Targeted next-generation sequencing of genes involved in Warfarin Pharmacodynamics and pharmacokinetics pathways using the Saudi Warfarin Pharmacogenetic study (SWAP).

BACKGROUND: Warfarin is an oral anticoagulant commonly used for treatment and prophylaxis against thromboembolic events. Warfarins's narrow therapeutic index window is one of the main challenges in clinical practice; thus, it requires frequent monitoring and dose adjustment to maintain patients' therapeutic range. Warfarin dose variation and response are attributed to several inter-and intra-individuals factors, including genetic variants in enzymes involved in warfarin pharmacokinetics (PK) and pharmacodynamics (PD) pathways. Thus, we aim to utilize the next-generation sequencing (NGS) approach to identify rare and common genetic variants that might be associated with warfarin responsiveness. METHOD AND RESULTS: A predesigned NGS panel that included 16 genes involved in Warfarin PK/PD pathways was used to sequence 786 patients from the Saudi Warfarin Pharmacogenetic Cohort (SWAP). Identified variants were annotated using several annotation tools to identify the pathogenicity and allele frequencies of these variants. We conducted variants-level association tests with warfarin dose. We identified 710 variants within the sequenced genes; 19% were novel variants, with the vast majority being scarce variants. The genetic association tests showed that VKORC1 (rs9923231, and rs61742245), CYP2C9 (rs98332238, rs9332172, rs1057910, rs9332230, rs1799853, rs1057911, and rs9332119), CYP2C19 (rs28399511, and rs3758581), and CYP2C8 (rs11572080 and rs10509681) were significantly associated with warfarin weekly dose. Our model included genetics, and non-genetic factors explained 40.1% of warfarin dose variation. CONCLUSION: The study identifies novel variants associated with warfarin dose in the Saudi population. These variants are more likely to be population-specific variants, suggesting that population-specific studies should be conducted before adopting a universal warfarin genotype-guided dosing algorithm.

In vitro assessment of the efficiency of the PIM-1 kinase pharmacological inhibitor as a potential treatment for Burkitt's lymphoma.

Burkitt's lymphoma is an aggressive form of lymphoma affecting B lymphocytes. It occurs endemically in Africa and sporadically in the rest of the world. Due to the high proliferation rate of this tumor, intensive multi-drug treatment is required; however, the risk of tumor syndrome lysis is high. Overexpression of the proto-oncogene proviral integration of the Moloney murine leukemia virus (PIM-1) kinase is associated with the development of hematological abnormalities, including Burkitt's lymphoma (BL). PIM-1 primarily exerts anti-apoptotic activities through BAD phosphorylation. The aim of the present study was to investigate the in vitro efficiency of a PIM-1 kinase pharmacological inhibitor (PIM1-1) in BL. The impact of PIM1-1 was evaluated in terms of the viability and apoptosis status of the BL B cell lines, Raji and Daudi, compared with K562 leukemia cells, which highly express PIM-1. Cell viability and apoptotic status were assessed with western blotting, and PIM-1 gene expression was assessed with reverse transcription-quantitative PCR. After 48 h of treatment, PIM1-1 inhibited the Daudi, Raji and K562 cell viability with a half-maximal inhibitory concentration corresponding to 10, 20 and 30 µM PIM1-1, respectively. A significant decrease of ERK phosphorylation was detected in PIM1-1-treated Daudi cells, confirming the antiproliferative effect. The addition of 10 µM PIM1-1 significantly decreased the PIM-1 protein and gene expression in Daudi cells. An inhibition of the pro-apoptotic BAD phosphorylation was observed in the Daudi cells treated with 0.1-1 µM PIM1-1 and 10 µM PIM1-1 decreased BAD phosphorylation in the Raji cells. The apoptotic status of both PIM1-1-treated cells lines were confirmed with the detection of cleaved capase-3. However, no change in cell viability and PIM-1 protein expression was observed in the 10 µM PIM1-1-treated K562 cells. In conclusion, the findings indicated that the PIM1-1 pharmacological inhibitor may have therapeutic potential in BL, but with lower efficiency in leukemia.

The effect of the VKORC1 promoter variant on warfarin responsiveness in the Saudi WArfarin Pharmacogenetic (SWAP) cohort.

Warfarin is a frequently prescribed oral anticoagulant with a narrow therapeutic index, requiring careful dosing and monitoring. However, patients respond with significant inter-individual variability in terms of the dose and responsiveness of warfarin, attributed to genetic polymorphisms within the genes responsible for the pharmacokinetics and pharmacodynamics of warfarin. Extensive warfarin pharmacogenetic studies have been conducted, including studies resulting in genotype-guided dosing guidelines, but few large scale studies have been conducted with the Saudi population. In this study, we report the study design and baseline characteristics of the Saudi WArfarin Pharmacogenomics (SWAP) cohort, as well as the association of the VKORC1 promoter variants with the warfarin dose and the time to a stable INR. In the 936 Saudi patients recruited in the SWAP study, the minor allele C of rs9923231 was significantly associated with a 8.45 mg higher weekly warfarin dose (p value = 4.0 × 10-46), as well as with a significant delay in achieving a stable INR level. The addition of the rs9923231 status to the model, containing all the significant clinical variables, doubled the warfarin dose explained variance to 31%. The SWAP cohort represents a valuable resource for future research with the objective of identifying rare and prevalent genetic variants, which can be incorporated in personalized anticoagulation therapy for the Saudi population.

Evolving sequence mutations in the Middle East Respiratory Syndrome Coronavirus (MERS-CoV).

BACKGROUND: Middle East respiratory syndrome coronavirus (MERS-CoV) has continued to cause sporadic outbreaks of severe respiratory tract infection over the last 8 years. METHODS: Complete genome sequencing using next-generation sequencing was performed for MERS-CoV isolates from cases that occurred in Riyadh between 2015 and 2019. Phylogenetic analysis and molecular mutational analysis were carried out to investigate disease severity. RESULTS: A total of eight MERS-CoV isolates were subjected to complete genome sequencing. Phylogenetic analysis resulted in the assembly of 7/8 sequences within lineage 3 and one sequence within lineage 4 showing complex genomic recombination. The isolates contained a variety of unique amino acid substitutions in ORF1ab (41), the N protein (10), the S protein (9) and ORF4b (5). CONCLUSION: Our study shows that MERS-CoV is evolving. The emergence of new variants carries the potential for increased virulence and could impose a challenge to the global health system. We recommend the sequencing every new MERS-CoV isolate to observe the changes in the virus and relate them to clinical outcomes.

Tracing the epidemic history of hepatitis C virus genotypes in Saudi Arabia.

HCV genotype 4 is highly prevalent in many Middle Eastern countries, yet little is known about the genotype's epidemic history at the subtype-level in this region. To address the dearth of data from Saudi Arabia (SA) we genotyped 230 HCV isolates in the core/E- and NS5B-region and analyzed using Bayesian phylogenetic approaches. HCV genotype 4 (HCV/4) was positive in 61.7% (142/230) of isolates belonging to 7 different subtypes with the predominance of 4d (73/142; 51.4%) followed by 4a (51/142; 35.9%). Phylogenetic analysis also revealed a distinct epidemiological cluster of HCV/4d for Saudi Arabia. HCV/1 appeared as the second most prevalent genotype positive in 31.3% (72/230) of isolates with the predominance of 1b (53/72; 73.6%) followed by 1a (16/72; 22.2%), and 1g (3/72; 4.1%). A small proportion of isolates belonged to HCV/3a (12/230; 5.2%), and HCV/2a (4/230; 1.7%). We estimate that the genotype 4 common ancestor existed around 1935 (1850-1985). Genotype 4 originated plausibly in Central Africa and multiple subtypes disseminated across African borders since ~1970, including subtype 4d which dominates current HCV infections in Saudi Arabia. The Bayesian skyline plot (BSP) analysis showed that genotype 4d entered the Saudi population in 1900. The effective number of HCV infections grew gradually until the second half of the 1950s and more rapidly until the early-80s through the use of imported blood units and blood products. Subsequently, the rate of HCV infection in the Saudi Arabian population was stabilized through effective screening of blood and infection control measures.

Analysis of CCR5 gene polymorphisms in 321 healthy Saudis using Next Generation Sequencing.

AIMS: To investigate the extent of CCR5 polymorphism in the healthy Saudi population. METHOD: A total of 321 healthy Saudi individuals were sequenced using the ion Ampliseq™ Exome kit (Life Technologies, USA) on genomic DNA following manufacturer's protocol. Whole Exome Sequencing (WES) reads were aligned to the human reference genome (hg19 build) with Torrent Suite Software (v5.0.2) and the variants were called using the Torrent Variant Caller plugin (v5.0) and imported into Ion Reporter Server (v5.0) for the annotation. CCR5 coding exons variants were filtered and checked against the NHLBI GO Exome Sequencing Project (NHLBI), NCBI Reference dbSNPs database, 1000 genomes and Exome Aggregation Consortium datasets (ExAC). RESULTS: A total of 475 variants were identified. Table 1 shows polymorphisms/mutations detected within exons that introduced an amino acid change, deletion or copy number variants (CNV). Three mutations are predicted to influence CCR5 function, including the 32bp deletion (Rs333). Four polymorphisms were detected, plus two CNV. CONCLUSIONS: This is the first report on sequencing the full CCR5 gene using NGS in the Saudi population. Here we demonstrate seven polymorphisms/mutations that were reported before. All were detected within very low frequency including the delta 32 mutation. However, we report for the first time copy number variants at two CCR5 gene locations; 45072265 and 38591712.

CD95-mediated apoptosis in Burkitt's lymphoma B-cells is associated with Pim-1 down-regulation.

B-cells of the high-grade non-Hodgkin lymphoma Burkitt's lymphoma (BL) overexpress survival oncoproteins, including the proviral integration site for Moloney murine leukaemia virus kinase (Pim)-1, and become apoptosis resistant. Activated death receptor CD95 after ligation with anti-CD95 monoclonal antibody (mAb) resulted in the regression of BL via induction of apoptosis, suggesting a decrease of survival protein expression. Here, CD95-mediated apoptotic pathways in BL B-cell lines (Raji and Daudi) following treatment with anti-CD95 mAb was investigated with the cause-and-effects on pim-1 gene expression, in comparison with leukemic cell line (K562) used as CD95-negative cells. Immunohistochemical staining for CD95 and Pim-1 was performed, and the effects of anti-CD95 mAb on apoptotic signalling using western blotting, on caspase activity and cell survival of BL B-cell and leukemic cell lines were determined. We showed that Raji cells expressed more CD95 receptors than Daudi cells. Half of each population underwent apoptosis accompanied by decreased cell viability after anti-CD95 mAb treatment. Distinct extrinsic and intrinsic CD95-mediated apoptotic pathways in Raji and Daudi cells were revealed by high caspase activity and mitochondrial outer membrane permeabilization, respectively. We observed decreased Pim-1 transcript and protein expression levels with increased heat-shock protein (Hsp)70 and decreased Hsp90 expression in anti-CD95 mAb-treated cells. Throughout the study, K562 cells did not undergo apoptosis upon anti-CD95 mAb treatment. Pim-1 knockdown following to stable transfection with plasmid vectors induced apoptosis and decreased viability of BL and K562 cells. Therefore, CD95-mediated apoptosis induces Pim-1 down-regulation in BL B-cells, but Pim-1 down-regulation cannot fully eradicate BL and leukaemia.

A report of two cases of Al-Awadi Raas-Rothschild syndrome (AARRS) supporting that "apparent" Phocomelia differentiates AARRS from Schinzel Phocomelia syndrome (SPS).

Although there is a long list of syndromes with phocomelia, there are only two syndromes in which there is concurrent pelvic dysplasia and phocomelia: Al-Awadi-Raas-Rothschild syndrome (AARRS) and Schinzel phocomelia syndrome (SPS). Currently, there is a diagnostic confusion between the two syndromes and both have the same MIM entry (MIM 276820). We believe that the two syndromes are different entities and we also believe that the limb defect in SPS is a "true" phocomelia while the limb defect in AARRS is an "apparent" phocomelia. "Apparent" phocomelia describes the most severe form of ulnar ray deficiency in which there is absent ulna with radio-humeral synostosis. "Apparent" phocomelia is diagnosed radiologically by three radiological features: the apparently single bone occupying the arm/forearm appears relatively long, the area of radio-humeral synostosis will have thicker cortex with or without slight angulation, and the lower end of the bone resembles the lower end of a radius and not a humerus. In this paper, we present two new cases of AARRS from two different Saudi Arabian tribes: one case with R292C mutation of WNT7A with bilateral "apparent" phocomelia and a second case with a novel c.814G>T mutation of the WNT7A gene (resulting in wnt7a protein truncation at position 272) with unilateral "apparent" phocomelia. We reviewed previously reported cases of AARRS and SPS to further delineate the differences between these two syndromes. We make the argument that these two syndromes are two different entities and hence require two different MIM entries.

Liebenberg syndrome is caused by a deletion upstream to the PITX1 gene resulting in transformation of the upper limbs to reflect lower limb characteristics.

Liebenberg syndrome (MIM 186550) is a very rare autosomal dominant condition characterized by three main features: dysplasia of all of the bony components of the elbow joint, abnormalities in the shape of carpal bones, and brachydactyly. In this paper, we report a Saudi Arabian family with Liebenberg syndrome. Comparative genomic hybridization (CGH) revealed a 275-kb deletion within the cytogenetic band 5q31.1 which contains the H2AFY gene and 190,428bp of its downstream region. The deleted region is upstream to the PITX1 gene. The radiological features in the upper limbs of all affected members of the family were almost identical to the phenotype in the mouse model with ectopic expression of Pitx1 in the forelimbs. We therefore re-define the phenotype of Liebenberg syndrome as a transformation of the upper limbs to reflect lower limb characteristics and speculate that the area of deletion contains a regulatory sequence that suppresses the expression of PITX1 in the upper limb buds.