CYP2D6 Genotyping for Personalized Therapy of Tamoxifen in Indonesian Women with ER+ Breast Cancer

PurposeTamoxifen, common adjuvant therapy prescribed in estrogen receptor positive (ER+) breast cancer, is metabolized by CYP2D6 enzyme into endoxifen. The phenotypes of CYP2D6, a highly polymorphic gene, vary from ultrarapid (UM), normal (NM), intermediate (IM), and poor metabolizers (PM). Studies showed that reduced CYP2D6 activity in IMs and PMs resulted in lower endoxifen level, thereby reducing therapy efficacy. This study aims to observe the distribution of CYP2D6 profiles and their corresponding endoxifen levels in Indonesian ER+ breast cancer patients.Methods151 patients who have received tamoxifen therapy for ≥8 weeks were recruited prospectively. DNA and blood samples were collected with buccal swab and finger-prick methods, respectively. Genotyping was performed using the qPCR method while metabolites measurement was performed using HPLC-tandem MS. Patients with IM/PM CYP2D6 profile were advised to increase their tamoxifen dose or switch to aromatase inhibitor, while patients with UM or NM CYP2D6 profile remained on 20 mg daily dose. Tamoxifen metabolites levels of those given 40 mg/day of tamoxifen were measured eight weeks post dose adjustment.ResultsWe found that 40.7% of patients recruited were IM. CYP2D6*10 was the most abundant allele (28.8%) and *10/*36 was the most frequently observed diplotype (23.6%). Endoxifen levels between the NM-PM, NM-IM, and IM-PM were statistically significant, and dose increase of tamoxifen successfully increased endoxifen levels in IMs to a similar level with NMs at baseline.ConclusionIndonesian women have a relatively high proportion of IMs. The correlation between CYP2D6 genotype and phenotype was shown in the significant difference in endoxifen levels among NMs, IMs, and PMs. Dose adjustment of tamoxifen to 40 mg daily positively increased endoxifen levels in IMs to a similar level as NMs. Implementing pharmacogenomics testing of CYP2D6 on ER+ breast cancer women taking tamoxifen can potentially increase the likelihood of achieving better treatment efficacy.Trial RegistrationThe trial was retrospectively registered at ClinicalTrials.gov on 18 March 2020 with identifier NCT04312347 (accessible at: https://clinicaltrials.gov/ct2/show/NCT04312347).

Polymorphism of 16s rRNA Gene: Any Effect on the Biomolecular Quantitation of the Honey Bee (Apis mellifera L., 1758) Pathogen Nosema ceranae?

The microsporidian Nosema ceranae is a severe threat to the western honey bee Apis mellifera, as it is responsible for nosemosis type C, which leads the colonies to dwindle and collapse. Infection quantification is essential to clinical and research aims. Assessment is made often with molecular assays based on rRNA genes, which are present in the N. ceranae genome as multiple and polymorphic copies. This study aims to compare two different methods of Real-Time PCR (qPCR), respectively relying on the 16S rRNA and Hsp70 genes, the first of which is described as a multiple and polymorphic gene. Young worker bees, hatched in the laboratory and artificially inoculated with N. ceranae spores, were incubated at 33 °C and subject to different treatment regimens. Samples were taken post-infection and analyzed with both qPCR methods. Compared to Hsp70, the 16S rRNA method systematically detected higher abundance. Straightforward conversion between the two methods is made impossible by erratic 16s rRNA/Hsp70 ratios. The 16s rRNA polymorphism showed an increase around the inoculated dose, where a higher prevalence of ungerminated spores was expected due to the treatment effects. The possible genetic background of that irregular distribution is discussed in detail. The polymorphic nature of 16S rRNA showed to be a limit in the infection quantification. More reliably, the N. ceranae abundance can be assessed in honey bee samples with methods based on the single-copy gene Hsp70.

Enhanced Thrombotic Responses Are Associated With Striatin Deficiency and Aldosterone

Background In addition to its role on blood pressure, aldosterone (ALDO) also affects the hemostatic system leading to increased experimental thrombosis. Striatin is an intermediate in the rapid, nongenomic actions of ALDO. Striatin heterozygote knockout ( Strn +/‐ ) mice have salt sensitivity of blood pressure and mildly chronically increased ALDO levels. In addition, in humans, striatin polymorphic gene variants are associated with increased salt sensitivity of blood pressure. Thus, we hypothesized that striatin deficiency would be associated with an increased prothrombotic response. Methods and Results Strn +/ ‐ mice and wild‐type littermates were maintained on a liberal sodium diet (1.6%). We measured in vivo thrombus formation following laser‐induced injury in cremaster arterioles using intravital microscopy. Mice were randomized to intravenous administration of ALDO or its vehicle. Acutely, ALDO increased thrombotic responses in wild‐type mice ( P <0.01) versus controls within minutes as determined by increased platelet accumulation and fibrin deposition at the site of laser injury. We then compared thrombus formation without ALDO administration in Strn +/‐ and wild‐type mice. Strn +/‐ mice showed highly significant increases in laser‐induced thrombosis ( P <0.001), as shown by increased platelet accumulation and fibrin deposition. Interestingly, the response in the Strn +/‐ mice basally was far greater than the wild‐type mice with ALDO administration, and ALDO administration produced no additional effect on thrombus responses in Strn +/‐ mice. Conclusions These results demonstrate a novel protective role of striatin in experimental thrombosis. Such a protective effect may be reduced in human striatin risk allele carriers, given the similar salt sensitivity of blood pressure in these individuals and Strn +/‐ mice.

Haplotype analysis of polymorphic genes of lipid metabolism and its association with an increased risk of the first non-cardioembolic ischemic stroke

Aim We studied the effect of haplotype variations in lipid metabolism genes on the risk of first non-cardioembolic ischemic stroke in 206 patients and 206 controls. Material and methods The alleles frequencies and genotypes assessed for 5 mono-nucleotide polymorphic gene variants (APOB (rs1042031), APOEB (rs676210), APOC-IV (rs1132899), APOE (rs 7412), APOE (rs 429358), LP(a) (rs41267817)) in 206 patients, who had first non-cardioembolic ischemic stroke, and 206 persons with no stroke, comparable with age, gender, place of living and ethnicity. Genotyping of polymorphisms was done with the prepared TaqMan probes. Haplotype analysis was performed using the online tool SNPStat. Results Haplotype analysis revealed that CTGATT, CTGACT and CCAGTT, haplotypes of lipid metabolism genes polymorphisms are associated with risk of first non-cardioembolic ischemic stroke after multivariate adjustment. Conclusions These results show that haplotype of lipid metabolism genes polymorphisms are signifcantly associated with increased the development of the first non-cardioembolic ischemic stroke In the studied groups. FUNDunding Acknowledgement Type of funding sources: None.

C3435T Polymorphism of the ABCB1 gene in the Yakut Population

Background: The ABCB1 gene is responsible for resistance to various cytotoxic drugs. The product of the ABCB1 gene, P-glycoprotein (P-gp), acts as a transmembrane pump and influences the action of many drugs. More than 40 SNPs of the ABCB1 gene that alter the expression of P-gp have been identified. The ABCB1 rs1045642 SNP, designated as C3435T (C-the wild-type allele, T-the variant allele), correlates with the activity of P-gp. The aim of our research was to study the distribution of alleles and genotypes of the ABCB1 C3435T polymorphism in Yakuts, in comparison with other human populations. Methods and Results: The studied cohort included 149 healthy Yakut volunteers (36 men and 113 women). The average age of participants was 30.67±0.06 years. The ABCB1 gene is a highly polymorphic gene; the allele frequency of the C3435T polymorphism differs widely among the studied populations. The frequency of the mutant T-allele among the Yakuts was 51% .In the studied group of Yakuts, we revealed the prevalence of the heterozygous CT genotype (75.8%). The Yakuts have a relatively low frequency of CC (10.7%) and TT (13.4%) genotypes. This preliminary study did not include the objective of proving the relationship between the ABCB1 C3435T polymorphism and addictive disorders in Yakuts. The further search for functional polymorphisms of the ABCB1 gene and associations with addictive behavior using a systematic approach on larger samples is of great practical importance.

Polymorphism of Block3 Region of Merozoite Surface Protein-2 Gene and Multiplicity of Infection in Plasmodium Falciparum in Urban and Rural Settings of Adama and Its Surroundings, Oromia, Ethiopia.

Background: Despite significant progress achieved globally in reducing malaria burden, still it is one of the major public health problems in Ethiopia. Furthermore, better understanding of genetic polymorphism of P. falciparum: the most virulent and predominant malaria parasite primarily targeted in malaria control and elimination program is paramount. Analysis of block 3 region of msp-2 gene of P. falciparum provides strong molecular evidence to evaluate the real picture of malaria epidemiology to fine-tune the ongoing control and elimination programs in the region.Thus, this study aimed to examine the status of such polymorphic gene and its implications in Adama and its surrounding.Methods: A total of 171 Dry Blood Spot (DBS) samples were collected from uncomplicated falciparum malaria patients from September 2019 to August 2020. Tween® 20 and Chelex method was employed for parasite DNA extraction. A total of 148 samples were successfully amplified by nested PCR targeting msp-2 alleles (IC/3D7 and FC27) followed by gel electrophoresis for fragment analysis. Results: Seventeen different polymorphic forms of msp-2 allelic fragments were detected in the study area. Moreover, a total of 47 (31.8%) and 41(27.7%) were detected for IC/3D7 and FC27 allelic family, respectively. Furthermore, the multi-clonal allele type accounted for 60(40.5%). The overall MOI was 1.4 and the expected heterozygosity is 0.49 indicating nearly intermediate malaria transmission in the study area.Conclusions: The study revealed nearly intermediate genetic diversity and polyclonal infection of P. falciparum in the study area, demanding further scale up of the ongoing control and elimination efforts.

MHC class IIa haplotypes derived by high throughput SNP screening in an isolated sheep population

Investigating the current evolutionary processes acting on a highly polymorphic gene region, such as the major histocompatibility complex (MHC), requires extensive population data for both genotypes and phenotypes. The MHC consists of several tightly linked loci with both allelic and gene content variation, making it challenging to genotype. Eight class IIa haplotypes have previously been identified in the Soay sheep (Ovis aries) of St. Kilda using Sanger sequencing and cloning, but no single locus is representative of all haplotypes. Here, we exploit the closed nature of the island population of Soay sheep and its limited haplotypic variation to identify a panel of SNPs that enable imputation of MHC haplotypes. We compared MHC class IIa haplotypes determined by Sanger sequence-based genotyping of 135 individuals to their SNP profiles generated using the Ovine Infinium HD BeadChip. A panel of 11 SNPs could reliably determine MHC diplotypes, and two additional SNPs within the DQA1 gene enabled detection of a recombinant haplotype affecting only the SNPs downstream of the expressed genes. The panel of 13 SNPs was genotyped in 5951 Soay sheep, of which 5349 passed quality control. Using the Soay sheep pedigree, we were able to trace the origin and inheritance of the recombinant SNP haplotype. This SNP-based method has enabled the rapid generation of locus-specific MHC genotypes for large numbers of Soay sheep. This volume of high-quality genotypes in a well-characterized population of free-living sheep will be valuable for investigating the mechanisms maintaining diversity at the MHC.

HLA Allele Imputation with Multitask Deep Convolutional Neural Network

The Human leukocyte antigen (HLA) system is a highly polymorphic gene complex encoding the major histocompatibility complex proteins in humans. HLA alleles are of strong epidemiological interest for their large effect sizes in associations with autoimmune diseases, infectious diseases, severe drug reactions, and transplant medicine. Since HLA genotyping can be time-consuming and cost-prohibitive, methods to impute HLA alleles from SNP genotype data have been developed, including HLA Genotype Imputation with Attribute Bagging (HIBAG), HLA*IMP:02, and SNP2HLA. However, limitations of these imputation programs include imputation accuracy, computational runtime, and ability to impute HLA allele haplotypes. We present a deep learning framework for HLA allele imputation using a multitask convolutional neural network (CNN) architecture. In this approach, we use phased SNP genotype data flanking ±250 kb from each HLA locus to simultaneously impute HLA allele haplotyes across loci HLA-A, -B, -C, -DQA1, -DQB1, -DPA1, -DPB1, and -DRB1. We start by tokenizing phased genotype sequences into k-mers that serve as input to the model. The CNN architecture starts with a shared embedding layer for learning low-dimensional representations of k-mers, shared convolutional layers for detecting genotype motifs, and branches off into separate densely-connected layers for imputing each HLA loci. We present evidence that the CNN used information from known tag SNPs to impute HLA alleles, and demonstrate the architecture is robust against a selection of hyperparameters. On the T1DGC dataset, our model achieved 97.6% imputation accuracy, which was superior to SNP2HLA's performance and comparable to HIBAG's performance. However, unlike HIBAG, our method can impute an entire HLA haplotype sequence instead of imputing one locus at a time. Additionally, by separating the training and inference steps, our imputation program provides user flexibility to reduce usage time.

Confirmation of a Gametophytic Self-Incompatibility in Oryza longistaminata

Oryza longistaminata, a wild species of African origin, has been reported to exhibit self-incompatibility (SI). However, the genetic pattern of its SI remained unknown. In this study, we conducted self-pollination and reciprocal cross-pollination experiments to verify that O. longistaminata is a strictly self-incompatible species. The staining of pollen with aniline blue following self-pollination revealed that although pollen could germinate on the stigma, the pollen tube was unable to enter the style to complete pollination, thereby resulting in gametophytic self-incompatibility (GSI). LpSDUF247, a S-locus male determinant in the gametophytic SI system of perennial ryegrass, is predicted to encode a DUF247 protein. On the basic of chromosome alignment with LpSDUF247, we identified OlSS1 and OlSS2 as Self-Incompatibility Stamen candidate genes in O. longistaminata. Chromosome segment analysis revealed that the Self-Incompatibility Pistil candidate gene of O. longistaminata (OlSP) is a polymorphic gene located in a region flanking OlSS1. OlSS1 was expressed mainly in the stamens, whereas OlSS2 was expressed in both the stamens and pistils. OlSP was specifically highly expressed in the pistils, as revealed by RT-PCR and qRT-PCR analyses. Collectively, our observations indicate the occurrence of GSI in O. longistaminata and that this process is potentially controlled by OlSS1, OlSS2, and OlSP. These findings provide further insights into the genetic mechanisms underlying self-compatibility in plants.