Somatic point mutations are enriched in non-coding RNAs with possible regulatory function in breast cancer

Non-coding RNAs (ncRNAs) form a large portion of the mammalian genome. However, their biological functions are poorly characterized in cancers. In this study, using a newly developed tool, SomaGene, we analyze de novo somatic point mutations from the International Cancer Genome Consortium (ICGC) whole-genome sequencing data of 1,855 breast cancer samples. We identify 1030 candidates of ncRNAs that are significantly and explicitly mutated in breast cancer samples. By integrating data from the ENCODE regulatory features and FANTOM5 expression atlas, we show that the candidate ncRNAs significantly enrich active chromatin histone marks (1.9 times), CTCF binding sites (2.45 times), DNase accessibility (1.76 times), HMM predicted enhancers (2.26 times) and eQTL polymorphisms (1.77 times). Importantly, we show that the 1030 ncRNAs contain a much higher level (3.64 times) of breast cancer-associated genome-wide association (GWAS) single nucleotide polymorphisms (SNPs) than genome-wide expectation. Such enrichment has not been seen with GWAS SNPs from other cancers. Using breast cell line related Hi-C data, we then show that 82% of our candidate ncRNAs (1.9 times) significantly interact with the promoter of protein-coding genes, including previously known cancer-associated genes, suggesting the critical role of candidate ncRNA genes in the activation of essential regulators of development and differentiation in breast cancer. We provide an extensive web-based resource (https://www.ihealthe.unsw.edu.au/research) to communicate our results with the research community. Our list of breast cancer-specific ncRNA genes has the potential to provide a better understanding of the underlying genetic causes of breast cancer. Lastly, the tool developed in this study can be used to analyze somatic mutations in all cancers.

The SomaGene tool is developed to identify non-coding RNAs (ncRNAs) mutated in breast cancer but can be used for other cancers. Candidate ncRNAs are shown to be enriched for regulatory features and to contain specific trait loci polymorphisms.

Impact of Particle Size and Polydispersity Index on the Clinical Applications of Lipidic Nanocarrier Systems

Lipid-based drug delivery systems, or lipidic carriers, are being extensively employed to enhance the bioavailability of poorly-soluble drugs. They have the ability to incorporate both lipophilic and hydrophilic molecules and protecting them against degradation in vitro and in vivo. There is a number of physical attributes of lipid-based nanocarriers that determine their safety, stability, efficacy, as well as their in vitro and in vivo behaviour. These include average particle size/diameter and the polydispersity index (PDI), which is an indication of their quality with respect to the size distribution. The suitability of nanocarrier formulations for a particular route of drug administration depends on their average diameter, PDI and size stability, among other parameters. Controlling and validating these parameters are of key importance for the effective clinical applications of nanocarrier formulations. This review highlights the significance of size and PDI in the successful design, formulation and development of nanosystems for pharmaceutical, nutraceutical and other applications. Liposomes, nanoliposomes, vesicular phospholipid gels, solid lipid nanoparticles, transfersomes and tocosomes are presented as frequently-used lipidic drug carriers. The advantages and limitations of a range of available analytical techniques used to characterize lipidic nanocarrier formulations are also covered.

A synthetic co-crystal prepared by cooperative single-crystal-to-single-crystal solid-state Diels–Alder reaction

Solid-state Diels–Alder reaction in a 2 : 1 donor to acceptor charge-transfer complex leads to a synthetic co-crystal composed of product and unreacted donor. Analysis of close contacts and DFT energy calculations indicate that the reaction occurs cooperatively where the arrangement of molecules shown in (ii) is favoured.

A single-crystal-to-single-crystal Diels–Alder reaction with mixed topochemical and topotactic behaviour

During a SCSC solid-state Diels–Alder reaction, voids are created, followed by conformational change and crystal annealing that lead to the formation of new weak interactions.