Y-Chromosome and mtDNA Genetics Reveal Significant Contrasts in Affinities of Modern Middle Eastern Populations with European and African Populations

The Middle East was a funnel of human expansion out of Africa, a staging area for the Neolithic Agricultural Revolution, and the home to some of the earliest world empires. Post LGM expansions into the region and subsequent population movements created a striking genetic mosaic with distinct sex-based genetic differentiation. While prior studies have examined the mtDNA and Y-chromosome contrast in focal populations in the Middle East, none have undertaken a broad-spectrum survey including North and sub-Saharan Africa, Europe, and Middle Eastern populations. In this study 5,174 mtDNA and 4,658 Y-chromosome samples were investigated using PCA, MDS, mean-linkage clustering, AMOVA, and Fisher exact tests of FST's, RST's, and haplogroup frequencies. Geographic differentiation in affinities of Middle Eastern populations with Africa and Europe showed distinct contrasts between mtDNA and Y-chromosome data. Specifically, Lebanon's mtDNA shows a very strong association to Europe, while Yemen shows very strong affinity with Egypt and North and East Africa. Previous Y-chromosome results showed a Levantine coastal-inland contrast marked by J1 and J2, and a very strong North African component was evident throughout the Middle East. Neither of these patterns were observed in the mtDNA. While J2 has penetrated into Europe, the pattern of Y-chromosome diversity in Lebanon does not show the widespread affinities with Europe indicated by the mtDNA data. Lastly, while each population shows evidence of connections with expansions that now define the Middle East, Africa, and Europe, many of the populations in the Middle East show distinctive mtDNA and Y-haplogroup characteristics that indicate long standing settlement with relatively little impact from and movement into other populations

Genome-Wide Association Study in a Lebanese Cohort Confirms PHACTR1 as a Major Determinant of Coronary Artery Stenosis

The manifestation of coronary artery disease (CAD) follows a well-choreographed series of events that includes damage of arterial endothelial cells and deposition of lipids in the sub-endothelial layers. Genome-wide association studies (GWAS) of multiple populations with distinctive genetic and lifestyle backgrounds are a crucial step in understanding global CAD pathophysiology. In this study, we report a GWAS on the genetic basis of arterial stenosis as measured by cardiac catheterization in a Lebanese population. The locus of the phosphatase and actin regulator 1 gene (PHACTR1) showed association with coronary stenosis in a discovery experiment with genome wide data in 1,949 individuals (rs9349379, OR = 1.37, p = 1.57×10−5). The association was replicated in an additional 2,547 individuals (OR = 1.31, p = 8.85×10−6), leading to genome-wide significant association in a combined analysis (OR = 1.34, p = 8.02×10−10). Results from this GWAS support a central role of PHACTR1 in CAD susceptibility irrespective of lifestyle and ethnic divergences. This association provides a plausible component for understanding molecular mechanisms involved in the formation of stenosis in cardiac vessels and a potential drug target against CAD

Large Scale Association Analysis Identifies Three Susceptibility Loci for Coronary Artery Disease

Genome wide association studies (GWAS) and their replications that have associated DNA variants with myocardial infarction (MI) and/or coronary artery disease (CAD) are predominantly based on populations of European or Eastern Asian descent. Replication of the most significantly associated polymorphisms in multiple populations with distinctive genetic backgrounds and lifestyles is crucial to the understanding of the pathophysiology of a multifactorial disease like CAD. We have used our Lebanese cohort to perform a replication study of nine previously identified CAD/MI susceptibility loci (LTA, CDKN2A-CDKN2B, CELSR2-PSRC1-SORT1, CXCL12, MTHFD1L, WDR12, PCSK9, SH2B3, and SLC22A3), and 88 genes in related phenotypes. The study was conducted on 2,002 patients with detailed demographic, clinical characteristics, and cardiac catheterization results. One marker, rs6922269, in MTHFD1L was significantly protective against MI (OR = 0.68, p = 0.0035), while the variant rs4977574 in CDKN2A-CDKN2B was significantly associated with MI (OR = 1.33, p = 0.0086). Associations were detected after adjustment for family history of CAD, gender, hypertension, hyperlipidemia, diabetes, and smoking. The parallel study of 88 previously published genes in related phenotypes encompassed 20,225 markers, three quarters of which with imputed genotypes The study was based on our genome-wide genotype data set, with imputation across the whole genome to HapMap II release 22 using HapMap CEU population as a reference. Analysis was conducted on both the genotyped and imputed variants in the 88 regions covering selected genes. This approach replicated HNRNPA3P1-CXCL12 association with CAD and identified new significant associations of CDKAL1, ST6GAL1, and PTPRD with CAD. Our study provides evidence for the importance of the multifactorial aspect of CAD/MI and describes genes predisposing to their etiology

Y-Chromosome and mtDNA Genetics Reveal Significant Contrasts in Affinities of Modern Middle Eastern Populations with European and African Populations

Badro, Danielle A. et al.-- The Genographic ConsortiumThe Middle East was a funnel of human expansion out of Africa, a staging area for the Neolithic Agricultural Revolution, and the home to some of the earliest world empires. Post LGM expansions into the region and subsequent population movements created a striking genetic mosaic with distinct sex-based genetic differentiation. While prior studies have examined the mtDNA and Y-chromosome contrast in focal populations in the Middle East, none have undertaken a broad-spectrum survey including North and sub-Saharan Africa, Europe, and Middle Eastern populations. In this study 5,174 mtDNA and 4,658 Y-chromosome samples were investigated using PCA, MDS, mean-linkage clustering, AMOVA, and Fisher exact tests of FST's, RST's, and haplogroup frequencies. Geographic differentiation in affinities of Middle Eastern populations with Africa and Europe showed distinct contrasts between mtDNA and Y-chromosome data. Specifically, Lebanon's mtDNA shows a very strong association to Europe, while Yemen shows very strong affinity with Egypt and North and East Africa. Previous Y-chromosome results showed a Levantine coastal-inland contrast marked by J1 and J2, and a very strong North African component was evident throughout the Middle East. Neither of these patterns were observed in the mtDNA. While J2 has penetrated into Europe, the pattern of Y-chromosome diversity in Lebanon does not show the widespread affinities with Europe indicated by the mtDNA data. Lastly, while each population shows evidence of connections with expansions that now define the Middle East, Africa, and Europe, many of the populations in the Middle East show distinctive mtDNA and Y-haplogroup characteristics that indicate long standing settlement with relatively little impact from and movement into other populations. © 2013 Badro et al.The Genographic Project is supported by funding from the National Geographic Society, IBM and the Waitt Family Foundation.Peer Reviewe

Good pharmacy practice assessment among community pharmacies in Lebanon

Objective: This study aims to assess good pharmacy practice (GPP) aspects and compare GPP scores among community pharmacies in Lebanon, using a tool developed jointly by the International Pharmaceutical Federation (FIP) and the World Health Organization (WHO) to improve and maintain standards of pharmacy practice. Methods: Data collection was carried out between July and October 2018 by a team of 10 licensed inspectors who work at the Lebanese Order of Pharmacists (OPL) and visited community pharmacies across Lebanon. The questionnaire was adapted to the Lebanese context and included 109 questions organized under five sections: socio-demographics, Indicator A (data management and data recording), Indicator B (services and health promotion), Indicator C (dispensing, preparation and administration of medicines), and Indicator D (storage and facilities). The value of 75% was considered as the cutoff point for adherence to indicators. Results: Out of 276 pharmacies visited, a total of 250 (90.58%) pharmacists participated in the study with one pharmacist being interviewed in every pharmacy. Results showed that 18.8% of pharmacists were generally adherents to GPP guidelines (scores above the 75% cutoff): 23.3% were adherent to indicator A, 21.6% to indicator B, 14.8% to indicator C and 13.2% to indicator D. Moreover, comparison of GPP scores across geographical regions revealed a higher adherence among community pharmacists working in the Beirut region compared to the North region, the South region, Mount Lebanon, and the Bekaa. Conclusions: Our study shows that community pharmacists in Lebanon do not fulfill GPP criteria set by FIP/WHO, and that this poor adherence is a trend across the country’s geographical regions. Therefore, efforts should be made to raise awareness among pharmacists about the necessity to adhere to GPP guidelines and standards, and train them and support them appropriately to reach that goal. This is the first indicator-based comprehensive pilot assessment to evaluate GPP adherence in community pharmacies across Lebanon. Working on the optimization of this assessment tool is also warranted

Validation of the Arabic and French Versions of a Knowledge, Attitudes and Practices (KAP) Questionnaire on Tranquilizer Misuse

Tranquilizer misuse is an emerging international public health concern. The psychosocial determinants of this misuse remain understudied. Instruments to measure the Knowledge, Attitudes and Practices (KAP) of tranquilizer misuse are unavailable, except for a recently published questionnaire validated in the Spanish language. We translated the KAP questionnaire into Arabic and French, adapted it and undertook a complete validation procedure in the general adult population in Lebanon. The content validity indicators were good: item content validity index ranged between 0.89 and 1.00, the content validity index scale average was ≥0.95 and the modified Kappa statistic for each of the KAP items was equal to I-CVI. The intra-class correlation coefficient values (n = 100) were ≥0.62 for all Knowledge and Attitudes items, demonstrating the item reliability. Confirmatory factorial analysis (n = 1450) showed that the selected model of Knowledge and Attitude constructs has adequate fit indicators and encompassed three factors that showed acceptable internal reliability: Knowledge (Cronbach’s alpha = 0.72), personal Attitudes towards tranquilizers (Cronbach’s alpha = 0.79) and Attitudes towards healthcare providers (Cronbach’s alpha = 0.65). The Arabic/French questionnaire was highly accepted, with a response rate of 95.72% and item non-response rate ≤3.6%. The availability of a cross-cultural adapted and multilingual validated questionnaire would stimulate research on tranquilizer misuse

Y-chromosome R-M343 African lineages and sickle cell disease reveal structured assimilation in Lebanon

We have sought to identify signals of assimilation of African male lines in Lebanon by exploring the association of sickle cell disease in Lebanon with Y-chromosome haplogroups that are informative of the disease origin and its exclusivity to the Muslim community. A total of 732 samples were analyzed including 33 sickle cell disease patients from Lebanon genotyped for 28 binary markers and 19 short tandem repeats on the non-recombinant segment of the Y chromosome. Genetic organization was identified using populations known to have influenced the genetic structure of the Lebanese population, in addition to African populations with high incidence of sickle cell disease. Y-chromosome haplogroup R-M343 sub-lineages distinguish between sub-Saharan African and Lebanese Y chromosomes. We detected a limited penetration of sickle cell disease into Lebanese R-M343 carriers, restricted to Lebanese Muslims. We suggest that this penetration brought the sickle cell gene along with the African R-M343, probably with the Saharan caravan slave trade

Development and Validation of a Knowledge, Attitude and Practice Questionnaire on Antibiotic Use in Arabic and French Languages in Lebanon

Objectives: Validated knowledge–attitude–practice (KAP) questionnaires are essential to design and evaluate intervention programs on antibiotic use. Recently, we validated the first KAP questionnaire on antibiotics in Spain. Cross-cultural adaptation and validation of research tools increase their universal usefulness. Here, we aimed to validate the questionnaire in a developing country with different socioeconomic characteristics from that of Spain. Methods: We translated the previously developed KAP-questionnaire into Arabic and French, tailored it and then validated it in adult population in Lebanon. The item content validity index (I-CVI), scale content validity index (S-CVI/Ave) and modified Kappa (k*) were calculated. The construct validity of the questionnaire was evaluated using confirmatory factorial analysis (CFA, N = 1460) and its reliability was assessed using intraclass correlation coefficients (ICC, N = 100) and Cronbach’s alpha statistic. Results: ICV-I (>0.78), k* (equal to ICV-I for all items) and S-CVI/Ave (≥0.95) confirmed the questionnaire content validity. Pilot testing (N = 40) and face validity showed the understandability of the questionnaire by the population. Test–retest reliability analysis (N = 100) yielded ICC ≥ 0.59 for all knowledge and attitude items, showing the capacity of the questionnaire to generate reproducible results. CFA evidenced adequate fit of the chosen model, thus establishing the construct validity of the questionnaire (root mean squared error approximation = 0.053, standardized root mean square residual = 0.045, comparative fit index = 0.92 and Tucker–Lewis index = 0.90). The questionnaire showed an acceptable internal reliability (Cronbach’s alpha = 0.62) and was highly accepted in Lebanon (response rate = 96% and item response rates ≥ 94%). Conclusions: The validity of the KAP-questionnaire on antibiotics in Arabic and French was demonstrated in Lebanon

WT1 controls antagonistic FGF and BMP-pSMAD pathways in early renal progenitors.

International audienceKidney organogenesis requires the tight control of proliferation, differentiation and apoptosis of renal progenitor cells. How the balance between these cellular decisions is achieved remains elusive. The Wilms' tumour suppressor Wt1 is required for progenitor survival, but the molecular cause for renal agenesis in mutants is poorly understood. Here we demonstrate that lack of Wt1 abolishes fibroblast growth factor (FGF) and induces BMP/pSMAD signalling within the metanephric mesenchyme. Addition of recombinant FGFs or inhibition of pSMAD signalling rescues progenitor cell apoptosis induced by the loss of Wt1. We further show that recombinant BMP4, but not BMP7, induces an apoptotic response within the early kidney that can be suppressed by simultaneous addition of FGFs. These data reveal a hitherto unknown sensitivity of early renal progenitors to pSMAD signalling, establishes FGF and pSMAD signalling as antagonistic forces in early kidney development and places WT1 as a key regulator of pro-survival FGF signalling pathway genes

p53 Restoration in Induction and Maintenance of Senescence: Differential Effects in Premalignant and Malignant Tumor Cells

International audienceThe restoration of p53 has been suggested as a therapeutic approach in tumors. However, the timing of p53 restoration in relation to its efficacy during tumor progression still is unclear. We now show that the restoration of p53 in murine premalignant proliferating pineal lesions resulted in cellular senescence, while p53 restoration in invasive pineal tumors did not. The effectiveness of p53 restoration was not dependent on p19 Arf expression but showed an inverse correlation with Mdm2 expression. In tumor cells, p53 restoration became effective when paired with either DNA-damaging therapy or with nutlin, an inhibitor of p53-Mdm2 interaction. Interestingly, the inactivation of p53 after senescence resulted in reentry into the cell cycle and rapid tumor progression. The evaluation of a panel of human supratentorial primitive neuroectodermal tumors (sPNET) showed low activity of the p53 pathway. Together, these data suggest that the restoration of the p53 pathway has different effects in premalignant versus invasive pineal tumors, and that p53 activation needs to be continually sustained, as reversion from senescence occurs rapidly with aggressive tumor growth when p53 is lost again. Finally, p53 restoration approaches may be worth exploring in sPNET, where the p53 gene is intact but the pathway is inactive in the majority of examined tumors