Non-coding RNAs as regulators in epigenetics

Role of lncRNA PVT1 in the progression of urological cancers: Novel insights into signaling pathways and clinical opportunities

Urologic malignancies, encompassing cancers of the kidney, bladder, and prostate, represent approximately 25 % of all cancer cases. Recent advances have enhanced our understanding of PVT1's crucial functions. Long noncoding RNAs influence both the onset and development of cancer, as well as epigenetic alterations. Recent findings have focused on PVT1's mechanism of action across several malignancies, particularly urologic cancers. Understanding the various functions of PVT1 linked to cancer is necessary for the development of cancer detection and treatment when PVT1 is dysregulated. Furthermore, recent advancements in genomic and epigenetic research have elucidated the complex regulatory networks that control PVT1 expression. Comprehending the intricate role of PVT1 Understanding the complex function of PVT1 in urologic cancers has substantial clinical implications. Here, we summarize some of the most recent findings about the carcinogenic effects of PVT1 signaling pathways and the possible treatment strategies for urological malignancies that target these pathways.

Roles of non-coding RNAs and exosomal non-coding RNAs, particularly microRNAs, long non-coding RNAs, and circular RNAs, in pathogenic mechanisms behind chronic pain: A review

Chronic pain is a significant public health concern that diminishes patients' quality of life and imposes considerable socioeconomic costs. Effective pharmacological treatments for ongoing pain are limited. Recent studies have indicated that various models of chronic pain-such as neuropathic pain, inflammatory pain, and pain associated with cancer-have abnormal levels of long noncoding RNAs (lncRNAs). Research has explored how these abnormal lncRNAs influence the activation of inflammatory cytokines, microRNAs, and other related molecules, which are crucial to the development of chronic pain. These findings suggest that these lncRNAs are vital in chronic pain mechanisms within the spinal cord and dorsal root ganglion following nerve injury. Additionally, exosomes, which can traverse the blood-brain barrier, are considered carriers of noncoding RNAs (ncRNAs) from neurons to systemic circulation. This study aims to summarize the existing knowledge on ncRNAs and exosomal ncRNAs in the context of chronic pain, highlighting potential biomarkers for diagnosis, regulatory roles in disease progression, therapeutic strategies, and clinical implications.

Advancing Ischemic Stroke Prognosis: Key Role of MiR-155 Non-Coding RNA

Ischemic stroke (IS) is the leading cause of long-term disability and the second leading cause of death worldwide. It remains a significant clinical problem because only supportive therapies exist, such as thrombolytic agents and surgical thrombectomy, which do not restore function. Understanding the molecular pathogenesis of IS, including dysfunction in oxidative homeostasis, apoptosis, neuroinflammation and neuroprotection, is crucial to developing therapies. Non-coding RNAs (ncRNAs) are master regulators, and one ncRNA that stands out is miR-155, a pro-inflammatory micro-RNA elevated in stroke. This review addresses the biological mechanisms reported in the literature that support using miR-155 as a biomarker and therapeutic agent to treat IS in patients.

Tumor heterogeneity in retinoblastoma: a literature review

Tumor heterogeneity, characterized by the presence of diverse cell populations within a tumor, is a key feature of the complex nature of cancer. This diversity arises from the emergence of cells with varying genomic, epigenetic, transcriptomic, and phenotypic profiles over the course of the disease. Host factors and the tumor microenvironment play crucial roles in driving both inter-patient and intra-patient heterogeneity. These diverse cell populations can exhibit different behaviors, such as varying rates of proliferation, responses to treatment, and potential for metastasis. Both inter-patient heterogeneity and intra-patient heterogeneity pose significant challenges to cancer therapeutics and management. In retinoblastoma, while heterogeneity at the clinical presentation level has been recognized for some time, recent attention has shifted towards understanding the underlying cellular heterogeneity. This review primarily focuses on retinoblastoma heterogeneity and its implications for therapeutic strategies and disease management, emphasizing the need for further research and exploration in this complex and challenging area.

Exploring the Fanconi Anemia Gene Expression and Regulation by MicroRNAs in Gilthead Seabream (Sparus aurata) at Different Gonadal Development Stages

Fanconi anaemia (FA) is a rare autosomal recessive disease in humans that is distributed worldwide. Fanconi anemia complementation (Fanc) proteins are essential for the appropriate functioning of the FA DNA repair pathway. They are also linked to a number of other biological processes, including oxygen metabolism, cell cycle regulation, haematopoiesis and apoptosis. So far, little research has been conducted on teleosts, but evidence shows that Fanc proteins play a significant role in immune response and sex reversal. For the examination of the expression of three fanc genes (fancc, fancl, and fancd2), as well as the potential regulation of these genes by microRNAs (miRNAs) in gonadal tissues at different stages of development, the present study has selected the gilthead seabream (Sparus aurata), a significant aquaculture species that exhibits protandrous hermaphroditism. The obtained data suggested the role of fancl and fancd2 in the maturation of female gonads and the miRNAs miR-210, miR-217 and miR-10926 have been identified as putative regulators of fancd2, fancc and fancl, respectively. Overall, the data indicated the potential use of fancl and fancd2 genes as sex biomarkers in conjunction with their respective regulation by miRNAs. To the best of our knowledge, this is the first study demonstrating the importance of fanc genes, along with putative regulatory miRNAs, in the reproduction of an important marine aquaculture species.

Epigenetic Symphony in Diffuse Large B-Cell Lymphoma: Orchestrating the Tumor Microenvironment

DLBCL is a testament to the complexity of nature. It is characterized by remarkable diversity in its molecular and pathological subtypes and clinical manifestations. Despite the strides made in DLBCL treatment and the introduction of innovative drugs, around one-third of patients face a relapse or develop refractory disease. Recent findings over the past ten years have highlighted the critical interplay between the evolution of DLBCL and various epigenetic mechanisms, including chromatin remodeling, DNA methylation, histone modifications, and the regulatory roles of non-coding RNAs. These epigenetic alterations are integral to the pathways of oncogenesis, tumor progression, and the development of therapeutic resistance. In the past decade, the identification of dysregulated epigenetic mechanisms in lymphomas has paved the way for an exciting field of epigenetic therapies. Crucially, these epigenetic transformations span beyond tumor cells to include the sophisticated network within the tumor microenvironment (TME). While the exploration of epigenetic dysregulation in lymphoma cells is thriving, the mechanisms affecting the functions of immune cells in the TME invite further investigation. This review is dedicated to weaving together the narrative of epigenetic alterations impacting both lymphoma cells with a focus on their infiltrating immune companions.

Premature aging and metabolic diseases: the impact of telomere attrition

Driven by genetic and environmental factors, aging is a physiological process responsible for age-related degenerative changes in the body, cognitive decline, and impaired overall wellbeing. Notably, premature aging as well as the emergence of progeroid syndromes have posed concerns regarding chronic health conditions and comorbidities in the aging population. Accelerated telomere attrition is also implicated in metabolic dysfunction and the development of metabolic disorders. Impaired metabolic homeostasis arises secondary to age-related increases in the synthesis of free radicals, decreased oxidative capacity, impaired antioxidant defense, and disrupted energy metabolism. In particular, several cellular and molecular mechanisms of aging have been identified to decipher the influence of premature aging on metabolic diseases. These include defective DNA repair, telomere attrition, epigenetic alterations, and dysregulation of nutrient-sensing pathways. The role of telomere attrition premature aging in the pathogenesis of metabolic diseases has been largely attributed to pro-inflammatory states that promote telomere shortening, genetic mutations in the telomerase reverse transcriptase, epigenetic alteration, oxidative stress, and mitochondrial dysfunctions. Nonetheless, the therapeutic interventions focus on restoring the length of telomeres and may include treatment approaches to restore telomerase enzyme activity, promote alternative lengthening of telomeres, counter oxidative stress, and decrease the concentration of pro-inflammatory cytokines. Given the significance and robust potential of delaying telomere attrition in age-related metabolic diseases, this review aimed to explore the molecular and cellular mechanisms of aging underlying premature telomere attrition and metabolic diseases, assimilating evidence from both human and animal studies.

Mechanism of non-coding RNA regulation of DNMT3A

BACKGROUND

De novo DNA methylation by DNMT3A is a fundamental epigenetic modification for transcriptional regulation. Histone tails and regulatory proteins regulate DNMT3A, and the crosstalk between these epigenetic mechanisms ensures appropriate DNA methylation patterning. Based on findings showing that Fos ecRNA inhibits DNMT3A activity in neurons, we sought to characterize the contribution of this regulatory RNA in the modulation of DNMT3A in the presence of regulatory proteins and histone tails.

RESULTS

We show that Fos ecRNA and mRNA strongly correlate in primary cortical neurons on a single cell level and provide evidence that Fos ecRNA modulation of DNMT3A at these actively transcribed sites occurs in a sequence-independent manner. Further characterization of the Fos ecRNA-DNMT3A interaction showed that Fos-1 ecRNA binds the DNMT3A tetramer interface and clinically relevant DNMT3A substitutions that disrupt the inhibition of DNMT3A activity by Fos-1 ecRNA are restored by the formation of heterotetramers with DNMT3L. Lastly, using DNMT3L and Fos ecRNA in the presence of synthetic histone H3 tails or reconstituted polynucleosomes, we found that regulatory RNAs play dominant roles in the modulation of DNMT3A activity.

CONCLUSION

Our results are consistent with a model for RNA regulation of DNMT3A that involves localized production of short RNAs binding to a nonspecific site on the protein, rather than formation of localized RNA/DNA structures. We propose that regulatory RNAs play a dominant role in the regulation of DNMT3A catalytic activity at sites with increased production of regulatory RNAs.

Non-coding RNAs as key regulators of epithelial-mesenchymal transition in breast cancer

This study examines the critical role of non-coding RNAs (ncRNAs) in regulating epithelial-mesenchymal transition (EMT) in breast cancer, a prevalent malignancy with significant metastatic potential. EMT, wherein cancer cells acquire mesenchymal traits, is fundamental to metastasis. ncRNAs-such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs)-modulate EMT by influencing gene expression and signaling pathways, affecting cancer cell migration and invasion. This review consolidates recent findings on ncRNA-mediated EMT regulation and explores their diagnostic and therapeutic potential. Specifically, miRNAs inhibit EMT-related transcription factors, while lncRNAs and circRNAs regulate gene expression through interactions with miRNAs, impacting EMT progression. Given the influence of ncRNAs on metastasis and therapeutic resistance, advancing ncRNA-based biomarkers and treatments holds promise for improving breast cancer outcomes.

Roles of microRNAs in cardiorenal syndrome

Cardiac and kidney diseases are intimately linked through numerous pathophysiological pathways, frequently exerting reciprocal influences on one another. This interconnection often culminates in heightened morbidity and mortality rates within the clinical spectrum of cardiorenal syndrome (CRS). CRS is categorized into five types based on the primary organ involved and the chronicity of the condition. Each type of CRS encompasses a complex array of pathophysiological mechanisms. In recent years, the field of microRNAs (miRNAs) has risen to prominence, playing a crucial role in the pathogenesis of a multitude of diseases. By uncovering novel therapeutic targets through the study of miRNAs that influence the expression of the CRS genes, the prognostic outcomes for patients could be significantly improved. This article provides a comprehensive review, examining the pathophysiological underpinnings of CRS, miRNAs alterations and their associated mechanisms in various forms of CRS, as well as the potential of miRNAs in precision medicine and the use of miRNAs for the diagnosis of the disease.

Genomic insights into pigeon breeding: GWAS for economic traits and the development of a high-throughput liquid phase array chip

Due to the monogamous mating system and late maturity of pigeons, their breeding cycle is longer compared to that of other poultry species, which has hindered the optimization of growth traits and meat quality. While traditional breeding methods are commonly used, they lack precision and are time-consuming. This study integrates phenotypic data from Tarim pigeons and White King pigeons with genomic information, using genome-wide association analysis (GWAS) to identify genetic markers associated with key economic traits, thereby accelerating the breeding process. The results reveal significant correlations between body type characteristics (e.g., live weight and chest depth) and carcass traits, supporting their use as indirect selection criteria. GWAS identified several candidate genes, including PPARGC1A and ADGRA3, linked to muscle development and metabolic regulation. To enhance breeding efficiency, this study developed a Liquid Phase Chip (LPC), designed to use high-throughput technology for identifying genetic markers related to carcass traits. Although the LPC is not yet commercially available, the 50 K pigeon LPC from this study could provide crucial theoretical support for its future application. Ultimately, the LPC will serve as an important tool for precision and efficiency in pigeon breeding, driving the development and optimization of the pigeon industry.

Innovative perspectives on glioblastoma: the emerging role of long non-coding RNAs

Glioblastoma (GBM) is a highly aggressive and treatment-resistant brain tumor. Recent advancements have highlighted the crucial role of long noncoding RNAs (lncRNAs) in GBM's molecular biology. Unlike protein-coding RNAs, lncRNAs regulate gene expression through transcription, post-transcriptional modifications, and chromatin remodeling. Some lncRNAs, like HOTAIR, CCAT2, CRNDE, and MALAT1, promote GBM development by affecting tumor suppressors and various signaling pathways like PI3K/Akt, mTOR, EGFR, NF-κB, and Wnt/β-catenin. Conversely, certain lncRNAs such as TUG1, MEG3, and GAS8-AS1 act as tumor suppressors and are associated with better prognosis. The study presented in the manuscript aims to explore the involvement of lncRNAs in GBM, focusing on their roles in tumor progression, proliferation, invasion, and potential implications for early detection and immunotherapy. The research seeks to elucidate the mechanisms by which specific lncRNAs influence GBM characteristics and highlight their potential as therapeutic targets or biomarkers in managing this aggressive form of brain cancer.

Energy Stress-Induced circEPB41(2) Promotes Lipogenesis in Hepatocellular Carcinoma

The tumor microenvironment plays a pivotal role in the metabolic reprogramming of cancer cells. A better understanding of the underlying mechanisms regulating cancer metabolism could help identify potential therapeutic targets. Here, we identified circEPB41(2) as a metabolically regulated circular RNA that mediates lipid metabolism in hepatocellular carcinoma (HCC). circEPB41(2) was induced in response to glucose deprivation via HNRNPA1-dependent alternative splicing. Upregulation of circEPB41(2) led to enhanced lipogenic gene expression that promoted lipogenesis. Mechanistically, circEPB41(2) cooperated with the N6-methyladenosine demethylase FTO to decrease the mRNA stability of the histone deacetylase sirtuin 6, thereby increasing histone H3 lysine 9 acetylation and histone H3 lysine 27 acetylation levels to activate lipogenic gene expression. Silencing of circEPB41(2) inhibited both in vitro proliferation of HCC cells and in vivo growth of tumor xenografts. Clinically, circEPB41(2) was elevated in HCC, and high circEPB41(2) expression was associated with poor patient prognosis. Overall, this study reveals that circEPB41(2) is an important regulator of lipid metabolic reprogramming and indicates that targeting the circEPB41(2)-FTO-sirtuin 6 axis could represent a promising anticancer strategy for treating HCC. Significance: circEPB41(2) is induced by glucose deprivation and mediates epigenetic alterations to drive lipogenesis and tumor growth in hepatocellular carcinoma, suggesting circEPB41(2) could be a potential therapeutic target in liver cancer.

Toward Understanding and Halting Legacies of Trauma

Echoes of natural and anthropogenic stressors not only reverberate within the physiology, biology, and neurobiology of the generation directly exposed to them but also within the biology of future generations. With the intent of understanding this phenomenon, significant efforts have been made to establish how exposure to psychosocial stress, chemicals, over- and undernutrition, and chemosensory experiences exert multigenerational influences. From these studies, we are gaining new appreciation for how negative environmental events experienced by one generation impact future generations. In this review, we first outline the need to operationally define dimensions of negative environmental events in the laboratory and the routes by which the impact of such events are felt through generations. Next, we discuss molecular processes that cause the effects of negative environmental events to be initiated in the exposed generation and then perpetuated across generations. Finally, we discuss how legacies of flourishing can be engineered to halt or reverse multigenerational influences of negative environmental events. In summary, this review synthesizes our current understanding of the concept, causes, and consequences of multigenerational echoes of stress and looks for opportunities to halt them.

Molecular Mechanisms of Immune Regulation: A Review

BACKGROUND

The immune system must carefully balance fighting pathogens with minimization of inflammation and avoidance of autoimmune responses. Over the past ten years, researchers have extensively studied the mechanisms regulating this delicate balance. Comprehending these mechanisms is essential for developing treatments for inflammatory conditions.

AIM

This review aims to synthesize knowledge of immunoregulatory processes published from 2014-2024 and to highlight discoveries that provide fresh perspectives on this complex balance.

METHODS

The keywords "molecular mechanisms", "immune regulation", "immune signaling pathways", and "immune homeostasis" were used to search PubMed for articles published between 2014 and 2024, with a preference for articles published in the past three years.

RESULTS

Recent research has pinpointed the impact of factors such as cytokine signaling, T-cell regulation, epigenetic regulation, and immunometabolism on immune function.

DISCUSSION

New research highlights the intricate interactions between the immune system and other molecular elements. A key area of interest is the impact of non-coding RNAs and metabolic pathways on the regulation of immune responses.

CONCLUSIONS

Exploring the mechanisms by which the immune system is regulated will provide new avenues for developing treatments to address autoimmune and inflammatory conditions.

Histone demethylase inhibitor KDM5-C70 regulates metabolomic and lipidomic programming during an astrocyte differentiation of rat neural stem cell

Lysine-specific histone demethylase (KDM) 5 inhibition by KDM5-C70 induces astrocytogenesis and highlights the importance of modulation of histone methylation in cell fate specification. This study investigated the role of the histone demethylase inhibitor KDM5-C70 in modulating the metabolic and lipidomic landscape during astrocyte differentiation of rat neural stem cells (NSCs). Using chemical derivatisation combined with gas chromatography-mass spectrometry, 42 metabolites were detected, indicating potential regulation of phospholipid metabolism. Subsequent lipidomic analysis, employing reverse-phase liquid chromatography with high-resolution quadrupole time-of-flight mass spectrometry, identified 180 lipid species and 9 lipid subclasses. Integrative analysis revealed that KDM5-C70 promoted astrocytogenesis through epigenetic changes linked to the attenuation of phosphatidylethanolamine (PE) biosynthesis pathways. The reduced expression of transcripts related to PE highlighted the significance of the PE pathway in influencing cell fate decisions. These quantitative metabolomic and lipidomic analyses not only advance our understanding of NSC differentiation but also lay the groundwork for potential therapeutic strategies targeting metabolic pathways in neurodegenerative diseases and neural injuries.

Long non-coding RNA involved in the carcinogenesis of human female cancer - a comprehensive review

Recent years have seen an increase in our understanding of lncRNA and their role in various disease states. lncRNA molecules have been shown to contribute to carcinogenesis and influence the various cancer hallmarks and signalling pathways. It is pertinent to understand the specific contributions and mechanisms of action of these molecules in various cancers. This review provides an overview of the various lncRNA entities that influence and regulate the gynaecological cancers, namely, cervical, breast, ovarian and uterine cancers. The review curates a list of the key players and their effect on cellular processes. lncRNA molecules show immense potential to be used as diagnostic and prognostic indicators and in therapeutic strategies. Several phytochemicals, small molecules, RNA-based regulators, oligos and gene editing tools show promise as a therapeutic strategy. While this review highlights the promising developments in this field, it also underscores the necessity for further research to delineate the complex role of lncRNAs in cancer.

Cellular Epigenetic Targets and Epidrugs in Breast Cancer Therapy: Mechanisms, Challenges, and Future Perspectives

Breast cancer is the most common malignancy affecting women, manifesting as a heterogeneous disease with diverse molecular characteristics and clinical presentations. Recent studies have elucidated the role of epigenetic modifications in the pathogenesis of breast cancer, including drug resistance and efflux characteristics, offering potential new diagnostic and prognostic markers, treatment efficacy predictors, and therapeutic agents. Key modifications include DNA cytosine methylation and the covalent modification of histone proteins. Unlike genetic mutations, reprogramming the epigenetic landscape of the cancer epigenome is a promising targeted therapy for the treatment and reversal of drug resistance. Epidrugs, which target DNA methylation and histone modifications, can provide novel options for the treatment of breast cancer by reversing the acquired resistance to treatment. Currently, the most promising approach involves combination therapies consisting of epidrugs with immune checkpoint inhibitors. This review examines the aberrant epigenetic regulation of breast cancer initiation and progression, focusing on modifications related to estrogen signaling, drug resistance, cancer progression, and the epithelial-mesenchymal transition (EMT). It examines existing epigenetic drugs for treating breast cancer, including agents that modify DNA, inhibitors of histone acetyltransferases, histone deacetylases, histone methyltransferases, and histone demethyltransferases. It also delves into ongoing studies on combining epidrugs with other therapies and addresses the upcoming obstacles in this field.

Aberrant expression of messenger and small noncoding RNAomes in aged skin of rats

The exact mechanisms and key functional molecules involved in skin ageing remain largely unknown. Studies linking the expression of messenger RNAs (mRNAs) and small noncoding RNAs (sncRNAs) to skin ageing are limited. In this study, we performed RNA sequencing to assess the effects of ageing on the expression of mRNAs and sncRNAs in rat skin. Our results revealed that 241 mRNAs, 109 microRNAs (miRNAs), 20 piwi-interacting RNAs (piRNAs), 45 small nucleolar RNAs (snoRNAs), and 7 small nuclear RNAs (snRNAs) were significantly differentially expressed in the skin of aged rats compared to their younger counterparts. Histological validation using RT-qPCR further verified the significant differential expression of 13 mRNAs, 7 miRNAs, 2 piRNAs, 15 snoRNAs, and 1 snRNA. Additionally, several sncRNAs showed differential expression across various tissues, suggesting that they may have broad correlations with ageing. After establishing cellular senescence in skin fibroblasts, we identified 4 mRNAs, 4 miRNAs, and 10 snoRNAs that may mediate skin ageing by modulating fibroblast senescence. Notably, overexpression or knockdown of some differentially expressed RNAs in fibroblasts influenced cellular senescence, indicating that these RNAs could play an important role in the skin ageing process. These findings highlight their potential significance for future treatments of age-related skin disorders.

Innate Immune Response and Epigenetic Regulation: A Closely Intertwined Tale in Inflammation

Maintenance of delicate homeostasis is very important in various diseases because it ensures appropriate immune surveillance against pathogens and prevents excessive inflammation. In a disturbed homeostatic condition, hyperactivation of immune cells takes place and interplay between these cells triggers a plethora of signaling pathways, releasing various pro-inflammatory cytokines such as Tumor necrosis factor alpha (TNFα), Interferon-gamma (IFNƴ), Interleukin-6 (IL-6), and Interleukin-1 beta (IL-1β), which marks cytokine storm formation. To be precise, dysregulated balance can impede or increase susceptibility to various pathogens. Pathogens have the ability to hijack the host immune system by interfering with the host's chromatin architecture for their survival and replication in the host cell. Cytokines, particularly IL-6, Interleukin-17 (IL-17), and Interleukin-23 (IL-23), play a key role in orchestrating innate immune responses and shaping adaptive immunity. Understanding the interplay between immune response and the role of epigenetic modification to maintain immune homeostasis and the structural aspects of IL-6, IL-17, and IL-23 can be illuminating for a novel therapeutic regimen to treat various infectious diseases. In this review, the light is shed on how the orchestration of epigenetic regulation facilitates immune homeostasis.

Non-coding RNA biosensors for early detection of brain cancer

Brain cancer remains a formidable challenge with limited treatment options. Non-coding RNAs (ncRNAs) have emerged as promising biomarkers due to their dysregulation in tumorigenesis. This review explores the potential of biosensors for early detection of brain cancer by targeting ncRNAs. We discuss the classification and functions of ncRNAs, emphasizing their involvement in key cancer-related processes. Additionally, we delve into recent advancements in biosensor technology, focusing on their ability to accurately detect specific ncRNA biomarkers associated with brain cancer. Our findings underscore the potential of biosensors to revolutionize brain cancer diagnosis, enabling personalized medicine and improving patient outcomes. Future research should focus on refining biosensor technology and expanding their clinical application.

The Role of Chronic Inflammation in Pediatric Cancer

Inflammation plays a crucial role in wound healing and the host immune response following pathogenic invasion. However, unresolved chronic inflammation can result in tissue fibrosis and genetic alterations that contribute to the pathogenesis of human diseases such as cancer. Recent scientific advancements exploring the underlying mechanisms of malignant cellular transformations and cancer progression have exposed significant disparities between pediatric and adult-onset cancers. For instance, pediatric cancers tend to have lower mutational burdens and arise in actively developing tissues, where cell-cycle dysregulation leads to gene, chromosomal, and fusion gene development not seen in adult-onset counterparts. As such, scientific findings in adult cancers cannot be directly applied to pediatric cancers, where unique mutations and inherent etiologies remain poorly understood. Here, we review the role of chronic inflammation in processes of genetic and chromosomal instability, the tumor microenvironment, and immune response that result in pediatric tumorigenesis transformation and explore current and developing therapeutic interventions to maintain and/or restore inflammatory homeostasis.

Adaptive Significance of Non-coding RNAs: Insights from Cancer Biology

The molecular basis of adaptive evolution and cancer progression are both complex processes that share many striking similarities. The potential adaptive significance of environmentally-induced epigenetic changes is currently an area of great interest in both evolutionary and cancer biology. In the field of cancer biology intense effort has been focused on the contribution of stress-induced non-coding RNAs (ncRNAs) in the activation of epigenetic changes associated with elevated mutation rates and the acquisition of environmentally adaptive traits. Examples of this process are presented and combined with more recent findings demonstrating that stress-induced ncRNAs are transferable from somatic to germline cells leading to cross-generational inheritance of acquired adaptive traits. The fact that ncRNAs have been implicated in the transient adaptive response of various plants and animals to environmental stress is consistent with findings in cancer biology. Based on these collective observations, a general model as well as specific and testable hypotheses are proposed on how transient ncRNA-mediated adaptive responses may facilitate the transition to long-term biological adaptation in both cancer and evolution.

DNA Methylation in Alzheimer's Disease

To date, DNA methylation is the best characterized epigenetic modification in Alzheimer's disease. Involving the addition of a methyl group to the fifth carbon of the cytosine pyrimidine base, DNA methylation is generally thought to be associated with the silencing of gene expression. It has been hypothesized that epigenetics may mediate the interaction between genes and the environment in the manifestation of Alzheimer's disease, and therefore studies investigating DNA methylation could elucidate novel disease mechanisms. This chapter comprehensively reviews epigenomic studies, undertaken in human brain tissue and purified brain cell types, focusing on global methylation levels, candidate genes, epigenome wide approaches, and recent meta-analyses. We discuss key differentially methylated genes and pathways that have been highlighted to date, with a discussion on how new technologies and the integration of multiomic data may further advance the field.

Scientific investigation of non-coding RNAs in mitochondrial epigenetic and aging disorders: Current nanoengineered approaches for their therapeutic improvement

Genetic control is vital for the growth of cells and tissues, and it also helps living things, from single-celled organisms to complex creatures, maintain a stable internal environment. Within cells, structures called mitochondria act like tiny power plants, producing energy and keeping the cell balanced. The two primary categories of RNA are messenger RNA (mRNA) and non-coding RNA (ncRNA). mRNA carries the instructions for building proteins, while ncRNA does various jobs at the RNA level. There are different kinds of ncRNA, each with a specific role. Some help put RNA molecules together correctly, while others modify other RNAs or cut them into smaller pieces. Still others control how much protein is made from a gene. Scientists have recently discovered many more ncRNAs than previously known, and their functions are still being explored. This article analyzes the RNA molecules present within mitochondria, which have a crucial purpose in the operation of mitochondria. We'll also discuss how genes can be turned on and off without changing their DNA code, and how this process might be linked to mitochondrial RNA. Finally, we'll explore how scientists are using engineered particles to silence genes and develop new treatments based on manipulating ncRNA.

Gut microbiome-gut brain axis-depression: interconnection

OBJECTIVES

The relationship between the gut microbiome and mental health, particularly depression, has gained significant attention. This review explores the connection between microbial metabolites, dysbiosis, and depression. The gut microbiome, comprising diverse microorganisms, maintains physiological balance and influences health through the gut-brain axis, a communication pathway between the gut and the central nervous system.

METHODS

Dysbiosis, an imbalance in the gut microbiome, disrupts this axis and worsens depressive symptoms. Factors like diet, antibiotics, and lifestyle can cause this imbalance, leading to changes in microbial composition, metabolism, and immune responses. This imbalance can induce inflammation, disrupt neurotransmitter regulation, and affect hormonal and epigenetic processes, all linked to depression.

RESULTS

Microbial metabolites, such as short-chain fatty acids and neurotransmitters, are key to gut-brain communication, influencing immune regulation and mood. The altered production of these metabolites is associated with depression. While progress has been made in understanding the gut-brain axis, more research is needed to clarify causative relationships and develop new treatments. The emerging field of psychobiotics and microbiome-targeted therapies shows promise for innovative depression treatments by harnessing the gut microbiome's potential.

CONCLUSIONS

Epigenetic mechanisms, including DNA methylation and histone modifications, are crucial in how the gut microbiota impacts mental health. Understanding these mechanisms offers new prospects for preventing and treating depression through the gut-brain axis.

Neuroprotective potential of Epigenetic modulators, its regulation and therapeutic approaches for the management of Parkinson's disease

The progressive degeneration of dopaminergic neurons in the substantia nigra region of the brain leads to a deficiency of dopamine and, ultimately, the onset of Parkinson's disease (PD). Since there is currently no cure for PD, patients all around the world are dealing with symptomatic management. PD progression is influenced by multiple elements, such as environmental, biological, chemical, genetic, and epigenetic factors. Epigenetics is gaining increased attention due to its role in controlling the expression of genes that contribute to PD. Recent advancements in our understanding of the brain network and its related conditions have shown that alterations in gene expression may occur independently of genetic abnormalities. Therefore, a thorough investigation has been carried out to explore the significance of epigenetics in all degenerative disorders. Epigenetic modifications are essential for regulating cellular homeostasis. Therefore, a deeper understanding of these modifications might provide valuable insights into many diseases and potentially serve as targets for therapeutic interventions. This review article focuses on diverse epigenetic alterations linked to the progression of PD. These abnormalities are supported by numerous research on the control of gene expression and encompass all the epigenetic processes. The beginning of PD is intricately associated with aberrant DNA methylation mechanisms. DNA methyltransferases are the enzymes that create and preserve various DNA methylation patterns. Integrating epigenetic data with existing clinical methods for diagnosing PD may aid in discovering potential curative medicines and novel drug development approaches. This article solely addresses the importance of epigenetic modulators in PD, primarily the mechanisms of DNMTs, their roles in the development of PD, and their therapeutic approaches; it bypasses other PD therapies.

Advances in CRISPR-Cas technology and its applications: revolutionising precision medicine

CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR-associated proteins) has undergone marked advancements since its discovery as an adaptive immune system in bacteria and archaea, emerged as a potent gene-editing tool after the successful engineering of its synthetic guide RNA (sgRNA) toward the targeting of specific DNA sequences with high accuracy. Besides its DNA editing ability, further-developed Cas variants can also edit the epigenome, rendering the CRISPR-Cas system a versatile tool for genome and epigenome manipulation and a pioneering force in precision medicine. This review explores the latest advancements in CRISPR-Cas technology and its therapeutic and biomedical applications, highlighting its transformative impact on precision medicine. Moreover, the current status of CRISPR therapeutics in clinical trials is discussed. Finally, we address the persisting challenges and prospects of CRISPR-Cas technology.

LncRNA DANCR-V1 is a novel regulator of Wnt/β-catenin and TGF-β1/SMAD signaling pathways in colorectal cancer: an in vitro and in silico study

BACKGROUND

DANCR is an oncogenic lncRNA associated with advanced colorectal cancer, one of the most common malignancies worldwide. This lncRNA has a new variant, DANCR-V1, whose function is not yet understood. In this study, we aimed to evaluate the expression pattern of DANCR-V1 and its regulatory mechanism in colorectal cancer.

METHOD AND RESULT

Bioinformatics analysis and RT-qPCR showed that DANCR-V1 expression was higher in colorectal cancer tissues than in normal pairs obtained from microarray data and 20 samples, respectively. LncRNA subcellular localization and hsa-miR-222 binding sites were predicted using bioinformatics tools. Dual luciferase assays confirmed that miR-222-mediated downregulation of DANCR-V1 through its targeting, and RT-qPCR showed that overexpression of miR-222 decreased the level of DANCR-V1. Functionally, Wnt/β-catenin and TGF-β1/SMAD-related genes changed under DANCR-V1 overexpression in the SW480 cell line, while their expression was reversed following miR-222 overexpression. Finally, at the cellular level, overexpression of DANCR-V1 elevated the proliferation and migration rates of SW480 cells, as determined using flow cytometry, western blotting and scratch assays.

CONCLUSION

Our data suggest that DANCR-V1 is a novel transcript variant that has crucial crosstalk with miR-222 via negative feedback and plays a critical role in colorectal cancer progression through Wnt/β-catenin and TGF-β1/SMAD signaling modulation.

Impact of Z chromosome inversions on gene expression in testis and liver tissues in the zebra finch

Chromosomal inversions have been identified in many natural populations and can be responsible for novel traits and rapid adaptation. In zebra finch, a large region on the Z chromosome has been subject to multiple inversions, which have pleiotropic effects on multiple traits but especially on sperm phenotypes, such as midpiece and flagellum length. To understand the effect, the Z inversion has on these traits, we examined testis and liver transcriptomes of young males at different maturation times. We compared gene expression differences among three inversion karyotypes: AA, B*B* and AB*, where B* denotes the inverted regions on Z with respect to A. In testis, 794 differentially expressed genes were found and most of them were located on chromosome Z. They were functionally enriched for sperm-related traits. We also identified clusters of co-expressed genes that matched with the inversion-related sperm phenotypes. In liver, there were some enriched functions and some overrepresentation on chromosome Z with similar location as in testis. In both tissues, the overrepresented genes were located near the distal end of Z but also in the middle of the chromosome. For the heterokaryotype, we observed several genes with one allele being dominantly expressed, similar to expression patterns in one or the other homokaryotype. This was confirmed with SNPs for three genes, and interestingly one gene, DMGDH, had allele-specific expression originating mainly from one inversion haplotype in the testis, yet both inversion haplotypes were expressed equally in the liver. This karyotype-specific difference in tissue-specific expression suggests a pleiotropic effect of the inversion and thus suggests a mechanism for divergent phenotypic effects resulting from an inversion.

The Effect of Maternal Diet and Lifestyle on the Risk of Childhood Obesity

Background/Objectives: Childhood obesity is a global health problem that affects at least 41 million children under the age of five. Increased BMI in children is associated with serious long-term health consequences, such as type 2 diabetes, cardiovascular disease, and psychological problems, including depression and low self-esteem. Although the etiology of obesity is complex, research suggests that the diet and lifestyle of pregnant women play a key role in shaping metabolic and epigenetic changes that can increase the risk of obesity in their children. Excessive gestational weight gain, unhealthy dietary patterns (including the Western diet), and pregnancy complications (such as gestational diabetes) are some of the modifiable factors that contribute to childhood obesity. The purpose of this narrative review is to summarize the most important and recent information on the impact of the diet and lifestyle of pregnant women on the risk of childhood obesity. Methods: This article is a narrative review that aims to summarize the available literature on the impact of pregnant women's diet and lifestyle on the risk of obesity in their offspring, with a focus on metabolic and epigenetic mechanisms. Results/Conclusions: Current evidence suggests that a pregnant woman's lifestyle and diet can significantly contribute to lowering the risk of obesity in their offspring. However, further high-quality research is needed to understand better the metabolic and epigenetic relationships concerning maternal factors that predispose offspring to obesity.

The Tumour Microenvironment and Epigenetic Regulation in BRCA1 Pathogenic Variant-Associated Breast Cancers

Background/Objectives: BRCA1 pathogenic variant (PV)-associated breast cancers are most commonly seen in hereditary genetic conditions such as the autosomal-dominant Hereditary Breast and Ovarian Cancer (HBOC) syndrome, and rarely in sporadic breast cancer. Such breast cancers tend to exhibit greater aggressiveness and poorer prognoses due to the influence of BRCA1 pathogenic variants (PVs) on the tumour microenvironment. Additionally, while the genetic basis of BRCA1 PV breast cancer is well-studied, the role of epigenetic mediators in the tumourigenesis of these hereditary breast cancers is also worth exploring. Results: PVs in the BRCA1 gene interact with stromal cells and immune cells, promoting epithelial-mesenchymal transition, angiogenesis, and affecting oestrogen levels. Additionally, BRCA1 PVs contribute to breast cancer development through epigenetic effects on cells, including DNA methylation and histone acetylation, leading to the suppression of proto-oncogenes and dysregulation of cytokines. In terms of epigenetics, lysine-specific demethylase 1 (LSD-1) is considered a master epigenetic regulator, governing both transcriptional repression and activation. It exerts epigenetic control over BRCA1 and, to a lesser extent, BRCA2 genes. The upregulation of LSD-1 is generally associated with a poorer prognosis in cancer patients. In the context of breast cancer in BRCA1/2 PV carriers, LSD-1 contributes to tumour development through various mechanisms. These include the maintenance of a hypoxic environment and direct suppression of BRCA1 gene expression. Conclusions: While LSD-1 itself does not directly cause mutations in BRCA1 or BRCA2 genes, its epigenetic influence sheds light on the potential role of LSD-1 inhibitors as a therapeutic approach in managing breast cancer, particularly in individuals with BRCA1/2 PVs. Targeting LSD-1 may help counteract its detrimental effects and provide a promising avenue for therapy in this specific subgroup of breast cancer.

Mechanisms Behind the Impact of PIWI Proteins on Cancer Cells: Literature Review

The P-Element-induced wimpy testis (PIWI) group of proteins plays a key role in RNA interference, particularly in the regulation of small non-coding RNAs. However, in recent years, PIWIs have gained attention in several diseases, mainly cancer. Therefore, the aim of this review was to evaluate current knowledge about the impact of PIWI proteins on cancer cells. PIWIs alter a number of pathways within cells, resulting in significant changes in cell behavior. Basic processes of cancer cells have been shown to be altered by either overexpression or inhibition of PIWIs. Regulation of apoptosis, metastasis, invasion, or proliferation of cancerous cells by these proteins proves their involvement in the progression of the malignancy. It has been revealed that PIWIs are also connected with cancer stem cells (CSCs), which proves their ability to become a therapeutic target. However, research on this topic is still fairly limited, and with significant differences between cancer types, it is necessary to refrain from making any decisive conclusions.

Mitochondria: the epigenetic regulators of ovarian aging and longevity

Ovarian aging is a major health concern for women. Ovarian aging is associated with reduced health span and longevity. Mitochondrial dysfunction is one of the hallmarks of ovarian aging. In addition to providing oocytes with optimal energy, the mitochondria provide a co-substrate that drives epigenetic processes. Studies show epigenetic alterations, both nuclear and mitochondrial contribute to ovarian aging. Both, nuclear and mitochondrial genomes cross-talk with each other, resulting in two ways orchestrated anterograde and retrograde response that involves epigenetic changes in nuclear and mitochondrial compartments. Epigenetic alterations causing changes in metabolism impact ovarian function. Key mitochondrial co-substrate includes acetyl CoA, NAD+, ATP, and α-KG. Thus, enhancing mitochondrial function in aging ovaries may preserve ovarian function and can lead to ovarian longevity and reproductive and better health outcomes in women. This article describes the role of mitochondria-led epigenetics involved in ovarian aging and discusses strategies to restore epigenetic reprogramming in oocytes by preserving, protecting, or promoting mitochondrial function.

Epigenetic Explorations of Neurological Disorders, the Identification Methods, and Therapeutic Avenues

Neurodegenerative disorders are major health concerns globally, especially in aging societies. The exploration of brain epigenomes, which consist of multiple forms of DNA methylation and covalent histone modifications, offers new and unanticipated perspective into the mechanisms of aging and neurodegenerative diseases. Initially, chromatin defects in the brain were thought to be static abnormalities from early development associated with rare genetic syndromes. However, it is now evident that mutations and the dysregulation of the epigenetic machinery extend across a broader spectrum, encompassing adult-onset neurodegenerative diseases. Hence, it is crucial to develop methodologies that can enhance epigenetic research. Several approaches have been created to investigate alterations in epigenetics on a spectrum of scales-ranging from low to high-with a particular focus on detecting DNA methylation and histone modifications. This article explores the burgeoning realm of neuroepigenetics, emphasizing its role in enhancing our mechanistic comprehension of neurodegenerative disorders and elucidating the predominant techniques employed for detecting modifications in the epigenome. Additionally, we ponder the potential influence of these advancements on shaping future therapeutic approaches.

Tumor Biology Hides Novel Therapeutic Approaches to Diffuse Large B-Cell Lymphoma: A Narrative Review

Diffuse large B-cell lymphoma (DLBCL) is a malignancy of immense biological and clinical heterogeneity. Based on the transcriptomic or genomic approach, several different classification schemes have evolved over the years to subdivide DLBCL into clinically (prognostically) relevant subsets, but each leaves unclassified samples. Herein, we outline the DLBCL tumor biology behind the actual and potential drug targets and address the challenges and drawbacks coupled with their (potential) use. Therapeutic modalities are discussed, including small-molecule inhibitors, naked antibodies, antibody-drug conjugates, chimeric antigen receptors, bispecific antibodies and T-cell engagers, and immune checkpoint inhibitors. Candidate drugs explored in ongoing clinical trials are coupled with diverse toxicity issues and refractoriness to drugs. According to the literature on DLBCL, the promise for new therapeutic targets lies in epigenetic alterations, B-cell receptor and NF-κB pathways. Herein, we present putative targets hiding in lipid pathways, ferroptosis, and the gut microbiome that could be used in addition to immuno-chemotherapy to improve the general health status of DLBCL patients, thus increasing the chance of being cured. It may be time to devote more effort to exploring DLBCL metabolism to discover novel druggable targets. We also performed a bibliometric and knowledge-map analysis of the literature on DLBCL published from 2014-2023.

HOXDeRNA activates a cancerous transcription program and super enhancers via genome-wide binding

The role of long non-coding RNAs (lncRNAs) in malignant cell transformation remains elusive. We previously identified an enhancer-associated lncRNA, LINC01116 (named HOXDeRNA), as a transformative factor converting human astrocytes into glioma-like cells. Employing a combination of CRISPR editing, chromatin isolation by RNA purification coupled with sequencing (ChIRP-seq), in situ mapping RNA-genome interactions (iMARGI), chromatin immunoprecipitation sequencing (ChIP-seq), HiC, and RNA/DNA FISH, we found that HOXDeRNA directly binds to CpG islands within the promoters of 35 glioma-specific transcription factors (TFs) distributed throughout the genome, including key stem cell TFs SOX2, OLIG2, POU3F2, and ASCL1, liberating them from PRC2 repression. This process requires a distinct RNA quadruplex structure and other segments of HOXDeRNA, interacting with EZH2 and CpGs, respectively. Subsequent transformation activates multiple oncogenes (e.g., EGFR, miR-21, and WEE1), driven by the SOX2- and OLIG2-dependent glioma-specific super enhancers. These results help reconstruct the sequence of events underlying the process of astrocyte transformation, highlighting HOXDeRNA's central genome-wide activity and suggesting a shared RNA-dependent mechanism in otherwise heterogeneous and multifactorial gliomagenesis.

Long non-coding RNA (LncRNA) and epigenetic factors: their role in regulating the adipocytes in bovine

Investigating the involvement of long non-coding RNAs (lncRNAs) and epigenetic processes in bovine adipocytes can provide valuable new insights into controlling adipogenesis in livestock. Long non-coding RNAs have been associated with forming chromatin loops that facilitate enhancer-promoter interactions during adipogenesis, as well as regulating important adipogenic transcription factors like C/EBPα and PPARγ. They significantly influence gene expression regulation at the post-transcriptional level and are extensively researched for their diverse roles in cellular functions. Epigenetic modifications such as chromatin reorganization, histone alterations, and DNA methylation subsequently affect the activation of genes related to adipogenesis and the progression of adipocyte differentiation. By investigating how fat deposition is epigenetically regulated in beef cattle, scientists aim to unravel molecular mechanisms, identify key regulatory genes and pathways, and develop targeted strategies for modifying fat deposition to enhance desirable traits such as marbling and meat tenderness. This review paper delves into lncRNAs and epigenetic factors and their role in regulating bovine adipocytes while focusing on their potential as targets for genetic improvement to increase production efficiency. Recent genomics advancements, including molecular markers and genetic variations, can boost animal productivity, meeting global demands for high-quality meat products. This review establishes a foundation for future research on understanding regulatory networks linked to lncRNAs and epigenetic changes, contributing to both scholarly knowledge advancement and practical applications within animal agriculture.

Early life epigenetics and childhood outcomes: a scoping review

Epigenetics is the study of changes in gene expression, without a change in the DNA sequence that are potentially heritable. Epigenetic mechanisms such as DNA methylation, histone modifications, and small non-coding RNA (sncRNA) changes have been studied in various childhood disorders. Causal links to maternal health and toxin exposures can introduce epigenetic modifications to the fetal DNA, which can be detected in the cord blood. Cord blood epigenetic modifications provide evidence of in-utero stressors and immediate postnatal changes, which can impact both short and long-term outcomes in children. The mechanisms of these epigenetic changes can be leveraged for prevention, early detection, and intervention, and to discover novel therapeutic modalities in childhood diseases. We report a scoping review of early life epigenetics, the influence of maternal health, maternal toxin, and drug exposures on the fetus, and its impact on perinatal, neonatal, and childhood outcomes. IMPACT STATEMENT: Epigenetic changes such as DNA methylation, histone modification, and non-coding RNA have been implicated in the pathophysiology of various disease processes. The fundamental changes to an offspring's epigenome can begin in utero, impacting the immediate postnatal period, childhood, adolescence, and adulthood. This scoping review summarizes current literature on the impact of early life epigenetics, especially DNA methylation on childhood health outcomes.

Non-Coding RNAs and Innate Immune Responses in Cancer

Non-coding RNAs (ncRNAs) and the innate immune system are closely related, acting as defense mechanisms and regulating gene expression and innate immunity. Both are modulators in the initiation, development and progression of cancer. We aimed to review the major types of ncRNAs, including small interfering RNAs (siRNAs), microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), and long non-coding RNAs (lncRNAs), with a focus on cancer, innate immunity, and inflammation. We found that ncRNAs are closely related to innate immunity, epigenetics, chronic inflammation, and cancer and share properties such as inducibility, specificity, memory, and transfer. These similarities and interrelationships suggest that ncRNAs and modulators of trained immunity, together with the control of chronic inflammation, can be combined to develop novel therapeutic approaches for personalized cancer treatment. In conclusion, the close relationship between ncRNAs, the innate immune system, and inflammation highlights their importance in cancer pathways and their potential as targets for novel therapeutic strategies.

Decoding the Epigenetics of Infertility: Mechanisms, Environmental Influences, and Therapeutic Strategies

Infertility is a complex condition caused by a combination of genetic, environmental, and lifestyle factors. Recent advances in epigenetics have highlighted the importance of epigenetic changes in fertility regulation. This review aims to provide a comprehensive overview of the epigenetic mechanisms involved in infertility, with a focus on DNA methylation, histone modification, and non-coding RNAs. We investigate the specific epigenetic events that occur during gametogenesis, with a focus on spermatogenesis and oogenesis as distinct processes. Furthermore, we investigate how environmental factors such as diet, stress, and toxin exposure can influence these epigenetic changes, potentially leading to infertility. The second part of the review explores epigenetic changes as therapeutic targets for infertility. Emerging therapies that modulate epigenetic marks present promising opportunities for fertility restoration, particularly in spermatogenesis. By summarizing current research findings, this review emphasizes the importance of understanding epigenetic contributions to infertility. Our discussion aims to lay the groundwork for future research directions and clinical applications in reproductive health.

LncRNA GAS8-AS1 dinucleotide genetic variantn.713A>G, n.714T>C is associated with early-stage disease, lymph node, and distant metastasis in differentiated thyroid cancer

PURPOSE

Long noncoding RNAs (lncRNAs) play an essential role in the epigenetic regulation of various key genes involved in vital cellular functions. A somatic dinucleotide mutation in the lncRNA GAS8-AS1 was reported in Chinese papillary thyroid cancer. However, GAS8-AS1 dinucleotide alteration and its impact have never been explored in differentiated thyroid cancers and other populations.

METHODS

We extracted genomic DNA from 265 DTCs and 97 normal healthy subjects, PCR amplified and Sanger sequenced to examine the GAS8-AS1 dinucleotide alteration. Calculated genotype/allele frequency to test Hardy-Weinberg Equilibrium (HWE) and performed a genetic model of inheritance to determine its association with DTC risk. Correlated the GAS8-AS1 dinucleotide variant distribution with clinical characteristics to find the association. Predicted GAS8-AS1 RNA secondary structure for wild type and variant using RemuRNA and RNAfold to assess the conformational changes.

RESULTS

GAS8-AS1 dinucleotide alteration (n.713A > G, rs55742939; n.714T > C, rs61118444) identified in DTCs is a germline variant not somatic. The GAS8-AS1 genotype and allele frequency significantly deviated for HWE in DTCs (χ2 = 37.954; p = 0.0001) though not associated with its risk. Dinucleotide variant distribution was remarkably associated with early-stage disease (p = 0.002), lymph node (p = 0.01), and distant metastasis (p = 0.01) in DTCs. The GAS8-AS1 bearing dinucleotide variant markedly showed conformational change compared to that of its wild type.

CONCLUSIONS

These findings indicate that GAS8-AS1 is genetically deregulated and implicated in several stages of DTC tumorigenesis suggesting it could be a promising prognostic biomarker in DTCs.

The effect of the loop on the thermodynamic and kinetic of single base pair in pseudoknot

RNA pseudoknots are RNA molecules with specialized three-dimensional structures that play important roles in various biological processes. To understand the functions and mechanisms of pseudoknots, it is essential to elucidate their structures and folding pathways. The most fundamental step in RNA folding is the opening and closing of a base pair. The effect of flexible loops on the base pair in pseudoknots remains unclear. In this work, we use molecular dynamics simulations and Markov state model to study the configurations, thermodynamic and kinetic of single base pair in pseudoknots. We find that the presence of the loop leads to a trap state. In addition, the rate-limiting step for the formation of base pair is the disruption of the trap state, rather than the open state to the closed state, which is quite different from the previous studies on non-pseudoknot RNA. For the thermodynamic parameters in pseudoknots, we find that the entropy difference upon opening the base pair between this simulation and the nearest-neighbor model results from the different entropy of different lengths of loop in solution. The thermodynamic parameters of the stack in pseudoknot are close to the nearest-neighbor parameters. The bases on the loop have different distribution patterns in different states, and the slow transition states of the loop are determined by the orientation of the bases.

Exploring potential roles of long non-coding RNAs in cancer immunotherapy: a comprehensive review

Cancer treatment has long been fraught with challenges, including drug resistance, metastasis, and recurrence, making it one of the most difficult diseases to treat effectively. Traditional therapeutic approaches often fall short due to their inability to target cancer stem cells and the complex genetic and epigenetic landscape of tumors. In recent years, cancer immunotherapy has revolutionized the field, offering new hope and viable alternatives to conventional treatments. A particularly promising area of research focuses on non-coding RNAs (ncRNAs), especially long non-coding RNAs (lncRNAs), and their role in cancer resistance and the modulation of signaling pathways. To address these challenges, we performed a comprehensive review of recent studies on lncRNAs and their impact on cancer immunotherapy. Our review highlights the crucial roles that lncRNAs play in affecting both innate and adaptive immunity, thereby influencing the outcomes of cancer treatments. Key observations from our review indicate that lncRNAs can modify the tumor immune microenvironment, enhance immune cell infiltration, and regulate cytokine production, all of which contribute to tumor growth and resistance to therapies. These insights suggest that lncRNAs could serve as potential targets for precision medicine, opening up new avenues for developing more effective cancer immunotherapies. By compiling recent research on lncRNAs across various cancers, this review aims to shed light on their mechanisms within the tumor immune microenvironment.

Contribution of the seminal microbiome to paternal programming

The field of Developmental Origins of Health and Disease has primarily focused on maternal programming of offspring health. However, emerging evidence suggests that paternal factors, including the seminal microbiome, could potentially play important roles in shaping the developmental trajectory and long-term offspring health outcomes. Historically, the microbes present in the semen were regarded as inherently pathogenic agents. However, this dogma has recently been challenged by the discovery of a diverse commensal microbial community within the semen of healthy males. In addition, recent studies suggest that the transmission of semen-associated microbes into the female reproductive tract during mating has potentials to not only influence female fertility and embryo development but could also contribute to paternal programming in the offspring. In this review, we summarize the current knowledge on the seminal microbiota in both humans and animals followed by discussing their potential involvement in paternal programming of offspring health. We also propose and discuss potential mechanisms through which paternal influences are transmitted to offspring via the seminal microbiome. Overall, this review provides insights into the seminal microbiome-based paternal programing, which will expand our understanding of the potential paternal programming mechanisms which are currently focused primarily on the epigenetic modifications, oxidative stresses, and cytokines.

Non-coding RNAs as regulators of autophagy in chondrocytes: Mechanisms and implications for osteoarthritis

Osteoarthritis (OA) is a chronic degenerative joint disease with multiple causative factors such as aging, mechanical injury, and obesity. Autophagy is a complex dynamic process that is involved in the degradation and modification of intracellular proteins and organelles under different pathophysiological conditions. Autophagy, as a cell survival mechanism under various stress conditions, plays a key role in regulating chondrocyte life cycle metabolism and cellular homeostasis. Non-coding RNAs (ncRNAs) are heterogeneous transcripts that do not possess protein-coding functions, but they can act as effective post-transcriptional and epigenetic regulators of gene and protein expression, thus participating in numerous fundamental biological processes. Increasing evidence suggests that ncRNAs, autophagy, and their crosstalk play crucial roles in OA pathogenesis. Therefore, we summarized the complex role of autophagy in OA chondrocytes and focused on the regulatory role of ncRNAs in OA-associated autophagy to elucidate the complex pathological mechanisms of the ncRNA-autophagy network in the development of OA, thus providing new research targets for the clinical diagnosis and treatment of OA.

Epigenetics Regulation in Responses to Abiotic Factors in Plant Species: A Systematic Review

Plants have several mechanisms to adapt or acclimate to environmental stress. Morphological, physiological, or genetic changes are examples of complex plant responses. In recent years, our understanding of the role of epigenetic regulation, which encompasses changes that do not alter the DNA sequence, as an adaptive mechanism in response to stressful conditions has advanced significantly. Some studies elucidated and synthesized epigenetic mechanisms and their relationships with environmental change, while others explored the interplay between epigenetic modifications and environmental shifts, aiming to deepen our understanding of these complex processes. In this study, we performed a systematic review of the literature to analyze the progression of epigenetics studies on plant species' responses to abiotic factors. We also aimed to identify the most studied species, the type of abiotic factor studied, and the epigenetic technique most used in the scientific literature. For this, a search for articles in databases was carried out, and after analyzing them using pre-established inclusion criteria, a total of 401 studies were found. The most studied species were Arabidopsis thaliana and Oryza sativa, highlighting the gap in studies of non-economic and tropical plant species. Methylome DNA sequencing is the main technique used for the detection of epigenetic interactions in published studies. Furthermore, most studies sought to understand the plant responses to abiotic changes in temperature, water, and salinity. It is worth emphasizing further research is necessary to establish a correlation between epigenetic responses and abiotic factors, such as extreme temperatures and light, associated with climate change.

Therapeutic Potential of Natural Compounds Acting through Epigenetic Mechanisms in Cardiovascular Diseases: Current Findings and Future Directions

Cardiovascular diseases (CVDs) remain a leading global cause of morbidity and mortality. These diseases have a multifaceted nature being influenced by a multitude of biochemical, genetic, environmental, and behavioral factors. Epigenetic modifications have a crucial role in the onset and progression of CVD. Epigenetics, which regulates gene activity without altering the DNA's primary structure, can modulate cardiovascular homeostasis through DNA methylation, histone modification, and non-coding RNA regulation. The effects of environmental stimuli on CVD are mediated by epigenetic changes, which can be reversible and, hence, are susceptible to pharmacological interventions. This represents an opportunity to prevent diseases by targeting harmful epigenetic modifications. Factors such as high-fat diets or nutrient deficiencies can influence epigenetic enzymes, affecting fetal growth, metabolism, oxidative stress, inflammation, and atherosclerosis. Recent studies have shown that plant-derived bioactive compounds can modulate epigenetic regulators and inflammatory responses, contributing to the cardioprotective effects of diets. Understanding these nutriepigenetic effects and their reversibility is crucial for developing effective interventions to combat CVD. This review delves into the general mechanisms of epigenetics, its regulatory roles in CVD, and the potential of epigenetics as a CVD therapeutic strategy. It also examines the role of epigenetic natural compounds (ENCs) in CVD and their potential as intervention tools for prevention and therapy.

Childhood obesity from the genes to the epigenome

The prevalence of obesity and its associated comorbidities has surged dramatically in recent decades. Especially concerning is the increased rate of childhood obesity, resulting in diseases traditionally associated only with adulthood. While obesity fundamentally arises from energy imbalance, emerging evidence over the past decade has revealed the involvement of additional factors. Epidemiological and murine studies have provided extensive evidence linking parental obesity to increased offspring weight and subsequent cardiometabolic complications in adulthood. Offspring exposed to an obese environment during conception, pregnancy, and/or lactation often exhibit increased body weight and long-term metabolic health issues, suggesting a transgenerational inheritance of disease susceptibility through epigenetic mechanisms rather than solely classic genetic mutations. In this review, we explore the current understanding of the mechanisms mediating transgenerational and intergenerational transmission of obesity. We delve into recent findings regarding both paternal and maternal obesity, shedding light on the underlying mechanisms and potential sex differences in offspring outcomes. A deeper understanding of the mechanisms behind obesity inheritance holds promise for enhancing clinical management strategies in offspring and breaking the cycle of increased metabolic risk across generations.

High-Fat Diets Fed during Pregnancy Cause Changes to Pancreatic Tissue DNA Methylation and Protein Expression in the Offspring: A Multi-Omics Approach

Maternal obesity, caused by diets rich in fats and sugars during pregnancy, can predispose offspring to metabolic diseases such as diabetes. We hypothesized that obesity during pregnancy leads to increased DNA methylation and reduced protein expression in factors regulating β-cell function and apoptosis. Female C57BL/6J mice were fed a high-fat diet (HFD; 42% fat content; n = 3) or a control diet (CON; 16% fat content; n = 3) for fourteen weeks before and during pregnancy. Offspring were euthanized at 8 weeks and pancreatic tissue was collected. Isolated DNA was analyzed using whole-genome bisulfite sequencing. Protein expression was quantified using LC-MS. No significant differences in body weight were observed between HFD and control pups (p = 0.10). Whole-genome bisulfite sequencing identified 91,703 and 88,415 differentially methylated regions (DMRs) in CON vs. HFD male and female offspring. A total of 34 and 4 proteins were determined to have changes in expression that correlated with changes in DNA methylation in CON vs. HFD males and females, respectively. The majority of these factors were grouped into the metabolic function category via pathway analyses. This study illustrates the complex relationship between epigenetics, diet, and sex-specific responses, therefore offering insights into potential therapeutic targets and areas for further research.