 PMCID: PMC9245467 DOI: 10.3390/biotech10010003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/22/2021] [Accepted: 01/22/2021] [Indexed: 01/05/2023] Open
Abstract
Gene-environment (G×E) interaction is critical for understanding the genetic basis of complex disease beyond genetic and environment main effects. In addition to existing tools for interaction studies, penalized variable selection emerges as a promising alternative for dissecting G×E interactions. Despite the success, variable selection is limited in terms of accounting for multidimensional measurements. Published variable selection methods cannot accommodate structured sparsity in the framework of integrating multiomics data for disease outcomes. In this paper, we have developed a novel variable selection method in order to integrate multi-omics measurements in G×E interaction studies. Extensive studies have already revealed that analyzing omics data across multi-platforms is not only sensible biologically, but also resulting in improved identification and prediction performance. Our integrative model can efficiently pinpoint important regulators of gene expressions through sparse dimensionality reduction, and link the disease outcomes to multiple effects in the integrative G×E studies through accommodating a sparse bi-level structure. The simulation studies show the integrative model leads to better identification of G×E interactions and regulators than alternative methods. In two G×E lung cancer studies with high dimensional multi-omics data, the integrative model leads to an improved prediction and findings with important biological implications.
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12
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Plowman PN, Plowman CE. Onco-ontogeny recapitulates phylogeny - a consideration. Oncogene 2021; 40:1542-1550. [PMID: 33452457 DOI: 10.1038/s41388-020-01624-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 11/09/2022]
Affiliation(s)
- P N Plowman
- Department of Clinical Oncology, St. Bartholomew's Hospital, West Smithfield, London, UK.
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Su H, Chang C, Hao J, Xu X, Bao M, Luo S, Zhao C, Liu Q, Wang X, Zhou Z, Zhou H. Identification of Genomic Alterations of Perineural Invasion in Patients with Stage II Colorectal Cancer. Onco Targets Ther 2020; 13:11571-11582. [PMID: 33204110 PMCID: PMC7667198 DOI: 10.2147/ott.s264616] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 10/22/2020] [Indexed: 12/24/2022] Open
Abstract
Purpose The molecular mechanism of perineural invasion (PNI) in stage II colorectal cancer (CRC) remains not to be defined clearly. This study aims to identify the genomic aberrations related to PNI in stage II CRC. Patients and Methods Using array-based comparative genomic hybridization (array-CGH), primary tumor tissues and paracancerous normal tissues of stage II CRC with PNI and without PNI were analyzed. We identified genomic aberrations by using Genomic Workbench and MD-SeeGH and validated the aberrations of selected genes by real-time polymerase chain reaction (PCR). Gene ontology (GO) and pathway analysis were performed to determine the most likely biological effects of these genes. Results The most frequent gains in stage II CRC were at 7q11.21-q11.22, 8p11.21, 8p12-p11.23, 8q11.1-q11.22, 13q12.13-q12.2, and 20q11.21-q11.23 and the most frequent losses were at 17p13.1-p12, 8p23.2, and 118q11.2-q23. Four high-level amplifications at 8p11.23-p11.22, 18q21.1, 19q11-q12, and 20q11.21-q13.32 and homozygous deletions at 20p12.1 were discovered in Stage II CRC. Gains at 7q11.21-q22.1, 16p11.2, 17q23.3-q25.3, 19p13.3-p12, and 20p13-p11.1, and losses at 11q11-q12.1, 11p15.5-p15.1, 18p11.21, and 18q21.1-q23 were more commonly found in patients with PNI by frequency plot comparison together with detailed genomic analysis. It is also observed that gains at 8q11.1-q24.3, 9q13-q34.3, and 13q12.3-q13.1, and losses at 8p23.3-p12, 17p13.3-p11.2, and 21q22.12 occurred more frequently in patients without PNI. Further validation showed that the expression of FLT1, FBXW7, FGFR1, SLC20A2 and SERPINI1 was significantly up-regulated in the NPNI group compared to the PNI group. GO and pathway analysis revealed some genes enriched in specific pathways. Conclusion These involved genomic changes in the PNI of stage II CRC may be useful to reveal the mechanisms underlying PNI and provide candidate biomarkers.
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Affiliation(s)
- Hao Su
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, People's Republic of China
| | - Chen Chang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, People's Republic of China
| | - Jiajie Hao
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, People's Republic of China
| | - Xin Xu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, People's Republic of China
| | - Mandula Bao
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, People's Republic of China
| | - Shou Luo
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, People's Republic of China
| | - Chuanduo Zhao
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, People's Republic of China
| | - Qian Liu
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, People's Republic of China
| | - Xishan Wang
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, People's Republic of China
| | - Zhixiang Zhou
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, People's Republic of China
| | - Haitao Zhou
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, People's Republic of China
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14
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Zhang Y, Yu N. Design, Synthesis and Biological Evaluation: 5-amino-1H-pyrazole-1- carbonyl derivatives as FGFR Inhibitors. LETT DRUG DES DISCOV 2020. [DOI: 10.2174/1570180817999200608140628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Background:
Fibroblast growth factors (FGFs) and their high affinity receptors (FGFRs)
play a major role in cell proliferation, differentiation, migration, and apoptosis. Aberrant FGFR signaling
pathway might accelerate development in a broad panel of malignant solid tumors. However,
the full application of most existing small molecule FGFR inhibitors has become a challenge due to
the potential target mutation. Hence, it has attracted a great deal of attention from both academic and
industrial fields for hunting for novel FGFR inhibitors with potent inhibitory activities and high selectivity.
Objective:
Novel 5-amino-1H-pyrazole-1-carbonyl derivatives were designed, synthesized, and
evaluated as FGFR inhibitors.
Methods:
A series of 5-amino-1H-pyrazole-1-carbonyl derivatives were established by a condensation
of the suitable formyl acetonitrile derivatives with either hydrazine or hydrazide derivatives in
the presence of anhydrous ethanol or toluene. The inhibitory activities of the target compounds were
screened against the FGFRs and two representative cancer cell lines. Tests were carried out to observe
the inhibition of 8e against FGFR phosphorylation and downstream signal phosphorylation in
human gastric cancer cell lines (SNU-16). The molecular docking of all the compounds were performed
using Molecular Operating Environment in order to evaluate their binding abilities with the
corresponding protein kinase.
Results:
A series of 5-amino-1H-pyrazole-1-carbonyl derivatives have been designed and synthesized,
screened for their inhibitory activities against FGFRs and cancer cell lines. Most of the target
compounds showed moderate to good anti-proliferate activities against the tested enzymes and cell
lines. The most promising compounds 8e suppressed FGFR1-3 with IC50 values of 56.4, 35.2, 95.5 nM,
and potently inhibited the SNU-16 and MCF-7 cancer cells with IC50 values of 0.71 1.26 μM, respectively.
And 8e inhibited the growth of cancer cells containing FGFR activated by multiple mechanisms. In
addition, the binding interactions were quite similar in the molecular models between generated
compounds and Debio-1347 with the FGFR1.
Conclusion:
According to the experimental findings, 5-amino-1H-pyrazole-1-carbonyl might serve
as a promising template of an FGFR inhibitor.
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Affiliation(s)
- Yan Zhang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
| | - Niefang Yu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
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Qiao C, Qian H, Wang J, Zhao T, Ma P, Wang S, Zhang T, Liu X. PD173074 blocks G1/S transition via CUL3-mediated ubiquitin protease in HepG2 and Hep3B cells. PLoS One 2020; 15:e0234708. [PMID: 32555680 PMCID: PMC7302471 DOI: 10.1371/journal.pone.0234708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/31/2020] [Indexed: 11/24/2022] Open
Abstract
Fibroblast growth factor receptors (FGFRs) are frequently altered in a variety of human cancer cells and are overexpressed in hepatocellular carcinoma (HCC). Several literatures have proven that they are efficacious for HCC therapy, however, the underlying mechanism remains unclear. Here, we found FGFR4 was overexpressed in HCC cell lines HepG2 and Hep3B and we used PD173074, an FGFR4 inhibitor, to explore the role of FGFR4 and its underlying mechanism in these cell lines. The results showed that PD173074 significantly arrested HepG2 and Hep3B cells in G1 phase and inhibited cell proliferation. Furthermore, Western blot analysis revealed that PD173074 decreased the levels of P-FRS2α, P-ERK, CDK2, cyclin E and NF-κB (p65) in the nucleus while it increased the levels of ubiquitin and CUL3, an E3 ubiquitin ligase which involves in cyclin E degradation. Meanwhile, the data from RT-qPCR showed that PD173074 also decreased miR-141 level. In conclusion, these results suggest that FGFR4 is involved in HCC by ERK/CUL3/cyclin E signaling pathway, and the finding may provide a potential theoretical basis for treatment by targeting FGFR4 in HCC.
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Affiliation(s)
- Chuchu Qiao
- School of Pharmacy, Xi’an Jiaotong University Health Science Center, Xi’an, ShaanXi, China
| | - Hongyan Qian
- School of Forensic Science and Medicine, Xi’an Jiaotong University Health Science Center, Xi’an, ShaanXi, China
| | - Jue Wang
- School of Pharmacy, Xi’an Jiaotong University Health Science Center, Xi’an, ShaanXi, China
| | - Tingting Zhao
- School of Pharmacy, Xi’an Jiaotong University Health Science Center, Xi’an, ShaanXi, China
| | - Pengyu Ma
- School of Pharmacy, Xi’an Jiaotong University Health Science Center, Xi’an, ShaanXi, China
| | - Sicen Wang
- School of Pharmacy, Xi’an Jiaotong University Health Science Center, Xi’an, ShaanXi, China
| | - Tao Zhang
- School of Pharmacy, Xi’an Jiaotong University Health Science Center, Xi’an, ShaanXi, China
| | - Xinshe Liu
- School of Forensic Science and Medicine, Xi’an Jiaotong University Health Science Center, Xi’an, ShaanXi, China
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Li J, Zhang J, Hu H, Cai Y, Ling J, Wu Z, Deng Y. Gene Expression Signature to Predict Prognosis and Adjuvant Chemosensitivity of Colorectal Cancer Patients. Cancer Manag Res 2020; 12:3301-3310. [PMID: 32494194 PMCID: PMC7227814 DOI: 10.2147/cmar.s243490] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Accepted: 04/16/2020] [Indexed: 12/22/2022] Open
Abstract
Purpose Molecular characteristics using gene-expression profiling can undoubtedly improve the prediction of treatment responses, and ultimately, the clinical outcome of cancer patients. We aimed at developing a genetic signature to improve the prediction of chemosensitivity and prognosis of patients with colorectal cancer (CRC). Patients and Methods We analyzed microarray data of 32 CRC patients to explore the potential functions and pathways involved in the disease relapse in CRC. Gene expression profiles and clinical follow-up information of GSE39582, GSE17536, and GSE103479 were downloaded from the Gene Expression Omnibus database (GEO) to identify prognostic genes. Eventually, a model of 15-mRNA signature was established, in which its efficacy for predicting chemosensitivity and prognosis was examined. Results Based on the proposed model of 15-mRNA signature, the test series patients could be classified into high-risk or low-risk subgroup with significantly different overall survival (OS) rate (hazard ratio [HR]=1.48, 95% confidence interval [CI]=1.30–1.70, P≤0.001). The prognostic value of this 15-mRNA signature was confirmed in another validation series. Further analysis revealed that the prognostic value of this signature was independent of the TNM stage and can predict adjuvant chemosensitivity of patients with early-stage CRC. Conclusion We identified a novel 15-mRNA signature in patients with CRC, which could be clinically helpful in the prognosis evaluation and the process of selection of patients with early-stage CRC for undergoing adjuvant chemotherapy.
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Affiliation(s)
- Jianxia Li
- Department of Medical Oncology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangdong Province Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangzhou, Guangdong 510655, People's Republic of China
| | - Jianwei Zhang
- Department of Medical Oncology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangdong Province Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangzhou, Guangdong 510655, People's Republic of China
| | - Huabin Hu
- Department of Medical Oncology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangdong Province Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangzhou, Guangdong 510655, People's Republic of China
| | - Yue Cai
- Department of Medical Oncology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangdong Province Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangzhou, Guangdong 510655, People's Republic of China
| | - Jiayu Ling
- Department of Medical Oncology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangdong Province Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangzhou, Guangdong 510655, People's Republic of China
| | - Zehua Wu
- Department of Medical Oncology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangdong Province Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangzhou, Guangdong 510655, People's Republic of China
| | - Yanhong Deng
- Department of Medical Oncology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangdong Province Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangzhou, Guangdong 510655, People's Republic of China
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Chang Z, Miao X, Zhao W. Identification of Prognostic Dosage-Sensitive Genes in Colorectal Cancer Based on Multi-Omics. Front Genet 2020; 10:1310. [PMID: 31998369 PMCID: PMC6962299 DOI: 10.3389/fgene.2019.01310] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 11/27/2019] [Indexed: 01/13/2023] Open
Abstract
Several studies have already identified the prognostic markers in colorectal cancer (CRC) based on somatic copy number alteration (SCNA). However, very little information is available regarding their value as a prognostic marker. Gene dosage effect is one important mechanism of copy number and dosage-sensitive genes are more likely to behave like driver genes. In this work, we propose a new pipeline to identify the dosage-sensitive prognostic genes in CRC. The RNAseq data, the somatic copy number of CRC from TCGA were assayed to screen out the SCNAs. Wilcoxon rank-sum test was used to identify the differentially expressed genes in alteration samples with |SCNA| > 0.3. Cox-regression was used to find the candidate prognostic genes. An iterative algorithm was built to identify the stable prognostic genes. Finally, the Pearson correlation coefficient was calculated between gene expression and SCNA as the dosage effect score. The cell line data from CCLE was used to test the consistency of the dosage effect. The differential co-expression network was built to discover their function in CRC. A total of six amplified genes (NDUFB4, WDR5B, IQCB1, KPNA1, GTF2E1, and SEC22A) were found to be associated with poor prognosis. They demonstrate a stable prognostic classification in more than 50% threshold of SCNA. The average dosage effect score was 0.5918 ± 0.066, 0.5978 ± 0.082 in TCGA and CCLE, respectively. They also show great stability in different data sets. In the differential co-expression network, these six genes have the top degree and are connected to the driver and tumor suppressor genes. Function enrichment analysis revealed that gene NDUFB4 and GTF2E1 affect cancer-related functions such as transmembrane transport and transformation factors. In conclusion, the pipeline for identifying the prognostic dosage-sensitive genes in CRC was proved to be stable and reliable.
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Affiliation(s)
- Zhiqiang Chang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xiuxiu Miao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Wenyuan Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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