Variation In Gene Expression Profiles Research Articles

Transcriptome meta-analysis and validation to discovery of hub genes and pathways in focal and segmental glomerulosclerosis

BackgroundFocal segmental glomerulosclerosis (FSGS), a histologic pattern of injury in the glomerulus, is one of the leading glomerular causes of end-stage renal disease (ESRD) worldwide. Despite extensive research, the underlying biological alterations causing FSGS remain poorly understood. Studying variations in gene expression profiles offers a promising approach to gaining a comprehensive understanding of FSGS molecular pathogenicity and identifying key elements as potential therapeutic targets. This work is a meta-analysis of gene expression profiles from glomerular samples of FSGS patients. The main aims of this study are to establish a consensus list of differentially expressed genes in FSGS, validate these findings, understand the disease’s pathogenicity, and identify novel therapeutic targets.MethodsAfter a thorough search in the GEO database and subsequent quality control assessments, seven gene expression datasets were selected for the meta-analysis: GSE47183 (GPL14663), GSE47183 (GPL11670), GSE99340, GSE108109, GSE121233, GSE129973, and GSE104948. The random effect size method was applied to identify differentially expressed genes (meta-DEGs), which were then used to construct a regulatory network (STRING, MiRTarBase, and TRRUST) and perform various pathway enrichment analyses. The expression levels of several meta-DEGs, specifically ADAMTS1, PF4, EGR1, and EGF, known as angiogenesis regulators, were analyzed using quantitative reverse transcription polymerase chain reaction (RT-qPCR).ResultsThe identified 2,898 meta-DEGs, including 665 downregulated and 669 upregulated genes, were subjected to various analyses. A co-regulatory network comprising 2,859 DEGs, 2,688 microRNAs (miRNAs), and 374 transcription factors (TFs) was constructed, and the top molecules in the network were identified based on degree centrality. Part of the pathway enrichment analysis revealed significant disruption in the angiogenesis regulatory pathways in the FSGS kidney. The RT-qPCR results confirmed an imbalance in angiogenesis pathways by demonstrating the differential expression levels of ADAMTS1 and EGR1, two key angiogenesis regulators, in the FSGS condition.ConclusionIn addition to presenting a consensus list of differentially expressed genes in FSGS, this meta-analysis identified significant distortions in angiogenesis-related pathways and factors in the FSGS kidney. Targeting these factors may offer a viable strategy to impede the progression of FSGS.

A brief history of somatostatin interneuron taxonomy or: how many somatostatin subtypes are there, really?

We provide a brief (and unabashedly biased) overview of the pre-transcriptomic history of somatostatin interneuron taxonomy, followed by a chronological summary of the large-scale, NIH-supported effort over the last ten years to generate a comprehensive, single-cell RNA-seq-based taxonomy of cortical neurons. Focusing on somatostatin interneurons, we present the perspective of experimental neuroscientists trying to incorporate the new classification schemes into their own research while struggling to keep up with the ever-increasing number of proposed cell types, which seems to double every two years. We suggest that for experimental analysis, the most useful taxonomic level is the subdivision of somatostatin interneurons into ten or so "supertypes," which closely agrees with their more traditional classification by morphological, electrophysiological and neurochemical features. We argue that finer subdivisions ("t-types" or "clusters"), based on slight variations in gene expression profiles but lacking clear phenotypic differences, are less useful to researchers and may actually defeat the purpose of classifying neurons to begin with. We end by stressing the need for generating novel tools (mouse lines, viral vectors) for genetically targeting distinct supertypes for expression of fluorescent reporters, calcium sensors and excitatory or inhibitory opsins, allowing neuroscientists to chart the input and output synaptic connections of each proposed subtype, reveal the position they occupy in the cortical network and examine experimentally their roles in sensorimotor behaviors and cognitive brain functions.

Breast Cancer Plasticity after Chemotherapy Highlights the Need for Re-Evaluation of Subtyping in Residual Cancer and Metastatic Tissues.

This research paper presents a novel approach to identifying biomarkers that can be used to prognosticate patients with triple-negative breast cancer (TNBC) eligible for neoadjuvant therapy. The study utilized survival and RNA sequencing data from a cohort of TNBC patients and identified 276 genes whose expression was related to survival in such patients. The gene expression data were then used to classify patients into two major groups based on the presence or absence of Wingless/Integrated-pathway (Wnt-pathway) and mesenchymal (Mes) markers (Wnt/Mes). Patients with a low expression of Wnt/Mes-related genes had a favorable outcome, with no deaths observed during follow-up, while patients with a high expression of Wnt/Mes genes had a higher mortality rate of 50% within 19 months. The identified gene list could be validated and potentially used to shape treatment options for TNBC patients eligible for neoadjuvant therapy providing valuable insights into the development of more effective treatments for TNBC. Our data also showed significant variation in gene expression profiles before and after chemotherapy, with most tumors switching to a more mesenchymal/stem cell-like profile. To verify this observation, we performed an in silico analysis to classify breast cancer tumors in Prediction Analysis of Microarray 50 (PAM50) molecular classes before treatment and after treatment using gene expression data. Our findings demonstrate that following drug intervention and metastasis, certain tumors undergo a transition to alternative subtypes, resulting in diminished therapeutic efficacy. This underscores the necessity for reevaluation of patients who have experienced relapse or metastasis post-chemotherapy, with a focus on molecular subtyping. Tailoring treatment strategies based on these refined subtypes is imperative to optimize therapeutic outcomes for affected individuals.

An-Gong-Niu-Huang-Wan (AGNHW) regulates cerebral blood flow by improving hypoperfusion, cerebrovascular reactivity and microcirculation disturbances after stroke

BackgroundThe restoration of cerebrovascular regulation and improvement of cerebral blood flow in ischaemic regions are crucial for improving the clinical prognosis after stroke. An-Gong-Niu-Huang-Wan (AGNHW) is a famous traditional compound Chinese medicine that has been used for over 220 years to treat acute ischaemic stroke; however, its role in the regulation of cerebral blood flow is still unclear. The aim of the present study was to investigate the regulatory effect of AGNHW on cerebral blood flow and microcirculation after ischaemic stroke and to elucidate the underlying mechanisms involved.MethodsMale C57BL/6 mice were subjected to distal middle cerebral artery occlusion (dMCAO) and randomly assigned to the sham, MCAO, or AGNHW groups. AGNHW was administered intragastrically 1 h after dMCAO. The rotarod test was utilized to evaluate behavioural function; TTC was used to determine the infarct volume; and ischaemic injury was assessed by detecting brain levels of SOD, MDA and NO. Then, cortical perfusion and acetazolamide-induced cerebrovascular reactivity were assessed using laser speckle contrast imaging, and the velocity and flux of red blood cells in cortical capillaries were detected using two-photon laser scanning microscopy. In addition, we employed RNA-Seq to identify variations in gene expression profiles and assessed endothelium-dependent changes in microcirculatory dysfunction by measuring vasoactive mediator levels.ResultsAGNHW significantly increased cerebral blood flow, reduced the infarct volume, and promoted functional recovery after cerebral ischaemia. AGNHW increased the velocity and flux of red blood cells in capillaries and improved cerebrovascular reactivity in the ischaemic cortex. Furthermore, AGNHW regulated endothelium-dependent microcirculation, as evidenced by decreases in the expression of endothelins (Edn1, Edn3 and Ednrb) and the ratios of brain and serum TXB2/6-keto-PGF1α and ET-1/CGRP.ConclusionsAGNHW improved cerebral hypoperfusion, regulated cerebrovascular reactivity and attenuated microcirculatory dysfunction within the ischaemic cortex after stroke. This outstanding effect was achieved by modulating the expression of genes related to vascular endothelial cell function and regulating endothelium-dependent vasoactive mediators.

Prognostic impact of MYD88 and TP53 mutations in diffuse large B Cell lymphoma

Diffuse large B cell lymphoma (DLBCL) is the most common subtype of lymphoma. It is a highly heterogeneous lymphoid neoplasm, with variations in gene expression profiles and genetic alterations. MYD88 and TP53 genes are common to be expressed and mutated in DLBCL patients with controversy regarding their role in prognosis and survival. This study aims to determine the predictive and prognostic role of MYD88 and TP53 gene mutation in DLBCL. A prospective cohort study was conducted on 50 patients who were diagnosed with DLBCL and 30 healthy individuals to assess the sensitivity and specificity of MYD88 and TP53 genetic mutations. MYD88 and TP53 gene mutations were more sensitive, specific, and accurate in predicting overall mortality and disease progression in comparison with the international prognostic index. Mutant MYD88 and TP53 showed their prognostic importance for worse objective response rates and survival outcomes. Both mutant MYD88 and TP53 were associated with worse ORR. There was a significant statistical difference for both MYD88 and TP53 with regard to 2-year PFS and 2-year OS rate. Hence, both mutant MYD88 and TP53 can be used in predicting disease progression and overall mortality.

Acute ischemic stroke: how to investigate the association between disease etiology and gene expression profiles

Background: Acute ischemic stroke (AIS) represents one of the principal causes of neurological morbidity and mortality worldwide. For a prompt and efficient cerebral blood restoration, intravenous treatment with rt-PA is often combined with mechanical thrombectomy (MT) which provides cerebral thrombi (CT) as study material, allowing the investigation of its cellular composition, morphological and histopathological features. Indeed, the determination of stroke etiology, typically defined by the TOAST classification, is paramount for prognostic factors, outcome, and management of the event. Aim of the study is therefore to highlight and analyze gene expression profiles in thrombotic tissue and peripheral blood (PB) in the comparison between strokes of cardioembolic (CE) and atherosclerotic (LAA) origin. Methods: We performed gene expression profiles of 92 patients. CT were stored in RNA later and RNA was extracted by PAX gene blood miRNA kit. The global gene expression profile was assessed by Affymetrix technology using GeneChip Human Transcriptome Array 2.0 combined with Affymetrix Transcriptome Analysis Console (TAC) Software. Results: Currently, we focused our attention on CT data analysis. The analysis revealed a significant difference (p-value<0.05 and FoldChange=2 as threshold) in gene expression when comparing LAA and CE stroke. In particular, from CT of atherosclerotic origin emerges an overexpression of 1766 genes. Prominent among them are genes such as MMP-9, TGFB, TGFBR and CXCL1, primarily involved in neutrophil-mediated immunity, Blood-Brain Barrier (BBB) disruption processes, and associated with atherosclerotic plaque instability and related to poor neurological outcome, suggesting a deleterious role in human brain injury. As concerns CE patients, 57 genes mainly involved in transcriptional regulatory processes turn out to be significantly overexpressed. Conclusions: Transcriptome profiling is a powerful weapon for revealing expression patterns associated with complex disorders. The variation of gene expression profiles confirmed and extended several known pathophysiological mechanisms and may be one way of delineating different stroke etiology.

Comparative transcriptome analysis of molecular mechanisms underlying adventitious root developments in Huangshan Bitter tea (Camellia gymnogyna Chang) under red light quality.

As the formation of adventitious roots (AR) is an important component of in vitro regeneration of tea plants, the propagation and preservation of Huangshan Bitter tea (Camellia gymnogyna Chang) cuttings have been hindered due to its lower rooting rate. As light is a crucial environmental factor that affects AR formation, this study aimed to investigate the special role of red light (RL) in the formation of AR in Huangshan Bitter tea plants, which has not been well understood. Huangshan Bitter tea plants were induced with white light (control, WL) and red light (660 nm, RL) qualities 36 days after induced treatment (DAI) to investigate dynamic AR formation and development, anatomical observation, hormones content change, and weighted gene co-expression network analysis (WGCNA) of the transcriptome. Results showed that RL promoted the rooting rate and root characteristics compared to WL. Anatomical observations demonstrated that root primordium was induced earlier by RL at the 4 DAI. RL positively affected IAA, ZT and GA3 content and negatively influenced ABA from the 4 to 16 DAI. RNA-seq and analysis of differential expression genes (DEGs) exhibited extensive variation in gene expression profiles between RL and WL. Meanwhile, the results of WGCNA and correlation analysis identified three highly correlated modules and hub genes mainly participated in 'response to hormone', 'cellular glucan metabolic progress', and 'response to auxin'. Furthermore, the proportion of transcription factors (TFs) such as ethylene response factor (ERF), myeloblastosis (MYB), basic helix-loop-helix (bHLH), and WRKYGQK (WRKY) were the top four in DEGs. These results suggested that the AR-promoting potential of red light was due to complex hormone interactions in tea plants by regulating the expression of related genes. This study provided an important reference to shorten breeding cycles and accelerate superiority in tea plant propagation and preservation.

Biologic Relevance of Variable Immunoglobulin Gene Diversity in B-Lymphoblastic Leukemia

Background: It remains unclear whether the variable biologic features of B-lymphoblastic leukemia (B-ALL) reflect distinct cells of origin in the hierarchy of early B cell development. Recombination activating genes (RAG) rearrange the immunoglobulin heavy chain (IgH) locus in B lymphoid progenitors, resulting in unique variable (Vh), diversity (D), and joining (Jh) gene rearrangements. In B-ALL, dominant IgH sequences are used for clone detection and surveillance. Further, subclone diversity resulting from RAG-mediated Vh gene switching is a prevalent feature of many B-ALLs, but its biologic basis has not been determined. To test whether discrete properties of each B-ALL reflect derivation from distinct B cell stages, we assessed the relationship between IgH variable gene (IGHV) characteristics and gene expression. Methods: We used targeted IgH sequencing (Illumina MiSeq) to identify dominant IgH clones and to assess the extent of IgH subclone diversification in pre-treatment specimens from 22 patients with B-ALL. We compared the gene expression profile (GEP) of cases with Vh-switch-mediated subclone diversity to those without. We then used single-cell RNA sequencing (scRNAseq) of 5 patients' B-ALL to test whether the capacity to undergo IgH diversification is patient-specific or clone-intrinsic, and we characterized variation in GEP between intrapatient IgH clones. Results: We discovered that each B-ALL with at least 1 dominant IgH clone demonstrates either minimal or extensive RAG-mediated subclone evolution. Gene set enrichment analysis (GSEA) revealed that genes associated with distinct B cell developmental stages distinguish these 2 groups. We detected dominant IgH clones in 19 of 22 patients (86.4%). In patients with 'diverse' B-ALL characterized by RAG-mediated intra-clonal diversification (N=9; 40.9%), we observed extensive subclone evolution arising from Vh recombination (median: 482 subclones; range: 2-2600) and enriched expression of genes associated with regulation of a hematopoietic stem cell state. In those without diversity (N=10; 45.5%) - the 'homogeneous' cohort - leukemia cells showed enriched expression of genes involving cell fate commitment. GSEA further revealed biologically distinct phenotypes between groups, as reflected in enrichment in the diverse cohort of Hallmark gene sets involving key cellular metabolic pathways including oxidative phosphorylation and glycolysis. Furthermore, distinct dominant IgH clones from a single patient could be individually diverse or homogenous with respect to Vh-switch-mediated subclone evolution. scRNAseq revealed that dominant IgH clones inconsistently express IGHV mRNA and differ from one another in their gene expression. In 4 of 5 patients, we detected IgH complementarity-determining region 3 (CDR3) mRNA expression from at least 1 clone. The GEP of IGHV-expressing leukemia cells was clearly resolved from other B-ALL cells in 3 of these 4 cases, with distinctive gene expression characterized by RAG1 pathway up-expression. Conclusions: Tumor evolution requires genetic diversity and is a fundamental property of cancer. Using primary B-ALL specimens, we assessed RAG-mediated intraclonal IgH variation to characterize the extent of diversity in B-ALL and to discover how it relates to fundamental biologic features of this common pediatric malignancy. We found that B-ALL may be divided into 2 groups: leukemias with RAG-mediated intra-clonal IGHV sequence diversification ('diverse') and those lacking diversity ('homogeneous'). GEP suggests that the difference in diversity of the IGHV repertoire reflects the B cell stage at leukemic initiation: B-ALL specimens with subclone diversity had a GEP suggestive of an earlier differentiation state compared to specimens with a homogenous IGHV repertoire. Furthermore, we discovered that a single leukemia can be simultaneously composed of both genetically stable and genetically diverse clonal populations. Our single-cell GEP data reveal that: 1) even within a single patient's leukemia, genetically-distinct clonal populations demonstrate a distinct profile of mRNA expression, and 2) B-ALL cells which express IGHV mRNA are characterized by greater expression of RAG pathway-related genes. Our findings suggest that variability in IGHV diversification in B-ALL is a useful marker of biological properties related to the B cell stage of origin.

BIOM-49. A PILOT STUDY OF CEREBROSPINAL FLUID EXOSOMAL SMALL RNA-SEQUENCING IN PEDIATRIC MEDULLOBLASTOMA PATIENTS ON THE NEXT CONSORTIUM “HEAD START” 4 PROTOCOL

Abstract BACKGROUND Head Start 4 is a randomized clinical trial to determine whether dose-intensive tandem consolidation, compared with a single cycle, with autologous hematopoietic progenitor cell rescue provides a survival benefit in pediatric patients with medulloblastoma or other embryonal tumors. The trial incorporates upfront molecular subgrouping and non-mandatory, prospective blood and cerebrospinal fluid (CSF) collection. This pilot study aimed to identify exosomal non-coding RNAs (exo-ncRNAs) that might serve as novel diagnostic and/or treatment response biomarkers. METHODS CSF(1-2mLs) from 11 controls (non-tumor) and 27 medulloblastoma participants including 23 obtained at baseline, 22 at the end of induction, 3 post-consolidation, and 4 relapse time points, were profiled. Exosome isolation and small RNA-sequencing were performed by System Biosciences. Differential gene expression (DGE) was performed in R (DESeq2). Variations in gene expression profiles between samples were visualized using principal component analysis. RESULTS After limiting to ncRNAs with expression of 2 counts per million in 50% or more of the samples in each comparison, ~9,500 ncRNAs were detected. DGE analyses revealed 118 ncRNAs with log2 fold change(FC) >2 and 1 ncRNA with log2FC< -2 in baseline CSF samples compared to controls. In contrast, 11 ncRNAs(log2FC >2) and 1 ncRNA(log2FC< -2) were detected in end of induction CSF samples compared to controls. Comparing end of induction to baseline CSF samples accounting for paired samples, 0 ncRNAs(log2FC >2) and 52 ncRNAs(log2FC< -2) were detected. CONCLUSIONS Overall, our data indicate that exosomal small RNA-sequencing of limited CSF volumes is feasible. Differential expression and distinct clustering between tumor baseline samples compared to non-tumor controls was observed. CSF-derived exo-ncRNAs at end of induction also demonstrated “normalization” of ncRNA profiles, signifying CSF biomarkers may serve a role in diagnosis and molecular response assessment. A comprehensive analysis including multi-marker predictive model development and molecular subgrouping will be undertaken at completion of study enrollment.

Phenotypic characterization of Ghanaian P. falciparum clinical isolates reveals a homogenous parasite population.

BackgroundErythrocyte invasion by P. falciparum involves functionally overlapping interactions between the parasite’s ligands and the erythrocyte surface receptors. While some P. falciparum isolates necessarily engage the sialic acid (SA) moieties of the erythrocytes during the invasion, others use ligands whose binding is independent of SA for successful invasion. Deciphering the major pathway used by P. falciparum clinical isolates represent a key step toward developing an efficient blood stage malaria vaccine.MethodsWe collected a total of 156 malaria-infected samples from Ghanaian children aged 2 to 14 years and used a two-color flow cytometry-based invasion assay to assess the invasion phenotype diversity of Ghanaian P. falciparum clinical isolates. Anti-human CR1 antibodies were used to determine the relative contribution of the PfRh4-CR1 interaction in the parasites invasion phenotype and RT-qPCR was used to assess the expression levels of key invasion-related ligands.ResultsOur findings show no clear association between demographic or clinical data and existing reports on the malaria transmission intensity. The complete invasion data obtained for 156 isolates, showed the predominance of SA-independent pathways in Ghanaian clinical isolates. Isolates from Hohoe and Navrongo had the highest diversity in invasion profile. Our data also confirmed that the PfRh4-CR1 mediated alternative pathway is important in Ghanaian clinical isolates. Furthermore, the transcript levels of ten invasion-related genes obtained in the study showed little variations in gene expression profiles within and between parasite populations across sites.ConclusionOur data suggest a low level of phenotypic diversity in Ghanaian clinical isolates across areas of varying endemicity and further highlight its importance in the quest for new intervention strategies, such as the investigation of blood-stage vaccine targets, particularly those targeting specific pathways and able to trigger the stimulation of broadly neutralizing invasion antibodies.

Low humidity altered the gene expression profile of keratinocytes in a three-dimensional skin model.

The skin is constantly exposed to various external stimuli including humidity variations. Low humidity affects skin properties such as decreased water content of the stratum corneum, reduced skin elasticity, and itching. However, the effects of humidity on the skin cells are not completely understood. This study aimed to investigatehow low humidity affects keratinocytes of the skin. In the present study, the effects of dry environment on the gene expression profile of epidermal keratinocytes were demonstrated using a three-dimensional skin model (3D-skin), composed of keratinocytes. Exposure of 3D-skin to low humidity (relative humidity ~ 10%) increased the expression levels of various genes, including those related to signal transduction and immune system. Accordingly, p38 mitogen-activated protein kinase (MAPK) signaling in keratinocytes of the 3D-skin was activated in response to low humidity for 30min. Additionally, several chemokines, such as chemokine (C-X-C motif) ligand 1 (CXCL1) and Chemokine (C-C motif) ligand 20 (CCL20), were up regulated after 3h of exposure to low humidity. We hypothesize that increased chemokine production may affect the immune system of the whole skin through chemoattractants. Our findings imply that keratinocytes sense low humidity and resultant activation of some cell-signaling pathways leads to variations in gene expression profiles including various chemokines. We provide evidence that keratinocytes adapt to external humidity variations.

Transcriptome-based identification and expression analysis of the glutathione S-transferase (GST) family in tree peony reveals a likely role in anthocyanin transport

For red-flowered cultivars of tree peony (Paeonia suffruticosa), anthocyanin content is a critical factor determining the different petal pigmentations. Glutathione S-transferases (GSTs) are ubiquitous and multifunctional conjugating proteins that may be responsible for the transport of anthocyanin pigments from the cytoplasm to vacuole. The underlying function of the GST family in tree peony, however, remains unclear. In this study, we systematically isolated and identified a total of 54 putative full-length PsGST genes through a combination of bioinformatics approaches from transcriptome databases. Intraspecific phylogenetic analyses revealed extensive differentiation in their coding sequences and divided them into 10 of the 14 known classes of plant GSTs. The phylogenetic relationships, evolutionary characteristics, protein domain, and motif organization were clearly conserved among the different phylogenetic subclasses. The results of the RNA-seq and quantitative real-time polymerase chain reaction experiments exhibited extensive variation in gene expression profiles among different developmental stages and varieties. Furthermore, the phylogenetic relationships, expression profiles, protein interactions, weighted gene co-expression network analysis, and correlation analysis results suggested that PsGSTF3 (Unigene 0064200) is a candidate participant in anthocyanin transport and the promotion of pigment accumulation, exhibiting a strong positive correlation with anthocyanin content among different tissues (r = 0.908⁎⁎) and an increasing rate of anthocyanin content during the flower developmental process (r = 0.961*). These results furthered our understanding of the transport and accumulation functions of the GST family as well as the enhancement of tree peony breeding through molecular biology techniques.

Identification of Hub Genes and Key Pathways Associated with Follicular Lymphoma

Follicular lymphoma (FL) is the second most prevalent form of non-Hodgkin lymphoma (NHL) and accounts for almost 20% of all NHL cases. Although FL patients' overall survival rates have steadily increased, there is still no accepted standard of care for individuals who experience recurrence or resistance to treatment. Hence, it is needed to evaluate the precise molecular cascades underlying FL to develop efficient diagnostic and treatment approaches. Herein, we aimed to evaluate variations in gene expression profiles, explore the underlying mechanisms, and find new FL targets. In the present study, Gene Expression Omnibus (GEO) database was employed to evaluate microarray datasets including GSE32018 and GSE55267. R software was employed to evaluate differentially expressed genes (DEGs) between FL and noncancer samples. The DEGs were evaluated using GO, KEGG pathway enrichment analysis, and PPI network to evaluate hub genes, which were then, examined using gene function enrichment analysis. According to the obtained results, a total of 190 upregulated and 162 downregulated DEGs were evaluated. Following the generation of PPI networks, 15 hub genes in highly connected upregulated DEGs were selected including FN1, MMP9, CCL2, CD8A, POSTN, CCR5, COL3A1, CXCL12, VCAM1, COL1A2, CCL5, SPARC, TIMP1, CXCL9, and IL18. The GO enrichment evaluation of the underlined hub genes indicated that the immunological response was the most considerably enriched term. Twelve significant cascades were found using the KEGG pathway analysis, most of which were linked to cellular structure and immunity. Our findings suggested that FN1, SPARC, POSTN, MMP9, and VCAM1 genes are potential biomarkers of FL, and cellular immunity contributes to the pathogenesis of FL. Moreover, the unique DEGs and cascades found in the present study may present new perspectives on the molecular basis of FL's underlying mechanisms as well as a new understanding of FL's future precise management.

Single-cell RNA sequencing of freshly isolated bovine milk cells and cultured primary mammary epithelial cells

Bovine mammary function at molecular level is often studied using mammary tissue or primary bovine mammary epithelial cells (pbMECs). However, bulk tissue and primary cells are heterogeneous with respect to cell populations, adding further transcriptional variation in addition to genetic background. Thus, understanding of the variation in gene expression profiles of cell populations and their effect on function are limited. To investigate the mononuclear cell composition in bovine milk, we analyzed a single-cell suspension from a milk sample. Additionally, we harvested cultured pbMECs to characterize gene expression in a homogeneous cell population. Using the Drop-seq technology, we generated single-cell RNA datasets of somatic milk cells and pbMECs. The final datasets after quality control filtering contained 7,119 and 10,549 cells, respectively. The pbMECs formed 14 indefinite clusters displaying intrapopulation heterogeneity, whereas the milk cells formed 14 more distinct clusters. Our datasets constitute a molecular cell atlas that provides a basis for future studies of milk cell composition and gene expression, and could serve as reference datasets for milk cell analysis.

Growth, phytochemical and gene expression changes related to the secondary metabolite synthesis of Solanum viarum Dunal

Solanum viarum Dunal, is an important medicinal plant widely used as a source of raw material for the steroidal drug industry. Out of various steroidal precursors, solasodine, an analogue of diosgenin is the most important source of raw material for the synthesis of steroidal drugs. In the present study, growth and phytochemical variations in different tissue (leaves, stem, roots, and berries) of two contrasting genotypes, prickled and prickleless Solanum viarum were evaluated under in vitro and field conditions. Significant variation in growth, yield and contents of glycoalkaloids, phenolics, and flavonoids were evident between two genotypes under in vitro and field conditions. Prickleless genotypes showed improved growth parameters both under in vitro and field conditions, that helps in contributing to higher yield over prickled plants. Tissue-specific chemical analysis revealed that the leaves and roots of prickleless plants serve as a better repertoire for bioactive phytomolecules. The vegetative parts of in vitro grown 50 days old prickleless plants showed comparable/higher metabolite content than 7–8 month old field-grown plants. Hence it can be used as an alternative production platform for further upscaling, elicitation, and precursor feeding targets that enhances its commercial utility. The expression analysis of seven genes involved in the regulation of important metabolite biosynthesis in both prickled and prickleless genotype of Solanum viarum was also examined. The diverse metabolite profiles are correlated with variations in gene expression profiles. This study provides information about the key metabolites and its biosynthetic pathway genes, which could be useful for the selection of an improved prickleless genotype (“Nishkantak”) of Solanum viarum.

PCR Array Technology in Biopsy Samples Identifies Up-Regulated mTOR Pathway Genes as Potential Rejection Biomarkers After Kidney Transplantation.

Background: Antibody-mediated rejection (AMR) is the major cause of kidney transplant rejection. The donor-specific human leukocyte antigen (HLA) antibody (DSA) response to a renal allograft is not fully understood yet. mTOR complex has been described in the accommodation or rejection of transplants and integrates responses from a wide variety of signals. The aim of this study was to analyze the expression of the mTOR pathway genes in a large cohort of kidney transplant patients to determine its possible influence on the transplant outcome.Methods: A total of 269 kidney transplant patients monitored for DSA were studied. The patients were divided into two groups, one with recipients that had transplant rejection (+DSA/+AMR) and a second group of recipients without rejection (+DSA/–AMR and –DSA/–AMR, controls). Total RNA was extracted from kidney biopsies and reverse transcribed to cDNA. Human mTOR-PCR array technology was used to determine the expression of 84 mTOR pathway genes. STRING and REVIGO software were used to simulate gene to gene interaction and to assign a molecular function.Results: The studied groups showed a different expression of the mTOR pathway related genes. Recipients that had transplant rejection showed an over-expressed transcript (≥5-fold) of AKT1S1, DDIT4, EIF4E, HRAS, IGF1, INS, IRS1, PIK3CD, PIK3CG, PRKAG3, PRKCB (>12-fold), PRKCG, RPS6KA2, TELO2, ULK1, and VEGFC, compared with patients that did not have rejection. AKT1S1 transcripts were more expressed in +DSA/–AMR biopsies compared with +DSA/+AMR. The main molecular functions of up-regulated gene products were phosphotransferase activity, insulin-like grown factor receptor and ribonucleoside phosphate binding. The group of patients with transplant rejection also showed an under-expressed transcript (≥5-fold) of VEGFA (>15-fold), RPS6, and RHOA compared with the group without rejection. The molecular function of down-regulated gene products such as protein kinase activity and carbohydrate derivative binding proteins was also analyzed.Conclusions: We have found a higher number of over-expressed mTOR pathway genes than under-expressed ones in biopsies from rejected kidney transplants (+DSA/+AMR) with respect to controls. In addition to this, the molecular function of both types of transcripts (over/under expressed) is different. Therefore, further studies are needed to determine if variations in gene expression profiles can act as predictors of graft loss, and a better understanding of the mechanisms of action of the involved proteins would be necessary.

Phenotypic and Transcriptomic Response of the Grasshopper Oedaleus asiaticus (Orthoptera: Acrididae) to Toxic Rutin.

Rutin, a widely distributed phytochemical flavonoid, can be used to control insect pests. In this study, we studied the growth performance of the grasshopper Oedaleus asiaticus Bey-Bienko given xenobiotic rutin using feeding experiments and transcriptomic analysis. O. asiaticus had reduced body size, lower survival rate, and reduced growth performance when fed with xenobiotic rutin. Rutin-fed nymphs had large variation in gene expression profiles, with a total of 308 genes significantly upregulated and 287 genes downregulated. The upregulated genes were significantly enriched in stress resistance-, immune-, and detoxification-related biological processes and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Downregulated genes mainly involved cuticle biosynthesis and nutrition metabolism-related pathways. The quantitative real-time PCR (qRT-PCR) analysis of 15 candidate genes also produced results consistent with the transcriptome data. These results suggested that grasshoppers’ capacity for biosynthesis and nutrition metabolism decreased, and stress resistance and metabolized capacity to toxic substances were significantly induced when O. asiaticus was fed on xenobiotic rutin. Rutin, as a phytotoxin, had detrimental effects and induced changes in gene expression profiles for O. asiaticus. This study can provide a molecular basis and offer future opportunities for the development of rutin-related insecticides and their application to grasshopper control.

Genetic alterations and their clinical implications in DLBCL.

Diffuse large B cell lymphoma (DLBCL) is a highly heterogeneous lymphoid neoplasm with variations in gene expression profiles and genetic alterations, which lead to substantial variations in clinical course and response to therapy. The advent of high-throughput genome sequencing platforms, and especially whole-exome sequencing, has helped to define the genetic landscape of DLBCL. In the past 10 years, these studies have identified many genetic alterations in DLBCL, some of which are specific to B cell lymphomas, whereas others can also be observed in other types of cancer. These aberrations result in altered activation of a wide range of signalling pathways and other cellular processes, including those involved in B cell differentiation, B cell receptor signalling, activation of the NF-κB pathway, apoptosis and epigenetic regulation. Further elaboration of the genetics of DLBCL will not only improve our understanding of disease pathogenesis but also provide further insight into disease classification, prognostication and therapeutic targets. In this Review, we describe the current understanding of the prevalence and causes of specific genetic alterations in DLBCL and their role in disease development and progression. We also summarize the available clinical data on therapies designed to target the aberrant pathways driven by these alterations.

Cold-induced stress alters the dynamics of T helper 1 and T helper 2 cytokine production in a mouse model during Chlamydia muridarum genital infection.

Chlamydia caused by Chlamydia trachomatis is the leading cause of bacterial STDs worldwide and the USA. Although there are more clinical and epidemiological studies of chlamydia genital infection, the effect of stress on chlamydia disease is not well explored. Previous results from our lab show that cold-induced stress results in increased intensity of chlamydia genital infection in mice; however, the mechanisms are unknown. Thelper 1(Th1) is known to be protective against chlamydia, whereas Th2 leads to infection. However, the differentiation of Th1 and Th2 during exposure to cold stress is not well understood. Several studies show GATA-3 and T-bet are associated with Th1 and Th2 cytokine production. The purpose of this study was to evaluate the effect of cold water on the activity off Th1 and Th2 during Chlamydia muridarum genital infection. We hypothesized that cold stress alters the differentiation and variation in gene expression profile of transcription factors and cytokine productions in T cells. T cells isolated from the genital tract were proliferated for 48 h incubated at 37OC and 5% CO2. The mRNA levels and detection of cytokines in culture supernatants was determined by quantitative real time PCR and ELISA, respectively. Our results showed increased IL-4 production, which was associated with upregulated expression of transcription factor GATA-3. In contrast, decreased gamma interferon production was associated with decreased T-bet gene expression in T cells. Based on this data, cold stress modulates the dynamics of signature Th1 and Th2 cytokine productions that are regulated by expression of GATA-3 and T-bet. This work was supported by NIH Grant P20GM103434 to the West Virginia IDeA Network for Biomedical Research Excellence and NIH Grant P20GM103434 awarded to Bluefield State College.

Quality control usage in high-density microarrays reveals differential gene expression profiles in ovarian cancer

There are several existing reports of microarray chip use for assessment of altered gene expression in different diseases. In fact, there have been over 1.5 million assays of this kind performed over the last twenty years, which have influenced clinical and translational research studies. The most commonly used DNA microarray platforms are Affymetrix GeneChip and Quality Control Software along with their GeneChip Probe Arrays. These chips are created using several quality controls to confirm the success of each assay, but their actual impact on gene expression profiles had not been previously analyzed until the appearance of several bioinformatics tools for this purpose. We here performed a data mining analysis, in this case specifically focused on ovarian cancer, as well as healthy ovarian tissue and ovarian cell lines, in order to confirm quality control results and associated variation in gene expression profiles. The microarray data used in our research were downloaded from ArrayExpress and Gene Expression Omnibus (GEO) and analyzed with Expression Console Software using RMA, MAS5 and Plier algorithms. The gene expression profiles were obtained using Partek Genomics Suite v6.6 and data were visualized using principal component analysis, heat map, and Venn diagrams. Microarray quality control analysis showed that roughly 40% of the microarray files were false negative, demonstrating over- and under-estimation of expressed genes. Additionally, we confirmed the results performing second analysis using independent samples. About 70% of the significant expressed genes were correlated in both analyses. These results demonstrate the importance of appropriate microarray processing to obtain a reliable gene expression profile.