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Integrated multi-omics analyses on patient-derived CRC organoids highlight altered molecular pathways in colorectal cancer progression involving PTEN. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:198. [PMID: 34154611 PMCID: PMC8215814 DOI: 10.1186/s13046-021-01986-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/16/2021] [Indexed: 12/23/2022]
Abstract
Background Colorectal cancer (CRC) represents the fourth leading cause of cancer-related deaths. The heterogeneity of CRC identity limits the usage of cell lines to study this type of tumor because of the limited representation of multiple features of the original malignancy. Patient-derived colon organoids (PDCOs) are a promising 3D-cell model to study tumor identity for personalized medicine, although this approach still lacks detailed characterization regarding molecular stability during culturing conditions. Correlation analysis that considers genomic, transcriptomic, and proteomic data, as well as thawing, timing, and culturing conditions, is missing. Methods Through integrated multi–omics strategies, we characterized PDCOs under different growing and timing conditions, to define their ability to recapitulate the original tumor. Results Whole Exome Sequencing allowed detecting temporal acquisition of somatic variants, in a patient-specific manner, having deleterious effects on driver genes CRC-associated. Moreover, the targeted NGS approach confirmed that organoids faithfully recapitulated patients’ tumor tissue. Using RNA-seq experiments, we identified 5125 differentially expressed transcripts in tumor versus normal organoids at different time points, in which the PTEN pathway resulted of particular interest, as also confirmed by further phospho-proteomics analysis. Interestingly, we identified the PTEN c.806_817dup (NM_000314) mutation, which has never been reported previously and is predicted to be deleterious according to the American College of Medical Genetics and Genomics (ACMG) classification. Conclusion The crosstalk of genomic, transcriptomic and phosphoproteomic data allowed to observe that PDCOs recapitulate, at the molecular level, the tumor of origin, accumulating mutations over time that potentially mimic the evolution of the patient’s tumor, underlining relevant potentialities of this 3D model. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-01986-8.
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Chen J, Lin M, Che Y, Guo J, Lin W. Key genes in youth colorectal cancer based on data mining and verification by reverse transcription-quantitative PCR. Oncol Lett 2021; 21:194. [PMID: 33574933 PMCID: PMC7816307 DOI: 10.3892/ol.2021.12455] [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: 07/10/2020] [Accepted: 12/07/2020] [Indexed: 12/24/2022] Open
Abstract
In recent years, among all patients with colorectal cancer, the proportion of young patients has been gradually increasing. However, the molecular mechanisms involved in colorectal cancer in the young are largely unknown. In the present study the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas datasets were integrated to elucidate the key gene biomarkers in these patients. The GSE41657 and GSE41258 datasets were downloaded from the GEO database. By screening for differentially expressed genes, Gene Ontology analysis, Kyoto Encyclopedia of Genes and Genomes pathway analysis, protein-protein interaction analysis, hub gene screening and survival analysis, two key genes, CXCL8 and VEGFA, which were enriched in cancer pathways, were obtained. Reverse transcription-quantitative (RT-q)PCR was performed to verify the outcome obtained by bioinformatics analysis. In conclusion, the present study identified two key genes using bioinformatics analysis and RT-qPCR validation. These results indicated that the candidate genes may be involved in the progression of colorectal cancer in young people, and these two genes may act as ideal prognostic indicators or therapeutic targets for colorectal cancer in the youth.
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Affiliation(s)
- Jianxin Chen
- The First Department of Gastrointestinal Surgery, The Affiliated Hospital of Putian University, Putian, Fujian 351100, P.R. China.,Gastrointestinal Surgery Research Institute, The Affiliated Hospital of Putian University, Putian, Fujian 351100, P.R. China
| | - Min Lin
- College of Information Engineering, Putian University, Putian, Fujian 351100, P.R. China
| | - Yan Che
- College of Information Engineering, Putian University, Putian, Fujian 351100, P.R. China.,Engineering Research Center of Big Data Application in Private Health Medicine, Fujian Province University, Putian, Fujian 351100, P.R. China
| | - Jian Guo
- The First Department of Gastrointestinal Surgery, The Affiliated Hospital of Putian University, Putian, Fujian 351100, P.R. China.,Gastrointestinal Surgery Research Institute, The Affiliated Hospital of Putian University, Putian, Fujian 351100, P.R. China
| | - Wei Lin
- The First Department of Gastrointestinal Surgery, The Affiliated Hospital of Putian University, Putian, Fujian 351100, P.R. China.,Gastrointestinal Surgery Research Institute, The Affiliated Hospital of Putian University, Putian, Fujian 351100, P.R. China
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Diethelm-Varela B. Using NMR Spectroscopy in the Fragment-Based Drug Discovery of Small-Molecule Anticancer Targeted Therapies. ChemMedChem 2020; 16:725-742. [PMID: 33236493 DOI: 10.1002/cmdc.202000756] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/21/2020] [Indexed: 12/19/2022]
Abstract
Against the challenge of providing personalized cancer care, the development of targeted therapies stands as a promising approach. The discovery of these agents can benefit from fragment-based drug discovery (FBDD) methods that help guide ligand design and provide key structural information on the targets of interest. In particular, nuclear magnetic resonance spectroscopy is a promising biophysical tool in fragment discovery due to its detection capabilities and versatility. This review provides an overview of FBDD, describes the basis of NMR-based fragment screening, summarizes some exciting technical advances reported over the past decades, and closes with a discussion of selected case studies where this technique has been used as part of drug discovery campaigns to produce lead compounds towards the design of anti-cancer targeted therapies.
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Affiliation(s)
- Benjamin Diethelm-Varela
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., Baltimore, MD 21201, USA
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Balibegloo M, Rezaei N. Development and clinical application of bispecific antibody in the treatment of colorectal cancer. Expert Rev Clin Immunol 2020; 16:689-709. [PMID: 32536227 DOI: 10.1080/1744666x.2020.1783249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Treatment of colorectal cancer as one of the most commonly diagnosed and a frequent cause of cancer-related deaths is of great challenges in health-related issues. AREAS COVERED Immunotherapy is the fourth pillar of cancer treatment which provides more novel therapeutic options with expanding investigational potentials. One of the modalities in immunotherapy is the use of bispecific antibodies. Despite demonstrating many promising roles, it still needs more advanced studies to identify the actual pros and cons. In this review, the application of bispecific antibody in the treatment of colorectal cancer has been explained, based on preclinical and clinical studies. The literature search was conducted mainly through PubMed in June and September 2019. EXPERT OPINION Bispecific antibody is in its early stages in colorectal cancer treatment, requiring modern technologies in manufacturing, better biomarkers and more specific target antigens, more studies on individual genetic variations, and conducting later phase clinical trials and systematic reviews to achieve better survival benefits.
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Affiliation(s)
- Maryam Balibegloo
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences , Tehran, Iran.,Cancer Immunology Project (CIP), Universal Scientific Education & Research Network (USERN) , Tehran, Iran
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences , Tehran, Iran.,Department of Immunology, School of Medicine, Tehran University of Medical Sciences , Tehran, Iran.,Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education & Research Network (USERN) , Tehran, Iran
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Campiotti L, Gariboldi MB, Mortara L, Noonan DM, Gallo D, Nigro O, Monti E, Piantanida E. Negative impact of high body mass index on cetuximab-mediated cellular cytotoxicity against human colon carcinoma cells. J Chemother 2020; 33:132-135. [PMID: 32544039 DOI: 10.1080/1120009x.2020.1777722] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
This study assessed the relationship between the ability of Natural Killer (NK) cells to activate antibody-dependent cellular cytotoxicity against human HT29 colorectal cancer cells exposed to cetuximab and the body mass index of the human subjects from whom the NK cells had been obtained. NK cells obtained from 73 human donors were co-incubated with HT-29 human colon cancer cells in the presence or absence of cetuximab. Antibody-dependent cellular cytotoxicity was assessed by measuring LDH release. A significant negative correlation was observed between body mass index and cetuximab-induced antibody-dependent cellular cytotoxicity. NK cells obtained from subjects who were overweight or with obesity were less efficient in killing cetuximab-treated HT29 cells than those derived from normal weight donors. Our results suggest that the success of cetuximab-containing regimens might be impaired in overweight and obese patients with colorectal cancer.
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Affiliation(s)
- Leonardo Campiotti
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | | | - Lorenzo Mortara
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Douglas McClain Noonan
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy.,Vascular Biology and Angiogenesis Laboratory, Science and Technology Pole (PST), IRCCS MultiMedica, Milano, Italy
| | - Daniela Gallo
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Olga Nigro
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Elena Monti
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Eliana Piantanida
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
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Du W, Liu N, Zhang Y, Liu X, Yang Y, Chen W, He Y. PLOD2 promotes aerobic glycolysis and cell progression in colorectal cancer by upregulating HK2. Biochem Cell Biol 2019; 98:386-395. [PMID: 31742425 DOI: 10.1139/bcb-2019-0256] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The purpose of this study was to characterize the expression of procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2 (PLOD2), a membrane-bound homodimeric enzyme that specifically hydroxylates lysine in the telopeptide of procollagens, and assess the clinical significance of PLOD2 in colorectal cancer (CRC). Our results show that PLOD2 is highly expressed in CRC tumor tissues and cell lines, both at the mRNA and protein levels. Next, we found that PLOD2 was positively correlated with tumor grade (P = 0.001), T stage (P = 0.001), N stage (P < 0.001), and an advanced TNM stage (P < 0.001). Knockdown of PLOD2 attenuated CRC cell proliferation, migration, and invasiveness, in vitro. Our analysis of the mechanism behind the effects of PLOD2 suggests that PLOD2 affected glycolysis by regulating the expression of hexokinase 2 (HK2). HK2 reverses the inhibitory effects of PLOD2 knockdown in CRC. Furthermore, the data suggest that PLOD2 regulates the expression of HK2 via the STAT3 signaling pathway. Survival analysis revealed that high expression levels of PLOD2 (HR = 3.800, P < 0.001) and HK2 expression (HR = 10.222, P < 0.001) correlated with the overall survival rate. After analyzing their expression and correlation, PLOD2 positively correlated with HK2 (r = 0.590, P < 0.001). Our findings have revealed that PLOD2 is a novel regulatory factor in glucose metabolism, exerted via controlling HK2 expression in CRC cells, suggesting PLOD2 as a promising therapeutic target for CRC treatment.
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Affiliation(s)
- Wenwu Du
- Department of Anus and Intestine Surgery, Suining Central Hospital, 127 West Desheng Road, Suining 629000, Sichuan, P.R. China.,Department of Anus and Intestine Surgery, Suining Central Hospital, 127 West Desheng Road, Suining 629000, Sichuan, P.R. China
| | - Ning Liu
- Department of Anus and Intestine Surgery, Suining Central Hospital, 127 West Desheng Road, Suining 629000, Sichuan, P.R. China.,Department of Anus and Intestine Surgery, Suining Central Hospital, 127 West Desheng Road, Suining 629000, Sichuan, P.R. China
| | - Yafeng Zhang
- Department of Anus and Intestine Surgery, Suining Central Hospital, 127 West Desheng Road, Suining 629000, Sichuan, P.R. China.,Department of Anus and Intestine Surgery, Suining Central Hospital, 127 West Desheng Road, Suining 629000, Sichuan, P.R. China
| | - Xi Liu
- Department of Anus and Intestine Surgery, Suining Central Hospital, 127 West Desheng Road, Suining 629000, Sichuan, P.R. China.,Department of Anus and Intestine Surgery, Suining Central Hospital, 127 West Desheng Road, Suining 629000, Sichuan, P.R. China
| | - Yuanhong Yang
- Department of Anus and Intestine Surgery, Suining Central Hospital, 127 West Desheng Road, Suining 629000, Sichuan, P.R. China.,Department of Anus and Intestine Surgery, Suining Central Hospital, 127 West Desheng Road, Suining 629000, Sichuan, P.R. China
| | - Wei Chen
- Department of Anus and Intestine Surgery, Suining Central Hospital, 127 West Desheng Road, Suining 629000, Sichuan, P.R. China.,Department of Anus and Intestine Surgery, Suining Central Hospital, 127 West Desheng Road, Suining 629000, Sichuan, P.R. China
| | - Yi He
- Department of Anus and Intestine Surgery, Suining Central Hospital, 127 West Desheng Road, Suining 629000, Sichuan, P.R. China.,Department of Anus and Intestine Surgery, Suining Central Hospital, 127 West Desheng Road, Suining 629000, Sichuan, P.R. China
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