Topic 173

tumors tumor cancer therapy patients immunotherapy checkpoint microenvironment resistance immune solid metastatic treatment progression cancers sequencing therapies clinical response samples analysis exhaustion clonal rna blockade tme cell neoplasms pd melanoma mechanisms polyclonal multiregional exist features signatures extranodal entd immunology profiling paired improved biology cells including pediatric microenvironments divergent seq mutations lymph heterogeneity performed recruited ith cd8 were infiltrating profiles myeloid exome colorectal greatly genes multi refractory bladder single prospective node tils sensitivity defining phenotypes dna malignant therapeutic histiocytic metastasis tcr differences cfdna alterations patient ctdna clonality ln intratumor sided materials scrna monocytes 206 g3 burden adenocarcinoma darwinian responses urothelial responders

30 items. Top items listed below.

Defining the transcriptional landscape of infiltrating immune cells in human and mouse bladder cancer. 173 148 14 9 3

Divergent resistance mechanisms to immunotherapy explains response in different skin cancers. 173 14 10 3

Circulating Clonally Expanded T Cells Reflect Functions of Tumor Infiltrating T Cells 173 88 14 9 3

Pan-cancer analysis identified inflamed microenvironment associated multi-omics signatures 173 14 9 3

Analysis of genetic signatures of tumor microenvironment yields insight into mechanisms of resistance to immunotherapy 173 14 10 9 3

Myeloid cell-associated resistance to PD-1/PD-L1 blockade in urothelial cancer revealed through bulk and single-cell RNA sequencing 173 14 9 3

Comparative analysis of clonal evolution among patients with right-sided colon cancer, left-sided colon cancer and rectal cancer 173 7 5

Intratumor Heterogeneity and Evolution of Colorectal Cancer 173 14 9

Mapping the evolution of T cell states during response and resistance to adoptive cellular therapy 173 14 10 9

Single-cell Characterization of Acute Myeloid Leukemia and its Microenvironment Following PD-1 Blockade Based Therapy 173 88 14 10 3

Tumor stiffening reversion through collagen crosslinking inhibition improves T cell migration and anti-PD-1 treatment 173 126 14 10 3

Multi-cancer analysis of clonality and the timing of systemic spread in paired primary tumors and metastases 173 14 10 9

CAR T cells for solid tumors: genome-wide dysfunction signature confirms value of c-Jun overexpression, but signals heterogeneity 173 14 10 9


An Integrative Genetic, Epigenetic and Proteomic Characterization of Pancreatic Neuroendocrine Neoplasms (PanNENs) defines Distinct Molecular Features of α- and β-cell like Subgroups 173 152 14 9

Surveying Brain Tumor Heterogeneity by Single-Cell RNA Sequencing of Multi-sector Biopsies 173 148 43 9

Evolutionary Dynamics of Non-Coding Regions in Pancreatic Ductal Adenocarcinoma 173 14 9

ScRNA-seq reveals tumor microenvironment remodeling induced by local intervention-based immunotherapy 173 88 27 14 10 3

Identification of Relevant Genetic Alterations in Cancer using Topological Data Analysis 173 142 14 9 4

Novel BRAF gene fusions in pediatric histiocytic neoplasms define distinct therapeutic responsiveness to RAF paradox breakers 173 14 3

Enhanced specificity of high sensitivity somatic variant profiling in cell-free DNA via paired normal sequencing: design, validation, and clinical experience of the MSK-ACCESS liquid biopsy assay 173 97 14 9 4

Dynamics of the cell-free DNA methylome of metastatic prostate cancer during androgen-targeting treatment 173 14 10 9

Interest of circulating tumor DNA as a biomarker for canine cancers: illustration in histiocytic sarcoma, oral malignant melanoma and multicentric lymphoma 173 14 10

PD-L1 lncRNA splice promotes lung adenocarcinoma progression via enhancing c-Myc activity 108 14 10 3

The Primary Tumor Immune Microenviornment Status Predicts the Response to Immunotherapy and Overall Survival in Breast Cancer 14 10 9

Circulating immune cell phenotype dynamics reflect the strength of tumor-immune cell interactions in patients during immunotherapy 14 10 9

Th17 cells contribute to combination MEK inhibitor and anti-PD-L1 therapy resistance in KRAS/p53 mutant lung cancers 126 14 10 3

Oncoprotein 18 is necessary for malignant cell proliferation in bladder cancer cells and serves as a G3-specific non-invasive diagnostic marker candidate in urinary RNA 173 14 10 9 3

A circulating T-cell differentiation marker to predict response to immune checkpoint inhibitors 126 14 10 3

Distinct CD8+ T Cell Programming in the Tumor Microenvironment Contributes to Sex Bias in Bladder Cancer Outcome 173 14 10 3

Single-cell analysis of patient-derived PDAC organoids reveals cell state heterogeneity and a conserved developmental hierarchy 152 14 9 3

Intertumoral Genetic Heterogeneity Generates Distinct Tumor Microenvironments in a Novel Murine Synchronous Melanoma Model 126 14 10 9 3

Stroma transcriptomic and proteomic profile of prostate cancer metastasis xenograft models reveals conservation of bonemicroenvironment signatures 152 14 9 3

Single cell analysis of colorectal cancer identifies mitogen-activated protein kinase as a key driver of tumor cell plasticity 152 148 142 14 9 3

Aging increases the systemic molecular degree of inflammatory perturbation in patients with tuberculosis 173 15 10

A novel mechanism of natural killer cell response to anti-CTLA-4 therapy identified by integrative analysis of mouse and human tumors 14 10 9 3

MethylationToActivity: a deep-learning framework that reveals promoter activity landscapes from DNA methylomes in individual tumors 173 26 4

Single-cell analyses identify circulating anti-tumor CD8 T cells and markers for their enrichment 88 14 9

Transcriptional subtype-specific microenvironmental crosstalk and tumor cell plasticity in metastatic pancreatic cancer 152 14 9 3

What is the storage effect, why should it occur in cancers, and how can it inform cancer therapy? 99 14 5

The cellular genomic diversity, regulatory states and networking of the metastatic colorectal cancer microenvironment 148 14 9 3

DNA methylation landscapes of matched primary and recurrent high grade serous ovarian cancers are preserved throughout disease progression and chemoresistance. 87 9

Biomarker-guided treatment strategies for ovarian cancer identified from a heterogeneous panel of patient-derived tumor xenografts 126 14 10 9

Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion 14 9 3

Redesigned Reporter Gene for Improved Proton Exchange-based Molecular MRI Contrast 173 18

Restructuring of the Immune Contexture Improves Checkpoint Blockade Efficacy in Murine Lung Cancer 126 14 10

Plasticity as an Underlying Mechanism of Tumor Heterogeneity in Breast Cancer 152 14 9

A single cell atlas reveals distinct immune landscapes in transplant and primary tumors that determine response or resistance to immunotherapy 126 14 10 3

Transcriptional mediators of treatment resistance in lethal prostate cancer 98 14 10 9 3

TISCH: a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment 43 9 4

Characterizing the tumor microenvironment of metastatic ovarian cancer by single cell transcriptomics 148 14 9 3

The capacity of the ovarian cancer tumor microenvironment to integrate inflammation signaling conveys a shorter disease-free interval 14 10 9 3

Aging interacts with tumor biology to produce major changes in the immune tumor microenvironment 14 9 3

RNA Editing Signatures Predict Response to Immunotherapies in Melanoma Patients 14 9 4

Whole exome precision oncology targeting synthetic lethal vulnerabilities across the tumor transcriptome 14 4

Relationship Between Neuroendocrine and Immune Gene Expression in Small Cell Lung Cancer 14 9 3

The genomic and epigenomic evolutionary history of papillary renal cell carcinomas 97 14 9 5

Tumor control via targeting PD-L1 with chimeric antigen receptor modified NK cells 126 88 14 10 3

Colon-specific immune microenvironment regulates cancer progression versus rejection 14 10 3

Elucidation of tumor-stromal heterogeneity and the ligand-receptor interactome by single cell transcriptomics in real-world pancreatic cancer biopsies 152 148 14 9 4

Predicting drug sensitivity of cancer cells based on DNA methylation levels 112 26 4

CD4+ follicular helper-like T cells are key players in anti-tumor immunity 88 14 10 3

Persistent cell proliferation signals correlates with increased glycolysis in tumor hypoxia microenvironment across cancer types 186 9

A multi-layered systems approach for renal cell carcinoma 14 9

Large scale analysis of smoking-induced changes in the tumor immune microenvironment 14 9

Kinetics of Plasma cfDNA Predicts Clinical Response in Non-Small Cell Lung Cancer Patients 126 14 10

Global computational alignment of tumor and cell line transcriptional profiles 43 14 9 4

Unsupervised machine learning reveals key immune cell subsets in COVID-19, rhinovirus infection, and cancer therapy 88 1

Chemotherapy but not the tumor-draining lymph nodes determine the immunotherapy response in secondary tumors 126 14 10 3

Ratio of the interferon-γ signature to the immunosuppression signature predicts anti-PD-1 therapy response in melanoma 14 10 9

Personalized in-silico drug response prediction based on the genetic landscape of muscle-invasive bladder cancer 112 14 4

Feasibility and promise of circulating tumor DNA analysis in dogs with naturally-occurring sarcoma. 14 9

Epigenetic therapy remodels the immune synaptic cytoskeleton to potentiate cancer susceptibility to γδ T cells 14 10 3

Response to CAR T cell therapy can be explained by ecological cell dynamics and stochastic extinction events 14 10

IL-4 receptor targeting as an effective immunotherapy against triple-negative breast cancer 126 14 10 3

Drosophila model of Anti-retroviral therapy Induced Peripheral Neuropathy and Nociceptive Hypersensitivity 173 10

Differing total mRNA expression shapes the molecular and clinical phenotype of cancer 9

Mutational processes impact the evolution of anti-EGFR antibody resistance in colorectal cancer 14 10 9

Patient-derived glioblastoma cells (GBM) exhibit distinct biomechanical profiles associated with altered activity in the cytoskeleton regulatory pathway 152 14 9 3

KALRN Mutations Promote Anti-tumor Immunity and Immunotherapy Response in Cancer 14 10 9 3

Individual cell-based modeling of tumor cell plasticity-induced immune escape after CAR-T therapy 126 14 10 3

Hematopoietic p53 loss cell-extrinsically defines an immune infiltrated microenvironment in leukemia and pre-leukemia 126 14 10 9 3

Tumor-specific EphA2 receptor tyrosine kinase inhibits anti-tumor immunity by recruiting suppressive myeloid populations in NSCLC 14 10 3

Single-cell transcriptomic profile reveals macrophage heterogeneity in medulloblastoma and their treatment-dependent recruitment 152 14 9 3

Epigenetic downregulation of HER2 during EMT leads to tumor resistance to HER2-targeted therapies in breast cancer 98 14 10 3

Profiling the Intratumoral Immune Landscapes of Primary and Syngeneic Kras-driven Sarcoma Mouse Models 7

Inhibition of the av integrin-TGF-b axis improves natural killer cell function against glioblastoma stem cells 152 14 10 3

Single-cell RNA-sequencing of peripheral neuroblastic tumors reveals an aggressive transitional cell state at the junction of an adrenergic-mesenchymal transdifferentiation trajectory 152 14 9 3

ATPIF1 inactivation promotes antitumor immunity through metabolic reprogramming of CD8+ T cells 14 10 3

Machine learning-based investigation of the cancer protein secretory pathway 112 14 9 4

The pleiotropic effects of the MNK1/2-eIF4E axis support immune suppression and metastasis in a model of postpartum breast cancer. 14 10 3

Quantitative in vivo analyses reveal a complex pharmacogenomic landscape in lung adenocarcinoma 14 9

Multi-organ signaling mobilizes tumor-associated erythroid cells expressing immune checkpoint molecules 14 10 3

Multiplex-inhibitor bead mass spectrometry reveals differential kinome signatures in newly diagnosed and recurrent glioblastoma 152 14 9 3

Clonal Evolution of Acute Myeloid Leukemia Revealed by High-Throughput Single-Cell Genomics 14 9

HDAC and MAPK/ERK inhibitors cooperate to reduce viability and stemness phenotype in medulloblastoma 186 108 14 10 3

Immune Response Drives Outcomes in Prostate Cancer: Implications for Immunotherapy 14 10 9

Deconvolution of Cell Type-Specific Drug Responses in Human Tumor Tissue with Single-Cell RNA-seq 14 9

Cancer-specific associations of driver genes with immunotherapy outcome 14 9

Immune profiling of gliomas reveals a connection with Tau function and the tumor vasculature. 14 10 3