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Zhang T, Qian C, Song M, Tang Y, Zhou Y, Dong G, Shen Q, Chen W, Wang A, Shen S, Zhao Y, Lu Y. Application Prospect of Induced Pluripotent Stem Cells in Organoids and Cell Therapy. Int J Mol Sci 2024; 25:2680. [PMID: 38473926 DOI: 10.3390/ijms25052680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/13/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Since its inception, induced pluripotent stem cell (iPSC) technology has been hailed as a powerful tool for comprehending disease etiology and advancing drug screening across various domains. While earlier iPSC-based disease modeling and drug assessment primarily operated at the cellular level, recent years have witnessed a significant shift towards organoid-based investigations. Organoids derived from iPSCs offer distinct advantages, particularly in enabling the observation of disease progression and drug metabolism in an in vivo-like environment, surpassing the capabilities of iPSC-derived cells. Furthermore, iPSC-based cell therapy has emerged as a focal point of clinical interest. In this review, we provide an extensive overview of non-integrative reprogramming methods that have evolved since the inception of iPSC technology. We also deliver a comprehensive examination of iPSC-derived organoids, spanning the realms of the nervous system, cardiovascular system, and oncology, as well as systematically elucidate recent advancements in iPSC-related cell therapies.
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Affiliation(s)
- Teng Zhang
- Jiangsu Joint International Research Laboratory of Chinese Medicine and Regenerative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Cheng Qian
- Jiangsu Joint International Research Laboratory of Chinese Medicine and Regenerative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Mengyao Song
- Jiangsu Joint International Research Laboratory of Chinese Medicine and Regenerative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yu Tang
- Jiangsu Joint International Research Laboratory of Chinese Medicine and Regenerative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yueke Zhou
- Jiangsu Joint International Research Laboratory of Chinese Medicine and Regenerative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Guanglu Dong
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Department of Biochemistry and Molecular Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Qiuhong Shen
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Department of Biochemistry and Molecular Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Wenxing Chen
- Jiangsu Joint International Research Laboratory of Chinese Medicine and Regenerative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Aiyun Wang
- Jiangsu Joint International Research Laboratory of Chinese Medicine and Regenerative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Sanbing Shen
- Regenerative Medicine Institute, School of Medicine, University of Galway, H91 W2TY Galway, Ireland
| | - Yang Zhao
- Jiangsu Joint International Research Laboratory of Chinese Medicine and Regenerative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Department of Biochemistry and Molecular Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yin Lu
- Jiangsu Joint International Research Laboratory of Chinese Medicine and Regenerative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
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Tejedor JR, Peñarroya A, Gancedo-Verdejo J, Santamarina-Ojeda P, Pérez RF, López-Tamargo S, Díez-Borge A, Alba-Linares JJ, González-Del-Rey N, Urdinguio RG, Mangas C, Roberti A, López V, Morales-Ruiz T, Ariza RR, Roldán-Arjona T, Meijón M, Valledor L, Cañal MJ, Fernández-Martínez D, Fernández-Hevia M, Jiménez-Fonseca P, García-Flórez LJ, Fernández AF, Fraga MF. CRISPR/dCAS9-mediated DNA demethylation screen identifies functional epigenetic determinants of colorectal cancer. Clin Epigenetics 2023; 15:133. [PMID: 37612734 PMCID: PMC10464368 DOI: 10.1186/s13148-023-01546-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 08/03/2023] [Indexed: 08/25/2023] Open
Abstract
BACKGROUND Promoter hypermethylation of tumour suppressor genes is frequently observed during the malignant transformation of colorectal cancer (CRC). However, whether this epigenetic mechanism is functional in cancer or is a mere consequence of the carcinogenic process remains to be elucidated. RESULTS In this work, we performed an integrative multi-omic approach to identify gene candidates with strong correlations between DNA methylation and gene expression in human CRC samples and a set of 8 colon cancer cell lines. As a proof of concept, we combined recent CRISPR-Cas9 epigenome editing tools (dCas9-TET1, dCas9-TET-IM) with a customized arrayed gRNA library to modulate the DNA methylation status of 56 promoters previously linked with strong epigenetic repression in CRC, and we monitored the potential functional consequences of this DNA methylation loss by means of a high-content cell proliferation screen. Overall, the epigenetic modulation of most of these DNA methylated regions had a mild impact on the reactivation of gene expression and on the viability of cancer cells. Interestingly, we found that epigenetic reactivation of RSPO2 in the tumour context was associated with a significant impairment in cell proliferation in p53-/- cancer cell lines, and further validation with human samples demonstrated that the epigenetic silencing of RSPO2 is a mid-late event in the adenoma to carcinoma sequence. CONCLUSIONS These results highlight the potential role of DNA methylation as a driver mechanism of CRC and paves the way for the identification of novel therapeutic windows based on the epigenetic reactivation of certain tumour suppressor genes.
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Affiliation(s)
- Juan Ramón Tejedor
- Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC), 33940, El Entrego, Asturias, Spain
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Spanish Biomedical Research Network in Rare Diseases (CIBERER), 28029, Madrid, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
| | - Alfonso Peñarroya
- Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC), 33940, El Entrego, Asturias, Spain
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
| | - Javier Gancedo-Verdejo
- Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC), 33940, El Entrego, Asturias, Spain
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Spanish Biomedical Research Network in Rare Diseases (CIBERER), 28029, Madrid, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
| | - Pablo Santamarina-Ojeda
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Spanish Biomedical Research Network in Rare Diseases (CIBERER), 28029, Madrid, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
| | - Raúl F Pérez
- Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC), 33940, El Entrego, Asturias, Spain
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Spanish Biomedical Research Network in Rare Diseases (CIBERER), 28029, Madrid, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
| | - Sara López-Tamargo
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
| | - Ana Díez-Borge
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Viralgen Vector Core, 20009, San Sebastián, Gipuzkoa, Spain
| | - Juan J Alba-Linares
- Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC), 33940, El Entrego, Asturias, Spain
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
| | - Nerea González-Del-Rey
- Department of Organisms and Systems Biology, Institute of Biotechnology of Asturias, University of Oviedo, 33071, Oviedo, Asturias, Spain
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Rocío G Urdinguio
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Spanish Biomedical Research Network in Rare Diseases (CIBERER), 28029, Madrid, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
| | - Cristina Mangas
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
| | - Annalisa Roberti
- Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC), 33940, El Entrego, Asturias, Spain
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
| | - Virginia López
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
| | - Teresa Morales-Ruiz
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071, Córdoba, Spain
- Department of Genetics, University of Córdoba, 14071, Córdoba, Spain
| | - Rafael R Ariza
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071, Córdoba, Spain
- Department of Genetics, University of Córdoba, 14071, Córdoba, Spain
| | - Teresa Roldán-Arjona
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071, Córdoba, Spain
- Department of Genetics, University of Córdoba, 14071, Córdoba, Spain
| | - Mónica Meijón
- Department of Organisms and Systems Biology, Institute of Biotechnology of Asturias, University of Oviedo, 33071, Oviedo, Asturias, Spain
| | - Luis Valledor
- Department of Organisms and Systems Biology, Institute of Biotechnology of Asturias, University of Oviedo, 33071, Oviedo, Asturias, Spain
| | - María Jesús Cañal
- Department of Organisms and Systems Biology, Institute of Biotechnology of Asturias, University of Oviedo, 33071, Oviedo, Asturias, Spain
| | - Daniel Fernández-Martínez
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
- Division of General Surgery, Department of Colorectal Surgery, Central University Hospital of Asturias (HUCA), 33011, Oviedo, Asturias, Spain
| | - María Fernández-Hevia
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
- Division of General Surgery, Department of Colorectal Surgery, Central University Hospital of Asturias (HUCA), 33011, Oviedo, Asturias, Spain
| | - Paula Jiménez-Fonseca
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Division of Oncology, Department of Medical Oncology, Central University Hospital of Asturias (HUCA), 33011, Oviedo, Asturias, Spain
| | - Luis J García-Flórez
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain
- Division of General Surgery, Department of Colorectal Surgery, Central University Hospital of Asturias (HUCA), 33011, Oviedo, Asturias, Spain
- Department of Surgery and Medical Surgical Specialties, University of Oviedo, 33006, Oviedo, Asturias, Spain
| | - Agustín F Fernández
- Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC), 33940, El Entrego, Asturias, Spain.
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain.
- Spanish Biomedical Research Network in Rare Diseases (CIBERER), 28029, Madrid, Spain.
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain.
| | - Mario F Fraga
- Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC), 33940, El Entrego, Asturias, Spain.
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain.
- Spanish Biomedical Research Network in Rare Diseases (CIBERER), 28029, Madrid, Spain.
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006, Oviedo, Asturias, Spain.
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Devall M, Eaton S, Yoshida C, Powell SM, Casey G, Li L. Assessment of Colorectal Cancer Risk Factors through the Application of Network-Based Approaches in a Racially Diverse Cohort of Colon Organoid Stem Cells. Cancers (Basel) 2023; 15:3550. [PMID: 37509213 PMCID: PMC10377524 DOI: 10.3390/cancers15143550] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/03/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Numerous demographic factors have been associated with colorectal cancer (CRC) risk. To better define biological mechanisms underlying these associations, we performed RNA sequencing of stem-cell-enriched organoids derived from the healthy colons of seven European Americans and eight African Americans. A weighted gene co-expression network analysis was performed following RNA sequencing. Module-trait relationships were determined through the association testing of each module and five CRC risk factors (age, body mass index, sex, smoking history, and race). Only modules that displayed a significantly positive correlation for gene significance and module membership were considered for further investigation. In total, 16 modules were associated with known CRC risk factors (p < 0.05). To contextualize the role of risk modules in CRC, publicly available RNA-sequencing data from TCGA-COAD were downloaded and re-analyzed. Differentially expressed genes identified between tumors and matched normal-adjacent tissue were overlaid across each module. Loci derived from CRC genome-wide association studies were additionally overlaid across modules to identify robust putative targets of risk. Among them, MYBL2 and RXRA represented strong plausible drivers through which cigarette smoking and BMI potentially modulated CRC risk, respectively. In summary, our findings highlight the potential of the colon organoid system in identifying novel CRC risk mechanisms in an ancestrally diverse and cellularly relevant population.
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Affiliation(s)
- Matthew Devall
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Stephen Eaton
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Cynthia Yoshida
- Digestive Health Center, University of Virginia, Charlottesville, VA 22903, USA
| | - Steven M Powell
- Digestive Health Center, University of Virginia, Charlottesville, VA 22903, USA
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
| | - Li Li
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
- University of Virginia Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
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Devall MA, Eaton S, Hu G, Sun X, Jakum E, Venkatesh S, Powell SM, Yoshida C, Weisenberger DJ, Cooper GS, Willis J, Ebrahim S, Zoellner J, Casey G, Li L. Potential role of fructose on human colon DNA methylation in racial disparities observed for colorectal cancer risk. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.31.23290777. [PMID: 37398462 PMCID: PMC10312841 DOI: 10.1101/2023.05.31.23290777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Background and aims An increasing body of observational studies has linked fructose intake to colorectal cancer (CRC). African Americans (AAs) are significantly more likely than European Americans to consume greater quantities of fructose and to develop right-side colon cancer. Yet, a mechanistic link between these two associations remains poorly defined. We aimed to identify differentially methylated regions (DMRs) associated with dietary fructose consumption measures obtained from food frequency questionnaires in a cohort of normal colon biopsies derived from AA men and women (n=79). Methods DNA methylation data from this study was obtained using the Illumina Infinium MethylationEPIC kit and is housed under accession GSE151732. DMR analysis was carried out using DMRcate in right and matched left colon, separately. Secondary analysis of CRC tumors was carried out using data derived from TCGA-COAD, GSE101764 and GSE193535. Differential expression analysis was carried out on CRC tumors from TCGA-COAD using DESeq2 . Results We identified 4,263 right-side fructose-DMRs. In contrast, only 24 DMRs survived multiple testing corrections (FDR<0.05) in matched, left colon. To identify targets by which dietary fructose drives CRC risk, we overlaid these findings with data from three CRC tumor datasets. Remarkably, almost 50% of right-side fructose-DMRs overlapped regions associated with CRC in at least one of three datasets. TNXB and CDX2 ranked among the most significant fructose risk DMRs in right and left colon respectively that also displayed altered gene expression in CRC tumors. Conclusions Our mechanistic data support the notion that fructose has a greater CRC-related effect in right than left AA colon, alluding to a potential role for fructose in contributing to racial disparities in CRC.
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Ditonno I, Novielli D, Celiberto F, Rizzi S, Rendina M, Ierardi E, Di Leo A, Losurdo G. Molecular Pathways of Carcinogenesis in Familial Adenomatous Polyposis. Int J Mol Sci 2023; 24:ijms24065687. [PMID: 36982759 PMCID: PMC10056005 DOI: 10.3390/ijms24065687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/11/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023] Open
Abstract
Familial adenomatous polyposis (FAP) is a genetic syndrome characterized by the presence of multiple polyps in the gastrointestinal tract and a wide range of systemic extra-intestinal manifestations. Patients affected will inevitably undergo abdominal surgery due to the malignant transformation of one or more adenomas. The pathogenesis of the disease is based on a loss of function mutation in adenomatous polyposis coli (APC), a tumor-suppressor gene, inherited following a Mendelian pattern. This gene is a key component of multiple cell functions that cooperate for homeostasis; when mutated, it contributes to the progression of colorectal adenoma into cancer. Recent studies have demonstrated that several additional mechanisms may influence this process, such as alterations in gut microbiota composition and mucosal barrier immunity, interaction with the immune microenvironment and inflammation, the hormone estrogen, and other signaling pathways. These factors represent promising targets of future therapies and chemoprevention, aiming to alter the progressive nature of the disease and improve the quality of life of families affected. Therefore, we performed a narrative review about the current knowledge of the aforementioned pathways involved in colorectal cancer pathogenesis in FAP, exploring the genetic and environmental factors that may contribute to the development of CRC in FAP.
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Affiliation(s)
- Ilaria Ditonno
- Section of Gastroenterology, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari, 70124 Bari, Italy
| | - Domenico Novielli
- Section of Gastroenterology, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari, 70124 Bari, Italy
| | - Francesca Celiberto
- Section of Gastroenterology, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari, 70124 Bari, Italy
- Course in Organs and Tissues Transplantation and Cellular Therapies, Department of Precision Medicine Jonic Area, University “Aldo Moro” of Bari, 70124 Bari, Italy
| | - Salvatore Rizzi
- Section of Gastroenterology, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari, 70124 Bari, Italy
| | - Maria Rendina
- Section of Gastroenterology, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari, 70124 Bari, Italy
| | - Enzo Ierardi
- Section of Gastroenterology, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari, 70124 Bari, Italy
| | - Alfredo Di Leo
- Section of Gastroenterology, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari, 70124 Bari, Italy
| | - Giuseppe Losurdo
- Section of Gastroenterology, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari, 70124 Bari, Italy
- Correspondence:
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Zhu Y, Pan B, Fei X, Hu Y, Yang M, Yu H, Li J, Xiong X. The Biological Characteristics and Differential Expression Patterns of TSSK1B Gene in Yak and Its Infertile Hybrid Offspring. Animals (Basel) 2023; 13:ani13020320. [PMID: 36670860 PMCID: PMC9854725 DOI: 10.3390/ani13020320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/05/2023] [Accepted: 01/14/2023] [Indexed: 01/18/2023] Open
Abstract
This study aimed to investigate the spatially and temporally expressed patterns and biological characteristics of TSSK1B in male yaks and explore the potential correlation between TSSK1B and male sterility of the yak hybrid offspring (termed cattle-yak). First, the coding sequence (CDS) of TSSK1B was cloned by RT-PCR, and bioinformatics analysis was conducted with relevant software. Quantitative real-time PCR (RT-qPCR) was employed to detect the expression profile of TSSK1B in various tissues of male adult yaks, the spatiotemporal expression of TSSK1B in different stages of yak testes, and the differential expression of TSSK1B between yak and cattle-yak testes. The cellular localization of TSSK1B was determined by immunohistochemistry (IHC). Furthermore, the methylation status of the TSSK1B promoter region was analyzed by bisulfite-sequencing PCR (BSP). The results showed that TSSK1B was 1235 bp long, including 1104 bp of the CDS region, which encoded 367 amino acids. It was a conserved gene sharing the highest homology with Bos mutus (99.67%). In addition, the bioinformatics analysis revealed that TSSK1B was an unstable hydrophilic protein mainly containing the alpha helix of 34.06% and a random coil of 44.41%, with a transmembrane structure of 29 amino acids long. The RT-qPCR results demonstrated that TSSK1B was specifically expressed in yak testes compared with that in other tissues and especially highly expressed in adult yak testes. On the contrary, TSSK1B was hardly expressed in the testis of adult cattle-yak. IHC confirmed that TSSK1B protein was more strongly expressed in the testes of adult yaks than in their fetal and juvenile counterparts. Interestingly, nearly no expression was observed in the testes of cattle-yak compared with the corresponding testes of yak. Bisulfite-sequencing PCR (BSP) revealed that the methylated CpG sites in the TSSK1B promoter region of cattle-yak was significantly higher than that in the yak. Taken together, this study revealed that TSSK1B was specifically expressed in yak testes and highly expressed upon sexual maturity. Moreover, the rare expression in cattle-yak may be related to the hypermethylation of the promoter region, thereby providing a basis for further studies on the regulatory mechanism of TSSK1B in male cattle-yak sterility.
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Affiliation(s)
- Yanjin Zhu
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu 610041, China
- Key Laboratory of Animal Science of National Ethnic Affairs Commission, Southwest Minzu University, Chengdu 610041, China
| | - Bangting Pan
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu 610041, China
| | - Xixi Fei
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu 610041, China
| | - Yulei Hu
- Key Laboratory of Animal Science of National Ethnic Affairs Commission, Southwest Minzu University, Chengdu 610041, China
| | - Manzhen Yang
- Key Laboratory of Animal Science of National Ethnic Affairs Commission, Southwest Minzu University, Chengdu 610041, China
| | - Hailing Yu
- Key Laboratory of Animal Science of National Ethnic Affairs Commission, Southwest Minzu University, Chengdu 610041, China
| | - Jian Li
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu 610041, China
- Key Laboratory of Animal Science of National Ethnic Affairs Commission, Southwest Minzu University, Chengdu 610041, China
| | - Xianrong Xiong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu 610041, China
- Key Laboratory of Animal Science of National Ethnic Affairs Commission, Southwest Minzu University, Chengdu 610041, China
- Correspondence:
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He R, Zhang H, Zhao H, Yin X, Lu J, Gu C, Gao J, Xu Q. Multiomics Analysis Reveals Cuproptosis-Related Signature for Evaluating Prognosis and Immunotherapy Efficacy in Colorectal Cancer. Cancers (Basel) 2023; 15:cancers15020387. [PMID: 36672336 PMCID: PMC9856392 DOI: 10.3390/cancers15020387] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/30/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Cuproptosis is a copper-induced form of mitochondrial cell death which is engaged in the proliferation and migration of a variety of tumors. Nevertheless, the role of cuproptosis in tumor microenvironment (TME) remodeling and antitumor therapy is still poorly understood. We characterized two diverse cuproptosis-associated molecular isoforms in CRC which exhibit distinct prognostic and TME characteristics. Subsequently, we constructed a cuproptosis-associated prognostic model containing five genes and divided the patients into a high CPS-score group and a low CPS-score group. Univariate and multivariate Cox analyses showed that the CPS score could be used as an independent prognostic factor. The nomogram, and its consequent calibration curves, indicated that this prognostic signature had good predictive power for CRC. The analysis of single-cell sequencing data showed the significant expression of HES4 and SPHK1 in various immune and stromal (including fibroblasts) cells. Further studies showed that tumor mutational burden (TMB), high microsatellite instability (MSI-H) ratio, immune checkpoint blockade (ICB), and human leukocyte antigen (HLA) gene expression all positively correlated with the CPS score, predicting a better reaction to immunotherapy in high CPS-core patients. The CPS score constructed from cuproptosis subtypes can be used as a predictive tool to evaluate the prognosis of CRC patients and their response to immunotherapy.
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Affiliation(s)
| | | | | | | | | | | | | | - Qing Xu
- Correspondence: ; Tel.: +86-13661778856
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Devall MA, Sun X, Eaton S, Cooper GS, Willis JE, Weisenberger DJ, Casey G, Li L. A Race-Specific, DNA Methylation Analysis of Aging in Normal Rectum: Implications for the Biology of Aging and Its Relationship to Rectal Cancer. Cancers (Basel) 2022; 15:cancers15010045. [PMID: 36612042 PMCID: PMC9817986 DOI: 10.3390/cancers15010045] [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: 10/22/2022] [Revised: 12/01/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Approximately 90% of colorectal cancer (CRC) develop over the age of 50, highlighting the important role of aging in CRC risk. African Americans (AAs) shoulder a greater CRC burden than European Americans (EA) and are more likely to develop CRC at a younger age. The effects of aging in AA and EA normal rectal tissue have yet to be defined. Here, we performed epigenome-wide DNA methylation analysis in the first, large-scale biracial cohort of normal rectum (n = 140 samples). We identified increased epigenetic age acceleration in EA than AA rectum (p = 3.91 × 10-4) using linear regression. We also identified differentially methylated regions (DMRs) associated with chronological aging in AA and EA, separately using DMRcate. Next, a consensus set of regions associated with cancer was identified through DMR analysis of two rectal cancer cohorts. The vast majority of AA DMRs were present in our analysis of aging in rectum of EA subjects, though rates of epigenetic drift were significantly greater in AA (p = 1.94 × 10-45). However, 3.66-fold more DMRs were associated with aging in rectum of EA subjects, many of which were also associated with rectal cancer. Our findings reveal a novel relationship between race, age, DNA methylation and rectal cancer risk that warrants further investigation.
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Affiliation(s)
- Matthew A. Devall
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Xiangqing Sun
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Stephen Eaton
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Gregory S. Cooper
- Department of Medicine, University Hospitals Cleveland Medical Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Joseph E. Willis
- Department of Pathology, Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Daniel J. Weisenberger
- Department of Biochemistry and Molecular Medicine, University of Southern California, Los Angeles, CA 90007, USA
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
- University of Virginia Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
| | - Li Li
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
- University of Virginia Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
- Correspondence: ; Tel.: +1-434-982-3975
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Devall MA, Eaton S, Ali MW, Powell SM, Li L, Casey G. Insights into Early Onset Colorectal Cancer through Analysis of Normal Colon Organoids of Familial Adenomatous Polyposis Patients. Cancers (Basel) 2022; 14:4138. [PMID: 36077675 PMCID: PMC9454756 DOI: 10.3390/cancers14174138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/22/2022] [Accepted: 08/25/2022] [Indexed: 01/07/2023] Open
Abstract
Early onset colorectal cancer (EOCRC) rates have increased in recent decades. While lowering the recommended age for routine colonoscopies to 45 may reduce this burden, such measures do not address those who develop CRC before that age. Additional measures are needed to identify individuals at-risk for CRC. To better define transcriptomic events that precede the development of CRC, we performed RNA-sequencing analysis in colon organoids derived from seven healthy and six familial adenomatous polyposis (FAP) patients. This led to the identification of 2635 significant differentially expressed genes (FDR < 0.05). Through secondary analysis of publicly available datasets, we found that these genes were enriched for significant genes also present in FAP CRC and non-hereditary CRC datasets, including a subset that were unique to EOCRC. By exposing FAP colon organoids to a three-day ethanol treatment, we found that two EOCRC-relevant genes were also targets of CRC related lifestyle factors. Our data provides unique insight into the potential, early mechanisms of CRC development in colon epithelial cells, which may provide biomarkers for patient monitoring. We also show how modifiable lifestyle factors may further alter genes relevant to EOCRC, adding weight to the hypothesis that such factors represent an important contributor to increased EOCRC incidence.
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Affiliation(s)
- Matthew A. Devall
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Stephen Eaton
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Mourad W. Ali
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Steven M. Powell
- Digestive Health Center, University of Virginia, Charlottesville, VA 22903, USA
| | - Li Li
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
- Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22911, USA
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
- Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22911, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
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