Beyond the disease itself: A cross-cutting educational initiative for patients and families with rare diseases

Rare diseases (RDs) as a whole affect a huge number of individuals although each specific condition comprises a low number of individuals. As a consequence, funds allocated to expand research to all conditions are often limited. Several initiatives have emerged to invest more resources for research in RDs, but patients express unmet needs regarding educational initiatives, awareness support, and psychosocial resources. We developed an educational training program in the format of weekly sessions covering basic medical scientific knowledge and psychosocial aspects of RDs. The aim of this initiative was to assess its overall impact regarding knowledge, psychological issues, and participant satisfaction. Items were evaluated through surveys before and after the sessions. Here, we report the experience and impact of two editions of this initiative with a total of 37 participants. Our results show improvements in knowledge and better management of the psychological impact. Moreover, participants were able to exchange experiences and concerns, most of which were shared even though the RDs were different. Overall, the program was evaluated by the participants as a highly beneficial experience and all of them were interested in attending advanced editions.

Chromosomal microarray analysis in fetuses with central nervous system anomalies: An 8-year long observational study from a tertiary care university hospital

OBJECTIVES

To evaluate the prevalence of DNA copy number variants (CNVs) detected with array comparative genomic hybridization (CGH) in fetuses with central nervous system (CNS) anomalies. Secondary objectives were to describe the prevalence of CNV in specific CNS abnormalities, in isolated defects or associated with other malformations or fetal growth restriction (FGR).

METHODS

Observational cohort study in 238 fetuses with CNS anomalies in which an array-CGH had been performed between January 2009 and December 2017. Pathogenic CNV and variants of unknown significance (VUS) were reported.

RESULTS

Pathogenic CNVs were found in 16/238 cases (6.7%), VUS in 18/238 (7.6%), and normal result in 204/238 (85.7%) cases. Pathogenic CNVs were more frequent in posterior fossa anomalies (cerebellar hypoplasia 33%, megacisterna magna 20%), moderate ventriculomegaly (11%) and spina bifida (3.7%). Pathogenic CNVs and VUS were found in 7/182 (3.8%) and 14/182 (7.7%) cases of isolated anomalies, in 9/49 (18.4%) and 4/49 (8.2%) presenting another malformation, and in 0/7 and 0/7 cases with associated FGR (P = .001, P = .741, respectively).

CONCLUSION

These results provide strong evidence toward performing array in fetuses with CNS anomalies, particular in cases of posterior fossa anomalies. The prevalence of pathogenic CNVs is higher in association with other malformations.

Utility of two SMN1 variants to improve spinal muscular atrophy carrier diagnosis and genetic counselling

Spinal muscular atrophy (SMA) is caused by deletions/mutations in SMN1. Most heterozygous SMA carriers have only one SMN1 copy in one of the alleles (1/0 carriers). However, a few carriers lack SMN1 in one of their chromosomes, but present two gene copies in the other. These "2/0 carriers" are undistinguishable from non-carrier individuals (1/1) with currently available methods. Previous association of SMN1 variants c.*3 + 80 T > G and c.*211_*212del with two SMN1 copies in cis in Ashkenazi population prompted us to analyze them in 270 Spanish individuals (SMA carriers, patients and general population). Both variants were much more frequently detected in chromosomes with 2 SMN1 copies in cis in comparison with chromosomes carrying one copy (17.9 vs. 0.7%; p < 0.001). In particular, one-fifth of 2/0 SMA carriers harboured one or both variants compared to none of 99 non-carriers with two SMN1 copies (p < 0.001). The c.*211_*212del variant was also much more frequent in exon 8 of SMN2-SMN1 hybrids than in that of intact SMN1 genes (20 vs. 0.83%, p < 0.001), suggesting its association with chromosomal rearrangements. Although absence of these variants does not exclude that a particular individual is a 2/0 SMA carrier, their presence is valuable to substantially increase residual risk in putative carriers, thus improving genetic counselling.

The transcription factor GATA6 enables self-renewal of colon adenoma stem cells by repressing BMP gene expression

Aberrant activation of WNT signalling and loss of BMP signals represent the two main alterations leading to the initiation of colorectal cancer (CRC). Here we screen for genes required for maintaining the tumour stem cell phenotype and identify the zinc-finger transcription factor GATA6 as a key regulator of the WNT and BMP pathways in CRC. GATA6 directly drives the expression of LGR5 in adenoma stem cells whereas it restricts BMP signalling to differentiated tumour cells. Genetic deletion of Gata6 from mouse colon adenomas increases the levels of BMP factors, which signal to block self-renewal of tumour stem cells. In human tumours, GATA6 competes with β-catenin/TCF4 for binding to a distal regulatory region of the BMP4 locus that has been linked to increased susceptibility to development of CRC. Hence, GATA6 creates an environment permissive for CRC initiation by lowering the threshold of BMP signalling required for tumour stem cell expansion.

Functional analysis of a large set of BRCA2 exon 7 variants highlights the predictive value of hexamer scores in detecting alterations of exonic splicing regulatory elements

Exonic variants can alter pre-mRNA splicing either by changing splice sites or by modifying splicing regulatory elements. Often these effects are difficult to predict and are only detected by performing RNA analyses. Here, we analyzed, in a minigene assay, 26 variants identified in the exon 7 of BRCA2, a cancer predisposition gene. Our results revealed eight new exon skipping mutations in this exon: one directly altering the 5' splice site and seven affecting potential regulatory elements. This brings the number of splicing regulatory mutations detected in BRCA2 exon 7 to a total of 11, a remarkably high number considering the total number of variants reported in this exon (n = 36), all tested in our minigene assay. We then exploited this large set of splicing data to test the predictive value of splicing regulator hexamers' scores recently established by Ke et al. (). Comparisons of hexamer-based predictions with our experimental data revealed high sensitivity in detecting variants that increased exon skipping, an important feature for prescreening variants before RNA analysis. In conclusion, hexamer scores represent a promising tool for predicting the biological consequences of exonic variants and may have important applications for the interpretation of variants detected by high-throughput sequencing.

Abstract 1334: Implication of the 3′UTR region of TGFβR1 with MSS HNPCC and sporadic colorectal cancer

Background: Colorectal cancer (CRC) is among all common malignancies one with the highest percentage of familial clustering. Thus almost 20% of cases develop in families with at least another affected member. Individuals in these families have a higher risk of developing CRC. Known mutations responsible for several CRC syndromes only explain a small proportion of familial cases but the underlying basis of most still remains unknown. Over half of CRCs that are highly suspicious for an autosomal dominant hereditary pattern of malignancy, as expressed by the Amsterdam criteria, are not explained by known genetic mutations. These cases are known as microsatellite stable hereditary non-polyposis CRC (MSS-HNPCC) or colorectal cancer type X. Aims: To identify new genetic variants that can potentially modulate CRC risk and contribute to hereditability. Methods: We sequenced the coding sequence of MGMT, AXIN2, CTNNB1, TGFβRI and TGFβRII genes and we genotyped 10 common low risk variants, in 30 MSS-HNPCC patients. Potentially relevant variants were genotyped in 308 sporadic cases and 425 cancer-free controls. Logistic regression was used to estimate cancer risk (OR (95%CI)) associated with the genetic variants identified using SPSS (IBM v20.0). Results: A haplotype containing 3 variants (rs67687202, rs868 and rs334354) in high linkage disequilibrium (LD) was found to be associated in a very strong manner with MSS-HNPCC patients and to a lesser degree with sporadic CRC. Thus both MSS-HNPCC and sporadic CRC showed a significantly lower minor allele frequency (MAF) than controls (MAF 0.07, MAF 0.23 vs MAF 0.29) for rs67687202. The AA genotype of rs868 associates with a strong risk for CRC in MSS-HNPCC patients (OR=7.9 (2.7-23.1) P&lt;0.001) and also in sporadic CRC patients but much more modestly (OR=1.6 (1.2-2.2) P=0.001). According to prediction models, the AA genotype for rs868 results in a tighter complementary binding for the family of let-7 miRNAs, which inhibits TGFβR1 translation. On the other hand, the GG genotype increases the hybridization energy of binding for miR-98 and let-7c and completely eliminates the binding for let-7d. We did not identify any association of 10 low risk variants or an accumulation of these risk alleles in MSS-HNPCC patients, which suggests that clustering of common risk alleles is not contributing to cancer development in these families. Conclusions: We describe for the first time a haplotype presumably involved in controlling TGFβR1 expression that has an extremely high association with MSS-HNPCC suggesting a deep contribution of this genetic component to familial CRC. The effect could be due to the more efficient binding of miRNA let-7, which inhibits the TGFβR1 transcript. This further supports other findings that suggest the important role of TGFβR1 as a susceptibility factor in CRC. An accumulation of low susceptibility variants is an unlikely explanation for the high cancer risk in MSS-HNPCC.

Citation Format: Rosa M. Munoz Xicola, Brian Doyle, Jamie Rawson, Pilar Garre, Anna Abuli, Esther Lee, Sathyaraj Murugappan, Xavier Bessa, Luis Bujanda, Francesc Balaguer, Sergi Castellvi-Bel, Juan Clofent, Cristina Alenda, Rodrigo Jover, Clara Ruiz-Ponte, Sapna Singal, Montserrat Andreu, Angel Carracedo, Antoni Castells, Nathan Ellis, Trinidad Caldes, Xavier LLor. Implication of the 3′UTR region of TGFβR1 with MSS HNPCC and sporadic colorectal cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1334. doi:10.1158/1538-7445.AM2013-1334