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Principal Investigator: Benjamin Izar
Organization: COLUMBIA UNIVERSITY HEALTH SCIENCES
Fiscal Year: 2024
Award: $657,805
Funding agency: National Cancer Institute
Brain metastasis (BM) occurs in up to 40% of patients with advanced cancers, most frequently arising from non-small cell lung cancer (NSCLC). Patients with BM frequently suffer from debilitating symptoms, have worse response rates to modern cancer therapies and are excluded from most clinical trials, resulting in an overall poor
prognosis. While the clinical significance of BM is broadly recognized, our understanding of underlying molecular,
cellular and microenvironmental mechanisms remains rudimentary. Here, through several innovations, we overcome experimental, technical, and analytical barriers to gain unprecedented insight into cellular and microenvironmental features of human BM. In an integrative analysis of multi-modal single-cell RNA, T cell receptor and
spatial transcriptomics of primary tumors and BM from patients with NSCLC, coupled with analyses of public
data sets, we identify chromosomal instability (CIN), and CIN-induced molecular adaptations as key driver of
brain-metastatic organotropism. The brain metastatic ecosystem is enriched with a pro-tumorigenic myeloid and
dysfunctional T cell compartment. In this proposal, we aim to define the mechanistic underpinnings of these
observations. In Aim 1, we will employ a fundamentally novel analytical tool, ContactTracing, to map at a systems level all cell-cell interactions in the BM ecosystem based on multi-modal single-cell sequencing. We assembled a large validation cohort of NSCLC specimen, including primary tumors, brain and extracranial metastases, that underwent whole-exome sequencing (WES) and RNA-seq which will be deconvolved to validate pre-
dictions derived from single-cell data. Furthermore, we assembled additional NSCLC for multiplexed immunofluorescence with established antibody panels to measure the rate of CIN, CIN-adaption, and their spatial association with myeloid and lymphoid immune infiltrates. In Aim 2, through functional imaging of human and murine
models we identify CIN as a defining feature of LKB1-deficient tumors. LKB1 loss (or deleterious mutation) is a
common genomic subtype of NSCLC (along with KRAS co-mutation) that frequently metastasizes to the brain
and is characterized by treatment resistance and poor prognosis. We find that CIN results in tonic activation of
the cGAS-STING pathway to promote BM. We will dissect underlying mechanisms of CIN-induced cellular adaptations that confer brain-metastatic organotropism through modulation of the brain-metastatic niche through
cGAMP hydrolysis to adenosine, which permeabilizes the blood-brain-barrier and creates an immunosuppressive environment. For this purpose, we will use in situ niche-labeling of in vivo BM models, coupled with single-cell/spatial transcriptomics to track the evolution of brain-metastatic ecosystem, and dynamics of cell interaction
networks using ContactTracing. Upon completion of this work, we will provide mechanistic and clinical insights
into genomic and multi-cellular features of the evolving brain-metastatic ecosystem. These insights are the first
step towards development of more effective therapies of affected patients.
Terms: <Address><Adenosine><Advanced Cancer><Advanced Malignant Neoplasm><Affect><Aneuploid><Aneuploidy><Antibodies><Assay><BBB permeabilization><BBB permeable><Bioassay><Biological Assay><Biology><Blood - brain barrier anatomy><Blood-Brain Barrier><Body Tissues><Brain><Brain Metastasis><Brain Nervous System><C-K-RAS><Cancer Cause><Cancer Etiology><Cancer Model><Cancer Patient><Cancer Treatment><CancerModel><Cancers><Cell Body><Cell Communication><Cell Communication and Signaling><Cell Compartmentation><Cell Compartmentations><Cell Function><Cell Interaction><Cell Physiology><Cell Process><Cell Signaling><Cell-to-Cell Interaction><Cells><Cellular Function><Cellular Physiology><Cellular Process><Cephalic><Cessation of life><Chromosomal Instability><Chromosome Instability><Chronic><Clinical><Clinical Trials><Communities><Coupled><Cranial><Cytosol><Data><Data Set><Death><Dependence><Development><Disease><Disorder><Double-Stranded DNA><Ecologic Systems><Ecological Systems><Ecosystem><Encephalon><Environment><Evolution><Exclusion><Exhibits><Functional Imaging><Genes><Genetic><Genetic Alteration><Genetic Change><Genetic defect><Genomics><Genotype><Goals><Hemato-Encephalic Barrier><Heterogeneity><Human><Hydrolysis><Immune><Immune Diseases><Immune Disorders><Immune Dysfunction><Immune System Diseases><Immune System Disorder><Immune System Dysfunction><Immune System and Related Disorders><Immune infiltrates><Immune response><Immunes><Immunocompetent><Immunocompromised><Immunocompromised Host><Immunocompromised Patient><Immunodeficiency and Immunosuppression Disorders><Immunofluorescence><Immunofluorescence Immunologic><Immunologic Diseases><Immunological Diseases><Immunological Dysfunction><Immunological System Dysfunction><Immunological response><Immunosuppressed Host><In Situ><Innate Immune Response><Intracellular Communication and Signaling><K-RAS2A><K-RAS2B><K-Ras><K-Ras 2A><K-Ras-2 Oncogene><KRAS><KRAS2><KRAS2 gene><Ki-RAS><Knock-out><Knockout><Knowledge><LKB1><LKB1/STK11 Gene><Label><Ligands><Link><Lung Carcinoma><Lymphoid><MHC Receptor><Major Histocompatibility Complex Receptor><Malignant Cell><Malignant Melanoma><Malignant Neoplasm Therapy><Malignant Neoplasm Treatment><Malignant Neoplasms><Malignant Tumor><Maps><Measures><Melanoma><Metabolic><Metastasis><Metastasize><Metastatic Lesion><Metastatic Mass><Metastatic Neoplasm><Metastatic Neoplasm to the Brain><Metastatic Tumor><Metastatic Tumor to the Brain><Metastatic malignant neoplasm to brain><Methods><Mice><Mice Mammals><Modeling><Modern Man><Modernization><Molecular><Murine><Mus><Mutation><Myelogenous><Myeloid><NSCLC><NSCLC - Non-Small Cell Lung Cancer><Nature><Neoplasm Metastasis><Non-Polyadenylated RNA><Non-Small Cell Lung Cancer><Non-Small-Cell Lung Carcinoma><Oncogene K-Ras><Pathway interactions><Patients><Phenotype><Physiologic Imaging><Primary Neoplasm><Primary Tumor><Prognosis><RASK2><RNA><RNA Gene Products><RNA Seq><RNA sequencing><RNAseq><Research><Research Specimen><Ribonucleic Acid><Role><Rupture><STK11><STK11 gene><Sampling><Secondary Neoplasm><Secondary Tumor><Shapes><Signal Transduction><Signal Transduction Systems><Signaling><Single cell seq><Specimen><Staining method><Stains><Stimulator of Interferon Genes><Subcellular Process><System><T-Cell Antigen Receptors><T-Cell Receptor><T-Cells><T-Lymphocyte><Testing><Tissues><Tumor Cell><Tumor-Derived><Validation><Work><analytical tool><anti-cancer therapy><biological signal transduction><blood-brain barrier permeabilization><blood-brain barrier permeable><bloodbrain barrier><bloodbrain barrier permeabilization><bloodbrain barrier permeable><brain micrometastasis><cGAMP STING><cGAMP-STING><cGAMP/STING><cGAS/STING><cancer cell><cancer metastasis><cancer microenvironment><cancer therapy><cancer-directed therapy><case control><case-controlled><cell type><clinical significance><clinically significant><cohort><cyclic GMP-AMP synthase/STING><debilitating symptom><developmental><ds-DNA><dsDNA><ecto-nucleotidase><effective therapy><effective treatment><exome sequencing><exome-seq><genome mutation><host response><human data><human model><immune cell infiltrate><immune competent><immune system response><immunoresponse><immunosuppressed patient><improved><in vivo><in vivo Model><innovate><innovation><innovative><insight><liver kinase B1><malignancy><micronucleus><model of human><mouse model><multi-modality><multimodality><murine model><neoplasm/cancer><neoplastic cell><new drug treatments><new drugs><new pharmacological therapeutic><new therapeutics><new therapy><next generation therapeutics><novel><novel drug treatments><novel drugs><novel pharmaco-therapeutic><novel pharmacological therapeutic><novel therapeutics><novel therapy><pathway><physiological imaging><programs><resistance to therapy><resistant to therapy><response><scRNA-seq><single cell RNA-seq><single cell RNAseq><single cell expression profiling><single cell next generation sequencing><single cell sequencing><single cell transcriptomic profiling><single-cell RNA sequencing><social role><spatiotemporal><therapeutic agent development><therapeutic development><therapeutic resistance><therapeutic target><therapy resistant><thymus derived lymphocyte><transcriptome sequencing><transcriptomic sequencing><transcriptomics><treatment resistance><tumor><tumor cell metastasis><tumor microenvironment><tumorigenic><v-Ki-RAS2 Kirsten Rat Sarcoma 2 Viral Oncogene Homolog><validations>