Genetic Profile Evaluation of Human Cell Lines Treated with Anastatica hierochuntica Using Forensic DNA Fingerprinting Markers

Cell line authentication using Short Tandem Repeats (STRs) is necessary to ensure the integrity of the cell for its continuous culture and to identify misidentification and cross-contamination issues. This study investigates the changes in the genetic profile of MCF-7 and HepG2 cell lines caused by the methanolic leaf extract of Anastatica hierochuntica (AH) using human identification based STR markers. MCF-7 and HepG2 cell lines were treated with various concentrations of AH extracts for three different periods. The treated and control cells' DNA was extracted using a QIAamp® DNA Micro Kit, quantified using a Quantifiler Duo DNA Quantification Kit, and amplified using an AmpFlSTR Identifiler plus PCR Amplification Kit. The concentrations of the DNA extracted from control and MCF-7 and HepG2 cell lines treated with AH extract at 300 to 2400 µg/ml for 24hr and 150 to 2400 µg/ml for 48 and 72hrs were statistically significant (p<0.05). Microsatellite instability (MSI), loss of heterozygosity (LOH), insertion/deletions changes in the STRs profile were observed in treated cell lines at 1200 and 2400 µg/ml in MCF-7 cells for 48 and 72hrs and HepG2 cells for 24, 48, and 72hrs. We conclude that the highest concentration of AH extracts affected the genotype of the cell lines leading to misidentification. Therefore, cell line authentication by forensic DNA analysis techniques plays a decisive role for cells tested with a high concentration of chemical compounds and gives the forensic investigator an insight into these changes in the STR genotype of a victim/suspect who has been been under long term chemotherapeutic treatment

Evaluation of Forensic Genetic Parameters of 24 STR Loci and Y indel in a Southern Region Saudi Population Sample Using GlobalFiler™ PCR Amplification Kit

The last three decades have seen rapid advances in the field of short tandem repeats (STRs) genotyping technology. Autosomal STRs have emerged as a  powerful tool in forensic identification and paternity investigations. The indigenous population of Saudi Arabia is irregularly distributed and has historically been organized into geographically distinct groups or tribes of patrilineal descent. So far, there has been no detailed investigation of the southern region Saudi population to assist in the interpretation of DNA-based forensic evidence and in the construction of DNA database. The objective of this study is to investigate the genetic structure in 154 unrelated healthy Saudi subjects within three generations from the southern Saudi regions using a GlobalFiler™ PCR Amplification kit. Intra- and Inter-population genetic diversity as well as the forensic genetics parameters were analyzed. Our results showed that SE33 and TPOX loci were the most and the least polymorphic loci, respectively. The PIC, PE, TPI, Ho and He varied from 0.56116 (TPOX) to 0.94393 (SE33), 0.26638 (TPOX) to 0.83859 (SE33), 1.1875 (TPOX) to 6.33333 (SE33), 0.57894 (TPOX) to 0.92105 (SE33) and 0.6169 (TPOX) to 0.952 (SE33), respectively. The highest PM was observed for D22S1045 (0.223944) and the highest PD for SE33 (0.98935). The combined PD was 99.99999999% and the combined PM was equal to 3.19021E-25. Phylogenetic parameters showed that the southern region Saudi population had the closest genetic relationship with the Saudi, Emirati, Kuwaiti, and Bahraini populations. The study offers some important insights into the southern region Saudi population structure using GlobalFiler™ PCR Amplification kit

Blood contains circulating cell-free respiratory competent mitochondria.

Mitochondria are considered as the power-generating units of the cell due to their key role in energy metabolism and cell signaling. However, mitochondrial components could be found in the extracellular space, as fragments or encapsulated in vesicles. In addition, this intact organelle has been recently reported to be released by platelets exclusively in specific conditions. Here, we demonstrate for the first time, that blood preparation with resting platelets, contains whole functional mitochondria in normal physiological state. Likewise, we show, that normal and tumor cultured cells are able to secrete their mitochondria. Using serial centrifugation or filtration followed by polymerase chain reaction-based methods, and Whole Genome Sequencing, we detect extracellular full-length mitochondrial DNA in particles over 0.22 µm holding specific mitochondrial membrane proteins. We identify these particles as intact cell-free mitochondria using fluorescence-activated cell sorting analysis, fluorescence microscopy, and transmission electron microscopy. Oxygen consumption analysis revealed that these mitochondria are respiratory competent. In view of previously described mitochondrial potential in intercellular transfer, this discovery could greatly widen the scope of cell-cell communication biology. Further steps should be developed to investigate the potential role of mitochondria as a signaling organelle outside the cell and to determine whether these circulating units could be relevant for early detection and prognosis of various diseases

Evaluation of circulating DNA analysis in the context of tumorigenesis and as a diagnostic tool

L’analyse de l’ADN circulant dans le contexte de la tumorogenèse et comme outil diagnostic Le projet de thèse ici décrit est fondé sur la découverte remarquable qu'une quantité importante d’ADN circule dans le sang de patients atteints de cancer [1-5]. Le développement d'une technologie basée sur la détection de l'ADN circulant représente une avancée scientifique et médicale pour le diagnostic et le suivi dans la prise en charge thérapeutique des patients atteints de cancer. Malgré de nombreuses études menées au cours des dix dernières années [4,5] sur l'ADN circulant, les origines de la libération de l'ADN circulant dans les liquides biologiques sont hypothétiques et sa structure n'est pas élucidée. Ces données ne valident pas jusqu'à présent l'ADN circulant en tant que biomarqueur. Pour cette raison, les objectifs du groupe dirigé par Alain Thierry sont axés sur l'élucidation des formes structurelles de l'ADN circulant. Ainsi, en utilisant des souris nude xénogreffées avec des lignées cellulaires tumorales humaines de cancer colorectal ainsi que des échantillons sanguins cliniques provenant de patients atteints de cancer colorectal, l'équipe a montré que la concentration en ADN circulant était corrélée positivement avec la taille de la tumeur [6, 7] et ces résultats se sont révélés optimaux pour des tailles inférieures à 100 pb. Une discrimination significative entre les individus sains et les patients du cancer a été observée grâce à l'analyse de la fragmentation de l'ADN circulant. L'originalité de ces découvertes a donné naissance à la technologie Intplex récemment breveté par le CNRS [8]. L'objectif de la thèse est de valider la quantification et la fragmentation de l'ADN circulant comme un outil de diagnostic et de suivi de la maladie dans la prise en charge du cancer en analysant de près les facteurs qui peuvent influencer la quantification et la fragmentation de l'ADN circulant. Grâce au modèle animal développé par l’équipe et l’étroite collaboration avec les centres anti-cancéreux, différents paramètres seront analysés. Une partie de la thèse se concentrera sur la comparaison et la standardisation des résultats en fonction de nombreux facteurs spécifiques à la tumeur, comme son type, sa progression, sa différenciation et sa localisation tissulaire. Le travail de thèse portera également sur l'influence de facteurs individuels pouvant affecter la quantité et la fragmentation de l'ADN circulant: âge, sexe, antécédents médicaux, états physiologiques spécifiques, situations physiopathologiques. L'influence du traitement sera également explorée. Des études seront menées afin de standardiser l'analyse biologique: influence du rythme circadien, prise de nourriture .... Techniquement, la variation analytique et l'influence des facteurs pré-analytiques seront déterminées afin d’établir un guide de bonnes pratiques analytiques pour éliminer tout artefact susceptible d’affecter la quantité et l'intégrité de l'ADN circulant dans les échantillons. Ces deux paramètres seront testés dans une évaluation clinique prospective multicentrique sur une cohorte de 450 patients atteints de cancer colorectal. Ce travail garantit un impact considérable dans la littérature et dans la pratique clinique comme test non invasif de diagnostic et de suivi et comme un outil pour améliorer les connaissances de base sur l'ADN circulant et le cancer.Analysis of circulating DNA circulating in the context of tumorigenesis and as a diagnostic tool The thesis project described here is based on the remarkable discovery that a significant amount of DNA circulates in blood of cancer patients [1-5]. The development of a technology based on the detection of circulating DNA represents a scientific and medical breakthrough for diagnosis and follow up in therapeutic care of cancer patients. Despite numerous studies conducted over the last decade [4,5] on circulating DNA, origins of release of circulating DNA in biological fluids are hypothetical and its structure is unclear. These data do not validate so far circulating DNA as a biomarker. For this reason, objectives of the group led by Alain Thierry are focused on elucidating structural forms of circulating DNA. Thus, using nude mice xenografted with human tumor cell lines of colorectal cancer as clinical samples from colorectal cancer patients, the team showed that the concentration was positively correlated with tumor size [6 , 7] and these results were optimal for sizes below 100 bp. A significative discrimination between healthy individuals and cancer patients was found by the analysis of circulating DNA fragmentation. The originality of these discoveries gave rise to the Intplex technology recently patented by the CNRS [8]. The aim of the thesis is to validate quantification and fragmentation of circulating DNA as a diagnostic and follow-up test in the management of cancer by closely analyzing the factors that may influence quantification and fragmentation of circulating DNA. Thanks to mouse model developed by the team and close collaboration with clinical cancer centers, different parameters will be analyzed. One part of the thesis will be focused on comparison and standardization of the different results depending on many factors specific to the tumor, such as its type, its progression, its differentiation and its tissue localization. The thesis work will also focus on the influence of individual factors that may affect the quantity and the fragmentation of circulating DNA: age, sex, medical history, specific physiological states, pathophysiological situations. The influence of treatment will also be explored. Studies will be undertaken in order to standardize the biological analysis: influence of circadian rhythm, food intake.... Technically, the analytical variation and the influence of pre-analytical factors will be determined to establish a good practice guide to eliminate any artifacts altering the amount and integrity of circulating DNA in the samples. These two parameters will be tested in a prospective multicentric clinical evaluation on a cohort including 450 patients with colorectal cancer. This work warrants a significant impact in the literature and in cancer clinical practice as a non invasive diagnostic and follow-up test and as a tool to improve the basic knowledge on circulating DNA and cancer

Multi-marker analysis of circulating cell-free DNA toward personalized medicine for colorectal cancer.

International audienceDevelopment of a Q-PCR-based assay for the high-performance analysis of circulating cell-free DNA (ccfDNA) requires good knowledge of its structure and size. In this work, we present the first visual determination of ccfDNA by Atomic Force Microscopy (AFM) on plasma samples from colorectal cancer (CRC) patients and healthy donors. In addition to the examination of fragment size distribution profile as performed by Q-PCR, this analysis confirms that ccfDNA is highly fragmented and that more than 80% of ccfDNA fragments in CRC plasma are below 145 bp. We adapted an Allele-Specific Blocker (ASB) Q-PCR to small ccfDNA fragments to determine simultaneously the total ccfDNA concentration, the presence of point mutation, the proportion of mutated allele, and a ccfDNA integrity index. The data validated analytically these four parameters in 124 CRC clinical samples and 71 healthy individuals. The multi-marker method, termed Intplex, enables sensitive and specific non-invasive analysis of tumor ccfDNA, which has great potential in terms of cost, quality control, and easy implementation in every clinical center laboratory

Population genetic data of the 21 autosomal STRs included in GlobalFiler kit of a population sample from the Kingdom of Bahrain.

Bahrain's population consists mainly of Arabs, Baharna and Persians leading Bahrain to become ethnically diverse. The exploration of the ethnic origin and genetic structure within the Bahraini population is fundamental mainly in the field of population genetics and forensic science. The purpose of the study was to investigate and conduct genetic studies in the population of Bahrain to assist in the interpretation of DNA-based forensic evidence and in the construction of appropriate databases. 24 short-tandem repeats in the GlobalFiler PCR Amplification kit including 21 autosomal STR loci and three gender determination loci were amplified to characterize different genetic and forensic population parameters in a cohort of 543 Bahraini unrelated healthy men. Samples were collected during the year 2017. The genotyping of the 21 autosomal STRs showed all of the loci were in Hardy-Weinberg Equilibrium (HWE) after applying Bonferroni's correction. We also found out no significant deviations from LD between pairwise STR loci in Bahraini population except when plotting for D3S1358-CSF1PO, CSF1PO-SE33, D19S433-D12S391, FGA-D2S1338, FGA-SE33, FGA-D7S820 and D7S820-SE33. The SE33 locus was the most polymorphic for the studied population and THO1 locus was the less polymorphic. The Allele 8 in TPOX scored the highest allele frequency of 0.496. The SE33 locus showed the highest power of discrimination (PD) in Bahraini population, whereas TPOX showed the lowest PD value. The 21 autosomal STRs showed a value of combined match probability (CMP) equal to 4.5633E-27, and a combined power of discrimination (CPD) of 99.99999999%. Off-ladders and tri-allelic variants were observed in various samples at D12S391, SE33 and D22S1045 loci. Additionally, pairwise genetic distances based on FST were calculated between Bahraini population and other populations extracted from the literature. Genetic distances were represented in a non-metric MDS plot and clustering of populations according to their geographic locations was detected. Phylogenetic tree was constructed to investigate the genetic relatedness between Bahraini population and the neighboring populations. Our study indicated that the twenty-one autosomal STRs are highly polymorphic in the Bahraini population and can be used as a powerful tool in forensics and population genetic analyses including paternity testing and familial DNA searching

Common polymorphisms of calpain-10 and the risk of Type 2 Diabetes in a Tunisian Arab population: a case-control study

Abstract Background Genetic variations in the calpain-10 gene (CAPN10), in particular the at-risk diplotype (112/121), were previously implicated with increased risk of type 2 diabetes (T2D). Methods We examined the association of CAPN10 UCSNP-43 (rs3792267), UCSNP-19 (rs3842570), and UCSNP-63 (rs5030952) SNPs with T2D in 917 Tunisian T2D patients and 748 non-diabetic controls. CAPN10 genotyping was done by PCR-RFLP. Results Enrichment of UCSNP-19 2R (minor) allele and 2R/2R genotype was found in T2D patients; the allele and genotype distribution of UCSNP-43 and UCSNP-63 alleles and genotypes were not significantly different between patient groups and non-diabetic control subjects. Regression analysis demonstrated progressive increases in T2D risk in 3R/2R [OR (95% CI) = 1.35 (1.08 - 1.68)] and 2R/2R [OR (95% CI) = 1.61 (1.20 - 2.18)] genotypes. Of the six haplotypes detected, enrichment of haplotype 111 (UCSNP-43/UCSNP-19/UCSNP-63) was seen in patients (Pc = 0.034); the distribution of the other haplotypes was comparable between patients and control subjects; neither haplotype 211 nor haplotype 212 was observed. Furthermore, the frequency of all CAPN10 diplotypes identified, including the "high-risk diplotype (112/121) reported for Mexican-Americans and Northern Europeans, were comparable between patients and controls. Conclusions CAPN10 UCSNP-19 variant, and the 111 haplotype contribute to the risk of T2D in Tunisian subjects; no significant associations between CAPN10 diplotypes and T2D were demonstrated for Tunisians.</p

Imidazoquinoxaline anticancer derivatives and imiquimod interact with tubulin: Characterization of molecular microtubule inhibiting mechanisms in correlation with cytotoxicity

International audienceDisplaying a strong antiproliferative activity on a wide variety of cancer cells, EAPB0203 and EAPB0503 belong to the imidazo[1,2-a]quinoxalines family of imiquimod structural analogues. EAPB0503 has been shown to inhibit tubulin polymerization. The aim of the present study is to characterize the interaction of EAPB0203 and EAPB0503 with tubulin. We combine experimental approaches at the cellular and the molecular level both in vitro and in silico in order to evaluate the interaction of EAPB0203 and EAPB0503 with tubulin. We examine the influence of EAPB0203 and EAPB0503 on the cell cycle and fate, explore the binding interaction with purified tubulin, and use a computational molecular docking model to determine the binding modes to the microtubule. We then use a drug combination study with other anti-microtubule agents to compare the binding site of EAPB0203 and EAPB0503 to known potent tubulin inhibitors. We demonstrate that EAPB0203 and EAPB0503 are capable of blocking human melanoma cells in G2 and M phases and inducing cell death and apoptosis. Second, we show that EAPB0203 and EAPB0503, but also unexpectedly imiquimod, bind directly to purified tubulin and inhibit tubulin polymerization. As suggested by molecular docking and binding competition studies, we identify the colchicine binding site on β-tubulin as the interaction pocket. Furthermore, we find that EAPB0203, EAPB0503 and imiquimod display antagonistic cytotoxic effect when combined with colchicine, and disrupt tubulin network in human melanoma cells. We conclude that EAPB0203, EAPB0503, as well as imiquimod, interact with tubulin through the colchicine binding site, and that the cytotoxic activity of EAPB0203, EAPB0503 and imiquimod is correlated to their tubulin inhibiting effect. These compounds appear as interesting anticancer drug candidates as suggested by their activity and mechanism of action, and deserve further investigation for their use in the clinic