Centromere protein I (CENPI) is a candidate gene for X-linked steroid sensitive nephrotic syndrome

Basit, Sulman; Al-Edressi, Howaida; Sairafi, Mona H.; Hashmi, Jamil Amjad; Alharby, Essa; Safar, R; Ramzan, Khushnooda

doi:10.1007/s40620-019-00692-1

Cited by 9 publications

(7 citation statements)

References 45 publications

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“…This protein regulated the recruitment of kinetochore-associated proteins that were required to generate the spindle checkpoint signal. The product of this gene was involved in the response of gonadal tissues to follicle-stimulating hormone [ 28 ]. CENPK was a subunit of a CENPH-CENPI-associated centromeric complex that targeted CENPA to centromeres and was required for proper kinetochore function and mitotic progression [ 29 ].…”

Section: Resultsmentioning

confidence: 99%

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Identification of key genes unique to the luminal a and basal-like breast cancer subtypes via bioinformatic analysis

Jia

Liang

et al. 2020

World J Surg Onc

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Background Breast cancer subtypes are statistically associated with prognosis. The search for markers of breast tumor heterogeneity and the development of precision medicine for patients are the current focuses of the field. Methods We used a bioinformatic approach to identify key disease-causing genes unique to the luminal A and basal-like subtypes of breast cancer. First, we retrieved gene expression data for luminal A breast cancer, basal-like breast cancer, and normal breast tissue samples from The Cancer Genome Atlas database. The differentially expressed genes unique to the 2 breast cancer subtypes were identified and subjected to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses. We constructed protein–protein interaction networks of the differentially expressed genes. Finally, we analyzed the key modules of the networks, which we combined with survival data to identify the unique cancer genes associated with each breast cancer subtype. Results We identified 1114 differentially expressed genes in luminal A breast cancer and 1042 differentially expressed genes in basal-like breast cancer, of which the subtypes shared 500. We observed 614 and 542 differentially expressed genes unique to luminal A and basal-like breast cancer, respectively. Through enrichment analyses, protein–protein interaction network analysis, and module mining, we identified 8 key differentially expressed genes unique to each subtype. Analysis of the gene expression data in the context of the survival data revealed that high expression of NMUR1 and NCAM1 in luminal A breast cancer statistically correlated with poor prognosis, whereas the low expression levels of CDC7, KIF18A, STIL, and CKS2 in basal-like breast cancer statistically correlated with poor prognosis. Conclusions NMUR1 and NCAM1 are novel key disease-causing genes for luminal A breast cancer, and STIL is a novel key disease-causing gene for basal-like breast cancer. These genes are potential targets for clinical treatment.

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Section: Resultsmentioning

confidence: 99%

Section: Ppi Network Constructionmentioning

confidence: 99%

Identification of key genes unique to the luminal a and basal-like breast cancer subtypes via bioinformatic analysis

Jia

Liang

et al. 2020

World J Surg Onc

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“…This protein regulated the recruitment of kinetochoreassociated proteins that were required to generate the spindle checkpoint signal. The product of this gene was involved in the response of gonadal tissues to follicle-stimulating hormone [28]. CENPK was a subunit of a CENPH-CENPI-associated centromeric complex that targeted CENPA to centromeres and was required for proper kinetochore function and mitotic progression [29].The protein encoded by CCNE2 belongs to the highly conserved cyclin family, whose members were characterized by a dramatic periodicity in protein abundance through the cell cycle.…”

Section: Ppi Network Constructionmentioning

confidence: 99%

Identification of key genes unique to the luminal A and basal-like breast cancer subtypes via bioinformatic analysis

Jia

Liang

et al. 2020

Preprint

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Background: Breast cancer subtypes are statistically associated with prognosis. The search for markers of breast tumor heterogeneity and the development of precision medicine for patients are the current focuses of the field.Methods: We used a bioinformatic approach to identify key disease-causing genes unique to the luminal A and basal-like subtypes of breast cancer. First, we retrieved gene expression data for luminal A breast cancer, basal-like breast cancer, and normal breast tissue samples from The Cancer Genome Atlas database. The differentially expressed genes unique to the 2 breast cancer subtypes were identified and subjected to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses. We constructed protein–protein interaction networks of the differentially expressed genes. Finally, we analyzed the key modules of the networks, which we combined with survival data to identify the unique cancer genes associated with each breast cancer subtype.Results: We identified 1,114 differentially expressed genes in luminal A breast cancer and 1,042 differentially expressed genes in basal-like breast cancer, of which the subtypes shared 500. We observed 614 and 542 differentially expressed genes unique to luminal A and basal-like breast cancer, respectively. Through enrichment analyses, protein–protein interaction network analysis, and module mining, we identified 8 key differentially expressed genes unique to each subtype. Analysis of the gene expression data in the context of the survival data revealed that high expression of NMUR1 and NCAM1 in luminal A breast cancer statistically correlated with poor prognosis, whereas the low expression levels of CDC7, KIF18A, STIL, and CKS2 in basal-like breast cancer statistically correlated with poor prognosis.Conclusions: NMUR1 and NCAM1 are novel key disease-causing genes for luminal A breast cancer, and STIL is a novel key disease-causing gene for basal-like breast cancer. These genes are potential targets for clinical treatment.

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“…Extracted DNA was further processed using the Illumina iScan system for scanning BeadChips array containing 2.5 M SNPs (Human Omni 2.5M array). Details of the SNP genotyping can be found elsewhere (Basit et al, 2020). AutoSNPa was used to determine the homozygous regions common to all three affected individuals.…”

Section: Genome-wide Homozygosity Mappingmentioning

confidence: 99%

A novel homozygous frameshift mutation in the DCC gene in a Pakistani family with autosomal recessive horizontal gaze palsy with progressive scoliosis‐2 with impaired intellectual development

Zaka

Shahzad

Rao

et al. 2020

American J of Med Genetics Pt A

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Horizontal Gaze Palsy with Progressive Scoliosis-2 with Impaired Intellectual Development (HGPPS2) is a rare congenital disorder characterized by absence of conjugate horizontal eye movements, and progressive scoliosis developing in childhood and adolescence. We report three new patients with HGPPS2 in a consanguineous Pakistani family, presenting varying degrees of progressive scoliosis, developmental delays, horizontal gaze palsy, agenesis of corpus callosum, and absence of cerebral commissures. Analysis of genotyping data identified shared loss of heterozygosity (LOH) region on chromosomes 5p15.33-15.31, 6q11.2-12, and 18q21.1-21.3. A hypothesis-free, unbiased exome data analysis detected an insertion of nucleotide A (c.2399dupA) in exon 16 of the DCC gene. The insertion is predicted to cause frameshift p.(Asn800Lysfs*11). Interestingly, DCC gene is present in the LOH region on chromosome 18. Variant (c.2399dupA) in the DCC gene is considered as the most probable candidate variant for HGPPS2 based on the presence of DCC in the LOH region, previously reported role of DCC in HGPPS2, perfect segregation of candidate variant with the disease, prediction of variant pathogenicity, and absence of variant in variation databases. Sanger Sequencing confirmed the presence of the novel homozygous mutation in all three patients; the parents were heterozygous carriers of the mutation, in accordance with an autosomal recessive inheritance pattern. DCC encodes a netrin-1 receptor protein; its role in the development of the CNS has recently been established. Biallelic DCC mutations have previously been shown to cause HGPPS2. A novel homozygous variant in patients of the reported family extend the genotypic and phenotypic spectrum of HGPPS2.

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Centromere protein I (CENPI) is a candidate gene for X-linked steroid sensitive nephrotic syndrome

Cited by 9 publications

References 45 publications

Identification of key genes unique to the luminal a and basal-like breast cancer subtypes via bioinformatic analysis

Identification of key genes unique to the luminal a and basal-like breast cancer subtypes via bioinformatic analysis

Identification of key genes unique to the luminal A and basal-like breast cancer subtypes via bioinformatic analysis

A novel homozygous frameshift mutation in the DCC gene in a Pakistani family with autosomal recessive horizontal gaze palsy with progressive scoliosis‐2 with impaired intellectual development

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