Revealing the human mutome

Chen JM, Férec C, Cooper DN. Revealing the human mutome. The number of known mutations in human nuclear genes, underlying or associated with human inherited disease, has now exceeded 100,000 in more than 3700 different genes (Human Gene Mutation Database). However, for a variety of reasons, this figure is likely to represent only a small proportion of the clinically relevant genetic variants that remain to be identified in the human genome (the ‘mutome’). With the advent of next‐generation sequencing, we are currently witnessing a revolution in medical genetics. In particular, whole‐genome sequencing (WGS) has the potential to identify all disease‐causing or disease‐associated DNA variants in a given individual. Here, we use examples of recent advances in our understanding of mutational/pathogenic mechanisms to guide our thinking about possible locations outwith gene‐coding sequences for those disease‐causing or disease‐associated variants that are likely so often to have been overlooked because of the inadequacy of current mutation screening protocols. Such considerations are important not only for improving mutation‐screening strategies but also for enhancing the interpretation of findings derived from genome‐wide association studies, whole‐exome sequencing and WGS. An improved understanding of the human mutome will not only lead to the development of improved diagnostic testing procedures but should also improve our understanding of human genome biology.     

Antimicrobial Activities of Skincare Preparations from Plant Extracts

In this study, Tithonia diversifolia Helms. (A Gray), Aloe secundiflora (Miller) and Azadirachta indica (A. Juss) plant extracts were used to make herbal soaps while Thevetia peruviana (Schum) seed oil was used to make a herbal lotion for skincare. The soaps were tested for the growth inhibition of Escherichia coli, and Candida albicans. The lotion was evaluated against Staphylococcus aureus and E.coli. Although Tithonia diversifolia soap exhibited the highest inhibitory effect on the test bacterial strains, it had the least inhibition against C. albicans. Results from this study indicated that the ‘Tithonia diversifolia’ soap would have superior skin protection against the tested bacteria but would offer the least skin protection against C. albicans. The herbal lotion inhibited S. aureus and E. coli in a concentration dependent manner, however, the inhibitory effect was more pronounced on S. aureus.     

p.R254Q mutation in the aquaporin‐2 water channel causing dominant nephrogenic diabetes insipidus is due to a lack of arginine vasopressin‐induced phosphorylation

Vasopressin regulates human water homeostasis by re‐distributing homotetrameric aquaporin‐2 (AQP2) water channels from intracellular vesicles to the apical membrane of renal principal cells, a process in which phosphorylation of AQP2 at S256 by cAMP‐dependent protein kinase A (PKA) is thought to be essential. Dominant nephrogenic diabetes insipidus (NDI), a disease in which the kidney is unable to concentrate urine in response to vasopressin, is caused by AQP2 gene mutations. Here, we investigated a reported patient case of dominant NDI caused by a novel p.R254Q mutation. Expressed in oocytes, AQP2‐p.R254Q appeared to be a functional water channel, but was impaired in its transport to the cell surface to the same degree as AQP2‐p.S256A, which mimics non‐phosphorylated AQP2. In polarized MDCK cells, AQP2‐p.R254Q was retained and was distributed similarly to that of unstimulated wt‐AQP2 or AQP2‐p.S256A. Upon co‐expression, AQP2‐p.R254Q interacted with, and retained wt‐AQP2 in intracellular vesicles. In contrast to wild‐type AQP2, forskolin did not increase AQP2‐p.R254Q phosphorylation at S256 or its translocation to the apical membrane. Mimicking constitutive phosphorylation in AQP2‐p.R254Q with the p.S256D mutation, however, rescued its apical membrane expression. These date indicate that a lack of S256 phosphorylation is the sole cause of dominant NDI here, and thereby, p.R254Q is a loss of function instead of a gain of function mutation in dominant NDI. © 2009 Wiley‐Liss, Inc.     

The salivary microbiota as a diagnostic indicator of oral cancer: A descriptive,non-randomized study of cancer-free and oral squamous cell carcinoma subjects

Background  

The purpose of the present investigation was to determine if the salivary counts of 40 common oral bacteria in subjects with an oral squamous cell carcinoma (OSCC) lesion would differ from those found in cancer-free (OSCC-free) controls.     

Mechanisms of enhanced prevalence of asthma and atopy in developed countries

Atopy — a T helper 2 cell driven hypersensitivity to innocuous antigens (allergens) which causes most cases of asthma — is of complex genetic and environmental origins. There is compelling epidemiological evidence for a rise in atopic disease in ‘westernised’ communities. The changing pattern of microbial exposure in early childhood is suggested to be the principal candidate mechanism for this rise.     

The role of recombination signal sequences in the preferential joining by deletion in DH-JH recombination and in the ordered rearrangement of the IgH locus

The bias favoring deletion over inversion in DH-JH rearrangement has been known for years, but the underlying mechanism has yet to be fully defined. It has been suggested that the ratio of deletion/inversion is determined by the combined effect of two factors: (i) the relative strengths of 5' and 3' recombination signal sequences (RSS) of a DH segment, and (ii) the efficiency with which the deletional product (one joint) forms relative to the inversional product (two joints). In this study, we analyzed for the first time the effect of factor 1 alone on the biased 3' RSS utilization in DH-JH joining by using deletional plasmids in an extrachromosomal substrate V(D)J recombination assay. It was found that the 3' RSS and associated coding end (12 bp) mediate recombination more efficiently than the 5' RSS/coding end DH-JH plasmids. These results demonstrate that the effect of the RSS/coding end alone can account, at least partially, for the predominant deletion in DH-JH recombination. The potential effect of the relative strength of RSS and associated coding end on the ordered rearrangement of DH-JH followed by VH to DH-JH was also assessed. When recombination frequencies of D-->J (3' DH to J3) were compared with frequencies of V-- >D (VHPJ14 to 3' DH or VHOX2 to 3' DH), it was found that V-->D joining was, if anything, more efficient than D-->J joining. Therefore, if all three segments were accessible, RSS/coding end effects would not contribute to the ordered rearrangement of the IgH locus.      

Expression of the apoptosis inhibitor, survivin, in nonmelanoma skin cancer and gene targeting in a keratinocyte cell line.

The recently described apoptosis inhibitor survivin is expressed in many human cancers, thus potentially contributing to disease progression and resistance to therapy. Its potential role in nonmelanoma skin cancer is unknown. By immunohistochemistry, survivin was expressed in 81% (17 of 21) of basal cell carcinomas (BCC) of both nodular and morpheaform subtypes, and in 92% (24 of 26) of cutaneous squamous cell carcinomas (SCC). Survivin was also expressed in 19 premalignant lesions of Bowen's disease (SCC in situ) and hypertrophic actinic keratosis (HAK), suggesting that its appearance occurs early during keratinocyte transformation. Survivin expression was detected by Western blotting in a model keratinocyte cell line, HaCat. Transfection of HaCat cells with green fluorescent protein (GFP)-conjugated survivin antisense or GFP-conjugated survivin dominant negative mutant (Cys84Ala) resulted in spontaneous apoptosis in the absence of other genotoxic stimuli. In GFP-conjugated survivin antisense transfectants, a decreased level of endogenous survivin was confirmed by flow cytometry. This was associated with a five-fold increase in the sub-G0/G1 fraction corresponding to apoptotic cells and a decrease in proliferating cells with 4N DNA content. These data demonstrate that apoptosis inhibition by survivin may participate in the onset and progression of both BCC and SCC, and suggest that therapeutic targeting of survivin may be beneficial in patients with recurrent or advanced disease.     

Physical activity modulates the effect of a lipoprotein lipase mutation (D9N) on plasma lipids and lipoproteins

We investigated interactions between a mutation (D9N) in the lipoprotein lipase (LPL) gene and physical activity, as well as other lifestyle factors, on lipid traits in a population-based sample of Dutch men and women (n = 379). We used questionnaire information to classify physical activity, alcohol consumption, and smoking habits, while overweight was defined as a body mass index (BMI) > 25 kg/m2. Non-fasting blood samples were used for the determination of lipid traits and the D9N genotype. Fifteen subjects (4%) carried the mutation. They presented with higher levels of total cholesterol, apolipoprotein (apo) B and triglycerides compared to non-carriers. While no interactions with overweight, alcohol consumption, and smoking were found, a strong interaction between the D9N mutation and physical activity became apparent. Physically inactive D9N carriers (n = 5) had considerably higher total cholesterol (+2 mmol/l, p < or = 0.0001) and apo B levels (+63 mg/dl, p < or = 0.0001) compared to non-carriers of this mutation, whereas their high-density lipoprotein (HDL)-cholesterol concentrations were lower (-0.22 mmol/l, p < 0.05). This was not the case for physically active D9N carriers (n = 10). In conclusion, a common variant of the LPL gene (D9N) adversely affects plasma lipid and lipoprotein profiles. However, the unfavorable consequences may be counteracted by physical activity.     

Differential returns from globalization to women smallholder coffee and food producers in rural Uganda

Background

Globalization-related measures to liberalize trade and stimulate export production were applied in Uganda in the late 1980s, including in the coffee production sector, to revitalize agricultural production, increase incomes to farmers and improve rural food security.

Objective

To explore the different effects of such measures on the health and dietary outcomes of female coffee and food small holder farmers in Uganda.

Methods

We gathered evidence through a cross-sectional comparative interview survey of 190 female coffee producers and 191 female food producers in Ntungamo district. The study mostly employed quantitative methods of data collection, targeting the sampled households. We also utilized qualitative data; collected three months after the household survey data had been collected and their analysis had been accomplished. Using qualitative interviews based on an unstructured interview guide, extra qualitative information was collected from key informants at national, district and community levels. This was among other underlying principles to avoid relying on snapshot information earlier collected at household level in order to draw valid and compelling conclusions from the study. We used indicators of production, income, access to food and dietary patterns, women''s health and health care. Of the two groups selected from the same area, female coffee producers represented a higher level of integration into liberalised export markets.

Results

Document review suggests that, although Uganda''s economy grew in the period, the household economic and social gains after the liberalization measures may have been less than expected. In the survey carried out, both food and coffee producers were similarly poor, involved in small-scale production, and of a similar age and education level. Coffee producers had greater land and livestock ownership, greater access to inputs and higher levels of income and used a wider variety of markets than food producers, but they had to work longer hours to obtain these economic returns, and spent more cash on health care and food from commercial sources. Their health outcomes were similar to those of the food producers, but with poorer dietary outcomes and greater food stress.

Conclusions

The small-scale women farmers who are producing food cannot rely on the economic infrastructure to give them support for meaningful levels of production. However, despite having higher incomes than their food producing counterparts, the evidence showed that women who are producing coffee in Uganda as an export commodity cannot rely on the income from their crops to guarantee their health and nutritional wellbeing, and that the income advantage gained in coffee-producing households has not translated into consistently better health or food security outcomes. Both groups have limited levels of autonomy and control to address these problems.