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Qi J, Li L, Gao B, Dai K, Shen K, Wu X, Li H, Yu Z, Wang Z, Wang Z. Prognostic prediction and immune checkpoint profiling in glioma patients through neddylation-associated features. Gene 2024; 930:148835. [PMID: 39127414 DOI: 10.1016/j.gene.2024.148835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 07/11/2024] [Accepted: 08/07/2024] [Indexed: 08/12/2024]
Abstract
BACKGROUND Gliomas are the most common primary malignant tumours of the central nervous system, and neddylation may be a potential target for the treatment of gliomas. Our study analysed neddylation's potential role in gliomas of different pathological types and its correlation with immunotherapy. METHODS Genes required for model construction were sourced from existing literature, and their expression data were extracted from the TCGA and CGGA databases. LASSO regression was employed to identify genes associated with the prognosis of glioma patients in TCGA and to establish a clinical prognostic model. Biological changes in glioma cell lines following intervention with hub genes were evaluated using the CCK-8 assay and transwell assay. The genes implicated in the model construction were validated across various cell lines using Western blot. We conducted analyses to examine correlations between model scores and clinical data, tumor microenvironments, and immune checkpoints. Furthermore, we investigated potential differences in molecular functions and mechanisms among different groups. RESULTS We identified 249 genes from the Reactome database and analysed their expression profiles in the TCGA and CGGA databases. After using LASSO-Cox, four genes (BRCA1, BIRC5, FBXL16 and KLHL25, p < 0.05) with significant correlations were identified. We selected FBXL16 for validation in in vitro experiments. Following FBXL16 overexpression, the proliferation, migration, and invasion abilities of glioma cell lines all showed a decrease. Then, we constructed the NEDD Index for gliomas. The nomogram indicated that this model could serve as an independent prognostic marker. Analysis of the tumour microenvironment and immune checkpoints revealed that the NEDD index was also correlated with immune cell infiltration and the expression levels of various immune checkpoints. CONCLUSION The NEDD index can serve as a practical tool for predicting the prognosis of glioma patients, and it is correlated with immune cell infiltration and the expression levels of immune checkpoints.
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Affiliation(s)
- Juxing Qi
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou 215006, China; Institute of Stroke Research, Soochow University, Suzhou, 215006, China
| | - Longyuan Li
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou 215006, China; Institute of Stroke Research, Soochow University, Suzhou, 215006, China
| | - Bixi Gao
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou 215006, China; Institute of Stroke Research, Soochow University, Suzhou, 215006, China
| | - Kun Dai
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou 215006, China; Institute of Stroke Research, Soochow University, Suzhou, 215006, China
| | - Kecheng Shen
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou 215006, China; Institute of Stroke Research, Soochow University, Suzhou, 215006, China
| | - Xin Wu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou 215006, China; Institute of Stroke Research, Soochow University, Suzhou, 215006, China
| | - Haiying Li
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou 215006, China; Institute of Stroke Research, Soochow University, Suzhou, 215006, China
| | - Zhengquan Yu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou 215006, China; Institute of Stroke Research, Soochow University, Suzhou, 215006, China
| | - Zongqi Wang
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou 215006, China; Institute of Stroke Research, Soochow University, Suzhou, 215006, China.
| | - Zhong Wang
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou 215006, China; Institute of Stroke Research, Soochow University, Suzhou, 215006, China.
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2
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Splichal RC, Chen K, Walton SP, Chan C. The Role of Endoplasmic Reticulum Stress on Reducing Recombinant Protein Production in Mammalian Cells. Biochem Eng J 2024; 210:109434. [PMID: 39220803 PMCID: PMC11360842 DOI: 10.1016/j.bej.2024.109434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Therapeutic recombinant protein production relies on industrial scale culture of mammalian cells to produce active proteins in quantities sufficient for clinical use. The combination of stresses from industrial cell culture environment and recombinant protein production can overwhelm the protein synthesis machinery in the endoplasmic reticulum (ER). This leads to a buildup of improperly folded proteins which induces ER stress. Cells respond to ER stress by activating the Unfolded Protein Response (UPR). To restore proteostasis, ER sensor proteins reduce global protein synthesis and increase chaperone protein synthesis, and if that is insufficient the proteins are degraded. If proteostasis is still not restored, apoptosis is initiated. Increasing evidence suggests crosstalk between ER proteostasis and DNA damage repair (DDR) pathways. External factors (e.g., metabolites) from the cellular environment as well as internal factors (e.g., transgene copy number) can impact genome stability. Failure to maintain genome integrity reduces cell viability and in turn protein production. This review focuses on the association between ER stress and processes that affect protein production and secretion. The processes mediated by ER stress, including inhibition of global protein translation, chaperone protein production, degradation of misfolded proteins, DNA repair, and protein secretion, impact recombinant protein production. Recombinant protein production can be reduced by ER stress through increased autophagy and protein degradation, reduced protein secretion, and reduced DDR response.
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Affiliation(s)
- R. Chauncey Splichal
- Department of Chemical Engineering and Materials Science, Michigan State University, MI, USA
| | - Kevin Chen
- Department of Chemical Engineering and Materials Science, Michigan State University, MI, USA
| | - S. Patrick Walton
- Department of Chemical Engineering and Materials Science, Michigan State University, MI, USA
| | - Christina Chan
- Department of Chemical Engineering and Materials Science, Michigan State University, MI, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, MI, USA
- Department of Computer Science and Engineering, Michigan State University, MI, USA
- Institute for Quantitative Health Science and Engineering, Division of Medical Devices, Michigan State University, MI, USA
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Xiang Z, Hou G, Zheng S, Lu M, Li T, Lin Q, Liu H, Wang X, Guan T, Wei Y, Zhang W, Zhang Y, Liu C, Li L, Lei QY, Hu Y. ER-associated degradation ligase HRD1 links ER stress to DNA damage repair by modulating the activity of DNA-PKcs. Proc Natl Acad Sci U S A 2024; 121:e2403038121. [PMID: 39226359 DOI: 10.1073/pnas.2403038121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 07/02/2024] [Indexed: 09/05/2024] Open
Abstract
Proteostasis and genomic integrity are respectively regulated by the endoplasmic reticulum-associated protein degradation (ERAD) and DNA damage repair signaling pathways, with both pathways essential for carcinogenesis and drug resistance. How these signaling pathways coordinate with each other remains unexplored. We found that ER stress specifically induces the DNA-PKcs-regulated nonhomologous end joining (NHEJ) pathway to amend DNA damage and impede cell death. Intriguingly, sustained ER stress rapidly decreased the activity of DNA-PKcs and DNA damage accumulated, facilitating a switch from adaptation to cell death. This DNA-PKcs inactivation was caused by increased KU70/KU80 protein degradation. Unexpectedly, the ERAD ligase HRD1 was found to efficiently destabilize the classic nuclear protein HDAC1 in the cytoplasm, by catalyzing HDAC1's polyubiquitination at lysine 74, at a late stage of ER stress. By abolishing HDAC1-mediated KU70/KU80 deacetylation, HRD1 transmits ER signals to the nucleus. The resulting enhanced KU70/KU80 acetylation provides binding sites for the nuclear E3 ligase TRIM25, resulting in the promotion of polyubiquitination and the degradation of KU70/KU80 proteins. Both in vitro and in vivo cancer models showed that genetic or pharmacological inhibition of HADC1 or DNA-PKcs sensitizes colon cancer cells to ER stress inducers, including the Food and Drug Administration-approved drug celecoxib. The antitumor effects of the combined approach were also observed in patient-derived xenograft models. These findings identify a mechanistic link between ER stress (ERAD) in the cytoplasm and DNA damage (NHEJ) pathways in the nucleus, indicating that combined anticancer strategies may be developed that induce severe ER stress while simultaneously inhibiting KU70/KU80/DNA-PKcs-mediated NHEJ signaling.
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Affiliation(s)
- Zhiyuan Xiang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
- Key Laboratory of Science and Engineering for the Multi-modal Prevention and Control of Major Chronic Diseases, Ministry of Industry and Information Technology, Harbin Institute of Technology Zhengzhou Research Institute, Zhengzhou 450000, China
| | - Guixue Hou
- Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China
| | - Shanliang Zheng
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Minqiao Lu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
- Key Laboratory of Science and Engineering for the Multi-modal Prevention and Control of Major Chronic Diseases, Ministry of Industry and Information Technology, Harbin Institute of Technology Zhengzhou Research Institute, Zhengzhou 450000, China
| | - Tianyu Li
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Qingyu Lin
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
- Key Laboratory of Science and Engineering for the Multi-modal Prevention and Control of Major Chronic Diseases, Ministry of Industry and Information Technology, Harbin Institute of Technology Zhengzhou Research Institute, Zhengzhou 450000, China
| | - Hao Liu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
- Key Laboratory of Science and Engineering for the Multi-modal Prevention and Control of Major Chronic Diseases, Ministry of Industry and Information Technology, Harbin Institute of Technology Zhengzhou Research Institute, Zhengzhou 450000, China
| | - Xingwen Wang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Tianqi Guan
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
- Key Laboratory of Science and Engineering for the Multi-modal Prevention and Control of Major Chronic Diseases, Ministry of Industry and Information Technology, Harbin Institute of Technology Zhengzhou Research Institute, Zhengzhou 450000, China
| | - Yuhan Wei
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Wenxin Zhang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
- Key Laboratory of Science and Engineering for the Multi-modal Prevention and Control of Major Chronic Diseases, Ministry of Industry and Information Technology, Harbin Institute of Technology Zhengzhou Research Institute, Zhengzhou 450000, China
| | - Yi Zhang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
- Key Laboratory of Science and Engineering for the Multi-modal Prevention and Control of Major Chronic Diseases, Ministry of Industry and Information Technology, Harbin Institute of Technology Zhengzhou Research Institute, Zhengzhou 450000, China
| | - Chaoran Liu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
- Key Laboratory of Science and Engineering for the Multi-modal Prevention and Control of Major Chronic Diseases, Ministry of Industry and Information Technology, Harbin Institute of Technology Zhengzhou Research Institute, Zhengzhou 450000, China
| | - Li Li
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin 150040, China
| | - Qun-Ying Lei
- Fudan University Shanghai Cancer Center and Cancer Metabolism Laboratory, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Ying Hu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
- Key Laboratory of Science and Engineering for the Multi-modal Prevention and Control of Major Chronic Diseases, Ministry of Industry and Information Technology, Harbin Institute of Technology Zhengzhou Research Institute, Zhengzhou 450000, China
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Ooki A, Osumi H, Yoshino K, Yamaguchi K. Potent therapeutic strategy in gastric cancer with microsatellite instability-high and/or deficient mismatch repair. Gastric Cancer 2024; 27:907-931. [PMID: 38922524 PMCID: PMC11335850 DOI: 10.1007/s10120-024-01523-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 06/12/2024] [Indexed: 06/27/2024]
Abstract
Gastric cancer (GC) is a common malignancy that presents challenges in patient care worldwide. The mismatch repair (MMR) system is a highly conserved DNA repair mechanism that protects genome integrity during replication. Deficient MMR (dMMR) results in an increased accumulation of genetic errors in microsatellite sequences, leading to the development of a microsatellite instability-high (MSI-H) phenotype. Most MSI-H/dMMR GCs arise sporadically, mainly due to MutL homolog 1 (MLH1) epigenetic silencing. Unlike microsatellite-stable (MSS)/proficient MMR (pMMR) GCs, MSI-H/dMMR GCs are relatively rare and represent a distinct subtype with genomic instability, a high somatic mutational burden, favorable immunogenicity, different responses to treatment, and prognosis. dMMR/MSI-H status is a robust predictive biomarker for treatment with immune checkpoint inhibitors (ICIs) due to high neoantigen load, prominent tumor-infiltrating lymphocytes, and programmed cell death ligand 1 (PD-L1) overexpression. However, a subset of MSI-H/dMMR GC patients does not benefit from immunotherapy, highlighting the need for further research into predictive biomarkers and resistance mechanisms. This review provides a comprehensive overview of the clinical, molecular, immunogenic, and therapeutic aspects of MSI-H/dMMR GC, with a focus on the impact of ICIs in immunotherapy and their potential as neoadjuvant therapies. Understanding the complexity and diversity of the molecular and immunological profiles of MSI-H/dMMR GC will drive the development of more effective therapeutic strategies and molecular targets for future precision medicine.
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Affiliation(s)
- Akira Ooki
- Department of Gastroenterological Chemotherapy, Cancer Institute Hospital of the Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-Ku, Tokyo, 135-8550, Japan.
| | - Hiroki Osumi
- Department of Gastroenterological Chemotherapy, Cancer Institute Hospital of the Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-Ku, Tokyo, 135-8550, Japan
| | - Koichiro Yoshino
- Department of Gastroenterological Chemotherapy, Cancer Institute Hospital of the Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-Ku, Tokyo, 135-8550, Japan
| | - Kensei Yamaguchi
- Department of Gastroenterological Chemotherapy, Cancer Institute Hospital of the Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-Ku, Tokyo, 135-8550, Japan
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Ahmad A, Braden A, Khan S, Xiao J, Khan MM. Crosstalk between the DNA damage response and cellular senescence drives aging and age-related diseases. Semin Immunopathol 2024; 46:10. [PMID: 39095660 DOI: 10.1007/s00281-024-01016-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 05/21/2024] [Indexed: 08/04/2024]
Abstract
Cellular senescence is a crucial process of irreversible cell-cycle arrest, in which cells remain alive, but permanently unable to proliferate in response to distinct types of stressors. Accumulating evidence suggests that DNA damage builds over time and triggers DNA damage response signaling, leading to cellular senescence. Cellular senescence serves as a platform for the perpetuation of inflammatory responses and is central to numerous age-related diseases. Defects in DNA repair genes or senescence can cause premature aging disease. Therapeutic approaches limiting DNA damage or senescence contribute to a rescued phenotype of longevity and neuroprotection, thus suggesting a mechanistic interaction between DNA damage and senescence. Here, we offer a unique perspective on the crosstalk between the DNA damage response pathway and senescence as well as their contribution to age-related diseases. We further summarize recent progress on the mechanisms and therapeutics of senescence, address existing challenges, and offering new insights and future directions in the senescence field.
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Affiliation(s)
- Ajmal Ahmad
- Department of Ophthalmology, College of Medicine, King Saud University Riyadh, Riyadh, Saudi Arabia
| | - Anneliesse Braden
- Department of Neurology, College of Medicine, University of Tennessee Health Science Center, 855 Monroe Avenue, Suite 415 Link Building, Memphis, TN, 38163, USA
- Neuroscience Institute, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Sazzad Khan
- Department of Neurology, College of Medicine, University of Tennessee Health Science Center, 855 Monroe Avenue, Suite 415 Link Building, Memphis, TN, 38163, USA
| | - Jianfeng Xiao
- Department of Neurology, College of Medicine, University of Tennessee Health Science Center, 855 Monroe Avenue, Suite 415 Link Building, Memphis, TN, 38163, USA
| | - Mohammad Moshahid Khan
- Department of Neurology, College of Medicine, University of Tennessee Health Science Center, 855 Monroe Avenue, Suite 415 Link Building, Memphis, TN, 38163, USA.
- Neuroscience Institute, University of Tennessee Health Science Center, Memphis, TN, USA.
- Center for Muscle, Metabolism and Neuropathology, Division of Regenerative and Rehabilitation Sciences, Department of Physical Therapy, College of Health Professions, University of Tennessee Health Science Center, Memphis, TN, USA.
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6
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Choi JW, Lee JO, Lee S. Detecting microsatellite instability by length comparison of microsatellites in the 3' untranslated region with RNA-seq. Brief Bioinform 2024; 25:bbae423. [PMID: 39210504 PMCID: PMC11361843 DOI: 10.1093/bib/bbae423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/30/2024] [Accepted: 08/09/2024] [Indexed: 09/04/2024] Open
Abstract
Microsatellite instability (MSI), a phenomenon caused by deoxyribonucleic acid (DNA) mismatch repair system deficiencies, is an important biomarker in cancer research and clinical diagnostics. MSI detection often involves next-generation sequencing data, with many studies focusing on DNA. Here, we introduce a novel approach by measuring microsatellite lengths directly from ribonucleic acid sequencing (RNA-seq) data and comparing its distribution to detect MSI. Our findings reveal distinct instability patterns between MSI-high (MSI-H) and microsatellite stable samples, indicating the efficacy of RNA-based MSI detection. Additionally, microsatellites in the 3'-untranslated regions showed the greatest predictive value for MSI detection. Notably, this efficacy extends to detecting MSI-H samples even in tumors not commonly associated with MSI. Our approach highlights the utility of RNA-seq data in MSI detection, facilitating more precise diagnostics through the integration of various biological data.
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Affiliation(s)
- Jin-Wook Choi
- Department of Health Science and Technology, Seoul National University, 1 Gwanak-ro, Gwanak-gu, 08826 Seoul, Republic of Korea
| | - Jin-Ok Lee
- Department of Health Science and Technology, Seoul National University, 1 Gwanak-ro, Gwanak-gu, 08826 Seoul, Republic of Korea
| | - Sejoon Lee
- Department of Health Science and Technology, Seoul National University, 1 Gwanak-ro, Gwanak-gu, 08826 Seoul, Republic of Korea
- Department of Pathology and Translational Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, 82 Gumi-ro 173beon-gil, Bundang-gu, 13620 Seongnam, Republic of Korea
- Precision Medicine Center, Seoul National University Bundang Hospital, 82 Gumi-ro, Bundang-gu, 13620 Seongnam, Republic of Korea
- Department of Genomic Medicine, Seoul National University Bundang Hospital, 82 Gumi-ro, Bundang-gu, 13620 Seongnam, Republic of Korea
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Gong X, Wu Q, Tan Z, Lin S, Zhou J, Lin S, Wang W, Han Z, Xie T, Zhou J. Identification and validation of cuproptosis and disulfidptosis related genes in colorectal cancer. Cell Signal 2024; 119:111185. [PMID: 38643947 DOI: 10.1016/j.cellsig.2024.111185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/11/2024] [Accepted: 04/17/2024] [Indexed: 04/23/2024]
Abstract
Colorectal cancer, the third most prevalent malignant cancer, is associated with poor prognosis. Recent studies have investigated the mechanisms underlying cuproptosis and disulfidptosis in colorectal cancer. However, whether genes linked to these processes impact the prognosis of colorectal cancer patients through analogous mechanisms remains unclear. In this study, we developed a model of cuproptosis and disulfidptosis in colorectal cancer and concurrently explored the role of the pivotal model gene HSPA8 in colorectal cancer cell lines. Our results revealed a positive correlation between cuproptosis and disulfidptosis, both of which are emerging as protective factors for the prognosis of CRC patients. Consequently, a prognostic model encompassing HSPA8, PDCL3, CBX3, ATP6V1G1, TAF1D, RPL4, and RPL14 was constructed. Notably, the key gene in our model, HSPA8, exhibited heightened expression and was validated as a protective prognostic factor in colorectal cancer, exerting inhibitory effects on colorectal cancer cell proliferation. This study offers novel insights into the interplay between cuproptosis and disulfidptosis. The application of the prognostic model holds promise for more effectively predicting the overall survival of colorectal cancer patients.
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Affiliation(s)
- Xiaoqing Gong
- Department of Gastroenterology, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China; Guangzhou Medical University, Guangzhou 511495, China
| | - Qixian Wu
- Department of Gastroenterology, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China; Guangzhou Medical University, Guangzhou 511495, China
| | - Zhenlin Tan
- Peking University Shenzhen Hospital, Shenzhen 518000, China
| | - Shumao Lin
- Department of Gastroenterology, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China; Guangzhou Medical University, Guangzhou 511495, China
| | - Jingdong Zhou
- Guangzhou Medical University, Guangzhou 511495, China
| | - Shihao Lin
- Guangzhou Medical University, Guangzhou 511495, China
| | - Weilin Wang
- Guangzhou Medical University, Guangzhou 511495, China
| | - Zhoujian Han
- Department of Gastroenterology, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China; Guangzhou Medical University, Guangzhou 511495, China
| | - Tingting Xie
- Department of Gastroenterology, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China.
| | - Jiyuan Zhou
- Department of Gastroenterology, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China.
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Wen X, Xu H, Woolley PR, Conway OM, Yao J, Matouschek A, Lambowitz AM, Paull TT. Senataxin deficiency disrupts proteostasis through nucleolar ncRNA-driven protein aggregation. J Cell Biol 2024; 223:e202309036. [PMID: 38717338 PMCID: PMC11080644 DOI: 10.1083/jcb.202309036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 01/19/2024] [Accepted: 03/13/2024] [Indexed: 05/12/2024] Open
Abstract
Senataxin is an evolutionarily conserved RNA-DNA helicase involved in DNA repair and transcription termination that is associated with human neurodegenerative disorders. Here, we investigated whether Senataxin loss affects protein homeostasis based on previous work showing R-loop-driven accumulation of DNA damage and protein aggregates in human cells. We find that Senataxin loss results in the accumulation of insoluble proteins, including many factors known to be prone to aggregation in neurodegenerative disorders. These aggregates are located primarily in the nucleolus and are promoted by upregulation of non-coding RNAs expressed from the intergenic spacer region of ribosomal DNA. We also map sites of R-loop accumulation in human cells lacking Senataxin and find higher RNA-DNA hybrids within the ribosomal DNA, peri-centromeric regions, and other intergenic sites but not at annotated protein-coding genes. These findings indicate that Senataxin loss affects the solubility of the proteome through the regulation of transcription-dependent lesions in the nucleus and the nucleolus.
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Affiliation(s)
- Xuemei Wen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Hengyi Xu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Phillip R. Woolley
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Olivia M. Conway
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jun Yao
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andreas Matouschek
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Alan M. Lambowitz
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - Tanya T. Paull
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
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Tang H, Pang X, Li S, Tang L. The Double-Edged Effects of MLN4924: Rethinking Anti-Cancer Drugs Targeting the Neddylation Pathway. Biomolecules 2024; 14:738. [PMID: 39062453 PMCID: PMC11274557 DOI: 10.3390/biom14070738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/11/2024] [Accepted: 06/18/2024] [Indexed: 07/28/2024] Open
Abstract
(1) Background: The neddylation pathway assumes a pivotal role in the initiation and progression of cancer. MLN4924, a potent small-molecule inhibitor of the NEDD8-activating enzyme (NAE), effectively intervenes in the early stages of the neddylation pathway. By instigating diverse cellular responses, such as senescence and apoptosis in cancer cells, MLN4924 also exerts regulatory effects on non-malignant cells within the tumor microenvironment (TME) and tumor virus-infected cells, thereby impeding the onset of tumors. Consequently, MLN4924 has been widely acknowledged as a potent anti-cancer drug. (2) Recent findings: Nevertheless, recent findings have illuminated additional facets of the neddylation pathway, revealing its active involvement in various biological processes detrimental to the survival of cancer cells. This newfound understanding underscores the dual role of MLN4924 in tumor therapy, characterized by both anti-cancer and pro-cancer effects. This dichotomy is herein referred to as the "double-edged effects" of MLN4924. This paper delves into the intricate relationship between the neddylation pathway and cancer, offering a mechanistic exploration and analysis of the causes underlying the double-edged effects of MLN4924-specifically, the accumulation of pro-cancer neddylation substrates. (3) Perspectives: Here, the objective is to furnish theoretical support and novel insights that can guide the development of next-generation anti-cancer drugs targeting the neddylation pathway.
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Affiliation(s)
- Haoming Tang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China; (H.T.); (X.P.)
| | - Xin Pang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China; (H.T.); (X.P.)
| | - Shun Li
- Department of Immunology, School of Basic Medical Sciences, Chengdu Medical College, Chengdu 610500, China
- Department of Spine Surgery, People’s Hospital of Longhua, Affiliated Hospital of Southern Medical University, Shenzhen 518109, China
| | - Liling Tang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China; (H.T.); (X.P.)
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Ke B, Jin P, Wang XJ, Liu N, Liang H, Zhang RP. Oncogenic and immunological role of EDIL3 in human tumours: From pan-cancer analysis to validation in gastric cancer. Heliyon 2024; 10:e32291. [PMID: 38882287 PMCID: PMC11180325 DOI: 10.1016/j.heliyon.2024.e32291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 05/30/2024] [Accepted: 05/31/2024] [Indexed: 06/18/2024] Open
Abstract
Background Epidermal growth factor-like repeats and discoidin I-like domains 3 (EDIL3) is a secreted extracellular matrix protein implicated in diverse physiological and pathological processes including embryonic development, angiogenesis, and anti-inflammatory responses. Recent reports have indicated that EDIL3 play critical roles in carcinogenesis and progression of many cancers. Herein, we performed a pan-cancer investigation to study the potential functions of EDIL3 in various cancers and experimentally validate its function in gastric cancer (GC). Methods We analysed EDIL3 expression profiles in different tumours using The Cancer Genome Atlas database. The Kaplan-Meier Plotter was used to investigate the prognostic value of EDIL3, while receiver operating characteristic curve was performed to analyze its diagnostic efficacy. Several bioinformatics tools were used to study the association between EDIL3 and promoter methylation, gene enrichment analysis, immune infiltration, immune-related genes, and drug sensitivity. Molecular biology experiments were conducted to validate the tumorigenic effects of EDIL3. Results EDIL3 is variably expressed in different cancers and is closely associated with clinical outcomes. An inverse correlation between EDIL3 and DNA methylation has been observed in 13 cancers. Enrichment analysis indicated that EDIL3 is correlated with many cellular pathways such as extracellular matrix receptor interactions and focal adhesion. EDIL3 was tightly associated with immune infiltration and immune checkpoints. EDIL3 knockdown can promote GC calls apoptosis while preventing proliferation, migration, and invasion in vitro. Conclusion EDIL3 is a promising prognostic, diagnostic, and immunological biomarker in various cancers, which could be applied as a new target for cancer therapy.
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Affiliation(s)
- Bin Ke
- Department of Gastric Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, 300060, Tianjin, China
| | - Peng Jin
- Department of Gastric Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, 300060, Tianjin, China
| | - Xue-Jun Wang
- Department of Gastric Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, 300060, Tianjin, China
| | - Ning Liu
- Department of Gastric Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, 300060, Tianjin, China
| | - Han Liang
- Department of Gastric Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, 300060, Tianjin, China
| | - Ru-Peng Zhang
- Department of Gastric Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, 300060, Tianjin, China
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11
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Zhao M, Dai B, Li X, Zhang Y, Qiao C, Qin Y, Li Z, Li Q, Wang S, Yang Y, Chen Y. RAPSYN-mediated neddylation of BCR-ABL alternatively determines the fate of Philadelphia chromosome-positive leukemia. eLife 2024; 12:RP88375. [PMID: 38865175 PMCID: PMC11168747 DOI: 10.7554/elife.88375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024] Open
Abstract
Philadelphia chromosome-positive (Ph+) leukemia is a fatal hematological malignancy. Although standard treatments with tyrosine kinase inhibitors (TKIs) have achieved remarkable success in prolonging patient survival, intolerance, relapse, and TKI resistance remain serious issues for patients with Ph+ leukemia. Here, we report a new leukemogenic process in which RAPSYN and BCR-ABL co-occur in Ph+ leukemia, and RAPSYN mediates the neddylation of BCR-ABL. Consequently, neddylated BCR-ABL enhances the stability by competing its c-CBL-mediated degradation. Furthermore, SRC phosphorylates RAPSYN to activate its NEDD8 E3 ligase activity, promoting BCR-ABL stabilization and disease progression. Moreover, in contrast to in vivo ineffectiveness of PROTAC-based degraders, depletion of RAPSYN expression, or its ligase activity decreased BCR-ABL stability and, in turn, inhibited tumor formation and growth. Collectively, these findings represent an alternative to tyrosine kinase activity for the oncoprotein and leukemogenic cells and generate a rationale of targeting RAPSYN-mediated BCR-ABL neddylation for the treatment of Ph+ leukemia.
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MESH Headings
- Animals
- Humans
- Mice
- Cell Line, Tumor
- Fusion Proteins, bcr-abl/metabolism
- Fusion Proteins, bcr-abl/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- NEDD8 Protein/metabolism
- NEDD8 Protein/genetics
- Ubiquitin-Protein Ligases/metabolism
- Ubiquitin-Protein Ligases/genetics
- Muscle Proteins/metabolism
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Affiliation(s)
- Mengya Zhao
- Laboratory of Chemical Biology, School of Life Science and Technology, China Pharmaceutical UniversityNanjingChina
| | - Beiying Dai
- State Key Laboratory of Natural Medicines, China Pharmaceutical UniversityNanjingChina
| | - Xiaodong Li
- Laboratory of Chemical Biology, School of Life Science and Technology, China Pharmaceutical UniversityNanjingChina
| | - Yixin Zhang
- State Key Laboratory of Natural Medicines, China Pharmaceutical UniversityNanjingChina
| | - Chun Qiao
- State Key Laboratory of Natural Medicines, China Pharmaceutical UniversityNanjingChina
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province HospitalNanjingChina
| | - Yaru Qin
- State Key Laboratory of Natural Medicines, China Pharmaceutical UniversityNanjingChina
| | - Zhao Li
- Laboratory of Chemical Biology, School of Life Science and Technology, China Pharmaceutical UniversityNanjingChina
| | - Qingmei Li
- Laboratory of Chemical Biology, School of Life Science and Technology, China Pharmaceutical UniversityNanjingChina
| | - Shuzhen Wang
- Laboratory of Chemical Biology, School of Life Science and Technology, China Pharmaceutical UniversityNanjingChina
| | - Yong Yang
- State Key Laboratory of Natural Medicines, China Pharmaceutical UniversityNanjingChina
| | - Yijun Chen
- Laboratory of Chemical Biology, School of Life Science and Technology, China Pharmaceutical UniversityNanjingChina
- State Key Laboratory of Natural Medicines, China Pharmaceutical UniversityNanjingChina
- Chongqing Innovation Institute of China Pharmaceutical UniversityChongqingChina
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12
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Feng H, Zhao Q, Zhao N, Liang Z, Huang Y, Zhang X, Zhang L, Liu Y. A Cell-Permeable Photosensitizer for Selective Proximity Labeling and Crosslinking of Aggregated Proteome. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306950. [PMID: 38441365 PMCID: PMC11095223 DOI: 10.1002/advs.202306950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 02/08/2024] [Indexed: 05/16/2024]
Abstract
Intracellular proteome aggregation is a ubiquitous disease hallmark with its composition associated with pathogenicity. Herein, this work reports on a cell-permeable photosensitizer (P8, Rose Bengal derivative) for selective photo induced proximity labeling and crosslinking of cellular aggregated proteome. Rose Bengal is identified out of common photosensitizer scaffolds for its unique intrinsic binding affinity to various protein aggregates driven by the hydrophobic effect. Further acetylation permeabilizes Rose Bengal to selectively image, label, and crosslink aggregated proteome in live stressed cells. A combination of photo-chemical, tandem mass spectrometry, and protein biochemistry characterizations reveals the complexity in photosensitizing pathways (both Type I & II), modification sites and labeling mechanisms. The diverse labeling sites and reaction types result in highly effective enrichment and identification of aggregated proteome. Finally, aggregated proteomics and interaction analyses thereby reveal extensive entangling of proteostasis network components mediated by HSP70 chaperone (HSPA1B) and active participation of autophagy pathway in combating proteasome inhibition. Overall, this work exemplifies the first photo induced proximity labeling and crosslinking method (namely AggID) to profile intracellular aggregated proteome and analyze its interactions.
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Affiliation(s)
- Huan Feng
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qun Zhao
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Nan Zhao
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Zhen Liang
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Yanan Huang
- Department of Chemistry and Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, China
| | - Xin Zhang
- Department of Chemistry and Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, China
| | - Lihua Zhang
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Yu Liu
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
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13
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Papakyriacou I, Kutkaite G, Rúbies Bedós M, Nagarajan D, Alford LP, Menden MP, Mao Y. Loss of NEDD8 in cancer cells causes vulnerability to immune checkpoint blockade in triple-negative breast cancer. Nat Commun 2024; 15:3581. [PMID: 38678024 PMCID: PMC11055868 DOI: 10.1038/s41467-024-47987-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 04/17/2024] [Indexed: 04/29/2024] Open
Abstract
Immune checkpoint blockade therapy aims to activate the immune system to eliminate cancer cells. However, clinical benefits are only recorded in a subset of patients. Here, we leverage genome-wide CRISPR/Cas9 screens in a Tumor-Immune co-Culture System focusing on triple-negative breast cancer (TNBC). We reveal that NEDD8 loss in cancer cells causes a vulnerability to nivolumab (anti-PD-1). Genetic deletion of NEDD8 only delays cell division initially but cell proliferation is unaffected after recovery. Since the NEDD8 gene is commonly essential, we validate this observation with additional CRISPR screens and uncover enhanced immunogenicity in NEDD8 deficient cells using proteomics. In female immunocompetent mice, PD-1 blockade lacks efficacy against established EO771 breast cancer tumors. In contrast, we observe tumor regression mediated by CD8+ T cells against Nedd8 deficient EO771 tumors after PD-1 blockade. In essence, we provide evidence that NEDD8 is conditionally essential in TNBC and presents as a synergistic drug target for PD-1/L1 blockade therapy.
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Affiliation(s)
- Irineos Papakyriacou
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Ginte Kutkaite
- Computational Health Center, Helmholtz Munich, Neuherberg, Germany
- Department of Biology, Ludwig-Maximilians University Munich, Martinsried, Germany
| | - Marta Rúbies Bedós
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Divya Nagarajan
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Liam P Alford
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Michael P Menden
- Computational Health Center, Helmholtz Munich, Neuherberg, Germany
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, Australia
| | - Yumeng Mao
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
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14
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Zhang S, Yu Q, Li Z, Zhao Y, Sun Y. Protein neddylation and its role in health and diseases. Signal Transduct Target Ther 2024; 9:85. [PMID: 38575611 PMCID: PMC10995212 DOI: 10.1038/s41392-024-01800-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/22/2024] [Accepted: 03/04/2024] [Indexed: 04/06/2024] Open
Abstract
NEDD8 (Neural precursor cell expressed developmentally downregulated protein 8) is an ubiquitin-like protein that is covalently attached to a lysine residue of a protein substrate through a process known as neddylation, catalyzed by the enzyme cascade, namely NEDD8 activating enzyme (E1), NEDD8 conjugating enzyme (E2), and NEDD8 ligase (E3). The substrates of neddylation are categorized into cullins and non-cullin proteins. Neddylation of cullins activates CRLs (cullin RING ligases), the largest family of E3 ligases, whereas neddylation of non-cullin substrates alters their stability and activity, as well as subcellular localization. Significantly, the neddylation pathway and/or many neddylation substrates are abnormally activated or over-expressed in various human diseases, such as metabolic disorders, liver dysfunction, neurodegenerative disorders, and cancers, among others. Thus, targeting neddylation becomes an attractive strategy for the treatment of these diseases. In this review, we first provide a general introduction on the neddylation cascade, its biochemical process and regulation, and the crystal structures of neddylation enzymes in complex with cullin substrates; then discuss how neddylation governs various key biological processes via the modification of cullins and non-cullin substrates. We further review the literature data on dysregulated neddylation in several human diseases, particularly cancer, followed by an outline of current efforts in the discovery of small molecule inhibitors of neddylation as a promising therapeutic approach. Finally, few perspectives were proposed for extensive future investigations.
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Affiliation(s)
- Shizhen Zhang
- Department of Breast Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China
| | - Qing Yu
- Department of Thyroid Surgery, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
- Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou, 310022, China
| | - Zhijian Li
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China
| | - Yongchao Zhao
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China.
- Department of Hepatobiliary and Pancreatic Surgery, Zhejiang University School of Medicine, Hangzhou, 310029, China.
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China.
- Zhejiang University Cancer Center, Hangzhou, 310029, China.
| | - Yi Sun
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China.
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China.
- Zhejiang University Cancer Center, Hangzhou, 310029, China.
- Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang, Hangzhou, 310024, China.
- Research Center for Life Science and Human Health, Binjiang Institute of Zhejiang University, Hangzhou, 310053, China.
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15
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Wang T, Li X, Ma R, Sun J, Huang S, Sun Z, Wang M. Advancements in colorectal cancer research: Unveiling the cellular and molecular mechanisms of neddylation (Review). Int J Oncol 2024; 64:39. [PMID: 38391033 PMCID: PMC10919758 DOI: 10.3892/ijo.2024.5627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 01/22/2024] [Indexed: 02/24/2024] Open
Abstract
Neddylation, akin to ubiquitination, represents a post‑translational modification of proteins wherein neural precursor cell‑expressed developmentally downregulated protein 8 (NEDD8) is modified on the substrate protein through a series of reactions. Neddylation plays a pivotal role in the growth and proliferation of animal cells. In colorectal cancer (CRC), it predominantly contributes to the proliferation, metastasis and survival of tumor cells, decreasing overall patient survival. The strategic manipulation of the NEDD8‑mediated neddylation pathway holds immense therapeutic promise in terms of the potential to modulate the growth of tumors by regulating diverse biological responses within cancer cells, such as DNA damage response and apoptosis, among others. MLN4924 is an inhibitor of NEDD8, and its combined use with platinum drugs and irinotecan, as well as cycle inhibitors and NEDD activating enzyme inhibitors screened by drug repurposing, has been found to exert promising antitumor effects. The present review summarizes the recent progress made in the understanding of the role of NEDD8 in the advancement of CRC, suggesting that NEDD8 is a promising anti‑CRC target.
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Affiliation(s)
- Tianyu Wang
- School of Clinical and Basic Medical Sciences, Shandong First Medical University, Jinan, Shandong 250117, P.R. China
| | - Xiaobing Li
- School of Clinical and Basic Medical Sciences, Shandong First Medical University, Jinan, Shandong 250117, P.R. China
| | - Ruijie Ma
- Department of Thoracic Surgery, Jinan Central Hospital, Shandong University, Jinan, Shandong 250013, P.R. China
| | - Jian Sun
- Department of General Surgery, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250014, P.R. China
- First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250013, P.R. China
| | - Shuhong Huang
- School of Clinical and Basic Medical Sciences, Shandong First Medical University, Jinan, Shandong 250117, P.R. China
- Science and Technology Innovation Center, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250117, P.R. China
| | - Zhigang Sun
- Department of Thoracic Surgery, Jinan Central Hospital, Shandong University, Jinan, Shandong 250013, P.R. China
- Department of Thoracic Surgery, Central Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250013, P.R. China
| | - Meng Wang
- Department of General Surgery, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250014, P.R. China
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16
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Zhan PC, Yang S, Liu X, Zhang YY, Wang R, Wang JX, Qiu QY, Gao Y, Lv DB, Li LM, Luo CL, Hu ZW, Li Z, Lyu PJ, Liang P, Gao JB. A radiomics signature derived from CT imaging to predict MSI status and immunotherapy outcomes in gastric cancer: a multi-cohort study. BMC Cancer 2024; 24:404. [PMID: 38561648 PMCID: PMC10985890 DOI: 10.1186/s12885-024-12174-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 03/22/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Accurate microsatellite instability (MSI) testing is essential for identifying gastric cancer (GC) patients eligible for immunotherapy. We aimed to develop and validate a CT-based radiomics signature to predict MSI and immunotherapy outcomes in GC. METHODS This retrospective multicohort study included a total of 457 GC patients from two independent medical centers in China and The Cancer Imaging Archive (TCIA) databases. The primary cohort (n = 201, center 1, 2017-2022), was used for signature development via Least Absolute Shrinkage and Selection Operator (LASSO) and logistic regression analysis. Two independent immunotherapy cohorts, one from center 1 (n = 184, 2018-2021) and another from center 2 (n = 43, 2020-2021), were utilized to assess the signature's association with immunotherapy response and survival. Diagnostic efficiency was evaluated using the area under the receiver operating characteristic curve (AUC), and survival outcomes were analyzed via the Kaplan-Meier method. The TCIA cohort (n = 29) was included to evaluate the immune infiltration landscape of the radiomics signature subgroups using both CT images and mRNA sequencing data. RESULTS Nine radiomics features were identified for signature development, exhibiting excellent discriminative performance in both the training (AUC: 0.851, 95%CI: 0.782, 0.919) and validation cohorts (AUC: 0.816, 95%CI: 0.706, 0.926). The radscore, calculated using the signature, demonstrated strong predictive abilities for objective response in immunotherapy cohorts (AUC: 0.734, 95%CI: 0.662, 0.806; AUC: 0.724, 95%CI: 0.572, 0.877). Additionally, the radscore showed a significant association with PFS and OS, with GC patients with a low radscore experiencing a significant survival benefit from immunotherapy. Immune infiltration analysis revealed significantly higher levels of CD8 + T cells, activated CD4 + B cells, and TNFRSF18 expression in the low radscore group, while the high radscore group exhibited higher levels of T cells regulatory and HHLA2 expression. CONCLUSION This study developed a robust radiomics signature with the potential to serve as a non-invasive biomarker for GC's MSI status and immunotherapy response, demonstrating notable links to post-immunotherapy PFS and OS. Additionally, distinct immune profiles were observed between low and high radscore groups, highlighting their potential clinical implications.
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Affiliation(s)
- Peng-Chao Zhan
- Department of Radiology, The First Affiliated Hospital of Zhengzhou University, No.1 Jianshe Road, 450052, Zhengzhou, Henan, PR China
| | - Shuo Yang
- Department of Radiology, The Second Hospital, Cheello College of Medicine, Shandong University, 250033, Jinan, PR China
| | - Xing Liu
- Department of Radiology, The First Affiliated Hospital of Zhengzhou University, No.1 Jianshe Road, 450052, Zhengzhou, Henan, PR China
| | - Yu-Yuan Zhang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, PR China
| | - Rui Wang
- Department of Radiology, The First Affiliated Hospital of Zhengzhou University, No.1 Jianshe Road, 450052, Zhengzhou, Henan, PR China
| | - Jia-Xing Wang
- Department of Interventional Medicine, The Second Hospital, Cheello College of Medicine, Shandong University, 250033, Jinan, Shandong, PR China
| | - Qing-Ya Qiu
- Zhengzhou University Medical College, 450052, Zhengzhou, Henan, PR China
| | - Yu Gao
- Department of Radiology, The First Affiliated Hospital of Zhengzhou University, No.1 Jianshe Road, 450052, Zhengzhou, Henan, PR China
| | - Dong-Bo Lv
- Department of Radiology, The First Affiliated Hospital of Zhengzhou University, No.1 Jianshe Road, 450052, Zhengzhou, Henan, PR China
| | - Li-Ming Li
- Department of Radiology, The First Affiliated Hospital of Zhengzhou University, No.1 Jianshe Road, 450052, Zhengzhou, Henan, PR China
| | - Cheng-Long Luo
- Department of Radiology, The First Affiliated Hospital of Zhengzhou University, No.1 Jianshe Road, 450052, Zhengzhou, Henan, PR China
| | - Zhi-Wei Hu
- Department of Radiology, The First Affiliated Hospital of Zhengzhou University, No.1 Jianshe Road, 450052, Zhengzhou, Henan, PR China
| | - Zhen Li
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, PR China
| | - Pei-Jie Lyu
- Department of Radiology, The First Affiliated Hospital of Zhengzhou University, No.1 Jianshe Road, 450052, Zhengzhou, Henan, PR China
| | - Pan Liang
- Department of Radiology, The First Affiliated Hospital of Zhengzhou University, No.1 Jianshe Road, 450052, Zhengzhou, Henan, PR China
| | - Jian-Bo Gao
- Department of Radiology, The First Affiliated Hospital of Zhengzhou University, No.1 Jianshe Road, 450052, Zhengzhou, Henan, PR China.
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17
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Yang W, Wang S, Tong S, Zhang WD, Qin JJ. Expanding the ubiquitin code in pancreatic cancer. Biochim Biophys Acta Mol Basis Dis 2024; 1870:166884. [PMID: 37704111 DOI: 10.1016/j.bbadis.2023.166884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/23/2023] [Accepted: 09/06/2023] [Indexed: 09/15/2023]
Abstract
The ubiquitin-proteasome system (UPS) is a fundamental regulatory mechanism in cells, vital for maintaining cellular homeostasis, compiling signaling transduction, and determining cell fates. These biological processes require the coordinated signal cascades of UPS members, including ubiquitin ligases, ubiquitin-conjugating enzymes, deubiquitinases, and proteasomes, to ubiquitination and de-ubiquitination on substrates. Recent studies indicate that ubiquitination code rewriting is particularly prominent in pancreatic cancer. High frequency mutation or aberrant hyperexpression of UPS members dysregulates ferroptosis, tumor microenvironment, and metabolic rewiring processes and contribute to tumor growth, metastasis, immune evasion, and acquired drug resistance. We conduct an in-depth overview of ubiquitination process in pancreatic cancer, highlighting the role of ubiquitin code in tumor-promoting and tumor-suppressor pathways. Furthermore, we review current UPS modulators and analyze the potential of UPS modulators as cancer therapy.
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Affiliation(s)
- Wenyan Yang
- College of Pharmaceutical Science, Zhejiang University of Technology, Huzhou 313200, China; Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Shiqun Wang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Shengqiang Tong
- College of Pharmaceutical Science, Zhejiang University of Technology, Huzhou 313200, China
| | - Wei-Dong Zhang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Jiang-Jiang Qin
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China; Key Laboratory of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer of Zhejiang Province, Hangzhou 310022, China.
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18
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Yan J, Fang Z, Shi M, Tu C, Zhang S, Jiang C, Li Q, Shao Y. Clinical Significance of Disulfidptosis-related Genes and Functional Analysis in Gastric Cancer. J Cancer 2024; 15:1053-1066. [PMID: 38230212 PMCID: PMC10788733 DOI: 10.7150/jca.91796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 12/13/2023] [Indexed: 01/18/2024] Open
Abstract
Background: Worldwide, gastric cancer (GC) remains intractable due to its poor prognosis and high morbidity and mortality. Disulfidptosis is a novel kind of cell death mediated by abnormal accumulation of intracellular disulphides. The correlation between disulfidptosis and GC is still unknown. Therefore, it is necessary to elucidate the pathogenesis and mechanism of disulfidptosis and GC for clinical diagnosis and intervention. Methods: RNA-sequencing data from several public data portals and clinical samples were collected. We compared the expression levels of four key genes of disulfidptosis, including SLC7A11, SLC3A2, RPN1, and NCKAP1, in GC and selected prognostic genes to build a novel GC prognosis-related nomogram model. The biological functions and immune landscape of the identified prognostic genes were explored. Results: Overexpressed NCKAP1 and SLC7A11 were prognostic disulfidptosis-related genes in GC. We combined these genes and several clinicopathological factors to build a prognostic nomogram model for GC. Meanwhile, the ROC curves showed that NCKAP1 and SLC7A11 were promising biomarkers for GC screening. The biological and cellular functions were focused on actin activities, GTPase and immunoreaction. The tumour immune microenvironment and immune therapy targets were identified. Competing endogenous RNA network was built to explore the downstream regulatory mechanisms. Finally, the elevated NCKAP1 and SLC7A11 expression in GC was validated via qRT-PCR in a cell line and tissue line. Conclusion: In conclusion, NCKAP1 and SLC7A11 are promising prognostic and diagnostic biomarkers for GC that correlate with the activities of actin, energy metabolism of GTPase, immune infiltration and immunotherapy.
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Affiliation(s)
- Jianing Yan
- Department of Gastroenterology, The First Affiliated Hospital of Ningbo University, Ningbo 315020, China
| | - Ziyi Fang
- Department of Gastroenterology, The First Affiliated Hospital of Ningbo University, Ningbo 315020, China
| | - Meiqi Shi
- Department of Gastroenterology, The First Affiliated Hospital of Ningbo University, Ningbo 315020, China
| | - Can Tu
- Department of Gastroenterology, The First Affiliated Hospital of Ningbo University, Ningbo 315020, China
| | - Shengke Zhang
- Clinical Medical College, Southwest Medical University, Luzhou 646000, China
| | - Chenglu Jiang
- Clinical Medical College, Southwest Medical University, Luzhou 646000, China
| | - Qier Li
- Department of Gastroenterology, The First Affiliated Hospital of Ningbo University, Ningbo 315020, China
| | - Yongfu Shao
- Department of Gastroenterology, The First Affiliated Hospital of Ningbo University, Ningbo 315020, China
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19
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Zhang W, Yang J, Wang B, Lu Y, Yang J, Zhong W, Yu Z, Qin Z, Xiao B, Wang K, Ma YY, Amaravadi R, Herlyn M, Kim J, Xu X, Guo W. HRS mediates tumor immune evasion by regulating proteostasis-associated interferon pathway activation. Cell Rep 2023; 42:113352. [PMID: 37948180 PMCID: PMC10748463 DOI: 10.1016/j.celrep.2023.113352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 08/31/2023] [Accepted: 10/11/2023] [Indexed: 11/12/2023] Open
Abstract
By sorting receptor tyrosine kinases into endolysosomes, the endosomal sorting complexes required for transport (ESCRTs) are thought to attenuate oncogenic signaling in tumor cells. Paradoxically, ESCRT members are upregulated in tumors. Here, we show that disruption of hepatocyte growth factor-regulated tyrosine kinase substrate (HRS), a pivotal ESCRT component, inhibited tumor growth by promoting CD8+ T cell infiltration in melanoma and colon cancer mouse models. HRS ablation led to misfolded protein accumulation and triggered endoplasmic reticulum (ER) stress, resulting in the activation of the type I interferon pathway in an inositol-requiring enzyme-1α (IRE1α)/X-box binding protein 1 (XBP1)-dependent manner. HRS was upregulated in tumor cells with high tumor mutational burden (TMB). HRS expression associates with the response to PD-L1/PD-1 blockade therapy in melanoma patients with high TMB tumors. HRS ablation sensitized anti-PD-1 treatment in mouse melanoma models. Our study shows a mechanism by which tumor cells with high TMB evade immune surveillance and suggests HRS as a promising target to improve immunotherapy.
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Affiliation(s)
- Wei Zhang
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jiegang Yang
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Beike Wang
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Youtao Lu
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jingbo Yang
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wenqun Zhong
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ziyan Yu
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zhiyuan Qin
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bolin Xiao
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China
| | - Kuiming Wang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China
| | - Yi Y Ma
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ravi Amaravadi
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Meenhard Herlyn
- Molecular and Cellular Oncogenesis Program and Melanoma Research Center, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Junhyong Kim
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xiaowei Xu
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wei Guo
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA.
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20
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Gervaso L, Bottiglieri L, Meneses-Medina MI, Pellicori S, Biffi R, Fumagalli Romario U, De Pascale S, Sala I, Bagnardi V, Barberis M, Cella CA, Fazio N. Role of microsatellite instability and HER2 positivity in locally advanced esophago-gastric cancer patients treated with peri-operative chemotherapy. Clin Transl Oncol 2023; 25:3287-3295. [PMID: 37084152 DOI: 10.1007/s12094-023-03179-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 03/28/2023] [Indexed: 04/22/2023]
Abstract
PURPOSE Neoadjuvant chemotherapy (NAC) significantly improved the prognosis of patients with locally advanced gastric cancer (LAGC). Several biomarkers, including HER2 and MMR/MSI are crucial for treatment decisions in the advanced stage but, currently, no biomarkers can guide the choice of NAC in clinical practice. Our aim was to evaluate the role of MSI and HER2 status on clinical outcomes. METHODS We retrospectively collected LAGC patients treated with NAC and surgery +/- adjuvant chemotherapy from 2006 to 2018. HER2 and MSI were assessed on endoscopic and surgical samples. Pathologic complete response (pCR) rate, overall survival (OS), and event-free survival (EFS) were estimated and evaluated for association with downstaging and MSI. RESULTS We included 76 patients, 8% were classified as MSI-H, entirely consistent between endoscopic and surgical samples. Six percent of patients were HER2 positive on endoscopic and 4% on surgical samples. Tumor downstaging was observed in 52.5% of cases, with three pCR (5.1%), none in MSI-H cancers. According to MSI status, event-free survival (EFS) and overall survival (OS) were higher for MSI-H patients to MSS [EFS not reached vs 30.0 months, p = 0.08; OS not reached vs 39.6 months, p = 0.10]. CONCLUSION Our work confirms the positive prognostic effect of MSI-H in the curative setting of LAGC, not correlated with pathologic tumor downstaging. Prospective ad-hoc trial and tumor molecular profiling are eagerly needed.
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Affiliation(s)
- Lorenzo Gervaso
- Division of Gastrointestinal Medical Oncology and Neuroendocrine Tumors, European Institute of Oncology, IEO IRCCS, Via Ripamonti 435, Milan, Italy.
- Molecular Medicine Department, University of Pavia, Pavia, Italy.
| | - Luca Bottiglieri
- Division of Pathology, European Institute of Oncology IRCCS, Milan, Italy
| | - Monica Isabel Meneses-Medina
- Division of Gastrointestinal Medical Oncology and Neuroendocrine Tumors, European Institute of Oncology, IEO IRCCS, Via Ripamonti 435, Milan, Italy
- Department of Hematology and Oncology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Stefania Pellicori
- Division of Gastrointestinal Medical Oncology and Neuroendocrine Tumors, European Institute of Oncology, IEO IRCCS, Via Ripamonti 435, Milan, Italy
| | - Roberto Biffi
- Division of Digestive Surgery, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | | | - Stefano De Pascale
- Division of Digestive Surgery, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Isabella Sala
- Department of Statistics and Quantitative Methods, University of Milan-Bicocca, Milan, Italy
| | - Vincenzo Bagnardi
- Department of Statistics and Quantitative Methods, University of Milan-Bicocca, Milan, Italy
| | - Massimo Barberis
- Pathology Unit, European Institute of Oncology IRCCS, Milan, Italy
| | - Chiara Alessandra Cella
- Division of Gastrointestinal Medical Oncology and Neuroendocrine Tumors, European Institute of Oncology, IEO IRCCS, Via Ripamonti 435, Milan, Italy
| | - Nicola Fazio
- Division of Gastrointestinal Medical Oncology and Neuroendocrine Tumors, European Institute of Oncology, IEO IRCCS, Via Ripamonti 435, Milan, Italy.
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21
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Qin Z, Huang Y, Li Z, Pan G, Zheng L, Xiao X, Wang F, Chen J, Chen X, Lin X, Li K, Yan G, Zhang H, Xing F. Glioblastoma Vascular Plasticity Limits Effector T-cell Infiltration and Is Blocked by cAMP Activation. Cancer Immunol Res 2023; 11:1351-1366. [PMID: 37540804 DOI: 10.1158/2326-6066.cir-22-0872] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 04/20/2023] [Accepted: 07/28/2023] [Indexed: 08/06/2023]
Abstract
Glioblastoma (GBM) is the deadliest form of brain cancer. It is a highly angiogenic and immunosuppressive malignancy. Although immune checkpoint blockade therapies have revolutionized treatment for many types of cancer, their therapeutic efficacy in GBM has been far less than expected or even ineffective. In this study, we found that the genomic signature of glioma-derived endothelial cells (GdEC) correlates with an immunosuppressive state and poor prognosis of patients with glioma. We established an in vitro model of GdEC differentiation for drug screening and used this to determine that cyclic adenosine monophosphate (cAMP) activators could effectively block GdEC formation by inducing oxidative stress. Furthermore, cAMP activators impaired GdEC differentiation in vivo, normalized the tumor vessels, and altered the tumor immune profile, especially increasing the influx and function of CD8+ effector T cells. Dual blockade of GdECs and PD-1 induced tumor regression and established antitumor immune memory. Thus, our study reveals that endothelial transdifferentiation of GBM shapes an endothelial immune cell barrier and supports the clinical development of combining GdEC blockade and immunotherapy for GBM. See related Spotlight by Lee et al., p. 1300.
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Affiliation(s)
- Zixi Qin
- Department of Pharmacology, School of Medicine, Jinan University, Guangzhou, P.R. China
| | - Youwei Huang
- Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, P.R. China
| | - Zeying Li
- National Clinical Research Center for Metabolic Diseases, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Guopeng Pan
- Department of Pharmacology, School of Medicine, Jinan University, Guangzhou, P.R. China
| | - Liangying Zheng
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, P.R. China
| | - Xiao Xiao
- Department of Pharmacy, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, P.R. China
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Fang Wang
- Department of Pharmacology, School of Medicine, Jinan University, Guangzhou, P.R. China
| | - Jiahong Chen
- Department of Pharmacology, School of Medicine, Jinan University, Guangzhou, P.R. China
| | - Xueqin Chen
- Department of Pharmacology, School of Medicine, Jinan University, Guangzhou, P.R. China
| | - Xi Lin
- Department of Pharmacology, School of Medicine, Jinan University, Guangzhou, P.R. China
| | - Kai Li
- Guangdong Research Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, P.R. China
| | - Guangmei Yan
- Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P.R. China
| | - Haipeng Zhang
- Department of Pharmacology, School of Medicine, Jinan University, Guangzhou, P.R. China
| | - Fan Xing
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, P.R. China
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong, P.R. China
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22
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Liu Y, Liu J, Peng N, Hai S, Zhang S, Zhao H, Liu W. Role of non-canonical post-translational modifications in gastrointestinal tumors. Cancer Cell Int 2023; 23:225. [PMID: 37777749 PMCID: PMC10544213 DOI: 10.1186/s12935-023-03062-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/08/2023] [Indexed: 10/02/2023] Open
Abstract
Post-translational modifications (PTMs) of proteins contribute to the occurrence and development of tumors. Previous studies have suggested that canonical PTMs such as ubiquitination, glycosylation, and phosphorylation are closely implicated in different aspects of gastrointestinal tumors. Recently, emerging evidence showed that non-canonical PTMs play an essential role in the carcinogenesis, metastasis and treatment of gastrointestinal tumors. Therefore, we summarized recent advances in sumoylation, neddylation, isoprenylation, succinylation and other non-canonical PTMs in gastrointestinal tumors, which comprehensively describe the mechanisms and functions of non-classical PTMs in gastrointestinal tumors. It is anticipated that targeting specific PTMs could benefit the treatment as well as improve the prognosis of gastrointestinal tumors.
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Affiliation(s)
- Yihong Liu
- Department of Gastroenterology, the First Affiliated Hospital of China Medical University, 155# North Nanjing Street, Heping District, Shenyang City, 110001, Liaoning Province, China
| | - Jingwei Liu
- Department of Anus and Intestine Surgery, the First Affiliated Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Na Peng
- Department of Gastroenterology, the First Affiliated Hospital of China Medical University, 155# North Nanjing Street, Heping District, Shenyang City, 110001, Liaoning Province, China
| | - Shuangshuang Hai
- Department of Gastroenterology, the First Affiliated Hospital of China Medical University, 155# North Nanjing Street, Heping District, Shenyang City, 110001, Liaoning Province, China
| | - Shen Zhang
- Department of Gastroenterology, the Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Haibo Zhao
- Department of Gastroenterology, the First Affiliated Hospital of China Medical University, 155# North Nanjing Street, Heping District, Shenyang City, 110001, Liaoning Province, China
| | - Weixin Liu
- Department of Gastroenterology, the First Affiliated Hospital of China Medical University, 155# North Nanjing Street, Heping District, Shenyang City, 110001, Liaoning Province, China.
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23
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Aubry A, Pearson JD, Charish J, Yu T, Sivak JM, Xirodimas DP, Avet-Loiseau H, Corre J, Monnier PP, Bremner R. Deneddylation of ribosomal proteins promotes synergy between MLN4924 and chemotherapy to elicit complete therapeutic responses. Cell Rep 2023; 42:112925. [PMID: 37552601 DOI: 10.1016/j.celrep.2023.112925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 05/29/2023] [Accepted: 07/18/2023] [Indexed: 08/10/2023] Open
Abstract
The neddylation inhibitor MLN4924/Pevonedistat is in clinical trials for multiple cancers. Efficacy is generally attributed to cullin RING ligase (CRL) inhibition, but the contribution of non-CRL targets is unknown. Here, CRISPR screens map MLN4924-monotherapy sensitivity in retinoblastoma to a classic DNA damage-induced p53/E2F3/BAX-dependent death effector network, which synergizes with Nutlin3a or Navitoclax. In monotherapy-resistant cells, MLN4924 plus standard-of-care topotecan overcomes resistance, but reduces DNA damage, instead harnessing ribosomal protein nucleolar-expulsion to engage an RPL11/p21/MYCN/E2F3/p53/BAX synergy network that exhibits extensive cross-regulation. Strikingly, unneddylatable RPL11 substitutes for MLN4924 to perturb nucleolar function and enhance topotecan efficacy. Orthotopic tumors exhibit complete responses while preserving visual function. Moreover, MLN4924 plus melphalan deploy this DNA damage-independent strategy to synergistically kill multiple myeloma cells. Thus, MLN4924 synergizes with standard-of-care drugs to unlock a nucleolar death effector network across cancer types implying broad therapeutic relevance.
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Affiliation(s)
- Arthur Aubry
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada; Department of Lab Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Centre Hospitalo-universitaire (CHU) de Toulouse, Institut Universitaire du Cancer de Toulouse-Oncopole (IUCT-O), Université de Toulouse, UPS, Unité de Génomique du Myélome, Toulouse, France
| | - Joel D Pearson
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Jason Charish
- Department of Ophthalmology and Vision Science, University of Toronto, Toronto, ON, Canada; Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Tao Yu
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Jeremy M Sivak
- Department of Lab Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Ophthalmology and Vision Science, University of Toronto, Toronto, ON, Canada; Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | | | - Hervé Avet-Loiseau
- Centre Hospitalo-universitaire (CHU) de Toulouse, Institut Universitaire du Cancer de Toulouse-Oncopole (IUCT-O), Université de Toulouse, UPS, Unité de Génomique du Myélome, Toulouse, France; Centre de Recherches en Cancérologie de Toulouse (CRCT), INSERM, Toulouse, France
| | - Jill Corre
- Centre Hospitalo-universitaire (CHU) de Toulouse, Institut Universitaire du Cancer de Toulouse-Oncopole (IUCT-O), Université de Toulouse, UPS, Unité de Génomique du Myélome, Toulouse, France; Centre de Recherches en Cancérologie de Toulouse (CRCT), INSERM, Toulouse, France
| | - Philippe P Monnier
- Department of Ophthalmology and Vision Science, University of Toronto, Toronto, ON, Canada; Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Rod Bremner
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada; Department of Lab Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Ophthalmology and Vision Science, University of Toronto, Toronto, ON, Canada.
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24
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Li X, Poire A, Jeong KJ, Zhang D, Chen G, Sun C, Mills GB. Single-cell trajectory analysis reveals a CD9 positive state to contribute to exit from stem cell-like and embryonic diapause states and transit to drug-resistant states. Cell Death Discov 2023; 9:285. [PMID: 37542044 PMCID: PMC10403509 DOI: 10.1038/s41420-023-01586-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/12/2023] [Accepted: 07/27/2023] [Indexed: 08/06/2023] Open
Abstract
Bromo- and extra-terminal domain (BET) inhibitors (BETi) have been shown to decrease tumor growth in preclinical models and clinical trials. However, toxicity and rapid emergence of resistance have limited their clinical implementation. To identify state changes underlying acquisition of resistance to the JQ1 BETi, we reanalyzed single-cell RNAseq data from JQ1 sensitive and resistant SUM149 and SUM159 triple-negative breast cancer cell lines. Parental and JQ1-resistant SUM149 and SUM159 exhibited a stem cell-like and embryonic diapause (SCLED) cell state as well as a transitional cell state between the SCLED state that is present in both treatment naïve and JQ1 treated cells, and a number of JQ1 resistant cell states. A transitional cell state transcriptional signature but not a SCLED state transcriptional signature predicted worsened outcomes in basal-like breast cancer patients suggesting that transit from the SCLED state to drug-resistant states contributes to patient outcomes. Entry of SUM149 and SUM159 into the transitional cell state was characterized by elevated expression of the CD9 tetraspanin. Knockdown or inhibition of CD9-sensitized cells to multiple targeted and cytotoxic drugs in vitro. Importantly, CD9 knockdown or blockade sensitized SUM149 to JQ1 in vivo by trapping cells in the SCLED state and limiting transit to resistant cell states. Thus, CD9 appears to be critical for the transition from a SCLED state into treatment-resistant cell states and warrants exploration as a therapeutic target in basal-like breast cancer.
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Affiliation(s)
- Xi Li
- Division of Oncological Sciences Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97201, USA.
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China.
| | - Alfonso Poire
- Division of Oncological Sciences Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97201, USA
| | - Kang Jin Jeong
- Division of Oncological Sciences Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97201, USA
| | - Dong Zhang
- Division of Oncological Sciences Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97201, USA
| | - Gang Chen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Chaoyang Sun
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Gordon B Mills
- Division of Oncological Sciences Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97201, USA
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25
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Janssen K, Duran-Romaña R, Bottu G, Guharoy M, Botzki A, Rousseau F, Schymkowitz J. SNPeffect 5.0: large-scale structural phenotyping of protein coding variants extracted from next-generation sequencing data using AlphaFold models. BMC Bioinformatics 2023; 24:287. [PMID: 37464277 DOI: 10.1186/s12859-023-05407-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 07/10/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Next-generation sequencing technologies yield large numbers of genetic alterations, of which a subset are missense variants that alter an amino acid in the protein product. These variants can have a potentially destabilizing effect leading to an increased risk of misfolding and aggregation. Multiple software tools exist to predict the effect of single-nucleotide variants on proteins, however, a pipeline integrating these tools while starting from an NGS data output list of variants is lacking. RESULTS The previous version SNPeffect 4.0 (De Baets in Nucleic Acids Res 40(D1):D935-D939, 2011) provided an online database containing pre-calculated variant effects and low-throughput custom variant analysis. Here, we built an automated and parallelized pipeline that analyzes the impact of missense variants on the aggregation propensity and structural stability of proteins starting from the Variant Call Format as input. The pipeline incorporates the AlphaFold Protein Structure Database to achieve high coverage for structural stability analyses using the FoldX force field. The effect on aggregation-propensity is analyzed using the established predictors TANGO and WALTZ. The pipeline focuses solely on the human proteome and can be used to analyze proteome stability/damage in a given sample based on sequencing results. CONCLUSION We provide a bioinformatics pipeline that allows structural phenotyping from sequencing data using established stability and aggregation predictors including FoldX, TANGO, and WALTZ; and structural proteome coverage provided by the AlphaFold database. The pipeline and installation guide are freely available for academic users on https://github.com/vibbits/snpeffect and requires a computer cluster.
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Affiliation(s)
- Kobe Janssen
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Ramon Duran-Romaña
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Guy Bottu
- VIB Bioinformatics Core, VIB, Rijvisschestraat 120, 9052, Ghent, Belgium
| | - Mainak Guharoy
- VIB Bioinformatics Core, VIB, Rijvisschestraat 120, 9052, Ghent, Belgium
| | - Alexander Botzki
- VIB Bioinformatics Core, VIB, Rijvisschestraat 120, 9052, Ghent, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium.
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
| | - Joost Schymkowitz
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium.
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
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26
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Wang X, Chen C, Vuong D, Rodriguez-Rodriguez S, Lam V, Roleder C, Wang JH, Kambhampati S, Berger A, Pennock N, Torka P, Hernandez-Ilizaliturri F, Siddiqi T, Wang L, Xia Z, Danilov AV. Pharmacologic targeting of Nedd8-activating enzyme reinvigorates T-cell responses in lymphoid neoplasia. Leukemia 2023; 37:1324-1335. [PMID: 37031300 PMCID: PMC10244170 DOI: 10.1038/s41375-023-01889-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 04/10/2023]
Abstract
Neddylation is a sequential enzyme-based process which regulates the function of E3 Cullin-RING ligase (CRL) and thus degradation of substrate proteins. Here we show that CD8+ T cells are a direct target for therapeutically relevant anti-lymphoma activity of pevonedistat, a Nedd8-activating enzyme (NAE) inhibitor. Pevonedistat-treated patient-derived CD8+ T cells upregulated TNFα and IFNγ and exhibited enhanced cytotoxicity. Pevonedistat induced CD8+ T-cell inflamed microenvironment and delayed tumor progression in A20 syngeneic lymphoma model. This anti-tumor effect lessened when CD8+ T cells lost the ability to engage tumors through MHC class I interactions, achieved either through CD8+ T-cell depletion or genetic knockout of B2M. Meanwhile, loss of UBE2M in tumor did not alter efficacy of pevonedistat. Concurrent blockade of NAE and PD-1 led to enhanced tumor immune infiltration, T-cell activation and chemokine expression and synergistically restricted tumor growth. shRNA-mediated knockdown of HIF-1α, a CRL substrate, abrogated the in vitro effects of pevonedistat, suggesting that NAE inhibition modulates T-cell function in HIF-1α-dependent manner. scRNA-Seq-based clinical analyses in lymphoma patients receiving pevonedistat therapy demonstrated upregulation of interferon response signatures in immune cells. Thus, targeting NAE enhances the inflammatory T-cell state, providing rationale for checkpoint blockade-based combination therapy.
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Affiliation(s)
| | - Canping Chen
- Computational Biology Program, Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
| | - Dan Vuong
- City of Hope National Medical Center, Duarte, CA, USA
| | | | - Vi Lam
- City of Hope National Medical Center, Duarte, CA, USA
| | - Carly Roleder
- City of Hope National Medical Center, Duarte, CA, USA
| | - Jing H Wang
- Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh, Pittsburgh, PA, USA
| | | | | | - Nathan Pennock
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Pallawi Torka
- Division of Hematology & Medical Oncology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | | | - Tanya Siddiqi
- City of Hope National Medical Center, Duarte, CA, USA
| | - Lili Wang
- City of Hope National Medical Center, Duarte, CA, USA
| | - Zheng Xia
- Computational Biology Program, Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
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Wen JH, He XH, Feng ZS, Li DY, Tang JX, Liu HF. Cellular Protein Aggregates: Formation, Biological Effects, and Ways of Elimination. Int J Mol Sci 2023; 24:ijms24108593. [PMID: 37239937 DOI: 10.3390/ijms24108593] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 05/06/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
The accumulation of protein aggregates is the hallmark of many neurodegenerative diseases. The dysregulation of protein homeostasis (or proteostasis) caused by acute proteotoxic stresses or chronic expression of mutant proteins can lead to protein aggregation. Protein aggregates can interfere with a variety of cellular biological processes and consume factors essential for maintaining proteostasis, leading to a further imbalance of proteostasis and further accumulation of protein aggregates, creating a vicious cycle that ultimately leads to aging and the progression of age-related neurodegenerative diseases. Over the long course of evolution, eukaryotic cells have evolved a variety of mechanisms to rescue or eliminate aggregated proteins. Here, we will briefly review the composition and causes of protein aggregation in mammalian cells, systematically summarize the role of protein aggregates in the organisms, and further highlight some of the clearance mechanisms of protein aggregates. Finally, we will discuss potential therapeutic strategies that target protein aggregates in the treatment of aging and age-related neurodegenerative diseases.
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Affiliation(s)
- Jun-Hao Wen
- Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Non-Communicable Diseases, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China
| | - Xiang-Hong He
- Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Non-Communicable Diseases, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China
| | - Ze-Sen Feng
- Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Non-Communicable Diseases, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China
| | - Dong-Yi Li
- Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Non-Communicable Diseases, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China
| | - Ji-Xin Tang
- Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Non-Communicable Diseases, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China
| | - Hua-Feng Liu
- Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Non-Communicable Diseases, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China
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Shi F, Huang X, Hong Z, Lu N, Huang X, Liu L, Liang T, Bai X. Improvement strategy for immune checkpoint blockade: A focus on the combination with immunogenic cell death inducers. Cancer Lett 2023; 562:216167. [PMID: 37031916 DOI: 10.1016/j.canlet.2023.216167] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/19/2023] [Accepted: 04/03/2023] [Indexed: 04/11/2023]
Abstract
Cancer immunotherapies have yielded promising outcomes in various malignant tumors by blocking specific immune checkpoint molecules, such as programmed cell death 1 and cytotoxic T lymphocyte antigen 4. However, only a few patients respond to immune checkpoint blockade therapy because of the poor immunogenicity of tumor cells and immune-suppressive tumor microenvironment. Accumulating evidence suggests that chemotherapeutic agents, including oxaliplatin and doxorubicin, not only mediate direct cytotoxicity in tumor cells but also induce immunogenic cancer cell death to stimulate a powerful anti-cancer immune response in the tumor microenvironment. In this review, we summarize the recent advances in cancer combination therapy based on immune checkpoint inhibitors plus immunogenic cell death inducers. Despite some clinical failures and challenges, immunogenic cell death inducers have displayed great potential when combined with immune checkpoint inhibitors for anti-cancer treatment in both preclinical studies and clinical trials.
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Affiliation(s)
- Fukang Shi
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Xing Huang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China; Cancer Center, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
| | - Zhengtao Hong
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Na Lu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Xin Huang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Lingyue Liu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China; Cancer Center, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
| | - Xueli Bai
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China; Cancer Center, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
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Fu Y, Yang B, Cui Y, Hu X, Li X, Lu F, Qin T, Zhang L, Hu Z, Guo E, Fan J, Xiao R, Li W, Qin X, Hu D, Peng W, Liu J, Wang B, Mills GB, Chen G, Sun C. BRD4 inhibition impairs DNA mismatch repair, induces mismatch repair mutation signatures and creates therapeutic vulnerability to immune checkpoint blockade in MMR-proficient tumors. J Immunother Cancer 2023; 11:jitc-2022-006070. [PMID: 37072347 PMCID: PMC10124306 DOI: 10.1136/jitc-2022-006070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2023] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND Mismatch repair deficiency (dMMR) is a well-recognized biomarker for response to immune checkpoint blockade (ICB). Strategies to convert MMR-proficient (pMMR) to dMMR phenotype with the goal of sensitizing tumors to ICB are highly sought. The combination of bromodomain containing 4 (BRD4) inhibition and ICB provides a promising antitumor effect. However, the mechanisms underlying remain unknown. Here, we identify that BRD4 inhibition induces a persistent dMMR phenotype in cancers. METHODS We confirmed the correlation between BRD4 and mismatch repair (MMR) by the bioinformatic analysis on The Cancer Genome Atlas and Clinical Proteomic Tumor Analysis Consortium data, and the statistical analysis on immunohistochemistry (IHC) scores of ovarian cancer specimens. The MMR genes (MLH1,MSH2,MSH6,PMS2) were measured by quantitative reverse transcription PCR, western blot, and IHC. The MMR status was confirmed by whole exome sequencing, RNA sequencing, MMR assay and hypoxanthine-guanine phosphoribosyl transferase gene mutation assay. The BRD4i AZD5153 resistant models were induced both in vitro and in vivo. The transcriptional effects of BRD4 on MMR genes were investigated by chromatin immunoprecipitation among cell lines and data from the Cistrome Data Browser. The therapeutic response to ICB was testified in vivo. The tumor immune microenvironment markers, such as CD4, CD8, TIM-3, FOXP3, were measured by flow cytometry. RESULTS We identified the positive correlation between BRD4 and MMR genes in transcriptional and translational aspects. Also, the inhibition of BRD4 transcriptionally reduced MMR genes expression, resulting in dMMR status and elevated mutation loads. Furthermore, prolonged exposure to AZD5153 promoted a persistent dMMR signature both in vitro and in vivo, enhancing tumor immunogenicity, and increased sensitivity to α-programmed death ligand-1 therapy despite the acquired drug resistance. CONCLUSIONS We demonstrated that BRD4 inhibition suppressed expression of genes critical to MMR, dampened MMR, and increased dMMR mutation signatures both in vitro and in vivo, sensitizing pMMR tumors to ICB. Importantly, even in BRD4 inhibitors (BRD4i)-resistant tumor models, the effects of BRD4i on MMR function were maintained rendering tumors sensitive to ICB. Together, these data identified a strategy to induce dMMR in pMMR tumors and further, indicated that BRD4i sensitive and resistant tumors could benefit from immunotherapy.
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Affiliation(s)
- Yu Fu
- Department of Gynecological Oncology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
- National Clinical Research Center for Gynecology and Obstetrics, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Bin Yang
- Department of Gynecological Oncology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
- National Clinical Research Center for Gynecology and Obstetrics, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Yaoyuan Cui
- Department of Gynecological Oncology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
- National Clinical Research Center for Gynecology and Obstetrics, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Xingyuan Hu
- Department of Gynecological Oncology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
- National Clinical Research Center for Gynecology and Obstetrics, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Xi Li
- Department of Gynecological Oncology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
- National Clinical Research Center for Gynecology and Obstetrics, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Funian Lu
- Department of Gynecological Oncology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
- National Clinical Research Center for Gynecology and Obstetrics, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Tianyu Qin
- Department of Gynecological Oncology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
- National Clinical Research Center for Gynecology and Obstetrics, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Li Zhang
- Department of Gynecological Oncology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
- National Clinical Research Center for Gynecology and Obstetrics, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Zhe Hu
- Department of Gynecological Oncology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
- National Clinical Research Center for Gynecology and Obstetrics, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Ensong Guo
- Department of Gynecological Oncology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
- National Clinical Research Center for Gynecology and Obstetrics, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Junpeng Fan
- Department of Gynecological Oncology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
- National Clinical Research Center for Gynecology and Obstetrics, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Rourou Xiao
- Department of Obstetrics and Gynecology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Wenting Li
- Department of Gynecological Oncology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
- National Clinical Research Center for Gynecology and Obstetrics, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Shihezi University, Shihezi, Xinjiang, People's Republic of China
| | - Xu Qin
- National Clinical Research Center for Gynecology and Obstetrics, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
- Department of Stomatology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Dianxing Hu
- Department of Gynecological Oncology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
- National Clinical Research Center for Gynecology and Obstetrics, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Wenju Peng
- Department of Gynecological Oncology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
- National Clinical Research Center for Gynecology and Obstetrics, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Jingbo Liu
- Department of Gynecological Oncology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
- National Clinical Research Center for Gynecology and Obstetrics, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Beibei Wang
- Department of Gynecological Oncology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
- National Clinical Research Center for Gynecology and Obstetrics, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Gordon B Mills
- Department of Cell, Development and Cancer Biology, Oregon Health & Science University Knight Cancer Institute, Portland, Oregon, USA
| | - Gang Chen
- Department of Gynecological Oncology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
- National Clinical Research Center for Gynecology and Obstetrics, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Chaoyang Sun
- Department of Gynecological Oncology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
- National Clinical Research Center for Gynecology and Obstetrics, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
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Zhou Y, Gao M, Jing Y, Wang X. Pan-cancer analyses reveal IGSF10 as an immunological and prognostic biomarker. Front Genet 2023; 13:1032382. [PMID: 36685968 PMCID: PMC9845414 DOI: 10.3389/fgene.2022.1032382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/29/2022] [Indexed: 01/06/2023] Open
Abstract
Background: IGSF10 is a member of the immunoglobulin superfamily. Over the previous decade, growing proof has validated definitive correlations between individuals of the immunoglobulin superfamily and human diseases. However, the function of IGSF10 in pan-cancer stays unclear. We aimed to analyze the immunological and prognostic value of IGSF10 in pan-cancer. Methods: We utilized a vary of bioinformatic ways to inspect the function of IGSF10 in pan-cancer, including its correlation with prognosis, immune cell infiltration, tumor mutational burden (TMB), microsatellite instability (MSI), mismatch repair (MMR), DNA methyltransferases, genetic alteration, drug sensitivity, etc. Results: We noticed low expression of IGSF10 in most cancer types. IGSF10 expression in tumor samples correlates with prognosis in most cancers. In most cancer types, IGSF10 expression was strongly related to immune cells infiltration, immune checkpoints, immune modulators, TMB, MSI, MMR, and DNA methyltransferases, among others. Functional enrichment analyses indicated that IGSF10 expression was involved in lymphocyte differentiation, cell molecules adhesion, etc. Furthermore, low IGSF10 expression could increase the drug sensitivity of many drugs. Conclusion: IGSF10 could serve as a novel prognostic marker and attainable immunotherapy target for several malignancies.
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Affiliation(s)
- Yongxia Zhou
- Department of Hematology, Tianjin Medical University Cancer Institute & Hospital, Tianjin, China,Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, China,Tianjin’s Clinical Research Center for Cancer, Tianjin, China,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China,Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
| | - Manzhi Gao
- Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, China,Tianjin’s Clinical Research Center for Cancer, Tianjin, China,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China,Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
| | - Yaoyao Jing
- Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, China,Tianjin’s Clinical Research Center for Cancer, Tianjin, China,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China,Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China,Day Ward of Tianjin Medical University Cancer Institute & Hospital, Tianjin, China
| | - Xiaofang Wang
- Department of Hematology, Tianjin Medical University Cancer Institute & Hospital, Tianjin, China,Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, China,Tianjin’s Clinical Research Center for Cancer, Tianjin, China,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China,Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China,*Correspondence: Xiaofang Wang,
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31
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Jiang G, Wu Q, Li B. Evaluation of immunotherapy efficacy in gynecologic cancer. Front Immunol 2023; 14:1061761. [PMID: 36793735 PMCID: PMC9922993 DOI: 10.3389/fimmu.2023.1061761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/16/2023] [Indexed: 01/31/2023] Open
Abstract
Various immunotherapies have demonstrated remarkable success over the past few decades, and have been approved for the treatment of different cancer types. However, patient responses to immunotherapy are variable, and approximately 50% of cases are refractory to these agents. Tumor biomarker-based stratification of cases may therefore help identify subpopulations that are sensitive/resistant to immunotherapy; it may also improve prediction of response in various cancers including gynecologic cancer. These biomarkers include the tumor mutational burden, microsatellite instability, mismatch repair deficiency, T cell-inflamed gene expression profile, programmed cell death protein 1 ligand 1, tumor-infiltrating lymphocytes, and numerous other genomic alterations. Future directions in the treatment of gynecologic cancer include the utilization of these biomarkers to select ideal candidates. This review focused on recent advances in the predictive ability of molecular biomarkers in patients with gynecologic cancer who undergo immunotherapy. The most recent developments in combined immunotherapy and targeted therapy strategies and novel immune interventions against gynecologic cancers have also been discussed.
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Affiliation(s)
- Genyi Jiang
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Qianhua Wu
- School of Medicine, Tongji University, Shanghai, China
| | - Bilan Li
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
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32
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Li Y, Niu JH, Wang Y. Machine learning-based neddylation landscape indicates different prognosis and immune microenvironment in endometrial cancer. Front Oncol 2023; 13:1084523. [PMID: 36910623 PMCID: PMC9992729 DOI: 10.3389/fonc.2023.1084523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 02/13/2023] [Indexed: 02/24/2023] Open
Abstract
Endometrial cancer (EC) is women's fourth most common malignant tumor. Neddylation plays a significant role in many diseases; however, the effect of neddylation and neddylation-related genes (NRGs) on EC is rarely reported. In this study, we first used MLN4924 to affect the activation of neddylation in different cell lines (Ishikawa and HEC-1-A) and determined the critical role of neddylation-related pathways for EC progression. Subsequently, we screened 17 prognostic NRGs based on expression files of the TCGA-UCEC cohort. Based on unsupervised consensus clustering analysis, patients with EC were classified into two neddylation patterns (C1 and C2). In terms of prognosis, substantial differences were observed between the two patterns. Compared with C2, C1 exhibited low levels of immune infiltration and promoted tumor progression. More importantly, based on the expression of 17 prognostic NRGs, we transformed nine machine-learning algorithms into 89 combinations. The random forest (RSF) was selected to construct the neddylation-related risk score according to the average C-index of different cohorts. Notably, our score had important clinical implications for EC. Patients with high scores have poor prognoses and a cold tumor state. In conclusion, neddylation-related patterns and scores can distinguish tumor microenvironment (TME) and prognosis and guide personalized treatment in patients with EC.
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Affiliation(s)
- Yi Li
- Department of Gynecology, The Affiliated Jiangsu Shengze Hospital of Nanjing Medical University & Jiangsu Shengze Hospital, Suzhou, China
| | - Jiang-Hua Niu
- Department of Gynecology, The Affiliated Jiangsu Shengze Hospital of Nanjing Medical University & Jiangsu Shengze Hospital, Suzhou, China
| | - Yan Wang
- Department of Gynecology, The Affiliated Jiangsu Shengze Hospital of Nanjing Medical University & Jiangsu Shengze Hospital, Suzhou, China
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Torchiaro E, Petti C, Arena S, Sassi F, Migliardi G, Mellano A, Porporato R, Basiricò M, Gammaitoni L, Berrino E, Montone M, Corti G, Crisafulli G, Marchiò C, Bardelli A, Medico E. Case report: Preclinical efficacy of NEDD8 and proteasome inhibitors in patient-derived models of signet ring high-grade mucinous colorectal cancer from a Lynch syndrome patient. Front Oncol 2023; 13:1130852. [PMID: 36816936 PMCID: PMC9932521 DOI: 10.3389/fonc.2023.1130852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 01/12/2023] [Indexed: 02/05/2023] Open
Abstract
High-grade mucinous colorectal cancer (HGM CRC) is particularly aggressive, prone to metastasis and treatment resistance, frequently accompanied by "signet ring" cancer cells. A sizeable fraction of HGM CRCs (20-40%) arises in the context of the Lynch Syndrome, an autosomal hereditary syndrome that predisposes to microsatellite instable (MSI) CRC. Development of patient-derived preclinical models for this challenging subtype of colorectal cancer represents an unmet need in oncology. We describe here successful propagation of preclinical models from a case of early-onset, MSI-positive metastatic colorectal cancer in a male Lynch syndrome patient, refractory to standard care (FOLFOX6, FOLFIRI-Panitumumab) and, surprisingly, also to immunotherapy. Surgical material from a debulking operation was implanted in NOD/SCID mice, successfully yielding one patient-derived xenograft (PDX). PDX explants were subsequently used to generate 2D and 3D cell cultures. Histologically, all models resembled the tumor of origin, displaying a high-grade mucinous phenotype with signet ring cells. For preclinical exploration of alternative treatments, in light of recent findings, we considered inhibition of the proteasome by bortezomib and of the related NEDD8 pathway by pevonedistat. Indeed, sensitivity to bortezomib was observed in mucinous adenocarcinoma of the lung, and we previously found that HGM CRC is preferentially sensitive to pevonedistat in models with low or absent expression of cadherin 17 (CDH17), a differentiation marker. We therefore performed IHC on the tumor and models, and observed no CDH17 expression, suggesting sensitivity to pevonedistat. Both bortezomib and pevonedistat showed strong activity on 2D cells at 72 hours and on 3D organoids at 7 days, thus providing valid options for in vivo testing. Accordingly, three PDX cohorts were treated for four weeks, respectively with vehicle, bortezomib and pevonedistat. Both drugs significantly reduced tumor growth, as compared to the vehicle group. Interestingly, while bortezomib was more effective in vitro, pevonedistat was more effective in vivo. Drug efficacy was further substantiated by a reduction of cellularity and of Ki67-positive cells in the treated tumors. These results highlight proteasome and NEDD8 inhibition as potentially effective therapeutic approaches against Lynch syndrome-associated HGM CRC, also when the disease is refractory to all available treatment options.
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Affiliation(s)
- Erica Torchiaro
- Candiolo Cancer Institute, Fondazione del Piemonte per l'Oncologia (FPO) - IRCCS, Candiolo, Italy
| | - Consalvo Petti
- Candiolo Cancer Institute, Fondazione del Piemonte per l'Oncologia (FPO) - IRCCS, Candiolo, Italy
| | - Sabrina Arena
- Candiolo Cancer Institute, Fondazione del Piemonte per l'Oncologia (FPO) - IRCCS, Candiolo, Italy.,Department of Oncology, University of Torino, Candiolo, Italy
| | - Francesco Sassi
- Candiolo Cancer Institute, Fondazione del Piemonte per l'Oncologia (FPO) - IRCCS, Candiolo, Italy
| | - Giorgia Migliardi
- Candiolo Cancer Institute, Fondazione del Piemonte per l'Oncologia (FPO) - IRCCS, Candiolo, Italy
| | - Alfredo Mellano
- Candiolo Cancer Institute, Fondazione del Piemonte per l'Oncologia (FPO) - IRCCS, Candiolo, Italy
| | - Roberta Porporato
- Candiolo Cancer Institute, Fondazione del Piemonte per l'Oncologia (FPO) - IRCCS, Candiolo, Italy
| | - Marco Basiricò
- Candiolo Cancer Institute, Fondazione del Piemonte per l'Oncologia (FPO) - IRCCS, Candiolo, Italy
| | - Loretta Gammaitoni
- Candiolo Cancer Institute, Fondazione del Piemonte per l'Oncologia (FPO) - IRCCS, Candiolo, Italy
| | - Enrico Berrino
- Candiolo Cancer Institute, Fondazione del Piemonte per l'Oncologia (FPO) - IRCCS, Candiolo, Italy.,Department of Medical Sciences, University of Turin, Torino, Italy
| | - Monica Montone
- Candiolo Cancer Institute, Fondazione del Piemonte per l'Oncologia (FPO) - IRCCS, Candiolo, Italy
| | - Giorgio Corti
- Department of Oncology, University of Torino, Candiolo, Italy
| | | | - Caterina Marchiò
- Candiolo Cancer Institute, Fondazione del Piemonte per l'Oncologia (FPO) - IRCCS, Candiolo, Italy.,Department of Medical Sciences, University of Turin, Torino, Italy
| | - Alberto Bardelli
- Candiolo Cancer Institute, Fondazione del Piemonte per l'Oncologia (FPO) - IRCCS, Candiolo, Italy.,Department of Oncology, University of Torino, Candiolo, Italy
| | - Enzo Medico
- Candiolo Cancer Institute, Fondazione del Piemonte per l'Oncologia (FPO) - IRCCS, Candiolo, Italy.,Department of Oncology, University of Torino, Candiolo, Italy
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Lin Z, Wang T, Li H, Xiao M, Ma X, Gu Y, Qiang J. Magnetic resonance-based radiomics nomogram for predicting microsatellite instability status in endometrial cancer. Quant Imaging Med Surg 2023; 13:108-120. [PMID: 36620141 PMCID: PMC9816750 DOI: 10.21037/qims-22-255] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 09/05/2022] [Indexed: 11/30/2022]
Abstract
Background Microsatellite instability (MSI) status is an important indicator for screening patients with endometrial cancer (EC) who have potential Lynch syndrome (LS) and may benefit from immunotherapy. This study aimed to develop a magnetic resonance imaging (MRI)-based radiomics nomogram for the prediction of MSI status in EC. Methods A total of 296 patients with histopathologically diagnosed EC were enrolled, and their MSI status was determined using immunohistochemical (IHC) analysis. Patients were randomly divided into the training cohort (n=236) and the validation cohort (n=60) at a ratio of 8:2. To predict the MSI status in EC, the tumor radiomics features were extracted from T2-weighted images and contrast-enhanced T1-weighted images, which in turn were selected using one-way analysis of variance (ANOVA) and the least absolute shrinkage and selection operator (LASSO) algorithm to build the radiomics signature (radiomics score; radscore) model. Five clinicopathologic characteristics were used to construct a clinicopathologic model. Finally, the nomogram model combining radscore and clinicopathologic characteristics was constructed. The performance of the three models was evaluated using receiver operating characteristic (ROC), calibration, and decision curve analyses (DCA). Results Totals of 21 radiomics features and five clinicopathologic characteristics were selected to develop the radscore and clinicopathological models. The radscore and clinicopathologic models achieved an area under the curve (AUC) of 0.752 and 0.600, respectively, in the training cohort; and of 0.723 and 0.615, respectively, in the validation cohort. The radiomics nomogram model showed improved discrimination efficiency compared with the radscore and clinicopathologic models, with an AUC of 0.773 and 0.740 in the training and validation cohorts, respectively. The calibration curve analysis and DCA showed favorable calibration and clinical utility of the nomogram model. Conclusions The nomogram incorporating MRI-based radiomics features and clinicopathologic characteristics could be a potential tool for the prediction of MSI status in EC.
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Affiliation(s)
- Zijing Lin
- Department of Radiology, Jinshan Hospital, Fudan University, Shanghai, China
- Department of Radiology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ting Wang
- Department of Radiology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Haiming Li
- Department of Radiology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Meiling Xiao
- Department of Radiology, Jinshan Hospital, Fudan University, Shanghai, China
| | - Xiaoliang Ma
- Department of Radiology, Jinshan Hospital, Fudan University, Shanghai, China
| | - Yajia Gu
- Department of Radiology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jinwei Qiang
- Department of Radiology, Jinshan Hospital, Fudan University, Shanghai, China
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Zhao C, Xiong K, Bi D, Zhao F, Lan Y, Jin X, Li X. Redox-associated messenger RNAs identify novel prognostic values and influence the tumor immune microenvironment of lung adenocarcinoma. Front Genet 2023; 14:1079035. [PMID: 36873939 PMCID: PMC9977811 DOI: 10.3389/fgene.2023.1079035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/30/2023] [Indexed: 02/18/2023] Open
Abstract
Background: An imbalance of redox homeostasis participates in tumorigenesis, proliferation, and metastasis, which results from the production of reactive oxygen species (ROS). However, the biological mechanism and prognostic significance of redox-associated messenger RNAs (ramRNAs) in lung adenocarcinoma (LUAD) still remain unclear. Methods: Transcriptional profiles and clinicopathological information were retrieved from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) of LUAD patients. A total of 31 overlapped ramRNAs were determined, and patients were separated into three subtypes by unsupervised consensus clustering. Biological functions and tumor immune-infiltrating levels were analyzed, and then, differentially expressed genes (DEGs) were identified. The TCGA cohort was divided into a training set and an internal validation set at a ratio of 6:4. Least absolute shrinkage and selection operator regression were used to compute the risk score and determine the risk cutoff in the training set. Both TCGA and GEO cohort were distinguished into a high-risk or low-risk group at the median cutoff, and then, relationships of mutation characteristics, tumor stemness, immune differences, and drug sensitivity were investigated. Results: Five optimal signatures (ANLN, HLA-DQA1, RHOV, TLR2, and TYMS) were selected. Patients in the high-risk group had poorer prognosis, higher tumor mutational burden, overexpression of PD-L1, and lower immune dysfunction and exclusion score compared with the low-risk group. Cisplatin, docetaxel, and gemcitabine had significantly lower IC50 in the high-risk group. Conclusion: This study constructed a novel predictive signature of LUAD based on redox-associated genes. Risk score based on ramRNAs served as a promising biomarker for prognosis, TME, and anti-cancer therapies of LUAD.
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Affiliation(s)
- Chen Zhao
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Kewei Xiong
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China.,School of Mathematics and Statistics, Central China Normal University, Wuhan, China
| | - Dong Bi
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Fangrui Zhao
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yanfang Lan
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xiaorui Jin
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xiangpan Li
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
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Chen B, Xi Y, Zhao J, Hong Y, Tian S, Zhai X, Chen Q, Ren X, Fan L, Xie X, Jiang C. m5C regulator-mediated modification patterns and tumor microenvironment infiltration characterization in colorectal cancer: One step closer to precision medicine. Front Immunol 2022; 13:1049435. [PMID: 36532062 PMCID: PMC9751490 DOI: 10.3389/fimmu.2022.1049435] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/09/2022] [Indexed: 12/04/2022] Open
Abstract
Background The RNA modification 5-methylcytosine (m5C) is one of the most prevalent post-transcriptional modifications, with increasing evidence demonstrating its extensive involvement in the tumorigenesis and progression of various cancers. Colorectal cancer (CRC) is the third most common cancer and second leading cause of cancer-related deaths worldwide. However, the role of m5C modulators in shaping tumor microenvironment (TME) heterogeneity and regulating immune cell infiltration in CRC requires further clarification. Results The transcriptomic sequencing data of 18 m5C regulators and clinical data of patients with CRC were obtained from The Cancer Genome Atlas (TCGA) and systematically evaluated. We found that 16 m5C regulators were differentially expressed between CRC and normal tissues. Unsupervised cluster analysis was then performed and revealed two distinct m5C modification patterns that yielded different clinical prognoses and biological functions in CRC. We demonstrated that the m5C score constructed from eight m5C-related genes showed excellent prognostic performance, with a subsequent independent analysis confirming its predictive ability in the CRC cohort. Then we developed a nomogram containing five clinical risk factors and the m5C risk score and found that the m5C score exhibited high prognostic prediction accuracy and favorable clinical applicability. Moreover, the CRC patients with low m5C score were characterized by "hot" TME exhibiting increased immune cell infiltration and higher immune checkpoint expression. These characteristics were highlighted as potential identifiers of suitable candidates for anticancer immunotherapy. Although the high m5C score represented the non-inflammatory phenotype, the CRC patients in this group exhibited high level of sensitivity to molecular-targeted therapy. Conclusion Our comprehensive analysis indicated that the novel m5C clusters and scoring system accurately reflected the distinct prognostic signature, clinicopathological characteristics, immunological phenotypes, and stratifying therapeutic opportunities of CRC. Our findings, therefore, offer valuable insights into factors that may be targeted in the development of precision medicine-based therapeutic strategies for CRC.
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Affiliation(s)
- Baoxiang Chen
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China,Clinical Center of Intestinal and Colorectal Diseases of Hubei Province (Zhongnan Hospital of Wuhan University), Wuhan, China,Hubei Key Laboratory of Intestinal and Colorectal Diseases (Zhongnan Hospital of Wuhan University), Wuhan, China
| | - Yiqing Xi
- Department of Breast and Thyroid Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jianhong Zhao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China,Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, China
| | - Yuntian Hong
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China,Clinical Center of Intestinal and Colorectal Diseases of Hubei Province (Zhongnan Hospital of Wuhan University), Wuhan, China,Hubei Key Laboratory of Intestinal and Colorectal Diseases (Zhongnan Hospital of Wuhan University), Wuhan, China
| | - Shunhua Tian
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China,Clinical Center of Intestinal and Colorectal Diseases of Hubei Province (Zhongnan Hospital of Wuhan University), Wuhan, China,Hubei Key Laboratory of Intestinal and Colorectal Diseases (Zhongnan Hospital of Wuhan University), Wuhan, China
| | - Xiang Zhai
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China,Clinical Center of Intestinal and Colorectal Diseases of Hubei Province (Zhongnan Hospital of Wuhan University), Wuhan, China,Hubei Key Laboratory of Intestinal and Colorectal Diseases (Zhongnan Hospital of Wuhan University), Wuhan, China
| | - Quanjiao Chen
- CAS Key Laboratory of Special Pathogens and Biosafety, CAS Center for Influenza Research and Early Warning, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Xianghai Ren
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China,Clinical Center of Intestinal and Colorectal Diseases of Hubei Province (Zhongnan Hospital of Wuhan University), Wuhan, China,Hubei Key Laboratory of Intestinal and Colorectal Diseases (Zhongnan Hospital of Wuhan University), Wuhan, China,*Correspondence: Congqing Jiang, ; Xiaoyu Xie, ; Lifang Fan, ; Xianghai Ren,
| | - Lifang Fan
- Department of Pathology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China,*Correspondence: Congqing Jiang, ; Xiaoyu Xie, ; Lifang Fan, ; Xianghai Ren,
| | - Xiaoyu Xie
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China,Clinical Center of Intestinal and Colorectal Diseases of Hubei Province (Zhongnan Hospital of Wuhan University), Wuhan, China,Hubei Key Laboratory of Intestinal and Colorectal Diseases (Zhongnan Hospital of Wuhan University), Wuhan, China,*Correspondence: Congqing Jiang, ; Xiaoyu Xie, ; Lifang Fan, ; Xianghai Ren,
| | - Congqing Jiang
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China,Clinical Center of Intestinal and Colorectal Diseases of Hubei Province (Zhongnan Hospital of Wuhan University), Wuhan, China,Hubei Key Laboratory of Intestinal and Colorectal Diseases (Zhongnan Hospital of Wuhan University), Wuhan, China,*Correspondence: Congqing Jiang, ; Xiaoyu Xie, ; Lifang Fan, ; Xianghai Ren,
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Meszka I, Polanowska J, Xirodimas DP. Mixed in chains: NEDD8 polymers in the Protein Quality Control system. Semin Cell Dev Biol 2022; 132:27-37. [PMID: 35078718 DOI: 10.1016/j.semcdb.2022.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/11/2022] [Accepted: 01/14/2022] [Indexed: 12/14/2022]
Abstract
Post-translational modification of proteins with the Ubiquitin-like molecule NEDD8 is a critical regulatory mechanism for several biological processes and a potential target for therapeutic intervention. The role of NEDD8 has been mainly characterised through its modification as single moiety on the cullin family of proteins and control of Cullin-Ring-Ligases, but also on non-cullin substrates. In addition to monoNEDDylation, recent studies have now revealed that NEDD8 can also generate diverse polymers. This is either through modification of the 9 available lysines in NEDD8 and the formation of polyNEDD8 chains, or NEDDylation of Ubiquitin and SUMO-2 for the generation of hybrid NEDD8 chains. Here, we review recent findings that characterise the formation of NEDD8 polymers under distinct modes of protein NEDDylation (canonical/atypical) and their potential role as regulatory signals of the proteotoxic stress response and the Protein Quality Control system.
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Affiliation(s)
- Igor Meszka
- CRBM, Univ. Montpellier, CNRS, Montpellier, France
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Xu Z, Liu J, Liu Z, Zhang H. MARCH1 as a novel immune-related prognostic biomarker that shapes an inflamed tumor microenvironment in lung adenocarcinoma. Front Oncol 2022; 12:1008753. [PMID: 36313698 PMCID: PMC9606618 DOI: 10.3389/fonc.2022.1008753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/07/2022] [Indexed: 11/25/2022] Open
Abstract
E3 ubiquitin ligases (E3s), the second most common cancer-related functional protein family, play vital roles in multiple tumors. However, their importance in prognosis and immunotherapy of lung adenocarcinoma (LUAD) is not clear. First, utilizing the data from The Cancer Genome Atlas (TCGA), we comprehensively assessed the expression profile and immunological association of 13 E3s in LUAD patients. Consequently, MARCH1 was considered a candidate for further study. Second, several algorithms were applied to assess the correlation between MARCH1 and immunological characteristics in the LUAD tumor microenvironment. Third, an immune risk score (IRS) was developed to predict the prognosis. Finally, the immunological relationship of MARCH1 in pan-cancer was also estimated. We found that E3s were disordered in LUAD. Among them, MARCH1 was positively correlated with most immunological characteristics, indicating that MARCH1 designed an inflamed TME in LUAD. Coincidently, LUAD with low MARCH1 expression had a poor prognosis and was not sensitive to immune checkpoint blockers. In addition, the IRS could accurately predict the prognosis. In pan-cancer, MARCH1 was also positively correlated with most immunological characteristics. In conclusion, MARCH1 could be a novel and promising biomarker for immune status and effectiveness of immunotherapy for LUAD patients.
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Affiliation(s)
- Zhiyong Xu
- Department of Oncology, the Second Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Radiotherapy, Southern Theater General Hospital, Guangzhou, China
| | - Jun Liu
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of South China University of Technology, Guangzhou, China
| | - Zichuan Liu
- Internal Medicine Section2, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
- *Correspondence: Zichuan Liu, ; Haibo Zhang,
| | - Haibo Zhang
- Department of Oncology, the Second Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China
- *Correspondence: Zichuan Liu, ; Haibo Zhang,
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Feng S, Liang X, Li J, Wang Z, Zhang H, Dai Z, Luo P, Liu Z, Zhang J, Xiao X, Cheng Q. Immunogenic cell death related risk model to delineate ferroptosis pathway and predict immunotherapy response of patients with GBM. Front Immunol 2022; 13:992855. [PMID: 36248827 PMCID: PMC9554879 DOI: 10.3389/fimmu.2022.992855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
Immunogenic cell death (ICD) is a type of cell death that leads to the regulation and activation of the immune response, which is marked by the exposure and delivery of damage‐associated molecular patterns (DAMPs) in the tumor microenvironment. Accumulating evidence has revealed the significance of ICD-related genes in tumor progression and therapeutic response. In this study, we obtained two ICD-related clusters for glioblastoma (GBM) by applying consensus clustering, and further constructed a risk signature on account of the prognostic ICD genes. Based on the risk signature, we found that higher risk scores were associated with worse patient prognosis. Besides, the results illustrated that ferroptosis regulators/markers were highly enriched the high-risk group, and ferroptosis were correlated with cytokine signaling pathway and other immune-related pathways. We also discovered that high-risk scores were correlated to specific immune infiltration patterns and good response to immune checkpoint blockade (ICB) treatment. In conclusion, our study highlights the significance of ICD-related genes as prognostic biomarkers and immune response indicators in GBM. And the risk signature integrating prognostic genes possessed significant potential value to predict the prognosis of patients and the efficacy of ICB treatment.
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Affiliation(s)
- Songshan Feng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha, China
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha, China
| | - Xisong Liang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Jing Li
- Department of Rehabilitation, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Zeyu Wang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Hao Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Ziyu Dai
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaoxiong Xiao
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Quan Cheng, ; Xiaoxiong Xiao,
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Quan Cheng, ; Xiaoxiong Xiao,
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Tilk S, Tkachenko S, Curtis C, Petrov DA, McFarland CD. Most cancers carry a substantial deleterious load due to Hill-Robertson interference. eLife 2022; 11:67790. [PMID: 36047771 PMCID: PMC9499534 DOI: 10.7554/elife.67790] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Cancer genomes exhibit surprisingly weak signatures of negative selection1,2. This may be because selective pressures are relaxed or because genome-wide linkage prevents deleterious mutations from being removed (Hill-Robertson interference)3. By stratifying tumors by their genome-wide mutational burden, we observe negative selection (dN/dS ~ 0.56) in low mutational burden tumors, while remaining cancers exhibit dN/dS ratios ~1. This suggests that most tumors do not remove deleterious passengers. To buffer against deleterious passengers, tumors upregulate heat shock pathways as their mutational burden increases. Finally, evolutionary modeling finds that Hill-Robertson interference alone can reproduce patterns of attenuated selection and estimates the total fitness cost of passengers to be 46% per cell on average. Collectively, our findings suggest that the lack of observed negative selection in most tumors is not due to relaxed selective pressures, but rather the inability of selection to remove deleterious mutations in the presence of genome-wide linkage.
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Affiliation(s)
- Susanne Tilk
- Department of Biology, Stanford University, Stanford, United States
| | - Svyatoslav Tkachenko
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, United States
| | - Christina Curtis
- Department of Genetics, Stanford University, Stanford, United States
| | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, United States
| | - Christopher D McFarland
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, United States
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Yang X, Li Q. Pan-Cancer Analysis of the Oncogenic and Immunological Role of Solute Carrier Family 6 Member 8 (SLC6A8). Front Genet 2022; 13:916439. [PMID: 36061183 PMCID: PMC9428493 DOI: 10.3389/fgene.2022.916439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
There is mounting evidence on the implication of SLC6A8 in the initiation and progression of human cancers. However, a comprehensive understanding of the role of SLC6A8 in pan-cancer remains elusive yet. Bioinformatics analysis was performed to investigate the expression and mutation profiles of SLC6A8 in cancers, and the association of SLC6A8 expression with cancer patients’ survival and immune cell infiltration. In general, SLC6A8 is significantly upregulated across multiple cancers. SLC6A8 expression was inconsistently prognostic in different types of cancer, albeit associated with favorable survival in the vast majority of cancers. The receiver operating characteristic curves showed that SLC6A8 was relatively accurate in identifying possible cancer patients. The genetic alteration of SLC6A8, including mutation, amplification and deletion, was frequently present across various types of cancer. Mechanistically, SLC6A8 might be involved in tumorigenesis through “carbon metabolism” and “HIF-1 signaling pathway.” Besides, SLC6A8 expression had significant correlation with immune checkpoints genes and tumor-infiltrating immune cell abundances. The present study offers a novel insight into the roles of SLC6A8 in the oncogenesis and development of multiple common cancers.
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Affiliation(s)
- Xin Yang
- Department of Surgery, People’s Hospital of Deyang City, Deyang, China
| | - Qiao Li
- Department of Pathology, People’s Hospital of Deyang City, Deyang, China
- *Correspondence: Qiao Li,
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Sialana F, Roumeliotis TI, Bouguenina H, Chan Wah Hak L, Wang H, Caldwell J, Collins I, Chopra R, Choudhary JS. SimPLIT: Simplified Sample Preparation for Large-Scale Isobaric Tagging Proteomics. J Proteome Res 2022; 21:1842-1856. [PMID: 35848491 PMCID: PMC9361352 DOI: 10.1021/acs.jproteome.2c00092] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Large scale proteomic profiling of cell lines can reveal molecular signatures attributed to variable genotypes or induced perturbations, enabling proteogenomic associations and elucidation of pharmacological mechanisms of action. Although isobaric labeling has increased the throughput of proteomic analysis, the commonly used sample preparation workflows often require time-consuming steps and costly consumables, limiting their suitability for large scale studies. Here, we present a simplified and cost-effective one-pot reaction workflow in a 96-well plate format (SimPLIT) that minimizes processing steps and demonstrates improved reproducibility compared to alternative approaches. The workflow is based on a sodium deoxycholate lysis buffer and a single detergent cleanup step after peptide labeling, followed by quick off-line fractionation and MS2 analysis. We showcase the applicability of the workflow in a panel of colorectal cancer cell lines and by performing target discovery for a set of molecular glue degraders in different cell lines, in a 96-sample assay. Using this workflow, we report frequently dysregulated proteins in colorectal cancer cells and uncover cell-dependent protein degradation profiles of seven cereblon E3 ligase modulators (CRL4CRBN). Overall, SimPLIT is a robust method that can be easily implemented in any proteomics laboratory for medium-to-large scale TMT-based studies for deep profiling of cell lines.
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Affiliation(s)
- Fernando
J. Sialana
- Functional
Proteomics Group, The Institute of Cancer Research, Chester Beatty Laboratories, London SW3 6JB, U.K.
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Theodoros I. Roumeliotis
- Functional
Proteomics Group, The Institute of Cancer Research, Chester Beatty Laboratories, London SW3 6JB, U.K.
| | - Habib Bouguenina
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Laura Chan Wah Hak
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Hannah Wang
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - John Caldwell
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Ian Collins
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Rajesh Chopra
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Jyoti S. Choudhary
- Functional
Proteomics Group, The Institute of Cancer Research, Chester Beatty Laboratories, London SW3 6JB, U.K.
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Xiao J, Liu T, Liu Z, Xiao C, Du J, Zuo S, Li H, Gu H. A Differentiation-Related Gene Prognostic Index Contributes to Prognosis and Immunotherapy Evaluation in Patients with Hepatocellular Carcinoma. Cells 2022; 11:cells11152302. [PMID: 35892599 PMCID: PMC9367442 DOI: 10.3390/cells11152302] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/14/2022] [Accepted: 07/21/2022] [Indexed: 12/04/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common gastrointestinal tumor with a poor prognosis, which is associated with poor differentiation of tumor cells. However, the potential value of cell differentiation-related molecules in predicting the benefit and prognosis of immune checkpoint inhibitors (ICI) therapy remains unknown. Herein, to investigate the differentiation trajectory of HCC cells and their clinical significance, a differentiation-related gene prognostic index (DRGPI) based on HCC differentiation-related genes (HDRGs) was constructed to elucidate the immune characteristics and therapeutic benefits of ICI in the HCC subgroup defined by DRGPI. Single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data from four HCC samples were integrated for bioinformatics analysis. Then, PON1, ADH4, SQSTM1, HSP90AA1, and STMN1 were screened out to construct a DRGPI. More intriguingly, RT-qPCR validation of the expression of these genes yielded consistent results with the TCGA database. Next, the risk scoring (RS) constructed based on DRGPI suggested that the overall survival (OS) of the DRGPI-high patients was significantly worse than that of the DRGPI-low patients. A nomogram was constructed based on DRGPI-RS and clinical characteristics, which showed strong predictive performance and high accuracy. The comprehensive results indicated that a low DRGPI score was associated with low TP53 mutation rates, high CD8 T cell infiltration, and more benefit from ICI therapy. Homoplastically, the high DRGPI score reflected the opposite results. Taken together, our study highlights the significance of HCC cell differentiation in predicting prognosis, indicating immune characteristics, and understanding the therapeutic benefits of ICI, and suggests that DRGPI is a valuable prognostic biomarker for HCC.
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Affiliation(s)
- Jingjing Xiao
- School of Clinical Medicine, Guizhou Medical University, Guiyang 550000, China; (J.X.); (T.L.); (C.X.); (J.D.); (S.Z.); (H.L.)
- Department of Hepatobiliary Surgery, Guizhou Provincial People’s Hospital, Guiyang 550002, China;
- Department of Pediatric Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang 550000, China
| | - Tao Liu
- School of Clinical Medicine, Guizhou Medical University, Guiyang 550000, China; (J.X.); (T.L.); (C.X.); (J.D.); (S.Z.); (H.L.)
- Department of Hepatobiliary Surgery, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi 445000, China
| | - Zhenhua Liu
- Department of Hepatobiliary Surgery, Guizhou Provincial People’s Hospital, Guiyang 550002, China;
| | - Chuan Xiao
- School of Clinical Medicine, Guizhou Medical University, Guiyang 550000, China; (J.X.); (T.L.); (C.X.); (J.D.); (S.Z.); (H.L.)
| | - Jun Du
- School of Clinical Medicine, Guizhou Medical University, Guiyang 550000, China; (J.X.); (T.L.); (C.X.); (J.D.); (S.Z.); (H.L.)
- Department of Pediatric Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang 550000, China
| | - Shi Zuo
- School of Clinical Medicine, Guizhou Medical University, Guiyang 550000, China; (J.X.); (T.L.); (C.X.); (J.D.); (S.Z.); (H.L.)
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang 550000, China
| | - Haiyang Li
- School of Clinical Medicine, Guizhou Medical University, Guiyang 550000, China; (J.X.); (T.L.); (C.X.); (J.D.); (S.Z.); (H.L.)
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang 550000, China
| | - Huajian Gu
- School of Clinical Medicine, Guizhou Medical University, Guiyang 550000, China; (J.X.); (T.L.); (C.X.); (J.D.); (S.Z.); (H.L.)
- Department of Pediatric Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang 550000, China
- Correspondence: ; Tel.: +86-851-8677-2723
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Zhu J, Wu W, Zhang Y, Lin S, Jiang Y, Liu R, Zhang H, Wang X. Computational Analysis of Pathological Image Enables Interpretable Prediction for Microsatellite Instability. Front Oncol 2022; 12:825353. [PMID: 35936712 PMCID: PMC9355712 DOI: 10.3389/fonc.2022.825353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 06/21/2022] [Indexed: 11/29/2022] Open
Abstract
Background Microsatellite instability (MSI) is associated with several tumor types and has become increasingly vital in guiding patient treatment decisions; however, reasonably distinguishing MSI from its counterpart is challenging in clinical practice. Methods In this study, interpretable pathological image analysis strategies are established to help medical experts to identify MSI. The strategies only require ubiquitous hematoxylin and eosin–stained whole-slide images and perform well in the three cohorts collected from The Cancer Genome Atlas. Equipped with machine learning and image processing technique, intelligent models are established to diagnose MSI based on pathological images, providing the rationale of the decision in both image level and pathological feature level. Findings The strategies achieve two levels of interpretability. First, the image-level interpretability is achieved by generating localization heat maps of important regions based on deep learning. Second, the feature-level interpretability is attained through feature importance and pathological feature interaction analysis. Interestingly, from both the image-level and feature-level interpretability, color and texture characteristics, as well as their interaction, are shown to be mostly contributed to the MSI prediction. Interpretation The developed transparent machine learning pipeline is able to detect MSI efficiently and provide comprehensive clinical insights to pathologists. The comprehensible heat maps and features in the intelligent pipeline reflect extra- and intra-cellular acid–base balance shift in MSI tumor.
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Affiliation(s)
- Jin Zhu
- Southern China Center for Statistical Science, School of Mathematics, Sun Yat-Sen University, Guangzhou, China
| | - Wangwei Wu
- Southern China Center for Statistical Science, School of Mathematics, Sun Yat-Sen University, Guangzhou, China
| | - Yuting Zhang
- Southern China Center for Statistical Science, School of Mathematics, Sun Yat-Sen University, Guangzhou, China
| | - Shiyun Lin
- Center for Statistical Science, School of Mathematical Sciences, Peking University, Beijing, China
| | - Yukang Jiang
- Southern China Center for Statistical Science, School of Mathematics, Sun Yat-Sen University, Guangzhou, China
| | - Ruixian Liu
- Department of Clinical Laboratory, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
- *Correspondence: Ruixian Liu, ; Heping Zhang, ; Xueqin Wang,
| | - Heping Zhang
- School of Public Health, Yale University, New Haven, CT, United States
- *Correspondence: Ruixian Liu, ; Heping Zhang, ; Xueqin Wang,
| | - Xueqin Wang
- Department of Statistics and Finance/International Institute of Finance, School of Management, University of Science and Technology of China, Hefei, China
- *Correspondence: Ruixian Liu, ; Heping Zhang, ; Xueqin Wang,
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45
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Long-Read Nanopore Sequencing Identifies Mismatch Repair-Deficient Related Genes with Alternative Splicing in Colorectal Cancer. DISEASE MARKERS 2022; 2022:4433270. [PMID: 35909892 PMCID: PMC9334049 DOI: 10.1155/2022/4433270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 06/15/2022] [Accepted: 06/23/2022] [Indexed: 11/17/2022]
Abstract
Background Alternative splicing (AS) plays a crucial role in regulating the progression of colorectal cancer (CRC), but its distribution remains to be explored. Here, we aim to investigate the genes edited by AS which show differential expression in patients with mismatch repair deficiency (dMMR)/microsatellite instability (MSI). Materials and Methods We applied long-read nanopore sequencing to determine the mRNA profiles and screen AS genes using Oxford Nanopore Technologies (ONT) method in ten paired CRC tissues. CRC tissue and plasma samples were used to validate the differential genes with AS using real-time fluorescent quantitative PCR, immunohistochemistry, and enzyme-linked immunosorbent assay. Results ONT sequencing identified 404 genes were downregulated, and 348 genes were upregulated in MSI cancer tissues compared with microsatellite stability (MSS) cancer tissues. In total, 6,200 AS events were identified in 2,728 mRNA transcripts. WGCNA revealed dMMR/MSI-correlated gene modules, including INHBA and RPL22L1, which were upregulated; conversely, HMGCS2 was downregulated in MSI cancer. Overexpression of RPL22L1, INHBA, and CAPZA1 was further confirmed in CRC tissues. INHBA was found to be associated with tumor lymphatic metastasis. Importantly, the levels of INHBA in CRC plasma were significantly increased compared with those in noncancer plasma. INHBA showed a higher level in dMMR/MSI CRC than in MSS CRC, indicating that INHBA is a useful biomarker. Conclusion Our results showed that ONT-identified genes provide a pool to explore AS-associated markers for dMMR/MSI CRC. We demonstrated INHBA as a promising signature for clinical application in predicting tumor lymphatic metastasis and screening dMMR/MSI candidates.
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Nargund AM, Xu C, Mandoli A, Okabe A, Chen GB, Huang KK, Sheng T, Yao X, Teo JMN, Sundar R, Kok YJ, See YX, Xing M, Li Z, Yong CH, Anand A, A I ZF, Poon LF, Ng MSW, Koh JYP, Ooi WF, Tay ST, Ong X, Tan ALK, Grabsch HI, Fullwood MJ, Teh TB, Bi X, Kaneda A, Li S, Tan P. Chromatin Rewiring by Mismatch Repair Protein MSH2 Alters Cell Adhesion Pathways and Sensitivity to BET Inhibition in Gastric Cancer. Cancer Res 2022; 82:2538-2551. [PMID: 35583999 DOI: 10.1158/0008-5472.can-21-2072] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 04/04/2022] [Accepted: 05/09/2022] [Indexed: 12/24/2022]
Abstract
Mutations in the DNA mismatch repair gene MSH2 are causative of microsatellite instability (MSI) in multiple cancers. Here, we discovered that besides its well-established role in DNA repair, MSH2 exerts a novel epigenomic function in gastric cancer. Unbiased CRISPR-based mass spectrometry combined with genome-wide CRISPR functional screening revealed that in early-stage gastric cancer MSH2 genomic binding is not randomly distributed but rather is associated specifically with tumor-associated super-enhancers controlling the expression of cell adhesion genes. At these loci, MSH2 genomic binding was required for chromatin rewiring, de novo enhancer-promoter interactions, maintenance of histone acetylation levels, and regulation of cell adhesion pathway expression. The chromatin function of MSH2 was independent of its DNA repair catalytic activity but required MSH6, another DNA repair gene, and recruitment to gene loci by the SWI/SNF chromatin remodeler SMARCA4/BRG1. Loss of MSH2 in advanced gastric cancers was accompanied by deficient cell adhesion pathway expression, epithelial-mesenchymal transition, and enhanced tumorigenesis in vitro and in vivo. However, MSH2-deficient gastric cancers also displayed addiction to BAZ1B, a bromodomain-containing family member, and consequent synthetic lethality to bromodomain and extraterminal motif (BET) inhibition. Our results reveal a role for MSH2 in gastric cancer epigenomic regulation and identify BET inhibition as a potential therapy in MSH2-deficient gastric malignancies. SIGNIFICANCE DNA repair protein MSH2 binds and regulates cell adhesion genes by enabling enhancer-promoter interactions, and loss of MSH2 causes deficient cell adhesion and bromodomain and extraterminal motif inhibitor synthetic lethality in gastric cancer.
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Affiliation(s)
- Amrita M Nargund
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Chang Xu
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Amit Mandoli
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Atsushi Okabe
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Gao Bin Chen
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Kie Kyon Huang
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Taotao Sheng
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore.,Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Xiaosai Yao
- Institute of Molecular and Cell Biology, Singapore, Singapore
| | | | - Raghav Sundar
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore.,Department of Hematology-Oncology, National University Health System, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yee Jiun Kok
- Bioprocessing Technology Institute, Singapore, Singapore
| | - Yi Xiang See
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Manjie Xing
- Epigenetic and Epitranscriptomic Regulation, Genome Institute of Singapore, Singapore, Singapore
| | - Zhimei Li
- Division of Medical Science, Laboratory of Cancer Epigenome, National Cancer Center, Singapore, Singapore
| | - Chern Han Yong
- Division of Medical Science, Laboratory of Cancer Epigenome, National Cancer Center, Singapore, Singapore
| | - Aparna Anand
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | | | - Lai Fong Poon
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | | | - Javier Yu Peng Koh
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Wen Fong Ooi
- Epigenetic and Epitranscriptomic Regulation, Genome Institute of Singapore, Singapore, Singapore
| | - Su Ting Tay
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Xuewen Ong
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Angie Lay Keng Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Heike I Grabsch
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands.,Division of Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Melissa J Fullwood
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Tean Bin Teh
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore.,Division of Medical Science, Laboratory of Cancer Epigenome, National Cancer Center, Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre, Singapore, Singapore
| | - Xuezhi Bi
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore.,Bioprocessing Technology Institute, Singapore, Singapore
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Shang Li
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Patrick Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore.,Epigenetic and Epitranscriptomic Regulation, Genome Institute of Singapore, Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre, Singapore, Singapore
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Dai Z, Peng X, Guo Y, Shen X, Ding W, Fu J, Liang Z, Song J. Metabolic pathway-based molecular subtyping of colon cancer reveals clinical immunotherapy potential and prognosis. J Cancer Res Clin Oncol 2022; 149:2393-2416. [PMID: 35731273 DOI: 10.1007/s00432-022-04070-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 05/11/2022] [Indexed: 11/28/2022]
Abstract
PURPOSE Colon cancer presents challenges to clinical diagnosis and management due to its high heterogeneity. For more efficient and convenient diagnosis and treatment of colon cancer, we are committed to characterizing the molecular features of colon cancer by pioneering a classification system based on metabolic pathways. METHODS Based on the 113 metabolic pathways and genes collected in the previous stage, we scored and filtered the metabolic pathways of each sample in the training set by ssGSEA, and obtained 16 metabolic pathways related to colon cancer recurrence. In consistent clustering of training set samples with recurrence-related metabolic pathway scores, we identified two robust molecular subtypes of colon cancer (MC1 and MC2). Furthermore, we performed multi-angle analysis on the survival differences of subtypes, metabolic characteristics, clinical characteristics, functional enrichment, immune infiltration, differences with other subtypes, stemness indices, TIDE prediction, and drug sensitivity, and finally constructed colon cancer prognostic model. RESULTS The results showed that the MC1 subtype had a poor prognosis based on higher immune activity and immune checkpoint gene expression. The MC2 subtype is associated with high metabolic activity and low expression of immune checkpoint genes and a better prognosis. The MC2 subtype was more responsive to PD-L1 immunotherapy than the MC1 subclass. However, we did not observe significant differences in tumor mutational burden between the two. CONCLUSION Two molecular subtypes of colon cancer based on metabolic pathways have distinct immune signatures. Constructing prognostic models based on subtype differential genes provides valuable reference for personalized therapy targeting unique tumor metabolic signatures.
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Affiliation(s)
- Zhujiang Dai
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China.,Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China
| | - Xiang Peng
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China.,Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China
| | - Yuegui Guo
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China.,Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China
| | - Xia Shen
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China.,Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China
| | - Wenjun Ding
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China.,Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China
| | - Jihong Fu
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China.,Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China
| | - Zhonglin Liang
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China. .,Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China.
| | - Jinglue Song
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China. .,Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China.
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Sun J, Ye L, Shi Y, Wang X, Zhao X, Ren S, Fan J, Shao H, Qin B. MiR-6511b-5p suppresses metastasis of pMMR colorectal cancer through methylation of CD44 by directly targeting BRG1. Clin Transl Oncol 2022; 24:1940-1953. [PMID: 35590122 PMCID: PMC9418090 DOI: 10.1007/s12094-022-02845-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 04/19/2022] [Indexed: 11/27/2022]
Abstract
PURPOSE Distal metastases are a major cause of poor prognosis in colorectal cancer patients. Approximately 95% of metastatic colorectal cancers are defined as DNA mismatch repair proficient (pMMR). Our previous study found that miR-6511b-5p was downregulated in pMMR colorectal cancer. However, the mechanism of miR-6511b-5p in pMMR colorectal cancer metastases remain unclear. METHODS We first used quantitative real-time PCR to evaluate the role of miR-6511b-5p in colorectal cancer. Second, we conducted invasion assays and wound healing assays to investigate the role of miR-6511b-5p and CD44 in colorectal cancer cells metastases. Third, luciferase reporter assay, in situ hybridization (ISH), and immunohistochemistry assays were performed to study the relationship between miR-6511b-5p and BRG1. Finally, real-time quantitative PCR, immunohistochemistry, and chromatin immunoprecipitation (ChIP) assays were performed to analyze the relationship between BRG1 and CD44 in colorectal cancer. RESULTS We found that lower expression of miR-6511b-5p appeared more often in pMMR colorectal cancer patients compared with dMMR (mismatch repair deficient) cases, and was positively correlated with metastases. In vitro, overexpression of miR-6511b-5p inhibited metastasis by decreasing CD44 expression via directly targeting BRG1 in colorectal cancer. Furthermore, BRG1 knockdown decreased the expression of CD44 by promoting CD44 methylation in colorectal cancer cells. CONCLUSION Our data suggest that miR-6511b-5p may act as a promising biomarker and treatment target for pMMR colorectal cancer, particularly in metastatic patients. Mechanistically, miR-6511b-5p suppresses invasion and migration of colorectal cancer cells through methylation of CD44 via directly targeting BRG1.
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Affiliation(s)
- JinMing Sun
- Department of Critical Care Medicine, Henan Key Laboratory for Critical Care Medicine, Zhengzhou Key Laboratory for Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou, 450003, Henan, China
- Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Ling Ye
- Department of Critical Care Medicine, Henan Key Laboratory for Critical Care Medicine, Zhengzhou Key Laboratory for Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou, 450003, Henan, China
- Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Yuan Shi
- Department of Critical Care Medicine, Henan Key Laboratory for Critical Care Medicine, Zhengzhou Key Laboratory for Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou, 450003, Henan, China
- Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, 450003, Henan, China
| | - XingWei Wang
- Department of Critical Care Medicine, Henan Key Laboratory for Critical Care Medicine, Zhengzhou Key Laboratory for Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou, 450003, Henan, China
- Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, 450003, Henan, China
| | - XiaFei Zhao
- Department of Critical Care Medicine, Henan Key Laboratory for Critical Care Medicine, Zhengzhou Key Laboratory for Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou, 450003, Henan, China
- Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, 450003, Henan, China
| | - ShengYong Ren
- Department of Critical Care Medicine, Henan Key Laboratory for Critical Care Medicine, Zhengzhou Key Laboratory for Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou, 450003, Henan, China
- Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, 450003, Henan, China
| | - JunWei Fan
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - HuanZhang Shao
- Department of Critical Care Medicine, Henan Key Laboratory for Critical Care Medicine, Zhengzhou Key Laboratory for Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou, 450003, Henan, China.
- Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, 450003, Henan, China.
| | - BingYu Qin
- Department of Critical Care Medicine, Henan Key Laboratory for Critical Care Medicine, Zhengzhou Key Laboratory for Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou, 450003, Henan, China.
- Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, 450003, Henan, China.
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Vijayasimha K, Leestemaker-Palmer AL, Gibbs JS, Yewdell JW, Dolan BP. MLN4924 Inhibits Defective Ribosomal Product Antigen Presentation Independently of Direct NEDDylation of Protein Antigens. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:2273-2282. [PMID: 35428693 PMCID: PMC9288214 DOI: 10.4049/jimmunol.2100584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 03/01/2022] [Indexed: 05/17/2023]
Abstract
Successful direct MHC class I Ag presentation is dependent on the protein degradation machinery of the cell to generate antigenic peptides that can be loaded onto MHC class I molecules for surveillance by CD8+ T cells of the immune system. Most often this process involves the ubiquitin (Ub)-proteasome system; however, other Ub-like proteins have also been implicated in protein degradation and direct Ag presentation. In this article, we examine the role of neuronal precursor cell-expressed developmentally downregulated protein 8 (NEDD8) in direct Ag presentation in mouse cells. NEDD8 is the Ub-like protein with highest similarity to Ub, and fusion of NEDD8 to the N terminus of a target protein can lead to the degradation of target proteins. We find that appending NEDD8 to the N terminus of the model Ag OVA resulted in degradation by both the proteasome and the autophagy protein degradation pathways, but only proteasomal degradation, involving the proteasomal subunit NEDD8 ultimate buster 1, resulted in peptide presentation. When directly compared with Ub, NEDD8 fusion was less efficient at generating peptides. However, inactivation of the NEDD8-conugation machinery by treating cells with MLN4924 inhibited the presentation of peptides from the defective ribosomal product-derived form of a model Ag. These results demonstrate that NEDD8 activity in the cell is important for direct Ag presentation, but not by directly targeting proteins for degradation.
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Affiliation(s)
- Kartikeya Vijayasimha
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR; and
| | - Amy L Leestemaker-Palmer
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR; and
| | - James S Gibbs
- Laboratory of Viral Diseases, National Institutes of Allergy and Infectious Diseases, Bethesda, MD
| | - Jonathan W Yewdell
- Laboratory of Viral Diseases, National Institutes of Allergy and Infectious Diseases, Bethesda, MD
| | - Brian P Dolan
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR; and
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Zhu J, Chu F, Zhang M, Sun W, Zhou F. Association Between Neddylation and Immune Response. Front Cell Dev Biol 2022; 10:890121. [PMID: 35602593 PMCID: PMC9117624 DOI: 10.3389/fcell.2022.890121] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 03/30/2022] [Indexed: 11/13/2022] Open
Abstract
Neddylation is a ubiquitin-like post-translational protein modification. It occurs via the activation of the neural precursor cell expressed, developmentally downregulated protein 8 (NEDD8) by three enzymes: activating enzyme, conjugating enzyme, and ligase. NEDD8 was first isolated from the mouse brain in 1992 and was initially considered important for the development and differentiation of the central nervous system. Previously, the downregulation of neddylation was associated with some human diseases, such as neurodegenerative disorders and cancers. In recent years, neddylation has also been proven to be pivotal in various processes of the human immune system, including the regulation of inflammation, bacterial infection, viral infection, and T cell function. Additionally, NEDD8 was found to act on proteins that can affect viral transcription, leading to impaired infectivity. Here, we focused on the influence of neddylation on the innate and adaptive immune responses.
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