R_Scripts

R scripts used for data analysis and Figure productio

Table S1_SiteDescription

Geographical site coordinate

AFLPdata

Presence/absence data of 345 AFLP markers for 85 Silene acaulis cushion plant

Data from: Differences in the fungal communities nursed by two genetic groups of the alpine cushion plant, Silene acaulis

Foundation plants shape the composition of local biotic communities and abiotic environments, but the impact of a plant’s intraspecific variations on these processes is poorly understood. We examined these links in the alpine cushion moss campion (Silene acaulis) on two neighboring mountain ranges in the French Alps. Genotyping of cushion plants revealed two genetic clusters matching known subspecies. The exscapa subspecies was found on both limestone and granite while the longiscapa one was only found on limestone. Even on similar limestone bedrock, cushion soils from the two S. acaulis subspecies deeply differed in their impact on soil abiotic conditions. They further strikingly differed from each other and from the surrounding bare soils in fungal community composition. Plant genotype variations accounted for a large part of the fungal composition variability in cushion soils, even when considering geography or soil chemistry, and particularly for the dominant molecular operational taxonomic units (MOTUs). Both saprophytic and biotrophic fungal taxa were related to the MOTUs recurrently associated with a single plant genetic cluster. Moreover, the putative phytopathogens were abundant, and within the same genus (Cladosporium) or species (Pyrenopeziza brassicae), MOTUs showing specificity for each plant subspecies were found. Our study highlights the combined influences of bedrock and plant genotype on fungal recruitment into cushion soils and suggests the coexistence of two mechanisms, an indirect selection resulting from the colonization of an engineered soil by free-living saprobes, and a direct selection resulting from direct plant-fungi interactions

README1

a file describing the content of the other files in this archiv

FungITS1_mrseq98.ecotag.unite.fasta

Most represented fungal ITS1 sequence for each of the 9379 MOTUs defined at the 98% identity threshold. Annotations further contain the taxonomic assignation on UNITE DB release V7, 2017-01 (see also Table S2 in Supplemental Data). Use 'obigrep' (OBITOOLS) to fetch sequences of interest. Use 'obigrep' (OBITOOLS) to fetch sequences of interest

Serum CD95L level correlates with tumor immune infiltration and is a positive prognostic marker for advanced high grade serous ovarian cancer

International audienceSoluble CD95L (s-CD95L) is a chemoattractant for certain lymphocyte subpopulations. We examined whether this ligand is a prognostic marker for high grade serous ovarian cancer (HGSOC) and whether it is associated with accumulation of immune cells in the tumor. Serum s-CD95L levels in 51 patients with advanced ovarian cancer were tested by ELISA. Immunohistochemical staining of CD3, CD4, CD8, CD20, CD163, CD31, FoxP3, CCR6, IL-17, Granzyme B, PD-L1, and membrane CD95L was used to assess tumor-infiltrating immune cells. Although the intensity of CD3, CD8, CD4, CD20, and CD163 in tumor tissues remained constant regardless of membrane CD95L expression, tumors in HGSOC patients with s-CD95L levels > 516 pg/ml showed increased infiltration by CD3+ T cells (p = 0.001), comprising both cytotoxic CD8+ (p = 0.01) and CD4+ (p = 0.0062) cells including FoxP3+ regulatory T cells (p = 0.0044). Also, the number of tumor-infiltrating CD20+ B cells (p = 0.0094) increased in these patients. Multivariate analyses revealed that low s-CD95L concentrations (6000 CD3+ cells (HR, 0.34; 95% CI, 0.15-0.79) was a good prognostic factor. Thus, low levels of s-CD95L (<516 pg/mL) are correlated with lower numbers of tumor-infiltrating lymphocytes (CD3+ and CD8+, but also CD4 and FoxP3 T cells) in advanced HGSOC and are a poor prognostic marker. Implications Serum s-CD95L is correlated with the number of tumor-infiltrating immune cells in HGSOC and could be used as a non-invasive marker of tumor immune infiltration to select patients referred for immunotherapy trials that evaluate checkpoint inhibitor treatment

Prognostic Impact of pT3 Subclassification in a Multicentre Cohort of Patients with Urothelial Carcinoma of the Renal Pelvicalyceal System Undergoing Radical Nephroureterectomy: A Propensity Score-weighted Analysis After Central Pathology Review

International audienceBackgroundThe current pathological tumour-node-metastasis (pTNM) classification for upper tract urothelial carcinoma (UTUC) does not include any risk stratification of pT3 renal pelvicalyceal tumours.ObjectiveTo assess the prognostic impact of pT3 subclassification in a multicentre cohort of patients with UTUC of the renal pelvicalyceal system undergoing radical nephroureterectomy (RNU).Design, setting, and participantsData from all consecutive patients treated with RNU for pT3 renal pelvicalyceal UTUC at 14 French centres from 1995 to 2013 were reviewed retrospectively.InterventionA central pathology review (CPR) was used to stratify pT3 patients into those with infiltration of the renal parenchyma on a microscopic level (pT3a) versus those with infiltration of the renal parenchyma visible on gross inspection of the resection specimen and/or invasion of peripelvic fat (pT3b).Outcome measurements and statistical analysisInverse probability weighting (IPW)-adjusted Cox regression analyses were used to compare recurrence-free survival (RFS) and cancer-specific survival (CSS) between pT3a and pT3b patients.Results and limitationsOverall, 202 patients were included and further stratified into pT3a (n = 98; 48.5%) and pT3b (n = 104; 51.5%) subgroups. Median time to follow-up in the weighted population was 68 (interquartile range, 50–95) mo. In IPW-adjusted Cox regression analyses, pT3b versus pT3a substage was associated with a significant adverse effect on RFS (hazard ratio [HR] = 2.02; 95% confidence interval [CI] = [1.36–3.01]; p < 0.001) and CSS (HR = 1.84; 95% CI = [1.20–2.82]; p = 0.005). The study is limited by its retrospective design.ConclusionsUsing IPW-adjusted analyses after the CPR, we observed that RNU patients with pT3b renal pelvicalyceal UTUC had adverse prognosis as compared with those with pT3a disease. As such, this subclassification could help refine the current pTNM system for UTUC