Dysregulation Of Gene Expression Research Articles

Intestinal flora induces depression by mediating the dysregulation of cerebral cortex gene expression and regulating the metabolism of stroke patients.

Post-stroke depression (PSD) is a common cerebrovascular complication characterized by complex pathogenesis and poor treatment effects. Here, we tested the influence of differentially expressed genes (DEGs), non-targeted metabolites, and intestinal microbes on the occurrence and development of PSD. We acquired gene expression profiles for stroke patients, depression patients, and healthy controls from the Gene Expression Omnibus database. After screening for DEGs using differential expression analysis, we identified common DEGs in stroke and depression patients that were considered to form the molecular basis of PSD. Functional enrichment analysis of DEGs also revealed that the majority of biological functions were closely related to metabolism, immunity, the nervous system, and microorganisms, and we also collected blood and stool samples from healthy controls, stroke patients, and PSD patients and performed 16S rDNA sequencing and untargeted metabolomics. After evaluating the quality of the sequencing data, we compared the diversity of the metabolites and intestinal flora within and between groups. Metabolic pathway enrichment analysis was used to identify metabolic pathways that were significantly involved in stroke and PSD, and a global metabolic network was constructed to explore the pathogenesis of PSD. Additionally, we constructed a global regulatory network based on 16S rDNA sequencing, non-targeted metabolomics, and transcriptomics to explore the pathogenesis of PSD through correlation analysis. Our results suggest that intestinal flora associates the dysregulation of cerebral cortex gene expression and could potentially promote the occurrence of depression by affecting the metabolism of stroke patients. Our findings may be helpful in identifying new targets for the prevention and treatment of PSD.

Executive Editor-in-Chief’s introduction for This Special Issue

Executive Editor-in-Chief’s introduction for This Special Issue

Dysregulation of Gene Expressions in Multiple Sclerosis: TNFSF13B and Other Candidate Genes.

In previous investigations of combined miRNAs/mRNAs expressions in neurodegenerative diseases like Multiple Sclerosis (MS) and Amyotrophic Lateral Sclerosis (ALS) we have targeted some interesting genes and molecular pathways that needed further confirmation. By nanofluidic qPCR analysis, we aimed to verify the expression of genes that resulted differentially expressed in the previous analyses. Data from MS patients - either the pediatric and the adult occurrence of the disease (adMS and pedMS, respectively) - was compared to age-matched healthy groups. As neurological controls we recruited a cohort of ALS subjects, considering published searches of possible genetic similarities between the two diseases. The main results confirmed the involvement of most of the investigated genes in pedMS and adMS, like BACH2 and MICAL3. On the other hand, suggestive MS candidate genes like TNFSF13B showed an interesting trend possibly influenced by interfering factors, such as concomitant disease-modifying treatments; it is worth noting that TNFSF13B was one of the genes upregulated in ALS compared to age-matched adMS patients, together with the transcription factor TFDP1. Although with caution due to the small sample size, this study confirms the interest in transcriptomic analysis supported by integrated and educated bioinformatics evaluations, to shed further light in complex neurological diseases.

A pleiotropic hypoxia-sensitive EPAS1 enhancer is disrupted by adaptive alleles in Tibetans.

In Tibetans, noncoding alleles in EPAS1-whose protein product hypoxia-inducible factor 2α (HIF-2α) drives the response to hypoxia-carry strong signatures of positive selection; however, their functional mechanism has not been systematically examined. Here, we report that high-altitude alleles disrupt the activity of four EPAS1 enhancers in one or more cell types. We further characterize one enhancer (ENH5) whose activity is both allele specific and hypoxia dependent. Deletion of ENH5 results in down-regulation of EPAS1 and HIF-2α targets in acute hypoxia and in a blunting of the transcriptional response to sustained hypoxia. Deletion of ENH5 in mice results in dysregulation of gene expression across multiple tissues. We propose that pleiotropic adaptive effects of the Tibetan alleles in EPAS1 underlie the strong selective signal at this gene.

Epigenetic Regulation in Chromium-, Nickel- and Cadmium-Induced Carcinogenesis

Environmental and occupational exposure to heavy metals, such as hexavalent chromium, nickel, and cadmium, are major health concerns worldwide. Some heavy metals are well-documented human carcinogens. Multiple mechanisms, including DNA damage, dysregulated gene expression, and aberrant cancer-related signaling, have been shown to contribute to metal-induced carcinogenesis. However, the molecular mechanisms accounting for heavy metal-induced carcinogenesis and angiogenesis are still not fully understood. In recent years, an increasing number of studies have indicated that in addition to genotoxicity and genetic mutations, epigenetic mechanisms play critical roles in metal-induced cancers. Epigenetics refers to the reversible modification of genomes without changing DNA sequences; epigenetic modifications generally involve DNA methylation, histone modification, chromatin remodeling, and non-coding RNAs. Epigenetic regulation is essential for maintaining normal gene expression patterns; the disruption of epigenetic modifications may lead to altered cellular function and even malignant transformation. Therefore, aberrant epigenetic modifications are widely involved in metal-induced cancer formation, development, and angiogenesis. Notably, the role of epigenetic mechanisms in heavy metal-induced carcinogenesis and angiogenesis remains largely unknown, and further studies are urgently required. In this review, we highlight the current advances in understanding the roles of epigenetic mechanisms in heavy metal-induced carcinogenesis, cancer progression, and angiogenesis.

Prognosis of Pediatric Acute Myeloid Leukemia with KMT2A-MLLT3 According to DNA Methylation Patterns: Jccg JPLSG AML-05 Study

Introduction Acute myeloid leukemia (AML) is a heterogeneous hematologic malignancy characterized by cytogenetic abnormalities, including fusion genes, mutations, epigenetic modifications, and dysregulated gene expression. DNA methylation patterns have recently been appeared to be associated with molecular subtypes, chromosomal abnormalities, gene fusion, and AML prognosis. DNA methylation pattern of adult AML has also been proposed as a novel biomarker for AML prognosis. However, few studies have discussed the influence of DNA methylation status on the clinical features of pediatric AML. We analyzed genome-wide DNA methylation in 127 pediatric patients with AML to determine its association with clinical features, genetic alterations, and prognostic impact. Methods Between 2006 and 2010, 443 pediatric patients with de novo AML (0-17 years) participated in the Japanese AML-05 trial of the Japanese Pediatric Leukemia/Lymphoma Study Group. Of these patients, 127 patients were enrolled in this study. Their cytogenetic features were as follows: normal karyotype, 26 patients; RUNX1-RUNX1T1, 11; CBFB-MYH11, 5; KMT2A rearrangement, 47 (22 of 47 had KMT2A-MLLT3); NUP98-NSD1, 8; NUP98-KDM5A, 5; CBFA2T3-GLIS2, 4; FUS-ERG, 4; and other cytogenetics, 18. This cohort included 35 patients with FLT3-internal tandem duplication (ITD), 9 with CEBPA biallelic mutations, 15 with high MECOM (also known as EVI1) expression, and 29 with high PRDM16 (also known as MEL1) expression. In all patients, genome-wide DNA methylation analysis using Infinium MethylationEPIC BeadChip (Illumina) was performed. Results and Discussion Based on unsupervised hierarchical clustering, patients were divided into six clusters (cluster 1-6) associated with genetic alterations. Cluster 1 (n = 28) was characterized by the presence of KMT2A rearrangement with low MECOM expression. CBFA2T3-GLIS2 and NUP98-KDM5A considered as adverse prognostic factors were included in cluster 2 (n = 15). Cluster 3 (n = 16) comprised 11 RUNX1-RUNX1T1 and 5 CBFB-MYH11. No CBF-AML was included in other clusters. All nine patients with biallelic CEBPA mutations, which indicated a favorable outcome, were classified under cluster 4 (n = 18). Interestingly, all four patients with FUS-ERG were also classified under cluster 4. Clusters 5 (n = 15) and 6 (n = 35) comprised patients with molecular features related to adverse outcomes, such as FLT3-ITD, KMT2A-MLLT3 with high MECOM expression, and high PRDM16 expression. All seven patients with NUP98-NSD1 were classified under cluster 6. Patients with AML with KMT2A rearrangement showed a significant difference in DNA methylation levels at 500 CpG sites compared with those without. Patients were categorized into four clusters (clusters A-D) based on the methylation values of the 500 CpG sites that were significantly different between patients with AML with or without KMT2A rearrangement, and 96% (45 of 47) of patients with AML with KMT2A rearrangement were classified under clusters A (n = 32) or B (n = 13). The remaining two patients were classified under clusters C (n = 1) and D (n = 1). Interestingly, all 32 patients with AML with KMT2A rearrangement classified under cluster A showed low MECOM expression. Moreover, 22 patients with AML with KMT2A-MLLT3 were classified under clusters A (n = 14) and B (n = 8). Patients with KMT2A-MLLT3 in cluster B had a significantly worse prognosis than those in cluster A (5-year overall survival, 30% vs. 100%; P = 0.001, and 5-year event-free survival, 0% vs. 100%; P < 0.001). All eight patients with KMT2A-MLLT3 in cluster B had high MECOM expression, whereas all 14 patients in cluster A had low MECOM expression. These results indicate that the methylation pattern corresponded to MECOM expression. Our findings suggest that DNA methylation levels at specific CpG sites are useful biomarkers for the prognosis of pediatric patients with AML.

Single-Cell RNA-Sequencing of 245 Tumor Samples from Patients with MGUS and Smoldering Multiple Myeloma Reveals Novel Insights into Malignant Plasma Cell Biology

Introduction Patients with Monoclonal Gammopathy of Undetermined Significance (MGUS) and Smoldering Multiple Myeloma (SMM) exhibit variable risk of progression to full-blown Multiple Myeloma (MM), which cannot be fully explained by differences in tumor burden or genetic alterations. Therefore, characterizing non-genetic changes in malignant plasma cells may help to identify novel mechanisms of disease progression and improve prognostication. Our current understanding of transcriptomic alterations in patients with MGUS and SMM is based on bulk RNA-sequencing or microarray studies, which are affected by sample purity and interpatient variability. Here, we present results from the largest single-cell RNA-sequencing cohort (n=245) of tumor samples from patients with MGUS and SMM. Methods We performed single-cell RNA- and V(D)J-sequencing on 245 samples from 36 patients with MGUS, 136 patients with SMM, 37 patients with MM, and 25 healthy donors. Libraries were prepared with the Chromium Single-cell 5' and V(D)J enrichment kit by 10X Genomics and sequenced on NovaSeq at the Genomics Platform of the Broad Institute of MIT and Harvard (Cambridge, MA). CellRanger v.6.0.1. was used to extract FASTQ files and produce count matrices. Droplets with more than 15% of UMIs mapped to mitochondrial genes or fewer than 200 detected genes were removed, and doublets were identified using Scrublet, SCDS, and scDblFinder. Samples were integrated using Harmony, and plasma cells were annotated as malignant or normal based on the matched V(D)J clonotype information. Differential expression was performed at the single-cell level using Wilcoxon's rank-sum test. Results Overall, we sequenced 1,318,218 plasma cells, including 960,998 malignant and 357,220 normal plasma cells. Each patient's tumor formed a unique cluster, and tumors with similar cytogenetics clustered adjacent to each other. By comparing expression levels between malignant and normal plasma cells for each patient, we were able to identify differentially expressed genes per tumor and assess how frequently each gene is dysregulated across the cohort. This approach can provide a rationale for the prioritization of target validation and can potentially uncover clinically meaningful differences between disease stages. As hypothesized, our analysis recovered established markers of plasma cell malignancy that are useful diagnostically, such as the downregulation of CD27 (rank 1), CD99 (rank 2), and CD81 (rank 5), or therapeutically, such as the upregulation of GPRC5D (rank 9). Moreover, we discovered frequent downregulation of SH3BGRL3 (rank 3), a gene associated with cell migration, and SSR4 (rank 9), SELENOK (rank 11), OSTC (rank 15), and SPCS3 (rank 18), genes associated with protein folding and the regulation of endoplasmic reticulum (ER) stress. Interestingly, PDK1 (rank 17), an inhibitor of pyruvate dehydrogenase that is highly expressed in normal plasma cells, was frequently downregulated in malignant plasma cells, suggesting that the balance between oxidative phosphorylation and aerobic glycolysis may be different in malignant plasma cells. The most common upregulated genes were the oncogene MLLT3 (rank 1), the growth factor IGF1 (rank 2), and the proteasome regulator TJP1 (rank 3). By comparing the frequency of dysregulation between patients with SMM and MGUS, we observed that malignant plasma cells from patients with SMM were more likely to upregulate MYC, which is concordant with the known increase in MYC genetic alterations as the disease progresses. Furthermore, patients with SMM are more likely to show upregulation of CD47, which promotes immune evasion. Lastly, patients with MM were more likely to exhibit upregulation of the RNA helicase DDX21, the therapeutic target SLAMF7, the ER factor TXNDC11, and NFkB signaling factors PIM2 and IRF9, compared to patients with SMM. Discussion In conclusion, by leveraging the largest single-cell RNA-sequencing cohort of bone marrow samples from patients with MGUS and SMM, we uncovered novel insights into plasma cell malignancy, as well as differences in gene expression dysregulation between disease stages. Observations gleaned from this dataset could be used to nominate novel targets and prioritize target validation for the development of novel therapeutics for the treatment or prevention of MM.

Bone Sialoprotein Is Critical for Alveolar Bone Healing in Mice

Bone sialoprotein (BSP) is an extracellular matrix (ECM) protein associated with mineralized tissues, particularly bone and cementum. BSP includes functional domains implicated in collagen binding, hydroxyapatite nucleation, and cell signaling, although its function(s) in osteoblast and osteoclast differentiation and function remain incompletely understood. Genetic ablation of BSP in Ibsp knockout (Ibsp–/–) mice results in developmental bone mineralization and remodeling defects, with alveolar bone more severely affected than the femurs and tibias of the postcranial skeleton. The role of BSP in alveolar bone healing has not been studied. We hypothesized that BSP ablation would cause defective alveolar bone healing. We employed a maxillary first molar extraction socket healing model in 42-d postnatalIbsp–/– and wild-type (WT) control mice. Tissues were collected at 0, 7, 14, 21, and 56 d postprocedure (dpp) for analysis by micro–computed tomography (microCT), histology, in situ hybridization (ISH), immunohistochemistry (IHC), and quantitative polymerase chain reaction (qPCR) array. As expected, alveolar bone healing progressed in WT mice with increasing bone volume fraction (BV/TV), bone mineral density (BMD), and tissue mineral density (TMD), transitioning from woven to mature bone from 7 to 56 dpp. Ibsp messenger RNA (mRNA) and BSP protein were strongly expressed during alveolar bone healing in parallel with other osteogenic markers. Compared to WT, Ibsp–/– mice exhibited 50% to 70% reduced BV/TV and BMD at all time points, 7% reduced TMD at 21 dpp, abnormally increased Col1a1 and Alpl mRNA expression, and persistent presence of woven bone and increased bone marrow in healing sockets. qPCR revealed substantially dysregulated gene expression in alveolar bone of Ibsp–/– versus WT mice, with significantly disrupted expression of 45% of tested genes in functional groups, including markers for osteoblasts, osteoclasts, mineralization, ECM, cell signaling, and inflammation. We conclude that BSP is a critical and nonredundant factor for alveolar bone healing, and its absence disrupts multiple major pathways involved in appropriate healing.

Influence of Sex and Strain on Hepatic and Adipose Tissue Trace Element Concentrations and Gene Expression in C57BL/6J and DBA/2J High Fat Diet Models.

The objective of this study was to determine the influence of sex and strain on the dysregulation of trace element concentration and associative gene expression due to diet induced obesity in adipose tissue and the liver. Male and female C57BL/6J (B6J) and DBA/2J (D2J) were randomly assigned to a normal-fat diet (NFD) containing 10% kcal fat/g or a mineral-matched high-fat diet (HFD) containing 60% kcal fat/g for 16 weeks. Liver and adipose tissue were assessed for copper, iron, manganese, and zinc concentrations and related changes in gene expression. Notable findings include three-way interactions of diet, sex, and strain amongst adipose tissue iron concentrations (p = 0.005), adipose hepcidin expression (p = 0.007), and hepatic iron regulatory protein (IRP) expression (p = 0.012). Cd11c to Cd163 ratio was increased in adipose tissue due to HFD amongst all biological groups except B6J females, for which tissue iron concentrations were reduced due to HFD (p = 0.002). Liver divalent metal transporter 1 (DMT-1) expression was increased due to HFD amongst B6J males (p &lt; 0.005) and females (p &lt; 0.004), which coincides with the reduction in hepatic iron concentrations found in these biological groups (p &lt; 0.001). Sex, strain, and diet affected trace element concentration, the expression of genes that regulate trace element homeostasis, and the expression of macrophages that contribute to tissue iron-handling in adipose tissue. These findings suggest that sex and strain may be key factors that influence the adaptive capacity of iron mismanagement in adipose tissue and its subsequent consequences, such as insulin resistance.

SNPs in 3'UTR miRNA Target Sequences Associated with Individual Drug Susceptibility.

The complementary interaction of microRNAs (miRNAs) with their binding sites in the 3'untranslated regions (3'UTRs) of target gene mRNAs represses translation, playing a leading role in gene expression control. MiRNA recognition elements (MREs) in the 3'UTRs of genes often contain single nucleotide polymorphisms (SNPs), which can change the binding affinity for target miRNAs leading to dysregulated gene expression. Accumulated data suggest that these SNPs can be associated with various human pathologies (cancer, diabetes, neuropsychiatric disorders, and cardiovascular diseases) by disturbing the interaction of miRNAs with their MREs located in mRNA 3'UTRs. Numerous data show the role of SNPs in 3'UTR MREs in individual drug susceptibility and drug resistance mechanisms. In this review, we brief the data on such SNPs focusing on the most rigorously proven cases. Some SNPs belong to conventional genes from the drug-metabolizing system (in particular, the genes coding for cytochromes P450 (CYP 450), phase II enzymes (SULT1A1 and UGT1A), and ABCB3 transporter and their expression regulators (PXR and GATA4)). Other examples of SNPs are related to the genes involved in DNA repair, RNA editing, and specific drug metabolisms. We discuss the gene-by-gene studies and genome-wide approaches utilized or potentially utilizable to detect the MRE SNPs associated with individual response to drugs.

Combination of common mtDNA variants results in mitochondrial dysfunction and a connective tissue dysregulation

Mitochondrial dysfunction can be associated with a range of clinical manifestations. Here, we report a family with a complex phenotype including combinations of connective tissue, neurological, and metabolic symptoms that were passed on to all surviving children. Analysis of the maternally inherited mtDNA revealed a novel genotype encompassing the haplogroup J - defining mitochondrial DNA (mtDNA) ND5 m.13708G>A (A458T) variant arising on the mtDNA haplogroup H7A background, an extremely rare combination. Analysis of transmitochondrial cybrids with the 13708A-H7 mtDNA revealed a lower mitochondrial respiration, increased reactive oxygen species production (mROS), and dysregulation of connective tissue gene expression. The mitochondrial dysfunction was exacerbated by histamine, explaining why all eight surviving children inherited the dysfunctional histidine decarboxylase allele (W327X) from the father. Thus, certain combinations of common mtDNA variants can cause mitochondrial dysfunction, mitochondrial dysfunction can affect extracellular matrix gene expression, and histamine-activated mROS production can augment the severity of mitochondrial dysfunction. Most important, we have identified a previously unreported genetic cause of mitochondrial disorder arising from the incompatibility of common, nonpathogenic mtDNA variants.

Epigenetic modification of Kiss1 gene expression in the AVPV is essential for female reproductive aging.

Female reproductive senescence is heralded by hypothalamus region-specific changes in the transcription of genes such as Kiss1 under estradiol (E2) positive feedback, associated with luteinizing hormone (LH) surge dysfunction and reproductive decline. The current study explored whether the anteroventral periventricular nucleus (AVPV) displayed epigenetic changes mediated by age-related dysregulation of gene expression and whether an epigenetic-based intervention could alleviate an aging-related neuroendocrine disorder. Chromatin immunoprecipitation sequencing (ChIP-seq) and ChIP-qPCR were used to assess the differential acetylation of histone H3 in the AVPV and the expression of genes in hormone-primed middle-aged rats. The association between acetylated histone H3 and Kiss1 expression and the underlying mechanisms of dysregulation were determined using pharmacological inhibitors and molecular experiments in vitro and in vivo. An AVPV gene expression program failed to initiate in middle-aged females displaying typical genome-wide hypoacetylation of histone H3, and this coincided with decreased LH. Hypoacetylation of histone H3 at the 3' intergenic region of Kiss1 in particular was associated with enhanced chromatin looping between the promoter and enhancer. Restoration of physiological histone H3 acetylation by intracerebroventricular injection of trichostatin A (TSA) restored the expression of Kiss1 by modifying chromatin looping and led to the restoration of Kiss1 neuronal activation and Kiss1 synthesis as well as circulating LH. These findings have revealed novel epigenetic-associated changes in gene expression in female reproductive aging. These results also suggest that HDAC enzyme-based treatment is a potential therapeutic approach for insufficient preovulatory LH release in aging females.

Common signatures of differential microRNA expression in Parkinson's and Alzheimer's disease brains.

Dysregulation of microRNA gene expression has been implicated in many neurodegenerative diseases, including Parkinson's disease. However, the individual dysregulated microRNAs remain largely unknown. Previous meta-analyses have highlighted several microRNAs being differentially expressed in post-mortem Parkinson's disease and Alzheimer's disease brains versus controls, but they were based on small sample sizes. In this study, we quantified the expression of the most compelling Parkinson's and Alzheimer's disease microRNAs from these meta-analyses ('candidate miRNAs') in one of the largest Parkinson's/Alzheimer's disease case-control post-mortem brain collections available (n = 451), thereby quadruplicating previously investigated sample sizes. Parkinson's disease candidate microRNA hsa-miR-132-3p was differentially expressed in our Parkinson's (P = 4.89E-06) and Alzheimer's disease samples (P = 3.20E-24) compared with controls. Alzheimer's disease candidate microRNAs hsa-miR-132-5p (P = 4.52E-06) and hsa-miR-129-5p (P = 0.0379) were differentially expressed in our Parkinson's disease samples. Combining these novel data with previously published data substantially improved the statistical support (α = 3.85E-03) of the corresponding meta-analyses, clearly implicating these microRNAs in both Parkinson's and Alzheimer's disease. Furthermore, hsa-miR-132-3p/-5p (but not hsa-miR-129-5p) showed association with α-synuclein neuropathological Braak staging (P = 3.51E-03/P = 0.0117), suggesting that hsa-miR-132-3p/-5p play a role in α-synuclein aggregation beyond the early disease phase. Our study represents the largest independent assessment of recently highlighted candidate microRNAs in Parkinson's and Alzheimer's disease brains, to date. Our results implicate hsa-miR-132-3p/-5p and hsa-miR-129-5p to be differentially expressed in both Parkinson's and Alzheimer's disease, pinpointing shared pathogenic mechanisms across these neurodegenerative diseases. Intriguingly, based on publicly available high-throughput sequencing of RNA isolated by cross-linking immunoprecipitation data, hsa-miR-132 may interact with SNCA messenger RNA in the human brain, possibly pinpointing novel therapeutic approaches in fighting Parkinson's disease.

Tuning neurodegeneration-linked gene expression, one (edited) base at a time

Dysregulated gene expression is a frequent hallmark of neurodegenerative diseases. Thus, strategies that enable precise and targeted tuning of endogenous gene expression represent an attractive approach for neurodegenerative-focused gene therapies. In this issue, Lim et al.1 employ CRISPR base editors to modify cis-regulatory sequences that govern the expression of two key genes involved in neurodegenerative diseases - the HTT gene for Huntington’s disease (HD), and the APP gene for Alzheimer’s disease (AD).

Druggable transcriptomic pathways revealed in Parkinson’s patient-derived midbrain neurons

Complex genetic predispositions accelerate the chronic degeneration of midbrain substantia nigra neurons in Parkinson’s disease (PD). Deciphering the human molecular makeup of PD pathophysiology can guide the discovery of therapeutics to slow the disease progression. However, insights from human postmortem brain studies only portray the latter stages of PD, and there is a lack of data surrounding molecular events preceding the neuronal loss in patients. We address this gap by identifying the gene dysregulation of live midbrain neurons reprogrammed in vitro from the skin cells of 42 individuals, including sporadic and familial PD patients and matched healthy controls. To minimize bias resulting from neuronal reprogramming and RNA-seq methods, we developed an analysis pipeline integrating PD transcriptomes from different RNA-seq datasets (unsorted and sorted bulk vs. single-cell and Patch-seq) and reprogramming strategies (induced pluripotency vs. direct conversion). This PD cohort’s transcriptome is enriched for human genes associated with known clinical phenotypes of PD, regulation of locomotion, bradykinesia and rigidity. Dysregulated gene expression emerges strongest in pathways underlying synaptic transmission, metabolism, intracellular trafficking, neural morphogenesis and cellular stress/immune responses. We confirmed a synaptic impairment with patch-clamping and identified pesticides and endoplasmic reticulum stressors as the most significant gene-chemical interactions in PD. Subsequently, we associated the PD transcriptomic profile with candidate pharmaceuticals in a large database and a registry of current clinical trials. This study highlights human transcriptomic pathways that can be targeted therapeutically before the irreversible neuronal loss. Furthermore, it demonstrates the preclinical relevance of unbiased large transcriptomic assays of reprogrammed patient neurons.

HDAC inhibitors suppress protein poly(ADP-ribosyl)ation and DNA repair protein levels and phosphorylation status in hematologic cancer cells: implications for their use in combination with PARP inhibitors and chemotherapeutic drugs.

The therapeutic efficacy of histone deacetylase inhibitors (HDACi) for hematologic malignancies and solid tumors is attributed to their ability to remodel chromatin, normalize dysregulated gene expression, and inhibit repair of damaged DNA. Studies on the interactions of HDACi with PARP inhibitors in hematologic cancers are limited, especially when combined with chemotherapeutic agents. Exposure of hematologic cancer cell lines and patient-derived cell samples to various HDACi resulted in a significant caspase-independent inhibition of protein PARylation, mainly catalyzed by PARP1. HDACi affected the expression of PARP1 at the transcription and/or post-translation levels in a cell line-dependent manner. HDACi-mediated inhibition of PARylation correlated with decreased levels and phosphorylation of major proteins involved in DNA repair. Combination of HDAC and PARP1 inhibitors provided synergistic cytotoxicity, which was further enhanced when combined with a chemotherapeutic regimen containing gemcitabine, busulfan and melphalan as observed in lymphoma cell lines. Our results indicate that the anti-tumor efficacy of HDACi is partly due to down-regulation of PARylation, which negatively affects the status of DNA repair proteins. This repair inhibition, combined with the high levels of oxidative and DNA replication stress characteristic of cancer cells, could have conferred these hematologic cancer cells not only with a high sensitivity to HDACi but also with a heightened dependence on PARP and therefore with extreme sensitivity to combined HDACi/PARPi treatment and, by extension, to their combination with conventional DNA-damaging chemotherapeutic agents. The observed synergism of these drugs could have a major significance in improving treatment of these cancers.

Dysregulation of gene expression of PTEN and AKT signaling pathway in patients of ovarian cancer: A pilot study

ObjectivePI3K/AKT/mTOR signaling pathway has a crucial role in chemo- and radiotherapy resistance, and tumorigenesis of ovarian cancer. Some of the genes of this pathway are also linked with progression of disease in association of different miRNAs. The main objective of the current research was to determine the level of mRNA expression of different genes along with their respective microRNA (miRNAs) in ovarian cancer and apparently healthy women. MethodsSamples from 46 ovarian cancer and 46 healthy females were obtained from a local cancer hospital. mRNA and miRNAs were extracted and gene expression of mRNA and miRNA were analyzed by qPCR. All data was analyzed using SPSS version 22 and CFX96 manager software for comparative gene analysis. ResultsThe relative mRNA expression levels of AKT, PI3K, PDK1, NFkB, and mTOR were high (2.14, 1.93, 1.93, 3.31, and 1.82 folds, respectively) as compared to healthy controls, whereas expression of PTEN was down-regulated (0.10-fold) in patients. There was a significant difference (p = 0.0019) in serum levels of phosphorylated-Akt in patients and controls. The expression of miR-29b was up-regulated in patients of ovarian cancer. ConclusionGene expression of PTEN/AKT pathway is deregulated in ovarian cancer patients. Moreover, the phosphorylated level of AKT, expression of mTOR or miRNAs may be a marker for the disease.

TCDD induces cleft palate through exosomes derived from mesenchymal cells.

TCDD (2,3,7,8-tetrachlorodibenzo-p-dioxin) is a ubiquitous environmental toxicant and a notable teratogenic agent for cleft palate (CP), a common congenital structural malformation that can result from abnormalities during palatal shelf connection and/or fusion. The development of the palate requires precise coordination between mesenchymal and epithelial cells. Exosomes are vesicles secreted by cells and participate in organ development by transferring various bioactive molecules between cells and regulating cell proliferation, migration, apoptosis, and epithelial-mesenchymal transition (EMT); these vesicles represent a new method of intercellular communication. To explore how TCDD could influence palatal cell behaviors and communication, we treated mesenchymal cells with TCDD, collected the exosomes secreted by the cells, assessed the 2 types of palatal cells, and then observed the effects of TCDD-induced exosomes. We found that the effects of TCDD-induced exosomes were equal to those of TCDD. Thus, TCDD might change the genetic materials of palatal cells and exosomes to cause dysregulated gene expression from parental cells, affect cellular information communicators, and induce abnormal cellular behaviors that could lead to CP.

Epigenetic Modulation of Opioid Receptors by Drugs of Abuse.

Chronic exposure to drugs of abuse produces profound changes in gene expression and neural activity associated with drug-seeking and taking behavior. Dysregulation of opioid receptor gene expression is commonly observed across a variety of abused substances including opioids, cocaine, and alcohol. Early studies in cultured cells showed that the spatial and temporal gene expression of opioid receptors are regulated by epigenetic mechanisms including DNA and histone modifications and non-coding RNAs. Accumulating evidence indicate that drugs of abuse can modulate opioid receptor gene expression by targeting various epigenetic regulatory networks. Based on current cellular and animal models of substance use disorder and clinical evidence, this review summarizes how chronic drug exposure alters the gene expression of mu, delta, kappa, and nociceptin receptors via DNA and histone modifications. The influence of drugs of abuse on epigenetic modulators, such as non-coding RNAs and transcription factors, is also presented. Finally, the therapeutic potential of manipulating epigenetic processes as an avenue to treat substance use disorder is discussed.

Integrative weighted molecular network construction from transcriptomics and genome wide association data to identify shared genetic biomarkers for COPD and lung cancer.

Chronic obstructive pulmonary disease (COPD) is a multifactorial progressive airflow obstruction in the lungs, accounting for high morbidity and mortality across the world. This study aims to identify potential COPD blood-based biomarkers by analyzing the dysregulated gene expression patterns in blood and lung tissues with the help of robust computational approaches. The microarray gene expression datasets from blood (136 COPD and 6 controls) and lung tissues (16 COPD and 19 controls) were analyzed to detect shared differentially expressed genes (DEGs). Then these DEGs were used to construct COPD protein network-clusters and functionally enrich them against gene ontology annotation terms. The hub genes in the COPD network clusters were then queried in GWAS catalog and in several cancer expression databases to explore their pathogenic roles in lung cancers. The comparison of blood and lung tissue datasets revealed 63 shared DEGs. Of these DEGs, 12 COPD hub gene-network clusters (SREK1, TMEM67, IRAK2, MECOM, ASB4, C1QTNF2, CDC42BPA, DPF3, DET1, CCDC74B, KHK, and DDX3Y) connected to dysregulations of protein degradation, inflammatory cytokine production, airway remodeling, and immune cell activity were prioritized with the help of protein interactome and functional enrichment analysis. Interestingly, IRAK2 and MECOM hub genes from these COPD network clusters are known for their involvement in different pulmonary diseases. Additional COPD hub genes like SREK1, TMEM67, CDC42BPA, DPF3, and ASB4 were identified as prognostic markers in lung cancer, which is reported in 1% of COPD patients. This study identified 12 gene network- clusters as potential blood based genetic biomarkers for COPD diagnosis and prognosis.