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NatureCancer BiologyPeer-reviewed journal article

Functional interrogation uncovers a critical role for a high-plasticity cell state in lung adenocarcinoma

Jason Earl ChaniD, Chun‐Hao PaniD, Jonathan RubiD, Gary GuzmaniD, Klavdija BastliD, Emma Brown, Zeda ZhangiD, Hannah C. StyersiD, Griffin G. HartmanniD, Zhuxuan LiiD, Xueqian ZhuangiD, Scott W. LoweiD, Doron BeteliD, Yan YaniD, Tuomas TammelaiD

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Abstract

Plasticity--the ability of cells to undergo phenotypic transitions--drives cancer progression and therapy resistance1-3. To date, strategies targeting cancer plasticity have not advanced to the clinic due to a lack of fundamental understanding of the underlying mechanisms. Recent studies have suggested that plasticity in solid tumors is concentrated in a minority subset of cancer cells4-6, yet functional studies interrogating this high plasticity cell state (HPCS) in situ are lacking. Here, we developed mouse models enabling detection, longitudinal lineage tracing, and ablation of the HPCS in autochthonous lung tumors in vivo. Using lineage tracing, we uncover the HPCS cells are dedifferentiated but possess high capacity for cell state transitions, giving rise to both early neoplastic (differentiated) and advanced lung cancer cell states in situ. Longitudinal lineage tracing using secreted luciferases reveals HPCS-derived cells harbor high capacity for growth when compared to bulk cancer cells or another defined cancer cell state with features of differentiated lung epithelium. Suicide gene-mediated ablation of the HPCS in early neoplasias abrogates tumor progression. Ablating HPCS cells in established tumors by suicide gene or HPCS-directed CAR T cells robustly reduces tumor burden, whereas ablation of a differentiated lung cancer cell state had no effect. We further demonstrate that the HPCS gives rise to therapy-resistant cell states, whereas ablation of the HPCS abrogates resistance to chemotherapy and oncoprotein-targeted therapy. Interestingly, an HPCS-like state is ubiquitous in regenerating epithelia and in carcinomas of multiple other tissues, revealing a convergence of plasticity programs. Our work establishes the HPCS as a critical hub enabling reciprocal transitions between cancer cell states, including acquisition of states adapted to cancer therapies. Targeting the HPCS in lung cancer and in other carcinomas may suppress cancer progression and eradicate treatment resistance.

In-depth summary

Claude Opus 5.5 · xhigh effort · 5 Nov 2026 · from the full text of version 1 (6 Oct 2025)

In vivo lineage tracing and targeted ablation in autochthonous mouse lung adenocarcinoma establish the Slc4a11+ high-plasticity cell state as a bidirectional transition hub driving tumor progression and therapy resistance.

Single-cell transcriptomics has nominated candidate transitional cell states in solid tumors, but static snapshots could not test whether plasticity is functionally concentrated in a specific cellular subset in vivo. Using knock-in reporters for longitudinal secreted-luciferase tracing and suicide-gene or CAR T ablation, this study proves that the high-plasticity cell state fuels intratumoral heterogeneity, tumor growth, and resistance to chemotherapy and KRAS(G12D) inhibition.

Key results

  1. ShownThe Slc4a11-MCD knock-in allele specifically marks a dedifferentiated high-plasticity cell state (HPCS) whose abundance increases with tumor grade.

    In autochthonous KPfrt lung tumors at 15-16 weeks post-initiation, mScarlet+ cells comprised 16.98 +/- 4.29% of GFP+ cancer cells (matching 13.1 +/- 3.80% by scRNA-seq) with 84.25-99.82% specificity, co-expressed integrin alpha-2 (78.41 +/- 1.66%), lost NKX2.1, and induced HMGA2. · Development of novel multifunctional reporter…; The Slc4a11MCD/+ reporter system faithfully…; Figure legends

  2. ShownThe HPCS functions as a bidirectional transition hub that generates all lung adenocarcinoma states and can be re-acquired by non-HPCS cells.

    Tamoxifen tracing in 6-week adenomas (>93% initial HPCS labeling) and 12-week adenocarcinomas (>67% initial labeling) showed rapid exit into all tumor states and expanded phenotypic volume over 14 days, whereas Hopx+ AT1-like traced cells contracted; orthotopically transplanted mScarlet- non-HPCS cells reconstituted the parent mScarlet+ fraction. · The HPCS is a hub for cell state transitions in…; The HPCS can be acquired by non-HPCS cells; Figure legends

  3. ShownQuiescent HPCS cells produce highly proliferative derivatives and are required for early adenoma progression and established tumor maintenance.

    While mScarlet+ HPCS cells are quiescent, exiting traced cells increased Ki67 positivity from 9.13 +/- 2.73% at day 3 to 15.11 +/- 1.76% at day 14 (vs 10.21 +/- 0.98% in untraced cells), outcompeted random or Hopx+ cells in plasma C-Luc/G-Luc assays, and diphtheria toxin ablation reduced lesions >0.15 mm^2 and allograft volume. · The HPCS drives tumor growth and progression; Figure legends

  4. ShownDrug-resistant minimal residual disease originates from the HPCS and is eradicated by combining standard therapy with HPCS ablation or uPAR-directed CAR T cells.

    During 3 weeks of cisplatin (1.5 mg/kg every 3 days) or MRTX1133 (30 mg/kg twice daily), non-traced G-Luc+ cells regressed while HPCS-derived C-Luc+ cells expanded into AT2-like/hybrid (cisplatin) or AT1-like (MRTX1133) states; diphtheria toxin ablation plus drug nearly eradicated tumors, and uPAR CAR T cells depleted uPAR+/integrin alpha-2+ cells and shrank allografts. · Drug-resistant cell states originate from the…; Administration of DT, MRTX1133, and cisplatin; Figure legends

  5. ShownAn Slc4a11+ and Plaur+ HPCS-like transcriptional program recurs across human carcinomas and injury-induced regenerating epithelia.

    The HPCS signature correlated with the pan-cancer Stress archetype and plastic/drug-resistant states in colorectal, pancreatic, prostate, and squamous cancers, as well as regenerating alveolar AT2 cells in mouse lungs 7 days after 32-hour >85% O2 hyperoxia injury. · An HPCS-like state marked by Slc4a11 and uPAR…; Hyperoxia lung injury; Figure legends

Methods, data and reproducibility

Knocked Flp-activatable Slc4a11-FSF-MCD (mScarlet-CreERT2-DTR), Hopx-FSF-MACD (mScarlet-AkaLuc-CreERT2-DTR), and Hipp11-FSF-GGCB dual-luciferase alleles into Kras(FSF-G12D/+); Trp53(frt/frt) mouse ESCs. Performed tamoxifen pulse-chase lineage tracing, longitudinal plasma luciferase monitoring, 10x scRNA-seq with TotalSeq B hashing, diphtheria toxin ablation, cisplatin/MRTX1133 therapy, and uPAR CAR T cell treatment.

  • 10x scRNA-seq, TotalSeq B hashing, flow cytometry, plasma luciferase, and histology from KPfrt lung tumors and NSG allografts across tracing, ablation, chemo, MRTX1133, and CAR T trials · mouse · n = n = 3 to 15 mice per group (~4,000-50,000 cells per scRNA-seq library) · GSE277777
  • Published longitudinal SmartSeq2 scRNA-seq dataset of wild-type AT2 cells, KP adenomas, and KP adenocarcinomas at 2, 12, 20, and 30 weeks post-tumor induction · mouse · GSE152607
  • Published pan-cancer human and mouse scRNA-seq datasets, epithelial injury scRNA-seq datasets, and human LUAD immunofluorescence sections · human, mouse
Methods & tools
CellRanger (v>=6.2), SCANPY (v>=1.9), scDblFinder, scikit-learn (v>=1.13), leidenalg (v0.10.2), Moscot, CellRank (v2.0.7), Palantir (v1.4.1), pingouin (v0.5.4), gseapy (v1.1.1), Aiforia (NSCLC_v25), Fiji (v2.14.0)
Software & environment
Python with SCANPY (>=1.9), Cellrank (2.0.7), Palantir (1.4.1), pingouin (0.5.4), gseapy (1.1.1), leidenalg (0.10.2), matplotlib (3.8.4), and scikit-learn (>=1.13); R (4.3.3); Fiji (2.14.0); CellRanger (>=6.2).
Limitations (3)
  • Incomplete FlpO-mediated excision of the FSF stop cassette in autochthonous KPfrt; Slc4a11^(MCD/+) lung tumors allowed some Slc4a11+ cancer cells lacking DTR expression to escape diphtheria toxin ablation. · stated by the authors
  • Detection sensitivity for Slc4a11 in 10x droplet scRNA-seq is 9.26% (compared with 65.4% in SmartSeq2), and the Hopx reporter has lower specificity for the AT1-like state (82.2% vs 99.7% for Slc4a11) due to expression in some AT2-like cells. · stated by the authors
  • A fraction of lineage-traced Slc4a11+ cells already exit the HPCS during the initial 3-day tamoxifen washout window, particularly in advanced 12-to-14 week adenocarcinomas. · stated by the authors

Read this if you study cancer cell plasticity, lineage tracing, or therapeutic strategies to prevent drug-tolerant residual disease in lung adenocarcinoma and other carcinomas.

Citations
38
FWCI
113.25
Field percentile
top 1%

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