CRACD loss promotes small cell lung cancer tumorigenesis via EZH2-mediated immune evasion

The mechanisms underlying immune evasion and immunotherapy resistance in small cell lung cancer (SCLC) remain unclear. Herein, we investigate the role of CRACD tumor suppressor in SCLC. We found that CRACD is frequently inactivated in SCLC, and Cracd knockout (KO) significantly accelerates SCLC development driven by loss of Rb1, Trp53, and Rbl2. Notably, the Cracd-deficient SCLC tumors display CD8+ T cell depletion and suppression of antigen presentation pathway. Mechanistically, CRACD loss silences the MHC-I pathway through EZH2. EZH2 blockade is sufficient to restore the MHC-I pathway and inhibit CRACD loss-associated SCLC tumorigenesis. Unsupervised single-cell transcriptomic analysis identifies SCLC patient tumors with concomitant inactivation of CRACD, impairment of tumor antigen presentation, and downregulation of EZH2 target genes. Our findings define CRACD loss as a new molecular signature associated with immune evasion of SCLC cells and proposed EZH2 blockade as a viable option for CRACD-negative SCLC treatment.

[1]  Kwon-Sik Park,et al.  WNT5A-RHOA signaling is a driver of tumorigenesis and represents a therapeutically actionable vulnerability in small cell lung cancer. , 2022, Cancer Research.

[2]  Joseph B Hiatt,et al.  Inhibition of LSD1 with bomedemstat sensitizes small cell lung cancer to immune checkpoint blockade and T cell killing. , 2022, Clinical cancer research : an official journal of the American Association for Cancer Research.

[3]  Vianne R. Gao,et al.  Signatures of plasticity, metastasis, and immunosuppression in an atlas of human small cell lung cancer. , 2021, Cancer cell.

[4]  C. Hammer,et al.  Antigen presentation in cancer: insights into tumour immunogenicity and immune evasion , 2021, Nature Reviews Cancer.

[5]  P. Robson,et al.  Patterns of transcription factor programs and immune pathway activation define four major subtypes of SCLC with distinct therapeutic vulnerabilities. , 2021, Cancer cell.

[6]  Raphael Gottardo,et al.  Integrated analysis of multimodal single-cell data , 2020, Cell.

[7]  W. Hwang,et al.  Gene signature of antigen processing and presentation machinery predicts response to checkpoint blockade in non-small cell lung cancer (NSCLC) and melanoma , 2020, Journal for ImmunoTherapy of Cancer.

[8]  C. Robert A decade of immune-checkpoint inhibitors in cancer therapy , 2020, Nature Communications.

[9]  Lihua Zhang,et al.  Inference and analysis of cell-cell communication using CellChat , 2020, Nature Communications.

[10]  Junnian Zheng,et al.  Turning Cold into Hot: Firing up the Tumor Microenvironment. , 2020, Trends in cancer.

[11]  M. Ragavan,et al.  Systemic Therapy of Extensive Stage Small Cell Lung Cancer in the Era of Immunotherapy , 2020, Current Treatment Options in Oncology.

[12]  Gabor Marth,et al.  MYC Drives Temporal Evolution of Small Cell Lung Cancer Subtypes by Reprogramming Neuroendocrine Fate. , 2020, Cancer cell.

[13]  M. Hellmann,et al.  Acquired Resistance to Immune Checkpoint Inhibitors. , 2020, Cancer cell.

[14]  V. Kok Current Understanding of the Mechanisms Underlying Immune Evasion From PD-1/PD-L1 Immune Checkpoint Blockade in Head and Neck Cancer , 2020, Frontiers in Oncology.

[15]  L. Horn,et al.  Immunotherapeutic approaches for small-cell lung cancer , 2020, Nature Reviews Clinical Oncology.

[16]  T. Jacks,et al.  CRISPR-mediated modeling and functional validation of candidate tumor suppressor genes in small cell lung cancer , 2019, Proceedings of the National Academy of Sciences.

[17]  Fabian J Theis,et al.  Generalizing RNA velocity to transient cell states through dynamical modeling , 2019, Nature Biotechnology.

[18]  Gennady Korotkevich,et al.  Fast gene set enrichment analysis , 2019, bioRxiv.

[19]  R. Tothill,et al.  An Evolutionarily Conserved Function of Polycomb Silences the MHC Class I Antigen Presentation Pathway and Enables Immune Evasion in Cancer , 2019, Cancer cell.

[20]  J. Weissman,et al.  Mapping Transcriptomic Vector Fields of Single Cells , 2022, Cell.

[21]  Aaron M. Newman,et al.  Single-cell transcriptional diversity is a hallmark of developmental potential , 2019, Science.

[22]  Fabian J Theis,et al.  PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells , 2019, Genome Biology.

[23]  Vincent A. Traag,et al.  From Louvain to Leiden: guaranteeing well-connected communities , 2018, Scientific Reports.

[24]  H. Bolouri,et al.  Crebbp Loss Drives Small Cell Lung Cancer and Increases Sensitivity to HDAC Inhibition. , 2018, Cancer discovery.

[25]  Erik Sundström,et al.  RNA velocity of single cells , 2018, Nature.

[26]  Fabian J Theis,et al.  SCANPY: large-scale single-cell gene expression data analysis , 2018, Genome Biology.

[27]  Byoung Choul Kim,et al.  Notch-Jagged complex structure implicates a catch bond in tuning ligand sensitivity , 2017, Science.

[28]  Aristeidis G. Telonis,et al.  GPRC5A is a potential oncogene in pancreatic ductal adenocarcinoma cells that is upregulated by gemcitabine with help from HuR , 2016, Cell Death and Disease.

[29]  J. Taube,et al.  Mechanism-driven biomarkers to guide immune checkpoint blockade in cancer therapy , 2016, Nature Reviews Cancer.

[30]  G. Giaccone,et al.  Small Cell Lung Cancer: Can Recent Advances in Biology and Molecular Biology Be Translated into Improved Outcomes? , 2022 .

[31]  S. Horvath,et al.  High expression of AGR2 in lung cancer is predictive of poor survival , 2015, BMC Cancer.

[32]  N. Perrimon,et al.  Mechanical Allostery: Evidence for a Force Requirement in the Proteolytic Activation of Notch. , 2015, Developmental cell.

[33]  T. Jacks,et al.  The Comparative Pathology of Genetically Engineered Mouse Models for Neuroendocrine Carcinomas of the Lung , 2015, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

[34]  R. Boldrini,et al.  IRF1 and NF-kB Restore MHC Class I-Restricted Tumor Antigen Processing and Presentation to Cytotoxic T Cells in Aggressive Neuroblastoma , 2012, PloS one.

[35]  K. Cibulskis,et al.  Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer , 2012, Nature Genetics.

[36]  E. Botvinick,et al.  Notch ligand endocytosis generates mechanical pulling force dependent on dynamin, epsins, and actin. , 2012, Developmental cell.

[37]  J. Tschopp,et al.  NLRC5 Deficiency Selectively Impairs MHC Class I- Dependent Lymphocyte Killing by Cytotoxic T Cells , 2012, The Journal of Immunology.

[38]  T. Jacks,et al.  Conditional mouse lung cancer models using adenoviral or lentiviral delivery of Cre recombinase , 2009, Nature Protocols.

[39]  J. Joyce,et al.  Therapeutic Targeting of the Tumor Microenvironment. , 2021, Cancer discovery.

[40]  R. Herrmann,et al.  Expression of CEACAM6 in resectable colorectal cancer: a factor of independent prognostic significance. , 2003, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[41]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[42]  I. Witz,et al.  The Tumor Microenvironment: Methods and Protocols , 2023, Methods in Molecular Biology.

[43]  Minoru Kanehisa,et al.  Toward Pathway Engineering: A New Database of Genetic and Molecular Pathways , 1997 .