This review aimed to arrange the process of a systematic review of genome-wide association studies in order to practice and apply a genome-wide meta-analysis (GWMA). The process has a series of five steps: searching and selection, extraction of related information, evaluation of validity, meta-analysis by type of genetic model, and evaluation of heterogeneity. In contrast to intervention meta-analyses, GWMA has to evaluate the Hardy-Weinberg equilibrium (HWE) in the third step and conduct meta-analyses by five potential genetic models, including dominant, recessive, homozygote contrast, heterozygote contrast, and allelic contrast in the fourth step. The 'genhwcci' and 'metan' commands of STATA software evaluate the HWE and calculate a summary effect size, respectively. A meta-regression using the 'metareg' command of STATA should be conducted to evaluate related factors of heterogeneities.

Endothelin-1 (ET-1) is a hormone peptide widely expressed and is involved in several biological processes, important not only for normal cell function but also for tumor development, including cell proliferation, invasion, metastasis, angiogenesis and osteogenesis. In accordance, ET-1 was already shown to contribute to the growth and progression of many different solid cancers. We recently demonstrated that ET-1 has a role in the pathogenesis of chronic lymphocytic leukemia (CLL) where it is abnormally expressed. In the context of this malignancy, ET-1 is able to mediate survival, drug-resistance and growth signals in leukemic cells. Previous studies, not conducted in CLL, have shown that ET-1 regulatory mechanisms are numerous and cell specific. Here, we valued the expression of ET-1 in CLL, in relation to DNA methylation but also in response to stimulation of some important pathways for the dialogue between CLL and microenvironment. We found that a high methylation of ET-1 first intron affects the basal expression of ET-1 in CLL. Moreover, we showed that the activation of CD40 or Toll-like receptor (TLR) by extracellular stimuli produces an augment of ET-1 level in CLL cells. Finally, we demonstrated the fundamental role of NF-kB signalling pathway in promoting and maintaining ET-1 expression in CLL cells, both in basal conditions and after CD40 activation.

Gene silencing through RNA interference (RNAi) has emerged as a potential strategy in manipulating cancer causing genes by complementary base-pairing mechanism. Small interfering RNA (siRNA) is an important RNAi tool that has found significant application in cancer therapy. However due to lack of stability, poor cellular uptake and high probability of loss-of-function due to degradation, siRNA therapeutic strategies seek safe and efficient delivery vehicles for in vivo applications. The current review discusses various nanoparticle systems currently used for siRNA delivery for cancer therapy, with emphasis on liposome based gene delivery systems. The discussion also includes various methods availed to improve nanoparticle based-siRNA delivery with target specificity and superior efficiency. Further this review describes challenges and perspectives on the development of safe and efficient nanoparticle based-siRNA-delivery systems for cancer therapy.

DNA repair by homologous recombination (HR) underpins cell survival and fuels genome instability, cancer, and evolution. However, the main kinds and sources of DNA damage repaired by HR in somatic cells and the roles of important HR proteins remain elusive. We present engineered proteins that trap, map, and quantify Holliday junctions (HJs), a central DNA intermediate in HR, based on catalytically deficient mutant RuvC protein of Escherichia coli. We use RuvCDefGFP (RDG) to map genomic footprints of HR at defined DNA breaks in E. coli and demonstrate genome-scale directionality of double-strand break (DSB) repair along the chromosome. Unexpectedly, most spontaneous HR-HJ foci are instigated, not by DSBs, but rather by single-stranded DNA damage generated by replication. We show that RecQ, the E. coli ortholog of five human cancer proteins, nonredundantly promotes HR-HJ formation in single cells and, in a novel junction-guardian role, also prevents apparent non-HR-HJs promoted by RecA overproduction. We propose that one or more human RecQ orthologs may act similarly in human cancers overexpressing the RecA ortholog RAD51 and find that cancer genome expression data implicate the orthologs BLM and RECQL4 in conjunction with EME1 and GEN1 as probable HJ reducers in such cancers. Our results support RecA-overproducing E. coli as a model of the many human tumors with up-regulated RAD51 and provide the first glimpses of important, previously elusive reaction intermediates in DNA replication and repair in single living cells.

Information on the cancer genome has accumulated rapidly, since approximately 2009, with the use of second-generation sequencing technology. Malignant lymphoma is no exception. In mature B-cell lymphomas, which constitute the vast majority of non-Hodgkin lymphomas, frequent mutations are identified in genes involved in signaling pathways, histone-modifying molecules, the DNA damage-response pathway, etc. The signaling pathways in which multiple genes are mutated include immune cell-specific pathways such as the B-cell receptor, the Toll-like receptor, and their downstream NF-κB signaling pathways, as well as the NOTCH signaling pathway. In mature T/NK-cell lymphomas, mutations accumulate in genes involved in the T-cell receptor pathway and its downstream NF-κB signaling pathway, regulators of DNA methylation, the JAK-STAT pathway, etc. Many of these mutations are found in multiple types of lymphomas but the frequencies of each gene mutation differ among diseases, demonstrating characteristic profiles. This cumulative and growing fund of knowledge provides an important basis for the development of new molecular-targeted drugs.

Acute myeloid leukemia (AML) is a heterogeneous disease, the onset of which involves a variety of chromosomal abnormalities and gene mutations. In recent years, the use of next-generation sequencers has facilitated intensive exploration of gene mutations resulting in the discovery of many AML-related gene mutations, and in clarifying the clonal evolution process of relapse. Epigenetic regulatory gene mutations have occurred in pre-leukemic cells with normal differentiation potential, and the acquisition of numerous genetic mutations was found to be strongly associated with AML onset, with further co-mutations contributing to clonal diversity and leading to the generation of treatment-resistant clones. As a result of these fruitful findings, the gene mutations of AML are becoming useful as not only prognostic factors but also the targets of molecular medicines such as FLT3 and IDH inhibitors. Most notably, several guidelines have proposed a prognostic classification that groups FLT3ITD, NPM1 mutation, and CEBPA mutation together under conventional chromosomal aberrations. This review outlines recent findings pertaining to the gene mutations in AML.

This review outlines recent advances in the understanding of gene alterations and the genetic background associated with myeloproliferative neoplasms (MPNs), as well as describing the roles of these genetic factors in the development of MPNs. JAK2, CALR, and MPL mutations that are specifically found in patients with MPNs have been shown to constitutively activate cytokine receptors. Other mutations that are commonly found in hematopoietic malignancies have been demonstrated to synergize with disease-specific mutations and to accelerate the development of MPN, or to define the disease subtype. However, some of these mutations are found in healthy elderly persons, such that the mechanism of MPN development remains elusive. Further analyses including those for genetic factors associated with the occurrence of MPN will lead to a complete understanding of MPN development.

Controversy exists regarding the effectiveness of early adjuvant versus salvage radiation therapy after prostatectomy for prostate cancer. Estimates of prostate cancer progression from the Decipher genomic classifier (GC) could guide informed decision-making and improve the outcomes for patients.

The clinical responsiveness to epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) in non-small-cell lung cancer (NSCLC) patients with exon 19 insertion and the specific exon 20 insertion (A763_Y764 insFQEA) are still not well known.

Cytogenetic analysis aides in risk stratification for patients with multiple myeloma (MM). Although several cytogenetic aberrations have been reported to be prognostic, less is known about the association between the presence of monosomies and prognosis. The present study evaluated the prevalence and prognostic implications of monosomies in patients with MM.