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Zhang F, Chen XL, Wang HF, Guo T, Yao J, Jiang ZS, Pei Q. The prognostic significance of ubiquitination-related genes in multiple myeloma by bioinformatics analysis. BMC Med Genomics 2024; 17:164. [PMID: 38898455 PMCID: PMC11186196 DOI: 10.1186/s12920-024-01937-0] [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: 10/11/2023] [Accepted: 06/14/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND Immunoregulatory drugs regulate the ubiquitin-proteasome system, which is the main treatment for multiple myeloma (MM) at present. In this study, bioinformatics analysis was used to construct the risk model and evaluate the prognostic value of ubiquitination-related genes in MM. METHODS AND RESULTS The data on ubiquitination-related genes and MM samples were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. The consistent cluster analysis and ESTIMATE algorithm were used to create distinct clusters. The MM prognostic risk model was constructed through single-factor and multiple-factor analysis. The ROC curve was plotted to compare the survival difference between high- and low-risk groups. The nomogram was used to validate the predictive capability of the risk model. A total of 87 ubiquitination-related genes were obtained, with 47 genes showing high expression in the MM group. According to the consistent cluster analysis, 4 clusters were determined. The immune infiltration, survival, and prognosis differed significantly among the 4 clusters. The tumor purity was higher in clusters 1 and 3 than in clusters 2 and 4, while the immune score and stromal score were lower in clusters 1 and 3. The proportion of B cells memory, plasma cells, and T cells CD4 naïve was the lowest in cluster 4. The model genes KLHL24, HERC6, USP3, TNIP1, and CISH were highly expressed in the high-risk group. AICAr and BMS.754,807 exhibited higher drug sensitivity in the low-risk group, whereas Bleomycin showed higher drug sensitivity in the high-risk group. The nomogram of the risk model demonstrated good efficacy in predicting the survival of MM patients using TCGA and GEO datasets. CONCLUSIONS The risk model constructed by ubiquitination-related genes can be effectively used to predict the prognosis of MM patients. KLHL24, HERC6, USP3, TNIP1, and CISH genes in MM warrant further investigation as therapeutic targets and to combat drug resistance.
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Affiliation(s)
- Feng Zhang
- Department of Hematology, Kunming First People's Hospital, Kunming, 650051, China.
| | - Xiao-Lei Chen
- Department of Endocrinology, Kunming First People's Hospital, Kunming, 650051, China
| | - Hong-Fang Wang
- Department of Hematology, Kunming First People's Hospital, Kunming, 650051, China
| | - Tao Guo
- Department of Hematology, Kunming First People's Hospital, Kunming, 650051, China
| | - Jin Yao
- Multidisciplinary Diagnosis and Treatment Center for Oncology, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650101, China
| | - Zong-Sheng Jiang
- Department of Hematology, Kunming First People's Hospital, Kunming, 650051, China
| | - Qiang Pei
- Department of Hematology, The First People's Hospital of Yunnan Province, Kunming, 650032, China
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Wang Y, Wang Y, Patel H, Chen J, Wang J, Chen ZS, Wang H. Epigenetic modification of m 6A regulator proteins in cancer. Mol Cancer 2023; 22:102. [PMID: 37391814 PMCID: PMC10311752 DOI: 10.1186/s12943-023-01810-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/19/2023] [Indexed: 07/02/2023] Open
Abstract
Divergent N6-methyladenosine (m6A) modifications are dynamic and reversible posttranscriptional RNA modifications that are mediated by m6A regulators or m6A RNA methylation regulators, i.e., methyltransferases ("writers"), demethylases ("erasers"), and m6A-binding proteins ("readers"). Aberrant m6A modifications are associated with cancer occurrence, development, progression, and prognosis. Numerous studies have established that aberrant m6A regulators function as either tumor suppressors or oncogenes in multiple tumor types. However, the functions and mechanisms of m6A regulators in cancer remain largely elusive and should be explored. Emerging studies suggest that m6A regulators can be modulated by epigenetic modifications, namely, ubiquitination, SUMOylation, acetylation, methylation, phosphorylation, O-GlcNAcylation, ISGylation, and lactylation or via noncoding RNA action, in cancer. This review summarizes the current roles of m6A regulators in cancer. The roles and mechanisms for epigenetic modification of m6A regulators in cancer genesis are segregated. The review will improve the understanding of the epigenetic regulatory mechanisms of m6A regulators.
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Affiliation(s)
- Yumin Wang
- Department of Respiratory and Critical Care Medicine, Aerospace Center Hospital, Peking University Aerospace School of Clinical Medicine, Beijing, 100049, China
| | - Yan Wang
- Hunan Provincial Key Laboratory of Hepatobiliary Disease Research, Division of Hepato-Biliary-Pancreatic Surgery, Department of Surgery, The Second Xiangya Hospital of Central South University, Changsha, 410008, China
| | - Harsh Patel
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, 11439, USA
| | - Jichao Chen
- Department of Respiratory and Critical Care Medicine, Aerospace Center Hospital, Peking University Aerospace School of Clinical Medicine, Beijing, 100049, China
| | - Jinhua Wang
- Beijing Key Laboratory of Drug Target and Screening Research, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, 11439, USA.
| | - Hongquan Wang
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China.
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Guo X, Chen S, Wang X, Liu X. Immune-related pulmonary toxicities of checkpoint inhibitors in non-small cell lung cancer: Diagnosis, mechanism, and treatment strategies. Front Immunol 2023; 14:1138483. [PMID: 37081866 PMCID: PMC10110908 DOI: 10.3389/fimmu.2023.1138483] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/23/2023] [Indexed: 04/22/2023] Open
Abstract
Immune checkpoint inhibitors (ICI) therapy based on programmed cell death-1 (PD-1) and programmed cell death ligand 1 (PD-L1) has changed the treatment paradigm of advanced non-small cell lung cancer (NSCLC) and improved the survival expectancy of patients. However, it also leads to immune-related adverse events (iRAEs), which result in multiple organ damage. Among them, the most common one with the highest mortality in NSCLC patients treated with ICI is checkpoint inhibitor pneumonitis (CIP). The respiratory signs of CIP are highly coincident and overlap with those in primary lung cancer, which causes difficulties in detecting, diagnosing, managing, and treating. In clinical management, patients with serious CIP should receive immunosuppressive treatment and even discontinue immunotherapy, which impairs the clinical benefits of ICIs and potentially results in tumor recrudesce. Therefore, accurate diagnosis, detailedly dissecting the pathogenesis, and developing reasonable treatment strategies for CIP are essential to prolong patient survival and expand the application of ICI. Herein, we first summarized the diagnosis strategies of CIP in NSCLC, including the classical radiology examination and the rising serological test, pathology test, and artificial intelligence aids. Then, we dissected the potential pathogenic mechanisms of CIP, including disordered T cell subsets, the increase of autoantibodies, cross-antigens reactivity, and the potential role of other immune cells. Moreover, we explored therapeutic approaches beyond first-line steroid therapy and future direction based on targeted signaling pathways. Finally, we discussed the current impediments, future trends, and challenges in fighting ICI-related pneumonitis.
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Poggi A. 10th Anniversary of Cells: Advances in Cellular Immunology-Regulation of Autoimmune Response and Antitumor Reactivity: Are They Two Side of the Same Coin? Cells 2022; 11:cells11244122. [PMID: 36552886 PMCID: PMC9776996 DOI: 10.3390/cells11244122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
The innate and adaptive arms of the immune system are involved in maintaining organism homeostasis [...].
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Affiliation(s)
- Alessandro Poggi
- Molecular Oncology and Angiogensesis Unit, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
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Boudin L, De Nonneville A, Finetti P, Guittard G, Nunes JA, Birnbaum D, Mamessier E, Bertucci F. CISH Expression Is Associated with Metastasis-Free Interval in Triple-Negative Breast Cancer and Refines the Prognostic Value of PDL1 Expression. Cancers (Basel) 2022; 14:3356. [PMID: 35884417 PMCID: PMC9316839 DOI: 10.3390/cancers14143356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/01/2022] [Accepted: 07/08/2022] [Indexed: 11/16/2022] Open
Abstract
Strategies are being explored to increase the efficiency of immune checkpoint inhibitors (ICIs) targeting PD1/PDL1 in triple-negative breast cancer (TNBC), including combination with therapies inhibiting intracellular immune checkpoints such as CISH (Cytokine-induced SH2 protein). Correlation between CISH expression and TNBC features is unknown. We retrospectively analyzed CISH expression in 1936 clinical TNBC samples and searched for correlations with clinical variables, including metastasis-free interval (MFI). Among TNBCs, 44% were identified as "CISH-up" and 56% "CISH-down". High expression was associated with pathological axillary lymph node involvement, more adjuvant chemotherapy, and Lehmann's immunomodulatory and luminal AR subtypes. The "CISH-up" class showed longer 5-year MFI (72%) than the "CISH-down" class (60%; p = 2.8 × 10-2). CISH upregulation was associated with activation of IFNα and IFNγ pathways, antitumor cytotoxic immune response, and signatures predictive for ICI response. When CISH and PDL1 were upregulated together, the 5-year MFI was 81% versus 52% when not upregulated (p = 6.21 × 10-6). The two-gene model provided more prognostic information than each gene alone and maintained its prognostic value in multivariate analysis. CISH expression is associated with longer MFI in TNBC and refines the prognostic value of PDL1 expression. Such observation might reinforce the therapeutic relevance of combining CISH inhibition with an anti-PD1/PDL1 ICI.
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Affiliation(s)
- Laurys Boudin
- Laboratory of Predictive Oncology, Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes, Aix-Marseille Université, Inserm UMR1068, CNRS UMR725, 13009 Marseille, France; (L.B.); (A.D.N.); (P.F.); (D.B.); (E.M.)
- Department of Medical Oncology, Hôpital d’Instruction des Armées Sainte-Anne, 83000 Toulon, France
| | - Alexandre De Nonneville
- Laboratory of Predictive Oncology, Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes, Aix-Marseille Université, Inserm UMR1068, CNRS UMR725, 13009 Marseille, France; (L.B.); (A.D.N.); (P.F.); (D.B.); (E.M.)
- Department of Medical Oncology, Institut Paoli-Calmettes, 13009 Marseille, France
| | - Pascal Finetti
- Laboratory of Predictive Oncology, Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes, Aix-Marseille Université, Inserm UMR1068, CNRS UMR725, 13009 Marseille, France; (L.B.); (A.D.N.); (P.F.); (D.B.); (E.M.)
| | - Geoffrey Guittard
- Immunity and Cancer Team, Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes, Aix-Marseille Université, Inserm UMR1068, CNRS UMR725, 13009 Marseille, France; (G.G.); (J.A.N.)
| | - Jacques A. Nunes
- Immunity and Cancer Team, Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes, Aix-Marseille Université, Inserm UMR1068, CNRS UMR725, 13009 Marseille, France; (G.G.); (J.A.N.)
| | - Daniel Birnbaum
- Laboratory of Predictive Oncology, Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes, Aix-Marseille Université, Inserm UMR1068, CNRS UMR725, 13009 Marseille, France; (L.B.); (A.D.N.); (P.F.); (D.B.); (E.M.)
| | - Emilie Mamessier
- Laboratory of Predictive Oncology, Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes, Aix-Marseille Université, Inserm UMR1068, CNRS UMR725, 13009 Marseille, France; (L.B.); (A.D.N.); (P.F.); (D.B.); (E.M.)
| | - François Bertucci
- Laboratory of Predictive Oncology, Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes, Aix-Marseille Université, Inserm UMR1068, CNRS UMR725, 13009 Marseille, France; (L.B.); (A.D.N.); (P.F.); (D.B.); (E.M.)
- Department of Medical Oncology, Institut Paoli-Calmettes, 13009 Marseille, France
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Huang C, Zhu Y, Xu Q, Chen S, Huang Y, Zhao G, Ni X, Liu B, Zhao W, Yin X. YTHDF2 promotes intrahepatic cholangiocarcinoma progression and desensitises cisplatin treatment by increasing CDKN1B mRNA degradation. Clin Transl Med 2022; 12:e848. [PMID: 35696608 PMCID: PMC9191870 DOI: 10.1002/ctm2.848] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 04/08/2022] [Accepted: 04/14/2022] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Intrahepatic cholangiocarcinoma (ICC) is an aggressive cancer with exceedingly poor prognosis, and chemoresistance is a huge challenge for treatment. N6-methyladenosine (m6 A) modification plays an important role in the progression and chemoresistance of cancers. We aimed to investigate the oncogenic function and therapeutic significance of the m6 A binding protein, YTH domain family 2 (YTHDF2), in ICC progression and cisplatin-based chemotherapy. METHODS Several independent data sets were used to assess the expression of YTHDF2 in ICC, particularly in chemoresistant ICC. Knockdown and overexpression were used to evaluate the effects of YTHDF2 on tumourigenesis and cisplatin response in ICC. Multi-omics sequencing was performed to identify target genes. RIP, dual luciferase reporter, RNA stability experiment and loss-of-function assays were conducted to study the mechanisms underlying the oncogenic function of YTHDF2. Furthermore, patient-derived xenograft (PDX) model was established to determine the effect of combination treatment of YTHDF2 siRNA and cisplatin in ICC. RESULTS Our study showed that YTHDF2 was upregulated in ICC tissues, particularly in chemoresistant ICC tissues, and correlated with poor prognosis. Furthermore, silencing YTHDF2 led to inhibited proliferation, promoted apoptosis and G0/G1 cell cycle arrest. Its downregulation also enhanced DNA damage and sensitised ICC cells to cisplatin. YTHDF2 overexpression exerted the opposite results. Integration analysis using RNA-seq, MeRIP-seq and anti-YTHDF2 RIP-seq elucidated the role of YTHDF2 in tumourigenesis and cisplatin-desensitising function by promoting the degradation of cyclin-dependent kinase inhibitor 1B (CDKN1B) mRNA in an m6 A-dependent manner. Downregulation of CDKN1B increased the YTHDF2 silencing-induced influence on tumourigenesis and cisplatin response to ICC. In addition, the combination treatment of YTHDF2 siRNA and cisplatin significantly enhanced the anti-tumour effect of cisplatin in a chemoresistant ICC PDX model. CONCLUSIONS YTHDF2 exhibits tumour oncogenic and cisplatin-desensitising properties, which may offer insight into the development of novel combination therapeutic strategies for ICC.
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Affiliation(s)
- Chen‐Song Huang
- Department of Pancreato‐Biliary SurgeryThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina
| | - Ying‐Qin Zhu
- Department of Pancreato‐Biliary SurgeryThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina
| | - Qiong‐Cong Xu
- Department of Pancreato‐Biliary SurgeryThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina
| | - Siyun Chen
- Key Laboratory of Stem Cells and Tissue EngineeringMinistry of EducationSun Yat‐sen UniversityGuangzhouChina
| | - Yue Huang
- Department of BiotherapySun Yat‐sen University Cancer CenterGuangzhouChina
| | - Guangyin Zhao
- Department of Animal Experiment CenterThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina
| | - Xuhao Ni
- Department of Pancreato‐Biliary SurgeryThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina
| | - Bo Liu
- Key Laboratory of Stem Cells and Tissue EngineeringMinistry of EducationSun Yat‐sen UniversityGuangzhouChina
| | - Wei Zhao
- Key Laboratory of Stem Cells and Tissue EngineeringMinistry of EducationSun Yat‐sen UniversityGuangzhouChina
| | - Xiao‐Yu Yin
- Department of Pancreato‐Biliary SurgeryThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina
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7
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Singh DD, Sharma A, Lee HJ, Yadav DK. SARS-CoV-2: Recent Variants and Clinical Efficacy of Antibody-Based Therapy. Front Cell Infect Microbiol 2022; 12:839170. [PMID: 35237535 PMCID: PMC8883582 DOI: 10.3389/fcimb.2022.839170] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 01/20/2022] [Indexed: 12/29/2022] Open
Abstract
Multiple variants of SARS-CoV-2 have emerged and are now prevalent at the global level. Currently designated variants of concern (VOCs) are B.1.1.7, B1.351, P.1, B.1.617.2 variants and B.1.1.529. Possible options for VOC are urgently required as they carry mutations in the virus spike protein that allow them to spread more easily and cause more serious illness. The primary targets for most therapeutic methods against SARS-CoV-2 are the S (Spike) protein and RBD (Receptor-Binding Domain), which alter the binding to ACE2 (Angiotensin-Converting Enzyme 2). The most popular of these strategies involves the use of drug development targeting the RBD and the NTD (N-terminal domain) of the spike protein and multiple epitopes of the S protein. Various types of mutations have been observed in the RBDs of B.1.1.7, B1.351, P. and B.1.620. The incidence of RBD mutations increases the binding affinity to the ACE2 receptor. The high binding affinity of RBD and ACE2 has provided a structural basis for future evaluation of antibodies and drug development. Here we discuss the variants of SARS-CoV-2 and recent updates on the clinical evaluation of antibody-based treatment options. Presently, most of the antibody-based treatments have been effective in patients with SARS-CoV-2. However, there are still significant challenges in verifying independence, and the need for further clinical evaluation.
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Affiliation(s)
- Desh Deepak Singh
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Anshul Sharma
- Department of Food and Nutrition, College of Bionanotechnology, Gachon University, Gyeonggi-do, South Korea
| | - Hae-Jeung Lee
- Department of Food and Nutrition, College of Bionanotechnology, Gachon University, Gyeonggi-do, South Korea
- Institute for Aging and Clinical Nutrition Research, Gachon University, Gyeonggi-do, South Korea
- Gachon Advanced Institute for Health Sciences and Technology, Gachon University, Incheon, South Korea
- *Correspondence: Hae-Jeung Lee, ; Dharmendra K. Yadav,
| | - Dharmendra K. Yadav
- Department of Pharmacy, Gachon Institute of Pharmaceutical Science, College of Pharmacy, Gachon University, Incheon, South Korea
- *Correspondence: Hae-Jeung Lee, ; Dharmendra K. Yadav,
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