LATE QUATERNARY CLIMATE HISTORY OF COASTAL ANTARCTIC ENVIRONMENTS: A MULTI-PROXY APPROACH (LAQUAN) (EV/01)

Novel biological proxies and inference models were developed to reconstruct past environmental changes in Antarctic ice-free regions. Reference datasets of cyanobacterial sequences, diatoms and pigments were constructed in order to study the present diversity and distribution of biota in benthic microbial mats from Antarctic lakes. These datasets were subsequently used for comparison between living and fossil floras or to develop inference models to quantitatively reconstruct past environmental changes in East Antarctica. Paleolimnological analyses and application of the models revealed the history of late Quaternary variation in climate, ultraviolet (UV) radiation, and relative sea-level in the Larsemann Hills. The study of modern cyanobacterial diversity showed that each lake is quite unique in terms of diversity. Every single lake studied resulted in the discovery of new Operational Taxonomic Units (OTUs), which suggests that there is a lot more diversity to discover. The majority of the genotypes are restricted to Antarctica and sometimes, even present only in one sample, which hints to the existence of endemic cyanobacteria. A taxonomic inventory of the diatom flora from the Larsemann Hills similarly revealed that Antarctic endemics account for about 40 % of all freshwater and brackish taxa. Fossil cyanobacterial sequences were found in layers of up to 9000 years old. The validation of fossil sequences of Progress and Heart Lake cores by both laboratories allowed us to assess that a majority of cyanobacterial sequences found in sedimentary core layers were really from fossil organisms. Comparison between the modern and fossil diversity revealed that most fossil sequences were also present in modern samples. The main problems encountered were related to the presence of good-quality bacterial DNA that act as competitor of fossil DNA during PCR, downcore degradation of fossil DNA, and the selective, group-specific resistance of cyanobacterial DNA to degradation. The main paleoenvironment-related results can be summarized as follows. During the Last Glacial Maximum one of the main peninsulas in the Larsemann Hills was only partly glaciated, as evidenced by uniquely long lake sedimentary records extending into the previous interglacial period (Eemian). Diatom-based inference models revealed that this interglacial was probably warmer and wetter than the Holocene, which was further supported by the presence of currently sub-Antarctic endemics in the Eemian diatom flora. The last glacial period was characterized by dry and cold conditions prevailing over the Larsemann Hills. The levels of the cyanobacterial UV-screening compound scytonemin in fossil microbial communities from this period were three times higher than the present-day values. Shortly after 13,500 yr BP, deglaciation of the Larsemann Hills and the continental shelf in Prydz Bay intensified. The collapse of this part of the East Antarctic Ice Sheet (EAIS) thuscoincided and may have contributed to melting water pulse 1A, which was one of the most rapid sea-level rises since the end of the last glacial period. During the Holocene, several warm periods were detected, coinciding with more productive coastal waters. Marine sediments in isolation basins from these periods are characterized by open water taxa and high chlorophyll a concentrations. Based on a relative sea level curve, we inferred that during the last warm period (the Hypsithermal) increased moisture supply to this part of the EAIS might have contributed to the global sea level fall between 4000 and 2500 yr BP. The high sediment accumulation rate in the isolation lakes further enabled us to identify several dry episodes and periods of higher UV radiation penetration during the past 2000 years. Together, our results highlight the potential of coastal Antarctic lakes for the reconstruction of past environmental changes and underscore the need for continued studies of lacustrine sediment sequences from this climate sensitive region.Projet EV/01 – “Late quaternary climate history of coastal antarctic environments: a multi-proxy approach (LAQUAN)

Structuring effects of climate-related environmental factors on Antarctic microbial mat communities

Both ground-based and satellite data show that parts of Antarctica have entered a period of rapid climate change, which already affects the functioning and productivity of limnetic ecosystems. To predict the consequences of future climate anomalies for lacustrine microbial communities, we not only need better baseline information on their biodiversity but also on the climate-related environmental factors structuring these communities. Here we applied denaturing gradient gel electrophoresis (DGGE) of the small subunit ribosomal DNA (SSU rDNA) to assess the genetic composition and distribution of Cyanobacteria and eukaryotes in 37 benthic microbial mat: samples from east Antarctic lakes. The lakes were selected to span a wide range of environmental gradients governed by differences in lake morphology and chemical limnology across 5 ice-free oases. Sequence analysis of selected DGGE bands revealed a high degree of potential endemism among the Cyanobacteria (mainly represented by Oscillatoriales and Nostocales), and the presence of a variety of protists (alveolates, stramenopiles and green algae), fungi, tardigrades and nematodes, which corroborates previous microscopy-based observations. Variation partitioning analyses revealed that the microbial mat community structure is largely regulated by both geographical and local environmental factors of which salinity (and related variables), lake water depth and nutrient concentrations are of major importance. These 3 groups of environmental variables have previously been shown to change drastically in Antarctica in response to climate change. Together, these results have obvious consequences for predicting the trajectory of biodiversity under changing climate conditions and call for the continued assessment of the biodiversity of these unique ecosystems

Tailored Digital PCR Follow-Up of Rare Fusion Transcripts after Initial Detection through RNA Sequencing in Hematological Malignancies

International audienceThe management of hematologic malignancies has entered a new era in which minimal residual disease (MRD) monitoring plays a pivotal role. Well-established molecular targets, such as PML::RARA, CBFB::MYH11, or RUNX1::RUNX1T1, are conventionally tracked by quantitative RT-PCR. Recently, a broader landscape of fusion transcripts has been unveiled through transcriptomic analysis. These newly discovered fusion transcripts may emerge as novel molecular markers for MRD quantification. In this study, we compared a targeted RNA-sequencing (RNA-seq) approach (FusionPlex) with a whole-transcriptomic strategy (Advanta RNA-Seq XT) for fusion detection in a training set of 21 samples. We evidenced a concordance of 100% for the detection of known fusions, and showed a good correlation for gene expression quantification between the two techniques (Spearman r = 0.77). Additionally, we prospectively evaluated the identification of fusions by targeted RNA-seq in a real-life series of 126 patients with hematological malignancy. At least one fusion transcript was detected for 60 patients (48%). We designed tailored digital PCR assays for 11 rare fusions, and validated this technique for MRD quantification with a limit of detection of <0.01%. The combination of RNA-seq and tailored digital PCR may become a new standard for MRD evaluation in patients lacking conventional molecular targets

Hypoxia regulates CD9 expression and dissemination of B lymphoblasts

International audienceAcute lymphoblastic leukemias (ALL) are the most frequent cancer in children and derive most often from B-cell precursors. Current survival rates roughly reach 90% at 10 years from diagnosis. However, 15-20% of children still relapse with a significant risk of death. Our previous work showed that the transmembrane protein CD9 plays a major role in lymphoblasts migration into sanctuary sites, especially in testis, through the activation of RAC1 signaling upon blasts stimulation with C-X-C chemokine ligand 12 (CXCL12). Here, we identified common factors shared by the bone marrow and extramedullary niches which could upregulate CD9 expression and function. We found that low oxygen levels enhance CD9 expression both at mRNA and protein levels. We further determined that Hypoxia Inducible Factor 1 alpha (HIF1 alpha), the master transcription factor involved in hypoxia response, binds directly CD9 promoter and induce CD9 transcription. We also showed that CD9 protein is crucial for leukemic cell adhesion and migration at low oxygen levels, possibly through its action on RAC1 signaling. Mouse xenograft experiments indicate that HIF1 alpha signaling pathway promotes ALL cells engraftment in a CD9-dependent manner. The present work increments our understanding of CD9 implication in ALL pathogenesis