# Deciphering lung adenocarcinoma evolution: Integrative single-cell genomics identifies the prognostic lung progression associated signature Researcher: Ge Zhang Chinese name: 张格 ORCID identity anchor: https://orcid.org/0000-0002-3116-3246 Canonical researcher: https://drgezhang.com/#person Journal: Journal of Cellular and Molecular Medicine Year: 2024 Type: Article DOI: 10.1111/jcmm.18408 Canonical page: https://drgezhang.com/papers/doi-10-1111-jcmm-18408.html Markdown record: https://drgezhang.com/papers/doi-10-1111-jcmm-18408.md ## Full Authors 1. Pengpeng Zhang 2. Zijun Yang 3. Zuo Liu 4. Ge Zhang 5. Lianmin Zhang 6. Zhenfa Zhang 7. Jun Fan ## Research & review context ### Research fields - Lung cancer molecular pathology - Computational oncology ### Review topics - Cell states in early lung adenocarcinoma - Transcriptomic survival risk signatures ### Scientific role Retrospective LUAD multi-dataset signature discovery with an ancillary PSMB1 cell-line perturbation study. ### Evidence position Observational transcriptomic/prognostic associations and in-vitro functional readouts; no prospective LPAS-guided therapy evidence. ### Related concepts - AIS–MIA–IAC comparison - LPAS nine-gene signature - PSMB1 siRNA ### Possible citation contexts - Reviews evaluating cross-sectional single-cell LUAD states and prognostic transcriptomic signatures. - Discussions distinguishing cell-line perturbation from clinical proof of a molecular therapeutic target. Possible literature-review contexts, not evidence of existing citations. Read the findings and Evidence Scope before citing the original article. ## Evidence Scale **Deciphering lung adenocarcinoma evolution: Integrative single-cell genomics identifies the prognostic lung progression associated signature** Integrative single-cell and bulk-transcriptomic analyses nominated a Cluster 6-related lung progression-associated signature (LPAS) associated with survival and inferred immune states in lung adenocarcinoma. PSMB1 silencing reduced proliferative and migratory phenotypes in cultured LUAD cells; these findings do not establish patient treatment efficacy. | Evidence | Value | | --- | --- | | Single-cell specimen scale | GSE189357 and GSE150938: 4 AIS, 8 MIA and 9 IAC specimens (21 reported across pathology groups) | | Independent survival-series list | GSE13213 (119), GSE29016 (39), GSE30219 (86), GSE31210 (227) and GSE68465 (443) as reported analyzed series | | Model discovery | TCGA-LUAD; cohort n not inferred from unspecified filtering | | Local stage-associated RNA sequencing | 14 LUAD surgical specimens (reported) | | LPAS signature | 9 genes | ### Counting note The 21 scRNA-seq specimens, 14 local RNA-seq specimens, TCGA cases, five survival cohorts and mixed-cancer immunotherapy datasets represent distinct analytic layers; neither cross-dataset independence nor a synthetic unique-patient total is inferred. ## Research Question Can cell-state patterns associated with adenocarcinoma in situ, minimally invasive adenocarcinoma and invasive lung adenocarcinoma inform a prognostic expression signature, and which experimental observations support prioritized genes? ## Author Evidence Summary The researchers integrated two public single-cell LUAD series, TCGA transcriptomic and survival data, five independent GEO survival series, exploratory immunotherapy-response datasets and cultured-cell knockdown assays. The prognostic evidence is observational; pseudotime, immune scores and therapy-response computations require separate interpretation from experiments. ## Key Findings ### KF1: Two single-cell series identified heterogeneous epithelial states across early LUAD pathological categories. Context: Single-cell cross-sectional profiles; inferCNV and trajectory scores estimate rather than observe clonal evolution. | Evidence | Value | | --- | --- | | Pathological specimens | 4 AIS, 8 MIA and 9 IAC in GSE189357/GSE150938 | | Computational annotation | 12 broad cell types; 8 re-clustered inferred tumor epithelial groups | Source locator: PMC11149493: Methods §2.1 Data set source (jcmm18408-sec-0003); Results §3.1 (jcmm18408-sec-0024); Figure 2A–H. ### KF2: Cluster 6-associated transcriptomic features were enriched during the reported AIS-to-IAC comparison. Context: Proportional and pseudotime associations do not establish observed within-patient malignant transformation. | Evidence | Value | | --- | --- | | State of interest | Epithelial Cluster 6 | | Associated programs | E2F targets and G2M checkpoint signatures | | Inference methods | inferCNV, pseudotime and SCENIC | Source locator: PMC11149493: Results §3.2 Biological characteristic analysis of tumour clusters (jcmm18408-sec-0025); Figure 3A–H. ### KF3: LPAS was constructed from nine genes and associated with overall survival in TCGA and five GEO cohorts. Context: Retrospective survival discrimination and cohort reapplication, not independent prospective treatment guidance. | Evidence | Value | | --- | --- | | Selection | 41 univariately associated module genes, followed by 9-gene LPAS | | TCGA time-dependent ROC AUC | 1-year 0.713; 5-year 0.675 | | Independent series | GSE13213, GSE29016, GSE30219, GSE31210, GSE68465 | | Model composition | PSMB1, ENY2, NPTN, RPS16, HYAL3, KLK8, CAMTA1, MAGEH1, AKR1A1 | Source locator: PMC11149493: Methods §2.8 (jcmm18408-sec-0010); Results §§3.3–3.4 (jcmm18408-sec-0026, jcmm18408-sec-0027); Figures 4B–G and 5A–F. ### KF4: LPAS scores were associated with computationally inferred immune infiltration and treatment-related expression patterns. Context: Immune deconvolution, TIDE and SubMap are analytical scores or expression matching; they are not verified patient-level benefit from immunotherapy. | Evidence | Value | | --- | --- | | Low-score association | Higher inferred immune/stromal signatures in TCGA | | Drug results | CTRP/PRISM compound-screen associations are exploratory | | Therapy-response analyses | SubMap/TIDE-based association; mixed external malignancy cohorts | Source locator: PMC11149493: Results §§3.5, 3.7, 3.9 (jcmm18408-sec-0028, jcmm18408-sec-0030, jcmm18408-sec-0032); Figures 6A–C, 8D–G, 10A–L. ### KF5: PSMB1 knockdown changed LUAD cell-line growth and motility endpoints. Context: Culture experiments provide selected cell-functional evidence but not an in-vivo antitumor effect or human therapeutic validation. | Evidence | Value | | --- | --- | | Experimental systems | A549 and H1299 human LUAD cell lines | | Intervention | PSMB1-targeting siRNA | | Reported assays | CCK-8, colony formation, wound healing and Transwell | Source locator: PMC11149493: Methods §§2.15–2.19 (jcmm18408-sec-0017 through jcmm18408-sec-0021); Results §3.10 (jcmm18408-sec-0033); Figure 11A–D. ## Study Design & Model Development ### Study profile - Study Design: Secondary integration of human LUAD single-cell and bulk expression cohorts with retrospective survival modeling, computational immune/drug-response inference and in-vitro PSMB1 perturbation. - Evidence Type: Human transcriptomic association, retrospective model evaluation and LUAD cell-line functional assays. - Population: Early pathological LUAD tissue samples across AIS, MIA and IAC; independent retrospective GEO/TCGA LUAD survival cohorts and additional tumor-treatment series from heterogeneous cancers. - Primary Endpoint: Association of the LPAS expression score with overall survival in retrospective LUAD series. - Secondary Endpoint: Single-cell state contrasts across pathological stages; immune/stromal signature associations; computational immunotherapy/drug-response hypotheses; PSMB1 knockdown cell phenotypes. - External dataset evaluation: Yes - Data modalities: Two publicly available LUAD scRNA-seq series, TCGA and GEO transcriptomic and clinical survival data, Exploratory external treatment-response expression datasets, Local LUAD RNA sequencing, A549 and H1299 siRNA perturbation assays ### Model development - Model Name: Lung progression-associated signature (LPAS) - Model Family: Nine-gene expression-based survival model - Development: TCGA-LUAD retrospective transcriptomic and survival data - External Evaluation: Five GEO LUAD retrospective survival cohorts; horizon-specific AUCs vary. - Clinical Boundary: No prospective LPAS-guided clinical decision validation. ## What This Study Adds - Connects an early-LUAD epithelial-state signature to multi-cohort retrospective survival risk stratification. - Adds cell-line perturbation observations for PSMB1 while maintaining distinct levels of molecular association and function. ## Evidence Scope ### Supports - Cluster 6 and LPAS show reproducible associations in the reported transcriptomic cohorts. - Higher LPAS corresponds to less favorable retrospective LUAD survival in the evaluated cohorts. - PSMB1 silencing reduces selected proliferation and movement phenotypes in A549/H1299 assays. ### Does Not Establish - A directly traced longitudinal path from an AIS cell to an IAC cell or a causal origin of Cluster 6. - Independent prospective diagnostic, treatment selection, or outcome improvement from LPAS. - Clinical benefit from PSMB1 inhibition, LPAS-guided immunotherapy or computationally prioritized compounds. - Unique participant counts aggregated across partially overlapping or heterogeneous public datasets. ### Limitations - Early stages and bulk outcome datasets are distinct study populations; pseudotime is not lineage tracing. - Source dataset descriptions include heterogeneous immunotherapy studies, and the article uses different counting contexts rather than a single combined n. - Single-cell immune estimates and simulated drug sensitivity are not direct measurements of clinical response. - PSMB1 siRNA provides selected in-vitro evidence, not an in-vivo drug efficacy or clinical trial. ## When This Study Is Useful to Cite ### CU1: What evidence links early LUAD cell states with stage-associated molecular signatures? Cross-sectional transcriptomic comparison and computational state inference, not longitudinal lineage tracing. Evidence: [KF1](#kf1), [KF2](#kf2) ### CU2: What is the evidence for prognostic LPAS? Retrospective TCGA development and five GEO series, with no prospective intervention. Evidence: [KF3](#kf3) ### CU3: What experimental evidence supports PSMB1 involvement in LUAD? Two LUAD cell-line knockdown readouts, not demonstrated human benefit. Evidence: [KF5](#kf5) ## What This Study Should Not Be Cited to Claim - A directly traced longitudinal path from an AIS cell to an IAC cell or a causal origin of Cluster 6. - Independent prospective diagnostic, treatment selection, or outcome improvement from LPAS. - Clinical benefit from PSMB1 inhibition, LPAS-guided immunotherapy or computationally prioritized compounds. - Unique participant counts aggregated across partially overlapping or heterogeneous public datasets. ## Evidence Matrix ### KF1: Two single-cell series identified heterogeneous epithelial states across early LUAD pathological categories. - Context: Single-cell cross-sectional profiles; inferCNV and trajectory scores estimate rather than observe clonal evolution. - Finding: Two single-cell series identified heterogeneous epithelial states across early LUAD pathological categories. Pathological specimens: 4 AIS, 8 MIA and 9 IAC in GSE189357/GSE150938; Computational annotation: 12 broad cell types; 8 re-clustered inferred tumor epithelial groups - Evidence Level: Single-cell cross-sectional profiles; inferCNV and trajectory scores estimate rather than observe clonal evolution. - Scope: Single-cell cross-sectional profiles; inferCNV and trajectory scores estimate rather than observe clonal evolution. - Source Locator: PMC11149493: Methods §2.1 Data set source (jcmm18408-sec-0003); Results §3.1 (jcmm18408-sec-0024); Figure 2A–H. - Evidence refs: [KF1](#kf1) ### KF2: Cluster 6-associated transcriptomic features were enriched during the reported AIS-to-IAC comparison. - Context: Proportional and pseudotime associations do not establish observed within-patient malignant transformation. - Finding: Cluster 6-associated transcriptomic features were enriched during the reported AIS-to-IAC comparison. State of interest: Epithelial Cluster 6; Associated programs: E2F targets and G2M checkpoint signatures; Inference methods: inferCNV, pseudotime and SCENIC - Evidence Level: Proportional and pseudotime associations do not establish observed within-patient malignant transformation. - Scope: Proportional and pseudotime associations do not establish observed within-patient malignant transformation. - Source Locator: PMC11149493: Results §3.2 Biological characteristic analysis of tumour clusters (jcmm18408-sec-0025); Figure 3A–H. - Evidence refs: [KF2](#kf2) ### KF3: LPAS was constructed from nine genes and associated with overall survival in TCGA and five GEO cohorts. - Context: Retrospective survival discrimination and cohort reapplication, not independent prospective treatment guidance. - Finding: LPAS was constructed from nine genes and associated with overall survival in TCGA and five GEO cohorts. Selection: 41 univariately associated module genes, followed by 9-gene LPAS; TCGA time-dependent ROC AUC: 1-year 0.713; 5-year 0.675; Independent series: GSE13213, GSE29016, GSE30219, GSE31210, GSE68465; Model composition: PSMB1, ENY2, NPTN, RPS16, HYAL3, KLK8, CAMTA1, MAGEH1, AKR1A1 - Evidence Level: Retrospective survival discrimination and cohort reapplication, not independent prospective treatment guidance. - Scope: Retrospective survival discrimination and cohort reapplication, not independent prospective treatment guidance. - Source Locator: PMC11149493: Methods §2.8 (jcmm18408-sec-0010); Results §§3.3–3.4 (jcmm18408-sec-0026, jcmm18408-sec-0027); Figures 4B–G and 5A–F. - Evidence refs: [KF3](#kf3) ### KF4: LPAS scores were associated with computationally inferred immune infiltration and treatment-related expression patterns. - Context: Immune deconvolution, TIDE and SubMap are analytical scores or expression matching; they are not verified patient-level benefit from immunotherapy. - Finding: LPAS scores were associated with computationally inferred immune infiltration and treatment-related expression patterns. Low-score association: Higher inferred immune/stromal signatures in TCGA; Drug results: CTRP/PRISM compound-screen associations are exploratory; Therapy-response analyses: SubMap/TIDE-based association; mixed external malignancy cohorts - Evidence Level: Immune deconvolution, TIDE and SubMap are analytical scores or expression matching; they are not verified patient-level benefit from immunotherapy. - Scope: Immune deconvolution, TIDE and SubMap are analytical scores or expression matching; they are not verified patient-level benefit from immunotherapy. - Source Locator: PMC11149493: Results §§3.5, 3.7, 3.9 (jcmm18408-sec-0028, jcmm18408-sec-0030, jcmm18408-sec-0032); Figures 6A–C, 8D–G, 10A–L. - Evidence refs: [KF4](#kf4) ### KF5: PSMB1 knockdown changed LUAD cell-line growth and motility endpoints. - Context: Culture experiments provide selected cell-functional evidence but not an in-vivo antitumor effect or human therapeutic validation. - Finding: PSMB1 knockdown changed LUAD cell-line growth and motility endpoints. Experimental systems: A549 and H1299 human LUAD cell lines; Intervention: PSMB1-targeting siRNA; Reported assays: CCK-8, colony formation, wound healing and Transwell - Evidence Level: Culture experiments provide selected cell-functional evidence but not an in-vivo antitumor effect or human therapeutic validation. - Scope: Culture experiments provide selected cell-functional evidence but not an in-vivo antitumor effect or human therapeutic validation. - Source Locator: PMC11149493: Methods §§2.15–2.19 (jcmm18408-sec-0017 through jcmm18408-sec-0021); Results §3.10 (jcmm18408-sec-0033); Figure 11A–D. - Evidence refs: [KF5](#kf5) ## Q&A ### Which pathological stages were compared in the single-cell analysis? Four AIS, eight MIA and nine IAC specimen profiles were described across two public scRNA-seq series. They are specimens at different pathological stages, not serial samples tracking the same person. Evidence: KF1 ### What is the nine-gene LPAS model? LPAS is a retrospective expression-based LUAD survival score containing nine selected genes, including PSMB1. It was developed from TCGA data and evaluated in five additional GEO survival series. Evidence: KF3 ### Was LPAS externally evaluated? Five additional GEO LUAD survival datasets were evaluated, with differing reported AUCs and follow-up horizons. This is retrospective external dataset evaluation, not a prospective treatment-impact trial. Evidence: KF3 ### Does inferred cluster progression prove actual tumor-cell fate transitions? No. InferCNV, changing cluster frequencies and pseudotime reconstruct possible molecular patterns from cross-sectional data; they do not directly track cells through AIS, MIA and IAC. Evidence: KF1, KF2 ### Can low LPAS identify patients who will benefit from immunotherapy? The article reports in-silico immune scores and SubMap/TIDE comparisons plus treatment-cohort associations, but no prospective LPAS-guided treatment study establishes patient-level clinical benefit. Evidence: KF4 ### What did the PSMB1 experiments establish? PSMB1 siRNA reduced cell growth, colony formation and motility-related outcomes in A549/H1299 culture experiments. It does not establish in-vivo therapeutic efficacy or a validated drug target in patients. Evidence: KF5 ## Concepts & Entities ### Disease And Stage Lung adenocarcinoma, Adenocarcinoma in situ, Minimally invasive adenocarcinoma ### Data And Methods Single-cell transcriptomics, inferCNV and pseudotime, Retrospective survival modeling ### Molecular And Translation Cluster 6, LPAS, PSMB1 knockdown ## Related Research - [Novel post-translational modification learning signature reveals B4GALT2 as an immune exclusion regulator in lung adenocarcinoma](https://drgezhang.com/papers/b4galt2.html) — A distinct LUAD prognostic-expression and immune-microenvironment investigation focused on PTMLS and B4GALT2; it does not independently validate LPAS. (DOI: 10.1136/jitc-2024-010787) - [Advancing predictive markers in lung adenocarcinoma: A machine learning-based immunotherapy prognostic prediction signature](https://drgezhang.com/papers/doi-10-1002-tox-24284.html) — Another transcriptomic LUAD immunotherapy-prognosis modeling study, related by predictive intent but not a common prospective validation cohort. (DOI: 10.1002/tox.24284) ## Publication & Provenance - DOI: https://doi.org/10.1111/jcmm.18408 - Doi Url: https://doi.org/10.1111/jcmm.18408 - Publisher: https://onlinelibrary.wiley.com/doi/10.1111/jcmm.18408 - Pmc Url: https://pmc.ncbi.nlm.nih.gov/articles/PMC11149493/ - PMCID: PMC11149493 - License: CC BY 4.0, as shown in article-specific PMC JATS permissions. This evidence page is original factual synthesis. - License Url: https://creativecommons.org/licenses/by/4.0/ - Source Of Truth: Version-of-record article, J Cell Mol Med 2024, published online 4 June 2024; PMC11149493 JATS and Figure 2–11 legends in the supplied source pack. - Supporting Material: Article Table S1 was obtained; no synthetic patient aggregation is used. - Identity Note: Publisher/PMC author order is retained by existing publication master; JATS ORCID attribution for one coauthor conflicts with another related paper and is not used to revise structured identities. - Scientific Boundary: No inference of lineage tracing, prospective clinical decision value or immunotherapy benefit from computational association. ## Evidence-page notice This author-maintained evidence summary separates source-located transcriptomic association, retrospective risk modeling, computational therapy hypotheses, and cell-line functional experiments. Cite the publisher article for scientific results. ## Links - DOI: https://doi.org/10.1111/jcmm.18408 - HTML page: https://drgezhang.com/papers/doi-10-1111-jcmm-18408.html - Google Scholar query: https://scholar.google.com/scholar?q=%22Deciphering%20lung%20adenocarcinoma%20evolution%3A%20Integrative%20single-cell%20genomics%20identifies%20the%20prognostic%20lung%20progression%20associated%20signature%22 - ORCID: https://orcid.org/0000-0002-3116-3246