Microarray analysis of RNA processing and modification

RNA modifications in physiology and pathology: Progressing towards application in clinical settings

The potential to modify individual nucleotides through chemical means in order to impact the electrostatic charge, hydrophobic properties, and base pairing of RNA molecules is harnessed in the medical application of stable synthetic RNAs like mRNA vaccines and synthetic small RNA molecules. These modifications are used to either increase or decrease the production of therapeutic proteins. Additionally, naturally occurring biochemical alterations of nucleotides play a role in regulating RNA metabolism and function, thereby modulating essential cellular processes. Research elucidating the mechanisms through which RNA modifications govern fundamental cellular functions in multicellular organisms has enhanced our comprehension of how irregular RNA modification profiles can lead to human diseases. Collectively, these fundamental scientific findings have unveiled the molecular and cellular functions of RNA modifications, offering new opportunities for therapeutic intervention and paving the way for a variety of innovative clinical strategies.

The essential roles of small non-coding RNAs and RNA modifications in normal and malignant hematopoiesis

Hematopoietic stem cells (HSCs) developing from mesoderm during embryogenesis are important for the blood circulatory system and immune system. Many factors such as genetic factors, chemical exposure, physical radiation, and viral infection, can lead to the dysfunction of HSCs. Hematological malignancies (involving leukemia, lymphoma, and myeloma) were diagnosed in more than 1.3 million people globally in 2021, taking up 7% of total newly-diagnosed cancer patients. Although many treatments like chemotherapy, bone marrow transplantation, and stem cell transplantation have been applied in clinical therapeutics, the average 5-year survival rate for leukemia, lymphoma, and myeloma is about 65%, 72%, and 54% respectively. Small non-coding RNAs play key roles in a variety of biological processes, including cell division and proliferation, immunological response and cell death. With the development of technologies in high-throughput sequencing and bioinformatic analysis, there is emerging research about modifications on small non-coding RNAs, as well as their functions in hematopoiesis and related diseases. In this study, we summarize the updated information of small non-coding RNAs and RNA modifications in normal and malignant hematopoiesis, which sheds lights into the future application of HSCs into the treatment of blood diseases.

Multifunctional electrochemical biosensor with "tetrahedral tripods" assisted multiple tandem hairpins assembly for ultra-sensitive detection of target DNA

Nucleic acids are genetic materials in the human body that play important roles in storing, copying, and transmitting genetic information. Abnormal nucleic acid sequences, base mutations, and genetic changes often lead to cancer and other diseases. Meanwhile, methylated DNA is one of the main epigenetic modifications, which is considered to be an excellent biomarker in the early detection, prognosis, and treatment of cancers. Therefore, a multifunctional electrochemical biosensor was constructed with sturdy tetrahedral tripods, which assisted multiple tandem hairpins through base complementary pairing and effective ultra-sensitive detection of targets (DNA, microRNA, and methylated DNA). In the experiments, experimental conditions were optimized, and different DNA concentrations in serum were detected to verify the sensitivity of the biosensor and the feasibility of this protocol. In addition, microRNA and DNA methylation were detected through different designs of tetrahedral tripods (TTs) that capture probes to prove the superiority of this scheme. A sturdy pyramid structure of TTs extremely enhanced the capture efficiency of targets. The targets triggered the one-step isothermal multi-tandem amplification reaction by incubating multiple hairpin assemblies. To our knowledge, a combination of two parts, which greatly reduced background interference and decreased non-specific substance interference, has appeared for the first time in this paper. Moreover, the load area of electrochemical substances was significantly increased than that in previous studies. This greatly increased the detection range and detection limit of targets. The electrochemical signal responses were generated in freely diffusing hexaammineruthenium(iii) chloride (RuHex). RuHex could adhere to the DNA phosphate backbone by a powerful electrostatic attraction, causing increased current responses.

Schematic illustration of the fabricated electrochemical biosensor. TTs assisted multiple tandem hairpins assembly for ultra-sensitive detection of target DNA.

Nucleic Acid Platform Technologies

Every microarray experiment is based on a common format. First, a large number of nucleotide "spots" are arrayed onto a substrate, typically a glass slide, a silicon chip, or microbeads. Second, a complex population of nucleic acids (isolated from cells, selected from in vitro-synthesized libraries, or obtained from another source) is labeled, typically with fluorescent dyes. Third, the labeled nucleic acids are allowed to hybridize to their complementary spot(s) on the microarray. Fourth, the hybridized microarray is washed, allowing the amount of hybridized label to then be quantified. Analysis of the raw data generates a readout of the levels of each species of RNA in the original complex population. This introduction includes several examples of microarray applications and provides a discussion of the basic steps of most microarray experiments.

Detection of Viral RNA Splicing in Diagnostic Virology

This chapter is the first one to introduce the detection of viral RNA splicing as a new tool for clinical diagnosis of virus infections. These include various infections caused by influenza viruses, human immunodeficiency viruses (HIV), human T-cell leukemia viruses (HTLV), Torque teno viruses (TTV), parvoviruses, adenoviruses, hepatitis B virus, polyomaviruses, herpesviruses, and papillomaviruses. Detection of viral RNA splicing for active viral gene expression in a clinical sample is a nucleic acid-based detection. The interpretation of the detected viral RNA splicing results is straightforward without concern for carry-over DNA contamination, because the spliced RNA is smaller than its corresponding DNA template.

Although many methods can be used, a simple method to detect viral RNA splicing is reverse transcription-polymerase chain reaction (RT-PCR). In principle, the detection of spliced RNA transcripts by RT-PCR depends on amplicon selection and primer design. The most common approach is the amplification over the intron regions by a set of primers in flanking exons. A larger product than the predicted size of smaller, spliced RNA is in general an unspliced RNA or contaminating viral genomic DNA. A spliced mRNA always gives a smaller RT-PCR product than its unspliced RNA due to removal of intron sequences by RNA splicing. The contaminating viral DNA can be determined by a minus RT amplification (PCR). Alternatively, specific amplification of a spliced RNA can be obtained by using an exon-exon junction primer because the sequence at exon-exon junction is not present in the unspliced RNA nor in viral genomic DNA.

CSF1R mutations link POLD and HDLS as a single disease entity

OBJECTIVE

Pigmented orthochromatic leukodystrophy (POLD) and hereditary diffuse leukoencephalopathy with axonal spheroids (HDLS) are rare neurodegenerative disorders characterized by cerebral white matter abnormalities, myelin loss, and axonal swellings. The striking overlap of clinical and pathologic features of these disorders suggested a common pathogenesis; however, no genetic or mechanistic link between POLD and HDLS has been established. Recently, we reported that mutations in the colony-stimulating factor 1 receptor (CSF1R) gene cause HDLS. In this study, we determined whether CSF1R mutations are also a cause of POLD.

METHODS

We performed sequencing of CSF1R in 2 pathologically confirmed POLD families. For the largest family (FTD368), a detailed case report was provided and brain samples from 2 affected family members previously diagnosed with POLD were re-evaluated to determine whether they had HDLS features. In vitro functional characterization of wild-type and mutant CSF1R was also performed.

RESULTS

We identified CSF1R mutations in both POLD families: in family 5901, we found c.2297T>C (p.M766T), previously reported by us in HDLS family CA1, and in family FTD368, we identified c.2345G>A (p.R782H), recently reported in a biopsy-proven HDLS case. Immunohistochemical examination in family FTD368 showed the typical neuronal and glial findings of HDLS. Functional analyses of CSF1R mutant p.R782H (identified in this study) and p.M875T (previously observed in HDLS), showed a similar loss of CSF1R autophosphorylation of selected tyrosine residues in the kinase domain for both mutations when compared with wild-type CSF1R.

CONCLUSIONS

We provide the first genetic and mechanistic evidence that POLD and HDLS are a single clinicopathologic entity.

Crosstalk between Wnt Signaling and RNA Processing in Colorectal Cancer

RNA processing involves a variety of processes affecting gene expression, including the removal of introns through RNA splicing, as well as 3' end processing (cleavage and polyadenylation). Alternative RNA processing is fundamentally important for gene regulation, and aberrant processing is associated with the initiation and progression of cancer. Deregulated Wnt signaling, which is the initiating event in the development of most cases of human colorectal cancer (CRC), has been linked to modified RNA processing, which may contribute to Wnt-mediated colonic carcinogenesis. Crosstalk between Wnt signaling and alternative RNA splicing with relevance to CRC includes effects on the expression of Rac1b, an alternatively spliced gene associated with tumorigenesis, which exhibits alternative RNA splicing that is influenced by Wnt activity. In addition, Tcf4, a crucial component of Wnt signaling, also exhibits alternative splicing, which is likely involved in colonic tumorigenesis. Modulation of 3' end formation, including of the Wnt target gene COX-2, also can influence the neoplastic process, with implications for CRC. While many human genes are dependent on introns and splicing for normal levels of gene expression, naturally intronless genes exist with a unique metabolism that allows for intron-independent gene expression. Effects of Wnt activity on the RNA metabolism of the intronless Wnt-target gene c-jun is a likely contributor to cancer development. Further, butyrate, a breakdown product of dietary fiber and a histone deacetylase inhibitor, upregulates Wnt activity in CRC cells, and also modulates RNA processing; therefore, the interplay between Wnt activity, the modulation of this activity by butyrate, and differential RNA metabolism in colonic cells can significantly influence tumorigenesis. Determining the role played by altered RNA processing in Wnt-mediated neoplasia may lead to novel interventions aimed at restoring normal RNA metabolism for therapeutic benefit. Therefore, this minireview presents a brief overview of several aspects of RNA processing of relevance to cancer, which potentially influence, or are influenced by, Wnt signaling activity.

Interrogating genomic and epigenomic data to understand prostate cancer

Major breakthroughs at the beginning of this century in high-throughput technologies have profoundly transformed biological research. Significant knowledge has been gained regarding our biological system and its disease such as malignant transformation. In this review, we summarize leading discoveries in prostate cancer research derived from the use of high-throughput approaches powered by microarrays and massively parallel next-generation sequencing (NGS). These include the seminal discovery of chromosomal translocations such as TMPRSS2-ERG gene fusions as well as the identification of critical oncogenes exemplified by the polycomb group protein EZH2. We then demonstrate the power of interrogating genomic and epigenomic data in understanding the plethora of mechanisms of transcriptional regulation. As an example, we review how androgen receptor (AR) binding events are mediated at multiple levels through protein-DNA interaction, histone and DNA modifications, as well as high-order chromatin structural changes.

Non-coding RNAs: identification of cancer-associated microRNAs by gene profiling

MicroRNAs (miRNAs) belong to the heterogeneous class of non-coding RNAs (ncRNAs), which are by definition RNA molecules that do not encode for proteins, but have instead important structural, catalytic or regulatory functions. In this review we first provide an overview of the different ncRNA families, focusing in particular on miRNAs and their relevance in tumour development and progression. Second we shortly describe the available ncRNA expression profiling methods, which comprise microarray, bead-based hybridization methods, in situ hybridization, quantitative real-time polymerase chain reaction, cloning and deep sequencing methods. Finally, we used the PubMed database to perform an extensive literature search for miRNA expression profiling research articles in cancer and identified 58 studies that were published between 2004 and 2009; we identified 70 miRNAs that were reported in at least five studies as being either up- or downregulated, depending on the type of cancer, and 192 miRNAs that were reported to be up- or downregulated in at least two reports. MiRNA expression profiling of human tumours has identified signatures associated with diagnosis, staging, progression, prognosis, and response to treatment. Based on the most important findings we discuss the possible use of miRNAs as clinical biomarkers in the management of cancer patients for diagnosis, prognosis, and response to therapy.

Modulation of inflammatory genes by natural dietary bioactive compounds

Several epidemiologic studies have shown that chronic inflammation predisposes individuals to various types of cancer. Many cancers arise from sites of infection, chronic irritation, and inflammation. Conversely, an oncogenic change induces an inflammatory microenvironment that promotes the development of tumors. Natural bioactive compounds in dietary plant products including fruits, vegetables, grains, legumes, tea, and wine are claimed to help prevent cancer, degenerative diseases, and chronic and acute inflammation. Modern methods in cell and molecular biology allow us to understand the interactions of different natural bioactive compounds with basic mechanisms of inflammatory response. The molecular pathways of this cancer-related inflammation are now unraveled. Natural bioactive compounds exert anti-inflammatory activity by modulating pro-inflammatory gene expressions have shown promising chemopreventive activity. This review summarizes current knowledge on natural bioactive compounds that act through the signaling pathways and modulate inflammatory gene expressions, thus providing evidence for these substances in cancer chemopreventive action.

Prediction and verification of mouse tRNA gene families

BACKGROUND

Transfer RNA (tRNA) gene predictions are complicated by challenges such as structural variation, limited sequence conservation and the presence of highly reiterated short interspersed sequences (SINEs) that originally derived from tRNA genes or tRNA-like transcription units. Annotation of "tRNA genes" in sequenced genomes generally have not been accompanied by experimental verification of the expression status of predicted sequences.

RESULTS

To address this for mouse tRNA genes, we have employed two programs, tRNAScan-SE and ARAGORN, to predict the tRNA genes in the nuclear genome, resulting in diverse but overlapping predicted gene sets. From these, we removed known SINE repeats and sorted the genes into predicted families and single-copy genes. In particular, four families of intron-containing tRNA genes were predicted for the first time in mouse, with introns in positions and structures similar to the well characterized intron-containing tRNA genes in yeast. We verified the expression of the predicted tRNA genes by microarray analysis. We then confirmed the expression of appropriately sized RNA for the four intron-containing tRNA gene families, as well as the other 30 tRNA gene families creating an index of expression-verified mouse tRNAs.

CONCLUSIONS

These confirmed tRNA genes represent all anticodons and all known mammalian tRNA structural groups, as well as a variety of predicted "rogue" tRNA genes within families with altered anticodon identities.

Regulation of multiple core spliceosomal proteins by alternative splicing-coupled nonsense-mediated mRNA decay

Alternative splicing (AS) can regulate gene expression by introducing premature termination codons (PTCs) into spliced mRNA that subsequently elicit transcript degradation by the nonsense-mediated mRNA decay (NMD) pathway. However, the range of cellular functions controlled by this process and the factors required are poorly understood. By quantitative AS microarray profiling, we find that there are significant overlaps among the sets of PTC-introducing AS events affected by individual knockdown of the three core human NMD factors, Up-Frameshift 1 (UPF1), UPF2, and UPF3X/B. However, the levels of some PTC-containing splice variants are less or not detectably affected by the knockdown of UPF2 and/or UPF3X, compared with the knockdown of UPF1. The intron sequences flanking the affected alternative exons are often highly conserved, suggesting important regulatory roles for these AS events. The corresponding genes represent diverse cellular functions, and surprisingly, many encode core spliceosomal proteins and assembly factors. We further show that conserved, PTC-introducing AS events are enriched in genes that encode core spliceosomal proteins. Where tested, altering the expression levels of these core spliceosomal components affects the regulation of PTC-containing splice variants from the corresponding genes. Together, our results show that AS-coupled NMD can have different UPF factor requirements and is likely to regulate many general components of the spliceosome. The results further implicate general spliceosomal components in AS regulation.

Chapter 11. Identification and analysis of tRNAs that are degraded in Saccharomyces cerevisiae due to lack of modifications

Mounting evidence shows that tRNA modifications play crucial roles in the maintenance of wild-type levels of several tRNA species. This chapter describes a generalized framework in which to study tRNA turnover in the yeast Saccharomyces cerevisiae as a consequence of a defect in tRNA modification status. It describes several approaches for the identification of tRNA species that are reduced as a consequence of a modification defect, methods for analysis of the rate of tRNA loss and analysis of its aminoacylation, and methods for initial characterization of tRNA turnover. These approaches have been used successfully for several modification defects that result in tRNA turnover.

Expression profiling of microRNA using oligo DNA arrays

After 12 years from its first application, microarray technology has become the reference technique to monitor gene expression of thousands of genes in the same experiment. In the past few years an increasing amount of evidence showed the importance of non-coding RNA (ncRNA) in different human diseases. The microRNAs (miRNAs) are one of the groups of ncRNA. They are small RNA fragments, 19-25 nucleotides long, with a main regulatory function on both protein coding genes and non-coding RNAs. The application of microarray platforms applied to miRNA profiling determined their deregulation in virtually all human diseases that have been studied. We previously developed a custom miRNA microarray platform, and here we describe the protocol we used to work with it including the oligo design strategy, the microarray printing protocol, the target-probe hybridization and the signal detection.

Coregulators: transducing signal from transcription to alternative splicing

Cells respond to many external stimuli by modulating gene expression. A key step in this regulation is the control of transcription, which determines the concentrations of pre-mRNA that are produced. A second level of control involves maturation of pre-mRNAs; many are alternatively spliced, which changes the exon content of transcripts and therefore the 'message' of the genes. Recent data indicate that the two control levels are linked. Here, we describe how transcriptional regulators and coregulators influence alternative splicing, with a focus on genes that are controlled by steroid hormones. Recent technical advances that help to elucidate the impact of stimuli on the exon content of regulated gene transcripts are also discussed.

Global analysis of alternative splicing during T-cell activation

The role of alternative splicing (AS) in eliciting immune responses is poorly understood. We used quantitative AS microarray profiling to survey changes in AS during activation of Jurkat cells, a leukemia-derived T-cell line. Our results indicate that approximately 10-15% of the profiled alternative exons undergo a >10% change in inclusion level during activation. The majority of the genes displaying differential AS levels are distinct from the set of genes displaying differential transcript levels. These two gene sets also have overlapping yet distinct functional roles. For example, genes that show differential AS patterns during T-cell activation are often closely associated with cell-cycle regulation, whereas genes with differential transcript levels are highly enriched in functions associated more directly with immune defense and cytoskeletal architecture. Previously unknown AS events were detected in genes that have important roles in T-cell activation, and these AS level changes were also observed during the activation of normal human peripheral CD4+ and CD8+ lymphocytes. In summary, by using AS microarray profiling, we have discovered many new AS changes associated with T-cell activation. Our results suggest an extensive role for AS in the regulation of the mammalian immune response.

[11] Sample Labeling: An Overview

It is not easy to write a critical review of the methods available for labeling RNA and DNA "extracts" for microarray studies. There are a number of reasons for this: Suppliers of the reagents and kits used for this purpose do research and development, quality control, and validation and then they provide a hard-wired, "optimized" product. They often give few details about the compositions of these products, are inclined to put the best face they can on what they sell and gloss over any deficiencies, and have no interest in paying for direct comparisons of their product to those of other companies. These comparisons can be expensive to perform, and there are few good examples in the literature. When comparative experiments have been done, it is not clear that each of the individual methods tested was executed with equal proficiency. Many experiments can be required to determine how best to hybridize any given labeled extract to a particular array and how to block, wash, and postprocess (e.g., stain) the array so that the signal-to-noise ratio is maximized. In addition, authors of comparative studies used different arrays, technical protocols (some of which are out of date), experimental designs, and analyses. Finally, some new techniques, which seem quite promising, have been employed so little that their strengths and shortcomings are difficult to assess.