Comparative Expression Analysis Research Articles

Neuronal activity regulates alternative exon usage

Neuronal activity-regulated gene transcription underlies plasticity-dependent changes in the molecular composition and structure of neurons. A large number of genes regulated by different neuronal plasticity inducing pathways have been identified, but altered gene expression levels represent only part of the complexity of the activity-regulated transcriptional program. Alternative splicing, the differential inclusion and exclusion of exonic sequence in mRNA, is an additional mechanism that is thought to define the activity-dependent transcriptome. Here, we present a genome wide microarray-based survey to identify exons with increased expression levels at 1, 4 or 8 h following neuronal activity in the murine hippocampus provoked by generalized seizures. We used two different bioinformatics approaches to identify alternative activity-induced exon usage and to predict alternative splicing, ANOSVA (ANalysis Of Splicing VAriation) which we here adjusted to accommodate data from different time points and FIRMA (Finding Isoforms using Robust Multichip Analysis). RNA sequencing, in situ hybridization and reverse transcription PCR validate selected activity-dependent splicing events of previously described and so far undescribed activity-regulated transcripts, including Homer1a, Homer1d, Ania3, Errfi1, Inhba, Dclk1, Rcan1, Cda, Tpm1 and Krt75. Taken together, our survey significantly adds to the comprehensive understanding of the complex activity-dependent neuronal transcriptomic signature. In addition, we provide data sets that will serve as rich resources for future comparative expression analyses.

Abstract IA04: The immune cell microenvironment of classical Hodgkin lymphoma by single-cell analysis

Abstract Background: Over the past decade knowledge about the mechanisms by which the neoplastic Hodgkin and Reed-Sternberg (HRS) cells recruit and manipulate the extensive tumor microenvironment (TME) of classical Hodgkin lymphoma (cHL) has significantly expanded. While some findings support the concept that characteristics of the host immune system contribute to the composition of the TME, there is increasing evidence that somatically acquired genetic alterations and phenotypes of HRS cells influence disease evolution and underlie specific TME interactions. Integrating these concepts, the cHL TME might be the reflection of a symbiotic ecosystem containing the malignant cells and host immune cells. Dissection of this symbiotic relationship at single-cell resolution will be critical for a better understanding of cHL pathogenesis with relevance for improved therapeutic targeting. Knowledge Gained: We present single-cell transcriptome sequencing data derived from cell suspensions of 22 Hodgkin lymphoma patients (representative of the nodular sclerosis and mixed cellularity subtype) that confirmed the previously identified predominance of Th1 polarized T regulatory cells in the TME. In comparison to 5 reactive lymph node samples, we describe a highly enriched, HL-specific T-cell subset that is characterized by high LAG3 expression and an immunosuppressive cytokine profile, consistent with type 1 regulatory (Tr1) T cells. Analyzing co-expression of inhibitory T-cell makers on the single-cell level, LAG3 expression occurred mostly in a mutually exclusive pattern to the canonical Treg marker FOXP3. Furthermore, using imaging mass cytometry and multicolor immunohistochemistry, we revealed a spatial pattern of rosetting LAG3+ cells in the direct vicinity of MHC-II negative HRS cells, suggesting differential microenvironment architecture dependent on malignant cell phenotypes. Comparative analysis of LAG3 expression across a spectrum of B-cell lymphomas confirmed the high abundance of these cells in cHL, but also suggest that LAG3+ CD4+ and LAG3+ CD8+ T-cell subsets play a role in the related entity of primary mediastinal large B-cell lymphoma (PMBCL) and diffuse large B-cell lymphoma (DLBCL). Expanding our studies to the lymphocyte-rich (LR) subtype of cHL, we also revealed subtype-specific differences in background B cell and T follicular helper (TFH) cell content, suggesting an important role of the CXCR5-CXCL13 axis in cHL. Significance: Characterization of the TME using multiparametric single-cell technologies, including multicolor immunohistochemistry, flow-based mass cytometry, imaging mass cytometry, single-cell RNAseq, and proximity ligation assays, has provided unprecedented insight into HL biology. These studies fuel hope for accelerated development of immunotherapies targeting the TME and predictive biomarker development that might guide the appropriate selection of checkpoint inhibitors. Citation Format: Christian Steidl. The immune cell microenvironment of classical Hodgkin lymphoma by single-cell analysis [abstract]. In: Proceedings of the AACR Virtual Meeting: Advances in Malignant Lymphoma; 2020 Aug 17-19. Philadelphia (PA): AACR; Blood Cancer Discov 2020;1(3_Suppl):Abstract nr IA04.

Comparative expression analysis of PD-1, PD-L1, and CD8A in lung adenocarcinoma.

BackgroundAs a new strategy for advanced lung adenocarcinoma (LUAD), programmed cell death protein 1 (PD-1) pathway inhibitors have been used in clinic for several years. However, the roles of PD-1, programmed cell death-ligand 1 (PD-L1), and CD8A in LUAD are still unclear. In the study, we aimed to assess the correlation between the mRNA expression of these three factors and the clinical characteristics of LUAD, and to explore the influence of the PD-1/PD-L1/CD8A axis on the prognosis of LUAD.MethodsThe mRNA expression data and clinical characteristics of LUAD patients were retrieved from The Cancer Genome Atlas (TCGA). The optimal cutoff value for PD-1, PD-L1, and CD8A was determined by Cutoff Finder. The chi-square test was used to compare categorical variables. The prognostic effects of variables were analyzed using the Kaplan­­-Meier method and the Cox proportional hazards model.ResultsA total of 484 cases were enrolled in this study according to the selection process. The optimal cutoff values for identifying high/low mRNA expression were defined as 27.4 for PD-1, 29.41 for PD-L1, and 95.52 for CD8A. The high expression of PD-1 (P=0.015) and PD-L1 (P=0.027) was more frequent in women than in men. The high expression of PD-1 (P=0.003), PD-L1 (P=0.002), and CD8A (P=0.003) was associated with early T status, whereas CD8A showed a significantly higher expression in both the early stage (P=0.006) and early N stage groups (P=0.031). PD-1, PD-L1, and CD8A were significantly positively correlated among pairs (P<0.001). High expression of each of the three genes was associated with better prognosis (P=0.030 for PD-1, P=0.046 for PD-L1, P=0.019 for CD8A), although the relation did not reach statistical significance in the Cox regression hazards model.ConclusionsThe study defined a group of cutoff values for PD-1, PD-L1, and CD8A to identify high and low mRNA expression in LUAD. The high expression of PD-1, PD-L1, and CD8A was associated with early T status, and CD8A showed significantly higher expression in both early stage and early N stage groups. Although the high expression of each of these three genes was associated with favorable overall survival (OS), they were not independent prognostic factors.

Comparative Analysis of Virulence and Toxin Expression of Vancomycin-Intermediate and Vancomycin-Sensitive Staphylococcus aureus Strains.

Previous studies on vancomycin-intermediate Staphylococcus aureus (VISA) have mainly focused on drug resistance, the evolution of differences in virulence between VISA and vancomycin-sensitive S. aureus (VSSA) requires further investigation. To address this issue, in this study, we compared the virulence and toxin profiles of pair groups of VISA and VSSA strains, including a series of vancomycin-resistant induced S. aureus strains—SA0534, SA0534-V8, and SA0534-V16. We established a mouse skin infection model to evaluate the invasive capacity of VISA strains, and found that although mice infected with VISA had smaller-sized abscesses than those infected with VSSA, the abscesses persisted for a longer period (up to 9 days). Infection with VISA strains was associated with a lower mortality rate in Galleria mellonella larvae compared to infection with VSSA strains (≥ 40% vs. ≤ 3% survival at 28 h). Additionally, VISA were more effective in colonizing the nasal passage of mice than VSSA, and in vitro experiments showed that while VISA strains were less virulent they showed enhanced intracellular survival compared to VSSA strains. RNA sequencing of VISA strains revealed significant differences in the expression levels of the agr, hla, cap, spa, clfB, and sbi genes and suggested that platelet activation is only weakly induced by VISA. Collectively, our findings indicate that VISA is less virulent than VSSA but has a greater capacity to colonize human hosts and evade destruction by the host innate immune system, resulting in persistent and chronic S. aureus infection.

Effects of NOD1 and NOD2 agonists polymuramyl as well as NOD2 agonist glucosaminylmuramyldipeptide on phenotype of neutrophile granulocyte CD64-CD16+CD32+CD11b+, CD16+CD62L+CD63-, CD16+CD62L+CD63+ subsets

Antimicrobial activity of neutrophilic granulocytes (NG) is based on effective recognition and elimination of microbial pathogens, as well as on complex intracellular signal transduction pathways interconnecting these processes. NG dysfunction leads to emergence of atypical infectious and inflammatory diseases recalcitrant to standard interventions, which requires new vector platforms aimed at restoring normal NG functioning and overcoming antibiotic resistance. Moreover, we emphasize about special interest paid to the NOD1 and NOD2 agonist polymuramyl and NOD2 agonist glucosaminylmuramyldipeptide. Objective of the study was to compare effects triggered by NOD1 and NOD2 agonist polymuramyl and NOD2 agonist glucosaminylmuramyldipeptide on phenotype of neutrophilic granulocyte subsets CD64- CD16+CD32+CD11b+, CD16+CD62L+CD63-, CD16+CD62L+CD63+ in the in vitro system. 64 samples of peripheral blood (PC) collected from 8 apparently healthy children (4 boys and 4 girls) aged 3 to 9 years were examined by flow cytometry (FC 500, Beckman Coulter, USA) assessing NG surface receptors CD64, CD16, CD32, CD11b, CD62L, CD63 with MonAb (Beckman Coulter International S. A., France) by analyzing NG number (%) expressing receptors examined, density of receptor expression measured as mean fluorescence intensity (MFI). For this, there were assessed intact peripheral blood NG from apparently healthy children (comparison group) as well as those exposed to polymuramyl (PM) (at concentration of 10-6 g/l) or glucosaminylmuramyl-dipeptide (GMDP) (at concentration of 10-6 g/l) for 60 minutes at 37 °С temperature. Comparative analysis of surface receptor expression was performed on CD64-CD16+CD32+CD11b+, CD16+CD62L+CD63- and CD16+CD62L+CD63+ NG subsets that suggested about positive transformation of activation parameters in circulating NG exposed to NOD1 and NOD2 agonist polymuramyl as well as NOD2 agonist glucosaminylmuramyldipeptide. At the same time, similar effects of varying intensity were revealed manifested as increased count of NG subsets CD16+CD62L+CD63+ bearing increased level of CD16 and reduced CD62L expression, as well as differences uncovered as significantly increased expression of surface membrane molecules CD16 and CD11b in CD64-CD16+CD32+CD11b+ NG subset from apparently healthy children exposed to polymuramyl as well as increased surface CD32 expression after incubation with GMDP.

Identification and analysis of key genes involved in methyl salicylate biosynthesis in different birch species.

Species of the perennial woody plant genus Betula dominate subalpine forests and play a significant role in preserving biological diversity. In addition to their conventional benefits, birches synthesize a wide range of secondary metabolites having pharmacological significance. Methyl salicylate (MeSA) is one of these naturally occurring compounds constitutively produced by different birch species. MeSA is therapeutically important in human medicine for muscle injuries and joint pain. However, MeSA is now mainly produced synthetically due to a lack of information relating to MeSA biosynthesis and regulation. In this study, we performed a comprehensive bioinformatics analysis of two candidate genes mediating MeSA biosynthesis, SALICYLIC ACID METHYLTRANSFERASE (SAMT) and SALICYLIC ACID-BINDING PROTEIN 2 (SABP2), of high (B. lenta, B. alleghaniensis, B. medwediewii, and B. grossa) and low (B. pendula, B. utilis, B. alnoides, and B. nana) MeSA-producing birch species. Phylogenetic analyses of SAMT and SABP2 genes and homologous genes from other plant species confirmed their evolutionary relationships. Multiple sequence alignments of the amino acid revealed the occurrence of important residues for substrate specificity in SAMT and SABP2. The analysis of cis elements in different birches indicated a functional multiplicity of SAMT and SABP2 and provided insights into the regulation of both genes. We successfully developed six prominent single nucleotide substitution markers that were validated with 38 additional birch individuals to differentiate high and low MeSA-producing birch species. Relative tissue-specific expression analysis of SAMT in leaf and bark tissue of two high and two low MeSA-synthesizing birches revealed a high expression in the bark of both high MeSA-synthesizing birches. In contrast, SABP2 expression in tissues revealed indifferent levels of expression between species belonging to the two groups. The comparative expression and bioinformatics analyses provided vital information that could be used to apply plant genetic engineering technology in the mass production of organic MeSA.

Trefoil factor 1 and gastrokine 2 inhibit Helicobacter pylori-induced proliferation and inflammation in gastric cardia and distal carcinogenesis.

Helicobacter pylori (H. pylori) infection has been associated with non-cardia adenocarcinoma in the stomach, while its role in gastric cardia adenocarcinoma (GCA) remains controversial. In addition, the association between H. pylori and the protective factors trefoil factor 1 (TFF1) and gastrokine 2 (GKN2) in gastroesophageal adenocarcinomas has not been fully investigated. Therefore, the mRNA and protein expression levels of TFF1 and GKN2 in GCA and distal gastric adenocarcinoma (DGA) were analyzed using quantitative PCR (qPCR) and immunohistochemistry, and the association with H. pylori infection was investigated. In addition, the effects of TFF1 and GKN2 overexpression on H. pylori-induced cells were investigated using western blot and reverse transcription-qPCR analysis. The comparative analysis of 16S rRNA-positive mRNA expression between GCA and DGA showed no statistically significant difference. However, the rate of the H. pylori vacuolating toxin A (VacA) genotype was significantly higher in GCA (49.2%) compared with that in DGA (26.9%; P<0.05). H. pylori infection downregulated the mRNA and protein expression levels of TFF1 and GKN2 in gastric tumor tissues, and the mRNA expression level of TFF1 and GKN2 was also markedly decreased in vitro. Furthermore, the cell proliferation varied in H. pylori total protein treatment group with the different doses. Notably, treatment with 20 µg/ml H. pylori total protein for 24 h resulted in the highest cellular proliferation rate. In addition, TFF1 and GKN2 overexpression inversely inhibited H. pylori-induced cell proliferation and upregulated NF-κB, tumor necrosis factor-α, IL-1β, IL-2, IL-4 and IL-6. The results of the present study indicate that H. pylori, particularly the VacA+ strain, plays an important role in GCA pathogenesis in high-risk areas of China, while TFF1/GKN2 inhibits H. pylori-induced cell proliferation and inflammation in GCA and DGA.

Transcriptome Analysis Shows Activation of Stress and Defense Responses by Silencing of Chlorophyll Biosynthetic Enzyme CHLI in Transgenic Tobacco.

In the present study, we have shown the transcriptional changes in a chlorosis model transgenic tobacco plant, i-amiCHLI, in which an artificial micro RNA is expressed in a chemically inducible manner to silence the expression of CHLI genes encoding a subunit of a chlorophyll biosynthetic enzyme. Comparison to the inducer-treated and untreated control non-transformants and untreated i-amiCHLI revealed that 3568 and 3582 genes were up- and down-regulated, respectively, in the inducer-treated i-amiCHLI plants. Gene Ontology enrichment analysis of these differentially expressed genes indicated the upregulation of the genes related to innate immune responses, and cell death pathways, and the downregulation of genes for photosynthesis, plastid organization, and primary and secondary metabolic pathways in the inducer-treated i-amiCHLI plants. The cell death in the chlorotic tissues with a preceding H2O2 production was observed in the inducer-treated i-amiCHLI plants, confirming the activation of the immune response. The involvement of activated innate immune response in the chlorosis development was supported by the comparative expression analysis between the two transgenic chlorosis model systems, i-amiCHLI and i-hpHSP90C, in which nuclear genes encoding different chloroplast proteins were similarly silenced.

Identification and comparative expression analysis of chalcone synthase, flavanone 3-hydroxylase and dihydroflavonol 4-reductase genes in wild pomegranate (Punica granatum L.) organs

Flavonoids are the predominant polyphenolic compounds which are ubiquitously present in plants, responsible for the colour development in different plant parts, thereby playing an important role in plant physiology. In order to understand chemo-diversity and biological functions of flavonoids, it is important to understand flavonoid biosynthetic pathway that involves various structural genes. Three structural genes of flavonoid biosynthetic pathway, chalcone synthase (PgCHS; GenBank accession no: KY498075), flavanone 3-hydroxylase (PgF3H; GenBank accession no: MG012857) and dihydroflavonol 4-reductase (PgDFR; GenBank accession no: MG366127) were isolated and characterized from the wild Punica granatum. Molecular modelling indicated that the secondary structures of PgCHS, PgF3H and PgDFR are mainly α-helix and random coils. HPLC analysis of flavonoids showed its accumulation in different tissues and fruits, thus corroborating well with the expression profile of PgCHS, PgF3H and PgDFR genes. PgF3H and PgDFR genes exhibited high transcripts levels in red fruits while expression of Pg CHS gene was highest in flowers. Further, it is speculated that expression of all these structural genes is independent of each other. This is the first study that provides a comparative expression pattern of flavonoid genes playing a significant role in fruit ripening in wild pomegranate.

Brief Report: Diminished Coinhibitory Molecule 2B4 Expression Is Associated With Preserved iNKT Cell Phenotype in HIV Long-Term Nonprogressors.

We have previously shown an association of elevated coinhibitory molecule 2B4 expression with iNKT cells alterations in HIV disease. Herein, we show a comparative analysis of 2B4 expression on iNKT cells of HIV long-term nonprogressors (LTNPs) and progressors. Antiretroviral therapy-naive HIV-seropositive individuals (progressors, n = 16) and LTNPs (n = 10) were recruited for this study. We used multicolor flow cytometry on frozen peripheral blood mononuclear cells to determine iNKT subset frequencies, the levels of coinhibitory 2B4 expression, and intracellular interferon-γ (IFN-γ) production. CD1d tetramer was used to characterize iNKT cells. We report significantly lower level of 2B4 expression on bulk LTNPs iNKT cells and on their CD4 subsets compared with HIV progressors. Furthermore, the iNKT cells from LTNPs produced higher amount of IFN-γ than HIV progressors as detected by intracellular cytokine staining. Interestingly, the frequency of 2B4iNKT cells of progressors but not LTNPs significantly correlates with CD4 T-cell count, HIV viral load, and IFN-γ production by iNKT cells. Our results suggest that in addition to suppressed HIV replication, diminished 2B4 expression and associated coinhibitory signaling, and substantial production of IFN-γ could contribute to preserved iNKT cell phenotype in LTNPs.

Comparative Immunofluorescent Analysis of Estrogen Receptor Beta Expression in Ovarian and Breast Cancer Cell Lines

Comparative quantitative evaluation of estrogen receptors β (ERβ) expression is performed by the immunofluorescence method using flow cytometry in the ovarian cancer cell lines COLO-704, OVCAR-3, EFO-21, and SK-OV-3, as well as the breast cancer cell line MCF-7. A high level of ERβ expression (88–91%) is revealed in all the cell cultures investigated, and significant differences were observed in the intensity of the marker’s expression between ovarian cancer cell cultures (in OVCAR-3, EFO-21, and SK-OV-3 they are higher than in COLO-704 cells by factors of 1.6, 2.3, and 3.5, respectively). Moreover, the intensity of ERβ expression was significantly higher in SK-OV-3, EFO-21, and OVCAR-3 than in MCF-7 cells: in 2.7; 1.4 and 1.9 times, respectively. The authors suggest that in contrast to breast cancer patients, ERβ rather than ERα could be the main target for antiestrogens in ovarian cancer patients. The revealed differences in the ERβ expression in a number of widely used ovarian cancer cell cultures lead us to recommend them for further fundamental research on ERβ to study the biological effects of antiestrogens.

Searching for Promoters to Drive Stable and Long-Term Transgene Expression in Fibroblasts for Syngeneic Mouse Tumor Models.

Tumor is a complex system of interactions between cancer cells and other cells of the tumor microenvironment. The cancer-associated fibroblasts (CAFs) of the tumor microenvironment remain in close contact with the cancer cells and play an important role in cancer progression. Genetically, CAFs are more stable than cancer cells, making them an attractive target for genetic modification in gene therapy. However, the efficiency of various promoters for transgene expression in fibroblasts is scarcely studied. We performed a comparative analysis of transgene long-term expression under the control of strong cytomegalovirus promoter (pCMV), constitutive cell promoter of the PCNA gene (pPCNA), and the potentially fibroblast-specific promoter of the IGFBP2 gene (pIGFBP2). In vitro expression of the transgene under the control of pCMV in fibroblasts was decreased soon after transduction, whereas the expression was more stable under the control of pIGFBP2 and pPCNA. The efficiency of transgene expression was higher under pPCNA than that under pIGFBP2. Additionally, in a mouse model, pPCNA provided more stable and increased transgene expression in fibroblasts as compared to that under pCMV. We conclude that PCNA promoter is the most efficient for long-term expression of transgenes in fibroblasts both in vitro and in vivo.

FOXI1 expression in chromophobe renal cell carcinoma and renal oncocytoma: a study of The Cancer Genome Atlas transcriptome-based outlier mining and immunohistochemistry.

FOXI1 is a forkhead family transcription factor that plays a key role in differentiation and functional maintenance for the renal intercalated cell (IC). The diagnostic utility of FOXI1 is rarely studied thus far. Comparative analyses of FOXI1 mRNA expression in normal kidney tissue and different renal neoplasms including chromophobe renal cell carcinoma (chRCC), renal oncocytoma (RO), and other renal cell carcinomas were conducted using transcriptomic data from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus, and single-cell RNA-seq datasets, in combination with integrative analyses using mutant data, karyotype data, and digital slides for cases with anomalous FOXI1 expression in TCGA. Formalin-fixed, paraffin-embedded whole-tissue slides of varied primary renal neoplasms (n = 367) were subjected to FOXI1 staining for validating FOXI1 transcription levels. We confirmed that FOXI1 was significantly upregulated at mRNA levels in ICs, chRCCs, and ROs compared with other renal tubule cell and renal cell carcinoma subtypes. Furthermore, most of the cases with FOXI1 expression outliers were misclassified in the TCGA kidney cancer project. An underlying novel entity with frequent mutations involved in the mTOR pathway was also found. FOXI1 immunoreactivity was consistently noted in ICs of the distal nephron. FOXI1 staining was positive in 85 of 93 chRCCs and 13 of 18 ROs, respectively. FOXI1 staining was not seen in renal neoplasms (n = 254) derived from non-ICs. In conclusion, FOXI1 expression in normal kidney tissue is restricted to ICs. This cell type-specific expression is retained during neoplastic transformation from ICs to chRCCs or ROs. FOXI1 is thereby a potential biomarker of IC-related tumors.

The Influence of Radical Prostatectomy on the Expression of Cell-Free MiRNA.

MiRNAs of blood and urine have been shown to represent a convenient source of biomarkers for prostate cancer (PCa) diagnosis and assessment of the therapy effectiveness due to their high stability and representation and the low invasiveness of sample collection. Here, we studied the influence of radical prostatectomy (RP) on the expression of 12 cell-free miRNAs previously shown as potential markers of PCa (i.e., miR-19b, miR-22, miR-92a, miR-378, miR-425, miR-30e, miR-31, miR-125b, miR-200b, miR-205, miR-375 and miR-660). The relative expression of the miRNAs combined into 31 paired ratios was evaluated in the urine extracellular vesicles (EVs), clarified urine (CU) and blood plasma of healthy donors, pre- and post-RP samples of PCa patients. Nineteen miRNA ratios based on combinations of ten of the miRNAs (miR-19b, miR-30e, miR-31, miR-125b, miR-200b, miR-205, miR-375, miR-378, miR-425, and miR-660) were altered by RP. The comparative expression analysis of the cell-free miRNA ratios between healthy donors and PCa patients revealed miR-125b/miR-30e and miR-375/miR-30e as potential markers for evaluating therapeutic efficacy. MiR-378/miR-19b, miR-425/miR-19b, miR-200/miR-30e, miR-660/miR-30e, and miR-205/miR-30e had minor prognostic value but could be used to increase the steadiness of the diagnostic system. The urine EVs had the highest potential as a source of markers.

Abstract 3853: The anti-tumor immune responses by active and quiescent tertiary lymphoid structures to breast cancer

Abstract There is a growing interest in active immune responses generated by tertiary lymphoid structures (TLS) arising in solid tumors; however, their clinical impact in breast cancer (BC) remains unclear. Several studies show that transcription factors contribute to TLS formation via their regulation of cytokine and chemokine production. The Forkhead box (FOX) protein 1 (FOXP1) has been shown to play critical roles in regulating immune cells, including our recent work revealing its effects on TIL migration. These data lead us to further investigate FOXP1 expression in tumor infiltrating lymphocytes (TIL) and TLS. We identify two types of TLS based on FOXP1 expression: 1) those that contain a germinal center (GC+) and those that do not (GC-). Comparative analysis of FOXP1 expression in secondary lymphoid organs, including more immune active tonsils (many GC) and less immune active spleens (primarily without GC) confirm differences in FOXP1 expression associated with GC. In BC, TLS containing tumors were more frequently GC- than GC+ (n=49), with triple-negative tumors having higher numbers of GC+ TLS compared to luminal or HER2+ tumors. Immunofluorescence and multiplex immunohistochemistry was used to closely examine the GC+ and GC- TLS, finding an immune active profile in the former, characterized by T follicular helper cells (PD1+CD4+ T), mature dendritic cells (CD21+ and CD23+), actively proliferating (Ki67+) B cells undergoing immunoglobulin (Ig) class switch recombination (AID+) and a plasma cell presence (CD138+). Analysis of Ig's in the primary tumor supernatants revealed that BC with ≥1 GC+ TLS (n=20) were characterized by increases in total Ig, IgG1, IgG2 and IgA, reflecting active humoral immunity, compared to BC containing only GC- TLS (n=29). Gene expression analysis of individual micro-dissected TLS demonstrated upregulation of Th1, Th2 and Tfh immune genes in the GC+ compared to the GC- TLS, suggesting the former also sustain cell-mediated immune responses. Immune infiltrates in tumors with ≥1 GC+ TLS are specifically characterized by high global TIL, CD3+, CD4+ or CD8+ T cell TIL and CD20+ TIL-B (n=29). Analysis of BC TIL spatial distribution identified increased stromal TIL (all subpopulations) while intratumoral TIL increases were predominantly CD3+ and CD8+ T cell TIL in tumors with GC+ TLS. Overall, our data indicate that GC+ TLS house active immune responses in BC while GC- TLS are quiescent. Citation Format: Pushpamali De Silva, Soizic Garaud, Cinzia Solinas, Grégory Noël, Mireille Langouo Fontsa, Anaïs Boisson, Alexandre de Wind, Vinu Jose, Gert Van den Eynden, Noemie Thomas, Hugues Duvillier, Céline Naveaux, Ligia Craciun, Dominique Bron, Martine Piccart-Gebhart, Denis Larsimont, Karen Willard-Gallo. The anti-tumor immune responses by active and quiescent tertiary lymphoid structures to breast cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3853.

Identification and comparative expression analysis of RIG‐I and MDA5 in Chinese giant salamander Andrias davidianus

Identification and comparative expression analysis of RIG‐I and MDA5 in Chinese giant salamander <i>Andrias davidianus</i>

A glimpse of potential transposable element impact on adaptation of the industrial yeast Saccharomyces cerevisiae.

The adapted industrial yeast strain Saccharomyces cerevisiae NRRL Y-50049 is able to in situ detoxify major toxic aldehyde compounds derived from sugar conversion of lignocellulosic biomass while producing ethanol. Pathway-based studies on its mechanisms of tolerance have been reported previously, however, little is known about transposable element (TE) involvement in its adaptation to inhibitory compounds. This work presents a comparative dynamic transcription expression analysis in response to a toxic treatment between Y-50049 and its progenitor, an industrial type strain NRRL Y-12632, using a time-course study. At least 77 TEs from Y-50049 showed significantly increased expression compared with its progenitor, especially during the late lag phase. Sequence analysis revealed significant differences in TE sequences between the two strains. Y-50049 was also found to have a transposons of yeast 2 (Ty2) long terminal repeat-linked YAT1 gene showing significantly higher copy number changes than its progenitor. These results raise awareness of potential TE involvement in the adaptation of industrial yeast to the tolerance of toxic chemicals.

Immune gene expression and genome-wide association analysis in rainbow trout with different resistance to Yersinia ruckeri infection

Selective breeding programmes involving marker assisted selection of innately pathogen resistant strains of rainbow trout rely on reliable controlled infection studies, extensive DNA typing of individual fish and recording of expression of relevant genes. We exposed juvenile rainbow trout (6 h bath to 2.6 × 105 CFU mL−1) to the fish pathogen Yersinia ruckeri serotype O1, biotype 2, eliciting Enteric Red Mouth Disease ERM, and followed the disease progression over 21 days. Cumulative mortality reached 42% at 12 days post challenge (dpc) after which no disease signs were recorded. All fish were sampled for DNA-typing (50 k SNP chip, Affymetrix®) throughout the course of infection when they showed clinical signs of disease (susceptible fish) or at day 21 when fish showed no clinical signs of disease (survivors - resistant fish). Genome-wide association analyses of 1027 trout applying single nucleotide polymorphisms (SNPs) as markers revealed an association between traits (susceptible/resistant) and certain regions of the trout genome. It was indicated that multiple genes are involved in rainbow trout resistance towards ERM whereby it is considered a polygenic trait. A corresponding trout group was kept as non-exposed controls and a comparative expression analysis of central innate and adaptive immune genes in gills, spleen and liver was performed for three fish groups: 1) moribund trout exhibiting clinical signs 7 dpc (CS), 2) exposed fish without clinical signs at the same sampling point (NCS) and 3) surviving fish at 21 dpc (survivors). Immune genes encoding inflammatory cytokines (IL-1β, IL-2A, IL-6A, IL-8, IL-10A, IL-12, IL-17A/F2A, IL-17C1, IL-17C2, IL-22, IFNγ, TNFα), acute phase reactants (SAA, C3, cathelicidins, lysozyme) were expressed differently in CS and NCS fish. Correlation (negative or positive) between expression of genes and bacterial load suggested involvement of immune genes in protection. Down-regulation of adaptive immune genes including IgDm, IgDs, IgT and TCR-β was seen primarily in CS and NCS fish whereas survivors showed up-regulation of effector molecule genes such as cathelicidins, complement and lysozyme suggesting their role in clearing the infection. In conclusion, SNP analyses indicated that ERM resistance in rainbow trout is a multi-locus trait. The gene expression in surviving fish suggested that several immune genes are associated with the trait conferring resistance.

Integrated Analysis of microRNA-mRNA Expression in Mouse Lungs Infected With H7N9 Influenza Virus: A Direct Comparison of Host-Adapting PB2 Mutants.

MicroRNAs (miRNAs) are important regulators involved in the antiviral response to influenza virus infection, however, an analytical comparison of miRNA and mRNA expression changes induced by several H7N9 host-adapting PB2 mutants remains undone. Here, miRNA microarray and transcriptome sequencing of BALB/c mouse lungs infected with A/Anhui/1/2013 (H7N9) [hereafter referred to as H7N9/AH1-PB2-627K(WT)] and mutant variants with PB2 amino acid substitutions (avian-like H7N9/AH1-PB2-627E and mammalian-adapted H7N9/AH1-PB2-627E/701N) were directly compared. The results showed that influenza virus infection induced dysregulation of numerous host cell processes. In a miRNA-mRNA network associated with immunity, changes in the expression of 38 miRNAs and 58 mRNAs were detected following influenza virus infection. Notably, the miRNAs of mmu-miR-188-5p, mmu-miR-511-5p, mmu-miR-483-5p, and mmu-miR-690 were specifically associated with the replication of the avian-like virus H7N9/AH1-PB2-627E. Likewise, the miRNAs of mmu-miR-691, mmu-miR-329-3p, and mmu-miR-144-3p were specifically associated with the mammalian-adapted virus H7N9/AH1-PB2-627E/701N. Finally, the miRNAs of mmu-miR-98-5p, mmu-miR-103-3p, mmu-miR-199a-5p, and mmu-miR-378a-3p were specifically associated with H7N9/AH1-PB2-627K(WT) virus replication. This is the first report of comparative integration analysis of miRNA-mRNA expression of these three H7N9 influenza viruses with different host-adapting PB2 mutations. Our results highlight potential miRNAs of importance in influenza virus pathogenesis.

Liquid profiling in plants: identification and analysis of extracellular metabolites and miRNAs in pollination drops of Ginkgo biloba.

The pollination drop (PD), also known as an ovular secretion, is a critical feature of most wind-pollinated gymnosperms and function as an essential component of pollination systems. However, the metabolome and small RNAs of gymnosperm PDs are largely unknown. We employed gas chromatography-mass spectrometry to identify a total of 101 metabolites in Ginkgo biloba L. PDs. The most abundant metabolites were sugars (45.70%), followed by organic acids (15.94%) and alcohols (15.39%) involved in carbohydrate metabolism, glycine, serine and threonine metabolism. Through pollen culture of the PDs, we further demonstrated that the metabolic components of PDs are indispensable for pollen germination and growth; in particular, organic acids and fatty acids play defensive roles against microbial activity. In addition, we successfully constructed a small RNA library and detected 45 known and 550 novel miRNAs in G. biloba PDs. Interestingly, in a comparative analysis of miRNA expression between PDs and ovules, we found that most of the known miRNAs identified in PDs were also expressed in the ovules, implying that miRNAs in PDs may originate from ovules. Further, combining with potential target prediction, degradome validation and transcriptome sequencing, we identified that the interactions of several known miRNAs and their targets in PDs are involved in carbohydrate metabolism, hormone signaling and defense response pathways, consistent with the metabolomics results. Our results broaden the knowledge of metabolite profiling and potential functional roles in gymnosperm PDs and provide the first evidence of extracellular miRNA functions in ovular secretions from gymnosperms.