Expression Of Selected Genes Research Articles

Jackfruit genome and population genomics provide insights into fruit evolution and domestication history in China.

As the largest known tree-borne fruit in the world, jackfruit (Artocarpus heterophyllus) is an important cultivated crop in tropical regions of South and Southeast Asia. The species has been cultivated in China for more than 1000 years, but the history of its introduction to the country remains unclear. We assembled a high-quality chromosome-level genome of jackfruit into 985.63 Mb with scaffold N50 of 32.81 Mb. We analyzed whole-genome resequencing data of 295 landraces to investigate the domestication history in China and agronomic trait evolution of jackfruit. Population structure analysis revealed that jackfruits of China could be traced back to originate from Southeast Asia and South Asia independently. Selection signals between jackfruit and its edible congener, cempedak (Artocarpus integer), revealed several important candidate genes associated with fruit development and ripening. Moreover, analyses of selective sweeps and gene expression revealed that the AhePG1 gene may be the major factor in determining fruit texture. This study not only resolves the origins of jackfruit of China, but also provides valuable genomic resources for jackfruit breeding improvement and offers insights into fruit size evolution and fruit texture changes.

Robust Heat Shock Response in Chlamydia Lacking a Typical Heat Shock Sigma Factor.

Cells reprogram their transcriptome in response to stress, such as heat shock. In free-living bacteria, the transcriptomic reprogramming is mediated by increased DNA-binding activity of heat shock sigma factors and activation of genes normally repressed by heat-induced transcription factors. In this study, we performed transcriptomic analyses to investigate heat shock response in the obligate intracellular bacterium Chlamydia trachomatis, whose genome encodes only three sigma factors and a single heat-induced transcription factor. Nearly one-third of C. trachomatis genes showed statistically significant (≥1.5-fold) expression changes 30 min after shifting from 37 to 45°C. Notably, chromosomal genes encoding chaperones, energy metabolism enzymes, type III secretion proteins, as well as most plasmid-encoded genes, were differentially upregulated. In contrast, genes with functions in protein synthesis were disproportionately downregulated. These findings suggest that facilitating protein folding, increasing energy production, manipulating host activities, upregulating plasmid-encoded gene expression, and decreasing general protein synthesis helps facilitate C. trachomatis survival under stress. In addition to relieving negative regulation by the heat-inducible transcriptional repressor HrcA, heat shock upregulated the chlamydial primary sigma factor σ66 and an alternative sigma factor σ28. Interestingly, we show for the first time that heat shock downregulates the other alternative sigma factor σ54 in a bacterium. Downregulation of σ54 was accompanied by increased expression of the σ54 RNA polymerase activator AtoC, thus suggesting a unique regulatory mechanism for reestablishing normal expression of select σ54 target genes. Taken together, our findings reveal that C. trachomatis utilizes multiple novel survival strategies to cope with environmental stress and even to replicate. Future strategies that can specifically target and disrupt Chlamydia’s heat shock response will likely be of therapeutic value.

Genetic variants in the Hedgehog signaling pathway genes are associated with gastric cancer risk in a Chinese Han population.

The Hedgehog signaling pathway participates in the occurrence and progression of cancers including gastric cancer. We conducted this study to evaluate whether genetic variants in the Hedgehog signaling pathway genes would affect gastric cancer risk. Multi-marker Analysis of GenoMic Annotation (MAGMA) was used to investigate the aggregated genetic effects of single nucleotide polymorphisms (SNPs) assigned to candidate genes. The relationship between SNPs and gastric cancer risk was estimated by multivariate logistic regression analyses. Gene expression was calculated using databases obtained from The Cancer Genome Atlas (TCGA) and The Gene Expression Omnibus (GEO). Kaplan‐Meier plotter was used to evaluate the association between gene expression with gastric cancer survival. Tumor Immune Estimation Resource 2.0 (TIMER 2.0) was applied to determine the correlation between selected gene expression and the immune cell infiltration degree. We identified that the G allele of rs2990912 in KIF27 was associated with higher gastric cancer risk, especially in the young and male subgroups. The expression ofKIF27 in gastric cancer tissues was higher than that in normal tissues, leading to poor survival in gastric cancer patients. Besides, KIF27 expression was related to immune cell infiltration and positively correlated with PD-L1 expression. Our findings highlight the key role of genetic variation in the Hedgehog signaling pathway genes in gastric cancer susceptibility, which may provide important insights into the diagnosis, prognosis, and treatment of gastric cancer.

Using a Transection Paradigm to Enhance the Repair Mechanisms of an Investigational Human Cell Therapy

One promising strategy in cell therapies for Parkinson’s disease (PD) is to harness a patient’s own cells to provide neuroprotection in areas of the brain affected by neurodegeneration. No treatment exists to replace cells in the brain. Thus, our goal has been to support sick neurons and slow neurodegeneration by transplanting living repair tissue from the peripheral nervous system into the substantia nigra of those with PD. Our group has pioneered the transplantation of transection-activated sural nerve fascicles into the brain of human subjects with PD. Our experience in sural nerve transplantation has supported the safety and feasibility of this approach. As part of a paradigm to assess the reparative properties of human sural nerve following a transection injury, we collected nerve tissue approximately 2 weeks after sural nerve transection for immunoassays from 15 participants, and collected samples from two additional participants for single nuclei RNA sequencing. We quantified the expression of key neuroprotective and select anti-apoptotic genes along with their corresponding protein levels using immunoassays. The single nuclei data clustered into 10 distinctive groups defined on the basis of previously published cell type-specific genes. Transection-induced reparative peripheral nerve tissue showed RNA expression of neuroprotective factors and anti-apoptotic factors across multiple cell types after nerve injury induction. Key proteins of interest (BDNF, GDNF, beta-NGF, PDGFB, and VEGF) were upregulated in reparative tissue. These results provide insight on this repair tissue’s utility as a neuroprotective cell therapy.

Changes in gene expression induced by Micro-Immunotherapy

Background: Metabolic syndrome (MS) is a metabolic disorder associated with obesity, type-II diabetes, and “low grade inflammation”, with the concomitant increased risk of cardiovascular events. As a chronic inflammatory process, MS results in a dysregulation of the cytokine profile. 2L®INFLAM, a Micro-immunotherapy (MI) medication formulated with highly diluted cytokines, is currently prescribed in Belgium for inflammatory diseases and potentially may be helpful for MS patients.
 Aims: To investigate the impact of 2L®INFLAM on selected gene expression markers (mRNA) in patients suffering from MS, in addition to biological and clinical parameters.
 Methodology: Four well characterized MS adult patients with stabilized body-weight were advised to take one capsule of 2L®INFLAM per day (by sublingual-oral route) for 6 months (composition in table 1). Concomitantly to biological and clinical examination, genes expression status was assessed by a DNA microarray technology (Oxygen™) comprising 200 genes involved mainly in oxidative stress and inflammation. Whole blood collection was performed before and after treatment (3-6 months) and mRNA levels measured. Gene expression was classified in 3 series (normally expressed, up or down-regulated) and genes related to diabetes predisposition were scored by using a proprietary Diascore (Probiox).
 Results: Before MI medication, a significant percentage of dysregulated genes (median: 16.3%) as well as a positive Diascore (median: 1.6) were noticed. Impressive correction of dysregulated genes (reaching 90% for one patient) was observed after 3 months of treatment (median: 2.3%) in addition to an improvement of Diascore in 3 MS patients out of 4 (median: 0.5). During the same period, both clinical and biological parameters remained unchanged.
 Conclusions: MS patients showing a high level of gene dysregulation efficiently normalized after 3 months of 2L®INFLAM (64%-90%), suggesting a biological regulatory effect of MI and a potential benefit of this medication for diabetic patients. Up and down-deregulated gene profiles were specific for each patient and not related to cytokine components of the formula. These preliminary data support the “domino effect” of MI sequential formula to restore in depth the immune homeostasis. DNA microarray technology may represent a promising tool for new provings as well as for biochemical comprehension of the “in vivo” effectiveness of highly diluted immune messengers.
 
 Table 1: 2L®INFLAM composition
 
 Compounds Dilutions
 
 Interleukin-1 (IL-1): 17 CH*
 Interleukin-1 Ra (IL-1 Ra): 3 CH
 Interleukin-2 (IL-2): 9 CH
 Interleukin-4 (IL-4): 7 CH
 Interleukin-6 (IL-6): 9 CH
 Interleukin-8 (IL-8): 9 CH
 Interleukin-10 (IL-10): 4 CH
 Interleukin-13 (IL-13): 9 CH
 Ciliary Neuro Trophic Factor (CNTF): 17 CH
 Leukemia Inhibitory Factor (LIF): 17 CH
 Oncostatine M (OSM): 9 CH
 Platelet Derived Growth Factor (PDGF): 5 CH
 Prostaglandine E2 (PgE2): 200 K**
 Rantes (Rantes): 17 CH
 Transforming Growth Factor beta(TGFβ): 5 CH 
 Tumor Necrosis Factor α (TNFα): 17 CH
 SNA INFLAMa-01 18 C
 SNA INFLAMb-01 18 CH
 
 * CH: Centesimal Hahnemannian (1/100)
 ** K: Centesimal Korsakovian (1/100)

Differential Expression of Polyamine Pathways in Human Pancreatic Tumor Progression and Effects of Polyamine Blockade on Tumor Microenvironment.

Simple SummaryPancreatic cancer has a five-year survival rate of less than 8% and is the fourth leading cause of cancer death in the United States. Existing therapeutics have failed to improve pancreatic ductal adenocarcinoma (PDAC) patient outcomes. There has been success with other tumor types in targeting aberrant polyamine upregulation as a therapeutic strategy. The present study identified dysregulation of polyamine pathways to be evident in human PDAC progression. Additionally, reduced survival of pancreatic cancer patients was associated with increased expression of specific polyamine-related genes. Polyamine blockade therapy significantly increased overall survival of pancreatic tumor-bearing mice, along with macrophage presence (F4/80) and significantly increased T-cell co-stimulatory marker (CD86) in the tumor microenvironment. Based on these findings, we hypothesized that a polyamine blockade therapy could potentially prime the tumor microenvironment to be more susceptible to existing therapeutics. Future studies which test polyamine blockade therapy with existing therapeutics could increase the molecular tools available to treat PDAC.Pancreatic cancer is the fourth leading cause of cancer death. Existing therapies only moderately improve pancreatic ductal adenocarcinoma (PDAC) patient prognosis. The present study investigates the importance of the polyamine metabolism in the pancreatic tumor microenvironment. Relative mRNA expression analysis identified differential expression of polyamine biosynthesis, homeostasis, and transport mediators in both pancreatic epithelial and stromal cells from low-grade pancreatic intraepithelial neoplasia (PanIN-1) or primary PDAC patient samples. We found dysregulated mRNA levels that encode for proteins associated with the polyamine pathway of PDAC tumors compared to early lesions. Next, bioinformatic databases were used to assess expression of select genes involved in polyamine metabolism and their impact on patient survival. Higher expression of pro-polyamine genes was associated with poor patient prognosis, supporting the use of a polyamine blockade therapy (PBT) strategy for inhibiting pancreatic tumor progression. Moreover, PBT treatment of syngeneic mice injected intra-pancreatic with PAN 02 tumor cells resulted in increased survival and decreased tumor weights of PDAC-bearing mice. Histological assessment of PBT-treated tumors revealed macrophage presence and significantly increased expression of CD86, a T cell co-stimulatory marker. Collectively, therapies which target polyamine metabolism can be used to disrupt tumor progression, modulate tumor microenvironment, and extend overall survival.

ZBP1 is a significant pyroptosis regulator for systemic lupus erythematosus.

BackgroundSystemic lupus erythematosus (SLE) is a common autoimmune disease that affects all organs. Recently, several studies have shown that pyroptosis playsa significant process in the occurrence and progression of SLE. However, no study has investigated the association between pyroptosis genes and SLE. We conducted this study to examine this association.MethodsThe GSE11090, GSE20864, and GSE112087 gene microarrays of normal and SLE patient samples were downloaded from the Gene Expression Omnibus database. A differentially expressed gene (DEG) analysis was performed using the LIMMA package in R software. Log2 fold change |logFC| >0.5 and a false discovery rate (FDR) <0.05 setting for DEGs’ screening value. We also performed an enrichment function analysis of the DEGs. To explore the role of pyroptosis genes in SLE, we selected pyroptosis genes that intersected with the DEGs for further analysis, we also examined the expression levels of the selected genes, their association with immune cell infiltration, and conducted western blotting and polymerase chain reaction analyses to confirm the selected genes expression levels in the SLE and normal samples.ResultsA total of 3,398 identical genes were obtained from 3 datasets for the differential analysis. 84 upregulated genes and 52 downregulated genes were identified in SLE. The enrichment function analysis revealed that DEGs act as key regulators of nicotinamide adenine dinucleotide (NADH) dehydrogenase activity, phospholipid scramblase activity, double-stranded ribonucleic acid (RNA) binding, and the interferon signaling pathway. We identified the SLE-related pyroptosis gene, Z-DNA binding protein 1 (ZBP1), by intersecting the DEGs of SLE and 40 pyroptosis genes. The differential analysis indicated that ZBP1 was more highly expressed in SLE patients compared to normal samples (P<0.001). Additionally, the expression of ZBP1 was higher in females than males (P=0.008). The SLE samples had different immune cell infiltration than the normal samples, and ZBP1 was significantly correlated with immune cell infiltration in the SLE samples. Finally, the validation experiments results showed that ZBP1 expression levels were significantly more highly expressed in female and SLE patients, than male and normal patients.ConclusionsZBP1 may indicate that females have a high incidence rate of SLE, and it plays a significant role in the occurrence and progression of SLE.

Abstract PO-120: Differential expression of polyamine pathways in human pancreatic tumor progression and effects of polyamine blockade therapy on the in vivo pancreatic tumor microenvironment

Abstract Pancreatic cancer is the fourth leading cause of cancer death in the United States, with a five-year survival rate of less than 8%. Existing therapies have failed to improve pancreatic ductal adenocarcinoma (PDAC) patient prognosis. The dense desmoplastic reaction which occurs in PDAC makes it challenging for drugs and immune cells to infiltrate the fibrotic barrier. There is a need to exploit lesser explored targets in PDAC that can influence both the tumor and its microenvironment. One such avenue could be via targeting polyamine metabolism which is upregulated in pancreatic tumors. Though aberrant polyamine upregulation in pancreatic tumors has been known for decades, there has been little progress in translating this information into a PDAC therapeutic strategy. Additionally, there is a dearth of information regarding the dysregulation of polyamine metabolism in human PDAC and its association with clinical outcomes. Thus far, preclinical studies targeting polyamines using polyamine blockade therapy (PBT) has improved survival of pancreatic tumor bearing mice. Literature shows effectiveness of PBT in eliciting an anti-tumor immune response in other tumor types. Whether these results translate to the immune-privileged PDAC microenvironment need to be determined. The present study explores polyamine gene expression in human PDAC samples by mRNA expression analysis of frozen PDAC and Pancreatic intraepithelial neoplasia (PanIN). The Cancer Genome Atlas in the public domain was used to identify clinical outcomes of PDAC patients associated with select polyamine gene expression. Further, the anti-tumor effects of PBT and associated tumor microenvironment changes were identified using in vivo PDAC models and histological assessment. Polyamine dysregulation was found to be evident in human PDAC progression. Also, increased expression of certain polyamine-related genes was associated with poorer survival of pancreatic cancer patients. When targeting polyamines using PBT in immunocompetent C57Bl/6 mice with Pan02 tumor cells injected in the pancreas, PBT significantly increased overall survival. PBT also resulted in an increase in the infiltration of macrophages (F4/80) and expression of T-cell co-stimulatory marker (CD86) as assessed by immunohistochemistry and further quantification of imaging. Based on these changes, we hypothesized that PBT could prime the tumor microenvironment to be more susceptible to existing therapeutics. In conclusion, targeting polyamines using PBT results in increased survival and immune modulation in PDAC. Citation Format: Sai Preethi Nakkina, Sarah B. Gitto, Veethika Pandey, Jignesh G. Parikh, Dirk Geerts, Kenneth P. Olive, Otto Phanstiel, Deborah A. Altomare, Carlo Maurer. Differential expression of polyamine pathways in human pancreatic tumor progression and effects of polyamine blockade therapy on the in vivo pancreatic tumor microenvironment [abstract]. In: Proceedings of the AACR Virtual Special Conference on Pancreatic Cancer; 2021 Sep 29-30. Philadelphia (PA): AACR; Cancer Res 2021;81(22 Suppl):Abstract nr PO-120.

The Transcriptional Differences of Avian CD4+CD8+ Double-Positive T Cells and CD8+ T Cells From Peripheral Blood of ALV-J Infected Chickens Revealed by Smart-Seq2.

It is well known that chicken CD8+ T cell response is vital to clearing viral infections. However, the differences between T cell subsets expressing CD8 receptors in chicken peripheral blood mononuclear cells (PBMCs) have not been compared. Herein, we used Smart-Seq2 scRNA-seq technology to characterize the difference of chicken CD8high+, CD8high αα+, CD8high αβ+, CD8medium+, and CD4+CD8low+ T cell subsets from PBMCs of avian leukosis virus subgroup J (ALV-J)-infected chickens. Weighted gene co-expression network analysis (WGCNA) and Trend analysis revealed that genes enriched in the “Cytokine–cytokine receptor interaction” pathway were most highly expressed in the CD8high αα+ T cell population, especially T cell activation or response-related genes including CD40LG, IL2RA, IL2RB, IL17A, IL1R1, TNFRSF25, and TNFRSF11, suggesting that CD8high αα+ T cells rather than other CD8 subpopulations were more responsive to ALV-J infections. On the other hand, genes involved in the “FoxO signaling pathway” and “TGF-beta signaling pathway” were most highly expressed in the CD4+CD8low+ (CD8low+) T cell population and the function of CD4+CD8low+ T cells may play roles in negatively regulating the functions of T cells based on the high expression of CCND1, ROCK1, FOXO1, FOXO3, TNFRSF18, and TNFRSF21. The selected gene expressions in CD8+ T cells and CD4+CD8low+ double-positive T cells confirmed by qRT-PCR matched the Smart-Seq2 data, indicating the reliability of the smart-seq results. The high expressions of Granzyme K, Granzyme A, and CCL5 indicated the positive response of CD8+ T cells. Conversely, CD4+CD8+ T cells may have the suppressor activity based on the low expression of activation molecules but high expression of T cell activity suppressor genes. These findings verified the heterogeneity and transcriptional differences of T cells expressing CD8 receptors in chicken PBMCs.

A tomato NAC transcription factor, SlNAM1, positively regulates ethylene biosynthesis and the onset of tomato fruit ripening.

Fruit ripening in tomato (Solanum lycopersicum) is the result of selective expression of ripening-related genes, which are regulated by transcription factors (TFs). The NAC (NAM, ATAF1/2, and CUC2) TF family is one of the largest families of plant-specific TFs and members are involved in a variety of plant physiological activities, including fruit ripening. Fruit ripening-associated NAC TFs studied in tomato to date include NAC-NOR (non-ripening), SlNOR-like1 (non-ripening like1), SlNAC1, and SlNAC4. Considering the large number of NAC genes in the tomato genome, there is little information about the possible roles of other NAC members in fruit ripening, and research on their target genes is lacking. In this study, we characterize SlNAM1, a NAC TF, which positively regulates the initiation of tomato fruit ripening via its regulation of ethylene biosynthesis. The onset of fruit ripening in slnam1-deficient mutants created by CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9) technology was delayed, whereas fruit ripening in OE-SlNAM1 lines was accelerated compared with the wild type. The results of RNA-sequencing (RNA-seq) and promoter analysis suggested that SlNAM1 directly binds to the promoters of two key ethylene biosynthesis genes (1-aminocyclopropane-1-carboxylate synthase: SlACS2 and SlACS4) and activates their expression. This hypothesis was confirmed by electrophoretic mobility shift assays and dual-luciferase reporter assay. Our findings provide insights into the mechanisms of ethylene production and enrich understanding of the tomato fruit ripening regulatory network.

PIM1 phosphorylation of the androgen receptor and 14-3-3 \u03b6 regulates gene transcription in prostate cancer

PIM1 is a serine/threonine kinase over-expressed in prostate cancer. We have previously shown that PIM1 phosphorylates the androgen receptor (AR), the primary therapeutic target in prostate cancer, at serine 213 (pS213), which alters expression of select AR target genes. Therefore, we sought to investigate the mechanism whereby PIM1 phosphorylation of AR alters its transcriptional activity. We previously identified the AR co-activator, 14-3-3 ζ, as an endogenous PIM1 substrate in LNCaP cells. Here, we show that PIM1 phosphorylation of AR and 14-3-3 ζ coordinates their interaction, and that they extensively occupy the same sites on chromatin in an AR-dependent manner. Their occupancy at a number of genes involved in cell migration and invasion results in a PIM1-dependent increase in the expression of these genes. We also use rapid immunoprecipitation and mass spectrometry of endogenous proteins on chromatin (RIME), to find that select AR co-regulators, such as hnRNPK and TRIM28, interact with both AR and 14-3-3 ζ in PIM1 over-expressing cells. We conclude that PIM1 phosphorylation of AR and 14-3-3 ζ coordinates their interaction, which in turn recruits additional co-regulatory proteins to alter AR transcriptional activity.

Cre driver mouse lines for thalamocortical circuit mapping.

Subpopulations of neurons and associated neural circuits can be targeted in mice with genetic tools in a highly selective manner for visualization and manipulation. However, there are not well-defined Cre "driver" lines that target the expression of Cre recombinase to thalamocortical (TC) neurons. Here, we characterize three Cre driver lines for the nuclei of the dorsal thalamus: Oligodendrocyte transcription factor 3 (Olig3)-Cre, histidine decarboxylase (HDC)-Cre, and corticotropin-releasing hormone (CRH)-Cre. We examined the postnatal distribution of Cre expression for each of these lines with the Cre-dependent reporter CAG-tdTomato (Ai9). Cre-dependent expression of tdTomato reveals that Olig3-Cre expresses broadly within the thalamus, including TC neurons and interneurons, while HDC-Cre and CRH-Cre each have unique patterns of expression restricted to TC neurons within and across the sensory relay nuclei of the dorsal thalamus. Cre expression is present by the time of natural birth in all three lines, underscoring their utility for developmental studies. To demonstrate the utility of these Cre drivers for studying sensory TC circuitry, we targeted the expression of channelrhodopsin-2 to thalamus from the CAG-COP4*H134R/EYFP (Ai32) allele with either HDC-Cre or CRH-Cre. Optogenetic activation of TC afferents in primary visual cortex was sufficient to measure frequency-dependent depression. Thus, these Cre drivers provide selective Cre-dependent gene expression in thalamus suitable for both anatomical and functional studies.

Pharmacological blockade of the EP3 prostaglandin E2 receptor in the setting of type 2 diabetes enhances β-cell proliferation and identity and relieves oxidative damage

ObjectiveType 2 diabetes is characterized by hyperglycemia and inflammation. Prostaglandin E2, which signals through four G protein-coupled receptors (EP1-4), is a mediator of inflammation and is upregulated in diabetes. We have shown previously that EP3 receptor blockade promotes β-cell proliferation and survival in isolated mouse and human islets ex vivo. Here, we analyzed whether systemic EP3 blockade could enhance β-cell mass and identity in the setting of type 2 diabetes using mice with a spontaneous mutation in the leptin receptor (Leprdb). MethodsFour- or six-week-old, db/+, and db/db male mice were treated with an EP3 antagonist daily for two weeks. Pancreata were analyzed for α-cell and β-cell proliferation and β-cell mass. Islets were isolated for transcriptomic analysis. Selected gene expression changes were validated by immunolabeling of the pancreatic tissue sections. ResultsEP3 blockade increased β-cell mass in db/db mice through enhanced β-cell proliferation. Importantly, there were no effects on α-cell proliferation. EP3 blockade reversed the changes in islet gene expression associated with the db/db phenotype and restored the islet architecture. Expression of the GLP-1 receptor was slightly increased by EP3 antagonist treatment in db/db mice. In addition, the transcription factor nuclear factor E2-related factor 2 (Nrf2) and downstream targets were increased in islets from db/db mice in response to treatment with an EP3 antagonist. The markers of oxidative stress were decreased. ConclusionsThe current study suggests that EP3 blockade promotes β-cell mass expansion in db/db mice. The beneficial effects of EP3 blockade may be mediated through Nrf2, which has recently emerged as a key mediator in the protection against cellular oxidative damage.

Characterization of Exosome-Related Gene Risk Model to Evaluate the Tumor Immune Microenvironment and Predict Prognosis in Triple-Negative Breast Cancer.

BackgroundAs a kind of small membrane vesicles, exosomes are secreted by most cell types from multivesicular endosomes, including tumor cells. The relationship between exosomes and immune response plays a vital role in the occurrence and development of tumors. Nevertheless, the interaction between exosomes and the microenvironment of tumors remains unclear. Therefore, we set out to study the influence of exosomes on the triple-negative breast cancer (TNBC) microenvironment.MethodOne hundred twenty-one exosome-related genes were downloaded from ExoBCD database, and IVL, CXCL13, and AP2S1 were final selected because of the association with TNBC prognosis. Based on the sum of the expression levels of these three genes, provided by The Cancer Genome Atlas (TCGA), and the regression coefficients, an exosome risk score model was established. With the median risk score value, the patients in the two databases were divided into high- and low-risk groups. R clusterProfiler package was employed to compare the different enrichment ways between the two groups. The ESTIMATE and CIBERSORT methods were employed to analyze ESTIMATE Score and immune cell infiltration. Finally, the correlation between the immune checkpoint-related gene expression levels and exosome-related risk was analyzed. The relationship between selected gene expression and drug sensitivity was also detected.ResultsDifferent risk groups exhibited distinct result of TNBC prognosis, with a higher survival rate in the low-risk group than in the high-risk group. The two groups were enriched by immune response and biological process pathways. A better overall survival (OS) was demonstrated in patients with high scores of immune and ESTIMATE rather than ones with low scores. Subsequently, we found that CD4+-activated memory T cells and M1 macrophages were both upregulated in the low-risk group, whereas M2 macrophages and activated mast cell were downregulated in the low-risk group in patients from the TCGA and GEO databases, respectively. Eventually, four genes previously proposed to be targets of immune checkpoint inhibitors were evaluated, resulting in the expression levels of CD274, CTLA4, LAG3, and TIM3 being higher in the low-risk group than high-risk group.ConclusionThe results of our study suggest that exosome-related risk model was related to the prognosis and ratio of immune cell infiltration in patients with TNBC. This discovery may make contributions to improve immunotherapy for TNBC.

MicroRNA Delivery by Graphene-Based Complexes into Glioblastoma Cells.

Glioblastoma (GBM) is the most common primary and aggressive tumour in brain cancer. Novel therapies, despite achievements in chemotherapy, radiation and surgical techniques, are needed to improve the treatment of GBM tumours and extend patients’ survival. Gene delivery therapy mostly uses the viral vector, which causes serious adverse events in gene therapy. Graphene-based complexes can reduce the potential side effect of viral carries, with high efficiency of microRNA (miRNA) or antisense miRNA delivery to GBM cells. The objective of this study was to use graphene-based complexes to induce deregulation of miRNA level in GBM cancer cells and to regulate the selected gene expression involved in apoptosis. The complexes were characterised by Fourier transform infrared spectroscopy (FTIR), scanning transmission electron microscopy and zeta potential. The efficiency of miRNA delivery to the cancer cells was analysed by flow cytometry. The effect of the anticancer activity of graphene-based complexes functionalised by the miRNA sequence was analysed using 2,3-bis-(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxyanilide salt (XTT) assays at the gene expression level. The results partly explain the mechanisms of miRNA deregulation stress, which is affected by graphene-based complexes together with the forced transport of mimic miR-124, miR-137 and antisense miR-21, -221 and -222 as an anticancer supportive therapy.

Infection of the Western Flower Thrips, Frankliniella occidentalis, by the Insect Pathogenic Fungus Beauveria bassiana

The western flower thrips, Frankliniella occidentalis, is an aggressive agricultural insect pest causing significant damage to a wide range of fruit, vegetable, and ornamental crops. Beauveria bassiana is a broad-host-range entomopathogenic fungus capable of infecting and killing F. occidentalis. Infection of thrips by B. bassiana strain BbYT12 using a concentration of 1 × 108 conidia/mL resulted in 81.48% mortality in adults in 6 d (LT50 = 90 ± 15.1 h). Scanning electron microscopy of the infection process revealed preferential adhesion and germination of fungal spores to inter-segmental folds or grooves on the insect body surface with penetrating germlings and extended hyphae visualized during the initial stages of infection (6–24 h). Histological analyses showed the appearance of in vivo hyphal bodies in sagittal sections and the fat body as early as 24 h post-infection. Within 72 h, hyphal bodies and hyphae could be found throughout the infected organism including in the midgut, Malphigian tubules, alimentary canal, ovarioles (in females), and an extended hyphal network could be seen on insect cadavers (&gt;72 h post-infection). Real-time RT-PCR analyses of the expression of select genes implicated in virulence including the Pr1 protease, beauvericin synthase, involved in the production of the secondary metabolite beauvericin, two cytochrome P450 monooxygenases implicated in cuticular hydrocarbon degradation, two multidrug efflux proteins, a perilipin involved in lipid storage, and the Hog1 MAP kinase and protein kinase A signaling factors revealed discrete patterns of infection-time dependent expression. These data provide basic insights into the process of B. bassiana infection of F. occidentalis.

In vitro Maturation of Buffalo Oocytes and Expression of Selected Biomarker Candidate Genes

Background: Number of genes expressed during in vitro maturation (IVM) of which selected genes can be used as the potential biomarkers of oocyte competence. Hence, this study was planned to evaluate selected gene expression of GDF9, HAS2, SPRY, ARHGAP22, COL18A1 and GPC4 in IVM and immature cumulus oocyte complexes (COCs). Methods: The COCs were recovered from slaughter origin ovaries of buffaloes. Of which first three grade COCs were randomly allotted in immature (IMT; n=217) and IVM group (n=272). IVM of COCs was performed under drops of BO-maturation media in CO2 incubator at 39.0°C for 24 hours. The expression of genes was evaluated using qPCR and the relative expression of each gene was calculated using the ΔΔCt method with efficiency correction. The logarithmic transformation of fold change of each candidate genes in the IVM group was computed against the IMT group using the Ct values. Result: The expression obtained for IVM group of earlier reported up-regulated genes (GDF9, HAS2, SPRY1) was higher (upto 10xfold) compared to the IMT group. Relatively lower expression was observed for the rest of the three candidate genes (ARHGAP22, COL18A1, GPC4) in the bovine transcripts of oocyte which were earlier also reported as down regulated.

Spaceflight Modulates the Expression of Key Oxidative Stress and Cell Cycle Related Genes in Heart.

Spaceflight causes cardiovascular changes due to microgravity-induced redistribution of body fluids and musculoskeletal unloading. Cardiac deconditioning and atrophy on Earth are associated with altered Trp53 and oxidative stress-related pathways, but the effects of spaceflight on cardiac changes at the molecular level are less understood. We tested the hypothesis that spaceflight alters the expression of key genes related to stress response pathways, which may contribute to cardiovascular deconditioning during extended spaceflight. Mice were exposed to spaceflight for 15 days or maintained on Earth (ground control). Ventricle tissue was harvested starting ~3 h post-landing. We measured expression of select genes implicated in oxidative stress pathways and Trp53 signaling by quantitative PCR. Cardiac expression levels of 37 of 168 genes tested were altered after spaceflight. Spaceflight downregulated transcription factor, Nfe2l2 (Nrf2), upregulated Nox1 and downregulated Ptgs2, suggesting a persistent increase in oxidative stress-related target genes. Spaceflight also substantially upregulated Cdkn1a (p21) and cell cycle/apoptosis-related gene Myc, and downregulated the inflammatory response gene Tnf. There were no changes in apoptosis-related genes such as Trp53. Spaceflight altered the expression of genes regulating redox balance, cell cycle and senescence in cardiac tissue of mice. Thus, spaceflight may contribute to cardiac dysfunction due to oxidative stress.

Oxidative Phosphorylation Is Dysregulated Within the Basocortical Circuit in a 6-month old Mouse Model of Down Syndrome and Alzheimer's Disease.

Down syndrome (DS) is the primary genetic cause of intellectual disability (ID), which is due to the triplication of human chromosome 21 (HSA21). In addition to ID, HSA21 trisomy results in a number of neurological and physiological pathologies in individuals with DS, including progressive cognitive dysfunction and learning and memory deficits which worsen with age. Further exacerbating neurological dysfunction associated with DS is the concomitant basal forebrain cholinergic neuron (BFCN) degeneration and onset of Alzheimer’s disease (AD) pathology in early mid-life. Recent single population RNA sequencing (RNA-seq) analysis in the Ts65Dn mouse model of DS, specifically the medial septal cholinergic neurons of the basal forebrain (BF), revealed the mitochondrial oxidative phosphorylation pathway was significantly impacted, with a large subset of genes within this pathway being downregulated. We further queried oxidative phosphorylation pathway dysregulation in Ts65Dn mice by examining genes and encoded proteins within brain regions comprising the basocortical system at the start of BFCN degeneration (6 months of age). In select Ts65Dn mice we demonstrate significant deficits in gene and/or encoded protein levels of Complex I-V of the mitochondrial oxidative phosphorylation pathway in the BF. In the frontal cortex (Fr Ctx) these complexes had concomitant alterations in select gene expression but not of the proteins queried from Complex I-V, suggesting that defects at this time point in the BF are more severe and occur prior to cortical dysfunction within the basocortical circuit. We propose dysregulation within mitochondrial oxidative phosphorylation complexes is an early marker of cognitive decline onset and specifically linked to BFCN degeneration that may propagate pathology throughout cortical memory and executive function circuits in DS and AD.

Molecular Characteristics of Choledochal Cysts in Children: Transcriptome Sequencing.

A choledochal cyst (CC) is a common congenital biliary disease in children, yet the underlying molecular bases for the cystic and fusiform clinical subtypes are unknown. RNA sequencing (RNA-seq) has been performed on 22 high-quality CC samples, including 12 cystic CC and 10 fusiform CC samples, to search for molecular features. Weighted gene co-expression network analysis (WGCNA) was performed to identify key modules associated with clinical subtypes. Bioinformatic analyses were conducted to elucidate potential mechanisms. Then, we constructed protein–protein interaction (PPI) networks to identify candidate hub genes related to CC. Finally, we used the support vector machine (SVM) to eliminate redundant features and screen out the hub genes. The selected gene expression was determined in CC patients through quantitative real-time polymerase chain reaction (PCR). A total of 6,463 genes were found to be aberrantly expressed between cystic CC and fusiform CC. Twelve co-expression modules that correlated with clinical subtypes of CC were identified and assigned representative colors. Among the 12 modules, the blue module was considered the key module. Two functionally distinct sets of dysregulated genes have been identified in two major subtypes, metabolism-related genes in cystic CC and immune-related genes in fusiform CC. A total of 20 candidate hub genes that were correlated with clinical subtypes were found in the blue module. In addition, we found ERBB2 and WNT11 that have not been studied in CC and verified their differential expression in CC through quantitative real-time PCR experiments. For the first time, we have described the transcriptome characteristics of CC. These results suggest that cystic CC and fusiform CC have different molecular mechanisms. The bi-omics-identified novel candidate genes and pathways might be helpful for personalized treatment and are of great clinical significance for CC.