Pan-cancer association of DNA repair deficiencies with whole-genome mutational patterns.

DNA repair deficiencies in cancers may result in characteristic mutational patterns, as exemplified by deficiency of BRCA1/2 and efficacy prediction for PARP inhibitors. We trained and evaluated predictive models for loss-of-function (LOF) of 145 individual DNA damage response genes based on genome-wide mutational patterns, including structural variants, indels, and base-substitution signatures. We identified 24 genes whose deficiency could be predicted with good accuracy, including expected mutational patterns for BRCA1/2, MSH3/6, TP53, and CDK12 LOF variants. CDK12 is associated with tandem duplications, and we here demonstrate that this association can accurately predict gene deficiency in prostate cancers (area under the receiver operator characteristic curve = 0.97). Our novel associations include mono- or biallelic LOF variants of ATRX, IDH1, HERC2, CDKN2A, PTEN, and SMARCA4, and our systematic approach yielded a catalogue of predictive models, which may provide targets for further research and development of treatment, and potentially help guide therapy.

Many different aspects of the environment ­ such as ultraviolet radiation, carcinogens in food and drink, and the ageing process itself ­ damage the DNA in human cells. Normally, cells can repair these sites by activating a mechanism known as the DNA damage response. However, the hundreds of genes that orchestrate this response are also themselves often lost or damaged, allowing the unrepaired sites to turn into permanent mutations that accumulate across the genome of the cancer cell. By studying the DNA of cancer cells, it has been possible to identify characteristic patterns of mutations, called mutational signatures, that appear in different types of cancer. One specific pattern has been linked to the loss of either the BRCA1 or BRCA2 gene, both of which are part of the DNA damage response. However, it remained unclear how many other genes involved in the DNA damage response also lead to detectable mutational signatures when lost. To investigate, Sørensen et al. computationally analysed data from over six thousand cancer patients. They looked for associations between over 700 DNA damage response genes and 80 different mutational signatures. As expected, the analysis revealed a strong connection between the loss of BRCA1/BRCA2 and their known mutational signature. However, it also found 23 other associations between DNA damage response genes that had been lost or damaged and particular patterns of mutations in a variety of cancers. These findings suggest that mutational signatures could be used more widely to predict which DNA damage response genes are no longer functioning in the genome of cancer cells. The mutational signature caused by the loss of BRAC1/BRAC2 has been shown to make patients more responsive to a certain type of chemotherapy. Further experiments are needed to determine whether the connections identified by Sørensen et al. could also provide information on which treatment would benefit a cancer patient the most. In the future, this might help medical practitioners provide more personalized treatment.

Novel noscapine derivatives stabilize the native state of insulin against fibrillation.

Protein aggregation to form amyloid is associated with many human diseases, increasing the need to develop inhibitors of this process. Here we evaluate the ability of derivatives of the small organic compound noscapine, derived from the opium poppy, to inhibit fibrillation of the model protein insulin. We combined biophysical methods to assess insulin stability and aggregation with computational docking and cell viability studies to identify the most potent derivatives. The best aggregation inhibitor (a phenyl derivative of N-nornoscapine) also demonstrated the highest ability to stabilize native insulin against thermal denaturation. This compound maintained insulin largely in the monomeric and natively folded state under fibrillation conditions and also decreased insulin aggregate toxicity against human neuroblastoma SH-SY5Y cells. The inhibitory effects were specific for insulin fibrillation, as the noscapine compounds did not inhibit fibrillation of other proteins such as α-synuclein, Aß, and FapC. Our data demonstrate that compounds which stabilize the folded native state of a protein can not only inhibit fibrillation but also decrease the toxicity of the mature fibrillar aggregates of insulin protein.