Section: New Results

Health

Rare Diseases. Splicing is an essential step in the process leading to gene expression because it not only removes the introns from the primary transcripts, but also generates a combination of mature transcripts through the differential inclusion/exclusion of exons and sometimes retention of introns. Some pathologies are associated to such abnormal splicing. This is the case of the Taybi-Linder Syndrome (TALS), a very rare malformative syndrome with autosomal recessive transmission, belonging to the group of microcephalic dwarfism and responsible for death usually before the age of 2 years. This pathology was recently found to be caused by mutations in RNU4ATAC, a small nuclear RNA, which is an essential component of the minor spliceosome. We started a collaboration with the group of Pr. P. Edery (who first identified this alteration in 2012) with the objective to establish a comprehensive catalog of splice alterations in several cohorts of TALS patients. In this work, we take advantage of our reference-free assembly approach of transcripts (KisSplice ) in order to detect new splicing alterations and to identify the associated deregulated signalling genes and pathways.

Cancer. Alain Viari has continued to develop a strong interaction with clinicians concerned with cancer, notably of the breast and in the early human embryo. A number of papers have appeared in 2017 that describe this work [7], [6], [10], [11], [12], [16], [17], [18]. We highlight here just two.

The first [7] refers to breast cancer. Mismatch repair (MMR)-deficient cancers have been discovered to be highly responsive to immune therapies such as PD-1 checkpoint blockade, making their definition in patients, where they may be relatively rare, paramount for treatment decisions. In the study published in [7], we utilised patterns of mutagenesis known as mutational signatures, which are imprints of the mutagenic processes associated with MMR deficiency, to identify MMR-deficient breast tumours from a whole-genome sequencing dataset comprising a cohort of 640 patients. We identified 11 of 640 tumours as MMR deficient, but only 2 of 11 exhibited germline mutations in MMR genes or Lynch Syndrome. Two additional tumours had a substantially reduced proportion of mutations attributed to MMR deficiency, where the predominant mutational signatures were related to APOBEC enzymatic activity. Overall, 6 of 11 of the MMR-deficient cases in this cohort were confirmed genetically or epigenetically as having abrogation of MMR genes. However, IHC analysis of MMR-related proteins revealed all but one of 10 samples available for testing as MMR deficient. Thus, the mutational signatures more faithfully reported MMR deficiency than sequencing of MMR genes, because they represent a direct pathophysiologic readout of repair pathway abnormalities. As whole-genome sequencing continues to become more affordable, it could be used to expose individually abnormal tumours in tissue types where MMR deficiency has been rarely detected, but also rarely sought.

The second [18] concerns early human embryo. Somatic cells acquire mutations throughout the course of an individual's life. Mutations occurring early in embryogenesis are often present in a substantial proportion of, but not all, cells in postnatal humans and thus have particular characteristics and effects. Depending on their location in the genome and the proportion of cells they are present in, these mosaic mutations can cause a wide range of genetic disease syndromes and predispose carriers to cancer. They have a high chance of being transmitted to offspring as de novo germline mutations and, in principle, can provide insights into early human embryonic cell lineages and their contributions to adult tissues. Although it is known that gross chromosomal abnormalities are remarkably common in early human embryos, our understanding of early embryonic somatic mutations is very limited. In this work, whole-genome sequences of normal blood from 241 adults was used to identify 163 early embryonic mutations. It was estimated that approximately three base substitution mutations occur per cell per cell-doubling event in early human embryogenesis and these are mainly attributable to two known mutational signatures. The mutations were then used to reconstruct developmental lineages of adult cells and demonstrate that the two daughter cells of many early embryonic cell-doubling events contribute asymmetrically to adult blood at an approximately 2:1 ratio. This study provided insights into the mutation rates, mutational processes and developmental outcomes of cell dynamics that operate during early human embryogenesis.