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Wang X, Zheng Q, Sun M, Liu L, Zhang H, Ying W. Signatures of necroptosis-related genes as diagnostic markers of endometriosis and their correlation with immune infiltration. BMC Womens Health 2023; 23:535. [PMID: 37817158 PMCID: PMC10566087 DOI: 10.1186/s12905-023-02668-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 09/21/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND Endometriosis (EMS) occurs when normal uterine tissue grows outside the uterus and causes chronic pelvic pain and infertility. Endometriosis-associated infertility is thought to be caused by unknown mechanisms. In this study, using necroptosis-related genes, we developed and validated multigene joint signatures to diagnose EMS and explored their biological roles. METHODS We downloaded two databases (GSE7305 and GSE1169) from the Gene Expression Omnibus (GEO) database and 630 necroptosis-related genes from the GeneCards and GSEA databases. The limma package in Rsoftware was used to identify differentially expressed genes (DEGs). We interleaved common differentially expressed genes (co-DEGs) and necroptosis-related genes (NRDEGs) in the endometriosis dataset. The DEGs functions were reflected by gene ontology analysis (GO), pathway enrichment analysis, and gene set enrichment analysis (GSEA). We used CIBERSORT to analyze the immune microenvironment differences between EMS patients and controls. Furthermore, a correlation was found between necroptosis-related differentially expressed genes and infiltrating immune cells to better understand the molecular immune mechanism. RESULTS Compared with the control group, this study revealed that 10 NRDEGs were identified in EMS. There were two types of immune cell infiltration abundance (activated NK cells and M2 macrophages) in these two datasets, and the correlation between different groups of samples was statistically significant (P < 0.05). MYO6 consistently correlated with activated NK cells in the two datasets. HOOK1 consistently demonstrated a high correlation with M2 Macrophages in two datasets. The immunohistochemical result indicated that the protein levels of MYO6 and HOOK1 were increased in patients with endometriosis, further suggesting that MYO6 and HOOK1 can be used as potential biomarkers for endometriosis. CONCLUSIONS We identified ten necroptosis-related genes in EMS and assessed their relationship with the immune microenvironment. MYO6 and HOOK1 may serve as novel biomarkers and treatment targets in the future.
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Affiliation(s)
- Xuezhen Wang
- Department of Gynecology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, 317000, China
| | - Qin Zheng
- Department of Gynecology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, 317000, China
| | - Man Sun
- School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Luotong Liu
- School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Huan Zhang
- School of Life Sciences, Jilin University, Changchun, 130012, China.
| | - Weiwei Ying
- Department of Gynecology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, 317000, China.
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Yin L, Li W, Chen X, Wang R, Zhang T, Meng J, Li Z, Xu L, Yin R, Cheng B, Yang H. HOOK1 Inhibits the Progression of Renal Cell Carcinoma via TGF-β and TNFSF13B/VEGF-A Axis. Adv Sci (Weinh) 2023; 10:e2206955. [PMID: 37085921 PMCID: PMC10265082 DOI: 10.1002/advs.202206955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 03/14/2023] [Indexed: 05/03/2023]
Abstract
Accumulating evidence shows HOOK1 disordered in human malignancies. However, the clinicopathological and biological significance of HOOK1 in renal cell carcinoma (RCC) remains rarely studied. In this study, the authors demonstrate that HOOK1 is downregulated in RCC samples with predicted poorer clinical prognosis. Mechanistically, HOOK1 inhibits tumor growth and metastasis via canonical TGF-β/ALK5/p-Smad3 and non-canonical TGF-β/MEK/ERK/c-Myc pathway. At the same time, HOOK1 inhibits RCC angiogenesis and sunitinib resistance by promoting degradation of TNFSF13B through the ubiquitin-proteasome pathway. In addition, HOOK1 is transcriptionally regulated by nuclear factor E2F3 in VHL dependent manner. Notably, an agonist of HOOK1, meletin, is screened and it shows antitumor activity more effectively when combined with sunitinib or nivolumab than it is used alone. The findings reveal a pivotal role of HOOK1 in anti-cancer treatment, and identify a novel therapeutic strategy for renal cell carcinoma.
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Affiliation(s)
- Lei Yin
- Department of UrologyPutuo People's HospitalTongji UniversityShanghai200060P. R. China
- Department of UrologyRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
| | - Wenjia Li
- Department of Cardiovascular MedicineRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
| | - Xuxiao Chen
- Department of General SurgeryHepatobiliary SurgeryShanghai Institute of Digestive SurgeryRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
| | - Ronghao Wang
- Department of Biochemistry and Molecular BiologySchool of Basic Medical SciencesSouthwest Medical UniversityLuzhou646000P. R. China
| | - Tao Zhang
- Department of UrologyPutuo People's HospitalTongji UniversityShanghai200060P. R. China
| | - Jialin Meng
- Department of UrologyThe First Affiliated Hospital of Anhui Medical UniversityAnhui Province Key Laboratory of Genitourinary DiseasesAnhui Medical UniversityHefei230032P. R. China
| | - Zhao Li
- Department of AnesthesiologyXiangya Hospital Central South UniversityChangsha410008P. R. China
| | - Li Xu
- Department of AnesthesiologyThe First People's Hospital of ChangdeChangde415000P. R. China
| | - Rui Yin
- Center for Reproductive MedicineShandong UniversityJinan250012P. R. China
| | - Bo Cheng
- Department of UrologyThe Affiliated Hospital of Southwest Medical UniversityLuzhou646000P. R. China
| | - Huan Yang
- Department of UrologyTongji HospitalTongji Medical College of Huazhong University of Science and TechnologyWuhan430030P. R. China
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Zhu Y, Liu N, Guo W, Pu X, Guo H, Gan W, Li D. ALK rearrangement in TFE3-positive renal cell carcinoma: Alternative diagnostic option to exclude Xp11.2 translocation carcinoma. Pathol Res Pract 2020; 216:153286. [PMID: 33197836 DOI: 10.1016/j.prp.2020.153286] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 12/18/2022]
Abstract
Anaplastic lymphoma kinase (ALK)-rearranged renal cell carcinoma (RCC) is a rare subtype of RCC with gene fusion involving ALK at 2p23. It was first included in the renal tumor classification system by WorldHealth organization (WHO) as a distinct emerging/provisional renal entity in 2016. To date, only a few cases of ALK-RCC have been reported. Here, we report an exceptional case of ALK-RCC in a 15-year-old girl and review the literature. The patient presented with gross hematuria and a tumor measured 7 cm × 6 cm was found in the left kidney by imaging examination. Then a laparoscopic radical nephrectomy combined with local lymph node dissection was performed. The pathologic stage of the tumor was pT1bN1Mx and postoperative pathology showed that the tumor corresponded to WHO/ISUP grade 3-4. Immunohistochemistry (IHC) demonstrated moderate nuclear expression of TFE3 protein. Interestingly, ALK gene rearrangement rather than TFE3 gene rearrangement was observed by fluorescence in situ hybridization (FISH). Now the girl is still alive without evidence of recurrence for 10 months follow-up. In conclusion, the positive expression of nuclear TFE3 in immunohistochemistry may be deceptive, the detection of ALK could be a diagnostic option if TFE3 was negative in FISH study. Large-scale and long-term studies are still needed to explore the biological behavior and molecular characteristic of ALK-RCC.
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Affiliation(s)
- Yiqi Zhu
- Department of Urology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Ning Liu
- Department of Urology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Wei Guo
- Department of Urology, Drum Tower Clinical Medical School of Nanjing Medical University, Nanjing, Jiangsu, China; Department of Urology, Jiangsu Taizhou People's Hospital, Taizhou, Jiangsu, China
| | - Xiaohong Pu
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Hongqian Guo
- Department of Urology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Weidong Gan
- Department of Urology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China.
| | - Dongmei Li
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu, China.
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Chen H, Zhu Y, Zhu Z, Zhi E, Lu K, Wang X, Liu F, Li Z, Xia W. Detection of heterozygous mutation in hook microtubule-tethering protein 1 in three patients with decapitated and decaudated spermatozoa syndrome. J Med Genet 2018; 55:150-157. [PMID: 29330334 DOI: 10.1136/jmedgenet-2016-104404] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 07/30/2017] [Accepted: 07/31/2017] [Indexed: 11/04/2022]
Abstract
BACKGROUND The mechanism of intramanchette transport is crucial to the transformation of sperm tail and the nuclear condensation during spermiogenesis. Although few dysfunctional proteins could result in abnormal junction between the head and tail of spermatozoon, little is known about the genetic cues in this process. OBJECTIVE Based on patients with severe decapitated and decaudated spermatozoa (DDS) syndrome, the study aimed to validate whether new mutation exists on their Hook microtubule-tethering protein 1 (HOOK1) genes and follow their results of assisted reproduction treatment (ART). METHODS 7 severe teratozoospermia patients with DDS (proportion >95%) and three relative members in one pedigree were collected to sequence the whole genomic DNA. The fertilisation rates (FRs) of these patients were followed. Morphological observation and interspecies intracytoplasmic sperm injection (ICSI) assays were applied. RESULTS A novel missense mutation of A to G (p.Q286R) in patients with DDS (n=3/7) was found in the HOOK1 gene, which was inherited from the mother in one patient. This variant was absent in 160 fertile population-matched control individuals. Morphological observation showed that almost all the DDS broke into decaudated heads and headless tails at the implantation fossa or the basal plate. The clinical studies indicated that the mutation might cause reduced FRs on both ART (FR=18.07%) and interspecies ICSI (FR=16.98%). CONCLUSIONS An unreported mutation in HOOK1 gene was identified, which might be responsible to some patients with DDS. Further studies need to uncover the molecular mechanism of spermiogenesis for genomic therapy.
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Affiliation(s)
- Huixing Chen
- School of Biomedical Engineering, Shanghai Jiao Tong University, Med-X Research Institute, Shanghai, China.,Department of Andrology, Urologic Medical Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yong Zhu
- Shanghai Human Sperm Bank, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zijue Zhu
- Department of Andrology, Urologic Medical Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Erlei Zhi
- Department of Andrology, Urologic Medical Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Keming Lu
- Shanghai Human Sperm Bank, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaobo Wang
- Shanghai Human Sperm Bank, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Feng Liu
- School of Biomedical Engineering, Shanghai Jiao Tong University, Med-X Research Institute, Shanghai, China.,Department of Andrology, Urologic Medical Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Human Sperm Bank, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zheng Li
- School of Biomedical Engineering, Shanghai Jiao Tong University, Med-X Research Institute, Shanghai, China.,Department of Andrology, Urologic Medical Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Human Sperm Bank, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Weiliang Xia
- School of Biomedical Engineering, Shanghai Jiao Tong University, Med-X Research Institute, Shanghai, China
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Labonne JDJ, Shen Y, Kong IK, Diamond MP, Layman LC, Kim HG. Comparative deletion mapping at 1p31.3-p32.2 implies NFIA responsible for intellectual disability coupled with macrocephaly and the presence of several other genes for syndromic intellectual disability. Mol Cytogenet 2016; 9:24. [PMID: 26997977 PMCID: PMC4797196 DOI: 10.1186/s13039-016-0234-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Accepted: 03/09/2016] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND While chromosome 1 is the largest chromosome in the human genome, less than two dozen cases of interstitial microdeletions in the short arm have been documented. More than half of the 1p microdeletion cases were reported in the pre-microarray era and as a result, the proximal and distal boundaries containing the exact number of genes involved in the microdeletions have not been clearly defined. RESULTS We revisited a previous case of a 10-year old female patient with a 1p32.1p32.3 microdeletion displaying syndromic intellectual disability. We performed microarray analysis as well as qPCR to define the proximal and distal deletion breakpoints and revised the karyotype from 1p32.1p32.3 to 1p31.3p32.2. The deleted chromosomal region contains at least 35 genes including NFIA. Comparative deletion mapping shows that this region can be dissected into five chromosomal segments containing at least six candidate genes (DAB1, HOOK1, NFIA, DOCK7, DNAJC6, and PDE4B) most likely responsible for syndromic intellectual disability, which was corroborated by their reduced transcript levels in RT-qPCR. Importantly, one patient with an intragenic microdeletion within NFIA and an additional patient with a balanced translocation disrupting NFIA display intellectual disability coupled with macrocephaly. CONCLUSION We propose NFIA is responsible for intellectual disability coupled with macrocephaly, and microdeletions at 1p31.3p32.2 constitute a contiguous gene syndrome with several genes contributing to syndromic intellectual disability.
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Affiliation(s)
- Jonathan D. J. Labonne
- />Department of Obstetrics & Gynecology, Augusta University, 1120 15th Street, Augusta, GA 30912 USA
- />Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA 30912 USA
| | - Yiping Shen
- />Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114 USA
| | - Il-Keun Kong
- />Department of Animal Science, Division of Applied Life Science (BK21plus), Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, Gyeongsangnam-do Korea
| | - Michael P. Diamond
- />Department of Obstetrics & Gynecology, Augusta University, 1120 15th Street, Augusta, GA 30912 USA
| | - Lawrence C. Layman
- />Department of Obstetrics & Gynecology, Augusta University, 1120 15th Street, Augusta, GA 30912 USA
- />Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA 30912 USA
- />Neuroscience Program, Medical College of Georgia, Augusta University, Augusta, GA 30912 USA
| | - Hyung-Goo Kim
- />Department of Obstetrics & Gynecology, Augusta University, 1120 15th Street, Augusta, GA 30912 USA
- />Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA 30912 USA
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Spinelli R, Pirola A, Redaelli S, Sharma N, Raman H, Valletta S, Magistroni V, Piazza R, Gambacorti-Passerini C. Identification of novel point mutations in splicing sites integrating whole-exome and RNA-seq data in myeloproliferative diseases. Mol Genet Genomic Med 2013; 1:246-59. [PMID: 24498620 PMCID: PMC3865592 DOI: 10.1002/mgg3.23] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 05/22/2013] [Accepted: 05/24/2013] [Indexed: 12/13/2022] Open
Abstract
Point mutations in intronic regions near mRNA splice junctions can affect the splicing process. To identify novel splicing variants from exome sequencing data, we developed a bioinformatics splice-site prediction procedure to analyze next-generation sequencing (NGS) data (SpliceFinder). SpliceFinder integrates two functional annotation tools for NGS, ANNOVAR and MutationTaster and two canonical splice site prediction programs for single mutation analysis, SSPNN and NetGene2. By SpliceFinder, we identified somatic mutations affecting RNA splicing in a colon cancer sample, in eight atypical chronic myeloid leukemia (aCML), and eight CML patients. A novel homozygous splicing mutation was found in APC (NM_000038.4:c.1312+5G>A) and six heterozygous in GNAQ (NM_002072.2:c.735+1C>T), ABCC3 (NM_003786.3:c.1783-1G>A), KLHDC1 (NM_172193.1:c.568-2A>G), HOOK1 (NM_015888.4:c.1662-1G>A), SMAD9 (NM_001127217.2:c.1004-1C>T), and DNAH9 (NM_001372.3:c.10242+5G>A). Integrating whole-exome and RNA sequencing in aCML and CML, we assessed the phenotypic effect of mutations on mRNA splicing for GNAQ, ABCC3, HOOK1. In ABCC3 and HOOK1, RNA-Seq showed the presence of aberrant transcripts with activation of a cryptic splice site or intron retention, validated by the reverse transcription-polymerase chain reaction (RT-PCR) in the case of HOOK1. In GNAQ, RNA-Seq showed 22% of wild-type transcript and 78% of mRNA skipping exon 5, resulting in a 4–6 frameshift fusion confirmed by RT-PCR. The pipeline can be useful to identify intronic variants affecting RNA sequence by complementing conventional exome analysis.
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Affiliation(s)
- Roberta Spinelli
- Department of Health Sciences, University of Milano-Bicocca, Monza, Italy
| | - Alessandra Pirola
- Department of Health Sciences, University of Milano-Bicocca Monza, Italy
| | - Sara Redaelli
- Department of Health Sciences, University of Milano-Bicocca Monza, Italy
| | - Nitesh Sharma
- Department of Health Sciences, University of Milano-Bicocca Monza, Italy
| | - Hima Raman
- Department of Health Sciences, University of Milano-Bicocca Monza, Italy
| | - Simona Valletta
- Department of Health Sciences, University of Milano-Bicocca Monza, Italy
| | - Vera Magistroni
- Department of Health Sciences, University of Milano-Bicocca Monza, Italy
| | - Rocco Piazza
- Department of Health Sciences, University of Milano-Bicocca Monza, Italy
| | - Carlo Gambacorti-Passerini
- Department of Health Sciences, University of Milano-Bicocca Monza, Italy ; Hematology and Clinical Research Unit, San Gerardo Hospital Monza, Italy
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