Systematic review and meta-analysis of bulk RNAseq studies in human Alzheimer's disease brain tissue

Abstract

We systematically reviewed and meta-analyzed bulk RNA sequencing (RNAseq) studies comparing Alzheimer's disease (AD) patients to controls in human brain tissue. We searched PubMed, Web of Science, and Scopus for human brain bulk RNAseq studies, excluding re-analyses and studies limited to small RNAs or gene panels. We developed 10 criteria for quality assessment and performed a meta-analysis on three high-quality datasets. Of 3266 records, 24 qualified for the systematic review, and one study with three datasets qualified for the meta-analysis. The meta-analysis identified 571 differentially expressed genes (DEGs) in the temporal lobe and 189 in the frontal lobe, including CLU and GFAP. Pathway analysis suggested reactivation of developmental processes in the adult AD brain. Limited data availability constrained the meta-analysis. These findings underscore the need for rigorous methods in AD transcriptomic research to better identify transcriptomic changes and advance biomarker and therapeutic development. This review is registered in PROSPERO (CRD42023466522).

Highlights: Comprehensive review: Conducted the first systematic review and meta-analysis of bulk RNA sequencing (RNAseq) studies comparing Alzheimer's disease (AD) patients with non-demented controls using primary human brain tissue.

Key findings: Identified 571 differentially expressed genes (DEGs) in the temporal lobe and 189 in the frontal lobe of patients with AD, revealing potential therapeutic targets. Pathway discovery: Highlighted key overlapping pathways such as "tube morphogenesis" and "neuroactive ligand-receptor interaction" that may play critical roles in AD.

Quality assessment: Emphasized the importance of methodological rigor in transcriptomic studies, including quality assessment tools to guide future research in AD.

Study limitation: Acknowledged limited access to complete data tables and lack of diversity in existing datasets, which constrained some of the analysis.

Keywords: Alzheimer's disease (AD); RNA sequencing (RNAseq); differentially expressed genes (DEGs); human brain tissue; meta‐analysis; systematic review.

FIGURE 1

PRISMA flow diagram and study design. Diagram illustrating the process to identify studies that met inclusion criteria. The diagram also shows the assessed brain regions in the systematic review and the corresponding number of studies for each region. The total number of studies across all brain regions exceeds the total number of included studies (n = 24) because some studies evaluated multiple brain regions. **Only three datasets from one study were included in the meta‐analysis for the following reasons: (1) the study had a significantly larger sample size compared to others; (2) it received the highest quality assessment score, reducing the risk of bias; and (3) only 5 of the remaining 23 studies provided a differential expression table suitable for meta‐analysis, all of which had relatively small sample sizes (n <50) or significant methodological issues, such as poorly defined AD status. AD, Alzheimer's disease; PRISMA, Preferred Reporting Items for Systematic Reviews and Meta‐Analyses.

FIGURE 2

Meta‐analysis for AD temporal lobe differential gene expression. (A) Differential gene expression results for the AD temporal lobe meta‐analysis (n = 319; 180 AD and 139 controls). The Manhattan plot shows −log10(p‐value) on the y‐axis and chromosome coordinates on the x‐axis. The dotted line represents the Bonferroni corrected p‐value threshold of 0.1 (equivalent to an unadjusted p‐value of 3.39 × 10^⁻6). Genes were considered significantly differentially expressed between AD subjects and controls if the Bonferroni corrected p‐value was less than to 0.1. Statistics were derived from the Inverse‐Variance Weighted Fixed‐Effects Model from METAL. Red dots indicate genes upregulated in AD, whereas blue dots indicate genes that are downregulated in AD. Selected DEGs are highlighted with their gene symbols for interest. (B) Number of temporal lobe meta‐analysis DEGs overlapping with other studies. The y‐axis represents the number of overlapping DEGs, whereas the x‐axis indicates how many of the eight temporal lobe studies each DEG overlapped with. A value of “0” on the x‐axis corresponds to DEGs that are unique to this meta‐analysis. More detailed information about DEG overlap for temporal lobe can be found in Table S8. (C) Metascape pathway convergence analysis for genes upregulated in the AD temporal lobe. Pathways are listed on the y‐axis, with −log10(p‐value) on the x‐axis. (D) Metascape pathway convergence analysis for genes downregulated in the AD temporal lobe. Pathways are listed on the y‐axis, with −log10(p‐value) on the x‐axis. AD, Alzheimer's disease; DEGs, differentially expressed genes.

FIGURE 3

Meta‐analysis for AD frontal lobe differential gene expression. (A) Differential gene expression results for the AD frontal lobe meta‐analysis (n = 599; 327 AD and 272 controls). The Manhattan plot shows −log10(p‐value) on the y‐axis and chromosome coordinates on the x‐axis. The dotted line represents the Bonferroni corrected p‐value threshold of 0.1 (equivalent to an unadjusted p‐value of 3.19 × 10^⁻6.). Genes were considered significantly differentially expressed between AD subjects and controls if the Bonferroni corrected p‐value was less than 0.1. Statistics were derived from the Inverse‐Variance Weighted Fixed‐Effects Model from METAL. Red dots indicate genes upregulated in AD, whereas blue dots indicate genes that are downregulated in AD. Selected DEGs are highlighted with their gene symbols. (B) Number of frontal lobe meta‐analysis DEGs overlapping with other studies. The y‐axis represents the number of overlapping DEGs, whereas the x‐axis indicates how many of the three frontal lobe studies each DEG overlapped with. A value of “0” on the x‐axis corresponds to DEGs that are unique to this meta‐analysis. (C) Metascape pathway convergence analysis for genes upregulated in the AD frontal lobe. Pathways are listed on the y‐axis, with −log10(p‐value) on the x‐axis. (D) Metascape pathway convergence analysis for genes downregulated in the AD frontal lobe. Pathways are listed on the y‐axis, with −log10(p‐value) on the x‐axis. AD, Alzheimer's disease; DEGs, differentially expressed genes.