The STAT3-DNMT1 connection

Blood transcriptome analysis suggests an indirect molecular association of early life adversities and adult social anxiety disorder by immune-related signal transduction

Social anxiety disorder (SAD) is a psychiatric disorder characterized by severe fear in social situations and avoidance of these. Multiple genetic as well as environmental factors contribute to the etiopathology of SAD. One of the main risk factors for SAD is stress, especially during early periods of life (early life adversity; ELA). ELA leads to structural and regulatory alterations contributing to disease vulnerability. This includes the dysregulation of the immune response. However, the molecular link between ELA and the risk for SAD in adulthood remains largely unclear. Evidence is emerging that long-lasting changes of gene expression patterns play an important role in the biological mechanisms linking ELA and SAD. Therefore, we conducted a transcriptome study of SAD and ELA performing RNA sequencing in peripheral blood samples. Analyzing differential gene expression between individuals suffering from SAD with high or low levels of ELA and healthy individuals with high or low levels of ELA, 13 significantly differentially expressed genes (DEGs) were identified with respect to SAD while no significant differences in expression were identified with respect to ELA. The most significantly expressed gene was MAPK3 (p = 0.003) being upregulated in the SAD group compared to control individuals. In contrary, weighted gene co-expression network analysis (WGCNA) identified only modules significantly associated with ELA (p ≤ 0.05), not with SAD. Furthermore, analyzing interaction networks of the genes from the ELA-associated modules and the SAD-related MAPK3 revealed complex interactions of those genes. Gene functional enrichment analyses indicate a role of signal transduction pathways as well as inflammatory responses supporting an involvement of the immune system in the association of ELA and SAD. In conclusion, we did not identify a direct molecular link between ELA and adult SAD by transcriptional changes. However, our data indicate an indirect association of ELA and SAD mediated by the interaction of genes involved in immune-related signal transduction.

Mixed model-based eQTL analysis reveals lncRNAs associated with regulation of genes involved in sex determination and spermatogenesis: The key to understanding human gender imbalance

BACKGROUND

An imbalance in the prenatal sex ratio in humans may be due to several factors affecting sperm physiology, including genetic features. In this study, we conducted a transcriptome-wide analysis of expression quantitative trait loci (eQTLs) to identify target genes associated with previously described QTLs associated with gender imbalance.

METHODS

A mixed model explaining polygenic effects by genomic covariance among individuals was used to identify the eQTLs using gene expression and genotype data from 462 European/African individuals.

RESULTS

Eight eGenes were associated with four QTLs (P < 4.00 × 10^-5), with strong associations found (P < 4.00 × 10^-8) between rs2485007 and eGenes ANKRD26P3 (P = 3.40 × 10^-9) and LINC00421 (P = 1.35 × 10^-9). ANKRD26P3 and LINC00421 are both lncRNAs associated with the control of testis-dominant genes PELP1, TAF15, NANOG, TEX14, TCF3, ZNF433, ZNF555, TEX37, FATE1, TCP11, and CYLC2 and Y-linked genes SRY and ZFY, as well as several genes with roles in spermatogenesis (ODF1, SPATC1, SPATA3, SPATA31E1, SPERT, SPATA16, MOSPD1, SPATA24, and SPO11) and sex determination (SOX family genes).

CONCLUSIONS

The above eGenes contribute directly or indirectly to gene regulation for sex determination and spermatogenesis, thereby serving as important functional clues for gender-biased selection.

Comprehensive analysis of regulation of DNA methyltransferase isoforms in human breast tumors

Significant reprogramming of epigenome is widely described during pathogenesis of breast cancer. Transformation of normal cell to hyperplastic cell and to neoplastic phenotype is associated with aberrant DNA (de)methylation, which, through promoter and enhancer methylation changes, activates oncogenes and silence tumor suppressor genes in variety of tumors including breast. DNA methylation, one of the major epigenetic mechanisms is catalyzed by evolutionarily conserved isoforms namely, DNMT1, DNMT3A and DNMT3B in humans. Over the years, studies have demonstrated intricate and complex regulation of DNMT isoforms at transcriptional, translational and post-translational levels. The recent findings of allosteric regulation of DNMT isoforms and regulation by other interacting chromatin modifying proteins emphasizes functional integrity and their contribution for the development of breast cancer and progression. DNMT isoforms are regulated by several intrinsic and extrinsic parameters. In the present review, we have extensively performed bioinformatics analysis of expression of DNMT isoforms along with their transcriptional and post-transcriptional regulators such as transcription factors, interacting proteins, hormones, cytokines and dietary elements along with their significance during pathogenesis of breast tumors. Our review manuscript provides a comprehensive understanding of key factors regulating DNMT isoforms in breast tumor pathology and documents unsolved issues.

Recent Advancements in the Mechanisms Underlying Resistance to PD-1/PD-L1 Blockade Immunotherapy

Simple Summary

Immune checkpoint blockade targeting PD-1/PD-L1 has a promising therapeutic efficacy in different tumors, but a significant percentage of patients cannot benefit from this therapy due to primary and acquired resistance during treatment. This review summarizes the recent findings of PD-L1 role in resistance to therapies through the PD-1/PD-L1 pathway and other correlating signaling pathways. A special focus will be given to the key mechanisms underlying resistance to the PD-1/PD-L1 blockade in cancer immunotherapy. Furthermore, we also discuss the promising combination of therapeutic strategies for patients resistant to the PD-1/PD-L1 blockade in order to enhance the efficacy of immune checkpoint inhibitors.

Abstract

Release of immunoreactive negative regulatory factors such as immune checkpoint limits antitumor responses. PD-L1 as a significant immunosuppressive factor has been involved in resistance to therapies such as chemotherapy and target therapy in various cancers. Via interacting with PD-1, PD-L1 can regulate other factors or lead to immune evasion of cancer cells. Besides, immune checkpoint blockade targeting PD-1/PD-L1 has promising therapeutic efficacy in the different tumors, but a significant percentage of patients cannot benefit from this therapy due to primary and acquired resistance during treatment. In this review, we described the utility of PD-L1 expression levels for predicting poor prognosis in some tumors and present evidence for a role of PD-L1 in resistance to therapies through PD-1/PD-L1 pathway and other correlating signaling pathways. Afterwards, we elaborate the key mechanisms underlying resistance to PD-1/PD-L1 blockade in cancer immunotherapy. Furthermore, promising combination of therapeutic strategies for patients resistant to PD-1/PD-L1 blockade therapy or other therapies associated with PD-L1 expression was also summarized.

Targeting Janus Kinases and Signal Transducer and Activator of Transcription 3 to Treat Inflammation, Fibrosis, and Cancer: Rationale, Progress, and Caution

Before it was molecularly cloned in 1994, acute-phase response factor or signal transducer and activator of transcription (STAT)3 was the focus of intense research into understanding the mammalian response to injury, particularly the acute-phase response. Although known to be essential for liver production of acute-phase reactant proteins, many of which augment innate immune responses, molecular cloning of acute-phase response factor or STAT3 and the research this enabled helped establish the central function of Janus kinase (JAK) family members in cytokine signaling and identified a multitude of cytokines and peptide hormones, beyond interleukin-6 and its family members, that activate JAKs and STAT3, as well as numerous new programs that their activation drives. Many, like the acute-phase response, are adaptive, whereas several are maladaptive and lead to chronic inflammation and adverse consequences, such as cachexia, fibrosis, organ dysfunction, and cancer. Molecular cloning of STAT3 also enabled the identification of other noncanonical roles for STAT3 in normal physiology, including its contribution to the function of the electron transport chain and oxidative phosphorylation, its basal and stress-related adaptive functions in mitochondria, its function as a scaffold in inflammation-enhanced platelet activation, and its contributions to endothelial permeability and calcium efflux from endoplasmic reticulum. In this review, we will summarize the molecular and cellular biology of JAK/STAT3 signaling and its functions under basal and stress conditions, which are adaptive, and then review maladaptive JAK/STAT3 signaling in animals and humans that lead to disease, as well as recent attempts to modulate them to treat these diseases. In addition, we will discuss how consideration of the noncanonical and stress-related functions of STAT3 cannot be ignored in efforts to target the canonical functions of STAT3, if the goal is to develop drugs that are not only effective but safe. SIGNIFICANCE STATEMENT: Key biological functions of Janus kinase (JAK)/signal transducer and activator of transcription (STAT)3 signaling can be delineated into two broad categories: those essential for normal cell and organ development and those activated in response to stress that are adaptive. Persistent or dysregulated JAK/STAT3 signaling, however, is maladaptive and contributes to many diseases, including diseases characterized by chronic inflammation and fibrosis, and cancer. A comprehensive understanding of JAK/STAT3 signaling in normal development, and in adaptive and maladaptive responses to stress, is essential for the continued development of safe and effective therapies that target this signaling pathway.

Effects of air pollution on the nervous system and its possible role in neurodevelopmental and neurodegenerative disorders

Recent extensive evidence indicates that air pollution, in addition to causing respiratory and cardiovascular diseases, may also negatively affect the brain and contribute to central nervous system diseases. Air pollution is comprised of ambient particulate matter (PM) of different sizes, gases, organic compounds, and metals. An important contributor to PM is represented by traffic-related air pollution, mostly ascribed to diesel exhaust (DE). Epidemiological and animal studies have shown that exposure to air pollution may be associated with multiple adverse effects on the central nervous system. In addition to a variety of behavioral abnormalities, the most prominent effects caused by air pollution are oxidative stress and neuro-inflammation, which are seen in both humans and animals, and are supported by in vitro studies. Among factors which can affect neurotoxic outcomes, age is considered most relevant. Human and animal studies suggest that air pollution may cause developmental neurotoxicity, and may contribute to the etiology of neurodevelopmental disorders, including autism spectrum disorder. In addition, air pollution exposure has been associated with increased expression of markers of neurodegenerative disease pathologies, such as alpha-synuclein or beta-amyloid, and may thus contribute to the etiopathogenesis of neurodegenerative diseases, particularly Alzheimer's disease and Parkinson's disease.

The Transcriptional Roles of ALK Fusion Proteins in Tumorigenesis

Anaplastic lymphoma kinase (ALK) is a tyrosine kinase involved in neuronal and gut development. Initially discovered in T cell lymphoma, ALK is frequently affected in diverse cancers by oncogenic translocations. These translocations involve different fusion partners that facilitate multimerisation and autophosphorylation of ALK, resulting in a constitutively active tyrosine kinase with oncogenic potential. ALK fusion proteins are involved in diverse cellular signalling pathways, such as Ras/extracellular signal-regulated kinase (ERK), phosphatidylinositol 3-kinase (PI3K)/Akt and Janus protein tyrosine kinase (JAK)/STAT. Furthermore, ALK is implicated in epigenetic regulation, including DNA methylation and miRNA expression, and an interaction with nuclear proteins has been described. Through these mechanisms, ALK fusion proteins enable a transcriptional programme that drives the pathogenesis of a range of ALK-related malignancies.

Developmental Neurotoxicity of Traffic-Related Air Pollution: Focus on Autism

PURPOSE OF REVIEW

Epidemiological and animal studies suggest that air pollution may negatively affect the central nervous system (CNS) and contribute to CNS diseases. Traffic-related air pollution is a major contributor to global air pollution, and diesel exhaust (DE) is its most important component.

RECENT FINDINGS

Several studies suggest that young individuals may be particularly susceptible to air pollution-induced neurotoxicity and that perinatal exposure may cause or contribute to developmental disabilities and behavioral abnormalities. In particular, a number of recent studies have found associations between exposures to traffic-related air pollution and autism spectrum disorders (ASD), which are characterized by impairment in socialization and in communication and by the presence of repetitive and unusual behaviors. The cause(s) of ASD are unknown, and while it may have a hereditary component, environmental factors are increasingly suspected as playing a pivotal role in its etiology, particularly in genetically susceptible individuals. Autistic children present higher levels of neuroinflammation and systemic inflammation, which are also hallmarks of exposure to traffic-related air pollution. Gene-environment interactions may play a relevant role in determining individual susceptibility to air pollution developmental neurotoxicity. Given the worldwide presence of elevated air pollution, studies on its effects and mechanisms on the developing brain, genetic susceptibility, role in neurodevelopmental disorders, and possible therapeutic interventions are certainly warranted.

Epigenetic regulation of the extrinsic oncosuppressor PTX3 gene in inflammation and cancer

PTX3 is a component of the humoral arm of innate immunity and an extrinsic oncosuppressor gene taming tumor-promoting inflammation. Here, we show that two enhancers differently regulate PTX3 expression: enhancer 1, located 230 kb upstream of PTX3 promoter, mediated the action of inflammatory transcription factors; and enhancer 2, encompassing PTX3 second exon, was implicated in pre-initiation complex assembly. Polycomb repressive complex 2 silenced these regulatory elements and the promoter in basal condition. Enhancer 1 was epigenetically inactivated in early colorectal cancer (CRC) stages, while the promoter and enhancer 2 showed increasingly DNA methylation during CRC progression from adenomas to stage II and III CRC. Inhibition of DNA methylation rescued PTX3 expression in CRC. Finally, enhancer 1 acquired the binding of STAT3 in stage I CRC, and inhibition of STAT3 phosphorylation restored PTX3 activity and decreased enhancer 1 methylation. Thus, the expression of PTX3 is under the control of two enhancers, which emerge as important fine regulators of PTX3 expression in inflammation and cancer.

Pivotal Importance of STAT3 in Protecting the Heart from Acute and Chronic Stress: New Advancement and Unresolved Issues

The transcription factor, signal transducer and activator of transcription 3 (STAT3), has been implicated in protecting the heart from acute ischemic injury under both basal conditions and as a crucial component of pre- and post-conditioning protocols. A number of anti-oxidant and antiapoptotic genes are upregulated by STAT3 via canonical means involving phosphorylation on Y705 and S727, although other incompletely defined posttranslational modifications are involved. In addition, STAT3 is now known to be present in cardiac mitochondria and to exert actions that regulate the electron transport chain, reactive oxygen species production, and mitochondrial permeability transition pore opening. These non-canonical actions of STAT3 are enhanced by S727 phosphorylation. The molecular basis for the mitochondrial actions of STAT3 is poorly understood, but STAT3 is known to interact with a critical subunit of complex I and to regulate complex I function. Dysfunctional complex I has been implicated in ischemic injury, heart failure, and the aging process. Evidence also indicates that STAT3 is protective to the heart under chronic stress conditions, including hypertension, pregnancy, and advanced age. Paradoxically, the accumulation of unphosphorylated STAT3 (U-STAT3) in the nucleus has been suggested to drive pathological cardiac hypertrophy and inflammation via non-canonical gene expression, perhaps involving a distinct acetylation profile. U-STAT3 may also regulate chromatin stability. Our understanding of how the non-canonical genomic and mitochondrial actions of STAT3 in the heart are regulated and coordinated with the canonical actions of STAT3 is rudimentary. Here, we present an overview of what is currently known about the pleotropic actions of STAT3 in the heart in order to highlight controversies and unresolved issues.

Modulation of learning and memory by cytokines: signaling mechanisms and long term consequences

This review describes the role of cytokines and their downstream signaling cascades on the modulation of learning and memory. Immune proteins are required for many key neural processes and dysregulation of these functions by systemic inflammation can result in impairments of memory that persist long after the resolution of inflammation. Recent research has demonstrated that manipulations of individual cytokines can modulate learning, memory, and synaptic plasticity. The many conflicting findings, however, have prevented a clear understanding of the precise role of cytokines in memory. Given the complexity of inflammatory signaling, understanding its modulatory role requires a shift in focus from single cytokines to a network of cytokine interactions and elucidation of the cytokine-dependent intracellular signaling cascades. Finally, we propose that whereas signal transduction and transcription may mediate short-term modulation of memory, long-lasting cellular and molecular mechanisms such as epigenetic modifications and altered neurogenesis may be required for the long lasting impact of inflammation on memory and cognition.

Genomic and computational approaches to dissect the mechanisms of STAT3's universal and cell type-specific functions

STAT3 is the quintessential pleiotropic transcription factor with many biological roles throughout development as well as in multiple adult tissues. Its functional heterogeneity is encoded in the range of genome-wide binding patterns that specify different regulatory networks in distinct cell types. However, STAT3 does not display remarkable DNA binding preferences that may help correlate specific motifs with individual biological functions or cell types. Therefore, achieving a detailed understanding of the regulatory mechanisms that endow STAT3 (or any other pleiotropic transcription factor) with such a rainbow of functions is not only a central problem in biology but also a fiendishly difficult one. Here we describe key genomic and computational approaches that have shed light into this question, and present the two current models of STAT3 binding (universal and cell type-specific). We also discuss the role that the local epigenetic environment plays in the selection of STAT3 binding sites.