Abstract
STUDY QUESTION
Does endometrium harbour functionally active microorganisms and whether the microbial composition differs between proliferative and mid-secretory phases?
SUMMARY ANSWER
...Endometrium harbours functionally alive microorganisms including bacteria, viruses, archaea and fungi whose composition and metabolic functions change along the menstrual cycle.
WHAT IS KNOWN ALREADY
Resident microbes in the endometrium have been detected, where microbial dysfunction has been associated with reproductive health and disease. Nevertheless, the core microorganismal composition in healthy endometrium is not determined and whether the identified bacterial DNA sequences refer to alive/functionally active microbes is not clear. Furthermore, whether there are cyclical changes in the microbial composition remains an open issue.
STUDY DESIGN, SIZE, DURATION
RNA sequencing (RNAseq) data from 14 endometrial paired samples from healthy women, 7 samples from the mid-secretory phase and 7 samples from the consecutive proliferative phase were analysed for the microbial RNA sequences.
PARTICIPANTS/MATERIALS, SETTING, METHODS
The raw RNAseq data were converted into FASTQ format using SRA Toolkit. The unmapped reads to human sequences were aligned to the reference database Kraken2 and visualised with Krona software. Menstrual phase taxonomic differences were performed by R package metagenomeSeq. The functional analysis of endometrial microbiota was obtained with HUMANn2 and the comparison between menstrual phases was conducted by one-way ANOVA. Human RNAseq analysis was performed using miARma-Seq and the functional enrichment analysis was carried out using gene set enrichment analysis (GSEA; HumanCyc). The integration of metabolic pathways between host and microbes was investigated. The developed method of active microbiota mapping was validated in independent sample set.
MAIN RESULTS AND THE ROLE OF CHANCE
With the novel metatranscriptomic approach, we mapped the entire alive microbiota composing of >5300 microorganisms within the endometrium of healthy women. Microbes such as bacteria, fungi, viruses and archaea were identified. The validation of three independent endometrial samples from different ethnicity confirmed the findings. Significant differences in the microbial abundances in the mid-secretory vs. proliferative phases were detected with possible metabolic activity in the host-microbiota crosstalk in receptive phase endometrium, specifically in the prostanoid biosynthesis pathway and L-tryptophan metabolism.
LARGE SCALE DATA
The raw RNAseq data used in the current study are available at GEO GSE86491 and at BioProject PRJNA379542.
LIMITATIONS, REASONS FOR CAUTION
These pioneering results should be confirmed in a bigger sample size.
WIDER IMPLICATIONS OF THE FINDINGS
Our study confirms the presence of active microbes, bacteria, fungi, viruses and archaea in the healthy human endometrium with implications in receptive phase endometrial functions, meaning that microbial dysfunction could impair the metabolic pathways important for endometrial receptivity. The results of this study contribute to the better understanding of endometrial microbiota composition in healthy women and its possible role in endometrial functions. In addition, our novel methodological pipeline for analysing alive microbes with transcriptional and metabolic activities could serve to inspire new analysis approaches in reproductive medicine.
STUDY FUNDING/COMPETING INTERESTS
This work is supported by the Spanish Ministry of Economy, Industry and Competitiveness (MINECO) and European Regional Development Fund (FEDER): grants RYC-2016-21199 and ENDORE SAF2017-87526-R; FEDER/Junta de Andalucía-Consejería de Economía y Conocimiento: MENDO (B-CTS-500-UGR18) and by the University of Granada Plan Propio de Investigación 2016 - Excellence actions: Unit of Excellence on Exercise and Health (UCEES) (SOMM17/6107/UGR). A.S.-L. and N.M.M. are funded by the Spanish Ministry of Science, Innovation and Universities (PRE2018-0854409 and FPU19/01638). S.A. has received honoraria for lectures from Merck. The funder had no role in this study.
Ewing sarcoma (EWS) is an aggressive bone and soft tissue tumor of children and young adults in which the principal driver is a fusion gene, EWSR1-FLI1. Although the essential role of EWSR1-FLI1 ...protein in the regulation of oncogenesis, survival, and tumor progression processes has been described in-depth, little is known about the regulation of chimeric fusion-gene expression. Here, we demonstrate that the active nuclear HDAC6 in EWS modulates the acetylation status of specificity protein 1 (SP1), consequently regulating the SP1/P300 activator complex binding to EWSR1 and EWSR1-FLI1 promoters. Selective inhibition of HDAC6 impairs binding of the activator complex SP1/P300, thereby inducing EWSR1-FLI1 downregulation and significantly reducing its oncogenic functions. In addition, sensitivity of EWS cell lines to HDAC6 inhibition is higher than other tumor or non-tumor cell lines. High expression of HDAC6 in primary EWS tumor samples from patients correlates with a poor prognosis in two independent series accounting 279 patients. Notably, a combination treatment of a selective HDAC6 and doxorubicin (a DNA damage agent used as a standard therapy of EWS patients) dramatically inhibits tumor growth in two EWS murine xenograft models. These results could lead to suitable and promising therapeutic alternatives for patients with EWS.
Circular RNAs (circRNAs) are a class of single-stranded RNAs derived from exonic, intronic, and intergenic regions from precursor messenger RNAs (pre-mRNA), where a noncanonical back-splicing event ...occurs, in which the 5' and 3' ends are attached by covalent bond. CircRNAs participate in the regulation of gene expression at the transcriptional and posttranscriptional level primarily as miRNA and RNA-binding protein (RBP) sponges, but also involved in the regulation of alternative RNA splicing and transcription. CircRNAs are widespread and abundant in plants where they have been involved in stress responses and development. Through the analysis of all publications in this field in the last five years, we can summarize that the identification of these molecules is carried out through next generation sequencing studies, where samples have been previously treated to eliminate DNA, rRNA, and linear RNAs as a means to enrich circRNAs. Once libraries are prepared, they are sequenced and subsequently studied from a bioinformatics point of view. Among the different tools for identifying circRNAs, we can highlight CIRI as the most used (in 60% of the published studies), as well as CIRCExplorer (20%) and find_circ (20%). Although it is recommended to use more than one program in combination, and preferably developed specifically to treat with plant samples, this is not always the case. It should also be noted that after identifying these circular RNAs, most of the authors validate their findings in the laboratory in order to obtain bona fide results.
List of abbreviations ALDH1A1 Aldehyde Dehydrogenase 1 Family Member A1 ANAPC1 Anaphase Promoting Complex Subunit 1 APC Adenomatous polyposis coli ATM Ataxia telangiectasia mutated AXIN2 Axin2, ...conductin BARD1 BRCA1 associated RING domain 1 BMPR1A Bone morphogenetic protein receptor type 1A BRCA1 Breast cancer type 1 susceptibility protein BRCA2 Breast cancer type 2 susceptibility protein CDH1 Cadherin1 CDK4 Cyclin-dependent kinase 4 CEACAM6 CEA Cell Adhesion Molecule 6 CHEK2 Checkpoint Kinase 2 CK1 kinases casein kinase 1 CTNNB1 β-catenin CYP1B1 Cytochrome P450 Family 1 Subfamily B Member 1 DE Differentially Expressed DICER1 Dicer 1, ribonuclease III DVL Dishevelled protein EAU European Association of Urology FZD Frizzled receptor GSK3β Glycogen synthase kinase-3β HIBCH 3-Hydroxyisobutyryl-CoA Hydrolase HLA-DQB2 Major Histocompatibility Complex, Class II, DQ Beta 2 JMJD6 Lysine Hydroxylase KEGG Kyoto Encyclopedia of Genes and Genomes KIFC1 Kinesin Family Member C1 LogFC Log2-fold change LRP Lipoprotein receptor-related protein LTF Lactotransferrin MLH1 MutL homolog 1 MOK MOK Protein Kinase MSH2 MutS homolog 2 MSH3 MutS homolog 3 MSH6 MutS homolog 6 MUTYH MutY DNA glycosylase NCCN National Comprehensive Cancer Network NF1 Neurofibromin 1 PC Prostate cancer PMS2 PMS1 homolog 2, mismatch repair system component POLD1 DNA polymerase delta 1, catalytic subunit POLE DNA polymerase epsilon, catalytic subunit PTEN Phosphatase and tensin homolog PTPN12 Protein Tyrosine Phosphatase Non-Receptor Type 12 RAD51C RAD51 paralog C RAD51D RAD51 paralog D RGS18 Regulator Of G Protein Signaling 18 RRM2 Ribonucleotide Reductase Regulatory Subunit M2 S100A8 S100 Calcium Binding Protein A8 SMAD4 SMAD family member 4 SNP Single Nucleotide Polymorphism SOCS3 Suppressor Of Cytokine Signaling 3 STK11 Serine/threonine kinase 11 TCF T cell factor/lymphoid enhancer-binding factor TP53 Tumor protein P53 VCAN Versican WNT Wingless-related integration site Dear Editor, Hereditary prostate cancer (PC) comprises 5%-10% of all PC cases. Each family is a small genetic unit that differs significantly from others with the same pathology but different genetic origins. ...individualized studies may be the key to unravel the heterogeneity of this disease. When increased cell survival is accompanied by low efficiency of cell cycle control genes in response to DNA damage, the ideal environment for cancer development is created. ...we also focused on highlighting the most frequently mutated gene, BARD1 (12.31%), in the present cohort (Supplementary Figure S3) and on previously published data 2. ...the integration of all the data showed significant correlation with immune system activation (Supplementary Figures S4 and S11
Giant cell arteritis (GCA) is an immune-mediated large-vessels vasculitis with complex etiology. Although the pathogenic mechanisms remain poorly understood, a central role for CD4+ T cells has been ...demonstrated. In this context, understanding the transcriptome dysregulation in GCA CD4+ T cells will yield new insights into its pathogenesis.
Transcriptome analysis was conducted on CD4+ T cells from 70 patients with GCA with different disease activity and treatment status (active patients before treatment and patients in remission with and without glucocorticoid treatment), and 28 healthy controls. The study also evaluated potential impacts of DNA methylation on gene expression alterations and assessed cross-talk with CD14+ monocytes.
This study has uncovered a substantial number of genes and pathways potentially contributing to the pathogenicity of CD4+ T cells in GCA. Specifically, CD4+ T cells from GCA patients with active disease exhibited altered expression levels of genes involved in multiple immune-related processes, including various interleukins (IL) signaling pathways. Notably, IL-2, a decisive interleukin for regulatory T cells homeostasis, was among the most significant. Additionally, impaired apoptotic pathways appear crucial in GCA development. Our findings also suggest that histone-related epigenetic pathways may be implicated in promoting an inflammatory phenotype in GCA active patients. Finally, our study observed altered signaling communication, such as the Jagged-Notch signaling, between CD4+ T cells and monocytes that could have pathogenic relevance in GCA.
Our study suggests the participation of novel cytokines and pathways and the occurrence of a disruption of monocyte-T cell crosstalk driving GCA pathogenesis.
•The pathogenic CD4+ T cells transcriptome in GCA prior any treatment reinforces the implication of IL-2 pathway.•The impairment of apoptotic processes could be crucial for GCA development.•Histone-related pathways may be implicated in promoting an inflammatory phenotype of CD4+ T cells in GCA.•Genes implicated in Wnt canonical signaling pathway appears to be less amenable to GC treatment.•Altered cross-talk between circulating CD4+ T cells and monocytes through Jagged-Notch signaling is key for GCA pathogenesis.
Premise of the study: We characterize 10 microsatellite loci in the endangered fern Vandenboschia speciosa (Hymenophyllaceae), enabling studies on the genetic population structure of this ...Macaronesian-European species using DNA hypervariable markers. Methods and Results: Ten primer sets were developed and tested on 47 individuals in a total of two Iberian populations of V. speciosa. The primers amplified di- and hexanucelotide repeats. The number of alleles ranged from two to eight, and the expected heterozygosity ranged from 0.107 to 0.807 among the populations analyzed. Conclusions: The 10 microsatellite markers developed will be useful in characterizing the genetic diversity of V. speciosa and understanding its population structure (including the possible structure between sporophyte and gametophyte phases) and biogeographic history, and will provide important genetic data for the conservation of this species.
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