Biology subjects

Cannet, C.

Publications and source records attributed to Cannet, C..

4 recordsLinked to original sources

bioRxiv2025

Quantification of Human DNA from Century-Old Archived FFPE Samples for Retrospective Genomic Studies

BackgroundFormalin-fixed, paraffin-embedded (FFPE) tissue archives are an invaluable resource for genomic research, offering the potential to link genomic data to long-term clinical outcomes. Their utility has however been limited by the degradation caused by fixation and long-term storage, particularly for samples archived for many decades. MethodsThis study evaluates a cohort of 79 FFPE tissue blocks collected and archived in 1973 from the Strasbourg Pathological Tissue Archive (SPTA), and a cohort of 51 FFPE tissue blocks from the Geneva Brain Bank (GBB), collected between 1928 and 1971. DNA was quantified using a forensic-grade quantitative PCR (qPCR) assay (QIAGEN Investigator Quantiplex Pro Kit on a Rotor-Gene Q) to precisely measure human DNA concentration, assess degradation, and detect PCR inhibition. ResultsA high proportion of the samples yielded human DNA fragments of 80bp and 95bp and very few fragments of 205bp. All organ samples treated with Bouin liquid (n=12) gave poor results, but among samples fixed in formalin (n=117), 58.1% showed over 0.25ng/{micro}L of 80bp human DNA fragments and 37.6% over 1ng/{micro}L. We propose a model to describe the decay of these samples and estimate the proportion of samples that should yield at least a 0.25ng/{micro}L concentration of fragments over 100bp to 45.1%. ConclusionsThis work demonstrates that automated extraction methods optimized for FFPE allow for the recovery of usable material even in century-old archived samples with inconsistent conditions of conservation. Our data suggests that the time spent in storage is much less influential on DNA quality than initial fixation time. Crucially, given the fragmented nature of the material recovered (an expected result), future analyses of this material will have to be conducted using next-generation sequencing (NGS) technologies and approaches that rely on short fragments.

genetics↗

bioRxiv2023

Maintained imbalance of triglycerides, apolipoproteins, energy metabolites and cytokines in long-term COVID-19 syndrome (LTCS) patients

Deep metabolomic, proteomic and immunologic phenotyping of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) patients have matched a wide diversity of clinical symptoms with potential biomarkers for coronavirus disease 2019 (COVID-19). Within here, several studies described the role of metabolites, lipoproteins and inflammation markers during infection and in recovered patients. In fact, after SARS-CoV-2 viral infection almost 20-30% of patients experience persistent symptoms even after 12 weeks of recovery which has been defined as long-term COVID-19 syndrome (LTCS). Emerging evidence revealed that a dysregulated immune system and persisting inflammation could be one of the key drivers of LTCS. However, how these small biomolecules such as metabolites, lipoprotein, cytokines and chemokines altogether govern pathophysiology is largely underexplored. Thus, a clear understanding how these parameters into an integrated fashion could predict the disease course may help to stratify LTCS patients from acute COVID-19 or recovered specimen and would help to elucidate a potential mechanistic role of these biomolecules during the disease course. Here, we report an integrated analysis of blood serum and plasma by in vitro diagnostics research NMR spectroscopy and flow cytometry-based cytokine quantification in a total of 125 individuals (healthy controls (HC; n=73), recovered (n=12), acute (n=7) and LTCS (n=33)). We identified that in LTCS patients lactate and pyruvate were significantly different from either healthy controls or acute COVID-19 patients. Further correlational analysis of cytokines and metabolites indicated that creatine, glutamine, and high-density lipoprotein (HDL) phospholipids were distributed differentially amongst patients or individuals. Of note, triglycerides and several lipoproteins (apolipoproteins Apo-A1 and A2) in LTCS patients demonstrate COVID-19-like alterations compared to HC. Interestingly, LTCS and acute COVID-19 samples were distinguished mostly by their creatinine, phenylalanine, succinate, 3-hydroxybutyrate (3-HB) and glucose concentrations, illustrating an imbalanced energy metabolism. Most of the cytokines and chemokines were present at low levels in LTCS patients compared with HC except IL-18 chemokine, which tended to be higher in LTCS patients and correlated positively with several amino acids (creatine, histidine, leucine, and valine), metabolites (lactate and 3-HB) and lipoproteins. The identification of these persisting plasma metabolites, lipoprotein and inflammation alterations will help to better stratify LTCS patients from other diseases and could help to predict ongoing severity of LTCS patients. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/523998v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@ecdeacorg.highwire.dtl.DTLVardef@10f0f80org.highwire.dtl.DTLVardef@1c2ddaborg.highwire.dtl.DTLVardef@672120_HPS_FORMAT_FIGEXP M_FIG C_FIG Layman summary & significance of the researchAlmost 20-30% of individuals infected with the SARS-CoV-2 virus regardless of hospitalization status experience long-term COVID-19 syndrome (LTCS). It is devasting for millions of individuals worldwide and hardly anything is known about why some people experience these symptoms even after 3 to 12 months after the acute phase. In this, we attempted to understand whether dysregulated metabolism and inflammation could be contributing factors to the ongoing symptoms in LTCS patients. Total blood triglycerides and the Cory cycle metabolites (lactate and pyruvate) were significantly higher, lipoproteins (Apo-A1 and A2) were drastically lower in LTCS patients compared to healthy controls. Correlation analysis revealed that either age or gender are positively correlated with several metabolites (citrate, glutamate, 3-hydroxybutyrate, glucose) and lipoproteins (Apo-A1, HDL Apo-A1, LDL triglycerides) in LTCS patients. Several cytokines and chemokines were also positively correlated with metabolites and lipoproteins thus, dysregulation in metabolism and inflammation could be a potential contributory factor for LTCS symptoms.

immunology↗

bioRxiv2022

Protein undernutrition reduces the efficacy of praziquantel in a murine model of Schistosoma mansoni infection

BackgroundUndernutrition and schistosomiasis are public health problems and often occur in low and middle-income countries. Protein undernutrition can alter the host-parasite environment system and aggravate the course of schistosomiasis. This study aimed to assess the impact of a protein-deficient diet on the efficacy of praziquantel. Methodology/principal findingsThirty-day-old mice were fed with a protein-deficient diet, and 40 days later, they were individually infected with fifty Schistosoma mansoni cercariae. A 28-day-treatment with praziquantel at 100 mg/kg for five consecutive days followed by distilled water begins at the 36th day post-infection. Mice were sacrificed on the 64th day post-infection. We determined the parasitological burden, liver and intestine histomorphometry, liver injury, and immunomodulation parameters. Praziquantel treatment of infected mice fed with a standard diet (IN-PZQ) resulted in a significant reduction of worm and egg burdens and a normalization of iron and calcium levels. The therapy also improved schistosomiasis-induced hepatopathy and oxidative stress. The anti-inflammatory and immunomodulatory activities of praziquantel were also significant in these mice. When infected mice receiving the protein-deficient diet were treated with praziquantel (ILP-PZQ), the body weight loss and hepatomegaly were not alleviated, and the worm and liver egg burdens were significantly higher than those of IN-PZQ mice (P < 0.001). The treatment did not reduce the increased activities of ALT and {gamma}-GGT, the high malondialdehyde concentration, and the liver granuloma volume. The iron and calcium levels were not ameliorated and differed from those of IN-PZQ mice (P < 0.001 and P < 0.05). Moreover, in these mice, praziquantel treatment did not reverse the high level of IL-5 and the low mRNA expression of CCL3/MIP-1 and CXCL-10/IP-10 induced by S. mansoni infection. Conclusion/significanceThese results demonstrated that a protein-deficient diet reduced the schistosomicidal, antioxidant, anti-inflammatory, and immunomodulatory activities of praziquantel. Authors summaryAlmost 90% of people requiring schistosomiasis preventive chemotherapy in 2018 lived in sub-Saharan Africa. Besides, 205.3 million children under five years suffer and die of undernutrition in low- and middle-income countries. The physiopathology of schistosomiasis mansoni involves liver damage, oxidative stress, and perturbation of the immune response. These disturbances are intensified by undernutrition. Praziquantel is used to treat schistosomiasis, but its efficacy on the comorbidity of S. mansoni infection and undernutrition has not been investigated. We conducted this study to assess the effectiveness of praziquantel on S. mansoni infection in mice fed with a protein-deficient diet. We recorded growth retardation, hepatomegaly, and high worm and egg burdens in mice fed with a protein-deficient diet and treated with PZQ. Moreover, the treatment did not reverse the liver function injury, oxidative stress, high iron level, and low calcium level. The proinflammatory cytokine IL-5 was still high, and the gene expression of some macrophage-associated chemokines was reduced. Therefore, this study demonstrated that in a murine model of a protein-deficient diet, the efficacy of praziquantel on S. mansoni infection was reduced. It also underlines the importance of targeting protein deficiency and malnutrition in populations living in schistosomiasis endemic areas for efficient disease control.

pathology↗

bioRxiv2017

Relationships between clans and genetic kin explain cultural similarities over vast distances: the case of Yakutia

Archaeological studies sample ancient human populations one site at a time, often limited to a fraction of the regions and periods occupied by a given group. While this bias is known and discussed in the literature, few model populations span areas as large and unforgiving as the Yakuts of Eastern Siberia. We systematically surveyed 31,000 square kilometres in the Sakha Republic (Yakutia) and completed the archaeological study of 174 frozen graves, assembled between the 15th and the 19th century. We analysed genetic data (autosomal genotypes, Y-chromosome haplotypes and mitochondrial haplotypes) for all ancient subjects and confronted these to data on 190 modern subjects from the same area and the same population. Ancient familial links were identified between graves up to 1500 km apart, as well as paternal clans. We provide new insights on the origins of the contemporary Yakut population and demonstrate that cultural similarities in the past were linked to (i) the expansion of specific paternal clans, (ii) preferential marriage among the elites and (iii) funeral choices that could constitute a bias in any ancient population study.

genetics↗