On the Reproducibility of MiRNA-Seq Differential Expression Analyses in Neuropsychiatric Diseases

Pérez-Rodríguez, Daniel; López-Fernández, Hugo; Agís‐Balboa, Roberto Carlos

doi:10.1007/978-3-030-86258-9_5

Cited by 3 publications

(4 citation statements)

References 22 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…As a consequence, in the last two decades, an increasing number of studies have made great efforts to find molecular mechanisms behind TRS and spot biomarkers for clinical use. However, the difficult access to neural tissues, the subtle definition of TRS, and the lack of standardization in the bioinformatic methodologies hindered such endeavors [15][16][17][18][19].…”

Section: Introductionmentioning

confidence: 99%

MiRNA Differences Related to Treatment-Resistant Schizophrenia

Pérez-Rodríguez

Penedo

Rivera-Baltanás

et al. 2023

IJMS

View full text Add to dashboard Cite

Schizophrenia (SZ) is a serious mental disorder that is typically treated with antipsychotic medication. Treatment-resistant schizophrenia (TRS) is the condition where symptoms remain after pharmacological intervention, resulting in long-lasting functional and social impairments. As the identification and treatment of a TRS patient requires previous failed treatments, early mechanisms of detection are needed in order to quicken the access to effective therapy, as well as improve treatment adherence. In this study, we aim to find a microRNA (miRNA) signature for TRS, as well as to shed some light on the molecular pathways potentially involved in this severe condition. To do this, we compared the blood miRNAs of schizophrenia patients that respond to medication and TRS patients, thus obtaining a 16-miRNA TRS profile. Then, we assessed the ability of this signature to separate responders and TRS patients using hierarchical clustering, observing that most of them are grouped correctly (~70% accuracy). We also conducted a network, pathway analysis, and bibliography search to spot molecular pathways potentially altered in TRS. We found that the response to stress seems to be a key factor in TRS and that proteins p53, SIRT1, MDM2, and TRIM28 could be the potential mediators of such responses. Finally, we suggest a molecular pathway potentially regulated by the miRNAs of the TRS profile.

show abstract

Section: Introductionmentioning

confidence: 99%

MiRNA Differences Related to Treatment-Resistant Schizophrenia

Pérez-Rodríguez

Penedo

Rivera-Baltanás

et al. 2023

IJMS

View full text Add to dashboard Cite

show abstract

“…However, the extensive use of the miRNA-Seq technology, together with the absence of a standardized methodology for bioinformatics analysis, has raised concerns about its reproducibility [ 17 ]. The main concerns are the great variability in the analysis procedures [ 18 , 19 ], the large influence that biological references have on the results [ 19 , 20 ], the application of generic RNA methods to miRNA data [ 21 ] and the biological variability itself, that makes the comparison between studies complex [ 22 , 23 ].…”

Section: Introductionmentioning

confidence: 99%

“…In this context, we present myBrain-Seq ( ), a highly modular pipeline for performing replicable miRNA-Seq analysis, from the preprocessing of the raw data to the generation of a network of miRNA–protein interactions. It covers most of the necessities of a miRNA-Seq study of neuropsychiatric data, which were identified by thoroughly reviewing current miRNA-Seq methodologies in the field [ 7 ] and translating that information into the pipeline design [ 17 , 38 ]. Finally, myBrain-Seq uses Docker technology, which ensures a stable environment regarding the dependencies and biological annotations used for data analysis, thus enhancing the replicability of the whole process [ 17 , 38 ].…”

Section: Introductionmentioning

confidence: 99%

“…In this context, we present myBrain-Seq (https://github.com/sing-group/my-brainseq), a highly modular pipeline for performing replicable miRNA-Seq analysis, from the preprocessing of the raw data to the generation of a network of miRNA-protein interactions. It covers most of the necessities of a miRNA-Seq study of neuropsychiatric data, which were identified by thoroughly reviewing current miRNA-Seq methodologies in the field [7] and translating that information into the pipeline design [17,38]. Finally, myBrain-Seq uses Docker technology, which ensures a stable environment regarding the dependencies and biological annotations used for data analysis, thus enhancing the replicability of the whole process [17,38].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

MyBrain-Seq: A Pipeline for MiRNA-Seq Data Analysis in Neuropsychiatric Disorders

2023

View full text Add to dashboard Cite

High-throughput sequencing of small RNA molecules such as microRNAs (miRNAs) has become a widely used approach for studying gene expression and regulation. However, analyzing miRNA-Seq data can be challenging because it requires multiple steps, from quality control and preprocessing to differential expression and pathway-enrichment analyses, with many tools and databases available for each step. Furthermore, reproducibility of the analysis pipeline is crucial to ensure that the results are accurate and reliable. Here, we present myBrain-Seq, a comprehensive and reproducible pipeline for analyzing miRNA-Seq data that incorporates miRNA-specific solutions at each step of the analysis. The pipeline was designed to be flexible and user-friendly, allowing researchers with different levels of expertise to perform the analysis in a standardized and reproducible manner, using the most common and widely used tools for each step. In this work, we describe the implementation of myBrain-Seq and demonstrate its capacity to consistently and reproducibly identify differentially expressed miRNAs and enriched pathways by applying it to a real case study in which we compared schizophrenia patients who responded to medication with treatment-resistant schizophrenia patients to obtain a 16-miRNA treatment-resistant schizophrenia profile.

show abstract

Towards a Flexible and Portable Workflow for Analyzing miRNA-Seq Neuropsychiatric Data: An Initial Replicability Assessment

Pérez-Rodríguez

Agís‐Balboa

et al. 2022

Practical Applications of Computational Biology and Bioinformatics, 16th International Conference (PACBB 2022)

View full text Add to dashboard Cite

On the Reproducibility of MiRNA-Seq Differential Expression Analyses in Neuropsychiatric Diseases

Cited by 3 publications

References 22 publications

MiRNA Differences Related to Treatment-Resistant Schizophrenia

MiRNA Differences Related to Treatment-Resistant Schizophrenia

MyBrain-Seq: A Pipeline for MiRNA-Seq Data Analysis in Neuropsychiatric Disorders

Towards a Flexible and Portable Workflow for Analyzing miRNA-Seq Neuropsychiatric Data: An Initial Replicability Assessment

Contact Info

Product

Resources

About