Identifying an Inversin as a Novel Prognostic Marker in Patients with Clear-Cell Renal Cell Carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39596188", "kind": "science-record", "revision": 4, "content_hash": "sha256:7d396ba5610705d981e50f7e999183fd8429b4c04ec4ade808c80b34af834de9", "created_at": "2026-11-01T20:29:52Z", "updated_at": "2026-11-01T22:55:41Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identifying an Inversin as a Novel Prognostic Marker in Patients with Clear-Cell Renal Cell Carcinoma.", "doi": "10.3390/ijms252212120", "pmid": "39596188", "authors": ["Ivanka Urlić", "Violeta Šoljić", "Martina Vukoja", "Inga Marijanović", "Marija Kraljević", "Marjan Urlić", "Sara Marić", "Katarina Vukojević", "Natalija Filipović"], "journal": "International journal of molecular sciences", "year": 2024, "abstract": "Precision medicine is a developing trend in oncology, and it includes the prognosis and treatment of advanced-stage ccRCC. New predictive factors and therapeutic targets for this disease are steadily needed. The aim of this study was to explore the tumor expression of inversin as a potential prognostic factor and/or therapeutic target in ccRCC. We compared the expression of inversin between primary ccRCC and normal renal tissues by using immunohistochemistry and rtPCR in our cohort, and we also analyzed publicly available data from the TCGA-KIRC cohort. We found that the expression of inversin was significantly lower in primary tumor tissue, in comparison to solid normal tissue. Data from the KIRC study confirmed that a lower INVS expression level in ccRCC was significantly related with the overall and disease-specific survival, as well as with a shorter progression-free interval (p < 0.05). Four out of ten inversin interactome partners were significantly related with the overall and disease-specific survival in ccRCC. A lower expression of ANKS6 was a negative survival predictor, while a higher expression of NPHP3, DVL1, or DVL3 was related with a lower survival. The expression of INVS and its interactome partners in ccRCC was correlated with the differentiation of the tumor and metastasis. The expression of INVS and its partners was also correlated with tumor leukocyte infiltration and the expression of immune checkpoint genes. The results of this study point to inversin and a distinguished group of its interactome partners as potential prognostic factors in ccRCC, with their predominant involvement in the modulation of the inflammatory infiltration of the tumor microenvironment and a strong relationship with the metastatic potential of the tumor.", "claims": [{"id": "claim-method", "statement": "Data from the primary tumor (533 samples) were used for a Kaplan–Meyer curve analysis. The median was used as the cut-off value. The different Kaplan–Meier curves were compared using the log-rank test and χ2, and the p-values (χ2 distribution) were reported. A differential expression analysis using Welch’s t-test was made to compare the M1 (N = 79) vs. M0 (N = 422) pathological M stages (for data with a known M stage). A one-way ANOVA was used to compare expression data according to a histological grade, after GX (N = 5) and null (N = 3) specimens were removed.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39596188", "locator": "sections[16] \"4.5. Survival and Statistical Analysis in the TCGA-KIRC Cohort\" paragraph 2", "quote": "Data from the primary tumor (533 samples) were used for a Kaplan–Meyer curve analysis. The median was used as the cut-off value. The different Kaplan–Meier curves were compared using the log-rank test and χ2, and the p-values (χ2 distribution) were reported. A differential expression analysis using Welch’s t-test was made to compare the M1 (N = 79) vs. M0 (N = 422) pathological M stages (for data with a known M stage). A one-way ANOVA was used to compare expression data according to a histological grade, after GX (N = 5) and null (N = 3) specimens were removed."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://docs.gdc.cancer.gov/Data/Release_Notes/Data_Release_Notes/#data-release-400; https://gdc-hub.s3.us-east-1.amazonaws.com/download/TCGA-KIRC.star_fpkm-uq.tsv.gz; Full metadata, TCGA_KIRC_exp_HiSeqV2; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131685, GSE131685.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39596188", "locator": "sections[24] \"notes\" paragraph 1", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://docs.gdc.cancer.gov/Data/Release_Notes/Data_Release_Notes/#data-release-400; https://gdc-hub.s3.us-east-1.amazonaws.com/download/TCGA-KIRC.star_fpkm-uq.tsv.gz; Full metadata, TCGA_KIRC_exp_HiSeqV2; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131685, GSE131685."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Lower INVS expression in ccRCC was significantly associated with poorer overall and disease-specific survival and a shorter progression-free interval.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "Data from the KIRC study confirmed that a lower INVS expression level in ccRCC was significantly related with the overall and disease-specific survival, as well as with a shorter progression-free interval (p < 0.05)."}, "evidence": [{"asset": "source:pmid:39596188", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data from the KIRC study confirmed that a lower INVS expression level in ccRCC was significantly related with the overall and disease-specific survival, as well as with a shorter progression-free interval (p < 0.05)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Lower INVS expression in ccRCC was significantly associated with poorer overall and disease-specific survival and a shorter progression-free interval.", "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:39596188"], "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:GSE131685"], "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:GSE131685"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39596188", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/ijms252212120", "sha256": "sha256:fd241e2d9204281c25fcb246de5f98b9e14317891e4f2fc16dbe8940f2ae8d97", "bytes": 40258, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/ijms252212120", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11594840", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE131685", "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=GSE131685", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE131685", "version": null, "note": "The datasets presented in this study can be found in online repositories. 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The median was used as the cut-off value. The different Kaplan–Meier curves were compared using the log-rank test and χ2, and the p-values (χ2 distribution) were reported. A differential expression analysis using Welch’s t-test was made to compare the M1 (N = 79) vs. M0 (N = 422) pathological M stages (for data with a known M stage). A one-way ANOVA was used to compare expression data according to a histological grade, after GX (N = 5) and null (N = 3) specimens were removed."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}