1
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Aparicio B, Theunissen P, Hervas-Stubbs S, Fortes P, Sarobe P. Relevance of mutation-derived neoantigens and non-classical antigens for anticancer therapies. Hum Vaccin Immunother 2024; 20:2303799. [PMID: 38346926 PMCID: PMC10863374 DOI: 10.1080/21645515.2024.2303799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 01/06/2024] [Indexed: 02/15/2024] Open
Abstract
Efficacy of cancer immunotherapies relies on correct recognition of tumor antigens by lymphocytes, eliciting thus functional responses capable of eliminating tumor cells. Therefore, important efforts have been carried out in antigen identification, with the aim of understanding mechanisms of response to immunotherapy and to design safer and more efficient strategies. In addition to classical tumor-associated antigens identified during the last decades, implementation of next-generation sequencing methodologies is enabling the identification of neoantigens (neoAgs) arising from mutations, leading to the development of new neoAg-directed therapies. Moreover, there are numerous non-classical tumor antigens originated from other sources and identified by new methodologies. Here, we review the relevance of neoAgs in different immunotherapies and the results obtained by applying neoAg-based strategies. In addition, the different types of non-classical tumor antigens and the best approaches for their identification are described. This will help to increase the spectrum of targetable molecules useful in cancer immunotherapies.
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Affiliation(s)
- Belen Aparicio
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
| | - Patrick Theunissen
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
- DNA and RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Sandra Hervas-Stubbs
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
| | - Puri Fortes
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
- DNA and RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
- Spanish Network for Advanced Therapies (TERAV ISCIII), Spain
| | - Pablo Sarobe
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
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2
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Krushkal J, Zhao Y, Roney K, Zhu W, Brooks A, Wilsker D, Parchment RE, McShane LM, Doroshow JH. Association of changes in expression of HDAC and SIRT genes after drug treatment with cancer cell line sensitivity to kinase inhibitors. Epigenetics 2024; 19:2309824. [PMID: 38369747 PMCID: PMC10878021 DOI: 10.1080/15592294.2024.2309824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/14/2024] [Indexed: 02/20/2024] Open
Abstract
Histone deacetylases (HDACs) and sirtuins (SIRTs) are important epigenetic regulators of cancer pathways. There is a limited understanding of how transcriptional regulation of their genes is affected by chemotherapeutic agents, and how such transcriptional changes affect tumour sensitivity to drug treatment. We investigated the concerted transcriptional response of HDAC and SIRT genes to 15 approved antitumor agents in the NCI-60 cancer cell line panel. Antitumor agents with diverse mechanisms of action induced upregulation or downregulation of multiple HDAC and SIRT genes. HDAC5 was upregulated by dasatinib and erlotinib in the majority of the cell lines. Tumour cell line sensitivity to kinase inhibitors was associated with upregulation of HDAC5, HDAC1, and several SIRT genes. We confirmed changes in HDAC and SIRT expression in independent datasets. We also experimentally validated the upregulation of HDAC5 mRNA and protein expression by dasatinib in the highly sensitive IGROV1 cell line. HDAC5 was not upregulated in the UACC-257 cell line resistant to dasatinib. The effects of cancer drug treatment on expression of HDAC and SIRT genes may influence chemosensitivity and may need to be considered during chemotherapy.
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Affiliation(s)
- Julia Krushkal
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA
| | - Yingdong Zhao
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA
| | - Kyle Roney
- Department of Biostatistics and Bioinformatics, George Washington University, Washington, DC, USA
| | - Weimin Zhu
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Alan Brooks
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Deborah Wilsker
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Ralph E. Parchment
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Lisa M. McShane
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA
| | - James H. Doroshow
- Division of Cancer Treatment and Diagnosis and Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
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3
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Lee NK, Chang JW. Manufacturing Cell and Gene Therapies: Challenges in Clinical Translation. Ann Lab Med 2024; 44:314-323. [PMID: 38361427 PMCID: PMC10961620 DOI: 10.3343/alm.2023.0382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/24/2023] [Accepted: 01/29/2024] [Indexed: 02/17/2024] Open
Abstract
The safety and efficacy of both cell and gene therapies have been demonstrated in numerous preclinical and clinical trials. Chimeric antigen receptor T (CAR-T) cell therapy, which leverages the technologies of both cell and gene therapies, has also shown great promise for treating various cancers. Advancements in pertinent fields have also highlighted challenges faced while manufacturing cell and gene therapy products. Potential problems and obstacles must be addressed to ease the clinical translation of individual therapies. Literature reviews of representative cell-based, gene-based, and cell-based gene therapies with regard to their general manufacturing processes, the challenges faced during manufacturing, and QC specifications are limited. We review the general manufacturing processes of cell and gene therapies, including those involving mesenchymal stem cells, viral vectors, and CAR-T cells. The complexities associated with the manufacturing processes and subsequent QC/validation processes may present challenges that could impede the clinical progression of the products. This article addresses these potential challenges. Further, we discuss the use of the manufacturing model and its impact on cell and gene therapy.
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Affiliation(s)
- Na Kyung Lee
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Seoul, Korea
- Cell and Gene Therapy Institute (CGTI), Research Institute for Future Medicine, Samsung Medical Center, Seoul, Korea
| | - Jong Wook Chang
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Seoul, Korea
- Cell and Gene Therapy Institute (CGTI), Research Institute for Future Medicine, Samsung Medical Center, Seoul, Korea
- Cell and Gene Therapy Institute, ENCell Co. Ltd., Seoul, Korea
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4
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Parande D, Suyal S, Bachhawat AK. ChaC1 upregulation reflects poor prognosis in a variety of cancers: analysis of the major missense SNPs of ChaC1 as an aid to refining prognosis. Gene 2024; 913:148386. [PMID: 38499213 DOI: 10.1016/j.gene.2024.148386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/13/2024] [Accepted: 03/15/2024] [Indexed: 03/20/2024]
Abstract
The ChaC1 enzyme that catalyzes cytosolic glutathione degradation is highly upregulated in several cancers. In a systematic review of gene signature panels for cancer prognosis based on oxidative stress and ferroptosis genes, we observed that ChaC1 was found in panels in a wide variety of different cancers, with the upregulation correlating with poor prognosis. Since SNPs can have an impact on functionality and prognosis, ChaC1 SNPs from various databases were also investigated. Six frequently observed missense SNPs were chosen for reconstruction, and their functionality was evaluated. Three out of six SNPs resulted in either a partial or complete loss of ChaC1 function, and these SNPs had the changes R72Q, A156V, and G173S in their proteins. This study highlights the importance of ChaC1 in cancer prognosis across a wide variety of cancers. Additionally, the information on the SNPs of ChaC1 with altered enzymatic activities would improve the prognostic ability of these panels and facilitate treatment regimens.
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Affiliation(s)
- Devraj Parande
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, S.A.S. Nagar, Punjab 140306, India
| | - Shradha Suyal
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, S.A.S. Nagar, Punjab 140306, India
| | - Anand K Bachhawat
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, S.A.S. Nagar, Punjab 140306, India.
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5
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Liu J, Hayden MR, Yang Y. Research progress of RP1L1 gene in disease. Gene 2024; 912:148367. [PMID: 38485037 DOI: 10.1016/j.gene.2024.148367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 03/07/2024] [Accepted: 03/11/2024] [Indexed: 03/22/2024]
Abstract
Retinitis pigmentosa 1-like 1 (RP1L1) is a component of photoreceptor cilia. Pathogenic variants in RP1L1 cause photoreceptor diseases, suggesting that RP1L1 plays an important role in photoreceptor biology, although its exact function is unknown. To date, RP1L1 variants have been associated with occult macular dystrophy (cone degeneration) and retinitis pigmentosa (rod degeneration). Here, we summarize the reported RP1L1-associated photoreceptor pathogenic mutations. The association between RP1L1 and other diseases (mainly several tumors) is also summarized and RP1L1 is included in a wider range of diseases. Finally, it is necessary to further explore the influence mechanism of RP1L1 gene on the health of photoreceptors and how it participates in the occurrence and development of tumors.
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Affiliation(s)
- Jiali Liu
- Department of Endocrinology, Affiliated Hospital of Yunnan University, Kunming, PR China
| | - Melvin R Hayden
- University of Missouri School of Medicine, Departments of Internal Medicine, Columbia, RP, USA
| | - Ying Yang
- Department of Endocrinology, Affiliated Hospital of Yunnan University, Kunming, PR China; University of Missouri School of Medicine, Departments of Internal Medicine, Columbia, RP, USA.
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6
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Zheng P, Raj P, Liang L, Wu L, Paidi SK, Kim JH, Barman I. Label-free plasmonic spectral profiling of serum DNA. Biosens Bioelectron 2024; 254:116199. [PMID: 38492362 DOI: 10.1016/j.bios.2024.116199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/07/2024] [Accepted: 03/07/2024] [Indexed: 03/18/2024]
Abstract
Genetic and epigenetic modifications are linked to the activation of oncogenes and inactivation of tumor suppressor genes. Likewise, the associated molecular alternations can best inform precision medicine for personalized tumor treatment. Therefore, performing characterization of genetic and epigenetic alternations at the molecular level represents a crucial step in early diagnosis and/or therapeutics of cancer. However, the prevailing methods for DNA analysis involve a series of tedious and complicated steps, in which important genetic and epigenetic information could be lost or altered. To provide a potential approach for non-invasive, direct, and efficient DNA analysis, herein, we present a promising strategy for label-free molecular profiling of serum DNA in its pristine form by fusing surface-enhanced Raman spectroscopy with machine learning on a superior plasmonic nanostructured platform. Using DNA methylation and single-point mutation as two case studies, the presented strategy allows a well-balanced sensitive and specific detection of epigenetic and genetic changes at the single-nucleotide level in serum. We envision the presented label-free strategy could serve as a versatile tool for direct molecular profiling in pristine forms of a wide range of biological markers and aid biomedical diagnostics as well as therapeutics.
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Affiliation(s)
- Peng Zheng
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, United States
| | - Piyush Raj
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, United States
| | - Le Liang
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, United States; The Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China; Department of Ophthalmology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Lintong Wu
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, United States
| | - Santosh Kumar Paidi
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, United States
| | - Jeong Hee Kim
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, United States
| | - Ishan Barman
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, United States; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, United States; The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, United States.
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7
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Zeng Q, Jiang T. The role of FHL1 in tumors. Gene 2024; 911:148347. [PMID: 38458365 DOI: 10.1016/j.gene.2024.148347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 02/01/2024] [Accepted: 03/04/2024] [Indexed: 03/10/2024]
Affiliation(s)
- Qun Zeng
- Department of Biochemistry and Molecular Biology, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, China
| | - Tingting Jiang
- Department of Clinical Laboratory, The Affiliated Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, China.
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8
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Yoon SB, Chen L, Robinson IE, Khatib TO, Arthur RA, Claussen H, Zohbi NM, Wu H, Mouw JK, Marcus AI. Subpopulation commensalism promotes Rac1-dependent invasion of single cells via laminin-332. J Cell Biol 2024; 223:e202308080. [PMID: 38551497 PMCID: PMC10982113 DOI: 10.1083/jcb.202308080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 02/02/2024] [Accepted: 03/11/2024] [Indexed: 04/02/2024] Open
Abstract
Phenotypic heterogeneity poses a significant hurdle for cancer treatment but is under-characterized in the context of tumor invasion. Amidst the range of phenotypic heterogeneity across solid tumor types, collectively invading cells and single cells have been extensively characterized as independent modes of invasion, but their intercellular interactions have rarely been explored. Here, we isolated collectively invading cells and single cells from the heterogeneous 4T1 cell line and observed extensive transcriptional and epigenetic diversity across these subpopulations. By integrating these datasets, we identified laminin-332 as a protein complex exclusively secreted by collectively invading cells. Live-cell imaging revealed that laminin-332 derived from collectively invading cells increased the velocity and directionality of single cells. Despite collectively invading and single cells having similar expression of the integrin α6β4 dimer, single cells demonstrated higher Rac1 activation upon laminin-332 binding to integrin α6β4. This mechanism suggests a novel commensal relationship between collectively invading and single cells, wherein collectively invading cells promote the invasive potential of single cells through a laminin-332/Rac1 axis.
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Affiliation(s)
- Sung Bo Yoon
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Luxiao Chen
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA
| | - Isaac E. Robinson
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Tala O. Khatib
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Robert A. Arthur
- Emory Integrated Computational Core, Emory University, Atlanta, GA, USA
| | - Henry Claussen
- Emory Integrated Computational Core, Emory University, Atlanta, GA, USA
| | - Najdat M. Zohbi
- Graduate Medical Education, Piedmont Macon Medical, Macon, GA, USA
| | - Hao Wu
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Janna K. Mouw
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Adam I. Marcus
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
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9
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Li Y, Liu LE, Han H, Yuan X, Ji J, Xue L, Wu Y, Yang R. A signal-switchable photoelectrochemical biosensor for ultrasensitive detection of long non-coding RNA in cancer cells. Talanta 2024; 273:125878. [PMID: 38492286 DOI: 10.1016/j.talanta.2024.125878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 01/12/2024] [Accepted: 03/04/2024] [Indexed: 03/18/2024]
Abstract
Long non-coding RNA (LncRNA) as an emerging tumor biomarker plays a key factor in the early diagnosis of cancer. Herein, an innovative signal-switchable photoelectrochemical (PEC) biosensor based on ZrO2@CuO bimetallic oxides and T7 Exo-assisted signal amplification is reported for the ultrasensitive and selective detection of lncRNA (HOX gene antisense intergenic RNA, HOTAIR) in cancer cells. Firstly, MOFs-derived TiO2 nanodisks as an excellent photoactive material show an anodic background signal. When target lncRNA exists, the abundant auxiliary DNA1 is freed from T7 Exo-assisted cycle signal amplification, and then competitively hybridizes with auxiliary DNA2 on the electrode. Subsequently, bimetallic MOFs-derived ZrO2@CuO octahedra with a high specific surface area and porous structure are introduced into TiO2 nanodisks-modified biosensor, which appears a cathodic photocurrent and achieves a switchable signal. The developed signal-switchable PEC biosensor shows ultrasensitive detection of lncRNA HOTAIR with a detection limit of 0.12 fM, and can eliminate the false interference. Importantly, the established PEC biosensor has good correlation with RT-qPCR analysis (P < 0.05) for the quantification of lncRNA HOTAIR in cancer cells, which has great potential application for biomarker detection in the early diagnosis of cancer.
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Affiliation(s)
- Yuling Li
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Li-E Liu
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Hangchen Han
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Xinxin Yuan
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Jiangying Ji
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Linsheng Xue
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Yongjun Wu
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Ruiying Yang
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China.
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10
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Rebhun RB, York D, De Graaf FMD, Yoon P, Batcher KL, Luker ME, Ryan S, Peyton J, Kent MS, Stern JA, Bannasch DL. A variant in the 5'UTR of ERBB4 is associated with lifespan in Golden Retrievers. GeroScience 2024; 46:2849-2862. [PMID: 37855863 PMCID: PMC11009206 DOI: 10.1007/s11357-023-00968-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 09/29/2023] [Indexed: 10/20/2023] Open
Abstract
Genome-wide association studies (GWAS) in long-lived human populations have led to identification of variants associated with Alzheimer's disease and cardiovascular disease, the latter being the most common cause of mortality in people worldwide. In contrast, naturally occurring cancer represents the leading cause of death in pet dogs, and specific breeds like the Golden Retriever (GR) carry up to a 65% cancer-related death rate. We hypothesized that GWAS of long-lived GRs might lead to the identification of genetic variants capable of modifying longevity within this cancer-predisposed breed. A GWAS was performed comparing GR dogs ≥ 14 years to dogs dying prior to age 12 which revealed a significant association to ERBB4, the only member of the epidermal growth factor receptor family capable of serving as both a tumor suppressor gene and an oncogene. No coding variants were identified, however, distinct haplotypes in the 5'UTR were associated with reduced lifespan in two separate populations of GR dogs. When all GR dogs were analyzed together (n = 304), the presence of haplotype 3 was associated with shorter survival (11.8 years vs. 12.8 years, p = 0.024). GRs homozygous for haplotype 3 had the shortest survival, and GRs homozygous for haplotype 1 had the longest survival (11.6 years vs. 13.5 years, p = 0.0008). Sub-analyses revealed that the difference in lifespan for GRs carrying at least 1 copy of haplotype 3 was specific to female dogs (p = 0.009), whereas survival remained significantly different in both male and female GRs homozygous for haplotype 1 or haplotype 3 (p = 0.026 and p = 0.009, respectively). Taken together, these findings implicate a potential role for ERBB4 in GR longevity and provide evidence that within-breed canine lifespan studies could serve as a mechanism to identify favorable or disease-modifying variants important to the axis of aging and cancer.
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Affiliation(s)
- Robert B Rebhun
- Department of Surgical and Radiological Sciences, University of California, Davis, CA, USA.
| | - Daniel York
- Department of Surgical and Radiological Sciences, University of California, Davis, CA, USA
| | - Flora M D De Graaf
- Department of Population Health and Reproduction, University of California, Davis, CA, USA
| | - Paula Yoon
- Veterinary Medical Teaching Hospital, University of California, Davis, CA, USA
| | - Kevin L Batcher
- Department of Population Health and Reproduction, University of California, Davis, CA, USA
| | - Madison E Luker
- Department of Surgical and Radiological Sciences, University of California, Davis, CA, USA
| | - Stephanie Ryan
- Department of Population Health and Reproduction, University of California, Davis, CA, USA
| | - Jamie Peyton
- Veterinary Medical Teaching Hospital, University of California, Davis, CA, USA
| | - Michael S Kent
- Department of Surgical and Radiological Sciences, University of California, Davis, CA, USA
| | - Joshua A Stern
- Department of Medicine and Epidemiology, University of California, Davis, CA, USA
| | - Danika L Bannasch
- Department of Population Health and Reproduction, University of California, Davis, CA, USA.
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11
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Ma T, Zhang Q, Zhang S, Yue D, Wang F, Ren Y, Zhang H, Wang Y, Wu Y, Liu LE, Yu F. Research progress of human key DNA and RNA methylation-related enzymes assay. Talanta 2024; 273:125872. [PMID: 38471421 DOI: 10.1016/j.talanta.2024.125872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/18/2024] [Accepted: 03/03/2024] [Indexed: 03/14/2024]
Abstract
Gene methylation-related enzymes (GMREs) are disfunction and aberrantly expressed in a variety of cancers, such as lung, gastric, and pancreatic cancers and have important implications for human health. Therefore,it is critical for early diagnosis and therapy of tumor to develop strategies that allow rapid and sensitive quantitative and qualitative detection of GMREs. With the development of modern analytical techniques and the application of various biosensors, there are numerous methods have been developed for analysis of GMREs. Therefore, this paper provides a systematic review of the strategies for level and activity assay of various GMREs including methyltransferases and demethylase. The detection methods mainly involve immunohistochemistry, colorimetry, fluorescence, chemiluminescence, electrochemistry, etc. Then, this review also addresses the coordinated role of various detection probes, novel nanomaterials, and signal amplification methods. The aim is to highlight potential challenges in the present field, to expand the analytical application of GMREs detection strategies, and to meet the urgent need for future disease diagnosis and intervention.
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Affiliation(s)
- Tiantian Ma
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Qiongwen Zhang
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Shuying Zhang
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Dan Yue
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Fanting Wang
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Yujie Ren
- School of Information Management, Zhengzhou University, Zhengzhou 450001, China
| | - Hengmiao Zhang
- School of Information Management, Zhengzhou University, Zhengzhou 450001, China
| | - Yinuo Wang
- Zhengzhou Foreign Language School, Zhengzhou 450001, China
| | - Yongjun Wu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Li-E Liu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Fei Yu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China.
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12
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Li R, Wang D, Yang H, Pu L, Li X, Yang F, Zhu R. Important role and underlying mechanism of non‑SMC condensin I complex subunit G in tumours (Review). Oncol Rep 2024; 51:77. [PMID: 38639175 DOI: 10.3892/or.2024.8736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 03/21/2024] [Indexed: 04/20/2024] Open
Abstract
At present, the incidence of tumours is increasing on a yearly basis, and tumourigenesis is usually associated with chromosomal instability and cell cycle dysregulation. Moreover, abnormalities in the chromosomal structure often lead to DNA damage, further exacerbating gene mutations and chromosomal rearrangements. However, the non‑SMC condensin I complex subunit G (NCAPG) of the structural maintenance of chromosomes family is known to exert a key role in tumour development. It has been shown that high expression of NCAPG is closely associated with tumour development and progression. Overexpression of NCAPG variously affects chromosome condensation and segregation during cell mitosis, influences cell cycle regulation, promotes tumour cell proliferation and invasion, and inhibits apoptosis. In addition, NCAPG has been associated with tumour cell stemness, tumour resistance and recurrence. The aim of the present review was to explore the underlying mechanisms of NCAPG during tumour development, with a view towards providing novel targets and strategies for tumour therapy, and through the elucidation of the mechanisms involved, to lay the foundation for future developments in health.
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Affiliation(s)
- Ruobing Li
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003, P.R. China
| | - Dechun Wang
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003, P.R. China
| | - Hong Yang
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003, P.R. China
| | - Leilei Pu
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003, P.R. China
| | - Xiaohong Li
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003, P.R. China
| | - Fumei Yang
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003, P.R. China
| | - Rong Zhu
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003, P.R. China
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13
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Aceti M, Caiata-Zufferey M, Pedrazzani C, Schweighoffer R, Kim SY, Baroutsou V, Katapodi MC, Kim S. Modes of responsibility in disclosing cancer genetic test results to relatives: An analysis of Swiss and Korean narrative data. Patient Educ Couns 2024; 123:108202. [PMID: 38395023 DOI: 10.1016/j.pec.2024.108202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 01/31/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024]
Abstract
OBJECTIVE We examined how responsibility (the "duty to inform relatives about genetic testing results") is understood and enacted among Swiss and Korean women carrying BRCA1 or BRCA2 pathogenic variants. METHODS In-depth interviews and/or focus groups with 46 Swiss and 22 Korean carriers were conducted, using an identical interview guide. Data were analyzed inductively and translated into English for cross-country comparisons. RESULTS We identified five modes of responsibility in both samples: Persuader, Enabler, Relayer, Delayer, and Decliner. The Enabler and Relayer modes were the most common in both countries. They followed the rational imperative of health and norms of competence and self-determination, respectively. The Relayer mode transmitted information without trying to influence relatives' decisions. The Delayer and Decliner modes withheld information, deeming it the best way to safeguard the family during that specific moment of its trajectory. Responsibility to disclose testing results was influenced by culturally diverging conceptions of the family unit and socio-contextual norms. CONCLUSION Responsibility primarily reflects the imperative of health prevention; findings demonstrate various interpretations, including the sense of family caring achieved through controlled disclosure of genetic information. PRACTICE IMPLICATIONS Findings offer healthcare providers socio-anthropological insights to assist probands navigate the disclosure of genetic information within their families. TRIAL REGISTRATION NUMBER NCT04214210 (registered Nov 2, 2020), KCT 0005643 (registered Nov 23, 2020).
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Affiliation(s)
- Monica Aceti
- Laboratory Sport and Social Sciences, University of Strasbourg, Strasbourg, France; Department of Clinical Research, University of Basel, Basel, Switzerland.
| | - Maria Caiata-Zufferey
- Department of Business Economics, Health and Social Care at the University of Applied Science and Arts of Southern Switzerland, Manno, Switzerland.
| | - Carla Pedrazzani
- Department of Business Economics, Health and Social Care at the University of Applied Science and Arts of Southern Switzerland, Manno, Switzerland.
| | - Reka Schweighoffer
- Department of Clinical Research, University of Basel, Basel, Switzerland.
| | - Soo Yeon Kim
- Korea Armed Forces Nursing Academy, Daejeon, South Korea; College of Nursing, Yonsei University, Seoul, South Korea.
| | - Vasiliki Baroutsou
- Department of Clinical Research, University of Basel, Basel, Switzerland.
| | - Maria C Katapodi
- Department of Clinical Research, University of Basel, Basel, Switzerland.
| | - Sue Kim
- College of Nursing, Mo-Im Kim Nursing Research Institute, Yonsei University, Seoul, South Korea.
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14
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Tedesco G, Santarosa M, Maestro R. Beyond self‑eating: Emerging autophagy‑independent functions for the autophagy molecules in cancer (Review). Int J Oncol 2024; 64:57. [PMID: 38606507 DOI: 10.3892/ijo.2024.5645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/21/2024] [Indexed: 04/13/2024] Open
Abstract
Autophagy is a conserved catabolic process that controls organelle quality, removes misfolded or abnormally aggregated proteins and is part of the defense mechanisms against intracellular pathogens. Autophagy contributes to the suppression of tumor initiation by promoting genome stability, cellular integrity, redox balance and proteostasis. On the other hand, once a tumor is established, autophagy can support cancer cell survival and promote epithelial‑to‑mesenchymal transition. A growing number of molecules involved in autophagy have been identified. In addition to their key canonical activity, several of these molecules, such as ATG5, ATG12 and Beclin‑1, also exert autophagy‑independent functions in a variety of biological processes. The present review aimed to summarize autophagy‑independent functions of molecules of the autophagy machinery and how the activity of these molecules can influence signaling pathways that are deregulated in cancer progression.
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Affiliation(s)
- Giulia Tedesco
- Unit of Oncogenetics and Functional Oncogenomics, CRO Aviano, National Cancer Institute, IRCCS, I‑33081 Aviano, Italy
| | - Manuela Santarosa
- Unit of Oncogenetics and Functional Oncogenomics, CRO Aviano, National Cancer Institute, IRCCS, I‑33081 Aviano, Italy
| | - Roberta Maestro
- Unit of Oncogenetics and Functional Oncogenomics, CRO Aviano, National Cancer Institute, IRCCS, I‑33081 Aviano, Italy
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15
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Hui San S, Ching Ngai S. E-cadherin re-expression: Its potential in combating TRAIL resistance and reversing epithelial-to-mesenchymal transition. Gene 2024; 909:148293. [PMID: 38373660 DOI: 10.1016/j.gene.2024.148293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 02/08/2024] [Accepted: 02/15/2024] [Indexed: 02/21/2024]
Abstract
The major limitation of conventional chemotherapy drugs is their lack of specificity for cancer cells. As a selective apoptosis-inducing agent, tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) has emerged as an attractive alternative. However, most of the cancer cells are found to be either intrinsically resistant to the TRAIL protein or may develop resistance after multiple treatments, and TRAIL resistance can induce epithelial-to-mesenchymal transition (EMT) at a later stage, promoting cancer invasion and migration. Interestingly, E-cadherin loss has been linked to TRAIL resistance and initiation of EMT, making E-cadherin re-expression a potential target to overcome these obstacles. Recent research suggests that re-expressing E-cadherin may reduce TRAIL resistance by enhancing TRAIL-induced apoptosis and preventing EMT by modulating EMT signalling factors. This reversal of EMT, can also aid in improving TRAIL-induced apoptosis. Therefore, this review provides remarkable insights into the mechanisms underlying E-cadherin re-expression, clinical implications, and potentiation, as well as the research gaps of E-cadherin re-expression in the current cancer treatment.
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Affiliation(s)
- Ser Hui San
- School of Biosciences, Faculty of Science and Engineering, University of Nottingham Malaysia, 43500 Semenyih, Selangor, Malaysia
| | - Siew Ching Ngai
- School of Biosciences, Faculty of Science and Engineering, University of Nottingham Malaysia, 43500 Semenyih, Selangor, Malaysia.
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16
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Du R, Li K, Guo K, Chen Z, Han L, Bian H. FSTL1: A double-edged sword in cancer development. Gene 2024; 906:148263. [PMID: 38346455 DOI: 10.1016/j.gene.2024.148263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/25/2024] [Accepted: 02/06/2024] [Indexed: 03/05/2024]
Abstract
Flolistatin-related protein 1 (FSTL1), a secreted glycoprotein that is involved in many physiological functions, has attracted much interest and has been implicated in a wide range of diseases, including heart diseases and inflammatory diseases. In recent years, the involvement of FSTL1 in cancer progression has been implicated and researched. FSTL1 plays a contradictory role in cancer, depending on the cancer type as well as the contents of the tumor microenvironment. As reviewed here, the structure and distribution of FSTL1 are first introduced. Subsequently, the expression and clinical significance of FSTL1 in various types of cancer as a tumor enhancer or inhibitor are addressed. Furthermore, we discuss the functional role of FSTL1 in various processes that involve tumor cell proliferation, metastasis, immune responses, stemness, cell apoptosis, and resistance to chemotherapy. FSTL1 expression is tightly controlled in cancer, and a multitude of cancer-related signaling cascades like TGF-β/BMP/Smad signaling, AKT, NF-κB, and Wnt-β-catenin signaling pathways are modulated by FSTL1. Finally, FSTL1 as a therapeutic target using monoclonal antibodies is stated. Herein, we review recent findings showing the double-edged characteristics and mechanisms of FSTL1 in cancer and elaborate on the current understanding of therapeutic approaches targeting FSTL1.
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Affiliation(s)
- Ruijuan Du
- Zhang Zhongjing School of Chinese Medicine, Nanyang Institute of Technology, Nanyang, 473004, PR China; Henan Key Laboratory of Zhang Zhongjing Formulae and Herbs for Immunoregulation, Nanyang Institute of Technology, No. 80, Changjiang Road, Nanyang 473004, Henan Province, PR China
| | - Kai Li
- Zhang Zhongjing School of Chinese Medicine, Nanyang Institute of Technology, Nanyang, 473004, PR China; Henan Key Laboratory of Zhang Zhongjing Formulae and Herbs for Immunoregulation, Nanyang Institute of Technology, No. 80, Changjiang Road, Nanyang 473004, Henan Province, PR China
| | - Kelei Guo
- Zhang Zhongjing School of Chinese Medicine, Nanyang Institute of Technology, Nanyang, 473004, PR China; Henan Key Laboratory of Zhang Zhongjing Formulae and Herbs for Immunoregulation, Nanyang Institute of Technology, No. 80, Changjiang Road, Nanyang 473004, Henan Province, PR China
| | - Zhiguo Chen
- Zhang Zhongjing School of Chinese Medicine, Nanyang Institute of Technology, Nanyang, 473004, PR China; Henan Key Laboratory of Zhang Zhongjing Formulae and Herbs for Immunoregulation, Nanyang Institute of Technology, No. 80, Changjiang Road, Nanyang 473004, Henan Province, PR China
| | - Li Han
- Zhang Zhongjing School of Chinese Medicine, Nanyang Institute of Technology, Nanyang, 473004, PR China; Henan Key Laboratory of Zhang Zhongjing Formulae and Herbs for Immunoregulation, Nanyang Institute of Technology, No. 80, Changjiang Road, Nanyang 473004, Henan Province, PR China.
| | - Hua Bian
- Zhang Zhongjing School of Chinese Medicine, Nanyang Institute of Technology, Nanyang, 473004, PR China; Henan Key Laboratory of Zhang Zhongjing Formulae and Herbs for Immunoregulation, Nanyang Institute of Technology, No. 80, Changjiang Road, Nanyang 473004, Henan Province, PR China.
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17
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Hu B, Chen S. The role of UBR5 in tumor proliferation and oncotherapy. Gene 2024; 906:148258. [PMID: 38331119 DOI: 10.1016/j.gene.2024.148258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/29/2024] [Accepted: 02/05/2024] [Indexed: 02/10/2024]
Abstract
Ubiquitin (Ub) protein ligase E3 component n-recognin 5 (UBR5), as a crucial Ub ligase, plays a pivotal role in the field of cell biology, attracting significant attention for its functions in regulating protein degradation and signaling pathways. This review delves into the fundamental characteristics and structure of UBR5. UBR5, through ubiquitination, regulates various key proteins, directly or indirectly participating in cell cycle control, thereby exerting a direct impact on the proliferation of tumor cells. Meanwhile, we comprehensively review the expression levels of UBR5 in different types of tumors and its relationship with tumor development, providing key clues for the role of UBR5 in cancer. Furthermore, we summarize the current research status of UBR5 in cancer treatment. Through literature review, we find that UBR5 may play a crucial role in the sensitivity of tumor cells to radiotherapy chemotherapy, and other anti-tumor treatment, providing new insights for optimizing cancer treatment strategies. Finally, we discuss the challenges faced by UBR5 in cancer treatment, and looks forward to the future research directions. With the continuous breakthroughs in technology and in-depth research, we hope to further study the biological functions of UBR5 and lay the foundation for its anti-tumor treatment.
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Affiliation(s)
- Bin Hu
- Department of Geriatrics, Beilun District People's Hospital, Ningbo 315800, China
| | - Shiyuan Chen
- Department of Geriatrics, Beilun District People's Hospital, Ningbo 315800, China.
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18
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Li Q, Yang L, Zhang C, Yuan J, Zhang J, Tao W, Zhou J. METTL16 deficiency attenuates apoptosis through translational control of extrinsic death receptor during nutrient deprivation. Biochem Biophys Res Commun 2024; 708:149802. [PMID: 38520913 DOI: 10.1016/j.bbrc.2024.149802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 03/18/2024] [Indexed: 03/25/2024]
Abstract
METTL16 is a well-characterized m6A methyltransferase that has been reported to contribute to tumorigenesis in various types of cancer. However, the effect of METTL16 on tumor progression under restricted nutrient conditions, which commonly occur in tumor microenvironment, has yet to be elucidated. Herein, our study initially reported the inhibitory effect of METTL16 depletion on apoptosis under amino acid starvation conditions. Mechanistically, we determined that the METTL16 knockdown represses the expression of extrinsic death receptors at both transcription and translation levels. Depletion of METTL16 prevented protein synthesis of GCN2, resulting in diminished ATF4 expression in a GCN2-eIF2α-dependent manner. Reduction of ATF4 further declined the expression of apoptotic receptor protein DR5. Meanwhile, METTL16 deficiency directly hampered protein synthesis of FADD and DR5, thereby impairing apoptosis and promoting cancer cell survival. Taken together, our study provides novel evidence for the involvement of METTL16 in regulating cancer progression, suggesting that METTL16 as a potential therapeutic target for cancer treatment.
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Affiliation(s)
- Qiujie Li
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu, 210009, China
| | - Lu Yang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu, 210009, China
| | - Chenxin Zhang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu, 210009, China
| | - Jingying Yuan
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu, 210009, China
| | - Jun Zhang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu, 210009, China
| | - Wenjun Tao
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu, 210009, China
| | - Jun Zhou
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu, 210009, China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, 210009, China; Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 21009, China.
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19
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Soleimani M, Harooni A, Erfani N, Khan AR, Saba T, Bahaj SA. Classification of cancer types based on microRNA expression using a hybrid radial basis function and particle swarm optimization algorithm. Microsc Res Tech 2024; 87:1052-1062. [PMID: 38230557 DOI: 10.1002/jemt.24492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 11/27/2023] [Accepted: 12/25/2023] [Indexed: 01/18/2024]
Abstract
The diagnosis and treatment of cancer is one of the most challenging aspects of the medical profession, despite advances in disease diagnosis. MicroRNAs are small noncoding RNA molecules involved in regulating gene expression and are associated with several cancer types. Therefore, the analysis of microRNA data has become one of the most important areas of cancer research in recent years. This paper presents an improved method for cancer-type classification based on microRNA expression data using a hybrid radial basis function (RBF) and particle swarm optimization (PSO) algorithm. Two datasets containing microRNA information were used, and preprocessing and normalization operations were performed on the raw data. Feature selection was carried out by using the PSO algorithm, which can identify the most relevant and informative features in the data along with helping to prioritize them. Using a PSO algorithm for feature selection is an effective approach to microRNA analysis. This enhances the accuracy and reliability of cancer-type classifications based on microRNA expression data. In the proposed method, we, respectively, achieved an accuracy of 0.95% and 0.91% on both datasets, with an average of 0.93%, using an improved RBF neural network classifier. These results demonstrate that the proposed method outperforms previous works. RESEARCH HIGHLIGHTS: To enhance the accuracy of cancer-type classifications based on microRNA expression data. We present a minimal feature selection method using particle swarm optimization to reduce computational load & radial basis function to improve accuracy.
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Affiliation(s)
- Masoumeh Soleimani
- Department of Mathematics and Statistical Sciences, Clemson University, Clemson, South Carolina, USA
| | - Aryan Harooni
- Department of Electrical and Computer Engineering, Isfahan University of Technology, Isfahan, Iran
| | - Nasim Erfani
- Department of Computer Engineering, Dolatabad Branch, Islamic Azad University, Isfahan, Iran
| | - Amjad Rehman Khan
- Artificial Intelligence & Data Analytics Lab CCIS Prince Sultan University, Riyadh, Saudi Arabia
| | - Tanzila Saba
- Artificial Intelligence & Data Analytics Lab CCIS Prince Sultan University, Riyadh, Saudi Arabia
| | - Saeed Ali Bahaj
- MIS Department College of Business Administration, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
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20
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Dai A, Zhang X, Wang X, Liu G, Wang Q, Yu F. Transcription factors in chimeric antigen receptor T-cell development. Hum Cell 2024; 37:571-581. [PMID: 38436882 DOI: 10.1007/s13577-024-01040-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/30/2024] [Indexed: 03/05/2024]
Abstract
Chimeric antigen receptor (CAR) T-cell therapy is a new and innovative approach to treating cancers that has shown promising results in the treatment of lymphoma. However, it has been found to be less effective in the treatment of solid tumors. To overcome the limitation, researchers have explored the use of combined CAR-T therapy with other complementary regimens that target specific genes or biomarkers, which would enhance the synergistic therapeutic effects. Transcription factors (TFs) have been identified as potential markers that can regulate gene expression in CAR-T cells to enhance their cytotoxicity and safety. TFs are known to bind DNA specifically and recruit cofactor proteins to regulate the expression of target genes. By targeting TFs, it is possible to improve the anti-tumor response of CAR-T cells by altering their phenotype and transcriptional map, thereby increasing their effector function, such as reducing the exhaustion, enhancing the survival, and cytotoxicity of CAR-T cells. This review summarizes the application of transcription factors in CART therapy to enhance the synergistic therapeutic effect of CAR-T cells in the treatment of solid tumors and improve their anti-tumor responses.
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Affiliation(s)
- Anran Dai
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, China
| | - Xiangzhi Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, China
| | - Xiaoyan Wang
- Department of Gastroenterology, Suqian First People's Hospital, Suqian, 223800, Jiangsu, China
| | - Guodong Liu
- Department of General Surgery, Suqian First People's Hospital, Suqian, 223800, Jiangsu, China
| | - Qiang Wang
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, China
| | - Feng Yu
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, China.
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21
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Yadav D, Yadav A, Bhattacharya S, Dagar A, Kumar V, Rani R. GLUT and HK: Two primary and essential key players in tumor glycolysis. Semin Cancer Biol 2024; 100:17-27. [PMID: 38494080 DOI: 10.1016/j.semcancer.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/02/2024] [Accepted: 03/09/2024] [Indexed: 03/19/2024]
Abstract
Cancer cells reprogram their metabolism to become "glycolysis-dominant," which enables them to meet their energy and macromolecule needs and enhancing their rate of survival. This glycolytic-dominancy is known as the "Warburg effect", a significant factor in the growth and invasion of malignant tumors. Many studies confirmed that members of the GLUT family, specifically HK-II from the HK family play a pivotal role in the Warburg effect, and are closely associated with glucose transportation followed by glucose metabolism in cancer cells. Overexpression of GLUTs and HK-II correlates with aggressive tumor behaviour and tumor microenvironment making them attractive therapeutic targets. Several studies have proven that the regulation of GLUTs and HK-II expression improves the treatment outcome for various tumors. Therefore, small molecule inhibitors targeting GLUT and HK-II show promise in sensitizing cancer cells to treatment, either alone or in combination with existing therapies including chemotherapy, radiotherapy, immunotherapy, and photodynamic therapy. Despite existing therapies, viable methods to target the glycolysis of cancer cells are currently lacking to increase the effectiveness of cancer treatment. This review explores the current understanding of GLUT and HK-II in cancer metabolism, recent inhibitor developments, and strategies for future drug development, offering insights into improving cancer treatment efficacy.
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Affiliation(s)
- Dhiraj Yadav
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University, Noida, Uttar Pradesh 201303, India; Drug Discovery, Jubilant Biosys, Greater Noida, Noida, Uttar Pradesh, India
| | - Anubha Yadav
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University, Noida, Uttar Pradesh 201303, India
| | - Sujata Bhattacharya
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University, Noida, Uttar Pradesh 201303, India
| | - Akansha Dagar
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-Ku, Yokohama 236-0027, Japan
| | - Vinit Kumar
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University, Noida, Uttar Pradesh 201303, India.
| | - Reshma Rani
- Drug Discovery, Jubilant Biosys, Greater Noida, Noida, Uttar Pradesh, India.
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Wang M, Peng M, Yang X, Zhang Y, Wu T, Wang Z, Wang K. Preoperative prediction of microsatellite instability status: development and validation of a pan-cancer PET/CT-based radiomics model. Nucl Med Commun 2024; 45:372-380. [PMID: 38312051 DOI: 10.1097/mnm.0000000000001816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
OBJECTIVE The purpose of this study is to verify the feasibility of preoperative prediction of patients' microsatellite instability status by applying a PET/CT-based radiation model. METHODS This retrospective study ultimately included 142 patients. Three prediction models have been developed. The predictive performance of all models was evaluated by the receiver operating characteristic curve and area under the curve values. The PET/CT radiological histology score (Radscore) was calculated to evaluate the microsatellite instability status, and the corresponding nomogram was established. The correlation between clinical factors and radiological characteristics was analyzed to verify the value of radiological characteristics in predicting microsatellite instability status. RESULTS Twelve features were retained to establish a comprehensive prediction model of radiological and clinical features. M phase of the tumor has been proven to be an independent predictor of microsatellite instability status. The receiver operating characteristic results showed that the area under the curve values of the training set and the validation set of the radiomics model were 0.82 and 0.75, respectively. The sensitivity, specificity, positive predictive value and negative predictive value of the training set were 0.72, 0.78, 0.83 and 0.66, respectively. The sensitivity, specificity, positive predictive value and negative predictive value of the validation set were 1.00, 0.50, 0.76 and 1.00, respectively. The risk of patients with microsatellite instability was calculated by Radscore and nomograph, and the cutoff value was -0.4385. The validity of the results was confirmed by the decision and calibration curves. CONCLUSION Radiological models based on PET/CT can provide clinical and practical noninvasive prediction of microsatellite instability status of several different cancer types, reducing or avoiding unnecessary biopsy to a certain extent.
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Affiliation(s)
- Menglu Wang
- Department of PET-CT, Harbin Medical University Cancer Hospital, Harbin and
| | - Mengye Peng
- Department of PET-CT, Harbin Medical University Cancer Hospital, Harbin and
| | - Xinyue Yang
- Department of PET-CT, Harbin Medical University Cancer Hospital, Harbin and
| | - Ying Zhang
- Department of PET-CT, Harbin Medical University Cancer Hospital, Harbin and
| | - Tingting Wu
- Department of PET-CT, Harbin Medical University Cancer Hospital, Harbin and
| | - Zeyu Wang
- The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Kezheng Wang
- Department of PET-CT, Harbin Medical University Cancer Hospital, Harbin and
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Rickles-Young M, Tinoco G, Tsuji J, Pollock S, Haynam M, Lefebvre H, Glover K, Owen DH, Collier KA, Ha G, Adalsteinsson VA, Cibulskis C, Lennon NJ, Stover DG. Assay Validation of Cell-Free DNA Shallow Whole-Genome Sequencing to Determine Tumor Fraction in Advanced Cancers. J Mol Diagn 2024; 26:413-422. [PMID: 38490303 DOI: 10.1016/j.jmoldx.2024.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 09/21/2023] [Accepted: 01/18/2024] [Indexed: 03/17/2024] Open
Abstract
Blood-based liquid biopsy is increasingly used in clinical care of patients with cancer, and fraction of tumor-derived DNA in circulation (tumor fraction; TFx) has demonstrated clinical validity across multiple cancer types. To determine TFx, shallow whole-genome sequencing of cell-free DNA (cfDNA) can be performed from a single blood sample, using an established computational pipeline (ichorCNA), without prior knowledge of tumor mutations, in a highly cost-effective manner. We describe assay validation of this approach to facilitate broad clinical application, including evaluation of assay sensitivity, precision, repeatability, reproducibility, pre-analytic factors, and DNA quality/quantity. Sensitivity to detect TFx of 3% (lower limit of detection) was 97.2% to 100% at 1× and 0.1× mean sequencing depth, respectively. Precision was demonstrated on distinct sequencing instruments (HiSeqX and NovaSeq) with no observable differences. The assay achieved prespecified 95% agreement of TFx across replicates of the same specimen (repeatability) and duplicate samples in different batches (reproducibility). Comparison of samples collected in EDTA and Streck tubes from single venipuncture in 23 patients demonstrated that EDTA or Streck tubes were comparable if processed within 8 hours. On the basis of a range of DNA inputs (1 to 50 ng), 20 ng cfDNA is the preferred input, with 5 ng minimum acceptable. Overall, this shallow whole-genome sequencing of cfDNA and ichorCNA approach offers sensitive, precise, and reproducible quantitation of TFx, facilitating assay application in clinical cancer care.
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Affiliation(s)
- Micah Rickles-Young
- Genomics Platform, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Gabriel Tinoco
- Division of Medical Oncology, The Ohio State University College of Medicine, Columbus, Ohio; Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Junko Tsuji
- Genomics Platform, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Sam Pollock
- Genomics Platform, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Marcy Haynam
- Ohio State University Comprehensive Cancer Center, Columbus, Ohio; Stefanie Spielman Comprehensive Breast Center, Columbus, Ohio
| | - Heather Lefebvre
- Ohio State University Comprehensive Cancer Center, Columbus, Ohio; Stefanie Spielman Comprehensive Breast Center, Columbus, Ohio
| | - Kristyn Glover
- Ohio State University Comprehensive Cancer Center, Columbus, Ohio; Stefanie Spielman Comprehensive Breast Center, Columbus, Ohio
| | - Dwight H Owen
- Division of Medical Oncology, The Ohio State University College of Medicine, Columbus, Ohio; Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Katharine A Collier
- Division of Medical Oncology, The Ohio State University College of Medicine, Columbus, Ohio; Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Gavin Ha
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Viktor A Adalsteinsson
- Genomics Platform, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Carrie Cibulskis
- Genomics Platform, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Niall J Lennon
- Genomics Platform, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts.
| | - Daniel G Stover
- Division of Medical Oncology, The Ohio State University College of Medicine, Columbus, Ohio; Ohio State University Comprehensive Cancer Center, Columbus, Ohio; Stefanie Spielman Comprehensive Breast Center, Columbus, Ohio.
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24
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Zhang G, Hou S, Li S, Wang Y, Cui W. Role of STAT3 in cancer cell epithelial‑mesenchymal transition (Review). Int J Oncol 2024; 64:48. [PMID: 38488027 PMCID: PMC11000535 DOI: 10.3892/ijo.2024.5636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 02/29/2024] [Indexed: 03/19/2024] Open
Abstract
Since its discovery, the role of the transcription factor, signal transducer and activator of transcription 3 (STAT3), in both normal physiology and the pathology of numerous diseases, including cancer, has been extensively studied. STAT3 is aberrantly activated in different types of cancer, fulfilling a critical role in cancer progression. The biological process, epithelial‑mesenchymal transition (EMT), is indispensable for embryonic morphogenesis. During the development of cancer, EMT is hijacked to confer motility, tumor cell stemness, drug resistance and adaptation to changes in the microenvironment. The aim of the present review was to outline recent advances in knowledge of the role of STAT3 in EMT, which may contribute to the understanding of the function of STAT3 in EMT in various types of cancer. Delineating the underlying mechanisms associated with the STAT3‑EMT signaling axis may generate novel diagnostic and therapeutic options for cancer treatment.
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Affiliation(s)
- Guoan Zhang
- Department of Forensic Genetics, Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Forensic Science Center of Jining Medical University, Jining, Shandong 272067, P.R. China
| | - Sen Hou
- Department of Forensic Genetics, Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Forensic Science Center of Jining Medical University, Jining, Shandong 272067, P.R. China
| | - Shuyue Li
- Department of Forensic Genetics, Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Forensic Science Center of Jining Medical University, Jining, Shandong 272067, P.R. China
| | - Yequan Wang
- Department of Forensic Genetics, Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Forensic Science Center of Jining Medical University, Jining, Shandong 272067, P.R. China
| | - Wen Cui
- Department of Forensic Pathology, Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Forensic Science Center of Jining Medical University, Jining, Shandong 272067, P.R. China
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25
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Gao K, Li X, Luo S, Zhao L. An overview of the regulatory role of annexin A1 in the tumor microenvironment and its prospective clinical application (Review). Int J Oncol 2024; 64:51. [PMID: 38516766 PMCID: PMC10997369 DOI: 10.3892/ijo.2024.5639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/06/2024] [Indexed: 03/23/2024] Open
Abstract
Although annexin A1 (ANXA1), a 37 kDa phospholipid‑binding anti‑inflammatory protein expressed in various tissues and cell types, has been investigated extensively for its regulatory role in cancer biology, studies have mainly focused on its intracellular role. However, cancer cells and stromal cells expressing ANXA1 have the ability to transmit signals within the tumor microenvironment (TME) through autocrine, juxtacrine, or paracrine signaling. This bidirectional crosstalk between cancer cells and their environment is also crucial for cancer progression, contributing to uncontrolled tumor proliferation, invasion, metastasis and resistance to therapy. The present review explored the important role of ANXA1 in regulating the cell‑specific crosstalk between various compartments of the TME and analyzed the guiding significance of the crosstalk effects in promotion or suppressing cancer progression in the development of cancer treatments. The literature shows that ANXA1 is critical for the regulation of the TME, indicating that ANXA1 signaling between cancer cells and the TME is a potential therapeutic target for the development of novel therapeutic approaches for impeding cancer development.
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Affiliation(s)
- Kuan Gao
- Department of Pharmacy, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Xinyang Li
- Department of Pharmacy, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Shuya Luo
- Department of Ion Channel Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Limei Zhao
- Department of Pharmacy, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
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26
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Eum HH, Jeong D, Kim N, Jo A, Na M, Kang H, Hong Y, Kong JS, Jeong GH, Yoo SA, Lee HO. Single-cell RNA sequencing reveals myeloid and T cell co-stimulation mediated by IL-7 anti-cancer immunotherapy. Br J Cancer 2024; 130:1388-1401. [PMID: 38424167 PMCID: PMC11014989 DOI: 10.1038/s41416-024-02617-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 02/03/2024] [Accepted: 02/08/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Immune checkpoint inhibitors unleash inhibitory signals on T cells conferred by tumors and surrounding stromal cells. Despite the clinical efficacy of checkpoint inhibitors, the lack of target expression and persistence of immunosuppressive cells limit the pervasive effectiveness of the therapy. These limitations may be overcome by alternative approaches that co-stimulate T cells and the immune microenvironment. METHODS We analyzed single-cell RNA sequencing data from multiple human cancers and a mouse tumor transplant model to discover the pleiotropic expression of the Interleukin 7 (IL-7) receptor on T cells, macrophages, and dendritic cells. RESULTS Our experiment on the mouse model demonstrated that recombinant IL-7 therapy induces tumor regression, expansion of effector CD8 T cells, and pro-inflammatory activation of macrophages. Moreover, spatial transcriptomic data support immunostimulatory interactions between macrophages and T cells. CONCLUSION These results indicate that IL-7 therapy induces anti-tumor immunity by activating T cells and pro-inflammatory myeloid cells, which may have diverse therapeutic applicability.
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Affiliation(s)
- Hye Hyeon Eum
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Dasom Jeong
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Nayoung Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Areum Jo
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Minsu Na
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Huiram Kang
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Yourae Hong
- Digestive Oncology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Jin-Sun Kong
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, 06591, Republic of Korea
- Center for Integrative Rheumatoid Transcriptomics and Dynamics, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Gi Heon Jeong
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, 06591, Republic of Korea
- Center for Integrative Rheumatoid Transcriptomics and Dynamics, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Seung-Ah Yoo
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, 06591, Republic of Korea
- Center for Integrative Rheumatoid Transcriptomics and Dynamics, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Hae-Ock Lee
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea.
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, 06591, Republic of Korea.
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27
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Hacisuleyman A, Erman B. Synergy and anti-cooperativity in allostery: Molecular dynamics study of WT and oncogenic KRAS-RGL1. Proteins 2024; 92:665-678. [PMID: 38153169 DOI: 10.1002/prot.26657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 11/03/2023] [Accepted: 12/15/2023] [Indexed: 12/29/2023]
Abstract
This study focuses on investigating the effects of an oncogenic mutation (G12V) on the stability and interactions within the KRAS-RGL1 protein complex. The KRAS-RGL1 complex is of particular interest due to its relevance to KRAS-associated cancers and the potential for developing targeted drugs against the KRAS system. The stability of the complex and the allosteric effects of specific residues are examined to understand their roles as modulators of complex stability and function. Using molecular dynamics simulations, we calculate the mutual information, MI, between two neighboring residues at the interface of the KRAS-RGL1 complex, and employ the concept of interaction information, II, to measure the contribution of a third residue to the interaction between interface residue pairs. Negative II indicates synergy, where the presence of the third residue strengthens the interaction, while positive II suggests anti-cooperativity. Our findings reveal that MI serves as a dominant factor in determining the results, with the G12V mutation increasing the MI between interface residues, indicating enhanced correlations due to the formation of a more compact structure in the complex. Interestingly, although II plays a role in understanding three-body interactions and the impact of distant residues, it is not significant enough to outweigh the influence of MI in determining the overall stability of the complex. Nevertheless, II may nonetheless be a relevant factor to consider in future drug design efforts. This study provides valuable insights into the mechanisms of complex stability and function, highlighting the significance of three-body interactions and the impact of distant residues on the binding stability of the complex. Additionally, our findings demonstrate that constraining the fluctuations of a third residue consistently increases the stability of the G12V variant, making it challenging to weaken complex formation of the mutated species through allosteric manipulation. The novel perspective offered by this approach on protein dynamics, function, and allostery has potential implications for understanding and targeting other protein complexes involved in vital cellular processes. The results contribute to our understanding of the effects of oncogenic mutations on protein-protein interactions and provide a foundation for future therapeutic interventions in the context of KRAS-associated cancers and beyond.
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Affiliation(s)
- Aysima Hacisuleyman
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Burak Erman
- Department of Chemical and Biological Engineering Koc University, Istanbul, Turkey
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28
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Wang Z, Zhang Y, Li K. Nuclear miRNAs as transcriptional regulators in processes related to various cancers (Review). Int J Oncol 2024; 64:56. [PMID: 38606502 PMCID: PMC11015916 DOI: 10.3892/ijo.2024.5644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 03/29/2024] [Indexed: 04/13/2024] Open
Abstract
MicroRNAs (miRNAs) are noncoding small nucleic acids that contain ~22 nucleotides and are considered to promote the degradation or inhibit the translation of mRNA by targeting its 3'‑untranslated region. However, growing evidence has revealed that nuclear miRNAs, combined with gene promoters or enhancers, are able to directly mediate gene transcription. These miRNAs exert a critical influence on cancer progression by affecting cell growth, migration and invasion. In this review, the direct regulation of gene expression by nuclear miRNAs at the transcriptional level was discussed and summarized, and their mechanisms of action in cancers were highlighted with reference to the various body systems.
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Affiliation(s)
- Ziqiang Wang
- Department of Nuclear Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, Shandong 250014, P.R. China
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, P.R. China
| | - Yu Zhang
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, P.R. China
| | - Kun Li
- Department of Nuclear Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, Shandong 250014, P.R. China
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29
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Benitez MBM, Navarro YP, Azuara-Liceaga E, Cruz AT, Flores JV, Lopez-Canovas L. Circular RNAs and the regulation of gene expression in diabetic nephropathy (Review). Int J Mol Med 2024; 53:44. [PMID: 38516776 PMCID: PMC10998718 DOI: 10.3892/ijmm.2024.5368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/14/2024] [Indexed: 03/23/2024] Open
Abstract
Circular RNAs (circRNAs) are non‑coding single‑stranded covalently closed RNA molecules that are considered important as regulators of gene expression at the transcriptional and post‑transcriptional levels. These molecules have been implicated in the initiation and progression of multiple human diseases, ranging from cancer to inflammatory and metabolic diseases, including diabetes mellitus and its vascular complications. The present article aimed to review the current knowledge on the biogenesis and functions of circRNAs, as well as their role in cell processes associated with diabetic nephropathy. In addition, novel potential interactions between circRNAs expressed in renal cells exposed to high‑glucose concentrations and the transcription factors c‑Jun and c‑Fos are reported.
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Affiliation(s)
- Maximo Berto Martinez Benitez
- Postgraduate Program in Genomic Sciences, Science and Technology School, Autonomous University of Mexico City, Mexico City, CP 03100, Mexico
| | - Yussel Pérez Navarro
- Postgraduate Program in Genomic Sciences, Science and Technology School, Autonomous University of Mexico City, Mexico City, CP 03100, Mexico
| | - Elisa Azuara-Liceaga
- Postgraduate Program in Genomic Sciences, Science and Technology School, Autonomous University of Mexico City, Mexico City, CP 03100, Mexico
| | - Angeles Tecalco Cruz
- Postgraduate Program in Genomic Sciences, Science and Technology School, Autonomous University of Mexico City, Mexico City, CP 03100, Mexico
| | - Jesús Valdés Flores
- Biochemistry Department, Center for Research and Advanced Studies, National Polytechnic Institute of Mexico, Mexico City, CP 07360, Mexico
| | - Lilia Lopez-Canovas
- Postgraduate Program in Genomic Sciences, Science and Technology School, Autonomous University of Mexico City, Mexico City, CP 03100, Mexico
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30
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Hou YJ, Yang XX, He L, Meng HX. Pathological mechanisms of cold and mechanical stress in modulating cancer progression. Hum Cell 2024; 37:593-606. [PMID: 38538930 DOI: 10.1007/s13577-024-01049-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/22/2024] [Indexed: 04/15/2024]
Abstract
Environmental temperature and cellular mechanical force are the inherent factors that participate in various biological processes and regulate cancer progress, which have been hot topics worldwide. They occupy a dominant part in the cancer tissues through different approaches. However, extensive investigation regarding pathological mechanisms in the carcinogenic field. After research, we found cold stress via two means to manipulate tumors: neuroscience and mechanically sensitive ion channels (MICHs) such as TRP families to regulate the physiological and pathological activities. Excessive cold stimulation mediated neuroscience acting on every cancer stage through the hypothalamus-pituitary-adrenocorticoid (HPA) to reach the target organs. Comparatively speaking, mechanical force via Piezo of MICHs controls cancer development. The progression of cancer depends on the internal activation of proto-oncogenes and the external tumorigenic factors; the above two means eventually lead to genetic disorders at the molecular level. This review summarizes the interaction of bidirectional communication between them and the tumor. It covers the main processes from cytoplasm to nucleus related to metastasis cascade and tumor immune escape.
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Affiliation(s)
- Yun-Jing Hou
- Harbin Medical University, Harbin, China
- Department of Precision Medicine Center, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xin-Xin Yang
- Harbin Medical University, Harbin, China
- Department of Precision Medicine Center, Harbin Medical University Cancer Hospital, Harbin, China
| | - Lin He
- Department of Stomatology, Heilongjiang Provincial Hospital, Harbin, China
| | - Hong-Xue Meng
- Harbin Medical University, Harbin, China.
- Department of Pathology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, China.
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31
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Chon E, Hendricks W, White M, Rodrigues L, Haworth D, Post G. Precision Medicine in Veterinary Science. Vet Clin North Am Small Anim Pract 2024; 54:501-521. [PMID: 38212188 DOI: 10.1016/j.cvsm.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Precision medicine focuses on the clinical management of the individual patient, not on population-based findings. Successes from human precision medicine inform veterinary oncology. Early evidence of success for canines shows how precision medicine can be integrated into practice. Decreasing genomic profiling costs will allow increased utilization and subsequent improvement of knowledge base from which to make better informed decisions. Utility of precision medicine in canine oncology will only increase for improved cancer characterization, enhanced therapy selection, and overall more successful management of canine cancer. As such, practitioners are called to interpret and leverage precision medicine reports for their patients.
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Affiliation(s)
- Esther Chon
- Vidium Animal Health, 7201 East Henkel Way, Suite 210, Scottsdale, AZ 85255, USA
| | - William Hendricks
- Vidium Animal Health, 7201 East Henkel Way, Suite 210, Scottsdale, AZ 85255, USA
| | - Michelle White
- OneHealthCompany, Inc, 530 Lytton Avenue, 2nd Floor, Palo Alto, CA 94301, USA
| | - Lucas Rodrigues
- OneHealthCompany, Inc, 530 Lytton Avenue, 2nd Floor, Palo Alto, CA 94301, USA
| | - David Haworth
- Vidium Animal Health, 7201 East Henkel Way, Suite 210, Scottsdale, AZ 85255, USA
| | - Gerald Post
- OneHealthCompany, Inc, 530 Lytton Avenue, 2nd Floor, Palo Alto, CA 94301, USA.
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32
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Khan AQ, Hasan A, Mir SS, Rashid K, Uddin S, Steinhoff M. Exploiting transcription factors to target EMT and cancer stem cells for tumor modulation and therapy. Semin Cancer Biol 2024; 100:1-16. [PMID: 38503384 DOI: 10.1016/j.semcancer.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/15/2024] [Accepted: 03/15/2024] [Indexed: 03/21/2024]
Abstract
Transcription factors (TFs) are essential in controlling gene regulatory networks that determine cellular fate during embryogenesis and tumor development. TFs are the major players in promoting cancer stemness by regulating the function of cancer stem cells (CSCs). Understanding how TFs interact with their downstream targets for determining cell fate during embryogenesis and tumor development is a critical area of research. CSCs are increasingly recognized for their significance in tumorigenesis and patient prognosis, as they play a significant role in cancer initiation, progression, metastasis, and treatment resistance. However, traditional therapies have limited effectiveness in eliminating this subset of cells, allowing CSCs to persist and potentially form secondary tumors. Recent studies have revealed that cancer cells and tumors with CSC-like features also exhibit genes related to the epithelial-to-mesenchymal transition (EMT). EMT-associated transcription factors (EMT-TFs) like TWIST and Snail/Slug can upregulate EMT-related genes and reprogram cancer cells into a stem-like phenotype. Importantly, the regulation of EMT-TFs, particularly through post-translational modifications (PTMs), plays a significant role in cancer metastasis and the acquisition of stem cell-like features. PTMs, including phosphorylation, ubiquitination, and SUMOylation, can alter the stability, localization, and activity of EMT-TFs, thereby modulating their ability to drive EMT and stemness properties in cancer cells. Although targeting EMT-TFs holds potential in tackling CSCs, current pharmacological approaches to do so directly are unavailable. Therefore, this review aims to explore the role of EMT- and CSC-TFs, their connection and impact in cellular development and cancer, emphasizing the potential of TF networks as targets for therapeutic intervention.
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Affiliation(s)
- Abdul Q Khan
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar.
| | - Adria Hasan
- Molecular Cell Biology Laboratory, Integral Information and Research Centre-4 (IIRC-4), Integral University, Kursi Road, Lucknow 226026, India; Department of Bioengineering, Faculty of Engineering, Integral University, Kursi Road, Lucknow 226026, India
| | - Snober S Mir
- Molecular Cell Biology Laboratory, Integral Information and Research Centre-4 (IIRC-4), Integral University, Kursi Road, Lucknow 226026, India; Department of Biosciences, Faculty of Science, Integral University, Kursi Road, Lucknow 226026, India
| | - Khalid Rashid
- Department of Urology,Feinberg School of Medicine, Northwestern University, 303 E Superior Street, Chicago, IL 60611, USA
| | - Shahab Uddin
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar; Department of Biosciences, Faculty of Science, Integral University, Kursi Road, Lucknow 226026, India; Laboratory Animal Research Center, Qatar University, Doha, Qatar; Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar
| | - Martin Steinhoff
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar; Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar; Department of Dermatology and Venereology, Rumailah Hospital, Hamad Medical Corporation, Doha 3050, Qatar; Department of Medicine, Weill Cornell Medicine Qatar, Qatar Foundation-Education City, Doha 24144, Qatar; Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA; College of Medicine, Qatar University, Doha 2713, Qatar
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33
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Oszwald A, Zisser L, Compérat E, Müllauer L. Panel Comparative Analysis Tool: An Open-Source Comparative Analysis Tool for Next-Generation Sequencing Panel Target Regions. J Mol Diagn 2024; 26:423-429. [PMID: 38508412 DOI: 10.1016/j.jmoldx.2024.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 11/15/2023] [Accepted: 01/29/2024] [Indexed: 03/22/2024] Open
Abstract
Multigene next-generation sequencing (NGS) panels have become a routine diagnostic method in the contemporary practice of personalized medicine. To avoid inadequate test choice or interpretation, a detailed understanding of the precise panel target regions is required. However, the necessary bioinformatic expertise is not always available, and publicly accessible and easily interpretable analyses of target regions are scarce. To address this critical knowledge gap, we present the Panel Comparative Analysis Tool (PanelCAT), an open-source application to analyze, visualize, and compare NGS panel DNA target regions. PanelCAT uses Reference Sequence, ClinVar, and Catalogue of Somatic Mutations in Cancer mutation census databases to quantify the exon and mutation coverage of target regions and provides interactive graphical representations and search functions to inspect the results. We demonstrate the utility of PanelCAT by analyzing two large NGS panels (TruSight Oncology 500 and Human Pan Cancer Panel) to validate the advertised target genes, quantify targeted exons and mutations, and identify differences between panels. PanelCAT will enable institutions and researchers to catalog and visualize NGS panel target regions independent of the manufacturer, promote transparency of panel limitations, and share this information with employees and requisitioners.
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Affiliation(s)
- André Oszwald
- Department of Pathology, Medical University of Vienna, Vienna, Austria.
| | - Lucia Zisser
- Division of Nuclear Medicine, Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, Vienna, Austria
| | - Eva Compérat
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Leonhard Müllauer
- Department of Pathology, Medical University of Vienna, Vienna, Austria
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Sun X, Zhao X, Xu Y, Yan Y, Han L, Wei M, He M. Potential therapeutic strategy for cancer: Multi-dimensional cross-talk between circRNAs and parental genes. Cancer Lett 2024; 588:216794. [PMID: 38453043 DOI: 10.1016/j.canlet.2024.216794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/27/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
In many ways, circular RNAs (circRNAs) have been demonstrated to be crucial in the onset and advancement of cancer throughout the last ten years and have become a new focus of intense research in the field of RNAs. Accumulating studies have demonstrated that circRNAs can regulate parental gene expression via a variety of biological pathways. Furthermore, research into the complex interactions between circRNAs and their parental genes will shed light on their biological roles and open up new avenues for circRNAs' potential clinical translational uses. However, to date, multi-dimensional cross-talk between circRNAs and parental genes have not been systematically elucidated. Particularly intriguing is circRNA's exploration of tumor targeting, and potential therapeutic uses based on the parental gene regulation perspective. Here, we discuss their biogenesis, take a fresh look at the molecular mechanisms through which circRNAs control the expression of their parental genes in cancer. We further highlight We further highlight the latest circRNA clinical translational applications, including prognostic diagnostic markers, cancer vaccines, gDNA, and so on. Demonstrating the potential benefits and future applications of circRNA therapy.
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Affiliation(s)
- Xiaoyu Sun
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China; Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China.
| | - Xinyi Zhao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China; Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China.
| | - Yan Xu
- Department of Urology, The First Hospital of China Medical University, Shenyang, China.
| | - Yuanyuan Yan
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China; Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China.
| | - Li Han
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China; Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China.
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China; Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China; Liaoning Medical Diagnosis and Treatment Center, Liaoning Province, China.
| | - Miao He
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China; Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China.
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Xu P, Gao Y, Jiang S, Cui Y, Xie Y, Kang Z, Chen YX, Sun D, Fang JY. CHEK2 deficiency increase the response to PD-1 inhibitors by affecting the tumor immune microenvironment. Cancer Lett 2024; 588:216595. [PMID: 38097135 DOI: 10.1016/j.canlet.2023.216595] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/13/2023] [Accepted: 12/06/2023] [Indexed: 03/12/2024]
Abstract
Immune checkpoint blockade (ICB) therapy has improved treatment effects in multiple cancers. Gene mutations in the DNA damage repair pathway (DDR) may cause genomic instability and may relate to the efficacy of ICB. Checkpoint kinase 2 (CHEK2) and polymerase epsilon (POLE) are important genes in the DDR. In this study, we aimed to study the impact of CHEK2 deficiency mutations on the response to ICB. We found that tumors with CHEK2 mutations had a significantly higher tumor mutational burden (TMB) compared to those with CHEK2-WT in a pancancer database. We noted that CHEK2 deficiency mutations potentiated the anti-tumor effect of anti-PD-1 therapy in MC38 and B16 tumor-bearing mice with the decrease of tumor volume and tumor weight after anti-PD-1 treatment. Mechanistically, CHEK2 deficiency tumors were with the increased cytotoxic CD8+ T-cell infiltration, especially cytotoxic CD8+ T cells, and modulated the tumor-immune microenvironment with an upregulated immune inflammatory pathway and antigen presentation pathway after anti-PD-1 treatment. Furthermore, murine models with POLE mutations confirmed that CHEK2 deficiency shaped similar mutational and immune landscapes as POLE mutations after anti-PD-1 treatment. Taken together, our results demonstrated that CHEK2 deficiency mutations may increase the response to ICB (eg. anti-PD-1) by influencing the tumor immune microenvironment. This indicated that CHEK2 deficiency mutations were a potentially predictive biomarker and CHEK2 deficiency may potentiate response to immunotherapy.
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Affiliation(s)
- Pingping Xu
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yaqi Gao
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shanshan Jiang
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yun Cui
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuanhong Xie
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ziran Kang
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ying-Xuan Chen
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Danfeng Sun
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jing-Yuan Fang
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Wu P, Li D, Zhang C, Dai B, Tang X, Liu J, Wu Y, Wang X, Shen A, Zhao J, Zi X, Li R, Sun N, He J. A unique circulating microRNA pairs signature serves as a superior tool for early diagnosis of pan-cancer. Cancer Lett 2024; 588:216655. [PMID: 38460724 DOI: 10.1016/j.canlet.2024.216655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 11/18/2023] [Accepted: 01/16/2024] [Indexed: 03/11/2024]
Abstract
Cancer remains a major burden globally and the critical role of early diagnosis is self-evident. Although various miRNA-based signatures have been developed in past decades, clinical utilization is limited due to a lack of precise cutoff value. Here, we innovatively developed a signature based on pairwise expression of miRNAs (miRPs) for pan-cancer diagnosis using machine learning approach. We analyzed miRNA spectrum of 15832 patients, who were divided into training, validation, test, and external test sets, with 13 different cancers from 10 cohorts. Five different machine-learning (ML) algorithms (XGBoost, SVM, RandomForest, LASSO, and Logistic) were adopted for signature construction. The best ML algorithm and the optimal number of miRPs included were identified using area under the curve (AUC) and youden index in validation set. The AUC of the best model was compared to previously published 25 signatures. Overall, Random Forest approach including 31 miRPs (31-miRP) was developed, proving highly efficient in cancer diagnosis across different datasets and cancer types (AUC range: 0.980-1.000). Regarding diagnosis of cancers at early stage, 31-miRP also exhibited high capacities, with AUC ranging from 0.961 to 0.998. Moreover, 31-miRP exhibited advantages in differentiating cancers from normal tissues (AUC range: 0.976-0.998) as well as differentiating cancers from corresponding benign lesions. Encouragingly, comparing to previously published 25 different signatures, 31-miRP also demonstrated clear advantages. In conclusion, 31-miRP acts as a powerful model for cancer diagnosis, characterized by high specificity and sensitivity as well as a clear cutoff value, thereby holding potential as a reliable tool for cancer diagnosis at early stage.
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Affiliation(s)
- Peng Wu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Dongyu Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China; 4+4 Medical Doctor Program, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Chaoqi Zhang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Bing Dai
- School of Software, Tsinghua University, Beijing, 100084, China
| | - Xiaoya Tang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jingjing Liu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yue Wu
- Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xingwu Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Ao Shen
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jiapeng Zhao
- 4+4 Medical Doctor Program, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xiaohui Zi
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Ruirui Li
- Department of Pathology, National Cancer Center/ National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Nan Sun
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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37
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Zhang Z, Yang N, Lu H, Chen Y, Xu L, Wang Z, Lu Q, Zhong K, Zhu Z, Wang G, Li H, Zheng M, Zhang W, Yang H, Peng X, Zhou L, Tong A. Improved antitumor effects elicited by an oncolytic HSV-1 expressing a novel B7H3nb/CD3 BsAb. Cancer Lett 2024; 588:216760. [PMID: 38428724 DOI: 10.1016/j.canlet.2024.216760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 02/06/2024] [Accepted: 02/22/2024] [Indexed: 03/03/2024]
Abstract
Oncolytic viruses have emerged as a promising modality for cancer treatment due to their unique abilities to directly destroy tumor cells and modulate the tumor microenvironment. Bispecific T-cell engagers (BsAbs) have been developed to activate and redirect cytotoxic T lymphocytes, enhancing the antitumor response. To take advantage of the specific infection capacity and carrying ability of exogenous genes, we generated a recombinant herpes simplex virus type 1 (HSV-1), HSV-1dko-B7H3nb/CD3 or HSV-1dko-B7H3nb/mCD3, carrying a B7H3nb/CD3 or B7H3nb/mCD3 BsAb that replicates and expresses BsAb in tumor cells in vitro and in vivo. The new generation of oncolytic viruses has been genetically modified using CRISPR/Cas9 technology and the cre-loxp system to increase the efficiency of HSV genome editing. Additionally, we used two fully immunocompetent models (GL261 and MC38) to assess the antitumor effect of HSV-1dko-B7H3nb/mCD3. Compared with the HSV-1dko control virus, HSV-1dko-B7H3nb/mCD3 induced enhanced anti-tumor immune responses and T-cell infiltration in both GL261 and MC38 models, resulting in improved treatment efficacy in the latter. Furthermore, flow cytometry analysis of the tumor microenvironment confirmed an increase in NK cells and effector CD8+ T cells, and a decrease in immunosuppressive cells, including FOXP3+ regulatory T cells (Tregs), myeloid-derived suppressor cells (MDSCs), and CD206+ macrophages (M2). Overall, our study identified a novel camel B7H3 nanobody and described the genetic modification of the HSV-1 genome using CRISPR/Cas9 technology and the cre-loxp system. Our findings indicate that expressing B7H3nb/CD3 BsAb could improve the antitumor effects of HSV-1 based oncolytic virus.
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Affiliation(s)
- Zongliang Zhang
- State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu Sichuan Province, 610041, China
| | - Nian Yang
- State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu Sichuan Province, 610041, China
| | - Huaqing Lu
- State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu Sichuan Province, 610041, China
| | - Yongdong Chen
- State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu Sichuan Province, 610041, China
| | - Long Xu
- State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu Sichuan Province, 610041, China
| | - Zeng Wang
- State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu Sichuan Province, 610041, China
| | - Qizhong Lu
- State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu Sichuan Province, 610041, China
| | - Kunhong Zhong
- State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu Sichuan Province, 610041, China
| | - Zhixiong Zhu
- State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu Sichuan Province, 610041, China
| | - Guoqing Wang
- Department of Ophthalmology, West China Hospital, Sichuan University, West China Medical School, Chengdu, Sichuan, 610041, China
| | - Hexian Li
- State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu Sichuan Province, 610041, China
| | - Meijun Zheng
- Department of Otolaryngology, Head and Neck Surgery, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Weiwei Zhang
- State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu Sichuan Province, 610041, China
| | - Hui Yang
- Department of Otolaryngology, Head and Neck Surgery, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Xingchen Peng
- State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu Sichuan Province, 610041, China.
| | - Liangxue Zhou
- Department of Neurosurgery, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, 610041, China; Department of Neurosurgery, Fifth People's Hospital of Ningxia Hui Autonomous Region, Shizuishan, Ningxia, 753000, China; Department of Neurosurgery, Mianyang Central Hospital, Mianyang, Sichuan, 621000, China.
| | - Aiping Tong
- State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu Sichuan Province, 610041, China; Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, 610212, China.
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Liu D, He W, Yang LL. Revitalizing antitumor immunity: Leveraging nucleic acid sensors as therapeutic targets. Cancer Lett 2024; 588:216729. [PMID: 38387757 DOI: 10.1016/j.canlet.2024.216729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/30/2024] [Accepted: 02/12/2024] [Indexed: 02/24/2024]
Abstract
Nucleic acid sensors play a critical role in recognizing and responding to pathogenic nucleic acids as danger signals. Upon activation, these sensors initiate downstream signaling cascades that lead to the production and release of pro-inflammatory cytokines, chemokines, and type I interferons. These immune mediators orchestrate diverse effector responses, including the activation of immune cells and the modulation of the tumor microenvironment. However, careful consideration must be given to balancing the activation of nucleic acid sensors to avoid unwanted autoimmune or inflammatory responses. In this review, we provide an overview of nucleic acid sensors and their role in combating cancer through the perception of various aberrant nucleic acids and activation of the immune system. We discuss the connections between different programmed cell death modes and nucleic acid sensors. Finally, we outline the development of nucleic acid sensor agonists, highlighting how their potential as therapeutic targets opens up new avenues for cancer immunotherapy.
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Affiliation(s)
- Danfeng Liu
- Department of Stomatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, PR China
| | - Wei He
- Department of Stomatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, PR China.
| | - Lei-Lei Yang
- Department of Stomatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, PR China.
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Cheng S, Li L, Yu X. PCTA, a pan-cancer cell line transcriptome atlas. Cancer Lett 2024; 588:216808. [PMID: 38462036 PMCID: PMC11019865 DOI: 10.1016/j.canlet.2024.216808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 03/12/2024]
Abstract
A substantial volume of RNA sequencing data have been generated from cancer cell lines. However, it requires specific bioinformatics skills to compare gene expression levels across cell lines. This has hindered non-bioinformaticians from fully utilizing these valuable datasets in their research. To bridge this gap, we established a curated Pan-cancer Cell Line Transcriptome Atlas (PCTA) dataset. This resource aims to provide a user-friendly platform, allowing researchers without extensive bioinformatics expertise to access and leverage the wealth of information within the dataset for their studies. The PCTA dataset encompasses the expression matrix of 24,965 genes, featuring data from 84,385 samples derived from 5677 studies. This comprehensive compilation spans 535 cell lines, representing a spectrum of 114 cancer types originating from 30 diverse tissue types. On UMAP plots, cell lines originating from the same type of tissue tend to cluster together, illustrating the dataset's ability to capture biological relationships. Additionally, an interactive and user-friendly web application (https://pcatools.shinyapps.io/PCTA_app/) was developed for researchers to explore the PCTA dataset. This platform allows users to examine the expression of their genes of interest across a diverse array of samples.
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Affiliation(s)
- Siyuan Cheng
- Department of Biochemistry & Molecular Biology, LSU Health Shreveport, United States; Feist Weiller Cancer Center, LSU Health Shreveport, United States.
| | - Lin Li
- Department of Biochemistry & Molecular Biology, LSU Health Shreveport, United States; Feist Weiller Cancer Center, LSU Health Shreveport, United States
| | - Xiuping Yu
- Department of Biochemistry & Molecular Biology, LSU Health Shreveport, United States; Feist Weiller Cancer Center, LSU Health Shreveport, United States; Department of Urology, LSU Health Shreveport, United States.
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Wu Y, Guo J, Li W, Xiu X, Thirunavukarasu D, Wang Y, Wang K, Chen W, Yu Zhang D, Yang X, Fan C, Song P. Enhanced Detection of Novel Low-Frequency Gene Fusions via High-Yield Ligation and Multiplexed Enrichment Sequencing. Angew Chem Int Ed Engl 2024; 63:e202316484. [PMID: 38494435 DOI: 10.1002/anie.202316484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 03/19/2024]
Abstract
Panel-based methods are commonly employed for the analysis of novel gene fusions in precision diagnostics and new drug development in cancer. However, these methods are constrained by limitations in ligation yield and the enrichment of novel gene fusions with low variant allele frequencies. In this study, we conducted a pioneering investigation into the stability of double-stranded adapter DNA, resulting in improved ligation yield and enhanced conversion efficiency. Additionally, we implemented blocker displacement amplification, achieving a remarkable 7-fold enrichment of novel gene fusions. Leveraging the pre-enrichment achieved with this approach, we successfully applied it to Nanopore sequencing, enabling ultra-fast analysis of novel gene fusions within one hour with high sensitivity. This method offers a robust and remarkably sensitive mean of analyzing novel gene fusions, promising the discovery of pivotal biomarkers that can significantly improve cancer diagnostics and the development of new therapeutic strategies.
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Affiliation(s)
- Yi Wu
- School of Biomedical Engineering, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jinxiao Guo
- Shanghai Sixth People's Hospital Affiliated to, Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
| | - Wenjun Li
- NuProbe USA, Inc., 2575 West Bellfort Avenue, Ste. 200 Houston, TX 77054, USA
| | - Xuehao Xiu
- School of Biomedical Engineering, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | | | - Yudong Wang
- Department of Gynecologic Oncology, The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Kai Wang
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, 322000, China
| | - Weiyu Chen
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, 322000, China
| | - David Yu Zhang
- NuProbe USA, Inc., 2575 West Bellfort Avenue, Ste. 200 Houston, TX 77054, USA
| | - Xiurong Yang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ping Song
- School of Biomedical Engineering, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
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Qian H, Ding CH, Liu F, Chen SJ, Huang CK, Xiao MC, Hong XL, Wang MC, Yan FZ, Ding K, Cui YL, Zheng BN, Ding J, Luo C, Zhang X, Xie WF. SRY-Box transcription factor 9 triggers YAP nuclear entry via direct interaction in tumors. Signal Transduct Target Ther 2024; 9:96. [PMID: 38653754 DOI: 10.1038/s41392-024-01805-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 01/27/2024] [Accepted: 03/13/2024] [Indexed: 04/25/2024] Open
Abstract
The translocation of YAP from the cytoplasm to the nucleus is critical for its activation and plays a key role in tumor progression. However, the precise molecular mechanisms governing the nuclear import of YAP are not fully understood. In this study, we have uncovered a crucial role of SOX9 in the activation of YAP. SOX9 promotes the nuclear translocation of YAP by direct interaction. Importantly, we have identified that the binding between Asp-125 of SOX9 and Arg-124 of YAP is essential for SOX9-YAP interaction and subsequent nuclear entry of YAP. Additionally, we have discovered a novel asymmetrical dimethylation of YAP at Arg-124 (YAP-R124me2a) catalyzed by PRMT1. YAP-R124me2a enhances the interaction between YAP and SOX9 and is associated with poor prognosis in multiple cancers. Furthermore, we disrupted the interaction between SOX9 and YAP using a competitive peptide, S-A1, which mimics an α-helix of SOX9 containing Asp-125. S-A1 significantly inhibits YAP nuclear translocation and effectively suppresses tumor growth. This study provides the first evidence of SOX9 as a pivotal regulator driving YAP nuclear translocation and presents a potential therapeutic strategy for YAP-driven human cancers by targeting SOX9-YAP interaction.
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Affiliation(s)
- Hui Qian
- Department of Gastroenterology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Chen-Hong Ding
- Department of Gastroenterology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Fang Liu
- Department of Gastroenterology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Shi-Jie Chen
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Chen-Kai Huang
- Department of Gastroenterology, First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Meng-Chao Xiao
- Department of Gastroenterology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xia-Lu Hong
- Department of Gastroenterology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Ming-Chen Wang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Fang-Zhi Yan
- Department of Gastroenterology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Kai Ding
- Department of Gastroenterology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Ya-Lu Cui
- Department of Gastroenterology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Bai-Nan Zheng
- Department of Gastroenterology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Jin Ding
- Clinical Cancer Institute, Center for Translational Medicine, Naval Medical University, Shanghai, China
| | - Cheng Luo
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
| | - Xin Zhang
- Department of Gastroenterology, Changzheng Hospital, Naval Medical University, Shanghai, China.
| | - Wei-Fen Xie
- Department of Gastroenterology, Changzheng Hospital, Naval Medical University, Shanghai, China.
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Molecular Pathology Collaboration Group of Tumor Pathology Committee of Chinese Anti-Cancer Association, Molecular Pathology Group of Chinese Society of Pathology. [Chinese expert consensus on the analytical validation of tumor comprehensive genomic profiling next generation sequencing testing (2024 edition)]. Zhonghua Zhong Liu Za Zhi 2024; 46:274-84. [PMID: 38644265 DOI: 10.3760/cma.j.cn112152-20231027-00277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
In hospital laboratories-developed testing is of great significance for the clinical testing products that has not been approved by the National Medical Product Administration and is urgently needed to meet clinical practice needs. With the development of cancer precision medicine in recent years, comprehensive genomic profiling (CGP) has become an important means and method for the detection of drug targets, precise molecular typing, and immunotherapy biomarkers in cancer patients. However, there is still a lack of unified understanding and consensus on clinical testing standards and application specifications for laboratory-developed testing in the hospitals. The Molecular Pathology Collaboration Group of the Cancer Experts Committee of the Chinese Anti-Cancer Association and the Molecular Pathology Group of the Pathology Branch of the Chinese Medical Association initiated the expert consensus on relevant specifications for analytical validation of CGP next-generation sequencing (NGS) testing in Chinese hospitals. Combined with domestic clinical practice, refer to domestic and foreign literatures, from the background of the laboratory-developed testing, analytical validation scenarios, evaluation indicators and variation ranges, sample types and quantities covered by analytical validation, clinical performance and drug efficacy determination, and site personnel for analytical validation, quality control, inter-laboratory quality evaluation and document management, etc. After the discussion by the expert group, 12 expert consensuses were formed to provide reference for the analytical validation and clinical application of tumor CGP NGS testing in Chinese hospitals, so as to promote the laboratory-developed testing applications in Chinese hospitals.
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Guérin C, Tulasne D. Recording and classifying MET receptor mutations in cancers. eLife 2024; 13:e92762. [PMID: 38652103 DOI: 10.7554/elife.92762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 04/04/2024] [Indexed: 04/25/2024] Open
Abstract
Tyrosine kinase inhibitors (TKI) directed against MET have been recently approved to treat advanced non-small cell lung cancer (NSCLC) harbouring activating MET mutations. This success is the consequence of a long characterization of MET mutations in cancers, which we propose to outline in this review. MET, a receptor tyrosine kinase (RTK), displays in a broad panel of cancers many deregulations liable to promote tumour progression. The first MET mutation was discovered in 1997, in hereditary papillary renal cancer (HPRC), providing the first direct link between MET mutations and cancer development. As in other RTKs, these mutations are located in the kinase domain, leading in most cases to ligand-independent MET activation. In 2014, novel MET mutations were identified in several advanced cancers, including lung cancers. These mutations alter splice sites of exon 14, causing in-frame exon 14 skipping and deletion of a regulatory domain. Because these mutations are not located in the kinase domain, they are original and their mode of action has yet to be fully elucidated. Less than five years after the discovery of such mutations, the efficacy of a MET TKI was evidenced in NSCLC patients displaying MET exon 14 skipping. Yet its use led to a resistance mechanism involving acquisition of novel and already characterized MET mutations. Furthermore, novel somatic MET mutations are constantly being discovered. The challenge is no longer to identify them but to characterize them in order to predict their transforming activity and their sensitivity or resistance to MET TKIs, in order to adapt treatment.
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Affiliation(s)
- Célia Guérin
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020 - UMR1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Lille, France
| | - David Tulasne
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020 - UMR1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Lille, France
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Chen H, Yan D, Sun J, Zhou M. Inference of Developmental Hierarchy and Functional States of Exhausted T Cells from Epigenetic Profiles with Deep Learning. J Chem Inf Model 2024; 64:3579-3591. [PMID: 38545680 DOI: 10.1021/acs.jcim.4c00261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Exhausted T cells are a key component of immune cells that play a crucial role in the immune response against cancer and influence the efficacy of immunotherapy. Accurate assessment and measurement of T-cell exhaustion (TEX) are critical for understanding the heterogeneity of TEX in the tumor microenvironment (TME) and tailoring individualized immunotherapeutic strategies. In this study, we introduced DeepEpiTEX, a novel computational framework based on deep neural networks, for inferring the developmental hierarchy and functional states of exhausted T cells in the TME from epigenetic profiles. DeepEpiTEX was trained using various modalities of epigenetic data, including DNA methylation data, microRNA expression data, and long non-coding RNA expression data from 30 bulk solid cancer types in the TCGA pan-cancer cohort, and identified five optimal TEX subsets with significant survival differences across the majority of cancer types. The performance of DeepEpiTEX was further evaluated and validated in external multi-center and multi-type cancer cohorts, consistently demonstrating its generalizability and applicability in different experimental settings. In addition, we discovered the potential relationship between TEX subsets identified by DeepEpiTEX and the response to immune checkpoint blockade therapy, indicating that individuals with immune-favorable TEX subsets may experience the greatest benefits. In conclusion, our study sheds light on the role of epigenetic regulation in TEX and provides a powerful and promising tool for categorizing TEX in different disease settings.
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Affiliation(s)
- Hongyan Chen
- School of Biomedical Engineering, National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Dongxue Yan
- School of Biomedical Engineering, National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Jie Sun
- School of Biomedical Engineering, National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Meng Zhou
- School of Biomedical Engineering, National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
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45
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Teschendorff AE. On epigenetic stochasticity, entropy and cancer risk. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230054. [PMID: 38432318 PMCID: PMC10909509 DOI: 10.1098/rstb.2023.0054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 09/26/2023] [Indexed: 03/05/2024] Open
Abstract
Epigenetic changes are known to accrue in normal cells as a result of ageing and cumulative exposure to cancer risk factors. Increasing evidence points towards age-related epigenetic changes being acquired in a quasi-stochastic manner, and that they may play a causal role in cancer development. Here, I describe the quasi-stochastic nature of DNA methylation (DNAm) changes in ageing cells as well as in normal cells at risk of neoplastic transformation, discussing the implications of this stochasticity for developing cancer risk prediction strategies, and in particular, how it may require a conceptual paradigm shift in how we select cancer risk markers. I also describe the mounting evidence that a significant proportion of DNAm changes in ageing and cancer development are related to cell proliferation, reflecting tissue-turnover and the opportunity this offers for predicting cancer risk via the development of epigenetic mitotic-like clocks. Finally, I describe how age-associated DNAm changes may be causally implicated in cancer development via an irreversible suppression of tissue-specific transcription factors that increases epigenetic and transcriptomic entropy, promoting a more plastic yet aberrant cancer stem-cell state. This article is part of a discussion meeting issue 'Causes and consequences of stochastic processes in development and disease'.
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Affiliation(s)
- Andrew E. Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, People's Republic of China
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46
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Meksiriporn B, Spangler JB. Directed-evolution approach to empower EGFR targeting for immunotherapy. Cell Rep Methods 2024; 4:100762. [PMID: 38631347 DOI: 10.1016/j.crmeth.2024.100762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 04/01/2024] [Accepted: 04/01/2024] [Indexed: 04/19/2024]
Abstract
Advances in directed-evolution technologies are enabling new strategies to isolate binding proteins that recognize disease-associated states of a target protein. In this issue of Cell Reports Methods, Dobersberger et al. devised a yeast display-based selection scheme to discover proteins that engage the cancer-associated activated state of a receptor to enable design of safe and effective immunotherapies.
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Affiliation(s)
- Bunyarit Meksiriporn
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Biology, School of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok 10520, Thailand
| | - Jamie B Spangler
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA; Bloomberg∼Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, MD, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Molecular Microbiology & Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA.
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47
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Pan H, Feng C, Zhou Z, Huang J, Deng J, Zhou Y, Wang Y, Mu X, Wang Q, Wang K, Lu Z. The causal association between artificial sweeteners and the risk of cancer: a Mendelian randomization study. Food Funct 2024; 15:4527-4537. [PMID: 38576413 DOI: 10.1039/d3fo05756a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Artificial sweeteners (ASs) have been widely added to food and beverages because of their properties of low calories and sweet taste. However, whether the consumption of ASs is causally associated with cancer risk is not clear. Here, we utilized the two-sample Mendelian randomization (MR) method to study the potential causal association. Genetic variants like single-nucleotide polymorphisms (SNPs) associated with exposure (AS consumption) were extracted from a genome-wide association study (GWAS) database including 64 949 Europeans and the influence of confounding was removed. The outcome was from 98 GWAS data and included several types of cancers like lung cancer, colorectal cancer, stomach cancer, breast cancer, and so on. The exposure-outcome SNPs were harmonized and then MR analysis was performed. The inverse-variance weighted (IVW) with random effects was used as the main analytical method accompanied by four complementary methods: MR Egger, weighted median, simple mode, and weighted mode. Sensitivity analyses consisted of heterogeneity, pleiotropy, and leave-one-out analysis. Our results demonstrated that ASs added to coffee had a positive association with high-grade and low-grade serous ovarian cancer; ASs added to tea had a positive association with oral cavity and pharyngeal cancers, but a negative association with malignant neoplasm of the bronchus and lungs. No other cancers had a genetic causal association with AS consumption. Our MR study revealed that AS consumption had no genetic causal association with major cancers. Larger MR studies or RCTs are needed to investigate small effects and support this conclusion.
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Affiliation(s)
- Haotian Pan
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Chenchen Feng
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, China
| | - Ziting Zhou
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Jiamin Huang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Jiasi Deng
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yuanyuan Zhou
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yuxuan Wang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Xinru Mu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Qian Wang
- School of International Education, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Ke Wang
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, China
| | - Zhigang Lu
- School of Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
- Key Laboratory of Acupuncture and Medicine Research of Ministry of Education, Nanjing University of Chinese Medicine, Nanjing, 210023, China
- Jiangsu Collaborative Innovation Center ofTraditional Chinese Medicine in Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing 210023, China
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Wang Q, Ma C, Wang N, Mao H. Effects of quercetin on the DNA methylation pattern in tumor therapy: an updated review. Food Funct 2024; 15:3897-3907. [PMID: 38535893 DOI: 10.1039/d3fo03831a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Quercetin is a unique bioactive flavonoid, and is an excellent antioxidant and has anti-tumor effects by regulating different tumor-related processes like proliferation, apoptosis, invasion, and spread. The latest investigations reveal that quercetin may have the capability to influence DNA methylation modification, one of the primary factors in the development of tumors. Despite the fact that quercetin has significant therapeutic properties, its use as an anti-tumor medicine is constrained by its poor solubility, short half-life, and ineffective tumor targeting. Here, we review the structure and properties of quercetin, its capacity for DNA methylation modification in tumors, and the possibility of nanoscale delivery of quercetin for future tumor treatment.
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Affiliation(s)
- Qin Wang
- School of Pharmacy, Southwest Minzu University, Chengdu, Sichuan 610225, China.
- BMI Center for Biomass Materials and Nanointerfaces, College of Biomass Science and Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Chen Ma
- School of Pharmacy, Southwest Minzu University, Chengdu, Sichuan 610225, China.
| | - Nan Wang
- School of Pharmacy, Southwest Minzu University, Chengdu, Sichuan 610225, China.
| | - Huixian Mao
- School of Pharmacy, Southwest Minzu University, Chengdu, Sichuan 610225, China.
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Yu D, Ma H, Li D, Tang H, Li W, Li M. Identification of SLC12A8 as a valuable prognostic biomarker and immunotherapeutic target by comprehensive pan-cancer analysis. Gene 2024; 903:148211. [PMID: 38280496 DOI: 10.1016/j.gene.2024.148211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/13/2023] [Accepted: 01/23/2024] [Indexed: 01/29/2024]
Abstract
Solute carrier family 12 member 8 (SLC12A8) is a nicotinamide mononucleotide transporter. Despite emerging evidence supporting its potential involvement in oncogenesis, a systematic pan-cancer analysis of SLC12A8 has not been performed. Thus, this research aimed to explore the prognostic implications of SLC12A8 and assess its possible immune-related functions across 33 different tumor types. And multiple datasets were retrieved from the databases of TCGA, GTEx, Broad Institute CCLE, TISCH, HPA, and GDSC2. After this data acquisition, bioinformatics analyses were conducted to assess the potential involvement of SLC12A8 in cancer pathogenesis. These analyses focused on examining the relationship between SLC12A8 and prognosis, drug sensitivity, chemotherapy response, immune checkpoints (ICPs), immune cell infiltration, and immunotherapy efficacy across various tumor types. Furthermore, experimental methods such as EdU assay, wound healing assay, and transwell assay were conducted to evaluate the cell proliferative and invasive abilities. Finally, the data analysis demonstrated that SLC12A8 was differentially expressed and predicted unfavorable survival outcomes in the majority of the tumor types in the TCGA dataset. Furthermore, a notable upregulation in the expression of SLC12A8 mRNA and protein was observed in cancer tissues compared to normal tissues. Additionally, the SLC12A8 levels demonstrated a strong association with ICPs, chemokines, immune-activating genes, immune-suppressive genes, chemokine receptors, chemotherapy response, and immunotherapy efficacy. In vitro experiments substantiated that knockdown of SLC12A8 restricted the malignant phenotypes of MDA-MB-231 and BT-549 cells. So SLC12A8 holds promise as a cancer biomarker with the capacity to interact with other ICPs to synergistically regulate the immune microenvironment. Thus, the identification of SLC12A8 contributes to the development of novel therapeutic strategies for enhancing the efficacy of immunotherapy.
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Affiliation(s)
- Dongmin Yu
- Department of Breast Disease Comprehensive Center, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, People's Republic of China.
| | - Hanhongfeng Ma
- General Surgery Ward 1. Bengbu First People's Hospital, Bengbu 233000, People's Republic of China
| | - Deping Li
- Department of Pharmacy, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, People's Republic of China
| | - Huiyang Tang
- Department of Breast Disease Comprehensive Center, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, People's Republic of China
| | - Wei Li
- General Surgery Ward 1. Bengbu First People's Hospital, Bengbu 233000, People's Republic of China
| | - Meifang Li
- Department of Breast Disease Comprehensive Center, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, People's Republic of China.
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50
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Zhao J, Xu L, Wei K, Jiang P, Chang C, Xu L, Shi Y, Zheng Y, Shan Y, Zheng Y, Shen Y, Liu J, Guo S, Wang R, He D. Identification of clinical characteristics biomarkers for rheumatoid arthritis through targeted DNA methylation sequencing. Int Immunopharmacol 2024; 131:111860. [PMID: 38508093 DOI: 10.1016/j.intimp.2024.111860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/24/2024] [Accepted: 03/11/2024] [Indexed: 03/22/2024]
Abstract
OBJECTIVES Rheumatoid arthritis (RA) is a complex disease with a challenging diagnosis, especially in seronegative patients. The aim of this study is to investigate whether the methylation sites associated with the overall immune response in RA can assist in clinical diagnosis, using targeted methylation sequencing technology on peripheral venous blood samples. METHODS The study enrolled 241 RA patients, 30 osteoarthritis patients (OA), and 30 healthy volunteers control (HC). Fifty significant cytosine guanine (CG) sites between undifferentiated arthritis and RA were selected and analyzed using targeted DNA methylation sequencing. Logistic regression models were used to establish diagnostic models for different clinical features of RA, and six machine learning methods (logit model, random forest, support vector machine, adaboost, naive bayes, and learning vector quantization) were used to construct clinical diagnostic models for different subtypes of RA. Least absolute shrinkage and selection operator regression and detrended correspondence analysis were utilized to screen for important CGs. Spearman correlation was used to calculate the correlation coefficient. RESULTS The study identified 16 important CG sites, including tumor necrosis factort receptor associated factor 5 (TRAF5) (chr1:211500151), mothers against decapentaplegic homolog 3 (SMAD3) (chr15:67357339), tumor endothelial marker 1 (CD248) (chr11:66083766), lysosomal trafficking regulator (LYST) (chr1:235998714), PR domain zinc finger protein 16 (PRDM16) (chr1:3307069), A-kinase anchoring protein 10 (AKAP10) (chr17:19850460), G protein subunit gamma 7 (GNG7) (chr19:2546620), yes1 associated transcriptional regulator (YAP1) (chr11:101980632), PRDM16 (chr1:3163969), histone deacetylase complex subunit sin3a (SIN3A) (chr15:75747445), prenylated rab acceptor protein 2 (ARL6IP5) (chr3:69134502), mitogen-activated protein kinase kinase kinase 4 (MAP3K4) (chr6:161412392), wnt family member 7A (WNT7A) (chr3:13895991), inhibin subunit beta B (INHBB) (chr2:121107018), deoxyribonucleic acid replication helicase/nuclease 2 (DNA2) (chr10:70231628) and chromosome 14 open reading frame 180 (C14orf180) (chr14:105055171). Seven CG sites showed abnormal changes between the three groups (P < 0.05), and 16 CG sites were significantly correlated with common clinical indicators (P < 0.05). Diagnostic models constructed using different CG sites had an area under the receiver operating characteristic curve (AUC) range of 0.64-0.78 for high-level clinical indicators of high clinical value, with specificity ranging from 0.42 to 0.77 and sensitivity ranging from 0.57 to 0.88. The AUC range for low-level clinical indicators of high clinical value was 0.63-0.72, with specificity ranging from 0.48 to 0.74 and sensitivity ranging from 0.72 to 0.88. Diagnostic models constructed using different CG sites showed good overall diagnostic accuracy for the four subtypes of RA, with an accuracy range of 0.61-0.96, a balanced accuracy range of 0.46-0.94, and an AUC range of 0.46-0.94. CONCLUSIONS This study identified potential clinical diagnostic biomarkers for RA and provided novel insights into the diagnosis and subtyping of RA. The use of targeted deoxyribonucleic acid (DNA) methylation sequencing and machine learning methods for establishing diagnostic models for different clinical features and subtypes of RA is innovative and can improve the accuracy and efficiency of RA diagnosis.
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Affiliation(s)
- Jianan Zhao
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Lingxia Xu
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Kai Wei
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Ping Jiang
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Cen Chang
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Linshuai Xu
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Yiming Shi
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Yixin Zheng
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Yu Shan
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Yuejuan Zheng
- The Research Center for Traditional Chinese Medicine, Shanghai Institute of Infectious Diseases and Biosecurity, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yi Shen
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Jia Liu
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Shicheng Guo
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Rongsheng Wang
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Dongyi He
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China.
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