Identification of Candidate Genes and Therapeutic Agents for Light Chain Amyloidosis Based on Bioinformatics Approach.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32099441", "kind": "science-record", "revision": 8, "content_hash": "sha256:b0a4eb68378cc59e61d12ae61f23a2b7f9add4dbcf8c8a33d8d5e6bfa41a7001", "created_at": "2026-11-01T15:40:56Z", "updated_at": "2026-11-01T22:01:19Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Candidate Genes and Therapeutic Agents for Light Chain Amyloidosis Based on Bioinformatics Approach.", "doi": "10.2147/PGPM.S228574", "pmid": "32099441", "authors": ["Wenxiang Bai", "Honghua Wang", "Hua Bai"], "journal": "Pharmacogenomics and personalized medicine", "year": 2019, "abstract": "OBJECTIVE: Systemic amyloid light chain (AL) amyloidosis is a rare plasma cell disease. However, the regulatory mechanisms of AL amyloidosis have not been thoroughly uncovered, identification of candidate genes and therapeutic agents for this disease is crucial to provide novel insights into exploring the regulatory mechanisms underlying AL amyloidosis.\nMETHODS: The gene expression profile of GSE73040, including 9 specimens from AL amyloidosis patients and 5 specimens from normal control, was downloaded from GEO datasets. Differentially expressed genes (DEGs) were sorted with regard to AL amyloidosis versus normal control group using Limma package. The gene enrichment analyses including GO and KEGG pathway were performed using DAVID website subsequently. Furthermore, the protein-protein interaction (PPI) network for DEGs was constructed by Cytoscape software and STRING database. DEGs were mapped to the connectivity map datasets to identify potential molecular agents of AL amyloidosis.\nRESULTS: A total of 1464 DEGs (727 up-regulated, 737 down-regulated) were identified in AL amyloidosis samples versus control samples, these dysregulated genes were associated with the dysfunction of ribosome biogenesis and immune response. PPI network and module analysis uncovered that several crucial genes were defined as candidate genes, including ITGAM, ITGB2, ITGAX, IMP3 and FBL. More importantly, we identified the small molecular agents (AT-9283, Ritonavir and PKC beta-inhibitor) as the potential drugs for AL amyloidosis.\nCONCLUSION: Using bioinformatics approach, we have identified candidate genes and pathways in AL amyloidosis, which can extend our understanding of the cause and molecular mechanisms, and these crucial genes and pathways could act as biomarkers and therapeutic targets for AL amyloidosis.", "claims": [{"id": "claim-data-access", "statement": "The microarray data of GSE73040 were downloaded from GEO datasets. GSE73040, which was based on Agilent GPL6244 platform, was submitted by Paiva et al11 GSE73040 dataset contained 14 samples, including 5 Control samples and 9 amyloidosis samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32099441", "locator": "sections[3] \"Affymetrix Microarray Data\" paragraph 2", "quote": "The microarray data of GSE73040 were downloaded from GEO datasets. GSE73040, which was based on Agilent GPL6244 platform, was submitted by Paiva et al11 GSE73040 dataset contained 14 samples, including 5 Control samples and 9 amyloidosis samples."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:32099441"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE73040"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE73040"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32099441", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/PGPM.S228574", "sha256": "sha256:1666025fee8661fb7bf6cadc8510613634bde75798e63e3f6c3436577a29fade", "bytes": 28551, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/PGPM.S228574", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6997413", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE73040", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73040", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE73040", "version": null, "note": "The microarray data of GSE73040 were downloaded from GEO datasets. GSE73040, which was based on Agilent GPL6244 platform, was submitted by Paiva et al11 GSE73040 dataset contained 14 samples, including 5 Control samples and 9 amyloidosis samples.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The microarray data of GSE73040 were downloaded from GEO datasets. GSE73040, which was based on Agilent GPL6244 platform, was submitted by Paiva et al11 GSE73040 dataset contained 14 samples, including 5 Control samples and 9 amyloidosis samples.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1881298", "GSM1881299", "GSM1881300", "GSM1881301", "GSM1881302", "GSM1881303", "GSM1881304", "GSM1881305", "GSM1881306", "GSM1881307", "GSM1881308", "GSM1881309", "GSM1881310", "GSM1881311"], "sample_count": 14, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Phenotypic, transcriptomic and genomic characterization of clonal plasma cells in light chain amyloidosis [Gene expression profiling]", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:32099441:1", "role": "table", "format": "jats-table", "media_type": 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limma_voom."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE73040"], "resolved_accessions": ["GSE73040"], "statements": ["The microarray data of GSE73040 were downloaded from GEO datasets. GSE73040, which was based on Agilent GPL6244 platform, was submitted by Paiva et al11 GSE73040 dataset contained 14 samples, including 5 Control samples and 9 amyloidosis samples."], "basis": "The paper names GSE73040 in NCBI Gene Expression Omnibus (GEO) and the accession resolves in the repository. 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