Pharmacogenetic landscape of Metabolic Syndrome components drug response in Tunisia and comparison with worldwide populations

<div><p>Genetic variation is an important determinant affecting either drug response or susceptibility to adverse drug reactions. Several studies have highlighted the importance of ethnicity in influencing drug response variability that should be considered during drug development. Our objective is to characterize the genetic variability of some pharmacogenes involved in the response to drugs used for the treatment of Metabolic Syndrome (MetS) in Tunisia and to compare our results to the worldwide populations. A set of 135 Tunisians was genotyped using the Affymetrix Chip 6.0 genotyping array. Variants located in 24 Very Important Pharmacogenes (VIP) involved in MetS drug response were extracted from the genotyping data. Analysis of variant distribution in Tunisian population compared to 20 worldwide populations publicly available was performed using R software packages. Common variants between Tunisians and the 20 investigated populations were extracted from genotyping data. Multidimensional screening showed that Tunisian population is clustered with North African and European populations. The greatest divergence was observed with the African and Asian population. In addition, we performed Inter-ethnic comparison based on the genotype frequencies of five VIP biomarkers. The genotype frequencies of the biomarkers rs3846662, rs1045642, rs7294 and rs12255372 located respectively in <i>HMGCR</i>, <i>ABCB1</i>, <i>VKORC1 and TCF7L2</i> are similar between Tunisian, Tuscan (TSI) and European (CEU). The genotype frequency of the variant rs776746 located in <i>CYP3A5</i> gene is similar between Tunisian and African populations and different from CEU and TSI. The present study shows that the genetic make up of the Tunisian population is relatively complex in regard to pharmacogenes and reflects previous historical events. It is important to consider this ethnic difference in drug prescription in order to optimize drug response to avoid serious adverse drug reactions. Taking into account similarities with other neighboring populations, our study has an impact not only on the Tunisian population but also on North African population which are underrepresented in pharmacogenomic studies.</p></div

STRUCTURE analysis of the genetic relationship between 24 populations.

<p>K is the possible numbers of parental population clusters. One color represents one parental population into different color segments. Best K level was observed at K = 3, where a vertical the proportion of each ancestral component in a single individual is represented by a vertical bar divided into 3 colors. 601 markers study—displaying results for runs with highest likelihood out of 27 runs in each cluster K3 to 10. Black vertical lines identify the population boundaries. The height extent of each color within an individual’s color bar corresponds to the estimated membership of the individual in one of the clusters; each cluster is assigned a separate <b>color</b>. The bars with multiple colors can be interpreted as genetic admixture or as relative probabilities of belonging to the different clusters.</p

Multidimensional scaling plot analysis of the Tunisian subpopulation and worldwide populations.

<p>The plot reveals three distinct clusters showing that the Tunisian population present a close affinity with the North Africans and Europeans and distinct from South Africans and Asians. Tunisian population; Capital Tunis TU_TC, coastal city of Monastir TU_MC (AffymetrixChip 6.0 genotyping array), African ancestry in the south Western USA (ASW); a northwestern European population (CEU); the Han Chinese in Beijing, China (CHB); a Chinese population of metropolitan Denver, Colorado, USA (CHD); the Gujarati Indians in Houston, Texas, USA (GIH); the Japanese population in Tokyo, Japan (JPT); the Luhya people in Webuye, Kenya (LWK); people of Mexican ancestry living in Los Angeles, California, USA (MEX); the Maasai people in Kinyawa, Kenya (MKK); the Tuscan people of Italy (TSI); and the Yoruba in Ibadan, Nigeria (YRI); data from HapMap were retrived in March 2016. It is available by FTP: <a target="_blank">ftp://ftp.ncbi.nlm.nih.gov/hapmap/</a> and Algeria (ALG), Egyptia (EGY), Libya (LIB), Tunisia Dwiret TUN_Ber, Lebanon (LIB), Morocco South (MCS), Morocco North (MCN), Spain South (SPS), Spain North (SPN), Spain Basc (SBA),: Sub-Saharan (SAH), Canary Island (CIS); data from the literature [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194842#pone.0194842.ref034" target="_blank">34</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194842#pone.0194842.ref035" target="_blank">35</a>].</p

Estimating of pairwise Fst among the 11 populations.

<p>Estimating of pairwise Fst among the 11 populations.</p

Genotype frequency of significant VIP variants in Tunisian population (n = 135) compared with ten HapMap populations.

<p>Genotype frequency of significant VIP variants in Tunisian population (n = 135) compared with ten HapMap populations.</p

Image1_Uncovering the clinical relevance of unclassified variants in DNA repair genes: a focus on BRCA negative Tunisian cancer families.pdf

Introduction: Recent advances in sequencing technologies have significantly increased our capability to acquire large amounts of genetic data. However, the clinical relevance of the generated data continues to be challenging particularly with the identification of Variants of Uncertain Significance (VUSs) whose pathogenicity remains unclear. In the current report, we aim to evaluate the clinical relevance and the pathogenicity of VUSs in DNA repair genes among Tunisian breast cancer families.Methods: A total of 67 unsolved breast cancer cases have been investigated. The pathogenicity of VUSs identified within 26 DNA repair genes was assessed using different in silico prediction tools including SIFT, PolyPhen2, Align-GVGD and VarSEAK. Effects on the 3D structure were evaluated using the stability predictor DynaMut and molecular dynamics simulation with NAMD. Family segregation analysis was also performed.Results: Among a total of 37 VUSs identified, 11 variants are likely deleterious affecting ATM, BLM, CHEK2, ERCC3, FANCC, FANCG, MSH2, PMS2 and RAD50 genes. The BLM variant, c.3254dupT, is novel and seems to be associated with increased risk of breast, endometrial and colon cancer. Moreover, c.6115G>A in ATM and c.592+3A>T in CHEK2 were of keen interest identified in families with multiple breast cancer cases and their familial cosegregation with disease has been also confirmed. In addition, functional in silico analyses revealed that the ATM variant may lead to protein immobilization and rigidification thus decreasing its activity. We have also shown that FANCC and FANCG variants may lead to protein destabilization and alteration of the structure compactness which may affect FANCC and FANCG protein activity.Conclusion: Our findings revealed that VUSs in DNA repair genes might be associated with increased cancer risk and highlight the need for variant reclassification for better disease management. This will help to improve the genetic diagnosis and therapeutic strategies of cancer patients not only in Tunisia but also in neighboring countries.</p

Table1_Uncovering the clinical relevance of unclassified variants in DNA repair genes: a focus on BRCA negative Tunisian cancer families.xlsx

Introduction: Recent advances in sequencing technologies have significantly increased our capability to acquire large amounts of genetic data. However, the clinical relevance of the generated data continues to be challenging particularly with the identification of Variants of Uncertain Significance (VUSs) whose pathogenicity remains unclear. In the current report, we aim to evaluate the clinical relevance and the pathogenicity of VUSs in DNA repair genes among Tunisian breast cancer families.Methods: A total of 67 unsolved breast cancer cases have been investigated. The pathogenicity of VUSs identified within 26 DNA repair genes was assessed using different in silico prediction tools including SIFT, PolyPhen2, Align-GVGD and VarSEAK. Effects on the 3D structure were evaluated using the stability predictor DynaMut and molecular dynamics simulation with NAMD. Family segregation analysis was also performed.Results: Among a total of 37 VUSs identified, 11 variants are likely deleterious affecting ATM, BLM, CHEK2, ERCC3, FANCC, FANCG, MSH2, PMS2 and RAD50 genes. The BLM variant, c.3254dupT, is novel and seems to be associated with increased risk of breast, endometrial and colon cancer. Moreover, c.6115G>A in ATM and c.592+3A>T in CHEK2 were of keen interest identified in families with multiple breast cancer cases and their familial cosegregation with disease has been also confirmed. In addition, functional in silico analyses revealed that the ATM variant may lead to protein immobilization and rigidification thus decreasing its activity. We have also shown that FANCC and FANCG variants may lead to protein destabilization and alteration of the structure compactness which may affect FANCC and FANCG protein activity.Conclusion: Our findings revealed that VUSs in DNA repair genes might be associated with increased cancer risk and highlight the need for variant reclassification for better disease management. This will help to improve the genetic diagnosis and therapeutic strategies of cancer patients not only in Tunisia but also in neighboring countries.</p

Analysis of potentially pathogenic <i>ABRAXAS</i> in-frame deletion or rare missense substitutions.

<p>Analysis of potentially pathogenic <i>ABRAXAS</i> in-frame deletion or rare missense substitutions.</p

Distribution of p.Thr141Ile, p.Ser7Ser and p.Ser11Ser by race/ethnicity.

<p>Distribution of p.Thr141Ile, p.Ser7Ser and p.Ser11Ser by race/ethnicity.</p

p.Gly39val and p.Thr141Ile ABRAXAS mutants have defects in gamma-H2AX formation.

<p>(A) Typical DNA damage foci of ABRAXAS in shABRAXAS (shABX145) MCF7 cells complemented with ABRAXAS-HA-Flag, ABRAXAS-HA-Flag pThr141Ile, or ABRAXAS-HA-Flag pGly39Val. The anti-Flag antibody was used to monitor ABRAXAS foci formation (green), anti-gamma-H2AX (red) and the merge picture is depicted. In blue, DAPI staining. (B) Quantification of gamma-H2AX foci formation in MCF7 cells after neocarzinostatin treatment and release. P-values were obtained with a Wilcoxon’s Test with N = 100 cells from four independent experiments.</p