Ribonucleic Acid Metabolism Research Articles

Multiplexed In Situ Imaging of Site-Specific m6A Methylation with Proximity Hybridization Followed by Primer Exchange Amplification (m6A-PHPEA).

Post-transcriptional modification of N6-methyladenosine (m6A) is crucial for ribonucleic acid (RNA) metabolism and cellular function. The ability to visualize site-specific m6A methylation at the single-cell level would markedly enhance our understanding of its pivotal regulatory functions in the field of epitranscriptomics. Despite this, current in situ imaging techniques for site-specific m6A are constrained, posing a significant barrier to epitranscriptomic studies and pathological diagnostics. Capitalizing on the precise targeting capability of deoxyribonucleic acid (DNA) hybridization and the high specificity of the m6A antibody, we present a method, termed proximity hybridization followed by primer exchange amplification (m6A-PHPEA), for the site-specific imaging of m6A methylation within cells. This approach enables high-resolution, single-cell imaging of m6A methylation across various RNA molecules coupled with efficient signal amplification. We successfully imaged three distinct m6A methylation sites concurrently in multiple cell types, revealing cell-to-cell variability in expression levels. This method promises to illuminate the dynamics of m6A-modified RNAs, potentially revolutionizing epitranscriptomic research and the development of advanced pathological diagnosis for chemical modifications.

Potential contribution of spinal interneurons to the etiopathogenesis of amyotrophic lateral sclerosis.

Amyotrophic lateral sclerosis (ALS) consists of a group of adult-onset fatal and incurable neurodegenerative disorders characterized by the progressive death of motor neurons (MNs) throughout the central nervous system (CNS). At first, ALS was considered to be an MN disease, caused by cell-autonomous mechanisms acting specifically in MNs. Accordingly, data from ALS patients and ALS animal models revealed alterations in excitability in multiple neuronal populations, including MNs, which were associated with a variety of cellular perturbations such as protein aggregation, ribonucleic acid (RNA) metabolism defects, calcium dyshomeostasis, modified electrophysiological properties, and autophagy malfunctions. However, experimental evidence rapidly demonstrated the involvement of other types of cells, including glial cells, in the etiopathogenesis of ALS through non-cell autonomous mechanisms. Surprisingly, the contribution of pre-motor interneurons (INs), which regulate MN activity and could therefore critically modulate their excitability at the onset or during the progression of the disease, has to date been severely underestimated. In this article, we review in detail how spinal pre-motor INs are affected in ALS and their possible involvement in the etiopathogenesis of the disease.

Assessing Partial Inhibition of Ribonuclease A Activity by Curcumin through Fluorescence Spectroscopy and Theoretical Studies.

Molecular interactions and controlled expression of enzymatic activities are fundamental to all cellular functions in an organism. The active polyphenol in turmeric known as curcumin (CCM) is known to exhibit diverse pharmacological activities. Ribonucleases(RNases) are the hydrolytic enzymes that plays important role in ribonucleic acid (RNA) metabolism. Uncontrolled and unwanted cleavage of RNA by RNases may be the cause of cell death leading to disease states. The protein ribonuclease A (RNase A) in the superfamily of RNases cleaves the RNA besides its role in different diseases like autoimmune diseases, and pancreatic disorders. Interaction of CCM with RNase A have been reported along with the possible role of CCM to inhibit the RNase A enzymatic activity. The interaction strength was found to be 104M-1 order from spectroscopic results. Quenching of RNase A fluorescence by CCM was 104M-1 order. Non-radiative energy transfer from RNase A (donor) to CCM (acceptor) suggested a distance of 2.42nm between the donor-acceptor pair. Circular dichroism studies revealed no structural changes in RNase A after binding. Binding-induced conformational variation in protein was observed from synchronous fluorescence studies. Agarose gel electrophoresis revealed a partial inhibition of the RNase A activity by CCM though not significant. Molecular docking and molecular dynamics studies suggested the residues of RNase A involved in the interaction with supporting the experimental finding for the partial inhibition of the enzyme activity. This study may help in designing new CCM analogues or related structures to understand their differential inhibition of the RNase A activity.

Novel molecular mechanism of high ribonucleic acid yield in Saccharomyces pastorianus revealed by transcriptomics

Ribonucleic acid (RNA) and its degradation products find widespread application across various industries, including the food condiments sector. This study employed comparative transcriptomics to investigate the genetic mechanisms underlying RNA synthesis in the mutant Saccharomyces pastorianus strain G03H8, which exhibited a high RNA yield. To identify genetically engineered targets, single gene over-expression and CRISPR/Cas9 gene editing technology were utilized. The differential enrichment results revealed a close association between RNA metabolism and cellular processes such as the cell cycle, purine metabolism, nucleotide metabolism, and other metabolic pathways. Subsequently, we selected the top nine most promising genes to evaluate their impact on RNA synthesis. In these nine targets, upon comparing the RNA yield of the genetically engineered strains, G03-TAL1, G03-PGM2, G03-ΔPRS5, and G03-△DBP8, with the parent strain G03, significant improvements of 31.7%, 41.8%, 72.1%, and 46.7% were observed, respectively. Furthermore, these four genes were found to enhance the strain's growth and augment the pentose phosphate pathway, thus demonstrating the considerable potential for enhancing RNA yield. Notably, this study represents the first instance of identifying the upregulation of TAL1, PGM2, PRS5, and DBP8 as a means to increase RNA content in S. pastorianus. Consequently, our findings present novel genetic targets for enhancing RNA production and contribute to a deeper understanding of the mechanisms involved in high RNA synthesis in S. pastorianus.

Deciphering molecular mechanisms of phase separation in RNA biology by single-molecule biophysical technologies.

Ribonucleic acid (RNA) biology has emerged as one of the most important areas in modern biology and biomedicine. RNA and RNA-binding proteins (RBPs) are involved in forming biomolecular condensates, which are crucial for RNA metabolism. To quantitively decipher the molecular mechanisms of RNP granules, researchers have turned to single-molecule biophysical techniques, such as single-molecule Förster resonance energy transfer (smFRET), in vivo single-molecule imaging technique with single particle tracking (SPT), DNA Curtains, optical tweezers, and atomic force microscopy (AFM). These methods are used to investigate the molecular biophysical properties within RNP granules, as well as the molecular interactions between RNA and RBPs and RBPs themselves, which are challenging to study using traditional experimental methods of the liquid-liquid phase separation (LLPS) field, such as fluorescence recovery after photobleaching (FRAP). In this work, we summarize the applications of single-molecule biophysical techniques in RNP granule studies and highlight how these methods can be used to reveal the molecular mechanisms of RNP granules.

A Systematic Pan-Cancer Analysis of YY1 Aberrations and their Relationship with Clinical Outcome, Tumor Microenvironment, and Therapeutic Targets.

Yin-Yang 1 (YY1) has a crucial function in the development of several malignancies, according to recent research. However, nothing is known about its aberrant expression and prognostic significance in human pan-cancer. We first explored the potential carcinogenic effect of YY1 in 33 cancers using the cancer genome atlas (TCGA) project and gene expression omnibus (GEO) datasets in this research. Then, we contained a variety of elements, for instance, gene expression, the state of survival, gene alterations, protein phosphorylation, immune infiltration, and related cellular pathways, and used a series of bioinformatics methods to investigate the underlying molecular mechanism of YY1 in the etiology or clinical prognosis of various malignancies. In most malignancies, YY1 was expressed at high levels, and the level of YY1 expression was statistically associated with the prognosis of tumor patients. The S118 site of YY1 implied higher phosphorylation expression in breast cancer, colon cancer, uterine corpus endometrial carcinoma (UCEC), and lung adenocarcinoma (LUAD) tumor tissues, but lower phosphorylation levels in ovarian cancer and clear cell carcinoma tumor tissues. For S247, higher phosphorylation levels were found in colon cancer, UCEC, and LUAD tumor tissue, and lower phosphorylation expression was found in clear cell carcinoma tumor tissue. In TCGA database, YY1 expression in BRCA, BRCA-LumA, BRCA-LumB, CESC, CHOL, COAD, ESCA, HNSC, HNSC-HPV-, KIRP, LGG, LIHC, and PAAD tumor tissues was a statistically significant positive connection of the estimated infiltration value of cancer-associated fibroblasts but a negative correlation in TGCT. In addition, the functional mechanism of YY1 also involves viral carcinogenesis and ribonucleic acid (RNA) metabolism related functions. Our first pan-cancer analysis offers a pretty comprehensive knowledge of YY1's oncogenic involvement in various cancers.

Development of Myotropic Extracellular Vesicles for Targeted Delivery of Therapeutics to Skeletal Muscle

Muscular pathologies comprise a family of diseases and disorders resulting in the degeneration of skeletal muscle tissue. Current therapeutics are non‐specific to skeletal muscle, which often reduces efficacy and causes harmful off‐target effects in patients. Thus, a myotropic (muscle‐targeted) drug delivery system is needed to shuttle therapeutics to muscle cells to improve efficacy and limit off‐target effects. The objective of this investigation was to develop biological lipid nanoparticles, extracellular vesicles (EVs), with enhanced myotropism. We hypothesized that displaying myotropic transmembrane proteins at the surface of EVs would improve delivery of molecular cargo into muscle cells. To this end, we displayed the myotropic transmembrane proteins MyoMaker (MYMK), MyoMixer (MYMX) and M‐Cadherin (M‐CAD) in the membranes of EVs from Human Embryonic Kidney (HEK293) cells. Using flow cytometry, we measured the incorporation of each protein candidate into the EVs via endogenous green fluorescent protein (GFP) tags included on the cytosolic c‐terminus of each protein. We then measured the delivery of fluorescently‐labeled protein by each myotropic EV candidate in mouse (C2C12) myotubes. In addition to using EVs as delivery vehicles for exogenously loaded therapeutics, the native EV cargo may also be of therapeutic relevance. Given this, we examined the endogenous protein cargo of non‐engineered HEK293‐EVs via mass spectrometry. MYMK displayed the highest degree of incorporation into EVs relative to control HEK293‐EVs (p = 0.006). The MYMK‐EV formulation displayed the greatest increase in protein cargo delivered into myotubes relative to control HEK293‐EVs (~125%, p = 0.0005). Proteomic analysis revealed the top biological processes and molecular functions of HEK293‐EV protein cargo to be ribonucleic acid binding, processing, and metabolism, potentially altering translation in recipient cells. The in vitro data in the present study establish the feasibility of using MYMK‐EVs as a myotropic delivery system. Future investigations are needed to fully elucidate the cell/tissue tropism and physiological effects of MYMK‐EVs in vivo.

Long Non-coding RNAs, Lnc(ing) RNA Metabolism to Cancer Biology.

The eukaryotic genome is represented by a vast proportion of non-coding regions, which in recent years have been attributed to have important functional roles in gene regulation through a myriad of processes, ranging from proper localization, correct folding and, most importantly, spatial and temporally regulated expression of genes. One of the major contributing factors in these processes is ribonucleic acid (RNA) metabolism, which comprises the RNA-nucleoprotein (RNP) complexes that interact with and instruct the genome to function. Long non-coding RNAs are an integral component of several RNPs, and herein we provide an overview of the understanding of the long non-coding RNAs, their characteristics, their function and their balancing act as dual modulators in cancer manifestation and progression.

Research Progress on the Omics of Methamphetamine Toxic Damage and Addiction.

The mechanism of methamphetamine toxicity and addiction is the key research direction of forensic toxicology, and the development of omics technology provides a new platform for further study of this direction. METH toxic damage and addiction are reflected differently in genes, ribonucleic acid (RNA) transcription, protein and metabolism. This article summarizes the achievements and shortcomings of multi-omics technologies such as genome, transcriptome, metabolome and proteome in the study of METH damage and addiction, and discusses the strategies and advantages of multi-omics combined analysis in the study of METH toxic damage and addiction mechanism, in order to provide more useful reference information for forensic toxicology of METH.

Dissecting the transcriptional program of phosphomannomutase 2-deficient cells: Lymphoblastoide B cell lines as a valuable model for congenital disorders of glycosylation studies.

Congenital disorders of glycosylation (CDG) include 150 genetically and clinically heterogeneous diseases, showing significant glycoprotein hypoglycosylation that leads to pathological consequences in multiple organs and systems whose underlying mechanisms are not yet understood. A few cellular and animal models have been used to study specific CDG characteristics, although they have given limited information due to the few CDG mutations tested and the still missing comprehensive molecular and cellular basic research. Here, we provide specific gene expression profiles, based on ribonucleic acid (RNA) microarray analysis, together with some biochemical and cellular characteristics of a total of nine control Epstein-Barr virus-transformed lymphoblastoid B cell lines (B-LCL) and 13 CDG B-LCL from patients carrying severe mutations in the phosphomannomutase 2 (PMM2) gene, strong serum protein hypoglycosylation and neurological symptoms. Significantly dysregulated genes in PMM2-CDG cells included those regulating stress responses, transcription factors, glycosylation, motility, cell junction and, importantly, those related to development and neuronal differentiation and synapse, such as carbonic anhydrase 2 (CA2) and ADAM23. PMM2-CDG-associated biological consequences involved the unfolded protein response, RNA metabolism and the endoplasmic reticulum, Golgi apparatus and mitochondria components. Changes in the transcriptional and CA2 protein levels are consistent with the CDG physiopathology. These results demonstrate the global transcriptional impact in phosphomannomutase 2-deficient cells, reveal CA2 as a potential cellular biomarker and confirm B-LCL as an advantageous model for CDG studies.

Poly(A)+ Sensing of Hybridization-Sensitive Fluorescent Oligonucleotide Probe Characterized by Fluorescence Correlation Methods.

Ribonucleic acid (RNA) plays an important role in many cellular processes. Thus, visualizing and quantifying the molecular dynamics of RNA directly in living cells is essential to uncovering their role in RNA metabolism. Among the wide variety of fluorescent probes available for RNA visualization, exciton-controlled hybridization-sensitive fluorescent oligonucleotide (ECHO) probes are useful because of their low fluorescence background. In this study, we apply fluorescence correlation methods to ECHO probes targeting the poly(A) tail of mRNA. In this way, we demonstrate not only the visualization but also the quantification of the interaction between the probe and the target, as well as of the change in the fluorescence brightness and the diffusion coefficient caused by the binding. In particular, the uptake of ECHO probes to detect mRNA is demonstrated in HeLa cells. These results are expected to provide new insights that help us better understand the metabolism of intracellular mRNA.

N6 -methyladenosine Steers RNA Metabolism and Regulation in Cancer.

As one of the most studied ribonucleic acid (RNA) modifications in eukaryotes, N6‐methyladenosine (m6A) has been shown to play a predominant role in controlling gene expression and influence physiological and pathological processes such as oncogenesis and tumor progression. Writer and eraser proteins, acting opposite to deposit and remove m6A epigenetic marks, respectively, shape the cellular m6A landscape, while reader proteins preferentially recognize m6A modifications and mediate fate decision of the methylated RNAs, including RNA synthesis, splicing, exportation, translation, and stability. Therefore, RNA metabolism in cells is greatly influenced by these three classes of m6A regulators. Aberrant expression of m6A regulators has been widely reported in various types of cancer, leading to cancer initiation, progression, and drug resistance. The close links between m6A and cancer shed light on the potential use of m6A methylation and its regulators as prognostic biomarkers and drug targets for cancer therapy. Given the notable effects of m6A in reversing chemoresistance and enhancing immune therapy, it is a promising target for combined therapy. Herein, we summarize the recent discoveries on m6A and its regulators, emphasizing their influences on RNA metabolism, their dysregulation and impacts in diverse malignancies, and discuss the clinical implications of m6A modification in cancer.

A Review Article: Categorization, Advancement and Obstacles of Genetic factors and types of Spinal Muscular Degeneration

SMA (Spinal muscular atrophies) are category of hereditary inflammation in the funiculars and lower brain stem, tissue fatigue, and degeneration characterized by motor neuron failure. The analytic and genetic phenotypes incorporate a diverse continuum distinguished depending on age of onset, tissue participation arrangement, and inheritance arrangement. Rapid advancements in genetic science have expedite the discovery of causative genes over the past few years, and provide significant access in awareness the biochemical and neurological basis of Spinal muscular atrophies and insights into the motor neurons' selective deficiency. Popular path physiological topics include Ribonucleic Acid metabolism and splicing abnormalities, axonal transmission, and motor neurons' advancement and communication. These also collectively revealed possible innovative prevention methods and comprehensive attempts are what benefits does the company offer? Although a range of promising therapeutic therapies for Spinal muscular atrophies is emerging, it is essential to identify therapeutic windows and establish responsive and appropriate biomarkers to promote future analytic trial success. This research offers a description of Spinal muscular atrophies' logical manifestations and genetics. It discusses recent advancements in learning—mechanisms for the pathogenesis of inflammation and new treatment methods.

Mitigation effects of CO2-driven ocean acidification on Cd toxicity to the marine diatom Skeletonema costatum

Ocean acidification (OA) is a global problem to marine ecosystems. Cadmium (Cd) is a typical metal pollutant, which is non-essential but extremely toxic to marine organisms. The combined effects of marine pollution and climate-driven ocean changes should be considered for the effective marine ecosystem management of coastal areas. Previous reports have separately investigated the influences of OA and Cd pollution on marine organisms. However, little is known of the potential combined effects of OA and Cd pollution on marine diatoms. We investigated the sole and combined influences of OA (1500 ppm CO2) and Cd exposure (0.4 and 1.2 mg/L) on the coastal diatom Skeletonema costatum. Our results clearly showed that OA significantly alleviated the toxicity of Cd to S. costatum growth and mitigated the oxidant stress, although the intercellular Cd accumulation still increased. OA partially rescued S. costatum from the inhibition of photosynthesis and pyruvate metabolism caused by Cd exposure. It also upregulated genes involved in gluconeogenesis, glycolysis, the citrate cycle (TCA), Ribonucleic acid (RNA) metabolism, and especially the biosynthesis of non-protein thiol compounds. These changes might contribute to algal growth and Cd resistance. Overall, this study demonstrates that OA can alleviate Cd toxicity to S. costatum and explores the potential underlying mechanisms at both the cellular and molecular levels. These results will ultimately help us understand the impacts of combined stresses of climate change and metal pollution on marine organisms and expand the knowledge of the ecological risks of OA.

Ubiquitin Signaling Regulates RNA Biogenesis, Processing, and Metabolism.

The fate of eukaryotic proteins, from their synthesis to destruction, is supervised by the ubiquitin-proteasome system (UPS). The UPS is the primary pathway responsible for selective proteolysis of intracellular proteins, which is guided by covalent attachment of ubiquitin to target proteins by E1 (activating), E2 (conjugating), and E3 (ligating) enzymes in a process known as ubiquitylation. The UPS can also regulate protein synthesis by influencing multiple steps of RNA (ribonucleic acid) metabolism. Here, recent publications concerning the interplay between the UPS and different types of RNA are reviewed. This interplay mainly involves specific RNA-binding E3 ligases that link RNA-dependent processes with protein ubiquitylation. The emerging understanding of their modes of RNA binding, their RNA targets, and their molecular and cellular functions are primarily focused on. It is discussed how the UPS adapted to interact with different types of RNA and how RNA molecules influence the ubiquitin signaling components.

ALS Yeast Models-Past Success Stories and New Opportunities.

In the past two decades, yeast models have delivered profound insights into basic mechanisms of protein misfolding and the dysfunction of key cellular pathways associated with amyotrophic lateral sclerosis (ALS). Expressing ALS-associated proteins, such as superoxide dismutase (SOD1), TAR DNA binding protein 43 (TDP-43) and Fused in sarcoma (FUS), in yeast recapitulates major hallmarks of ALS pathology, including protein aggregation, mislocalization and cellular toxicity. Results from yeast have consistently been recapitulated in other model systems and even specimens from human patients, thus providing evidence for the power and validity of ALS yeast models. Focusing on impaired ribonucleic acid (RNA) metabolism and protein misfolding and their cytotoxic consequences in ALS, we summarize exemplary discoveries that originated from work in yeast. We also propose previously unexplored experimental strategies to modernize ALS yeast models, which will help to decipher the basic pathomechanisms underlying ALS and thus, possibly contribute to finding a cure.

Characterization of the Catalytic Subunits of the RNA Exosome-like Complex in Plasmodium falciparum.

The eukaryotic ribonucleic acid (RNA) exosome is a versatile multiribonuclease complex that mediates the processing, surveillance, and degradation of virtually all classes of RNA in both the nucleus and cytoplasm. The complex, composed of 10 to 11 subunits, has been widely described in many organisms. Bioinformatic analyses revealed that there may be also an exosome‐like complex in Plasmodium falciparum, a parasite of great importance in public health, with eight predicted subunits having high sequence similarity to their counterparts in yeast and human. In this work, the putative RNA catalytic components, designated as PfRrp4, PfRrp41, PfDis3, and PfRrp6, were identified and systematically analyzed. Quantitative polymerase chain reaction (QPCR) analyses suggested that all of them were transcribed steadily throughout the asexual stage. The expression of these proteins was determined by Western blot, and their localization narrowed to the cytoplasm of the parasite by indirect immunofluorescence. The recombinant proteins of PfRrp41, PfDis3, and PfRrp6 exhibited catalytic activity for single‐stranded RNA (ssRNA), whereas PfRrp4 showed no processing activity of both ssRNA and dsRNA. The identification of these putative components of the RNA exosome complex opens up new perspectives for a deep understanding of RNA metabolism in the malarial parasite P. falciparum.

Diabetic neuropathy and the sensory neuron: New aspects of pathogenesis and their treatment implications.

Diabetic polyneuropathy (DPN) continues to be generally considered as a “microvascular” complication of diabetes mellitus alongside nephropathy and retinopathy. The microvascular hypothesis, however, might be tempered by the concept that diabetes directly targets dorsal root ganglion sensory neurons. This neuron‐specific concept, supported by accumulating evidence, might account for important features of DPN, such as its early sensory neuron degeneration. Diabetic sensory neurons develop neuronal atrophy alongside a series of messenger ribonucleic acid (RNA) changes related to declines in structural proteins, increases in heat shock protein, increases in the receptor for advanced glycation end‐products, declines in growth factor signaling and other changes. Insulin is recognized as a potent neurotrophic factor, and insulin ligation enhances neurite outgrowth through activation of the phosphoinositide 3‐kinase–protein kinase B pathway within sensory neurons and attenuates phenotypic features of experimental DPN. Several interventions, including glucagon‐like peptide‐1 agonism, and phosphatase and tensin homolog inhibition to activate growth signals in sensory neurons, or heat shock protein overexpression, prevent or reverse neuropathic abnormalities in experimental DPN. Diabetic sensory neurons show a unique pattern of microRNA alterations, a key element of messenger RNA silencing. For example, let‐7i is widely expressed in sensory neurons, supports their growth and is depleted in experimental DPN; its replenishment improves features of DPN models. Finally, impairment of pre‐messenger RNA splicing in diabetic sensory neurons including abnormal nuclear RNA metabolism and structure with loss of survival motor neuron protein, a neuron survival molecule, and overexpression of CWC22, a splicing factor, offer further novel insights. The present review addresses these new aspects of DPN sensory neurodegeneration.

Prognostic signature of early lung adenocarcinoma based on the expression of ribonucleic acid metabolism–related genes

ObjectiveThe current staging system for lung cancer is not sufficient to accurately identify those patients with early-stage tumors who would benefit from postsurgery chemotherapy. The objective of this study was to validate a prognostic signature based on the expression of 5 RNA (ribonucleic acid) metabolism-related genes. MethodsFive lung cancer microarray datasets, 3 from adenocarcinomas and 2 from squamous cell carcinomas, were analyzed. Kaplan-Meier survival curves and Cox proportional hazards models were used to evaluate the relationship between the classifier and recurrence and survival. ResultsStatistically significant differences in relapse-free survival and overall survival were observed when lung adenocarcinoma patients were divided into 3 risk groups. The prognostic information provided by the signature was independent from other demographic and disease variables, including stage. Significant differences in survival were observed between low- and high-risk groups in stage-IB patients: 5-year survival rates ranged from 83% to 100% in the low-risk groups, and from 30% to 71% in the high-risk groups, depending on the dataset. The RNA metabolism score additionally displayed an association with the benefit of adjuvant chemotherapy (P < .001), suggesting that those patients in the low-risk group are not good candidates for this treatment. ConclusionsThe RNA metabolism signature is a prognostic marker that may be useful for predicting survival and optimizing the benefit of adjuvant chemotherapy in patients with lung adenocarcinoma.

Analysis of Parkinson's disease pathophysiology using an integrated genomics-bioinformatics approach

The pathogenesis and pathophysiology of a disease determine how it should be diagnosed and treated. Yet, understanding the cause and mechanisms of progression often requires intensive human efforts, especially for diseases with complex etiology. The latest genomic technology coupled with advanced, large-scale data analysis in the field known as bioinformatics has promised a high-throughput approach that can quickly identify disease-affected genes and pathways by examining tissue samples collected from patients and control subjects. Furthermore, significant biological themes indicative of genomic events can be recognized on the basis of affected genes. However, given identified biological themes, it is not clear how to organize genomic events to arrive at a coherent pathophysiological explanation about the disease. To address this important issue, we have developed an innovative method named “Expression Data Up-Stream Analysis” (EDUSA) that can perform a bioinformatics analysis to identify and rank upstream processes effectively. We applied it to Parkinson's disease (PD) using a genomic data set available at a public data repository known as Gene Expression Omnibus (GEO). In this study, disease-affected genes were identified using GEO2R software, and disease-pertinent processes were identified using EASE software. Then the EDUSA program was used to determine the upstream versus downstream hierarchy of the processes. The results confirmed the current misfolded protein theory about the pathogenesis of PD, and provided new insights as well. Particularly, our program discovered that RNA (ribonucleic acid) metabolism pathology was a potential cause of PD, which in fact, is an emerging theory of neurodegenerative disorders. In addition, it was found that the dysfunction of the transport system seemed to occur in the early phase of neurodegeneration, whereas mitochondrial dysfunction appeared at a later stage. Using this methodology, we have demonstrated how to determine the stages of disease development with single-point data collection.