Number Of Non-synonymous Mutations Research Articles

Functional polymorphisms in cancer.

Germline variants (single nucleotide polymorphisms, SNPs) represent the vast majority of genetic changes occurring in cancer relative to the reference human genome. Two randomly chosen healthy individuals differ by approximately 20,000 germline variants in their exome [1]. In contrast, most solid tumors harbor an average of 30 to 100 somatic mutations that are considered potentially important in cancer biology. In breast cancer, the median number of non-synonymous mutations per cancer is 33 [1]. An unexpected observation from large scale sequencing efforts was the relative paucity of high frequency, recurrent somatic driver mutations in most solid tumors, which instead present a variable assortment of low frequency mutations in unique combinations in each cancer. These observations raise the possibility that inherited risk-modifying functional SNPs may interact with somatic mutations to collectively cause the malignant phenotype. Inter-individual physiological and anatomical differences, to a large extent, are attributable to differences in germline variants, which illustrates the biological importance of functional polymorphisms. Disease-causing mutations are a subtype of SNPs that have profound deleterious effect on health, whereas other germline variants increase the risk for cancer development (e.g. BRCA1, CHEK2, FGF receptors, etc.) [2, 3]. The biological functional effect of the vast majority of human SNPs has not been studied yet. However, there is an increasing list of germ line variants that have been shown experimentally to impact protein function, without detectable association with disease states. For example, the M326I variant (rs3730089) in the p85α regulatory subunit of Phosphatidylinositol 3-kinase (PI3K) results in reduced protein expression and constitutively increased activity of the PI3K pathway [4]. Similarly, the L1016S variant (rs61733127) in the PH domain and Leucine-rich repeat Protein Phosphatase 2 (PHLPP2) leads to reduced phosphatase activity and increased signaling through the AKT and Protein Kinase C (PKC) pathways (which are both substrates of PHLPP2) [5]. The article by Liu et al. adds to the growing list of publications that examine the functional impact of rare germline variants in the laboratory [6]. They studied a germline variant in the MET gene (Hepatocyte Growth Factor [HGF] Receptor), MET-T1010I (rs56391007), that occurs in <1% of the normal population but was observed in 2 % of metastatic breast cancer patients (n=240) in their study. It has also been previously linked to hereditary lung and colorectal cancer. They report that the expression of MET-T1010I in the MCF-10A immortalized breast epithelial cell line caused marked functional consequences including increased colony formation, cell migration, and invasion in-vitro. It also increased tumor growth in-vivo in human HGF transgenic mice. It is important to note that this SNP has not been associated with increased risk for developing breast cancer in large genome wide association studies and previous laboratory studies have reported conflicting functional effects for the T1010I variant in NIH3T3 fibroblast and murine myeloid BA/F3 cell line models as discussed by Liu et al. These observations support the hypothesis that the effect of this SNP, and probably many others, is genomic context dependent. What constitutes a somatic cancer driver event may depend on the constellation of polymorphisms already present in an individual's germline, which could explain the lack of high frequency recurrent oncogenic mutations in breast cancer (other than PI3K and P53). This could also explain the cell line-restricted, transforming effects of many known oncogenes because several studies have shown that oncogenes do not transform every type of cell or cell line even from the same tissue. To further support the important role of inherited genetic variants in the biology of sporadic cancers, several recent studies have demonstrated that the prognosis of early stage breast cancer tends to cluster by families, suggesting a hereditary component that is independent of tumor characteristics and treatment [7]. Better understanding of the functional interactions between germline and somatic genetic events represents a fertile ground for research, and could fundamentally change the way we think about cancer biology.

ARID1A Is Recurrently and Significantly Mutated in Follicular Lymphoma (FL) and Impairs DNA Repair Efficiency

FL is the most common indolent nodal lymphoma and considered incurable for the majority of patients. Virtually all patients eventually develop resistant disease, and up to 45% histologic transformation (tFL) with poor outcome. Alterations associated with progression to tFL include increased copy number variations (e.g. CDKN2A deletions, MYC amplification), acquisition of additional translocations (e.g. MYC or BCL6), and higher mutation load (including TP53). However the underlying molecular mechanisms promoting this genomic instability remain elusive. Interestingly, histologic transformation occurs at a remarkably constant rate of ~3% per year implying a rather stochastic process.We previously described convergent evolution for disruptive ARID1A mutations in FLs of a donor and the recipient patient following an allogeneic bone marrow transplantation (Weigert, Canc Discovery 2012). The independent acquisition of ARID1Aloss in two separate hosts after transplantation of an identical FL ancestor clone suggested (i) a later acquired event in the molecular ontogeny and (ii) functional relevance.ARID1A promotes the formation of SWI/SNF nucleosome remodeling complexes containing BRG1 or BRM, which catalyze disruption of DNA-histone contacts, thereby controlling chromatin condensation and DNA accessibility. Nucleosome-remodelling has been linked to DNA damage response, including nucleotide and base excision repair, homologous recombination and non-homologous end-joining (NHEJ). We thus hypothesized that ARID1Ahaplodeficiency might contribute to genetic and genomic instability in FL.In a cohort of 305 FL specimens, we identified 44 ARID1A mutations in 43 patients (14%). The majority of these mutations were disruptive (66%; 19 nonsense and 10 frame shift mutations), 6 cases harbored splice site mutations. MutSigCV analysis (Lawrence, Nature 2013) indicated that ARID1A was significantly mutated in FL, i.e. more often than expected by chance given background mutation processes. Consistent with our hypothesis, the number of non-synonymous mutations in 104 targeted genes was higher in ARID1A mutated FLs (5.6+0.34, mean+sem) compared to ARID1A wild-type (wt) FLs (4.7+0.12; p=0.0099), and similar compared to 17 FLs with TP53 mutations (5.6+0.12). Of note, ARID1A and TP53 mutations were mutually exclusive.For functional studies, we confirmed deleterious ARID1A alterations in 6 lymphoma cell lines (Namalwa, Karpas422, SUPHD-1, SU-DHL5, WSU-FSCCL, U-OH1). Immunoblotting showed decreased ARID1A protein expression in all 6 lines compared to 5 ARID1A wt lymphomas. Tet-induced re-expression of ARID1A in two tested ARID1A mutant cell lines (Namalwa and SUP-HD1) reduced cell proliferation compared to tet-induced control (LacZ), but had no effect in ARID1A wt OCI-Ly1.As a proof-of-principle experiment we assayed the impact of ARID1A loss on DNA double strand break (DSB) repair efficiency in genetically well defined mouse embryo fibroblasts (MEFs), avoiding uncontrolled bias introduced by the genetic and genomic complexity in lymphoma cell lines. Early passage MEFs from either wt or conditional ARID1A knock-out mice (ARID1Af/f; Gao, PNAS 2008) were transiently transfected or retrovirally transduced with self-excising Cre-recombinase (Silver&Livingston, Mol Cell 2001) or control, and irradiated with 2 Gy after 36 hrs. Cre-induced ARID1A loss was confirmed by Western blot. To assay NHEJ, the predominate DSB-repair pathway used by cells in G1 phase, we stained cells for γH2A.X and 53BP1. In 3 independent and blinded experiments, evaluation of >100 cells per condition demonstrated significantly more double-positive cells (>6 foci/cell) in ARID1A-/- MEFs (43+14%) compared to both ARID1Af/fMEFs (9+1%) and Cre-exposed wt MEFs (15+5%) at 16 hrs post irradiation, whereas there was no significant difference for ARID1Af/for wt MEFs with or without Cre at baseline (all <10%), and 1 hr post irradiation (all >50%). This data indicates that ARID1A loss slows the repair kinetics of NHEJ and delays the clearance of DSB.We conclude that ARID1A is recurrently and significantly mutated in FL. Most mutations are disruptive leading to functionally relevant ARID1A protein haplodeficiency. ARID1A loss impairs NHEJ, which might sensitize tumors to DNA damaging agents and irradiation, but also contribute to genetic and genomic instability promoting histologic transformation. DisclosuresNo relevant conflicts of interest to declare.

Competence in Streptococcus pneumoniae Is a Response to an Increasing Mutational Burden

Competence for genetic transformation in Streptococcus pneumoniae has previously been described as a quorum-sensing trait regulated by a secreted peptide pheromone. Recently we demonstrated that competence is also activated by reduction in the accuracy of protein biosynthesis. We have now investigated whether errors upstream of translation in the form of random genomic mutations can provide a similar stimulus. Here we show that generation of a mutator phenotype in S. pneumoniae through deletions of mutX, hexA or hexB enhanced the expression of competence. Similarly, chemical mutagenesis with the nucleotide analog dPTP promoted development of competence. To investigate the relationship between mutational load and the activation of competence, replicate lineages of the mutX strain were serially passaged under conditions of relaxed selection allowing random accumulation of secondary mutations. Competence increased with propagation in these lineages but not in control lineages having wild-type mutX. Resequencing of these derived strains revealed between 1 and 9 single nucleotide polymorphisms (SNPs) per lineage, which were broadly distributed across the genome and did not involve known regulators of competence. Notably, the frequency of competence development among the sequenced strains correlated significantly with the number of nonsynonymous mutations that had been acquired. Together, these observations provide support for the hypothesis that competence in S. pneumoniae is regulated in response to the accumulated burden of coding mutations in the bacterial genome. In contrast to previously described DNA damage response systems that are activated by physical lesions in the chromosome, this pneumococcal pathway may represent a unique stress response system that monitors the coding integrity of the genome.

DNA mutagenesis in 2- and 20-yr-old Panax ginseng cell cultures

Previously, Panax ginseng var. Mimaki C.A. Meyer had been shown to accumulate genetic mutations during long-term propagation of a callus culture over a period of 20 yr. In this study, we analyzed the mutation types and frequency in a 2-yr-old P. ginseng callus culture and compared it with the 20-yr-old callus culture, and leaves of cultivated plants. We analyzed the sequence variability between the Actin genes, which are a family of housekeeping genes; phenylalanine ammonia-lyase (PAL) and dammarenediol synthase (DDS), which actively participate in the biosynthesis of ginsenosides; and the somatic embryogenesis receptor kinases (SERK), which control plant development. The frequency of point mutations in the Actin, PAL, DDS, and SERK genes in the 2-yr-old P. ginseng callus culture was markedly higher than in cultivated plants, but lower than in the 20-yr-old callus culture. Most of the mutations in the 2-yr-old P. ginseng calli were A↔G and T↔C transitions, as in the 20-yr-old calli and intact P. ginseng plants. The number of nonsynonymous mutations was higher in the 2- and 20-yr-old callus cultures than the number of nonsynonymous mutations in cultivated P. ginseng. Interestingly, the total number of N→G or N→C substitutions in the analyzed genes was 1.6 times higher than the total number of N→A or N→T substitutions. Using a methylation-sensitive DNA fragmentation assay, we showed the level of methylcytosine to be higher in the DNA of the 20-yr-old P. ginseng calli that than in the DNA of the 2-yr-old cultures.

Comparison of novel MLB-clade, VA-clade and classic human astroviruses highlights constrained evolution of the classic human astrovirus nonstructural genes

Eight serotypes of human astroviruses (the classic human astroviruses) are causative agents of diarrhea. Recently, five additional astroviruses belonging to two distinct clades have been described in human stool, including astroviruses MLB1, MLB2, VA1, VA2 and VA3. We report the discovery in human stool of two novel astroviruses, astroviruses MLB3 and VA4. The complete genomes of these two viruses and the previously described astroviruses VA2 and VA3 were sequenced, affording seven complete genomes from the MLB and VA clades for comparative analysis to the classic human astroviruses. Comparison of the genetic distance, number of synonymous mutations per synonymous site (dS), number of non-synonymous mutations per non-synonymous site (dN) and the dN/dS ratio in the protease, polymerase and capsid of the classic human, MLB and VA clades suggests that the protease and polymerase of the classic human astroviruses are under distinct selective pressure.

Evidence for reduced selection pressure on the hepatitis B virus core gene in hepatitis B e antigen-negative chronic hepatitis B

The mechanisms underlying the high levels of hepatitis B virus (HBV) replication that cause hepatitis B e antigen (HBeAg)-negative chronic hepatitis B (e-CHB) are unknown. Impaired anti-HBV immunity, which may be measurable as a relaxation of selection pressure on the virus, is possible. A group of Tongans (n = 345) with a chronic HBV infection, including seven with e-CHB, were genotyped at HLA class I. The repertoire of HBV core-gene codons under positive selection pressure was defined by phylogenetic analysis (by using the paml program) of 708 cloned sequences extracted from the 67 of these 345 subjects with the same repertoire of HLA class I alleles as the seven e-CHB individuals and matched controls (see below). The frequency of non-synonymous mutations at these codons was measured in longitudinal data from 15 subjects. Finally, the number of non-synonymous mutations at these codons was compared in seven groups comprised of one subject with e-CHB and 1-3 HLA class I-matched controls with an inactive, HBeAg-negative chronic HBV infection (e-InD). Nineteen codons in the core gene were under positive selection pressure. There was a high frequency of new non-synonymous mutations at these codons (P<0.0001) in longitudinal data. The mean number of these 19 codons with non-synonymous mutations was lower (P = 0.02) in HBV from subjects with e-CHB (4.4±0.5 codons per subject) versus those with e-InD (6.4±0.4 codons per subject). There is a subtle relaxation in selection pressure on the HBV core gene in e-CHB. This may be due to impaired antiviral immunity, and could contribute to the high levels of viral replication that cause liver inflammation in this disease.

Genome variability and capsid structural constraints of hepatitis a virus.

The number of synonymous mutations per synonymous site (K(s)), the number of nonsynonymous mutations per nonsynonymous site (K(a)), and the codon usage statistic (N(c)) were calculated for several hepatitis A virus (HAV) isolates. While K(s) was similar to those of poliovirus (PV) and foot-and-mouth disease virus (FMDV), K(a) was 1 order of magnitude lower. The N(c) parameter provides information on codon usage bias and decreases when bias increases. The N(c) value in HAV was about 38, while in PV and FMDV, it was about 53. The emergence of 22 rare codons in front of 8 in PV and 7 in FMDV was detected. Most of the conserved rare codons of the P1 region were strategically located at the carboxy borders of beta barrels and alpha helices, their potential function being the assurance of proper folding of the capsid proteins through a decrease in the translation speed. This strategic location was not observed for amino acids encoded by the conserved rare codons of the 3D region. The percentage of bases with low pairing number values was higher in the latter region, suggesting a role of the conserved rare codons in the maintenance of RNA structure. Many of the rare codons in HAV are among the most frequent in humans, unlike in PV or in FMDV. This fact may be explained by the lack of cellular shutoff in HAV. One hypothesis is that HAV has evolved in order to avoid competition with its host for cellular tRNAs.