18 research outputs found
Depletion of somatic mutations in splicing-associated sequences in cancer genomes
Abstract Background An important goal of cancer genomics is to identify systematically cancer-causing mutations. A common approach is to identify sites with high ratios of non-synonymous to synonymous mutations; however, if synonymous mutations are under purifying selection, this methodology leads to identification of false-positive mutations. Here, using synonymous somatic mutations (SSMs) identified in over 4000 tumours across 15 different cancer types, we sought to test this assumption by focusing on coding regions required for splicing. Results Exon flanks, which are enriched for sequences required for splicing fidelity, haveâ~â17% lower SSM density compared to exonic cores, even after excluding canonical splice sites. While it is impossible to eliminate a mutation bias of unknown cause, multiple lines of evidence support a purifying selection model above a mutational bias explanation. The flank/core difference is not explained by skewed nucleotide content, replication timing, nucleosome occupancy or deficiency in mismatch repair. The depletion is not seen in tumour suppressors, consistent with their role in positive tumour selection, but is otherwise observed in cancer-associated and non-cancer genes, both essential and non-essential. Consistent with a role in splicing modulation, exonic splice enhancers have a lower SSM density before and after controlling for nucleotide composition; moreover, flanks at the 5â end of the exons have significantly lower SSM density than at the 3â end. Conclusions These results suggest that the observable mutational spectrum of cancer genomes is not simply a product of various mutational processes and positive selection, but might also be shaped by negative selection
The effect of the main physicochemical properties of polycyclic aromatic hydrocarbons on their water/sediments distribution
International audiencePolycyclic aromatic hydrocarbons (PAHs) are environmental contaminants that continue to attract researchers' attention until these days due to their toxicity and their multisource emission. In this study, levels of 17 active molecules of PAHs were investigated in marine and continental Lebanese aquatic systems. The results showed that Lebanese seawater is more contaminated than several other sites on the Mediterranean Sea. On the marine side, the total concentration of PAHs ranges from 55.7 to 2683.8 ng Lâ1 in water and from 19.09 to 2025.03 ng gâ1 in sediments. On the continental side, the total concentration ranges from 465.7 to 1399.9 ng Lâ1 in water and from 72.6 to 1074.7 ng gâ1 in sediments presenting higher contamination and detection frequency than the marine sites. Pearson test was applied to determine the preference of PAHs toward one of the phases and showed that when the number of rings, the molecular mass and the log Ko/w increase, PAHs accumulate in sediments, and when the water solubility and the vapor pressure of PAHs increase, they tend to remain in the aqueous phase. Moreover, PAHs in Lebanese sediments were combustion-originated and resulted mainly from industrial sites set next to aquatic systems and heavy traffic especially along the Lebanese coastline. Regarding the toxicity effect, the use of the ERL/ERM approach revealed that few sites have individual PAHs levels that may occasionally cause biological adverse effects to benthic organisms; nevertheless, the ecosystem risk of PAHs in Lebanese sediments is low
Clin Sci (Lond)
Autosomal dominant inherited Protein S deficiency (PSD) (MIM 612336) is a rare disorder caused by rare mutations, mainly located in the coding sequence of the structural PROS1 gene, and associated with an increased risk of venous thromboembolism. To identify the molecular defect underlying PSD observed in an extended French pedigree with seven PSD affected members in whom no candidate deleterious PROS1 mutation was detected by Sanger sequencing of PROS1 exons and their flanking intronic regions or via an multiplex ligation-dependent probe amplification (MLPA) approach, a whole genome sequencing strategy was adopted. This led to the identification of a never reported C to T substitution at c.-39 from the natural ATG codon of the PROS1 gene that completely segregates with PSD in the whole family. This substitution ACGâATG creates a new start codon upstream of the main ATG. We experimentally demonstrated in HeLa cells that the variant generates a novel overlapping upstream open reading frame (uORF) and inhibits the translation of the wild-type PS. This work describes the first example of 5âČUTR PROS1 mutation causing PSD through the creation of an uORF, a mutation that is not predicted to be deleterious by standard annotation softwares, and emphasizes the need for better exploration of such type of non-coding variations in clinical genomics
Combined genetic and splicing analysis of BRCA1 c.[594-2A>C; 641A>G] highlights the relevance of naturally occurring in-frame transcripts for developing disease gene variant classification algorithms
A recent analysis using family history weighting and co-observation classification modeling indicated that BRCA1 c.594-2A > C (IVS9-2A > C), previously described to cause exon 10 skipping (a truncating alteration), displays characteristics inconsistent with those of a high risk pathogenic BRCA1 variant. We used large-scale genetic and clinical resources from the ENIGMA, CIMBA and BCAC consortia to assess pathogenicity of c.594-2A > C. The combined odds for causality considering case-control, segregation and breast tumor pathology information was 3.23 Ă 10â»âž . Our data indicate that c.594-2A > C is always in cis with c.641A > G. The spliceogenic effect of c.[594-2A > C;641A > G] was characterized using RNA analysis of human samples and splicing minigenes. As expected, c.[594-2A > C; 641A > G] caused exon 10 skipping, albeit not due to c.594-2A > C impairing the acceptor site but rather by c.641A > G modifying exon 10 splicing regulatory element(s). Multiple blood-based RNA assays indicated that the variant allele did not produce detectable levels of full-length transcripts, with a per allele BRCA1 expression profile composed of â70â80% truncating transcripts, and â20â30% of in-frame Î9,10 transcripts predicted to encode a BRCA1 protein with tumor suppression function. We confirm that BRCA1 c.[594-2A > C;641A > G] should not be considered a high-risk pathogenic variant. Importantly, results from our detailed mRNA analysis suggest that BRCA-associated cancer risk is likely not markedly increased for individuals who carry a truncating variant in BRCA1 exons 9 or 10, or any other BRCA1 allele that permits 20â30% of tumor suppressor function. More generally, our findings highlight the importance of assessing naturally occurring alternative splicing for clinical evaluation of variants in disease-causing genes.Miguel de la Hoya ... Nicola Poplawski ... Niel Johnson ... et al
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Combined genetic and splicing analysis of BRCA1 c.[594-2A>C; 641A>G] highlights the relevance of naturally occurring in-frame transcripts for developing disease gene variant classification algorithms.
A recent analysis using family history weighting and co-observation classification modeling indicated that BRCA1 c.594-2A > C (IVS9-2A > C), previously described to cause exon 10 skipping (a truncating alteration), displays characteristics inconsistent with those of a high risk pathogenic BRCA1 variant. We used large-scale genetic and clinical resources from the ENIGMA, CIMBA and BCAC consortia to assess pathogenicity of c.594-2A > C. The combined odds for causality considering case-control, segregation and breast tumor pathology information was 3.23 Ă 10-8 Our data indicate that c.594-2A > C is always in cis with c.641A > G. The spliceogenic effect of c.[594-2A > C;641A > G] was characterized using RNA analysis of human samples and splicing minigenes. As expected, c.[594-2A > C; 641A > G] caused exon 10 skipping, albeit not due to c.594-2A > C impairing the acceptor site but rather by c.641A > G modifying exon 10 splicing regulatory element(s). Multiple blood-based RNA assays indicated that the variant allele did not produce detectable levels of full-length transcripts, with a per allele BRCA1 expression profile composed of â70-80% truncating transcripts, and â20-30% of in-frame Î9,10 transcripts predicted to encode a BRCA1 protein with tumor suppression function.We confirm that BRCA1c.[594-2A > C;641A > G] should not be considered a high-risk pathogenic variant. Importantly, results from our detailed mRNA analysis suggest that BRCA-associated cancer risk is likely not markedly increased for individuals who carry a truncating variant in BRCA1 exons 9 or 10, or any other BRCA1 allele that permits 20-30% of tumor suppressor function. More generally, our findings highlight the importance of assessing naturally occurring alternative splicing for clinical evaluation of variants in disease-causing genes.The research described was supported by Spanish Instituto de Salud Carlos III funding, an initiative of the Spanish Ministry of Economy and Innovation partially supported by European Regional Development FEDER Funds [PI12/00539 and PI15/00059 to M.d.H., PI13/02030 to A.V.]; the French Ministry of Higher Education and Research [to O.S.]; the University of Otago, Mackenzie Charitable Foundation, Maria Lupton, and .Health Research Council of New Zealand [to L.W.]; UK Higher Education Funding Council Senior Fellowship Scheme, the University of Southampton [to D.B.]; Cancer research UK [to D.B., M.R.]; FamilienHede Nielsen Foundation fund [to T.V.O.H.]; Cancer Research-UK Senior Cancer Research Fellowship [to A.C.A.]; National Institute of Health [CA128978 and CA11616 to F.J.C.]; an NIH specialized program of research excellence in breast cancer to the Mayo Clinic [P50 CA116201 to F.J.C.]; and the US Breast Cancer Research Foundation [to F.J.C.]; translational grant from the French National Cancer Institute and Direction GĂ©nĂ©rale de l'Offre des Soins (INCa-DGOS AAP/CFB/CI) and a grant from the French North-West Canceropole (CNO) [to A.M.]; The Cancer Council Queensland [APP1086286 to A.B.S.]; the NHMRC Senior Research Fellowship Scheme [ID 1061779 to A.B.S.]; NHMRC Project grant scheme [ID 1010719 to A.B.S.].
EMBRACE is supported by Cancer Research UK Grants C1287/A10118 and C1287/A11990.
The BBCS is funded by Cancer Research UK and Breakthrough Breast Cancer (recently merged with Breast Cancer Campaign forming Breast Cancer Now) and acknowledges NHS funding to the NIHR Biomedical Research Centre, and the National Cancer Research Network (NCRN).
SEARCH was supported by grants CRUK A490/A11021, C490/A16561.
CIMBA data management was supported by Cancer Research-UK grant C12292/A11174 and C1287/A10118.
BCAC is funded by Cancer Research UK [C1287/A10118, C1287/A12014] and by the European CommunitĂœs Seventh Framework Programme under grant agreement number 223175 (grant number HEALTH-F2-2009-223175) (COGS).This is the author accepted manuscript. The final version is available from Oxford University Press via http://dx.doi.org/10.1093/hmg/ddw09
Importance of muscle biopsy to establish pathogenicity of DMD missense and splice variants
Pseudomonas aeruginosa quorum sensing inhibition by clinical isolate Delftia tsuruhatensis 11304: involvement of N-octadecanoylhomoserine lactones
Combined genetic and splicing analysis of BRCA1 c.[594-2A>C; 641A>G] highlights the relevance of naturally occurring in-frame transcripts for developing disease gene variant classification algorithms.
A recent analysis using family history weighting and co-observation classification modeling indicated thatBRCA1c.594-2A>C (IVS9-2A>C), previously described to cause exon 10 skipping (a truncating alteration), displays characteristics inconsistent with those of a high risk pathogenicBRCA1variant. We used large-scale genetic and clinical resources from the ENIGMA, CIMBA and BCAC consortia to assess pathogenicity of c.594-2A>C. The combined odds for causality considering case-control, segregation, and breast tumor pathology information was 3.23x10(-8) Our data indicate that c.594-2A>C is always inciswith c.641A>G.The spliceogenic effect of c.[594-2A>C;641A>G] was characterized using RNA analysis of human samples and splicing minigenes. As expected, c.[594-2A>C; 641A>G] caused exon 10 skipping, albeit not due to c.594-2A>C impairing the acceptor site but rather by c.641A>G modifying exon 10 splicing regulatory element(s). Multiple blood-based RNA assays indicated that the variant allele did not produce detectable levels of full-length transcripts, with aper allele BRCA1expression profile comprised of â70-80% truncating transcripts, and â20-30% of in-frame Î9,10 transcripts predicted to encode a BRCA1 protein with tumor suppression function.We confirm thatBRCA1c.[594-2A>C;641A>G] should not be considered a high-risk pathogenic variant. Importantly, results from our detailed mRNA analysis suggest that BRCA-associated cancer risk is likely not markedly increased for individuals who carry a truncating variant inBRCA1exons 9 or 10, or any otherBRCA1allele that permits 20-30% of tumor suppressor function. More generally, our findings highlight the importance of assessing naturally occurring alternative splicing for clinical evaluation of variants in disease-causing genes.Accepted version, 12 month embargo, set statement