Integrated Transcriptome Analysis of Human Visceral Adipocytes Unravels Dysregulated microRNA-Long Non-coding RNA-mRNA Networks in Obesity and Colorectal Cancer

Association of lncRNA MEG3 rs941576 polymorphism, expression profile, and its related targets with the risk of obesity-related colorectal cancer: potential clinical insights

The identification of novel screening tools is imperative to empower the early detection of colorectal cancer (CRC). The influence of the long non-coding RNA maternally expressed gene 3 (MEG3) rs941576 single nucleotide polymorphism on CRC susceptibility remains uninvestigated. This research appraised MEG3 rs941576 association with the risk and clinical features of CRC and obesity-related CRC and its impact on serum MEG3 expression and its targets miR-27a/insulin-like growth factor 1 (IGF1)/IGF binding protein 3 (IGFBP3) and miR-181a/sirtuin 1 (SIRT1), along with the potential of these markers in obesity-related CRC diagnosis. 130 CRC patients (60 non-obese and 70 obese) and 120 cancer-free controls (64 non-obese and 56 obese) were enrolled. MEG3 targets were selected using bioinformatics analysis. MEG3 rs941576 was associated with magnified CRC risk in overall (OR (95% CI) 4.69(1.51-14.57), P = 0.0018) and stratified age and gender groups, but not with obesity-related CRC risk or MEG3/downstream targets' expression. Escalated miR-27a and IGFBP3 and reduced IGF1 serum levels were concomitant with MEG3 downregulation in overall CRC patients versus controls and obese versus non-obese CRC patients. Serum miR-181a and SIRT1 were upregulated in CRC patients versus controls but weren't altered in the obese versus non-obese comparison. Serum miR-181a and miR-27a were superior in overall and obesity-related CRC diagnosis, respectively; meanwhile, IGF1 was superior in distinguishing obese from non-obese CRC patients. Only serum miR-27a was associated with obesity-related CRC risk in multivariate logistic analysis. Among overall CRC patients, MEG3 rs941576 was associated with lymph node (LN) metastasis and tumor stage, serum MEG3 was negatively correlated with tumor stage, while SIRT1 was correlated with the anatomical site. Significant correlations were recorded between MEG3 and anatomical site, SIRT1 and tumor stage, and miR-27a/IGFBP3 and LN metastasis among obese CRC patients, while IGF1 was correlated with tumor stage and LN metastasis among non-obese CRC patients. Conclusively, this study advocates MEG3 rs941576 as a novel genetic marker of CRC susceptibility and prognosis. Our findings accentuate circulating MEG3/miR-27a/IGF1/IGFBP3, especially miR-27a as valuable markers for the early detection of obesity-related CRC. This axis along with SIRT1 could benefit obesity-related CRC prognosis.

Examining the effects of coronary artery disease- and mitochondrial biogenesis-related genes' and microRNAs' expression levels on metabolic disorders in epicardial adipose tissue

BACKGROUND AND AIMS

Epicardial adipose tissue (EAT) surrounds the heart and coronary arteries and is important for comprehending the pathogenesis of coronary artery disease (CAD). We aimed to evaluate the expressions of mitochondrial biogenesis- and CAD-related genes and miRNAs in EAT by comparing them to visceral adipose tissue (VAT) in CAD, diabetes, and obesity subgroups.

METHODS

In this study, a total of 93 individuals were recruited, and EAT samples (63 CAD; 30 non-CAD) and VAT samples from 65 individuals (46 CAD; 19 non-CAD) were collected. For further analysis, the study population was divided according to obesity and diabetes status. PRKAA1, PPARGC1A, SIRT1, RELA, TNFA, and miR-155-5p, let-7g-5p, miR-1247-5p, miR-326 expression levels were examined.

RESULTS

PRKAA1 and let-7g-5p were differentially expressed in EAT compared to VAT. TNFA expression was upregulated significantly in both tissues of CAD patients. In EAT, PRKAA1, PPARGC1A, and SIRT1 were downregulated with diabetes. Moreover, PPARGC1A expression is decreased under the condition of obesity in both tissues. EAT expressions of miR-1247-5p and miR-326 were downregulated with obesity, while miR-155-5p is decreased only in the VAT of obese. Also, miRNAs and genes were correlated with biochemical parameters and each other in EAT and VAT (p < 0.050).

CONCLUSIONS

The findings demonstrating distinct let-7g-5p and AMPKα1 mRNA expression between EAT and VAT underscores the importance of tissue-specific regulation in different clinical outcomes. In addition, the differential expressions of investigated genes and miRNAs highlight their responsiveness to obesity, DM, and CAD in adipose tissues.

Epigenetic modifications in obesity-associated diseases

The global prevalence of obesity has reached epidemic levels, significantly elevating the susceptibility to various cardiometabolic conditions and certain types of cancer. In addition to causing metabolic abnormalities such as insulin resistance (IR), elevated blood glucose and lipids, and ectopic fat deposition, obesity can also damage pancreatic islet cells, endothelial cells, and cardiomyocytes through chronic inflammation, and even promote the development of a microenvironment conducive to cancer initiation. Improper dietary habits and lack of physical exercise are important behavioral factors that increase the risk of obesity, which can affect gene expression through epigenetic modifications. Epigenetic alterations can occur in early stage of obesity, some of which are reversible, while others persist over time and lead to obesity-related complications. Therefore, the dynamic adjustability of epigenetic modifications can be leveraged to reverse the development of obesity-associated diseases through behavioral interventions, drugs, and bariatric surgery. This review provides a comprehensive summary of the impact of epigenetic regulation on the initiation and development of obesity-associated cancers, type 2 diabetes, and cardiovascular diseases, establishing a theoretical basis for prevention, diagnosis, and treatment of these conditions.

Genetic variants and haplotype structures of miRNA host genes in cancer and obesity

Cancer and obesity are two important public health problems. This study aimed to investigate the role of genetic variants and haplotypes of miRNA host genes in cancer and obesity. Data from the catalog of genome-wide association studies (GWAS) were used to find significant variants (index). Then, 1000-genome phase 3 data were used to find haplotypic variants (proxy) associated with these diseases. The candidate variants and haplotypes were identified from proxy and index variants. Finally, SNP function analysis was performed. All GWAS-significant cancer-associated miRNA host gene variants, including MIR4713HG, MIR663AHG, MIR99AHG and MIR4435-2HG, were also significantly associated with obesity. The rs703764 variant was common between cutaneous melanoma and obesity traits in the European population (P ≤ 5E-8). The rs2414098 variant was associated with endometrial cancer (P ≤ 5E-13), and the rs7173595 variant was associated with waist-hip ratio (P ≤ 5E-13) and new CGGCATCA haplotypic located at MIR4713HG was identified in the European population. In addition, the ATCTTGTT haplotype for rs17041868 in MIR4435-2HG was identified to be associated with obesity traits (waist-hip ratio and BMI) in the European population (P ≤ 5E-8). This study found that rs703764 is a common genetic marker between cancer and obesity. The CGGCATCA haplotype is common between endometrial cancer and waist-hip ratio. Also, ATCTTGTT haplotype is associated with obesity traits. These results indicate that the variants and haplotypes of miRNAs host genes play an important role between cancer and obesity in the European population. It is suggested to investigate the effect of these structures in other populations.Communicated by Ramaswamy H. Sarma.

On the road to colorectal cancer development: crosstalk between the gut microbiota, metabolic reprogramming, and epigenetic modifications

An increasing number of studies have reported the role of gut microbes in colorectal cancer (CRC) development, as they can be influenced by dietary metabolism and mediate alterations in host epigenetics, ultimately affecting CRC. Intake of specific dietary components can affect gut microbial composition and function, and their metabolism regulates important epigenetic functions that may influence CRC risk. Gut microbes can regulate epigenetic modifications through nutrient metabolism, including histone modification, DNA methylation, and noncoding RNAs. Epigenetics, in turn, determines the gut microbial composition and thus influences the risk of developing CRC. This review discusses the complex crosstalk between metabolic reprogramming, gut microbiota, and epigenetics in CRC and highlights the potential applications of the gut microbiota as a biomarker for the prevention, diagnosis, and therapy of CRC.

Colon cancer transcriptome

Over the last four decades, methodological innovations have continuously changed transcriptome profiling. It is now feasible to sequence and quantify the transcriptional outputs of individual cells or thousands of samples using RNA sequencing (RNA-seq). These transcriptomes serve as a connection between cellular behaviors and their underlying molecular mechanisms, such as mutations. This relationship, in the context of cancer, provides a chance to unravel tumor complexity and heterogeneity and uncover novel biomarkers or treatment options. Since colon cancer is one of the most frequent malignancies, its prognosis and diagnosis seem to be critical. The transcriptome technology is developing for an earlier and more accurate diagnosis of cancer which can provide better protectivity and prognostic utility to medical teams and patients. A transcriptome is a whole set of expressed coding and non-coding RNAs in an individual or cell population. The cancer transcriptome includes RNA-based changes. The combined genome and transcriptome of a patient may provide a comprehensive picture of their cancer, and this information is beginning to affect treatment decision-making in real-time. A full assessment of the transcriptome of colon (colorectal) cancer has been assessed in this review paper based on risk factors such as age, obesity, gender, alcohol use, race, and also different stages of cancer, as well as non-coding RNAs like circRNAs, miRNAs, lncRNAs, and siRNAs. Similarly, they have been examined independently in the transcriptome study of colon cancer.

The Acinetobacter baumannii model can explain the role of small non-coding RNAs as potential mediators of host-pathogen interactions

Bacterial small RNAs (sRNAs) research has accelerated over the past decade, boosted by advances in RNA-seq technologies and methodologies for capturing both protein-RNA and RNA-RNA interactions. The emerging picture is that these regulatory sRNAs play important roles in controlling complex physiological processes and are required to survive the antimicrobial challenge. In recent years, the RNA content of OMVs/EVs has also gained increasing attention, particularly in the context of infection. Secreted RNAs from several bacterial pathogens have been characterized but the exact mechanisms promoting pathogenicity remain elusive. In this review, we briefly discuss how secreted sRNAs interact with targets in infected cells, thus representing a novel perspective of host cell manipulation during bacterial infection. During the last decade, Acinetobacter baumannii became clinically relevant emerging pathogens responsible for nosocomial and community-acquired infections. Therefore, we also summarize recent findings of regulation by sRNAs in A. baumannii and discuss how this emerging bacterium utilizes many of these sRNAs to adapt to its niche and become successful human pathogen.

Long Noncoding RNAs in the Pathogenesis of Insulin Resistance

Insulin resistance (IR), designated as the blunted response of insulin target tissues to physiological level of insulin, plays crucial roles in the development and progression of diabetes, nonalcoholic fatty liver disease (NAFLD) and other diseases. So far, the distinct mechanism(s) of IR still needs further exploration. Long non-coding RNA (lncRNA) is a class of non-protein coding RNA molecules with a length greater than 200 nucleotides. LncRNAs are widely involved in many biological processes including cell differentiation, proliferation, apoptosis and metabolism. More recently, there has been increasing evidence that lncRNAs participated in the pathogenesis of IR, and the dysregulated lncRNA profile played important roles in the pathogenesis of metabolic diseases including obesity, diabetes and NAFLD. For example, the lncRNAs MEG3, H19, MALAT1, GAS5, lncSHGL and several other lncRNAs have been shown to regulate insulin signaling and glucose/lipid metabolism in various tissues. In this review, we briefly introduced the general features of lncRNA and the methods for lncRNA research, and then summarized and discussed the recent advances on the roles and mechanisms of lncRNAs in IR, particularly focused on liver, skeletal muscle and adipose tissues.

Identification of thermogenesis-related lncRNAs in small extracellular vesicles derived from adipose tissue

Background

Brown adipose tissue (BAT) is considered as a primary location of adaptive thermogenesis and the thermogenic activities of brown adipocytes are also connected to generating heat and counteracting obesity. Recent studies revealed that BAT could secrete certain batokines-like factors especially small extracellular vesicles (sEVs), which contributed to the systemic consequences of BAT activities. As a newly emerging class of mediators, some long non-coding RNAs (lncRNAs) have exhibited metabolic regulatory effects in adipocyte development. However, besides the well-studied lncRNAs, the lncRNAs carried by sEVs derived from brown adipose tissue (sEV-BAT) have not been identified yet. 

Results

In this study, we demonstrated that sEV-BAT could induce beige adipocyte differentiation both in ASCs and 3T3-L1 cells, while sEV-WAT had no corresponding effects. The lncRNA microarray assay on sEV-WAT and sEV-BAT revealed a total of 563 types of known lncRNAs were identified to be differentially expressed, among which 232 lncRNAs were upregulated and 331 lncRNAs were downregulated in sEV-BAT. Three novel candidates (AK029592, humanlincRNA1030 and ENSMUST00000152284) were selected for further validation. LncRNA–mRNA network analysis revealed candidate lncRNAs were largely embedded in cellular metabolic pathways. During adipogenic and thermogenic phenotype differentiation in ASCs and 3T3-L1 cells, only the expressions of AK029592 were upregulated. The three lncRNAs were all relatively enriched in brown adipose tissues and brown adipocytes. In different adipocytes, sEV and adipose tissue, the expression of AK029592 and ENSMUST00000152284 were remarkably decreased in obese mice compared to lean mice, while obesity state could not change the expression of humanlincRNA1030.

Conclusion

Collectively, our profiling study provided a comprehensive catalog for the study of lncRNAs specifically carried by sEV-BAT and indicated the potential regulatory role of certain sEV-BAT lncRNAs in thermogenesis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08883-0.

Using ncRNAs as Tools in Cancer Diagnosis and Treatment-The Way towards Personalized Medicine to Improve Patients' Health

Although the first discovery of a non-coding RNA (ncRNA) dates back to 1958, only in recent years has the complexity of the transcriptome started to be elucidated. However, its components are still under investigation and their identification is one of the challenges that scientists are presently facing. In addition, their function is still far from being fully understood. The non-coding portion of the genome is indeed the largest, both quantitatively and qualitatively. A large fraction of these ncRNAs have a regulatory role either in coding mRNAs or in other ncRNAs, creating an intracellular network of crossed interactions (competing endogenous RNA networks, or ceRNET) that fine-tune the gene expression in both health and disease. The alteration of the equilibrium among such interactions can be enough to cause a transition from health to disease, but the opposite is equally true, leading to the possibility of intervening based on these mechanisms to cure human conditions. In this review, we summarize the present knowledge on these mechanisms, illustrating how they can be used for disease treatment, the current challenges and pitfalls, and the roles of environmental and lifestyle-related contributing factors, in addition to the ethical, legal, and social issues arising from their (improper) use.

NcRNAs-mediated P2RX1 expression correlates with clinical outcomes and immune infiltration in patients with breast invasive carcinoma

The development of novel treatments for breast invasive carcinoma (BC) has been stagnant. P2RX1, a member of the purinergic receptor family, has been found to have a prognostic impact in several tumors. Therefore, we analyzed the expression pattern of P2RX1 in pan-cancers including BC and its impact on survival and found that the expression level of P2RX1 was lower in BC compared with para-cancerous tissues, and higher P2RX1 expression indicated better prognoses. But real-time quantitative reverse transcription PCR (RT-qPCR) and Western blot detected that the P2RX1 expression in normal mammary epithelial cells was lower than that in tumor cells. Then we comprehensively analyzed the regulatory mechanism and protein-protein interaction network, and found that P2RX1 was significantly positively linked with immune cell infiltration and immune checkpoints.

Association of miRNA targetome variants in LAMC1 and GNB3 genes with colorectal cancer and obesity

Background

Colorectal cancer (CRC) is one of the most common obesity‐associated cancers. Inflammation is also considered the most important factor between obesity and CRC. This study aimed to examine miRNAs binding sites variants on inflammatory genes identified using bioinformatics and systematic approach on clinical samples that were collected from CRC patients and controls.

Methods

The candidate variants related to CRC inflammatory genes were obtained from genome‐wide association studies and their population‐specific haplotypes. The variants were analyzed according to their genomic position on the miRNA targetome. Targetome variants in inflammation‐related genes were selected for genetic association study by TaqMan genotyping assay.

Results

The GG genotype of rs7473 decreased the risk of obesity (p < 0.05). Heterozygous genotype (GA) of rs1547715 decreased the risk of CRC (p < 0.05). In the rs7473/rs1547715 genotype and haplotype, the frequencies of AA/GA and GG/AA lessened in CRC and obesity, respectively (p < 0.05).

Conclusions

The variants of rs7473 and rs1547715 were associated with obesity and CRC, respectively. The above‐mentioned associations could be made based on the interactions of these variants with miRNAs.

The PPARα and PPARγ Epigenetic Landscape in Cancer and Immune and Metabolic Disorders

Peroxisome proliferator-activated receptors (PPARs) are ligand-modulated nuclear receptors that play pivotal roles in nutrient sensing, metabolism, and lipid-related processes. Correct control of their target genes requires tight regulation of the expression of different PPAR isoforms in each tissue, and the dysregulation of PPAR-dependent transcriptional programs is linked to disorders, such as metabolic and immune diseases or cancer. Several PPAR regulators and PPAR-regulated factors are epigenetic effectors, including non-coding RNAs, epigenetic enzymes, histone modifiers, and DNA methyltransferases. In this review, we examine advances in PPARα and PPARγ-related epigenetic regulation in metabolic disorders, including obesity and diabetes, immune disorders, such as sclerosis and lupus, and a variety of cancers, providing new insights into the possible therapeutic exploitation of PPAR epigenetic modulation.

Transcriptional characterization of subcutaneous adipose tissue in obesity affected women highlights metabolic dysfunction and implications for lncRNAs

Obesity is a complex disease with multifactorial causes, and its prevalence is becoming a serious health crisis. For this reason, there is a crucial need to identify novel targets and players. With this aim in mind, we analyzed via RNA-sequencing the subcutaneous adipose tissue of normal weight and obesity-affected women, highlighting the differential expression in the two tissues. We specifically focused on long non-coding RNAs, as 6 of these emerged as dysregulated in the diseased-tissue (COL4A2-AS2, RPS21-AS, PELATON, ITGB2-AS1, ACER2-AS and CTEPHA1). For each of them, we performed both a thorough in silico dissection and in vitro validation, to predict their function during adipogenesis. We report the lncRNAs expression during adipose derived stem cells differentiation to adipocytes as model of adipogenesis and their potential modulation by adipogenesis-related transcription factors (C/EBPs and PPARγ). Moreover, inhibiting CTEPHA1 expression we investigated its impact on adipogenesis-related transcription factors, showing its significative dysregulation of C/EBPα expression. Lastly, we dissected the subcellular localization, pathway involvement and disease-correlation for coding differentially expressed genes. Together, these findings highlight a transcriptional deregulation at the basis of obesity, impacted by both coding and long non-coding RNAs.

MicroRNAs: The Link between the Metabolic Syndrome and Oncogenesis

Metabolic syndrome (MetS) represents a cluster of disorders that increase the risk of a plethora of conditions, in particular type two diabetes, cardiovascular diseases, and certain types of cancers. MetS is a complex entity characterized by a chronic inflammatory state that implies dysregulations of adipokins and proinflammatory cytokins together with hormonal and growth factors imbalances. Of great interest is the implication of microRNA (miRNA, miR), non-coding RNA, in cancer genesis, progression, and metastasis. The adipose tissue serves as an important source of miRs, which represent a novel class of adipokines, that play a crucial role in carcinogenesis. Altered miRs secretion in the adipose tissue, in the context of MetS, might explain their implication in the oncogenesis. The interplay between miRs expressed in adipose tissue, their dysregulation and cancer pathogenesis are still intriguing, taking into consideration the fact that miRNAs show both carcinogenic and tumor suppressor effects. The aim of our review was to discuss the latest publications concerning the implication of miRs dysregulation in MetS and their significance in tumoral signaling pathways. Furthermore, we emphasized the role of miRNAs as potential target therapies and their implication in cancer progression and metastasis.

An updated overview and classification of bioinformatics tools for MicroRNA analysis, which one to choose?

The term 'MicroRNA' (miRNA) refers to a class of small endogenous non-coding RNAs (ncRNAs) regenerated from hairpin transcripts. Recent studies reveal miRNAs' regulatory involvement in essential biological processes through translational repression or mRNA degradation. Recently, there is a growing body of literature focusing on the importance of miRNAs and their functions. In this respect, several databases have been developed to manage the dispersed data produced. Therefore, it is necessary to know the parameters and characteristics of each database to benefit their data. Besides, selecting the correct database is of great importance to scientists who do not have enough experience in this field. A comprehensive classification along with an explanation of the information contained in each database leads to facilitating access to these resources. In this regard, we have classified relevant databases into several categories, including miRNA sequencing and annotation, validated/predicted miRNA targets, disease-related miRNA, SNP in miRNA sequence or target site, miRNA-related pathways, or gene ontology, and mRNA-miRNA interactions. Hence, this review introduces available miRNA databases and presents a convenient overview to inform researchers of different backgrounds to find suitable miRNA-related bioinformatics web tools and relevant information rapidly.

Transcriptome Analysis of Subcutaneous Adipose Tissue from Severely Obese Patients Highlights Deregulation Profiles in Coding and Non-Coding Oncogenes

Obesity is a major risk factor for a large number of secondary diseases, including cancer. Specific insights into the role of gender differences and secondary comorbidities, such as type 2 diabetes (T2D) and cancer risk, are yet to be fully identified. The aim of this study is thus to find a correlation between the transcriptional deregulation present in the subcutaneous adipose tissue of obese patients and the oncogenic signature present in multiple cancers, in the presence of T2D, and considering gender differences. The subcutaneous adipose tissue (SAT) of five healthy, normal-weight women, five obese women, five obese women with T2D and five obese men were subjected to RNA-sequencing, leading to the identification of deregulated coding and non-coding RNAs, classified for their oncogenic score. A panel of DE RNAs was validated via Real-Time PCR and oncogene expression levels correlated the oncogenes with anthropometrical parameters, highlighting significant trends. For each analyzed condition, we identified the deregulated pathways associated with cancer, the prediction of possible prognosis for different cancer types and the lncRNAs involved in oncogenic networks and tissues. Our results provided a comprehensive characterization of oncogenesis correlation in SAT, providing specific insights into the possible molecular targets implicated in this process. Indeed, the identification of deregulated oncogenes also in SAT highlights hypothetical targets implicated in the increased oncogenic risk in highly obese subjects. These results could shed light on new molecular targets to be specifically modulated in obesity and highlight which cancers should receive the most attention in terms of better prevention in obesity-affected patients.