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Li X, Lei Y. Construction of a prognostic risk model for Stomach adenocarcinoma based on endoplasmic reticulum stress genes. Wien Klin Wochenschr 2024; 136:319-330. [PMID: 37993598 DOI: 10.1007/s00508-023-02306-0] [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: 02/06/2023] [Accepted: 10/21/2023] [Indexed: 11/24/2023]
Abstract
OBJECTIVE Stomach adenocarcinoma (STAD) is caused by malignant transformation of gastric glandular cells and is characterized by a high incidence rate and a poor prognosis. This study was designed to establish a prognostic risk model for STAD according to endoplasmic reticulum (ER) stress feature genes as cancer cells are susceptible to ER stress. METHODS The TCGA-STAD dataset was downloaded to screen differentially expressed genes (DEGs). By intersecting DEGs with ER stress genes retrieved from GeneCards, ER stress-related DEGs in STAD were obtained. Kmeans cluster analysis of STAD subtypes and Single sample gene set enrichment analysis (ssGSEA) analysis of immune infiltration were performed. Cox regression analysis was utilized to construct a risk prognostic model. Samples were split into high-risk and low-risk groups according to the median risk score. Survival analysis and Receiver Operating Characteristic (ROC) curves were conducted to assess the validity of the model. Gene set enrichment analysis (GSEA) was performed to investigate differential pathways in the two risk groups. Cox analysis was performed to verify the independence of the risk model, and a nomogram was generated. RESULTS A total of 162 ER stress-related DEGs in STAD were identified by bioinformatics analysis. Kmeans cluster analysis showed that STAD was divided into 3 subgroups. The ssGSEA showed that the levels of immune infiltration in subgroups 2 and 3 were significantly higher than subgroup 1. With 12 prognostic genes (MATN3, ATP2A1, NOX4, AQP11, HP, CAV1, STARD3, FKBP10, EGF, F2, SERPINE1, CNGA3) selected from ER stress-related DEGs using Cox regression analysis, we then constructed a prognostic model. Kaplan-Meier (K‑M) survival curves and ROC curves showed good prediction performance of the model. Significant enrichment of genes in the high-risk group was found in extracellular matrix (ECM) receptor interaction. Cox regression analysis combined with clinical factors showed that the risk model could be used as an independent prognostic factor. The prediction correction curve showed that the good prediction ability of the nomogram. CONCLUSION The STAD could be divided into three subgroups, and the 12-gene model constructed by ER stress signatures had a good prognostic performance for STAD patients.
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Affiliation(s)
- Xi Li
- Department of General Surgery, Zigong Fourth People's Hospital, No. 19 Tanmulin Street, Ziliujing District, 643000, Zigong City, Sichuan Province, China
| | - Yuehua Lei
- Department of General Surgery, Zigong Fourth People's Hospital, No. 19 Tanmulin Street, Ziliujing District, 643000, Zigong City, Sichuan Province, China.
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Li H, Wang L, Zhang C. A rare case of dysferlinopathy with paternal isodisomy for chromosome 2 determined by exome sequencing. Mol Genet Genomic Med 2022; 11:e2110. [PMID: 36464789 PMCID: PMC9938747 DOI: 10.1002/mgg3.2110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 11/09/2022] [Indexed: 12/10/2022] Open
Abstract
BACKGROUND Dysferlinopathies are autosomal recessive muscular dystrophies resulting from defects in DYSF (MIM: 603009), which is located on chromosome 2p13 and encodes the dysferlin protein. METHODS We performed exome sequencing and subsequent trio-based analysis in a family with dysferlinopathy. RESULTS We report a young patient presenting with hyperCKemia and mild muscle weakness of the lower limbs. Exome sequencing of the proband revealed a homozygous frameshift mutation, NM_001130987.2:c.1471dupA(p.M491Nfs*15), in DYSF. The father was heterozygous for the mutation and the mother did not carry the mutation, as determined by genetic analyses, exome sequencing of parental samples, and a trio-based analysis. Further analysis revealed that the DYSF gene was not deleted; instead, the entire chromosome 2 of the proband was inherited from the father. Thus, the child had paternal uniparental isodisomy for chromosome 2 (uniparental disomy [UPD]2 pat). CONCLUSION We report the first case of dysferlinopathy caused by paternal isodisomy for chromosome 2. Furthermore, our findings highlight the importance of exome sequencing of the proband and parents and trio analyses in clinical settings, particularly when Mendelian inheritance cannot be confirmed, to identify the presence of UPD and to rule out large pathogenic deletions.
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Affiliation(s)
- Huan Li
- Department of Neurology, National Key Clinical Department and Key Discipline of NeurologyThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina
| | - Liang Wang
- Department of Neurology, National Key Clinical Department and Key Discipline of NeurologyThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina
| | - Cheng Zhang
- Department of Neurology, National Key Clinical Department and Key Discipline of NeurologyThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina
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Tachibana N, Hosono K, Nomura S, Arai S, Torii K, Kurata K, Sato M, Shimakawa S, Azuma N, Ogata T, Wada Y, Okamoto N, Saitsu H, Nishina S, Hotta Y. Maternal Uniparental Isodisomy of Chromosome 4 and 8 in Patients with Retinal Dystrophy: SRD5A3-Congenital Disorders of Glycosylation and RP1-Related Retinitis Pigmentosa. Genes (Basel) 2022; 13:genes13020359. [PMID: 35205402 PMCID: PMC8872353 DOI: 10.3390/genes13020359] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 01/27/2023] Open
Abstract
Purpose: Uniparental disomy (UPD) is a rare chromosomal abnormality. We performed whole-exosome sequencing (WES) in cases of early-onset retinal dystrophy and identified two cases likely caused by UPD. Herein, we report these two cases and attempt to clarify the clinical picture of retinal dystrophies caused by UPD. Methods: WES analysis was performed for two patients and their parents, who were not consanguineous. Functional analysis was performed in cases suspected of congenital disorders of glycosylation (CDG). We obtained clinical case data and reviewed the literature. Results: In case 1, a novel c.57G>C, p.(Trp19Cys) variant in SRD5A3 was detected homozygously. Genetic analysis suggested a maternal UPD on chromosome 4, and functional analysis confirmed CDG. Clinical findings showed early-onset retinal dystrophy, intellectual disability, and epilepsy. In case 2, an Alu insertion (c.4052_4053ins328, p.[Tyr1352Alafs]) in RP1 was detected homozygously. Maternal UPD on chromosome 8 was suspected. The clinical picture was consistent with RP1-related retinitis pigmentosa. Although the clinical features of retinal dystrophy by UPD may vary, most cases present with childhood onset. Conclusions: There have been limited reports of retinal dystrophy caused by UPD, suggesting that it is rare. Genetic counseling may be encouraged in pediatric cases of retinal dystrophy.
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Affiliation(s)
- Nobutaka Tachibana
- Department of Ophthalmology, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan; (N.T.); (K.H.); (S.N.); (S.A.); (K.T.); (K.K.); (M.S.)
| | - Katsuhiro Hosono
- Department of Ophthalmology, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan; (N.T.); (K.H.); (S.N.); (S.A.); (K.T.); (K.K.); (M.S.)
| | - Shuhei Nomura
- Department of Ophthalmology, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan; (N.T.); (K.H.); (S.N.); (S.A.); (K.T.); (K.K.); (M.S.)
| | - Shinji Arai
- Department of Ophthalmology, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan; (N.T.); (K.H.); (S.N.); (S.A.); (K.T.); (K.K.); (M.S.)
| | - Kaoruko Torii
- Department of Ophthalmology, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan; (N.T.); (K.H.); (S.N.); (S.A.); (K.T.); (K.K.); (M.S.)
| | - Kentaro Kurata
- Department of Ophthalmology, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan; (N.T.); (K.H.); (S.N.); (S.A.); (K.T.); (K.K.); (M.S.)
| | - Miho Sato
- Department of Ophthalmology, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan; (N.T.); (K.H.); (S.N.); (S.A.); (K.T.); (K.K.); (M.S.)
| | - Shuichi Shimakawa
- Department of Pediatrics, Osaka Medical and Pharmaceutical University Hospital, Takatsuki 569-8686, Japan;
| | - Noriyuki Azuma
- National Center for Child Health and Development, Department of Ophthalmology and Laboratory for Visual Science, Tokyo 157-8535, Japan; (N.A.); (S.N.)
| | - Tsutomu Ogata
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan; (T.O.); (H.S.)
- Hamamatsu Medical Center, Department of Pediatrics, Hamamatsu 432-8580, Japan
| | - Yoshinao Wada
- Department of Molecular Medicine, Osaka Women’s and Children’s Hospital, Izumi 594-1101, Japan; (Y.W.); (N.O.)
| | - Nobuhiko Okamoto
- Department of Molecular Medicine, Osaka Women’s and Children’s Hospital, Izumi 594-1101, Japan; (Y.W.); (N.O.)
- Department of Medical Genetics, Osaka Women’s and Children’s Hospital, Izumi 594-1101, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan; (T.O.); (H.S.)
| | - Sachiko Nishina
- National Center for Child Health and Development, Department of Ophthalmology and Laboratory for Visual Science, Tokyo 157-8535, Japan; (N.A.); (S.N.)
| | - Yoshihiro Hotta
- Department of Ophthalmology, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan; (N.T.); (K.H.); (S.N.); (S.A.); (K.T.); (K.K.); (M.S.)
- Correspondence: ; Tel.: +81-53-435-2256
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