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2022 ◽  
Vol 20 (1) ◽  
Author(s):  
Erika Prašnikar ◽  
Tanja Kunej ◽  
Mario Gorenjak ◽  
Uroš Potočnik ◽  
Borut Kovačič ◽  
...  

Abstract Background Women with uterine adenomyosis seeking assisted reproduction have been associated with compromised endometrial receptivity to embryo implantation. To understand the mechanisms involved in this process, we aimed to compare endometrial transcriptome profiles during the window of implantation (WOI) between women with and without adenomyosis. Methods We obtained endometrial biopsies LH-timed to the WOI from women with sonographic features of adenomyosis (n=10) and controls (n=10). Isolated RNA samples were subjected to RNA sequencing (RNA-seq) by the Illumina NovaSeq 6000 platform and endometrial receptivity classification with a molecular tool for menstrual cycle phase dating (beREADY®, CCHT). The program language R and Bioconductor packages were applied to analyse RNA-seq data in the setting of the result of accurate endometrial dating. To suggest robust candidate pathways, the identified differentially expressed genes (DEGs) associated with the adenomyosis group in the receptive phase were further integrated with 151, 173 and 42 extracted genes from published studies that were related to endometrial receptivity in healthy uterus, endometriosis and adenomyosis, respectively. Enrichment analyses were performed using Cytoscape ClueGO and CluePedia apps. Results Out of 20 endometrial samples, 2 were dated to the early receptive phase, 13 to the receptive phase and 5 to the late receptive phase. Comparison of the transcriptomics data from all 20 samples provided 909 DEGs (p<0.05; nonsignificant after adjusted p value) in the adenomyosis group but only 4 enriched pathways (Bonferroni p value < 0.05). The analysis of 13 samples only dated to the receptive phase provided suggestive 382 DEGs (p<0.05; nonsignificant after adjusted p value) in the adenomyosis group, leading to 33 enriched pathways (Bonferroni p value < 0.05). These included pathways were already associated with endometrial biology, such as “Expression of interferon (IFN)-induced genes” and “Response to IFN-alpha”. Data integration revealed pathways indicating a unique effect of adenomyosis on endometrial molecular organization (e.g., “Expression of IFN-induced genes”) and its interference with endometrial receptivity establishment (e.g., “Extracellular matrix organization” and “Tumour necrosis factor production”). Conclusions Accurate endometrial dating and RNA-seq analysis resulted in the identification of altered response to IFN signalling as the most promising candidate of impaired uterine receptivity in adenomyosis.


2021 ◽  
Author(s):  
Sayaka Imano ◽  
Mayuka Fushimi ◽  
Maurizio Camagna ◽  
Akiko Tsuyama-Koike ◽  
Hitoshi Mori ◽  
...  

Plants recognize molecular patterns unique to a certain group of microbes to induce effective resistance mechanisms. Elicitins are secretory proteins produced by plant pathogenic oomycete genera including Phytophthora and Pythium. Treatment of INF1 (an elicitin produced by P. infestans) induces a series of defense responses in Nicotiana species, including reactive oxygen species (ROS) production, hypersensitive cell death and accumulation of the sesquiterpenoid phytoalexin capsidiol. In this study, we analyzed the expression profiles of N. benthamiana genes after INF1 treatment by RNAseq analysis. Based on their expression patterns, N. benthamiana genes were categorized into 20 clusters and 4,761 (8.3%) out of 57,140 genes were assigned to the clusters for INF1-induced genes. All genes encoding enzymes dedicated for capsidiol production, 5-epi-aristolochene (EA) synthase (NbEAS, 10 copies) and EA dehydrogenase (NbEAH, 6 copies) and some genes for ethylene production, such as 1-aminocyclopropane 1-carboxylate (ACC) synthase (NbACS) and ACC oxidase (NbACO), were significantly upregulated by INF1 treatment. Analysis of NbEAS1 and NbEAS4 promoters revealed that AGACGCC (GCC box-like motif) is the essential cis-element required for INF1-induced expression of NbEAS genes. Given that the GCC box is known to be targeted by ERF (ethylene-responsive factor) transcription factors, we created a complete list of N. benthamiana genes encoding AP2/ERF family transcription factors, and identified 45 out of 337 AP2/ERF genes in the clusters for INF1-induced genes. Among INF1-induced NbERF genes, silencing of NbERF-IX-33 compromised resistance against P. infestans and INF1-induced production of capsidiol. Recombinant NbERF-IX-33 protein can bind to the promoter sequence of NbEAS4, suggesting that NbERF-IX-33 is a transcription factor directly regulating the expression of genes for phytoalexin production.


Biology Open ◽  
2021 ◽  
Vol 10 (11) ◽  
Author(s):  
Ekaterina V. Borvinskaya ◽  
Albina A. Kochneva ◽  
Polina B. Drozdova ◽  
Olga V. Balan ◽  
Victor G. Zgoda

ABSTRACT The protein composition of the cestode Schistocephalus solidus was measured in an experiment simulating the trophic transmission of the parasite from a cold-blooded to a warm-blooded host. The first hour of host colonisation was studied in a model experiment, in which sticklebacks Gasterosteus aculeatus infected with S. solidus were heated at 40°C for 1 h. As a result, a decrease in the content of one tegument protein was detected in the plerocercoids of S. solidus. Sexual maturation of the parasites was initiated in an experiment where S. solidus larvae were taken from fish and cultured in vitro at 40°C for 48 h. Temperature-independent changes in the parasite proteome were investigated by incubating plerocercoids at 22°C for 48 h in culture medium. Analysis of the proteome allowed us to distinguish the temperature-induced genes of S. solidus, as well as to specify the molecular markers of the plerocercoid and adult worms. The main conclusion of the study is that the key enzymes of long-term metabolic changes (glycogen consumption, protein production, etc.) in parasites during colonisation of a warm-blooded host are induced by temperature.


Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 1332-1332
Author(s):  
Wendy Cozen ◽  
Marta Epeldegui ◽  
David V. Conti ◽  
Amie E. Hwang ◽  
Jun Wang ◽  
...  

Abstract Background: We and others have demonstrated persistent differences in T cell function and cytokine responses in adolescent/ young adult Hodgkin lymphoma (AYAHL) survivors and their family members. To identify the transcription control pathways involved, we examined mRNA profiles from 17 pairs of long term AYA HL survivors and their unaffected twins. Methods: Blood samples were collected remotely from AYAHL survivors and their like-sex unaffected co-twin controls and shipped to the Epeldegui laboratory at UCLA. B and T cells were negatively separated using magnetic beads. RNA was extracted and sequenced using a high-efficiency mRNA-targeted assay system (Lexogen QuantSeq 3' FWD), with an average 6.7 million reads per sample mapped to the hg38 human transcriptome (99%) using the STAR aligner. Raw read counts for each gene transcript were normalized to transcripts per million total mapped reads and log2 transformed for analysis using linear statistical models including a random effect of twin pair. Analyses examined average expression of pre-specified sets of 17 genes in general immunologic activation (i.e., AP-1- and NF-kB-family transcripts) and 28 Type I IFN-responsive genes (e.g., IFI-, OAS-, and MX-family), as well as TELiS promoter-based bioinformatics analyses of all genes showing &gt;2-fold empirical differences in gene expression (focusing on activation-induced transcription factors, NF-kB and AP-1, and Type 1 interferon-related IRF transcription factors). Body mass index, history of therapeutic radiation, zygosity, sex, age at diagnosis and age at blood collection were included in the model. Results: The average age at diagnosis was 25 years with blood collected 33 years post-diagnosis. In T-cells, AYAHL survivors showed marginally lower expression of 12 activation-induced genes (average 0.41-fold, p = .038) and markedly lower expression of 28 Type 1 interferon-related genes (average 0.33-fold, p &lt; .001) relative to their unaffected co-twins. B cells showed similar reductions in activation-induced genes (0.33-fold, p &lt; .001) but no difference in Type 1 interferon genes (1.02-fold, p =. 942). Promoter-based bioinformatics analyses of all 151 genes found to be differentially expressed by &gt;2-fold in T cells between AYAHL survivors and their unaffected co-twin controls implicated IRF-family transcription factors in mediating observed differences, with IRF3 showing the most significant signal of decreased activity (0.68-fold, p = .059). We also identified marked up-regulation of multiple GATA family transcription factors (GATA3: p &lt; .001; GATA1: p = .009; GATA2: p = .032). Conclusions: Transcriptional indicators of immunologic activation and Type 1 interferon activity show persistent down-regulation in T lymphocytes from long-term adult AYAHL survivors compared to their unaffected like-sex co-twin controls. Incidental findings also identified persistent activation of other gene regulatory pathways mediating T-cell differentiation (e.g., GATA family). We have previously demonstrated higher Epstein-Barr virus (EBV) copy number in AYAHL long-term survivors compared to their unaffected co-twin controls, as well as lower levels of circulating interleukin-12, consistent with a decrease in the ability to control viral replication. The GATA family plays a major role in commitment to T cell lineage (GATA3) and upregulation of the T-helper-type 2 response, and possibly in control of EBV viral infection (GATA2), processes relevant to AYAHL. These differences further support the premise that abnormalities in T-cells play a strong role in etiology, pathogenesis, and survivorship. Disclosures No relevant conflicts of interest to declare.


2021 ◽  
Vol 23 (Supplement_6) ◽  
pp. vi211-vi211
Author(s):  
Valerie Marallano ◽  
Anirudh Sattiraju ◽  
Hongyan Zou ◽  
Roland Friedel

Abstract Hypoxia (low oxygen) has been associated with adverse effects in tumor biology by exaggerating the capabilities of invasion, proliferation, and survival of tumor cells within the tumor microenvironment. We engineered glioblastoma (GBM) proneural cells with a novel hypoxia reporter, HRE-UnaG, to study areas of tumor hypoxia and the effects that these hypoxic cells have on tumorigenesis. Single cell RNA-seq analysis from a mouse intracranially injected with our HRE dUnaG GBM cells revealed a shift to a mesenchymal state upon hypoxia (detected by expression of UnaG). Two genes, CXCR4 and NXPH4, were identified as being specifically induced in the hypoxic population. Our studies focus on the hypothesis that these two hypoxia induced genes, CXCR4 and NXPH4, are upregulated in hypoxic GBM cells, which may allow tumor cells to become more aggressive and resistant to conventional forms of therapies. GBM cells will be transduced with lentiviral vectors for Dox inducible shRNA knockdown of CXCR4 or NXPH4 to test specific contribution of these genes to the phenotype of the hypoxic population, with particular focus on the change in invasion and overall tumor burden upon gene silencing.


Author(s):  
S Couillard ◽  
J Melhorn ◽  
A Singhania ◽  
D Horowitz ◽  
R Djukanovíc ◽  
...  

Author(s):  
Michal Mastalerz ◽  
Elisabeth Dick ◽  
Ashesh Anjankumar Chakraborty ◽  
Elisabeth Hennen ◽  
Andrea C Schamberger ◽  
...  

Rationale. The bronchial epithelium is constantly challenged by inhalative insults including cigarette smoke (CS), a key risk factor for lung disease. In vitro exposure of bronchial epithelial cells using CS extract (CSE) is a widespread alternative to whole CS (wCS) exposure. However, CSE exposure protocols vary considerably between studies, precluding direct comparison of applied doses. Moreover, they are rarely validated in terms of physiological response in vivo and the relevance of the findings is often unclear. Methods. We tested six different exposure settings in primary human bronchial epithelial cells (phBECs), including five CSE protocols in comparison with wCS exposure. We quantified cell-delivered dose and directly compared all exposures using expression analysis of 10 well-established smoke-induced genes in bronchial epithelial cells. CSE exposure of phBECs was varied in terms of differentiation state, exposure route, duration of exposure, and dose. Gene expression was assessed by quantitative Real-Time PCR (qPCR) and Western Blot analysis. Cell type-specific expression of smoke-induced genes was analyzed by immunofluorescent analysis. Results. Three surprisingly dissimilar exposure types, namely chronic CSE treatment of differentiating phBECs, acute CSE treatment of submerged basal phBECs, and wCS exposure of differentiated phBECs performed best, resulting in significant upregulation of seven (chronic CSE) and six (acute wCS, acute submerged CSE exposure) out of 10 genes. Acute apical or basolateral exposure of differentiated phBECs with CSE was much less effective despite similar doses used. Conclusions. Our findings provide guidance for the design of human in vitro CS exposure models in experimental and translational lung research.


2021 ◽  
Author(s):  
Ashley L Waring ◽  
Joshua Hill ◽  
Brooke M Allen ◽  
Nicholas M Bretz ◽  
Nguyen Le ◽  
...  

Background: Organisms are commonly infected by a diverse array of pathogen types including bacteria, fungi, viruses, and parasites, and mount functionally distinct responses to each of these varied immune challenges. Host immune responses are characterized by the induction of gene expression in response to infection. However, the extent to which expression changes are shared among responses to distinct pathogens is largely unknown. Results: We performed meta-analysis of gene expression data collected from Drosophila melanogaster following infection with a wide array of pathogens. We identified 62 genes that are significantly induced by infection. While many of these infection-induced genes encode known immune response factors, we also identified 21 genes that have not been previously associated with host immunity. Examination of the upstream flanking sequences of the infection-induced genes lead to the identification of two conserved enhancer sites. These sites correspond to conserved binding sites for GATA and nuclear factor κB (NFκB) family transcription factors and are associated with higher levels of transcript induction. We further identified 31 genes with predicted functions in metabolism and organismal development that are significantly downregulated following infection by diverse pathogens. Conclusions: Our study identifies conserved gene expression changes in Drosophila melanogaster following infection with varied pathogens, and transcription factor families that may regulate this immune induction. These findings provide new insight into transcriptional changes that accompany Drosophila immunity. They may suggest possible roles for the differentially regulated genes in innate immune responses to diverse classes of pathogens, and serve to identify candidate genes for further empirical study of these processes.


BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Tyler W. Doughty ◽  
Rosemary Yu ◽  
Lucy Fang-I Chao ◽  
Zhongjun Qin ◽  
Verena Siewers ◽  
...  

Abstract Background Eukaryotic organisms, like the model yeast S. cerevisiae, have linear chromosomes that facilitate organization and protection of nuclear DNA. A recent work described a stepwise break/repair method that enabled fusion of the 16 chromosomes of S. cerevisiae into a single large chromosome. Construction of this strain resulted in the removal of 30 of 32 telomeres, over 300 kb of subtelomeric DNA, and 107 subtelomeric ORFs. Despite these changes, characterization of the single chromosome strain uncovered modest phenotypes compared to a reference strain. Results This study further characterized the single chromosome strain and found that it exhibited a longer lag phase, increased doubling time, and lower final biomass concentration compared with a reference strain when grown on YPD. These phenotypes were amplified when ethanol was added to the medium or used as the sole carbon source. RNAseq analysis showed poor induction of genes involved in diauxic shift, ethanol metabolism, and fatty-acid ß-oxidation during growth on ethanol compared to the reference strain. Enzyme-constrained metabolic modeling identified decreased flux through the enzymes that are encoded by these poorly induced genes as a likely cause of diminished biomass accumulation. The diminished growth on ethanol for the single chromosome strain was rescued by nicotinamide, an inhibitor of sirtuin family deacetylases, which have been shown to silence gene expression in heterochromatic regions. Conclusions Our results indicate that sirtuin-mediated silencing in the single chromosome strain interferes with growth on non-fermentable carbon sources. We propose that the removal of subtelomeric DNA that would otherwise be bound by sirtuins leads to silencing at other loci in the single chromosome strain. Further, we hypothesize that the poorly induced genes in the single chromosome strain during ethanol growth could be silenced by sirtuins in wildtype S. cerevisiae during growth on glucose.


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