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Ananya RG, Pandi C, Kannan B, Pandi A, Prasad P, Jayaseelan VP, Arumugam P. DYNC1I1 acts as a promising prognostic biomarker and is correlated with immune infiltration in head and neck squamous cell carcinoma. JOURNAL OF STOMATOLOGY, ORAL AND MAXILLOFACIAL SURGERY 2024; 125:101734. [PMID: 38072235 DOI: 10.1016/j.jormas.2023.101734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 12/07/2023] [Indexed: 08/28/2024]
Abstract
BACKGROUND/PURPOSE Dynein Cytoplasmic 1 Intermediate Chain 1 (DYNC1I1) is a crucial cytoplasmic dynein binding component, its high expression levels are associated with malignant progression and poor survival in different types of cancer; however, the oncogenic role of DYNC1I1 in Head and neck squamous cell carcinomas (HNSCC) remains to be elucidated. In our present study, we aimed to explore the potential role of DYNC1I1 expression in the tumorigenesis of HNSCC and the shaping of the immune microenvironment. MATERIALS AND METHODS The expression levels of DYNC1I1 were analyzed in The Cancer Genome Atlas Head-Neck Squamous Cell Carcinoma (TCGA-HNSC) dataset, and then real-time quantitative polymerase chain reaction (RT-qPCR) was used to validate the DYNC1I1 expression in oral squamous cell carcinoma (OSCC) tumor samples, one of the major types of HNSCC. The functional pathway, tumor immune infiltration, and gene expression correlation for DYNC1I1 were performed using different bioinformatic tools. RESULTS We found that the expression of DYNC1I1 was significantly increased in HNSCC and was a predictor of poor survival. The DYNC1I1 high expression has also been associated with an increased risk of HPV-negative HNSCC and decreased immune cell infiltration. Functional enrichment analysis identified that DYNC1I1 is involved in several important signaling pathways that contribute to the cancer cell's survival and proliferation. CONCLUSION Our findings indicate that DYNC1I1 plays an important role in the tumorigenesis of HNSCC, and could be a promising prognostic biomarker for HNSCC diagnosis and treatment.
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Affiliation(s)
- Reddy G Ananya
- Saveetha Medical College, and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, India
| | - Chandra Pandi
- Molecular Biology Lab, Centre for Cellular and Molecular Research, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, India
| | - Balachander Kannan
- Molecular Biology Lab, Centre for Cellular and Molecular Research, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, India
| | - Anitha Pandi
- Clinical Genetics Lab, Centre for Cellular and Molecular Research, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, India
| | - Prathibha Prasad
- College of Dentistry, Ajman University, Ajman, the United Arab Emirates; Center of Medical and Bio-allied Health Sciences Research, Ajman University, Ajman, the United Arab Emirates
| | - Vijayashree Priyadharsini Jayaseelan
- Clinical Genetics Lab, Centre for Cellular and Molecular Research, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, India
| | - Paramasivam Arumugam
- Molecular Biology Lab, Centre for Cellular and Molecular Research, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, India.
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2
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Stachelek K, Harutyunyan N, Lee S, Beck A, Kim J, Xu L, Berry JL, Nagiel A, Reynolds CP, Murphree AL, Lee TC, Aparicio JG, Cobrinik D. Non-synonymous, synonymous, and non-coding nucleotide variants contribute to recurrently altered biological processes during retinoblastoma progression. Genes Chromosomes Cancer 2023; 62:275-289. [PMID: 36550020 PMCID: PMC10006380 DOI: 10.1002/gcc.23120] [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: 10/12/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Retinoblastomas form in response to biallelic RB1 mutations or MYCN amplification and progress to more aggressive and therapy-resistant phenotypes through accumulation of secondary genomic changes. Progression-related changes include recurrent somatic copy number alterations and typically non-recurrent nucleotide variants, including synonymous and non-coding variants, whose significance has been unclear. To determine if nucleotide variants recurrently affect specific biological processes, we identified altered genes and over-represented variant gene ontologies in 168 exome or whole-genome-sequenced retinoblastomas and 12 tumor-matched cell lines. In addition to RB1 mutations, MYCN amplification, and established retinoblastoma somatic copy number alterations, the analyses revealed enrichment of variant genes related to diverse biological processes including histone monoubiquitination, mRNA processing (P) body assembly, and mitotic sister chromatid segregation and cytokinesis. Importantly, non-coding and synonymous variants increased the enrichment significance of each over-represented biological process term. To assess the effects of such mutations, we examined the consequences of a 3' UTR variant of PCGF3 (a BCOR-binding component of Polycomb repressive complex I), dual 3' UTR variants of CDC14B (a regulator of sister chromatid segregation), and a synonymous variant of DYNC1H1 (a regulator of P-body assembly). One PCGF3 and one of two CDC14B 3' UTR variants impaired gene expression whereas a base-edited DYNC1H1 synonymous variant altered protease sensitivity and stability. Retinoblastoma cell lines retained only ~50% of variants detected in tumors and enriched for new variants affecting p53 signaling. These findings reveal potentially important differences in retinoblastoma cell lines and tumors and implicate synonymous and non-coding variants, along with non-synonymous variants, in retinoblastoma oncogenesis.
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Affiliation(s)
- Kevin Stachelek
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
- Cancer Biology and Genomics Program, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Narine Harutyunyan
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
| | - Susan Lee
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
| | - Assaf Beck
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
| | - Jonathan Kim
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
- Department of Ophthalmology and Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Liya Xu
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
- Department of Ophthalmology and Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Jesse L. Berry
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
- Department of Ophthalmology and Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Aaron Nagiel
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
- Department of Ophthalmology and Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - C. Patrick Reynolds
- Department of Pediatrics and Cancer Center, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, TX
| | - A. Linn Murphree
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
- Department of Ophthalmology and Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Thomas C. Lee
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
- Department of Ophthalmology and Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Jennifer G. Aparicio
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
| | - David Cobrinik
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
- Department of Ophthalmology and Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA
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3
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Liu W, Cheng M, Zhu Y, Chen Y, Yang Y, Chen H, Niu X, Tian X, Yang X, Zhang Y. DYNC1H1-related epilepsy: Genotype-phenotype correlation. Dev Med Child Neurol 2023; 65:534-543. [PMID: 36175372 DOI: 10.1111/dmcn.15414] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/19/2022] [Accepted: 08/24/2022] [Indexed: 11/03/2022]
Abstract
AIM To explore the phenotypic spectrum and refine the genotype-phenotype correlation of DYNC1H1-related epilepsy. METHOD The clinical data of 15 patients with epilepsy in our cohort and 50 patients with epilepsy from 24 published studies with the DYNC1H1 variants were evaluated. RESULTS In our cohort, 13 variants were identified from 15 patients (seven males, eight females). Twelve variants were de novo and seven were new. Age at seizure onset ranged from 3 months to 4 years 5 months (median age 1 year). Common seizure types were epileptic spasms, focal seizures, tonic seizures, and myoclonic seizures. Mild-to-severe developmental delay was present in all patients. Six patients were diagnosed with West syndrome and one was diagnosed with epileptic encephalopathy with continuous spikes and waves during slow sleep (CSWS). Collectively, in our cohort and published studies, 17% had ophthalmic diseases, 31% of variants were located in the stalk domain, and 92% patients with epilepsy had a malformation of cortical development (MCD). INTERPRETATION The phenotypes of DYNC1H1-related epilepsy included multiple seizure types; the most common epileptic syndrome was West syndrome. CSWS is a new phenotype of DYNC1H1-related epilepsy. One-third of the variants in patients with epilepsy were located in the stalk domain. Most patients had a MCD and developmental delay. WHAT THIS PAPER ADDS Nearly 40% of patients with DYNC1H1 variants had epilepsy. Ninety-two percent of patients with DYNC1H1-related epilepsy had malformation of cortical development. More than 10% of patients with DYNC1H1-related epilepsy were diagnosed with West syndrome. Continuous spikes and waves during slow sleep could be a new phenotype of DYNC1H1 variants. One-third of the variants in patients with epilepsy were located in the stalk domain.
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Affiliation(s)
- Wenwei Liu
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Miaomiao Cheng
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Ying Zhu
- Department of Radiology, Peking University First Hospital, Beijing, China
| | - Yi Chen
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Ying Yang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Hui Chen
- Department of Neurology, Chengdu Women and Children's Central Hospital, Chengdu, China
| | - Xueyang Niu
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Xiaojuan Tian
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Xiaoling Yang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yuehua Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
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4
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Identification of Cancer Driver Genes by Integrating Multiomics Data with Graph Neural Networks. Metabolites 2023; 13:metabo13030339. [PMID: 36984779 PMCID: PMC10052551 DOI: 10.3390/metabo13030339] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
Cancer is a heterogeneous disease that is driven by the accumulation of both genetic and nongenetic alterations, so integrating multiomics data and extracting effective information from them is expected to be an effective way to predict cancer driver genes. In this paper, we first generate comprehensive instructive features for each gene from genomic, epigenomic, transcriptomic levels together with protein–protein interaction (PPI)-networks-derived attributes and then propose a novel semisupervised deep graph learning framework GGraphSAGE to predict cancer driver genes according to the impact of the alterations on a biological system. When applied to eight tumor types, experimental results suggest that GGraphSAGE outperforms several state-of-the-art computational methods for driver genes identification. Moreover, it broadens our current understanding of cancer driver genes from multiomics level and identifies driver genes specific to the tumor type rather than pan-cancer. We expect GGraphSAGE to open new avenues in precision medicine and even further predict drivers for other complex diseases.
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5
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Bai J, Yang B, Shi R, Shao X, Yang Y, Wang F, Xiao J, Qu X, Liu Y, Zhang Y, Li Z. Could microtubule inhibitors be the best choice of therapy in gastric cancer with high immune activity: mutant DYNC1H1 as a biomarker. Aging (Albany NY) 2020; 12:25101-25119. [PMID: 33221769 PMCID: PMC7803585 DOI: 10.18632/aging.104084] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 08/27/2020] [Indexed: 12/24/2022]
Abstract
Immune checkpoint blockade (ICB) has achieved unprecedented breakthroughs in various cancers, including gastric cancer (GC) with high immune activity (MSI-H or TMB-H), yet clinical benefits from ICB were moderate. Here we aimed to identify the most appropriate drugs which can improve outcomes in GC. We firstly compared MSI-H and TMB-H GC samples with normal samples in TCGA-STAD cohort, respectively. After that, Connectivity Map database repurposed nine candidate drugs (CMap score < -90). Then, microtubule inhibitors (MTIs) were screened as the significant candidate drugs with their representative gene sets strongly enriched (p < 0.05) via GSEA. GDSC database validated higher activities of some MTIs in GC cells with MSI-H and TMB-H (p < 0.05). Furthermore, some MTIs activities were positively associated with mutant Dynein Cytoplasmic 1 Heavy Chain 1 (DYNC1H1) (p < 0.05) based on NCI-60 cancer cell line panel. DYNC1H1 was high frequently alteration in GC and was positively associated with TMB-H and MSI-H. Mutant DYNC1H1 may be accompanied with down-regulation of MTIs-related genes in GC or change the binding pocket to sensitize MTIs. Overall, this study suggested that some MTIs may be the best candidate drugs to treat GC with high immune activity, especially patients with DYNC1H1 mutated.
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Affiliation(s)
- Jin Bai
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang 110001, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang 110001, China.,Liaoning Province Clinical Research Center for Cancer, Shenyang 110001, China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang 110001, China
| | - BoWen Yang
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang 110001, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang 110001, China.,Liaoning Province Clinical Research Center for Cancer, Shenyang 110001, China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang 110001, China
| | - Ruichuan Shi
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang 110001, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang 110001, China.,Liaoning Province Clinical Research Center for Cancer, Shenyang 110001, China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang 110001, China
| | - Xinye Shao
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang 110001, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang 110001, China.,Liaoning Province Clinical Research Center for Cancer, Shenyang 110001, China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang 110001, China
| | - Yujing Yang
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang 110001, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang 110001, China.,Liaoning Province Clinical Research Center for Cancer, Shenyang 110001, China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang 110001, China
| | - Fang Wang
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang 110001, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang 110001, China.,Liaoning Province Clinical Research Center for Cancer, Shenyang 110001, China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang 110001, China
| | - Jiawen Xiao
- Department of Medical Oncology, Shenyang Fifth People Hospital, Tiexi District, Shenyang 110001, China
| | - Xiujuan Qu
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang 110001, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang 110001, China.,Liaoning Province Clinical Research Center for Cancer, Shenyang 110001, China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang 110001, China
| | - Yunpeng Liu
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang 110001, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang 110001, China.,Liaoning Province Clinical Research Center for Cancer, Shenyang 110001, China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang 110001, China
| | - Ye Zhang
- Laboratory I of Cancer Institute, The First Hospital of China Medical University, Shenyang 110001, China
| | - Zhi Li
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang 110001, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang 110001, China.,Liaoning Province Clinical Research Center for Cancer, Shenyang 110001, China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang 110001, China
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6
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Fang YL, Li N, Zhi XF, Zheng J, Liu Y, Pu LJ, Gu CY, Shu JB, Cai CQ. Discovery of specific mutations in spinal muscular atrophy patients by next-generation sequencing. Neurol Sci 2020; 42:1827-1833. [PMID: 32895776 DOI: 10.1007/s10072-020-04697-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 08/28/2020] [Indexed: 12/28/2022]
Abstract
Spinal muscular atrophy (SMA) is a type of autosomal recessive genetic disease, which seriously threatens the health and lives of children and adolescents. We attempted to find some genes and mutations related to the onset of SMA. Eighty-three whole-blood samples were collected from 28 core families, including 28 probands with clinically suspected SMA (20 SMA patients, 5 non-SMA children, and 3 patients with unknown etiology) and their parents. The multiplex ligation probe amplification (MLPA) was performed for preliminary diagnosis. The high-throughput sequencing technology was used to conduct the whole-exome sequencing analysis. We analyzed the mutations in adjacent genes of SMN1 gene and the unique mutations that only occurred in SMA patients. According to the MLPA results, 20 probands were regarded as experimental group and 5 non-SMA children as control group. A total of 10 mutations were identified in the adjacent genes of SMN1 gene. GUSBP1 g.[69515863G>A], GUSBP1 g.[69515870C>T], and SMA4 g.[69515738C>A] were the top three most frequent sites. SMA4 g.[69515726A>G] and OCLN c.[818G>T] have not been reported in the existing relevant researches. Seventeen point mutations in the DYNC1H1 gene were only recognized in SMA children, and the top two most common mutations were c.[2869-34A>T] and c.[345-89A>G]; c.[7473+105C>T] was the splicing mutation that might change the mRNA splicing site. The mutations of SMA4 g.[69515726A>G], OCLN c.[818G>T], DYNC1H1 c.[2869-34A>T], DYNC1H1 c.[345-89A>G], and DYNC1H1 c.[7473+105C>T] in the adjacent genes of SMN1 gene and other genes might be related to the onset of SMA.
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Affiliation(s)
- Yu-Lian Fang
- Institute of Pediatrics, Tianjin Children's Hospital, 238 Longyan Road, Beichen District, Tianjin, 300134, China
| | - Na Li
- Department of Neonatology, The Pediatric Clinical College, Tianjin Medical University, Tianjin, 300134, China.,Department of Neonatology, Tianjin Children's Hospital, Tianjin, 300134, China
| | - Xiu-Fang Zhi
- Graduate School, Tianjin Medical University, Tianjin, 300070, China
| | - Jie Zheng
- Graduate School, Tianjin Medical University, Tianjin, 300070, China
| | - Yang Liu
- Department of Neonatology, The Pediatric Clinical College, Tianjin Medical University, Tianjin, 300134, China.,Department of Neonatology, Tianjin Children's Hospital, Tianjin, 300134, China
| | - Lin-Jie Pu
- Graduate School, Tianjin Medical University, Tianjin, 300070, China
| | - Chun-Yu Gu
- Graduate School, Tianjin Medical University, Tianjin, 300070, China
| | - Jian-Bo Shu
- Institute of Pediatrics, Tianjin Children's Hospital, 238 Longyan Road, Beichen District, Tianjin, 300134, China. .,Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, 300134, China.
| | - Chun-Quan Cai
- Institute of Pediatrics, Tianjin Children's Hospital, 238 Longyan Road, Beichen District, Tianjin, 300134, China. .,Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, 300134, China. .,Department of Neurosurgery, Tianjin Children's Hospital, Tianjin, 300134, China.
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7
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Peng C, Zheng Y, Huang DS. Capsule Network Based Modeling of Multi-omics Data for Discovery of Breast Cancer-Related Genes. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020; 17:1605-1612. [PMID: 30969931 DOI: 10.1109/tcbb.2019.2909905] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Breast cancer is one of the most common cancers all over the world, which bring about more than 450,000 deaths each year. Although this malignancy has been extensively studied by a large number of researchers, its prognosis is still poor. Since therapeutic advance can be obtained based on gene signatures, there is an urgent need to discover genes related to breast cancer that may help uncover the mechanisms in cancer progression. We propose a deep learning method for the discovery of breast cancer-related genes by using Capsule Network based Modeling of Multi-omics Data (CapsNetMMD). In CapsNetMMD, we make use of known breast cancer-related genes to transform the issue of gene identification into the issue of supervised classification. The features of genes are generated through comprehensive integration of multi-omics data, e.g., mRNA expression, z scores for mRNA expression, DNA methylation, and two forms of DNA copy-number alterations (CNAs). By modeling features based on the capsule network, we identify breast cancer-related genes with a significantly better performance than other existing machine learning methods. The predicted genes with prognostic values play potential important roles in breast cancer and may serve as candidates for biologists and medical scientists in the future studies of biomarkers.
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8
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Peng N, Li J, He J, Shi X, Huang H, Mo Y, Ye H, Wu G, Wu F, Xiang B, Zhong J, Li L, Zhu S. c-Myc-mediated SNRPB upregulation functions as an oncogene in hepatocellular carcinoma. Cell Biol Int 2020; 44:1103-1111. [PMID: 31930637 DOI: 10.1002/cbin.11307] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 01/10/2020] [Indexed: 01/09/2023]
Abstract
Dysregulation of genes involved in alternative splicing contributes to hepatocarcinogenesis. SNRPB, a component of spliceosome, is implicated in human cancers, yet its clinical significance and biological function in hepatocellular carcinoma (HCC) remains unknown. Here, we show that SNRPB expression is increased in HCC tissues, compared with the nontumorous tissues, at both messenger RNA and protein levels in two independent cohorts. High expression of SNRPB is significantly associated with higher pathological grade, vascular invasion, serum alpha-fetoprotein level, tumor metastasis, and poor disease-free and overall survivals. Luciferase reporter and chromatin immunoprecipitation assays demonstrate that SNRPB upregulation in HCC is mediated by c-Myc. Positive correlation is found between SNRPB and c-Myc expression in clinical samples. In vitro studies show that ectopic expression of SNRPB promotes HCC cell proliferation and migration, whereas knockdown of SNRPB results in the opposite phenotypes. Collectively, our data suggest SNRPB function as an oncogene and serve as a potential prognostic factor in HCC.
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Affiliation(s)
- Ningfu Peng
- Department of Hepatobiliary Surgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Jindu Li
- Department of Hepatobiliary Surgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Jingrong He
- Department of Hepatobiliary Surgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Xianmao Shi
- Department of Hepatobiliary Surgery, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, 530022, China
| | - Hao Huang
- Department of Hepatobiliary Surgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Yishuai Mo
- Department of Hepatobiliary Surgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Hang Ye
- Department of Hepatobiliary Surgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Guobin Wu
- Department of Hepatobiliary Surgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Feixiang Wu
- Department of Hepatobiliary Surgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Bangde Xiang
- Department of Hepatobiliary Surgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Jianhong Zhong
- Department of Hepatobiliary Surgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Lequn Li
- Department of Hepatobiliary Surgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Shaoliang Zhu
- Department of Hepatobiliary Surgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, 530021, China
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9
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Gong LB, Wen T, Li Z, Xin X, Che XF, Wang J, Liu YP, Qu XJ. DYNC1I1 Promotes the Proliferation and Migration of Gastric Cancer by Up-Regulating IL-6 Expression. Front Oncol 2019; 9:491. [PMID: 31249807 PMCID: PMC6582752 DOI: 10.3389/fonc.2019.00491] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 05/24/2019] [Indexed: 12/30/2022] Open
Abstract
Gastric cancer is one of the top five malignant tumors worldwide. At present, the molecular mechanisms of gastric cancer progression are still not completely clear. Cytoplasmic dynein regulates intracellular transport and mitotic spindle localization, and its abnormal function is crucial for tumorigenesis, promotes tumor cell cycle progression, and tumor migration. DYNC1I1 is an important binding subunit of cytoplasmic dynein. However, studies on DYNC1I1 in tumors are currently limited. In the current study, we found that high DYNC1I1 expression in gastric cancer is associated with poor prognosis and is an independent prognostic factor. DYNC1I1 promoted the proliferation and migration of gastric cancer cells both in vitro and in vivo. DYNC1I1 also upregulated IL-6 expression by increasing NF-κB nuclear translocation. Collectively, these data revealed an important role for the DYNC1I1-driven IL-6/STAT pathway in gastric cancer proliferation and migration, suggesting that DYNC1I1 may be a potential therapeutic target for gastric cancer.
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Affiliation(s)
- Li-Bao Gong
- Department of Medical Oncology, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, the First Hospital of China Medical University, Shenyang, China
| | - Ti Wen
- Department of Medical Oncology, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, the First Hospital of China Medical University, Shenyang, China
| | - Zhi Li
- Department of Medical Oncology, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, the First Hospital of China Medical University, Shenyang, China
| | - Xing Xin
- Department of Medical Oncology, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, the First Hospital of China Medical University, Shenyang, China
| | - Xiao-Fang Che
- Department of Medical Oncology, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, the First Hospital of China Medical University, Shenyang, China
| | - Jin Wang
- Department of Medical Oncology, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, the First Hospital of China Medical University, Shenyang, China
| | - Yun-Peng Liu
- Department of Medical Oncology, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, the First Hospital of China Medical University, Shenyang, China
| | - Xiu-Juan Qu
- Department of Medical Oncology, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, the First Hospital of China Medical University, Shenyang, China
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Synonymous mutation adenomatous polyposis coliΔ486s affects exon splicing and may predispose patients to adenomatous polyposis coli/mutY DNA glycosylase mutation‑negative familial adenomatous polyposis. Mol Med Rep 2018; 18:4931-4939. [PMID: 30272267 PMCID: PMC6236305 DOI: 10.3892/mmr.2018.9495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 08/23/2018] [Indexed: 12/20/2022] Open
Abstract
Familial adenomatous polyposis (FAP) is an autosomal dominant-inherited colorectal cancer. Recent advances in genetics have indicated that the majority of patients with FAP carry germline mutations of the adenomatous polyposis coli (APC) and mutY DNA glycosylase (MUTYH) genes. However, a large subset of families with a history of FAP have undetectable pathogenic alterations, termed APC/MUTYH mutation-negative FAP. To investigate the germline mutations in the APC and MUTYH genes in Chinese patients with FAP, 13 unrelated patients were enrolled. Through genetic sequencing, four known pathogenic alterations (Lys1061LysfsTer2, Glu1309AspfsTer4, Arg283Ter and Ser1196Ter) of APC and two novel disease-associated pathogenic mutations (Tyr152Ter and Ter522Gly) in MUTYH were identified in six individuals. For samples that did not present with pathogenic alterations, the functional effects of missense, synonymous and intronic mutations were analyzed using bioinformatics tools and databases. Bioinformatics prediction suggested that the synonymous mutation Tyr486Tyr in APC (APC∆486s) was likely a disease-causing polymorphism and may have induced the exon skipping of APC. A hybrid mini-gene assay was performed, which confirmed that the synonymous single nucleotide polymorphism APC∆486s induced major splicing defects with skipping of exon 12 in APC. The data of the present study suggested that the synonymous polymorphism APC∆486s was a potential pathogenic alteration that predisposed APC/MUTYH mutation-negative patients to FAP.
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Elango T, Sun J, Zhu C, Zhou F, Zhang Y, Sun L, Yang S, Zhang X. Mutational analysis of epidermal and hyperproliferative type I keratins in mild and moderate psoriasis vulgaris patients: a possible role in the pathogenesis of psoriasis along with disease severity. Hum Genomics 2018; 12:27. [PMID: 29784039 PMCID: PMC5963134 DOI: 10.1186/s40246-018-0158-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 05/09/2018] [Indexed: 02/08/2023] Open
Abstract
Background Mutations in keratin proteins have been vastly associated with a wide array of genodermatoses; however, mutations of keratins in psoriasis have not been fully investigated. The main aim of the current research was to identify the mutation in K14, K10, K16, and K17 genes in two stages of psoriasis patients. Methods Ninety-six psoriatic skin biopsies were collected. mRNA transcript of K14, K10, K16, and K17 was prepared, amplified, and sequenced. Sanger sequences of all keratins were further validated for mutational analysis using Mutation Surveyor and Alamut Visual. Then, in silico analysis of protein stability and protein and gene expression of all keratins was performed and validated. Results Out of 44 mutations, about 75% of keratins are highly pathogenic and deleterious. Remaining 25% mutations are less pathogenic and tolerated in nature. In these 33 deleterious mutations were immensely found to decrease keratin protein stability. We also found a correlation between keratin and Psoriasis Area and Severity Index score which added that alteration in keratin gene in skin causes severity of psoriasis. Conclusions We strongly concluded that acanthosis and abnormal terminal differentiation was mainly due to the mutation in epidermal keratins. In turn, disease severity and relapsing of psoriasis are mainly due to the mutation of hyperproliferative keratins. These novel keratin mutations in psoriatic epidermis might be one of the causative factors for psoriasis. Electronic supplementary material The online version of this article (10.1186/s40246-018-0158-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tamilselvi Elango
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China. .,Anhui Medical University, 81 Meishan Road, Hefei, Anhui Province, China.
| | - Jingying Sun
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - Caihong Zhu
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - Fusheng Zhou
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - Yaohua Zhang
- Institute of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Liangdan Sun
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China.,Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, China
| | - Sen Yang
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China.,Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, China
| | - Xuejun Zhang
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China. .,Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China. .,Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, China. .,Institute of Dermatology, Huashan Hospital, Fudan University, Shanghai, China. .,Anhui Medical University, 81 Meishan Road, Hefei, Anhui Province, China.
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