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Gangaram B, Lee V, Slavotinek A. Biallelic OTUD6B variants associated with a Kabuki syndrome-like disorder in three siblings: A clinical report and literature review. Am J Med Genet A 2024; 194:e63567. [PMID: 38389298 DOI: 10.1002/ajmg.a.63567] [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: 09/11/2023] [Revised: 01/19/2024] [Accepted: 02/01/2024] [Indexed: 02/24/2024]
Abstract
Biallelic variants in the OTUD6B gene have been reported in the literature in association with an intellectual developmental disorder featuring dysmorphic facies, seizures, and distal limb abnormalities. Physical differences described for affected individuals suggest that the disorder may be clinically recognizable, but previous publications have reported an initial clinical suspicion for Kabuki syndrome (KS) in some affected individuals. Here, we report on three siblings with biallelic variants in OTUD6B co-segregating with neurodevelopmental delay, shared physical differences, and other clinical findings similar to those of previously reported individuals. However, clinical manifestations such as long palpebral fissures, prominent and cupped ears, developmental delay, growth deficiency, persistent fetal fingertip pads, vertebral anomaly, and seizures in the proband were initially suggestive of KS. In addition, previously unreported clinical manifestations such as delayed eruption of primary dentition, soft doughy skin with reduced sweating, and mirror movements present in our patients suggest an expansion of the phenotype, and we perform a literature review to update on current information related to OTUD6B and human gene-disease association.
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Affiliation(s)
- Balram Gangaram
- Division of Medical Genetics, Department of Pediatrics, University of California, San Francisco, California, USA
| | - Virgina Lee
- Division of Child Neurology, University of California, San Francisco, California, USA
| | - Anne Slavotinek
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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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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Yang M, Wei Y, He X, Xia C. The deubiquitinating protein OTUD6B promotes lung adenocarcinoma progression by stabilizing RIPK1. Biol Direct 2024; 19:46. [PMID: 38880876 PMCID: PMC11181667 DOI: 10.1186/s13062-024-00489-8] [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: 04/19/2024] [Accepted: 06/12/2024] [Indexed: 06/18/2024] Open
Abstract
BACKGROUND There is growing evidence indicating that deubiquitinating enzymes may contribute to tumor progression and can serve as promising therapeutic targets. METHODS The overexpression of deubiquitinase OTUD6B in lung adenocarcinoma (LUAD) and its adjacent tissues was analyzed by immunohistochemistry and TCGA/GO database. Survival analysis further supported OTUD6B as a potential target for LUAD treatment. We assessed the effect of OTUD6B on LUAD cell growth using cell viability assays and conducted TUNEL staining, migration, and invasion experiments to investigate the impact of OTUD6B on the apoptosis and metastasis of LUAD cells. Additionally, we established a transplanted tumor model in nude mice to validate our findings in vivo. Finally, using IP mass spectrometry and co-IP experiments, we screened and confirmed the influence of RIPK1 as a substrate of OTUD6B in LUAD. RESULTS OTUD6B is highly overexpressed in human LUAD and predicts poor prognosis in LUAD patients. OTUD6B knockdown inhibited the proliferation of LUAD cells and enhanced apoptosis and inhibited metastasis in LUAD cells suppressed. A549 xenografts revealed that OTUD6B deletion can slow down tumour growth. Additionally, OTUD6B can bind to RIPK1, reduce its ubiquitination level and increase its protein stability. CONCLUSIONS Our results suggest that OTUD6B is a promising clinical target for LUAD treatment and that targeting OTUD6B may constitute an effective anti-LUAD strategy.
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Affiliation(s)
- Miaomiao Yang
- Department of Nephrology, Henan Provincial Key Laboratory of Kidney Disease and Immunology, Henan Provincial Clinical Research Center for Kidney Disease, Henan Provincial People's Hospital and People's Hospital of Zhengzhou University, 7 Weiwu Road, Zhengzhou, 450053, Henan, China.
| | - Yujie Wei
- National Engineering Laboratory for Internet Medical Systems and Applications, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No. 1 Jianshe Road, Erqi District, Zhengzhou, 450052, Henan, China
| | - Xin He
- Department of Clinical Laboratory, The Fifth Affiliated Hospital of Zhengzhou University, No.3 Kangfuqian Street, Erqi District, Zhengzhou, China
| | - Changwei Xia
- Heart Center of Henan Provincial People's Hospital, Central China Fuwai Hospital of Zhengzhou University, Fuwai Central China Cardiovascular Hospital and Central China Branch of National Center Fuwai Cardiovascular Diseases, Zhengzhou, China.
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Cosgrove BD, Bounds LR, Taylor CK, Su AL, Rizzo AJ, Barrera A, Crawford GE, Hoffman BD, Gersbach CA. Mechanosensitive genomic enhancers potentiate the cellular response to matrix stiffness. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.10.574997. [PMID: 38260455 PMCID: PMC10802421 DOI: 10.1101/2024.01.10.574997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Epigenetic control of cellular transcription and phenotype is influenced by changes in the cellular microenvironment, yet how mechanical cues from these microenvironments precisely influence epigenetic state to regulate transcription remains largely unmapped. Here, we combine genome-wide epigenome profiling, epigenome editing, and phenotypic and single-cell RNA-seq CRISPR screening to identify a new class of genomic enhancers that responds to the mechanical microenvironment. These 'mechanoenhancers' could be active on either soft or stiff extracellular matrix contexts, and regulated transcription to influence critical cell functions including apoptosis, mechanotransduction, proliferation, and migration. Epigenetic editing of mechanoenhancers on rigid materials tuned gene expression to levels observed on softer materials, thereby reprogramming the cellular response to the mechanical microenvironment. These editing approaches may enable the precise alteration of mechanically-driven disease states.
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Affiliation(s)
- Brian D. Cosgrove
- Department of Biomedical Engineering, Duke University; Durham, NC 27708, USA
- Center for Advanced Genomic Technologies, Duke University; Durham, NC 27708, USA
| | - Lexi R. Bounds
- Department of Biomedical Engineering, Duke University; Durham, NC 27708, USA
- Center for Advanced Genomic Technologies, Duke University; Durham, NC 27708, USA
| | - Carson Key Taylor
- Department of Biomedical Engineering, Duke University; Durham, NC 27708, USA
- Center for Advanced Genomic Technologies, Duke University; Durham, NC 27708, USA
| | - Alan L. Su
- Department of Biomedical Engineering, Duke University; Durham, NC 27708, USA
- Center for Advanced Genomic Technologies, Duke University; Durham, NC 27708, USA
| | - Anthony J. Rizzo
- Department of Biomedical Engineering, Duke University; Durham, NC 27708, USA
- Center for Advanced Genomic Technologies, Duke University; Durham, NC 27708, USA
| | - Alejandro Barrera
- Center for Advanced Genomic Technologies, Duke University; Durham, NC 27708, USA
- Department of Biostatistics and Bioinformatics, Duke University; Durham, NC 27708, USA
| | - Gregory E. Crawford
- Center for Advanced Genomic Technologies, Duke University; Durham, NC 27708, USA
- Department of Pediatrics, Duke University Medical Center; Durham, NC 27708, USA
| | - Brenton D. Hoffman
- Department of Biomedical Engineering, Duke University; Durham, NC 27708, USA
- Department of Cell Biology, Duke University; Durham, NC 27708, USA
| | - Charles A. Gersbach
- Department of Biomedical Engineering, Duke University; Durham, NC 27708, USA
- Center for Advanced Genomic Technologies, Duke University; Durham, NC 27708, USA
- Department of Cell Biology, Duke University; Durham, NC 27708, USA
- Department of Surgery, Duke University Medical Center; Durham, NC 27708, USA
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Ma B, Wei X, Zhou S, Yang M. MCTS1 enhances the proliferation of laryngeal squamous cell carcinoma via promoting OTUD6B-1 mediated LIN28B deubiquitination. Biochem Biophys Res Commun 2023; 678:128-134. [PMID: 37634410 DOI: 10.1016/j.bbrc.2023.08.036] [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: 08/07/2023] [Accepted: 08/16/2023] [Indexed: 08/29/2023]
Abstract
The aberrant upregulation of MCTS1 Re-Initiation and Release Factor (also known as Malignant T-cell-amplified sequence 1, MCTS1) can promote laryngeal squamous cell carcinoma (LSCC). It might act as a binding partner of multiple proteins. In this study, we further explored the expression of potential interaction between MCTS1 and OTU domain-containing protein 6B (OTUD6B) and its influence on the ubiquitination and degradation of OTUD6B's substrate in LSCC. LSCC cell lines AMC-HN-8 and TU177 were utilized for assessing protein-protein interaction, protein degradation and tumor growth in vitro and in vivo. The results showed that MCTS1 interacts with OUTD6B isoform 1 (OTUD6B-1) in the cell lines. Higher OTUD6B-1 expression is associated with significantly shorter progression-free interval in LSCC patients. OTUD6B positively modulated the expression of cyclin D1, cyclin E1 and c-Myc and LSCC cell proliferation in vitro and in vivo. MCTS1 negatively modulated the degradation of LIN28B in G1/S cells, via enhancing OTUD6B-mediated cleaving of K48-branched ubiquitin chains from LIN28B. OTUD6B or LIN28B shRNA weakened MCTS1 overexpression-induced cyclin D1 and c-Myc protein expression and LSCC cell proliferation. In summary, this study revealed that MCTS1 could enhance LSCC proliferation partially via the OTUD6B-LIN28B axis.
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Affiliation(s)
- Binjuan Ma
- Otorhinolaryngology-Head and Neck Surgery, Gansu Provincial Hospital, Lanzhou, China
| | - Xiaoquan Wei
- Otorhinolaryngology-Head and Neck Surgery, Gansu Provincial Hospital, Lanzhou, China
| | - Shijie Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Mengsheng Yang
- Otorhinolaryngology-Head and Neck Surgery, Gansu Provincial Hospital, Lanzhou, China.
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Vízkeleti L, Spisák S. Rewired Metabolism Caused by the Oncogenic Deregulation of MYC as an Attractive Therapeutic Target in Cancers. Cells 2023; 12:1745. [PMID: 37443779 PMCID: PMC10341379 DOI: 10.3390/cells12131745] [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: 04/10/2023] [Revised: 06/20/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
MYC is one of the most deregulated oncogenes on multiple levels in cancer. As a node transcription factor, MYC plays a diverse regulatory role in many cellular processes, including cell cycle and metabolism, both in physiological and pathological conditions. The relentless growth and proliferation of tumor cells lead to an insatiable demand for energy and nutrients, which requires the rewiring of cellular metabolism. As MYC can orchestrate all aspects of cellular metabolism, its altered regulation plays a central role in these processes, such as the Warburg effect, and is a well-established hallmark of cancer development. However, our current knowledge of MYC suggests that its spatial- and concentration-dependent contribution to tumorigenesis depends more on changes in the global or relative expression of target genes. As the direct targeting of MYC is proven to be challenging due to its relatively high toxicity, understanding its underlying regulatory mechanisms is essential for the development of tumor-selective targeted therapies. The aim of this review is to comprehensively summarize the diverse forms of MYC oncogenic deregulation, including DNA-, transcriptional- and post-translational level alterations, and their consequences for cellular metabolism. Furthermore, we also review the currently available and potentially attractive therapeutic options that exploit the vulnerability arising from the metabolic rearrangement of MYC-driven tumors.
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Affiliation(s)
- Laura Vízkeleti
- Department of Bioinformatics, Faculty of Medicine, Semmelweis University, 1094 Budapest, Hungary;
| | - Sándor Spisák
- Institute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, 1117 Budapest, Hungary
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