Neo-Darwinian Principles Exemplified in Cancer Genomics.

Within the last two decades, the advent of next-generation sequencing accompanied by single-cell technologies has enabled cancer researchers to study in detail mutations and other genetic aberrations that transpire during transformation of cells to a neoplastic state. This article covers the insights gained through these extensive studies where neo-Darwinian principles can be inferred to play roles throughout neoplastic transformation. The cells promoted during cancer development exhibit cancer hallmarks combined with the related enabling characteristics as outlined by Hanahan and Weinberg, analogous to natural selection and survival of the fittest. Selection of driver mutations that inactivate proteins encoded by tumor suppressor genes differs in profound ways from mutations that activate tumor promoter proteins. In most cases, the later stages of cancer development are characterized by sudden, extensive damage to chromosomes in a process that is not Darwinian in nature. Nevertheless, cells that survive these cataclysmic events remain subject to Darwinian selection promoting clones exhibiting the greatest rates of progression. Duplications of chromosomal segments containing oncogenes, deletions of segments harboring tumor suppressor genes, or distinctive chromosomal rearrangements are often found in cells progressing into later stages of cancer. In summary, the technological developments in genome sequencing since the start of the century have given us clear insights into genomic alterations promoting tumor progression where neo-Darwinian mechanisms of clonal selection can be inferred to play a primary role.

Standard operating procedures for serum and plasma collection: early detection research network consensus statement standard operating procedure integration working group.

Specimen collection is an integral component of clinical research. Specimens from subjects with various stages of cancers or other conditions, as well as those without disease, are critical tools in the hunt for biomarkers, predictors, or tests that will detect serious diseases earlier or more readily than currently possible. Analytic methodologies evolve quickly. Access to high-quality specimens, collected and handled in standardized ways that minimize potential bias or confounding factors, is key to the "bench to bedside" aim of translational research. It is essential that standard operating procedures, "the how" of creating the repositories, be defined prospectively when designing clinical trials. Small differences in the processing or handling of a specimen can have dramatic effects in analytical reliability and reproducibility, especially when multiplex methods are used. A representative working group, Standard Operating Procedures Internal Working Group (SOPIWG), comprised of members from across Early Detection Research Network (EDRN) was formed to develop standard operating procedures (SOPs) for various types of specimens collected and managed for our biomarker discovery and validation work. This report presents our consensus on SOPs for the collection, processing, handling, and storage of serum and plasma for biomarker discovery and validation.

Deletion of the NOT4 gene impairs hyphal development and pathogenicity in Candida albicans.

The Candida albicans NOT4 gene was disrupted in order to investigate the role of Not4p in growth, morphogenesis and pathogenicity. Heterozygote (NOT4/not4), null (not4/not4) and reconstructed heterozygote ([NOT4]/not4) strains of C. albicans, as well as CAF2-1, the parental strain, were grown under conditions that promote hyphal formation. When cultured in liquid medium 199 the heterozygote, reconstructed and wild-type strains began the yeast-to-hyphal transition within 3 h and continued hyphal growth for the duration of experiments. The null mutant also began hyphal growth within 3-5 h but hyphae tended to be shorter and distorted. Subsequently, hyphal growth was arrested and growth returned predominantly to the yeast form. Similar differences were observed when strains were grown on solid Spider medium and medium 199. The parental, heterozygote and reconstructed strains formed normal filamentous networks emanating from colonies. In contrast, the null mutant failed to form hyphae on all solid media tested. The ability of the NOT4 null strain to form biofilms was also investigated, and it was observed that biofilm development does not readily occur for this strain. Virulence of each strain was examined utilizing the mouse model of systemic candidiasis. Mice infected with CAF2-1 succumbed to infection within 3-7 days. All mice infected with the null strain survived for the duration of experiments, while the heterozygote and reconstructed heterozygote strains showed an intermediate level of virulence. These findings suggest that NOT4 may play a role in affecting strain pathogenicity, possibly by regulating expression of certain genes that effect cellular morphogenesis and virulence.