Translesion DNA synthesis-driven mutagenesis in very early embryogenesis of fast cleaving embryos.

In early embryogenesis of fast cleaving embryos, DNA synthesis is short and surveillance mechanisms preserving genome integrity are inefficient, implying the possible generation of mutations. We have analyzed mutagenesis in Xenopus laevis and Drosophila melanogaster early embryos. We report the occurrence of a high mutation rate in Xenopus and show that it is dependent upon the translesion DNA synthesis (TLS) master regulator Rad18. Unexpectedly, we observed a homology-directed repair contribution of Rad18 in reducing the mutation load. Genetic invalidation of TLS in the pre-blastoderm Drosophila embryo resulted in reduction of both the hatching rate and single-nucleotide variations on pericentromeric heterochromatin in adult flies. Altogether, these findings indicate that during very early Xenopus and Drosophila embryos TLS strongly contributes to the high mutation rate. This may constitute a previously unforeseen source of genetic diversity contributing to the polymorphisms of each individual with implications for genome evolution and species adaptation.

IRFinder-S: a comprehensive suite to discover and explore intron retention.

Accurate quantification and detection of intron retention levels require specialized software. Building on our previous software, we create a suite of tools called IRFinder-S, to analyze and explore intron retention events in multiple samples. Specifically, IRFinder-S allows a better identification of true intron retention events using a convolutional neural network, allows the sharing of intron retention results between labs, integrates a dynamic database to explore and contrast available samples, and provides a tested method to detect differential levels of intron retention.

A cell-to-patient machine learning transfer approach uncovers novel basal-like breast cancer prognostic markers amongst alternative splice variants.

BACKGROUND: Breast cancer is amongst the 10 first causes of death in women worldwide. Around 20% of patients are misdiagnosed leading to early metastasis, resistance to treatment and relapse. Many clinical and gene expression profiles have been successfully used to classify breast tumours into 5 major types with different prognosis and sensitivity to specific treatments. Unfortunately, these profiles have failed to subclassify breast tumours into more subtypes to improve diagnostics and survival rate. Alternative splicing is emerging as a new source of highly specific biomarkers to classify tumours in different grades. Taking advantage of extensive public transcriptomics datasets in breast cancer cell lines (CCLE) and breast cancer tumours (TCGA), we have addressed the capacity of alternative splice variants to subclassify highly aggressive breast cancers. RESULTS: Transcriptomics analysis of alternative splicing events between luminal, basal A and basal B breast cancer cell lines identified a unique splicing signature for a subtype of tumours, the basal B, whose classification is not in use in the clinic yet. Basal B cell lines, in contrast with luminal and basal A, are highly metastatic and express epithelial-to-mesenchymal (EMT) markers, which are hallmarks of cell invasion and resistance to drugs. By developing a semi-supervised machine learning approach, we transferred the molecular knowledge gained from these cell lines into patients to subclassify basal-like triple negative tumours into basal A- and basal B-like categories. Changes in splicing of 25 alternative exons, intimately related to EMT and cell invasion such as ENAH, CD44 and CTNND1, were sufficient to identify the basal-like patients with the worst prognosis. Moreover, patients expressing this basal B-specific splicing signature also expressed newly identified biomarkers of metastasis-initiating cells, like CD36, supporting a more invasive phenotype for this basal B-like breast cancer subtype. CONCLUSIONS: Using a novel machine learning approach, we have identified an EMT-related splicing signature capable of subclassifying the most aggressive type of breast cancer, which are basal-like triple negative tumours. This proof-of-concept demonstrates that the biological knowledge acquired from cell lines can be transferred to patients data for further clinical investigation. More studies, particularly in 3D culture and organoids, will increase the accuracy of this transfer of knowledge, which will open new perspectives into the development of novel therapeutic strategies and the further identification of specific biomarkers for drug resistance and cancer relapse.

iMOKA: k-mer based software to analyze large collections of sequencing data.

iMOKA (interactive multi-objective k-mer analysis) is a software that enables comprehensive analysis of sequencing data from large cohorts to generate robust classification models or explore specific genetic elements associated with disease etiology. iMOKA uses a fast and accurate feature reduction step that combines a Naïve Bayes classifier augmented by an adaptive entropy filter and a graph-based filter to rapidly reduce the search space. By using a flexible file format and distributed indexing, iMOKA can easily integrate data from multiple experiments and also reduces disk space requirements and identifies changes in transcript levels and single nucleotide variants. iMOKA is available at https://github.com/RitchieLabIGH/iMOKA and Zenodo https://doi.org/10.5281/zenodo.4008947 .

NF90 modulates processing of a subset of human pri-miRNAs.

MicroRNAs (miRNAs) are predicted to regulate the expression of >60% of mammalian genes and play fundamental roles in most biological processes. Deregulation of miRNA expression is a hallmark of most cancers and further investigation of mechanisms controlling miRNA biogenesis is needed. The double stranded RNA-binding protein, NF90 has been shown to act as a competitor of Microprocessor for a limited number of primary miRNAs (pri-miRNAs). Here, we show that NF90 has a more widespread effect on pri-miRNA biogenesis than previously thought. Genome-wide approaches revealed that NF90 is associated with the stem region of 38 pri-miRNAs, in a manner that is largely exclusive of Microprocessor. Following loss of NF90, 22 NF90-bound pri-miRNAs showed increased abundance of mature miRNA products. NF90-targeted pri-miRNAs are highly stable, having a lower free energy and fewer mismatches compared to all pri-miRNAs. Mutations leading to less stable structures reduced NF90 binding while increasing pri-miRNA stability led to acquisition of NF90 association, as determined by RNA electrophoretic mobility shift assay (EMSA). NF90-bound and downregulated pri-miRNAs are embedded in introns of host genes and expression of several host genes is concomitantly reduced. These data suggest that NF90 controls the processing of a subset of highly stable, intronic miRNAs.

GECKO is a genetic algorithm to classify and explore high throughput sequencing data.

Comparative analysis of high throughput sequencing data between multiple conditions often involves mapping of sequencing reads to a reference and downstream bioinformatics analyses. Both of these steps may introduce heavy bias and potential data loss. This is especially true in studies where patient transcriptomes or genomes may vary from their references, such as in cancer. Here we describe a novel approach and associated software that makes use of advances in genetic algorithms and feature selection to comprehensively explore massive volumes of sequencing data to classify and discover new sequences of interest without a mapping step and without intensive use of specialized bioinformatics pipelines. We demonstrate that our approach called GECKO for GEnetic Classification using k-mer Optimization is effective at classifying and extracting meaningful sequences from multiple types of sequencing approaches including mRNA, microRNA, and DNA methylome data.

Successful treatment of acute periprosthetic breast infection with curettage, pulse lavage, and immediate device exchange.

Acute periprosthetic breast infection in aesthetic surgical patients is a rare event. These patients would be expected to be less tolerant of the standard option of removing the infected implant and waiting 6 months (or possibly more) for tissue conditions to become favourable prior to reinsertion. This report provides confirmatory evidence of a controversial method of management that involves removal of the infected implant, curettage of granulation tissue within the breast implant pocket, pulsed lavage, then switching to a "clean" setup (including gloves, gowns, drapes and instruments) and reinsertion of a new device with suction drainage. The technique allows for immediate replacement of the implant and if successful, obviates the need for any waiting period. Surgeons are encouraged to consider this management option in specific cases where tissue vascularity and patient health are satisfactory.

Randomized, double-blind comparison of the efficacy of two hyaluronic acid derivatives, restylane perlane and hylaform, in the treatment of nasolabial folds.

BACKGROUND: Cross-linked hyaluronic acid gels may offer longer-lasting cosmetic correction and a lower risk of immunogenicity than other soft tissue augmentation agents. OBJECTIVE: To compare the efficacy and safety of a non-animal-stabilized hyaluronic acid gel (Restylane Perlane, Q-Med, Uppsala, Sweden) with that of a hylan B gel (Hylaform, Genzyme Corp., Cambridge, MA, USA), a cross-linked hyaluronic acid from chicken combs, for treatment of nasolabial folds. METHODS: One hundred fifty patients with moderate or severe nasolabial folds were randomized to contralateral treatment with Restylane Perlane and Hylaform. Efficacy was assessed using semi-objective outcome instruments at 3, 4.5, and 6 months after achievement of an "optimal cosmetic result". Patients subsequently underwent open-label bilateral retreatment with Restylane Perlane (if required) and were followed up for a further 6 months. RESULTS: The two products were equally effective in producing an optimal cosmetic result, although fewer treatment sessions were required with Restylane Perlane. At 6 months post-treatment, a higher proportion of patients showed a > or = 1-grade improvement in Wrinkle Severity Rating Scale (WSRS) score with Restylane Perlane (75%) than with Hylaform (38%). Restylane Perlane was considered superior in 64% of patients, whereas Hylaform was superior in 8% of patients. Treatment-related adverse events tended to be more frequent with Restylane Perlane. Local injection-site reactions were generally transient and mild or moderate in intensity and were no more frequent after Restylane Perlane retreatment. CONCLUSIONS: Restylane Perlane provides a more durable esthetic improvement than Hylaform and offers acceptable tolerability.