The Effects of Autophagy-Related Genes and lncRNAs in Therapy and Prognosis of Colorectal Cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33777735", "kind": "science-record", "revision": 3, "content_hash": "sha256:ab6af34085e2840328d94bba7a277c33eaa0ebdfdde376945b1940f21b85bf17", "created_at": "2026-11-01T15:41:30Z", "updated_at": "2026-11-01T21:25:00Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The Effects of Autophagy-Related Genes and lncRNAs in Therapy and Prognosis of Colorectal Cancer.", "doi": "10.3389/fonc.2021.582040", "pmid": "33777735", "authors": ["Yang Yang", "Mingyang Feng", "LiangLiang Bai", "Mengxi Zhang", "Kexun Zhou", "Weiting Liao", "Wanting Lei", "Nan Zhang", "Jiaxing Huang", "Qiu Li"], "journal": "Frontiers in oncology", "year": 2021, "abstract": "Cellular autophagy plays an important role in the occurrence and development of colorectal cancer (CRC). Whether autophagy-related genes and lncRNAs can be used as ideal markers in CRC is still controversial. The purpose of this study is to identify novel treatment and prognosis markers of CRC. We downloaded transcription and clinical data of CRC from the GEO (GSE40967, GSE12954, GSE17536) and TCGA database, screened for differentially autophagy-related genes (DEAGs) and lncRNAs, constructed prognostic model, and analyzed its relationship with immune infiltration. TCGA and GEO datasets (GSE12954 and GSE17536) were used to validate the effect of the model. Oncomine database and Human Protein Atlas verified the expression of DEAGs. We obtained a total of 151 DEAGs in three verification sets collaboratively. Then we constructed a risk prognostic model through Lasso regression to obtain 15 prognostic DEAGs from the training set and verified the risk prognostic model in three verification sets. The low-risk group survived longer than the high-risk group. Age, gender, pathological stage, and TNM stage were related to the prognostic risk of CRC. On the other hand, BRAF status, RFS event, and tumor location are considered as most significant risk factors of CRC in the training set. Furthermore, we found that the immune score of the low-risk group was higher. The content of CD8 + T cells, active NK cells, macrophages M0, macrophages M1, and active dendritic cells was noted more in the high-risk group. The content of plasma cells, resting memory CD4 + T cells, resting NK cells, resting mast cells, and neutrophil cells was higher in the low-risk group. After all, the Oncomine database and immunohistochemistry verified that the expression level of most key autophagy-related genes was consistent with the results that we found. In addition, we obtained six lncRNAs co-expressed with DEAGs from the training set and found that the survival time was longer in the low-risk group. This finding was verified in the verification set and showed same trend to the results mentioned above. In the final analysis, these results indicate that autophagy-related genes and lncRNAs can be used as prognostic and therapeutic markers for CRC.", "claims": [{"id": "claim-method", "statement": "We used the unicox to filter prognosis-related DEAGs and then Lasso regression to construct a risk prognosis model.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33777735", "locator": "sections[15] \"Construction and Verification of Risk Prognosis Model in Colorectal Cancer\" paragraph 2", "quote": "We used the unicox to filter prognosis-related DEAGs and then Lasso regression to construct a risk prognosis model."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. These data can be found here: The Cancer Genome Atlas (https://portal.gdc.cancer.gov/); the NCBI Gene Expression Omnibus (GSE40967).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33777735", "locator": "sections[20] \"Data Availability Statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. These data can be found here: The Cancer Genome Atlas (https://portal.gdc.cancer.gov/); the NCBI Gene Expression Omnibus (GSE40967)."}], "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:33777735"], "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:GSE12954"], "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:GSE12954"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33777735", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fonc.2021.582040", "sha256": "sha256:2d4fd8f3e613e2cc42091c9b9a3e28aea4f3d132abb79afd997bfaa1c0ed8ae6", "bytes": 55587, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fonc.2021.582040", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7991845", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE12954", "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=GSE12954", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE12954", "version": null, "note": "Publicly available datasets were analyzed in this study. These data can be found here: The Cancer Genome Atlas (https://portal.gdc.cancer.gov/); the NCBI Gene Expression Omnibus (GSE40967).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. These data can be found here: The Cancer Genome Atlas (https://portal.gdc.cancer.gov/); the NCBI Gene Expression Omnibus (GSE40967).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM321749", "GSM321750", "GSM321751", "GSM321752", "GSM321753", "GSM321754", "GSM321755", "GSM321756", "GSM321757", "GSM321758", "GSM321759", "GSM321760", "GSM321761", "GSM321762", "GSM321763", "GSM321764", "GSM321766", "GSM321767", "GSM321768", "GSM321769", "GSM321770", "GSM321771", "GSM321772", "GSM321773", "GSM321774", "GSM321775", "GSM321776", "GSM321778", "GSM321779", "GSM321780", "GSM321781"], "sample_count": 31, "group_sizes": null, "group_sizes_basis": null, "platform": "4937", "taxon": "Mus musculus", "title": "Expression Profiling of Dll1 mutant mouse line", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE17536", "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=GSE17536", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE17536", "version": null, "note": "Publicly available datasets were analyzed in this study. 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