Identification of long non-coding RNAs and RNA binding proteins in breast cancer subtypes

DCTPP1: A promising target in cancer therapy and prognosis through nucleotide metabolism

Deoxycytidine triphosphate pyrophosphatase 1 (DCTPP1) is an important deoxycytidine triphosphate (dCTP) hydrolase responsible for eliminating noncanonical dCTP and maintaining deoxyribonucleoside triphosphate (dNTP) pool homeostasis. This regulation is vital for proper DNA replication and genome stability. Emerging evidence highlights the considerable role of DCTPP1 in tumor progression, chemotherapy resistance, and prognostic prediction. Consequently, DCTPP1 has emerged as a promising nucleotide metabolism-related target for cancer therapy. In this review, we provide a comprehensive summary of the structural and cellular biological features of DCTPP1, its functions, and its role in cancer. In addition, we discuss recent advancments in small molecules targeting DCTPP1, and propose potential directions for future research.

Exploration of mRNA-modifying METTL3 oncogene as momentous prognostic biomarker responsible for colorectal cancer development

Background

Colorectal cancer (CRC) is a leading cause of cancer-related mortality worldwide, emphasizing the need for improved prognostic biomarkers. Recent studies have identified the mRNA-modifying METTL3 oncogene as a potential biomarker in CRC progression.

Objective

This study aimed to investigate the expression patterns of METTL3 in CRC, assess its association with clinical outcomes, identify interacting proteins and biological pathways, and explore its correlation with immune cell infiltration.

Methods

Comprehensive analyses were conducted using public datasets, including transcriptome profiles from The Cancer Genome Atlas and the GSE103512 dataset. Protein-protein interaction (PPI) networks, pathway enrichment, and immune infiltration analyses were performed to elucidate METTL3's role in CRC progression.

Results

METTL3 expression was significantly higher in CRC tissues compared to normal tissues (p < 0.001). Mutations in METTL3 were detected in approximately 6% of CRC cases, with fusion events involving the SRPK2 gene. PPI analysis identified ten interacting proteins, including METTL4, EIF3H, RBM15B1, CBLL1, WTAP, NCBP1, RBM15, ZC3H13, METTL14, and KIAA1429. METTL3 expression showed a positive correlation with METTL4, METTL14, NCBP1, and WTAP expression (R > 0.5, p < 0.001). Higher METTL3 expression was associated with immunosuppressive phenotypes, such as increased infiltration of tumor-associated macrophages, regulatory T cells, and cancer-associated fibroblasts (p < 0.001). Pathway enrichment analysis revealed METTL3's involvement in crucial pathways, including the cell cycle and renal cell carcinoma (p < 0.01). Gene ontology analysis highlighted its role in mRNA and RNA-related processes.

Conclusion

The study supports the potential of METTL3 as a prognostic biomarker in CRC and highlights its involvement in immune modulation and cancer progression. These findings lay the groundwork for future studies aimed at developing targeted therapies and improving patient outcomes.

Regulatory Effects of RNA-Protein Interactions Revealed by Reporter Assays of Bacteria Grown on Solid Media

Reporter systems are widely used to study biomolecular interactions and processes in vivo, representing one of the basic tools used to characterize synthetic regulatory circuits. Here, we developed a method that enables the monitoring of RNA-protein interactions through a reporter system in bacteria with high temporal resolution. For this, we used a Real-Time Protein Expression Assay (RT-PEA) technology for real-time monitoring of a fluorescent reporter protein, while having bacteria growing on solid media. Experimental results were analyzed by fitting a three-variable Gompertz growth model. To validate the method, the interactions between a set of RNA sequences and the RNA-binding protein (RBP) Musashi-1 (MSI1) were evaluated, as well as the allosteric modulation of the interaction by a small molecule (oleic acid). This new approach proved to be suitable to quantitatively characterize RNA-RBP interactions, thereby expanding the toolbox to study molecular interactions in living bacteria, including allosteric modulation, with special relevance for systems that are not suitable to be studied in liquid media.

Identification of sequence determinants for the ABHD14 enzymes

Over the course of evolution, enzymes have developed remarkable functional diversity in catalyzing important chemical reactions across various organisms, and understanding how new enzyme functions might have evolved remains an important question in modern enzymology. To systematically annotate functions, based on their protein sequences and available biochemical studies, enzymes with similar catalytic mechanisms have been clustered together into an enzyme superfamily. Typically, enzymes within a superfamily have similar overall three-dimensional structures, conserved catalytic residues, but large variations in substrate recognition sites and residues to accommodate the diverse biochemical reactions that are catalyzed within the superfamily. The serine hydrolases are an excellent example of such an enzyme superfamily. Based on known enzymatic activities and protein sequences, they are split almost equally into the serine proteases and metabolic serine hydrolases. Within the metabolic serine hydrolases, there are two outlying members, ABHD14A and ABHD14B, that have high sequence similarity, but their biological functions remained cryptic till recently. While ABHD14A still lacks any functional annotation to date, we recently showed that ABHD14B functions as a lysine deacetylase in mammals. Given their high sequence similarity, automated databases often wrongly assign ABHD14A and ABHD14B as the same enzyme, and therefore, annotating functions to them in various organisms has been problematic. In this article, we present a bioinformatics study coupled with biochemical experiments, which identifies key sequence determinants for both ABHD14A and ABHD14B, and enable better classification for them. In addition, we map these enzymes on an evolutionary timescale and provide a much-wanted resource for studying these interesting enzymes in different organisms.

The role of long noncoding RNA DGCR5 in cancers: Focus on molecular targets

Long noncoding RNAs (lncRNAs) are major components of cellular transcripts that are emerging as important players in various biological pathways. Due to their specific expression and functional diversity in a variety of cancers, lncRNAs have promising applications in cancer diagnosis, prognosis, and therapy. Studies have shown that lncRNA DiGeorge syndrome critical region gene 5 (DGCR5) with high specificity and accuracy has the potential to become biomarkers in cancers. LncRNA DGCR5 can be noninvasively extracted from body fluids, tissues, and cells, and can be used as independent or auxiliary biomarkers to improve the accuracy of diagnosis or prognosis. Now, the underlying mechanisms of lncRNAs such as DGCR5 were explored as therapeutic targets, which have been investigated in clinical trials of several cancers. The DGCR5 lacks an appropriate animal model, which is necessary to gain greater knowledge of their functions. While some studies on the uses of DGCR5 have been carried out, the small sample size makes them unreliable. In this review, we presented a compilation of recent publications addressing the potential of lncRNA DGCR5 that could be considered as biomarkers or therapeutic targets, with the hopes of providing promised implications for future cancer therapy.

Targeted mutation and inactivation of the kinesin light chain 3 protein-encoding gene have no impact on mouse fertility†

The kinesin light chain 3 protein (KLC3) is the only member of the kinesin light chain protein family that was identified in post-meiotic mouse male germ cells. It plays a role in the formation of the sperm midpiece through its association with both spermatid mitochondria and outer dense fibers (ODF). Previous studies showed a significant correlation between its expression level and sperm motility and quantitative semen parameters in humans, while the overexpression of a KLC3-mutant protein unable to bind ODF also affected the same traits in mice. To further assess the role of KLC3 in fertility, we used CRISPR/Cas9 genome editing in mice and investigated the phenotypes induced by the invalidation of the gene or of a functional domain of the protein. Both approaches gave similar results, i.e. no detectable change in male or female fertility. Testis histology, litter size and sperm count were not altered. Apart from the line-dependent alterations of Klc3 mRNA levels, testicular transcriptome analysis did not reveal any other changes in the genes tested. Western analysis supported the absence of KLC3 in the gonads of males homozygous for the inactivating mutation and a strong decrease in expression in males homozygous for the allele lacking one out of the five tetratricopeptide repeats. Overall, these observations raise questions about the supposedly critical role of this kinesin in reproduction, at least in mice where its gene mutation or inactivation did not translate into fertility impairment.

The potential use and experimental validation of genomic instability-related lncRNA in pancreatic carcinoma

This study explored the potential role of long noncoding RNA (lncRNAs) associated with genomic instability in the diagnosis and treatment of pancreatic adenocarcinoma (PAAD). Transcriptome and single-nucleotide variation data of PAAD samples were downloaded from the cancer genome atlas database to explore genomic instability-associated lncRNAs. We constructed a genomic instability-associated lncRNA prognostic signature. Then gene ontology and Kyoto encyclopedia of genes and genomes enrichment analyses were used to explore the physiological role of lncRNAs involved in genomic instability. Tumor microenvironments, immunotherapy response, immune cell infiltration, immune checkpoint, and drug sensitivity were compared between high-risk and low-risk groups. In vitro experiments were performed for external validation. Six lncRNAs associated with genomic instability were identified, capable of predicting the prognosis of PAAD. Patients were assigned to low-risk or high-risk groups using these biomarkers, with better or worse prognosis, respectively. The tumor immune score, immune cell infiltration, and efficacy of immunotherapy were worse in the high-risk group. A drug sensitivity analysis revealed the high- and low-risk groups had different half-maximal inhibitory concentrations. The expression of cancer susceptibility candidate 8 was significantly higher in tumor tissues than in normal tissues, while the expression of LYPLAL1-AS1 exhibited an opposite pattern. They may be potential diagnostic or prognostic biomarkers for patients with pancreatic cancer. Genomic instability-associated lncRNAs were explored in this study and predicted the prognosis of PAAD and stratified patients risk in PAAD. These lncRNAs also predicted the efficacy of immunotherapy and potential therapeutic targets in PAAD.

Investigation of putative roles of smoking-associated salivary microbiome alterations on carcinogenesis by integrative in silico analysis

Growing evidence suggests that cigarette smoking alters the salivary microbiome composition and affects the risk of various complex diseases including cancer. However, the potential role of the smoking-associated microbiome in cancer development remains unexplained. Here, the putative roles of smoking-related microbiome alterations in carcinogenesis were investigated by in silico analysis and suggested evidence can be further explored by experimental methodologies. The Disbiome database was used to extract smoking-associated microbial taxa in saliva and taxon set enrichment analysis (TSEA) was conducted to identify the gene sets associated with extracted microbial taxa. We further analyzed the expression profiles of identified genes by using RNA-sequencing data from TCGA and GTEx projects. Associations of the genes with smoking-related phenotypes in cancer datasets were analyzed to prioritize genes for their interplay between smoking-related microbiome and carcinogenesis. Thirty-eight microbial taxa associated with smoking were included in the TSEA and this revealed sixteen genes that were significantly associated with smoking-associated microbial taxa. All genes were found to be differentially expressed in at least one cancer dataset, yet the ELF3 and CTSH were the most common differentially expressed genes giving significant results for several cancer types. Moreover, C2CD3, CTSH, DSC3, ELF3, RHOT2, and WSB2 showed statistically significant associations with smoking-related phenotypes in cancer datasets. This study provides in silico evidence for the potential roles of the salivary microbiome on carcinogenesis. The results shed light on the importance of smoking cessation strategies for cancer management and interventions to stratify smokers for their risk of smoking-induced carcinogenesis.

Roles of RNA-binding proteins in neurological disorders, COVID-19, and cancer

RNA-binding proteins (RBPs) have emerged as important players in multiple biological processes including transcription regulation, splicing, R-loop homeostasis, DNA rearrangement, miRNA function, biogenesis, and ribosome biogenesis. A large number of RBPs had already been identified by different approaches in various organisms and exhibited regulatory functions on RNAs' fate. RBPs can either directly or indirectly interact with their target RNAs or mRNAs to assume a key biological function whose outcome may trigger disease or normal biological events. They also exert distinct functions related to their canonical and non-canonical forms. This review summarizes the current understanding of a wide range of RBPs' functions and highlights their emerging roles in the regulation of diverse pathways, different physiological processes, and their molecular links with diseases. Various types of diseases, encompassing colorectal carcinoma, non-small cell lung carcinoma, amyotrophic lateral sclerosis, and Severe acute respiratory syndrome coronavirus 2, aberrantly express RBPs. We also highlight some recent advances in the field that could prompt the development of RBPs-based therapeutic interventions.

Shared genetics between classes of obesity and psychiatric disorders: A large-scale genome-wide cross-trait analysis

AIMS

Epidemiological studies demonstrate an association between classes of obesity and psychiatric disorders, although little is known about shared genetics and causality of association. Thus, we aimed to investigate shared genetics and causal link between different classes of obesity and psychiatric disorders.

METHODS

We used genome-wide association study (GWAS) summary data range from 9725 to 500,199 sample sizes of European descent, conducted a large-scale genome-wide cross-trait association study to investigate genetic overlap between the classes of obesity and anorexia nervosa, attention-deficit/hyperactivity disorder, autism spectrum disorder, bipolar disorder, major depressive disorder, obsessive-compulsive disorder, schizophrenia, anxiety disorders and Tourette syndrome. We conducted transcriptome-wide association study analysis (TWAS) to identified variants regulated gene expression in those related disorders. Finally, pathway enrichment analysis to identified major pathways.

RESULTS

In the combined analysis, we replicated 211 previously reported loci and discovered 58 novel independent loci that were associated with all three classes of obesity and related psychiatric disorders. Functional analysis revealed that the identified variants regulated gene expression in major tissues belonging to exocrine/endocrine, digestive, circulatory, adipose, digestive, respiratory, and nervous systems, such as DCC, NEGR1, INO80E. Mendelian randomization analyses suggested that there may be a two-way or one-way causal relationship between obesity and psychiatric disorders.

CONCLUSION

This large-scale genome-wide cross-trait analysis identified shared genetics and potential causal links between classes of obesity and psychiatric disorders (attention deficit hyperactivity disorder, autism spectrum disorder, anorexia nervosa, major depressive disorder, schizophrenia, and obsessive-compulsive disorder). Such shared genetics suggests potential new biological functions in common among them.

Emerging Roles of Long Noncoding RNAs in Breast Cancer Epigenetics and Epitranscriptomics

Breast carcinogenesis is a multistep process that involves both genetic and epigenetic changes. Epigenetics refers to reversible changes in gene expression that are not accompanied by changes in gene sequence. In breast cancer (BC), dysregulated epigenetic changes, such as DNA methylation and histone modifications, are accompanied by epitranscriptomic changes, in particular adenine to inosine modifications within RNA molecules. Factors that trigger these phenomena are largely unknown, but there is evidence for widespread participation of long noncoding RNAs (lncRNAs) that already have been linked to virtually any aspect of BC biology, making them promising biomarkers and therapeutic targets in BC patients. Here, we provide a systematic review of known and possible roles of lncRNAs in epigenetic and epitranscriptomic processes, along with methods and tools to study them, followed by a brief overview of current challenges regarding the use of lncRNAs in medical applications.

MIR205HG/LEADR Long Noncoding RNA Binds to Primed Proximal Regulatory Regions in Prostate Basal Cells Through a Triplex- and Alu-Mediated Mechanism

Aside serving as host gene for miR-205, MIR205HG transcribes for a chromatin-associated long noncoding RNA (lncRNA) able to restrain the differentiation of prostate basal cells, thus being reannotated as LEADR (Long Epithelial Alu-interacting Differentiation-related RNA). We previously showed the presence of Alu sequences in the promoters of genes modulated upon MIR205HG/LEADR manipulation. Notably, an Alu element also spans the first and second exons of MIR205HG/LEADR, suggesting its possible involvement in target selection/binding. Here, we performed ChIRP-seq to map MIR205HG/LEADR chromatin occupancy at genome-wide level in prostate basal cells. Our results confirmed preferential binding to regions proximal to gene transcription start site (TSS). Moreover, enrichment of triplex-forming sequences was found upstream of MIR205HG/LEADR-bound genes, peaking at −1,500/−500 bp from TSS. Triplexes formed with one or two putative DNA binding sites within MIR205HG/LEADR sequence, located just upstream of the Alu element. Notably, triplex-forming regions of bound genes were themselves enriched in Alu elements. These data suggest, from one side, that triplex formation may be the prevalent mechanism by which MIR205HG/LEADR selects and physically interacts with target DNA, from the other that direct or protein-mediated Alu (RNA)/Alu (DNA) interaction may represent a further functional requirement. We also found that triplex-forming regions were enriched in specific histone modifications, including H3K4me1 in the absence of H3K27ac, H3K4me3 and H3K27me3, indicating that in prostate basal cells MIR205HG/LEADR may preferentially bind to primed proximal regulatory elements. This may underscore the need for basal cells to keep MIR205HG/LEADR target genes repressed but, at the same time, responsive to differentiation cues.

Uncovering the mechanisms of dandelion against triple-negative breast cancer using a combined network pharmacology, molecular pharmacology and metabolomics approach

BACKGROUND

Taraxacum mongolicum, also called dandelion, has been used for thousands of years as a remedy for mammary abscess, mammary gland hyperplasia, and various other diseases afflicting the breast. In modern pharmacological research, dandelion has been proven to be effective against triple-negative breast cancer (TNBC). However, the mechanisms of this anti-tumor effect have not been fully elucidated.

PURPOSE

The aim of this investigation was to understand the multi-target mechanisms through which dandelion counteracts TNBC via a network pharmacology strategy as well as to validate its effectiveness by means of molecular pharmacology and metabolomics assessments.

METHODS

A liquid chromatography coupled with quadrupole time-of-flight mass spectrometer (LC-Q-TOF/MS) was employed to identify the absorbed components of dandelion in rat plasma. The network pharmacology-based prediction was utilized to uncover the potential mechanisms through which dandelion counteracts TNBC, during which potential targets were identified and pathway enrichment analysis was performed. Subsequently, TNBC cells and 4T1 tumor-bearing mice were used to further verify the molecular mechanisms of dandelion.

RESULTS

Twelve active compounds were identified in rat plasma, which were connected with 50 TNBC-related targets. The pathway enrichment showed that dandelion could treat TNBC through regulating a series of biological processes involving cell cycle and metabolism. Experimentally, flow cytometry analysis revealed that dandelion could arrest the G0/G1 and G2/M cell cycles in 4T1 cells. Further western blot analysis evidenced that the protein expression of kinase 6 (CDK6) as well as cyclins B1 and B2 in mice tumor tissue were suppressed by dandelion. In addition, cell metabolomics analysis revealed the changes in the endogenous metabolite levels that result from dandelion treatments, such as the downregulation of arginine and spermine levels. All these findings were consistent with the predicted targets and pathways.

CONCLUSION

This study comprehensively demonstrates the multi-target mechanisms of dandelion against TNBC using network pharmacology, molecular pharmacology, and metabolomics approaches. These findings will provide important stepping stones for further mechanism investigations and may lead to the development of highly effective dandelion-based treatments for TNBC.