Effects of heat shock, hypoxia, post-mortem interval and glioma disease state on heat shock gene HSPA expression

Heat shock protein 70 (HSPA/HSP70) gene expression is induced by a wide range of cellular stress conditions. This study investigated HSPA/HSP70 expression in human cell lines exposed to hypoxic conditions, in cancerous and non-cancerous brain tissue specimens from 18 patients (gliomas and normal conditions), and in post mortem rat brain samples exposed to heat shock. Three human glioma cell lines were chosen for this study, each representing various types of glioma: (astrocytoma, oligodendroglioma and glioblastoma), with a normal human astrocyte cell line used as a control. In addition, 18 clinical brain tissue samples were also examined. HSPA RNA transcripts and proteins were examined in these samples using qRT-PCR, immunofluorescence and flow cytometry techniques. The average HSPA mRNA copy numbers detected in glioblastoma tissue were 1.8 and 8.8 fold higher respectively than in lower grade glioma and control tissues, which is suggestive of a grade related transcription profile. Similar patterns of grade related expression were also observed in corresponding cell lines. The percentage of cells showing positive for HSPA protein in normal cell lines increased from 0 to 33% immediately after exposure to hypoxia, and gradually declined to 11% 24 h after treatment. However, the effects of hypoxia were marginal in glioma cells, due to the already elevated levels of HSPA. Although hypoxia induced HSPA expression in normal cells, it did not achieve the same level of induction in cancer cells, suggesting that there are other factors which contribute to the induction of HSPA. These results suggest that HSPA is induced in cancer cells, not only by hypoxia, but also by other factors. In addition, this study indicated for the first time that HSPA expression in glioma cells may possibly be grade related, and thus may have value as a prognostic marker. However a greater sample size is needed to validate such findings. This study showed that HSPA is expressed at low levels in normal brain tissue, but was more highly expressed in brain tissue subjected to mild heat shock. The levels of HSPA transcripts in heat shocked post mortem brain tissue showed a marked increase in HSPA expression. GAPDH was used as a control gene for these studies, and exhibited a consistent level of expression in normal and tumourous cell lines and tissue samples under normal and hypoxic conditions, and also in post mortem tissues exposed to heat shock. For Homo sapiens GAPDH, the average transcript numbers for normal and tumourous cell lines and brain tissue samples were approximately 145,000 copies per sample. For Rattus norvegicus GAPDH, levels were higher than for human samples, at an average of 268,300 copies per sample. The consistency of these results confirms that GAPDH was a suitable candidate gene for the purpose of this study. Early in the post-mortem period, HSPA is expressed more highly in tissues subjected to single and multiple heat shocks compared to controls. However, later post-mortem intervals of between 3 - 24 h demonstrated inconsistent and irregular results, with no predictive or reproducible patterns. Therefore, although there is demonstrable de novo expression of HSPA in post mortem brain tissue in response to heat shock, it is difficult to predict the full parameters of this induction, probably as a result of other forms of cellular stress affecting these tissues under our experimental methodology. These initial studies indicate that the use of HSPA with the methodologies employed here are not suitable as an accurate indicator of post-mortem interval

The Genomic Architecture of Bladder Exstrophy Epispadias Complex

From MDPI via Jisc Publications RouterHistory: accepted 2021-07-21, pub-electronic 2021-07-28Publication status: PublishedThe bladder exstrophy–epispadias complex (BEEC) is an abdominal midline malformation comprising a spectrum of congenital genitourinary abnormalities of the abdominal wall, pelvis, urinary tract, genitalia, anus, and spine. The vast majority of BEEC cases are classified as non-syndromic and the etiology of this malformation is still unknown. This review presents the current knowledge on this multifactorial disorder, including phenotypic and anatomical characterization, epidemiology, proposed developmental mechanisms, existing animal models, and implicated genetic and environmental components

Biallelic TMEM260 variants cause truncus arteriosus, with or without renal defects

Only two families have been reported with biallelic TMEM260 variants segregating with structural heart defects and renal anomalies syndrome (SHDRA). With a combination of genome, exome sequencing and RNA studies, we identified eight individuals from five families with biallelic TMEM260 variants. Variants included one multi-exon deletion, four nonsense/frameshifts, two splicing changes and one missense change. Together with the published cases, analysis of clinical data revealed ventricular septal defects (12/12), mostly secondary to truncus arteriosus (10/12), elevated creatinine levels (6/12), horse-shoe kidneys (1/12) and renal cysts (1/12) in patients. Three pregnancies were terminated on detection of severe congenital anomalies. Six patients died between the ages of 6 weeks and 5 years. Using a range of stringencies, carrier frequency for SHDRA was estimated at 0.0007–0.007 across ancestries. In conclusion, this study confirms the genetic basis of SHDRA, expands its known mutational spectrum and clarifies its clinical features. We demonstrate that SHDRA is a severe condition associated with substantial mortality in early childhood and characterised by congenital cardiac malformations with a variable renal phenotype

Expanding the genotypic spectrum of TXNL4A variants in Burn‐McKeown syndrome

From Wiley via Jisc Publications RouterHistory: received 2021-09-06, rev-recd 2021-10-21, accepted 2021-10-23, pub-electronic 2021-11-05Article version: VoRPublication status: PublishedFunder: Biotechnology and Biological Sciences Research Council; Id: http://dx.doi.org/10.13039/501100000268; Grant(s): BB/N000358/1Funder: Health Education England Genomics Education ProgrammeFunder: Medical Research Council; Id: http://dx.doi.org/10.13039/501100007155; Grant(s): 1916606Funder: National Institute for Health Manchester Biomedical Research Centre; Grant(s): IS‐BRC‐1215‐20007Abstract: The developmental disorder Burn‐McKeown Syndrome (BMKS) is characterised by choanal atresia and specific craniofacial features. BMKS is caused by biallelic variants in the pre‐messenger RNA splicing factor TXNL4A. Most patients have a loss‐of‐function variant in trans with a 34‐base pair (bp) deletion (type 1 Δ34) in the promoter region. Here, we identified two patients with BMKS. One individual has a TXNL4A c.93_94delCC, p.His32Argfs *21 variant combined with a type 1 Δ34 promoter deletion. The other has an intronic TXNL4A splice site variant (c.258‐3C>G) and a type 1 Δ34 promoter deletion. We show the c.258‐3C>G variant and a previously reported c.258‐2A>G variant, cause skipping of the final exon of TXNL4A in a minigene splicing assay. Furthermore, we identify putative transcription factor binding sites within the 56 bp of the TXNL4A promoter affected by the type 1 and type 2 Δ34 and use dual luciferase assays to identify a 22 bp repeated motif essential for TXNL4A expression within this promoter region. We propose that additional variants affecting critical transcription factor binding nucleotides within the 22 bp repeated motif could be relevant to BMKS aetiology. Finally, our data emphasises the need to analyse the non‐coding sequence in individuals where a single likely pathogenic coding variant is identified in an autosomal recessive disorder consistent with the clinical presentation

A genome-wide association study with tissue transcriptomics identifies genetic drivers for classic bladder exstrophy

Classic bladder exstrophy represents the most severe end of all human congenital anomalies of the kidney and urinary tract and is associated with bladder cancer susceptibility. Previous genetic studies identified one locus to be involved in classic bladder exstrophy, but were limited to a restrict number of cohort. Here we show the largest classic bladder exstrophy genome-wide association analysis to date where we identify eight genome-wide significant loci, seven of which are novel. In these regions reside ten coding and four non-coding genes. Among the coding genes is EFNA1, strongly expressed in mouse embryonic genital tubercle, urethra, and primitive bladder. Re-sequence of EFNA1 in the investigated classic bladder exstrophy cohort of our study displays an enrichment of rare protein altering variants. We show that all coding genes are expressed and/or significantly regulated in both mouse and human embryonic developmental bladder stages. Furthermore, nine of the coding genes residing in the regions of genome-wide significance are differentially expressed in bladder cancers. Our data suggest genetic drivers for classic bladder exstrophy, as well as a possible role for these drivers to relevant bladder cancer susceptibility

A Dominantly Inherited 5' UTR Variant Causing Methylation-Associated Silencing of BRCA1 as a Cause of Breast and Ovarian Cancer

Pathogenic variants in BRCA1 or BRCA2 are identified in ∼20% of families with multiple individuals affected by early-onset breast and/or ovarian cancer. Extensive searches for additional highly penetrant genes or alternative mutational mechanisms altering BRCA1 or BRCA2 have not explained the missing heritability. Here, we report a dominantly inherited 5′ UTR variant associated with epigenetic BRCA1 silencing due to promoter hypermethylation in two families affected by breast and ovarian cancer. BRCA1 promoter methylation of ten CpG dinucleotides in families who are affected by breast and/or ovarian cancer but do not have germline BRCA1 or BRCA2 pathogenic variants was assessed by pyrosequencing and clonal bisulfite sequencing. RNA and DNA sequencing of BRCA1 from lymphocytes was undertaken to establish allelic expression and the presence of germline variants. BRCA1 promoter hypermethylation was identified in 2 of 49 families in which multiple women are affected by grade 3 breast cancer or high-grade serous ovarian cancer. Soma-wide BRCA1 promoter hypermethylation was confirmed in blood, buccal mucosa, and hair follicles. Pyrosequencing showed that DNA was ∼50% methylated, consistent with the silencing of one allele, which was confirmed by clonal bisulfite sequencing. RNA sequencing revealed the allelic loss of BRCA1 expression in both families and that this loss of expression segregated with the heterozygous variant c.−107A>T in the BRCA1 5′ UTR. Our results establish a mechanism whereby familial breast and ovarian cancer is caused by an in cis 5′ UTR variant associated with epigenetic silencing of the BRCA1 promoter in two independent families. We propose that methylation analyses be undertaken to establish the frequency of this mechanism in families affected by early-onset breast and/or ovarian cancer without a BRCA1 or BRCA2 pathogenic variant

ISL1 is a major susceptibility gene for classic bladder exstrophy and a regulator of urinary tract development.

Previously genome-wide association methods in patients with classic bladder exstrophy (CBE) found association with ISL1, a master control gene expressed in pericloacal mesenchyme. This study sought to further explore the genetics in a larger set of patients following-up on the most promising genomic regions previously reported. Genotypes of 12 markers obtained from 268 CBE patients of Australian, British, German Italian, Spanish and Swedish origin and 1,354 ethnically matched controls and from 92 CBE case-parent trios from North America were analysed. Only marker rs6874700 at the ISL1 locus showed association (p = 2.22 × 10-08). A meta-analysis of rs6874700 of our previous and present study showed a p value of 9.2 × 10-19. Developmental biology models were used to clarify the location of ISL1 activity in the forming urinary tract. Genetic lineage analysis of Isl1-expressing cells by the lineage tracer mouse model showed Isl1-expressing cells in the urinary tract of mouse embryos at E10.5 and distributed in the bladder at E15.5. Expression of isl1 in zebrafish larvae staged 48 hpf was detected in a small region of the developing pronephros. Our study supports ISL1 as a major susceptibility gene for CBE and as a regulator of urinary tract development

Biallelic TMEM260 variants cause truncus arteriosus, with or without renal defects

From Wiley via Jisc Publications RouterHistory: received 2021-08-18, rev-recd 2021-09-22, accepted 2021-10-02, pub-electronic 2021-10-11Article version: VoRPublication status: PublishedFunder: Cancer Research UK; Id: http://dx.doi.org/10.13039/501100000289Funder: European Union's Horizon 2020; Grant(s): 779257Funder: Medical Research Council; Id: http://dx.doi.org/10.13039/501100007155Funder: NHS EnglandFunder: NIHR Oxford Biomedical Research Centre ProgrammeFunder: Society for the Relief of Disabled Children, Hong KongFunder: Wellcome Trust; Id: http://dx.doi.org/10.13039/100010269; Grant(s): 203141/Z/16/ZAbstract: Only two families have been reported with biallelic TMEM260 variants segregating with structural heart defects and renal anomalies syndrome (SHDRA). With a combination of genome, exome sequencing and RNA studies, we identified eight individuals from five families with biallelic TMEM260 variants. Variants included one multi‐exon deletion, four nonsense/frameshifts, two splicing changes and one missense change. Together with the published cases, analysis of clinical data revealed ventricular septal defects (12/12), mostly secondary to truncus arteriosus (10/12), elevated creatinine levels (6/12), horse‐shoe kidneys (1/12) and renal cysts (1/12) in patients. Three pregnancies were terminated on detection of severe congenital anomalies. Six patients died between the ages of 6 weeks and 5 years. Using a range of stringencies, carrier frequency for SHDRA was estimated at 0.0007–0.007 across ancestries. In conclusion, this study confirms the genetic basis of SHDRA, expands its known mutational spectrum and clarifies its clinical features. We demonstrate that SHDRA is a severe condition associated with substantial mortality in early childhood and characterised by congenital cardiac malformations with a variable renal phenotype

Comparison of in silico strategies to prioritize rare genomic variants impacting RNA splicing for the diagnosis of genomic disorders

From Springer Nature via Jisc Publications RouterHistory: received 2021-03-09, accepted 2021-09-13, registration 2021-10-01, online 2021-10-18, pub-electronic 2021-10-18, collection 2021-12Publication status: PublishedFunder: Wellcome Trust; Grant(s): RP-2016-07-011, 200990/Z/16/ZFunder: Health Education EnglandAbstract: The development of computational methods to assess pathogenicity of pre-messenger RNA splicing variants is critical for diagnosis of human disease. We assessed the capability of eight algorithms, and a consensus approach, to prioritize 249 variants of uncertain significance (VUSs) that underwent splicing functional analyses. The capability of algorithms to differentiate VUSs away from the immediate splice site as being ‘pathogenic’ or ‘benign’ is likely to have substantial impact on diagnostic testing. We show that SpliceAI is the best single strategy in this regard, but that combined usage of tools using a weighted approach can increase accuracy further. We incorporated prioritization strategies alongside diagnostic testing for rare disorders. We show that 15% of 2783 referred individuals carry rare variants expected to impact splicing that were not initially identified as ‘pathogenic’ or ‘likely pathogenic’; one in five of these cases could lead to new or refined diagnoses