Positive Mutation Research Articles

Variegated RHOA mutations in adult T-cell leukemia/lymphoma

AbstractAdult T-cell leukemia/lymphoma (ATLL) is a distinct form of peripheral T-cell lymphoma with poor prognosis, which is caused by the human T-lymphotropic virus type 1 (HTLV-1). In contrast to the unequivocal importance of HTLV-1 infection in the pathogenesis of ATLL, the role of acquired mutations in HTLV-1 infected T cells has not been fully elucidated, with a handful of genes known to be recurrently mutated. In this study, we identified unique RHOA mutations in ATLL through whole genome sequencing of an index case, followed by deep sequencing of 203 ATLL samples. RHOA mutations showed distinct distribution and function from those found in other cancers. Involving 15% (30/203) of ATLL cases, RHOA mutations were widely distributed across the entire coding sequence but almost invariably located at the guanosine triphosphate (GTP)-binding pocket, with Cys16Arg being most frequently observed. Unexpectedly, depending on mutation types and positions, these RHOA mutants showed different or even opposite functional consequences in terms of GTP/guanosine diphosphate (GDP)-binding kinetics, regulation of actin fibers, and transcriptional activation. The Gly17Val mutant did not bind GTP/GDP and act as a dominant negative molecule, whereas other mutants (Cys16Arg and Ala161Pro) showed fast GTP/GDP cycling with enhanced transcriptional activation. These findings suggest that both loss- and gain-of-RHOA functions could be involved in ATLL leukemogenesis. In summary, our study not only provides a novel insight into the molecular pathogenesis of ATLL but also highlights a unique role of variegation of heterologous RHOA mutations in human cancers.

Model-based mutation testing—Approach and case studies

This paper rigorously introduces the concept of model-based mutation testing (MBMT) and positions it in the landscape of mutation testing. Two elementary mutation operators, insertion and omission, are exemplarily applied to a hierarchy of graph-based models of increasing expressive power including directed graphs, event sequence graphs, finite-state machines and statecharts. Test cases generated based on the mutated models (mutants) are used to determine not only whether each mutant can be killed but also whether there are any faults in the corresponding system under consideration (SUC) developed based on the original model. Novelties of our approach are: (1) evaluation of the fault detection capability (in terms of revealing faults in the SUC) of test sets generated based on the mutated models, and (2) superseding of the great variety of existing mutation operators by iterations and combinations of the two proposed elementary operators. Three case studies were conducted on industrial and commercial real-life systems to demonstrate the feasibility of using the proposed MBMT approach in detecting faults in SUC, and to analyze its characteristic features. Our experimental data suggest that test sets generated based on the mutated models created by insertion operators are more effective in revealing faults in SUC than those generated by omission operators. Worth noting is that test sets following the MBMT approach were able to detect faults in the systems that were tested by manufacturers and independent testing organizations before they were released.

Improving HIV proteome annotation: new features of BioAfrica HIV Proteomics Resource.

The Human Immunodeficiency Virus (HIV) is one of the pathogens that cause the greatest global concern, with approximately 35 million people currently infected with HIV. Extensive HIV research has been performed, generating a large amount of HIV and host genomic data. However, no effective vaccine that protects the host from HIV infection is available and HIV is still spreading at an alarming rate, despite effective antiretroviral (ARV) treatment. In order to develop effective therapies, we need to expand our knowledge of the interaction between HIV and host proteins. In contrast to virus proteins, which often rapidly evolve drug resistance mutations, the host proteins are essentially invariant within all humans. Thus, if we can identify the host proteins needed for virus replication, such as those involved in transporting viral proteins to the cell surface, we have a chance of interrupting viral replication. There is no proteome resource that summarizes this interaction, making research on this subject a difficult enterprise. In order to fill this gap in knowledge, we curated a resource presents detailed annotation on the interaction between the HIV proteome and host proteins. Our resource was produced in collaboration with ViralZone and used manual curation techniques developed by UniProtKB/Swiss-Prot. Our new website also used previous annotations of the BioAfrica HIV-1 Proteome Resource, which has been accessed by approximately 10 000 unique users a year since its inception in 2005. The novel features include a dedicated new page for each HIV protein, a graphic display of its function and a section on its interaction with host proteins. Our new webpages also add information on the genomic location of each HIV protein and the position of ARV drug resistance mutations. Our improved BioAfrica HIV-1 Proteome Resource fills a gap in the current knowledge of biocuration.Database URL: http://www.bioafrica.net/proteomics/HIVproteome.html

Analysis of α1 and α2 globin genes among patients with hemoglobin Adana in Malaysia.

Hemoglobin (Hb) Adana [HBA2: c179G>A (or HBA1); p.Gly60Asp] is a non-deletional α-thalassemia variant found in Malaysia. An improvement in the molecular techniques in recent years has made identification of Hb Adana much easier. For this study, a total of 26 Hb Adana α-thalassemia intermedia and 10 Hb Adana trait blood samples were collected from patients. Common deletional and non-deletional α-thalassemia genotypes were determined using multiplex gap polymerase chain reaction (PCR) and multiplex ARMS PCR techniques. Identification of the Hb Adana location on the α-globin gene was carried out using genomic sequencing and the location of the mutation was confirmed via restriction fragment length polymorphism-PCR. Among the 36 samples, 24 (66.7%) had the -α(3.7)/α(Cd59)α mutation, while the -α(3.7)/α(Cd59)α mutation accounted for 2 samples (5.6%) and the remaining 10 (27.8%) samples were α/α(Cd59)α. All 36 samples were found to have the Hb Adana mutation on the α2-globin gene. The position of the α-globin gene mutation found in our cases was similar to that reported in Indonesia (16%) but not to that in Turkey (0.6%). Our results showed that the Hb Adana mutation was preferentially present in the α2-globin genes in Malays compared to the other ethnicities in Malaysia. Thus, the Malays might have similar ancestry based on the similarities in the Hb Adana position.

COLD-PCR: Applications and Advantages.

Co-amplification at lower denaturation temperature-based polymerase chain reaction (COLD-PCR) is a single-step amplification method that results in the enhancement of both known and unknown minority alleles during PCR, irrespective of mutation type and position. This method is based on exploitation of the critical temperature, Tc, at which mutation-containing DNA is preferentially melted over wild type. COLD-PCR can be a good strategy for mutation detection in specimens with high nonneoplastic cell content, small specimens in which neoplastic cells are difficult to micro-dissect and therefore enrich, and whenever a mutation is suspected to be present but is undetectable using conventional PCR and sequencing methods. We describe in this chapter our COLD-PCR-based pyrosequencing method for KRAS mutation detection in various clinical samples using DNA extracted from either fresh or fixed paraffin-embedded tissue specimens.

Modification of Predicted Inhibitor Risk in Non-Severe Hemophilia-a By in silico Analysis of Human Proteome Homology with Wild-Type, FVIII-Derived Peptides

Neutralising antibodies (inhibitors) are increasingly recognized to be a life-time risk in non-severe hemophilia A patients exposed to factor VIII concentrates. It is currently not possible to reliably identify the variable inhibitor risk between individuals. Risk appears to differ between F8 genotypes but also for individuals living with the same F8 genotype. As a T cell dependent process, the wild-type, factor concentrate-derived peptide sequences spanning the F8 mutation position are presented by class II MHC and responsible for driving the T helper response and subsequent B cell response. We hypothesize that the primary sequences of the 20,469 proteins in the human proteome will, coincidentally, contain short primary sequences homologous to key immunogenic peptides derived from the therapeutic factor VIII. We present in silico data and correlation with published registry inhibitor data (Fisher's exact test) to demonstrate the potential impact of such "proteome protection" and future potential to more reliably stratify individuals between low/negligible risk and more significant risk of inhibitor formation.We utilize a well-validated, computational tool, NetMHC-II, to enable large scale, computational comparison of predicted antigen presentation between endogenous, mutated FVIII derived peptides and factor-concentrate derived, wild-type FVIII peptides spanning all 520 F8 missense mutations listed on www.hadb.org. NetMHC-II analyses peptide presentation by 14 class II MHC HLA-DR alleles, resulting in analysis of 7,280 (520 x 14) permutations of F8 -MHC-II. We identify 56% (n=4,077) of these permutations to be at low/negligible risk of inhibitor formation, at a binding threshold of 500nM, defined as absence of a novel peptide-MHC surface capable of driving a helper T cell response (p=0.005). When cross referenced with potential homologous sequences buried anywhere in the human proteome (http://www.ebi.ac.uk/reference_proteomes), a further 1,237 F8 -MHC-II combinations are afforded "proteome protection" due to direct sequence homology between FVIII-derived peptide and peptide(s) derived from other proteins. This increases the total number of F8 -MHC-II combinations predicted to be unable to drive a T cell response to 73% (n=5,314). The residual 1,966 (27%) F8 -MHC-II combinations are predicted to retain the ability to present novel-interface FVIII-derived peptides to T cells with an IC50<500nM (higher affinity).Previous work exploring in silico prediction of FVIII-derived peptide presentation may have overestimated the number of F8 -MHC II combinations deemed to be at risk of contributing to inhibitor formation. Our data suggests an additional mechanism "protecting" a larger proportion of those living with non-severe HA from inhibitor formation. The contribution of "proteome protection" further reduces the "at risk" F8 -MHC II permutations to be more representative of clinically observed inhibitor rates. We identify a potential novel tolerance mechanism and provide key data for future in vitro validation strategies. DisclosuresNo relevant conflicts of interest to declare.

Inverse birth cohort effects in ovarian cancer: Increasing risk in BRCA1/2 mutation carriers and decreasing risk in the general population

ObjectiveBRCA1/2 carriers are at increased risk of ovarian cancer, and some reports suggest an increasing risk in more recent birth cohorts. In contrast, decreasing incidences have been observed in the general population. The aim was to assess the birth cohort effect on ovarian cancer risk in BRCA1/2 carriers relative to their background general population. MethodsData on ovarian cancer incidence was collected for a cohort of 1050 BRCA1/2 mutation carriers ascertained by our regional clinic and retrieved from the general Dutch population cancer registry. Birth cohorts were categorized as pre-1935, 1935–1953, post-1953. Birth cohort effects on the ovarian cancer risk were estimated using hazard ratios (HRs) in BRCA1/2 carriers and Poisson rate ratios in the general population. Standardized incidence ratios (SIRs) were calculated to compare populations. HRs were adjusted for mutation position and family history. ResultsCompared to the pre-1935 cohort, BRCA1 carriers in the 1935–1953 and post-1953 cohorts had an increased ovarian cancer risk of HRadjusted 1.54 (95% CI 1.11–2.14) and 2.40 (95% CI 1.56–3.69), respectively. BRCA2 carriers in the 1935–1953 cohort had an HRadjusted of 3.01 (95% CI 1.47–6.13). The SIRs for the 1935–1953 and post-1953 cohorts were 1.7 and 2.7, respectively, for the BRCA1 carriers and 1.6 times and 2.4 times, respectively, for BRCA2 carriers. ConclusionsMutation carriers, particularly BRCA1 carriers, born in the most recent cohorts, have the highest additional ovarian cancer risk as compared to the general population.

Detecting Arbitrary DNA Mutations Using Graphene Oxide and Ethidium Bromide.

We propose a simple and fast method for detecting arbitrary DNA mutations. Single-stranded DNA probes labeled with fluorescein amidite (FAM-ssDNA), ethidium bromide (EB), and graphene oxide (GO) are employed in the sensing system. The detection is achieved in two steps. In the first step, the sensing system contains FAM-ssDNA probes and EB molecules. It exhibits different fluorescence emissions in the presence of perfectly matched, mismatched, and random DNA sequences. With the addition of GO in the second step, the fluorescence signal for perfectly matched and random DNA does not vary greatly, which, however, experiences a significant change for mismatched DNA targets. The signal ratio before and after the addition of GO can clearly distinguish mutations from normal and random DNA sequences. The detection method works well regardless of the mutation positions and only requires "mix-and-detect" steps, which are completed within 15 min.

A novel homozygous mutation in HSF4 causing autosomal recessive congenital cataract.

Cataract is defined as opacity in the crystalline lens and congenital cataract occurs during the first year of life. Until now, mutations of more than 50 genes in congenital cataract have been reported with various modes of inheritance. Among them, HSF4 mutations have been reported in autosomal dominant, autosomal recessive and age-related forms of cataract. The inheritance patterns of these mutations depend on their mutational positions in HSF4: autosomal dominant or recessive mutations are respectively found either in a DNA-binding domain or in (or downstream of) hydrophobic repeats. Here we report a novel homozygous HSF4 mutation (c.521T>C, p.Leu174Pro) in two affected sibs of an Iranian consanguineous family using whole exome sequencing. The mutation is predicted as highly pathogenic by in silico analysis (SIFT, Polyphen2 and MutationTaster) and is not found in any of control databases. This mutation is located in a hydrophobic repeat of the HSF4 protein, which is consistent with the mode of inheritance as an autosomal recessive trait.

The impact of mutation position on the gene and family history on ovarian cancer risk in BRCA1/2 mutation carriers

The impact of mutation position on the gene and family history on ovarian cancer risk in BRCA1/2 mutation carriers

An internal promoter underlies the difference in disease severity between N- and C-terminal truncation mutations of Titin in zebrafish.

Truncating mutations in the giant sarcomeric protein Titin result in dilated cardiomyopathy and skeletal myopathy. The most severely affected dilated cardiomyopathy patients harbor Titin truncations in the C-terminal two-thirds of the protein, suggesting that mutation position might influence disease mechanism. Using CRISPR/Cas9 technology, we generated six zebrafish lines with Titin truncations in the N-terminal and C-terminal regions. Although all exons were constitutive, C-terminal mutations caused severe myopathy whereas N-terminal mutations demonstrated mild phenotypes. Surprisingly, neither mutation type acted as a dominant negative. Instead, we found a conserved internal promoter at the precise position where divergence in disease severity occurs, with the resulting protein product partially rescuing N-terminal truncations. In addition to its clinical implications, our work may shed light on a long-standing mystery regarding the architecture of the sarcomere.

A novel mutation of GATA4 (K300T) associated with familial atrial septal defect

The GATA-binding protein 4 gene (GATA4) encodes a zinc-finger transcription factor that plays a key role in embryogenesis and cardiac development. Variants in the GATA4 gene have been implicated in several congenital heart diseases (CHD), such as the tetralogy of Fallot (ToF), atrial septal defect (ASD), ventricular septal defect (VSD), atrioventricular septal defect (AVSD), and dilated cardiomyopathy (DCM). We studied a four-generation Chinese ASD family and identified a novel GATA4 mutation (c.A899C, p.K300T) in all surviving affected members and two carriers with incomplete penetrance. Bioinformatics programs (PolyPhen-2, SIFT, and MutationTaster) predicted the mutation to be deleterious. The lysine at the mutation position was highly conserved from Drosophila to humans and was recognized as a methylation location in the GATA4 protein. The involvement of the lysine methylation in cardiogenesis by attenuating the transcriptional activity of GATA4 in mice has been previously examined. Our study broadens the mutation spectrum of the GATA4 gene and reveals for the first time a mutation at the methylation position of GATA4 associated with ASD.

Genetic determinants of white matter hyperintensities and amyloid angiopathy in familial Alzheimer's disease

Familial Alzheimer's disease (FAD) treatment trials raise interest in the variable occurrence of cerebral amyloid angiopathy (CAA); an emerging important factor in amyloid-modifying therapy. Previous pathological studies reported particularly severe CAA with postcodon 200 PSEN1 mutations and amyloid beta coding domain APP mutations. As CAA may manifest as white matter hyperintensities (WMH) on magnetic resonance imaging, particularly posteriorly, we investigated WMH in 52 symptomatic FAD patients for associations with mutation position. WMH were visually rated in 39 PSEN1 (18 precodon 200); 13 APP mutation carriers and 25 healthy controls. Ten PSEN1 mutation carriers (5 precodon 200) had postmortem examination. Increased WMH were observed in the PSEN1 postcodon 200 group and in the single APP patient with an amyloid beta coding domain (p.Ala692Gly, Flemish) mutation. WMH burden on MRI correlated with severity of CAA and cotton wool plaques in several areas. The precodon 200 group had younger ages at onset, decreased axonal density and/or integrity, and a greater T-lymphocytic response in occipital deep white matter. Mutation site contributes to the phenotypic and pathological heterogeneity witnessed in FAD.

The evolution of noncoding RNAs in the Drosophila melanogaster genome

Noncoding RNAs (ncRNAs) are important regulatory molecules that function owing to their specific secondary structures. The secondary structure depends on the RNA sequence and can be viewed as a combination of loops, stems, and pseudoknot regions. Each local RNA part, as well as the entire molecule, tends to achieve the minimal free energy by assuming a certain structure. New mutations may change the free energy of the current RNA structure so that another structure becomes optimal, thus altering the RNA function. The chance that a mutation will cause structural alterations depends on the mutation position in the RNA secondary structure. Divergence estimates have been found to differ between paired and unpaired regions, the difference arises because selection is aimed at preserving the ncRNA secondary structure. A more detailed analysis of the evolutionary differences between loops and stems in all of the most important ncRNA classes may be of interest for developing the algorithms to search a genome for ncRNA genes. This study focused on natural selection acting on the loop and stem regions in five ncRNA classes. An attempt was made to associate selection characteristics with changes in free energy. The Drosophila melanogaster genome was used as a model.

Proteins linked to autosomal dominant and autosomal recessive disorders harbor characteristic rare missense mutation distribution patterns.

The role of rare missense variants in disease causation remains difficult to interpret. We explore whether the clustering pattern of rare missense variants (MAF < 0.01) in a protein is associated with mode of inheritance. Mutations in genes associated with autosomal dominant (AD) conditions are known to result in either loss or gain of function, whereas mutations in genes associated with autosomal recessive (AR) conditions invariably result in loss-of-function. Loss-of-function mutations tend to be distributed uniformly along protein sequence, whereas gain-of-function mutations tend to localize to key regions. It has not previously been ascertained whether these patterns hold in general for rare missense mutations. We consider the extent to which rare missense variants are located within annotated protein domains and whether they form clusters, using a new unbiased method called CLUstering by Mutation Position. These approaches quantified a significant difference in clustering between AD and AR diseases. Proteins linked to AD diseases exhibited more clustering of rare missense mutations than those linked to AR diseases (Wilcoxon P = 5.7 × 10(-4), permutation P = 8.4 × 10(-4)). Rare missense mutation in proteins linked to either AD or AR diseases was more clustered than controls (1000G) (Wilcoxon P = 2.8 × 10(-15) for AD and P = 4.5 × 10(-4) for AR, permutation P = 3.1 × 10(-12) for AD and P = 0.03 for AR). The differences in clustering patterns persisted even after removal of the most prominent genes. Testing for such non-random patterns may reveal novel aspects of disease etiology in large sample studies.

Abstract 2860: Improved clinical response in patients with advanced melanoma treated with nivolumab combined with ipilimumab compared to ipilimumab alone

Abstract Background: Blockade of the immune checkpoints PD-1 and CTLA-4 each results in improved overall survival in patients (pts) with metastatic melanoma using monotherapy. In a phase 1 dose-escalation study, dual inhibition of these pathways by nivolumab (NIVO) and ipilimumab (IPI) demonstrated encouraging antitumor activity. Methods: Treatment-naïve pts with advanced melanoma were randomized (double-blind) 2:1 to IPI 3 mg/kg combined with either NIVO 1 mg/kg (NIVO+IPI combination group) or placebo (PBO; IPI alone group) every 3 weeks (Q3W) for 4 doses, followed by NIVO 3 mg/kg or PBO, respectively, Q2W until disease progression or unacceptable toxicity. Primary endpoint was investigator-assessed objective response rate (ORR) in BRAF wild-type (WT) pts. Secondary endpoints included progression-free survival (PFS), ORR in BRAF V600 mutation-positive (MT) pts, and safety. Results: In BRAF WT pts, ORR was 60% (43/72) in the NIVO+IPI group vs 11% (4/37) in the IPI group (P&amp;lt;0.0001); complete response reported in 12 (17%) and 0 pts, respectively. Median change in target lesions was 57% reduction for NIVO+IPI vs 4% increase for IPI alone. Median duration of response was not reached in either group. In BRAF WT pts, median PFS was 8.9 months for NIVO+IPI; 4.7 months for IPI (HR 0.40, 95% CI 0.22-0.71; P = 0.0012). Similar results for ORR and PFS favoring the combination were observed in BRAF MT pts (Table). A higher rate of drug-related grade 3-4 adverse events was observed in the NIVO+IPI group compared to IPI (Table), leading to more frequent discontinuation. Pts who discontinued NIVO+IPI due to study drug toxicity had a 67% response rate; most continue to respond. Immune-mediated AEs were manageable by standard treatment interventions, and the majority resolved with immune-modulating medication. Conclusion: NIVO+IPI significantly improved ORR and PFS compared to IPI alone in treatment-naïve pts with advanced melanoma, and had a manageable safety profile. Efficacy (evaluated in all randomized patients)BRAF WTBRAF WTBRAF MTNIVO+IPIIPINIVO+IPIIPIRandomized patients, N72372310ORR,% (95% CI)59.7 (47.5-71.1)a10.8 (3.0-25.4)a43.5 (23.2-65.5)0 (0-30.8)Best overall response, n (%)Complete response12 (16.7)04 (17.4)0Partial response31 (43.1)4 (10.8)6 (26.1)0Stable disease10 (13.9)12 (32.4)5 (21.7)2 (20.0)Progressive disease10 (13.9)16 (43.2)5 (21.7)7 (70.0)Median PFS, mo (95% CI)8.9 (7.0, NE)4.7 (2.8, 5.3)7.4 (2.8, NE)2.7 (0.99, 5.4)HR, (95% CI)0.40 (0.22-0.71) P = 0.00120.33 (0.1, 0.9)bSafety (evaluated in all treated patients)Patients reporting AE, n (%)NIVO+IPI (N = 94)IPI (N = 46)Any GradeGrade 3-4Any GradeGrade 3-4Treatment-related AEs86 (91.5)48 (51.1)42 (91.3)9 (19.6)aP&amp;lt;0.0001; estimated odds ratio for objective response 12.23 (95% CI, 3.69-51.40)bDue to the small sample size in the BRAF MT subgroup, no P-value is provided NE = not estimable Citation Format: F. Stephen Hodi, Michael A. Postow, Jason Chesney, Anna C. Pavlick, Caroline Robert, Kenneth Grossmann, David McDermott, Gerald Linette, Nicolas Meyer, Jeffrey Giguere, Sanjiv S. Agarwala, Montaser Shaheen, Marc S. Ernstoff, David R. Minor, April Salama, Matthew H. Taylor, Linda Rollin, Christine Horak, Paul Gagnier, Jedd D. Wolchok. Improved clinical response in patients with advanced melanoma treated with nivolumab combined with ipilimumab compared to ipilimumab alone. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2860. doi:10.1158/1538-7445.AM2015-2860

Missense mutation in the PTEN promoter of a patient with hemifacial hyperplasia

The cellular mechanisms involved in the asymmetric facial overgrowth syndrome, hemifacial hyperplasia (HFH), are not well understood. This study was conducted to compare primary cell cultures from hyperplastic and normal HFH bone for cellular and molecular differences. Primary cultures developed from biopsies of a patient with isolated HFH showed a twofold difference in cell size and cell number between hyperplastic and normal bone. Microarray data suggested a 40% suppression of PTEN (phosphatase-tensin homolog) transcripts. Sequencing of the PTEN gene and promoter identified novel C/G missense mutation (position -1053) in the regulatory region of the PTEN promoter. Western blots of downstream pathway components showed an increase in PKBa/Akt1 phosphorylation and TOR (target of rapamcyin) signal. Sirolimus, an inhibitor of TOR, when added to overgrowth cells reversed the cell size, cell number and total protein differences between hyperplastic and normal cells. In cases of facial overgrowth, which involve PTEN/Akt/TOR dysregulation, sirolimus could be used for limiting cell overgrowth.

Short Communication: In Vitro Accumulation of Drug Resistance Mutations in Chimeric Infectious Clones Containing Subtype B or C Reverse Transcriptase and Selected with Tenofovir or Didanosine.

Highly active antiretroviral therapy (HAART) contributed to the improvement in the life expectancy of HIV-infected patients. However, the emergence of drug-resistant mutations (DRM) is a major viral factor impacting therapeutic failure. Differences in DRM can occur among HIV-1 subtypes. We evaluate the kinetics of the selection of resistance mutations in vitro analyzing two chimeric clones that contain the reverse transcriptases of subtypes B or C (RTB' and RTC') in cells treated with increasing concentrations of tenofovir disoproxil fumarate (TDF) and didanosine (ddI). The mutation K65R is selected more quickly in RTC' than in RTB' viruses with TDF and ddI, and additional mutations (positions 45, 62, and 68) were selected after K65R fixation. Other primary mutations (M184V and Q151M) were selected with ddI treatment in conjunction with K65R only in RTC' viruses. Both patterns, M184V+K65R and Q151M+K65R, have a significant impact on NRTI resistance. Our data suggest that selection of TDF and ddI DRMs can occur earlier in subtype C HIV in patients when compared to subtype B.

Ovarian cancer in BRCA1/2 mutation carriers: The impact of mutation position and family history on the cancer risk

ObjectivesAssessing the combined impact of mutation position, regarding the ovarian cancer cluster region (OCCR), and type of cancer family history (FH) on age-related penetrance of ovarian cancer (OC) in women from BRCA1/2 families from the northern Netherlands. Study designA consecutive series of 1763 mutation carriers and their first-degree relatives from 355 proven BRCA1/2 families with a history of breast and/or ovarian cancer with in total 248 OC cases was included. Mutations were stratified for gene (BRCA1 or BRCA2) and location (within or outside the OCCR). FH was stratified for type of cancer occurring in first and second-degree relatives (OC only, breast cancer (BC) only or both OC and BC). Main outcome measuresCox-proportional hazard models were applied to estimate the OCCR effect, including and excluding a FH of cancer. ResultsAmong BRCA1 families, OC risks were higher in women with OCCR mutations versus those with non-OCCR mutations (HR=1.59, 95%CI=1.19–2.12). This effect remained significant after adjustment for the type of FH (HR=1.50, 95%CI=1.11–2.01). In BRCA2 families, mutation position did not significantly affect the OC risk (HR=1.50, 95%CI=0.74–3.04). However, in the BRCA2 group, a FH including only OC presented by itself a strong impact on OC risk (HR=4.63, 95%CI=2.38–9.02), which remained stable after adjustment for mutation position (HR=4.48, 95%CI=2.28–8.81). ConclusionOCCR mutations significantly increased the OC risk in BRCA1 families regardless of the type of FH, but in BRCA2 families, type of FH seems to have a higher impact than mutation position on OC risk.

Site-directed mutagenesis substituting cysteine for serine in 2-Cys peroxiredoxin (2-Cys Prx A) of Arabidopsis thaliana effectively improves its peroxidase and chaperone functions.

The 2-Cys peroxiredoxin (Prx) A protein of Arabidopsis thaliana performs the dual functions of a peroxidase and a molecular chaperone depending on its conformation and the metabolic conditions. However, the precise mechanism responsible for the functional switching of 2-Cys Prx A is poorly known. This study examines various serine-to-cysteine substitutions on α-helix regions of 2-Cys Prx A in Arabidopsis mutants and the effects they have on the dual function of the protein. Various mutants of 2-Cys Prx A were generated by replacing serine (Ser) with cysteine (Cys) at different locations by site-directed mutagenesis. The mutants were then over-expressed in Escherichia coli. The purified protein was further analysed by size exclusion chromatography, polyacrylamide gel electrophoresis, circular dichroism spectroscopy and transmission electron microscopy (TEM) and image analysis. Peroxidase activity, molecular chaperone activity and hydrophobicity of the proteins were also determined. Molecular modelling analysis was performed in order to demonstrate the relationship between mutation positions and switching of 2-Cys Prx A activity. Replacement of Ser(150) with Cys(150) led to a marked increase in holdase chaperone and peroxidase activities of 2-Cys Prx A, which was associated with a change in the structure of an important domain of the protein. Molecular modelling demonstrated the relationship between mutation positions and the switching of 2-Cys Prx A activity. Examination of the α2 helix, dimer-dimer interface and C-term loop indicated that the peroxidase function is associated with a fully folded α2 helix and easy formation of a stable reduced decamer, while a more flexible C-term loop makes the chaperone function less likely. Substitution of Cys for Ser at amino acid location 150 of the α-helix of 2-Cys Prx A regulates/enhances the dual enzymatic functions of the 2-Cys Prx A protein. If confirmed in planta, this leads to the potential for it to be used to maximize the functional utility of 2-Cys Prx A protein for improved metabolic functions and stress resistance in plants.