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Wang HY, Diao Y, Tan PZ, Liang H. Four centrosome-related genes to predict the prognosis and drug sensitivity of patients with colon cancer. World J Gastrointest Oncol 2024; 16:1908-1924. [PMID: 38764831 PMCID: PMC11099447 DOI: 10.4251/wjgo.v16.i5.1908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/08/2024] [Accepted: 02/22/2024] [Indexed: 05/09/2024] Open
Abstract
BACKGROUND As the primary microtubule organizing center in animal cells, centrosome abnormalities are involved in human colon cancer. AIM To explore the role of centrosome-related genes (CRGs) in colon cancer. METHODS CRGs were collected from public databases. Consensus clustering analysis was performed to separate the Cancer Genome Atlas cohort. Univariate Cox and least absolute shrinkage selection operator regression analyses were performed to identify candidate prognostic CRGs and construct a centrosome-related signature (CRS) to score colon cancer patients. A nomogram was developed to evaluate the CRS risk in colon cancer patients. An integrated bioinformatics analysis was conducted to explore the correlation between the CRS and tumor immune microenvironment and response to immunotherapy, chemotherapy, and targeted therapy. Single-cell transcriptome analysis was conducted to examine the immune cell landscape of core prognostic genes. RESULTS A total of 726 CRGs were collected from public databases. A CRS was constructed, which consisted of the following four genes: TSC1, AXIN2, COPS7A, and MTUS1. Colon cancer patients with a high-risk signature had poor survival. Patients with a high-risk signature exhibited decreased levels of plasma cells and activated memory CD4+ T cells. Regarding treatment response, patients with a high-risk signature were resistant to immunotherapy, chemotherapy, and targeted therapy. COPS7A expression was relatively high in endothelial cells and fibroblasts. MTUS1 expression was high in endothelial cells, fibroblasts, and malignant cells. CONCLUSION We constructed a centrosome-related prognostic signature that can accurately predict the prognosis of colon cancer patients, contributing to the development of individualized treatment for colon cancer.
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Affiliation(s)
- Hui-Yan Wang
- Department of Clinical Laboratory, Harbin Medical University Cancer Hospital, Harbin 150086, Heilongjiang Province, China
| | - Yan Diao
- Department of Clinical Laboratory, Heilongjiang Province Hospital, Harbin 150000, Heilongjiang Province, China
| | - Pei-Zhu Tan
- Translational Medicine Center of Northern China, Harbin Medical University, Harbin 150081, Heilongjiang Province, China
| | - Huan Liang
- Department of Clinical Laboratory, Harbin Medical University Cancer Hospital, Harbin 150086, Heilongjiang Province, China
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Zhang F, Yin T, Tang X, Ma S, Meng Q, Song J, Wang Y, Men S, Wang L. Prenatal diagnosis of a case with complete and uniform tetrasomy 12p by the utility of noninvasive prenatal testing. J Assist Reprod Genet 2023; 40:2233-2240. [PMID: 37501006 PMCID: PMC10440312 DOI: 10.1007/s10815-023-02896-8] [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: 04/26/2023] [Accepted: 07/18/2023] [Indexed: 07/29/2023] Open
Abstract
PURPOSE To report a rare type of Pallister-Killian syndrome (PKS) diagnosed prenatally by the utility of non-invasive prenatal testing (NIPT). METHODS NIPT was performed in the first trimester. Conventional karyotyping and chromosomal microarray analysis (CMA) were performed on the amniotic samples in the second trimester. Copy number variation sequencing (CNV-seq) was used for the validation of fetal skin and the placental tissue after pregnancy termination. RESULTS NIPT results showed increased signal from chromosome 12p. Subsequent prenatal diagnostic testing by karyotype revealed 47, XY, +i (12p), and CMA displayed four copies of 12p: 12p13.33-12p11.1(173786_34835641) × 4. The CNV-seq results of the fetal skin and the fetal side of placenta showed four copies of 12p13.33-p11 and an estimated chimeric duplication of 34.08 Mb (chimerism ratio: 10%) in 12 p13.33-p11, respectively. However, no abnormality was detected by CNV-seq at the maternal side of placenta. CONCLUSIONS Our findings suggest that a positive signal from chromosome 12p on NIPT should raise suspicion for PKS. With the wide application of NIPT, the true positive of incidental finding is expected to increase.
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Affiliation(s)
- Fang Zhang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, 222000, People's Republic of China
| | - Ting Yin
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, 222000, People's Republic of China
| | - Xinxin Tang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, 222000, People's Republic of China
| | - Shanshan Ma
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, 222000, People's Republic of China
| | - Qian Meng
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, 222000, People's Republic of China
| | - Jiedong Song
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, 222000, People's Republic of China
| | - Yongan Wang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, 222000, People's Republic of China
| | - Shuai Men
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, 222000, People's Republic of China
| | - Leilei Wang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, 222000, People's Republic of China.
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Xu D, Fang H, Liu J, Chen Y, Gu Y, Sun G, Xia B. ChIP-seq assay revealed histone modification H3K9ac involved in heat shock response of the sea cucumber Apostichopus japonicus. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 820:153168. [PMID: 35051475 DOI: 10.1016/j.scitotenv.2022.153168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/23/2021] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Heat stress poses an increasing threat for the marine invertebrate Apostichopus japonicus. Histone lysine acetylation is a central chromatin modification for epigenetic regulation of gene expression during stress response. In this study, a genome-wide characterization for acetylated lysine 9 on histone H3 (H3K9ac) binding regions in normal temperature (18 °C) and heat-stress conditions (26 °C) via ChIP-seq were carried out. The results that revealed H3K9ac was an extensive epigenetic modulation in A. japonicus. The GO terms "regulation of transcription, DNA-templated" and "transcription coactivator activity" were significantly enriched in both groups. Particularly, various transcriptional factors (TFs) families showed notable modification of H3K9ac. Differentially acetylated regions (DARs) with H3K9ac modification under heat stress were identified with 24 hyperacetylated and 23 hypoacetylated peaks, respectively. We further examined the transcriptional expression for 13 genes with dysregulated H3K9ac level in the promoter regions by qRT-PCR. Combined H3K9ac ChIP-seq characteristics with the transcriptional expression, 5 up-up genes (ZCCHC3, RPA70, MTRR, β-Gal and PHTF2) and 2 down-down genes (PRPF39 and BSL78_10147) were identified. Surprisingly, the increasing mRNA expression of NECAP1 under heat stress was negatively related to the decreasing H3K9ac level in its promoter region. Our research is the first genome-wide characterization for the epigenetic modification H3K9ac in A. japonicus, and will help to advance the understanding of the roles of H3K9ac in transcriptional regulation under heat-stress condition.
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Affiliation(s)
- Dongxue Xu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Huahua Fang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Ji Liu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Yanru Chen
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Yuanxue Gu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Guohua Sun
- School of Agriculture, Ludong University, Yantai, Shandong 264025, China
| | - Bin Xia
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong 266109, China.
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He X, Xiao H, Yang R, Chen H, Wang B. lncRNA LOC339524 inhibits the proliferation of bladder cancer cells by targeting the miR-875-5p/COPS7A signaling axis. Exp Ther Med 2021; 22:1202. [PMID: 34584547 PMCID: PMC8422399 DOI: 10.3892/etm.2021.10636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 07/21/2021] [Indexed: 12/28/2022] Open
Abstract
It has been reported that long non-coding RNAs (lncRNAs) play a crucial role in the progression of various types of cancer. The role of numerous lncRNAs in a variety of cancer types has been investigated. However, the underlying mechanisms of the majority of lncRNAs in bladder cancer (BCa) remain to be elucidated. In the present study, abnormally expressed lncRNAs in BCa and para-carcinoma tissues were identified through screening the Cancer RNA-Seq Nexus database and were validated using reverse transcription-quantitative PCR. It was found that LOC339524 expression levels were markedly downregulated in BCa tissues and cells (J82, T24, UM-UC-3 and 5637). LOC339524 overexpression was revealed to suppress the proliferation of BCa cells. LOC339524 was also discovered to act as a sponge for microRNA (miR)-875-5p, as identified using dual luciferase reporter assays and biotin pull-down analysis. LOC339524 downregulated the expression of miR-875-5p and knockdown of miR-875-5p expression inhibited the proliferation of bladder cancer cells. In addition, COP9 signalosome subunit 7A (COPS7A) was identified to be the target gene of miR-875-5p and COPS7A expression level was upregulated following LOC339524 overexpression. lncRNA LOC339524 was proposed to function as a competitive endogenous RNA to facilitate the expression of COPS7A by binding to miR-875-5p. In conclusion, the findings of the present study suggested that LOC339524 may inhibit cell proliferation in BCa by targeting the miR-875-5p/COPS7A signaling axis.
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Affiliation(s)
- Xuan He
- Department of Oncology, Daping Hospital, Army Medical University, Chongqing 400042, P.R. China
| | - He Xiao
- Department of Oncology, Daping Hospital, Army Medical University, Chongqing 400042, P.R. China
| | - Rui Yang
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Hang Chen
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Bin Wang
- Department of Oncology, Daping Hospital, Army Medical University, Chongqing 400042, P.R. China
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A case of a parthenogenetic 46,XX/46,XY chimera presenting ambiguous genitalia. J Hum Genet 2020; 65:705-709. [PMID: 32277176 DOI: 10.1038/s10038-020-0748-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/12/2020] [Accepted: 03/12/2020] [Indexed: 11/08/2022]
Abstract
Sex-chromosome discordant chimerism (XX/XY chimerism) is a rare chromosomal disorder in humans. We report a boy with ambiguous genitalia and hypospadias, showing 46,XY[26]/46,XX[4] in peripheral blood cells. To clarify the mechanism of how this chimerism took place, we carried out whole-genome genotyping using a SNP array and microsatellite analysis. The B-allele frequency of the SNP array showed a mixture of three and five allele combinations, which excluded mosaicism but not chimerism, and suggested the fusion of two embryos or a shared parental haplotype between the two parental cells. All microsatellite markers showed a single maternal allele. From these results, we concluded that this XX/XY chimera is composed of two different paternal alleles and a single duplicated maternal genome. This XX/XY chimera likely arose from a diploid maternal cell that was formed via endoduplication of the maternal genome just before fertilization, being fertilized with both X and Y sperm.
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Gunnarsson R, Dilorenzo S, Lundin-Ström KB, Olsson L, Biloglav A, Lilljebjörn H, Rissler M, Wahlberg P, Lundmark A, Castor A, Behrendtz M, Fioretos T, Paulsson K, Isaksson A, Johansson B. Mutation, methylation, and gene expression profiles in dup(1q)-positive pediatric B-cell precursor acute lymphoblastic leukemia. Leukemia 2018; 32:2117-2125. [PMID: 29626196 PMCID: PMC6170391 DOI: 10.1038/s41375-018-0092-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/19/2018] [Accepted: 02/01/2018] [Indexed: 12/19/2022]
Abstract
High-throughput sequencing was applied to investigate the mutation/methylation patterns on 1q and gene expression profiles in pediatric B-cell precursor acute lymphoblastic leukemia (BCP ALL) with/without (w/wo) dup(1q). Sequencing of the breakpoint regions and all exons on 1q in seven dup(1q)-positive cases revealed non-synonymous somatic single nucleotide variants (SNVs) in BLZF1, FMN2, KCNT2, LCE1C, NES, and PARP1. Deep sequencing of these in a validation cohort w (n = 17)/wo (n = 94) dup(1q) revealed similar SNV frequencies in the two groups (47% vs. 35%; P = 0.42). Only 0.6% of the 36,259 CpGs on 1q were differentially methylated between cases w (n = 14)/wo (n = 13) dup(1q). RNA sequencing of high hyperdiploid (HeH) and t(1;19)(q23;p13)-positive cases w (n = 14)/wo (n = 52) dup(1q) identified 252 and 424 differentially expressed genes, respectively; only seven overlapped. Of the overexpressed genes in the HeH and t(1;19) groups, 23 and 31%, respectively, mapped to 1q; 60-80% of these encode nucleic acid/protein binding factors or proteins with catalytic activity. We conclude that the pathogenetically important consequence of dup(1q) in BCP ALL is a gene-dosage effect, with the deregulated genes differing between genetic subtypes, but involving similar molecular functions, biological processes, and protein classes.
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Affiliation(s)
- Rebeqa Gunnarsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.
| | - Sebastian Dilorenzo
- Array and Analysis Facility, Department of Medical Sciences, Uppsala University, Uppsala, Sweden.,National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Kristina B Lundin-Ström
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Linda Olsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Department of Clinical Genetics and Pathology, Division of Laboratory Medicine, Lund, Sweden
| | - Andrea Biloglav
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Henrik Lilljebjörn
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Marianne Rissler
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Per Wahlberg
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anders Lundmark
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anders Castor
- Department of Pediatrics, Skåne University Hospital, Lund, Sweden
| | - Mikael Behrendtz
- Department of Pediatrics, Linköping University Hospital, Linköping, Sweden
| | - Thoas Fioretos
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Department of Clinical Genetics and Pathology, Division of Laboratory Medicine, Lund, Sweden
| | - Kajsa Paulsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Anders Isaksson
- Array and Analysis Facility, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Bertil Johansson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Department of Clinical Genetics and Pathology, Division of Laboratory Medicine, Lund, Sweden
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