Sub-Saharan African women often develop breast cancer at a younger age, with a high prevalence of aggressive subtypes such as triple-negative breast cancer and elevated mortality. Genetic factors may underlie these patterns, but African populations remain underrepresented in genomic research. As an initial step toward addressing this gap, we evaluated DNA extracted from formalin-fixed paraffin-embedded (FFPE) breast cancer blocks collected in anatomic pathology laboratories in Gabon, Togo, and Benin. Although DNA could be successfully extracted, its functional quality was significantly impaired. Quantitative PCR revealed progressive degradation, with poor amplification efficiency for larger fragments, and next-generation sequencing (NGS) libraries exhibited degraded electropherogram profiles, low coverage, and elevated duplication rates. These limitations likely stem from socio-economic constraints, including delayed processing and prolonged formalin fixation, which promote nucleic acid fragmentation and crosslinking. To overcome these barriers, we established a preservation protocol adapted to the resource and infrastructural limitations of the region: storage of biopsies in physiological saline at -20 °C. This method requires only basic equipment widely available in local hospitals, yet yielded DNA of high integrity, enabled efficient library construction, and produced significantly superior NGS performance compared with FFPE-derived DNA. This cost-effective and scalable approach provides a feasible solution for genomic research in resource-limited settings. Future efforts should focus on complementary strategies for RNA preservation and tumor enrichment to enable comprehensive molecular profiling and advance precision oncology in West Africa.

Marbling is one of the most important beef quality traits. An association between a non-synonymous variant located in EGFLAM (EGF-like fibronectin and laminin G) and marbling in Hanwoo cattle has recently been published. We therefore investigated the association between this SNP (rs109436056 SNP) and marbling in Limousin cattle. A total of 355 animals were phenotyped for marbling and genotyped for this SNP. Significant association (p < 0.05) was observed, in which genotype CC exhibited higher marbling. This SNP could be used for the genetic improvement of marbling in Limousin cattle.

PhexL222P mouse is a new ENU mouse model for XLH disease due to Leu to Pro amino acid modification at position 222. PhexL222P mouse is characterized by growth retardation, hypophosphatemia, hypocalcemia, reduced body bone length, and increased epiphyseal growth plate thickness and femur diameter despite the increase in PHEXL222P expression. Actually, PhexL222P mice show an increase in Fgf23, Dmp1, and Mepe and Slc34a1 (Na-Pi IIa cotransporter) mRNA expression similar to those observed in Hyp mice. Femoral osteocalcin and sclerostin and Slc34a1 do not show any significant variation in PhexL222P mice. Molecular dynamics simulations support the experimental data. P222 might locally break the E217-Q224 β-sheet, which in turn might disrupt inter-β-sheet interactions. We can thus expect local protein misfolding, which might be responsible for the experimentally observed PHEXL222P loss of function. This model could be a valuable addition to the existing XLH model for further comprehension of the disease occurrence and testing of new therapies.

BACKGROUND:Ischemia-related injury during the preimplantation period impacts kidney graft outcome. Evaluating these lesions by a noninvasive approach before transplantation could help us to understand graft injury mechanisms and identify potential biomarkers predictive of graft outcomes. This study aims to determine the metabolomic content of graft perfusion fluids and its dependence on preservation time and to explore whether tubular transporters are possibly involved in metabolomics variations.METHODS:Kidneys were stored on hypothermic perfusion machines. We evaluated the metabolomic profiles of perfusion fluids (n = 35) using liquid chromatography coupled with tandem mass spectrometry and studied the transcriptional expression of tubular transporters on preimplantation biopsies (n = 26), both collected at the end of graft perfusion. We used univariate and multivariate analyses to assess the impact of perfusion time on these parameters and their relationship with graft outcome.RESULTS:Seventy-two metabolites were found in preservation fluids at the end of perfusion, of which 40% were already present in the native conservation solution. We observed an increase of 23 metabolites with a longer perfusion time and a decrease of 8. The predictive model for time-dependent variation of metabolomics content showed good performance (R 2  = 76%, Q 2  = 54%, accuracy = 41%, and permutation test significant). Perfusion time did not affect the mRNA expression of transporters. We found no correlation between metabolomics and transporters expression. Neither the metabolomics content nor transporter expression was predictive of graft outcome.CONCLUSIONS:Our results call for further studies, focusing on both intra- and extratissue metabolome, to investigate whether transporter alterations can explain the variations observed in the preimplantation period.

BISCEm (https://www.unilim.fr/biscem/), acronyme de Biologie Intégrative Santé Chimie Environnement, est une plateforme technologique créée par l’Institut de recherche GEIST en 2017. La plateforme regroupe des équipements de pointe permettant la réalisation d’analyses moléculaires, cellulaires et tissulaires et d’expériences sur des animaux, dans le strict respect de la règlementation en vigueur et du bien-être animal. La réalisation des prestations, la formation à l’utilisation des équipements, les conseils dans la conception des expériences et dans l’interprétation des résutats, la veille technologique et la gestion de la plateforme sont assurés par une équipe d’une vingtaine d’agents hautement qualifiés. La plateforme est ouverte à toutes les structures de recherche, publiques ou privées.

Le cancer du sein est le premier cancer chez la femme au Benin aussi bien en termes d’incidence que de mortalite et affecte des patientes jeunes. Bien que la connaissance des types moleculaires de cancer du sein des femmes beninoises reste encore limitee, les etudes disponibles montrent clairement que ces femmes font plus de cancers triples negatifs, formes particulierement agressives. Objectifs: Actuellement, aucune analyse genetique du cancer du sein au Benin n’a ete effectuee et donc aucune information sur les genes qui abritent le plus souvent des mutations pathogenes dans cette population n’est disponible. Les objectifs de nos travaux sont d’evaluer la survie en fonction du stade de diagnostic, de l’acces au traitement mais aussi d’identifier les genes du cancer du sein qui abritent le plus souvent des mutations pathogenes dans la population beninoise. Methodes/Resultats: Les progres technologiques permettent aujourd’hui de rechercher des mutations sur plusieurs genes de facon simultanee. Une etude prospective et retrospective a partir de bloc de paraffine est realisee, le sequencage a haut debit va nous permettre de tester un ensemble de genes susceptibles d’intervenir dans la predisposition au cancer du sein et d’identifier des variations dont il faudra definir le caractere deletere ou non (selon la classification en 5 classes). Afin de classer les variants de signification inconnue potentiellement identifies lors de cette etude, des tests fonctionnels seront developpes. Conclusion: Compte tenu des ressources limitees pour le depistage chez les beninoises par mammographie, ces informations genetiques sont d’autant plus importantes pour l'identification des femmes presentant un risque particulierement eleve de cancer du sein, utile pour concentrer les efforts de depistage et leur proposer un suivi personnalise.

The aim of this study was to identify relevant biomarkers for the prognosis of glioma considering current molecular changes such as IDH mutation and 1p19q deletion. Gene expression profiling was performed using the TaqMan Low Density Array and hierarchical clustering using 96 selected genes in 64 patients with newly diagnosed glioma. The expression dataset was validated on a large independent cohort from The Cancer Genome Atlas (TCGA) database. A differential expression panel of 26 genes discriminated two prognostic groups regardless of grade and molecular groups of tumors: Patients having a poor prognosis with a median overall survival (OS) of 23.0 ± 9.6 months (group A) and patients having a good prognosis with a median OS of 115.0 ± 6.6 months (group B) (p = 0.007). Hierarchical clustering of the glioma TCGA cohort supported the prognostic value of these 26 genes (p < 0.0001). Among these genes, CHI3L1 and NTRK2 were identified as factors that can be associated with IDH status and 1p/19q co-deletion to distinguish between prognostic groups of glioma from the TCGA cohort. Therefore, CHI3L1 associated with NTRK2 seemed to be able to provide new information on glioma prognosis.

The transcriptional co-activator PGC-1α has been reported to play a key role in adaptive thermogenesis and to influence muscle homeostasis and growth in mouse and human. PGC-1α has a complex structure with multiple protein domains whose gene is controlled by two promoters and is subject to alternative splicing events. In cattle, very little is currently known about PGC-1α, the only available data are putative transcripts. So, the aim of our study was to investigate the presence and the structure of bovine PGC-1α alternative transcripts. We found different transcripts, two full-length isoforms named PGC-1α-a and PGC-1α-b, and two truncated forms, NT-PGC-1α and PGC-1α4. In basal conditions, our results showed that the truncated forms are the most expressed in bovine muscle. In addition, the transcripts derived from the proximal promoter are predominant, suggesting that NT-PGC-1α would be the main form. Finally, we showed that the overexpression of either full-length or truncated isoforms of bovine PGC-1α enhances myoblasts differentiation. The multiplicity of isoforms resulting from PGC-1α as well as their implication in myogenesis makes PGC-1α as a gene of interest for the study of the muscular phenotypic variability found in different cattle breeds.

Earlier diagnosis and longitudinal monitoring of diffuse low-grade gliomas (DLGG) increase overall survival by maximizing surgery efficacy and optimizing time for an adjuvant treatment when resection is incomplete. Presently, only imaging permits the non-invasive detection and monitoring of DLGG, but it lacks sensitivity. Measure of circulating microRNAs levels could represent a non-invasive alternative. We hypothesized that slow-growing DLGG induce overtime a systemic reaction impacting blood cells microRNA profiles, while the intact blood–brain barrier restricts the passage of tumor microRNAs into bloodstream. In 15 DLGG patients and 15 healthy controls, expression levels of 758 microRNAs were measured by the TaqMan OpenArray RT-qPCR platform, on preoperative whole blood, containing both cell-free and blood cells microRNAs. Normalized data were computed by a Student t test with a p value threshold allowing a 10% rate of false positive. Statistical analysis retained fifteen microRNAs, all overexpressed in patients. MiR-20a, miR-106a, miR-20b, and miR-93 belong to clusters genetically related. As miR-223 and miR-let7e, they target the transcription factor STAT3. MicroRNA expression levels were not correlated to preoperative tumor volume. A signature composed of miR-93, miR-590-3p, and miR-454 enabled to nearly perfectly separate patients from controls. Our study performed on a homogeneous cohort was designed accordingly to DLGG particularities and provided the first microRNAs signature proposal. Functional convergence on STAT3 and overexpression of miR-223, factors respectively involved in myeloid-derived suppressor cells and granulocytes, argued for a systemic peripheral response. Overexpressed microRNAs and tumor volume were uncorrelated, making a tumor origin elusive.

Chimpanzees are susceptible to experimental infection by human deficiency virus (HIV)-1, but unlike humans, they exceptionally develop an immunodeficiency syndrome after HIV-1 inoculation. To explore the difference between human and chimpanzee, we analyzed the expression of 1547 genes of various functions in human or chimpanzee CD4+ lymphoblasts inoculated in vitro with HIV-1. We observed that, 1 day after HIV inoculation, fifty-eight genes were up-regulated in lymphoblasts of the three humans while their expression remained unchanged in lymphoblasts of the three chimpanzees. One gene is involved in adhesion of HIV (catenin-alpha), three in the immune response (semaphorin 4D, placental growth factor, IL-6), three in apoptosis (deleted in colorectal carcinoma, caspase 9 and FOXO1A). No difference between species was revealed for the expression of 373 genes related to glycosylation pathways. The in vitro human/chimpanzee comparison reveals new candidate genes up-regulated after inoculation with HIV-1 only in human lymphoblasts and which could be related to the higher sensitivity of human to HIV-induced AIDS.

α1-Antichymotrypsin is encoded by the unique SERPINA3 gene in humans, while it is encoded by a cluster of eight closely related genes in cattle. BovSERPINA3 proteins present a high degree of similarity and significant divergences in the reactive centre loop (RCL) domains which are responsible for the antiprotease activity. In this study, we analysed their expression patterns in a range of cattle tissues. Even if their expression is ubiquitous, we showed that the expression levels of each serpin vary in different tissues of 15-month-old Charolais bulls. Our results led us to focus on bovSERPINA3-7, one of the two most divergent members of the bovSERPINA3 family. Expression analyses showed that bovSERPINA3-7 protein presents different tissue-specific patterns with diverse degrees of N-glycosylation. Using a specific antibody raised against bovSERPINA3-7, Western blot analysis revealed a specific 96 kDa band in skeletal muscle. BovSERPINA3-7 immunoprecipitation and mass spectrometry revealed that this 96 kDa band corresponds to a complex of bovSERPINA3-7 and creatine kinase M-type. Finally, we reported that the bovSERPINA3-7 protein is present in slow-twitch skeletal myofibres. Precisely, bovSERPINA3-7 specifically colocalized with myomesin at the M-band region of sarcomeres where it could interact with other components such as creatine kinase M-type. This study opens new prospects on the bovSERPINA3-7 function in skeletal muscle and promotes opportunities for further understanding of the physiological role(s) of serpins.

BACKGROUND:Transcriptome sequencing is a powerful tool for measuring gene expression, but as well as some other technologies, various artifacts and biases affect the quantification. In order to correct some of them, several normalization approaches have emerged, differing both in the statistical strategy employed and in the type of corrected biases. However, there is no clear standard normalization method.RESULTS:We present a novel methodology to normalize RNA-Seq data, taking into account transcript size, GC content, and sequencing depth, which are the major quantification-related biases. In this study, we found that transcripts shorter than 600 bp have an underestimated expression level, while longer transcripts are even more overestimated that they are long. Second, it was well known that the higher the GC content (>50%), the more the transcripts are underestimated. Third, we demonstrated that the sequencing depth impacts the size bias and proposed a correction allowing the comparison of expression levels among many samples. The efficiency of our approach was then tested by comparing the correlation between normalized RNA-Seq data and qRT-PCR expression measurements. All the steps are automated in a program written in Perl and available on request.CONCLUSIONS:The methodology presented in this article identifies and corrects different biases that influence RNA-Seq quantification, and provides more accurate estimations of gene expression levels. This method can be applied to compare expression quantifications from many samples, but preferentially from the same tissue. In order to compare samples from different tissue, a calibration using several reference genes will be required.

Protease-activated receptor-2 (PAR-2) is a trypsin-activated member of the PAR receptor family. Following cleavage, the newly created N-terminus acts as a tethered receptor-activating ligand. PAR-2 is expressed in keratinocytes and enhances the phagocytosis rate of keratinocytes, which leads to increased melanosome transfer and skin pigmentation. Here, we investigated to see whether the bovine bPAR-2 plays a role in pigmentation of cattle skins resulting in shades ranging from dark-black to white. We have identifiedtwo bPAR-2natural variants located in the tethered ligand for the first time. Surprisingly, none of these seems to affect the receptor activity in relation to skin pigmentation as suggested by tethered ligand structure-activity relationships studies. Furthermore, we also showed for the first timethatbPAR-2is regulated at a post-transcriptional level in pigmentation-skin dependent manner. Modulation of PAR-2 activity enhances or decreases melanosome transfer from melanocytes to keratinocytes which results in a variation in skin pigmentation. In this study, we found that bPAR-2 was subjected to post-transcriptional regulation in pigmentation-skin dependent manner and that two variants affecting its tethered ligand did not affect skin pigmentation. Understanding the regulation of PAR-2 expression and the activity of its tethered ligand is important, because PAR-2 is involved in a key step of skin pigmentation and plays a role in lightening or darkening of the skin.

Myostatin is essential for proper regulation of myogenesis, and inactivation of Myostatin results in muscle hypertrophy. Here, we identified an unexpected mutation in the myostatin gene which is almost fixed in Blonde d'Aquitaine cattle. In skeletal muscle, the mutant allele was highly expressed leading to an abnormal transcript consisting of a 41-bp inclusion and premature termination codons and to residual levels of a correctly spliced transcript. This expression pattern, caused by a leaky intronic mutation with regard to spliceosome activity and its apparent stability with regard to surveillance mechanisms, could contribute to the moderate muscle hypertrophy in this cattle breed. This finding is of importance for genetic counseling for meat quantity and quality in livestock production and possibly to manipulate myostatin pre-mRNA in human muscle diseases.

In Arabidopsis thaliana, two genes encoding phytochelatin synthase (PCS; EC 2.3.2.15), AtPCS1 and AtPCS2, have been identified. Until now, only AtPCS1 was shown to play a role in response to Cd. To gain insight into the putative role of AtPCS2, three Cd concentrations (50, 100 and 200 μM) and long-term exposure (7 days) were tested on 1-week-old A. thaliana ecotype Wassilewskija (Ws) seedlings. Since 100 μM Cd did not alter seedling metabolism, as shown by unchanged total soluble protein and free proline contents, we investigated plantlet response to this concentration in addition to Cd accumulation. Seedlings accumulated Cd in roots and shoots. As phytochelatins and glutathione (GSH) contents increased in treated seedlings, we suggested that Cd might be translocated via the phytochelatin pathway. Specific enzymatic activities of γ-glutamylcysteine synthetase (GCS; EC 6.3.2.2), glutathione synthetase (GS; EC 6.3.2.3) and PCS were twice much more stimulated in shoots and roots after Cd exposure except GS that remained constant in shoots. As expression of genes encoding GCS and GS was unchanged in response to Cd, we suggested a regulation at translational or post-translational level. Surprisingly, AtPCS1 and AtPCS2 were differentially up-regulated after Cd treatment: AtPCS1 in shoots and AtPCS2 in whole plantlets. This last result suggests that PCS2 could be involved in plant response to high concentration of Cd in Ws ecotype and supports a putative role of PCS2, not redundant with PCS1, in a long-term response to Cd.

Tailings and slag residues from the most important antimony mine of the French Massif Central were analysed for their mineralogical and chemical contents by conventional X-ray powder diffraction and synchrotron-based X-ray microdiffraction (μ-XRD). Results show that ∼2000 metric tons of Sb are still present at the abandoned mining site. Mean concentrations of Sb in slags and tailings are 1700 and 5000mgkg−1, respectively. In addition, smaller quantities of As were also measured (∼800mgkg−1 in tailings). Toxicity tests of As and Sb indicate that the growth of bacteria is severely affected at these concentrations. In particular, Sb was observed to cause negative effects for several types of bacteria. Almost all primary minerals carrying trivalent Sb disappeared during weathering at the expense of phases in which Sb5+ is the most abundant form. Instead of sulphides, Sb-bearing Fe hydroxides (goethite and lepidocrocite) are now present in the residues together with Sb-bearing jarosite and Sb(-Fe) oxides and hydroxides such as tripuhyite, senarmontite, romeite, cervantite, and valentinite. Water analyses of the main local stream indicate little remobilization of Sb downstream the site and despite the acidic pH of the surface tailings, pH values show neutral or near-neutral values on all locations of the site.

Glioblastoma Multiforme (GBM) is the most frequent malignant brain tumor with still poor prognosis. Tumor initiation, growth and recurrences might depend on Brain Tumor Stem Cells (BTSCs) which can promote tumor aggressiveness and potentially affords new therapeutic target. Recent works emphasized aberrant cell-surface glyco-conjugate expression in brain tumors suggesting that altered glycosylation is closely linked to cancer tumor metastasis and invasive process. Post-translational changes might play a key role in determining the fates of most aggressive and undifferentiated cells such as self-renewal, proliferation and differentiation. In order to characterize the glycosylation-related genes involved in differentiation status of the BTSCs, two glioblastoma cell lines, U87-MG and U251 have been cultured according to two conditions leading to undifferentiated floating cells or differentiated adherent cells. The expression level of 559 glycosylation related genes has been analyzed by Taqman Low Density Array (TLDA) analysis and allowed to isolate eight up-regulated genes specific of a subpopulation of undifferentiated cells. Protein expression has been confirmed. Among main selected genes, five are also over-expressed in the undifferentiated condition in primary cultures provided by three GBM freshly isolated from patient. This work suggests that new Glycosylation-related gene signature might improve the characterization of the most aggressive and undifferentiated cells and supports that in future, N-linked glycosylation might provide new target to develop therapeutic strategy for inhibiting tumor growth.

BACKGROUND:In the domestic rabbit (Oryctolagus cuniculus), classical genetic studies have identified five alleles at the Extension locus: ED (dominant black), ES (steel, weaker version of ED), E (wild type, normal extension of black), eJ(Japanese brindling, mosaic distribution of black and yellow) and e (non-extension of black, yellow/red with white belly). Sequencing almost the complete coding sequence (CDS) of the rabbit MC1R gene, we recently identified two in-frame deletions associated with dominant black (c.280_285del6; alleles ED or ES) and recessive red (c.304_333del30; allele e) coat colours. It remained to characterize the eJallele whose phenotypic effect is similar to the Orange and Sex-linked yellow loci of cat and Syrian hamster.RESULTS:We sequenced the whole CDS in 25 rabbits of different coat colours including 10 Japanese and 10 Rhinelander (tricolour) rabbits and identified another 6 bp-in frame deletion flanked by a G > A transition in 5' (c.[124G>A;125_130del6]) that was present in all animals with Japanese brindling coat colour and pattern. These mutations eliminate two amino acids in the first transmembrane domain and, in addition, cause an amino acid substitution at position 44 of the wild type sequence. Genotyping 371 rabbits of 31 breeds with different coat colour this allele (eJ) was present in homozygous state in Japanese, Rhinelander and Dutch tricolour rabbits only (except one albino rabbit). Rabbits with eJ/eJ genotype were non fixed at the non-agouti mutation we previously identified in the ASIP gene. Segregation in F1 and F2 families confirmed the order of dominance already determined by classical genetic experiments with a possible dose effect evident comparing eJ/eJ and eJ/e animals. MC1R mRNA was expressed in black hair skin regions only.CONCLUSIONS:The c.[124A;125_130del6] allele may be responsible for a MC1R variant determining eumelanin production in the black areas. However, the mechanism determining the presence of both red and black hairs in the same animal seems more complex. Expression analyses of the c.[124A;125_130del6] allele suggest that MC1R transcription may be regulated epigenetically in rabbits with the Japanese brindling phenotype. Further studies are needed to clarify this issue.