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Opposing immune and genetic forces shape oncogenic programs in synovial sarcoma

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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T‐cell infiltration and clonality correlate with programmed cell death protein 1 and programmed death‐ligand 1 expression in patients with soft tissue sarcomas

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Oncotator: Cancer Variant Annotation Tool

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Synovial Sarcoma Is a Stem Cell Malignancy

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Significant growth suppression of synovial sarcomas by the histone deacetylase inhibitor FK228 in vitro and in vivo

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The SS18-SSX Oncoprotein Hijacks KDM2B-PRC1.1 to Drive Synovial Sarcoma

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The SS18-SSX Fusion Oncoprotein Hijacks BAF Complex Targeting and Function to Drive Synovial Sarcoma

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Deconstruction of the SS18-SSX Fusion Oncoprotein Complex: Insights into Disease Etiology and Therapeutics

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Reversible Disruption of mSWI/SNF (BAF) Complexes by the SS18-SSX Oncogenic Fusion in Synovial Sarcoma

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Genomic Classification of Cutaneous Melanoma

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Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas

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Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Head and Neck Cancer

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A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade

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Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma

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Cancer-testis antigen expression in synovial sarcoma: NY-ESO-1, PRAME, MAGEA4, and MAGEA1

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The anatomy of a large-scale hypertextual Web search engine

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Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals

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Melanoma-intrinsic β-catenin signalling prevents anti-tumour immunity

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Massively parallel digital transcriptional profiling of single cells

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A draft network of ligand–receptor-mediated multicellular signalling in human

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Functional classification of memory CD8+ T cells by CX3CR1 expression

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T cell fate and clonality inference from single-cell transcriptomes

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SCENIC: single-cell regulatory network inference and clustering

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Full-length RNA-seq from single cells using Smart-seq2

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The immune contexture in human tumours: impact on clinical outcome

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Inhibition of cyclin-dependent kinase 4 as a potential therapeutic strategy for treatment of synovial sarcoma

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RNA velocity of single cells

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Mutations in the SWI/SNF complex induce a targetable dependence on oxidative phosphorylation in lung cancer

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TRRUST: a reference database of human transcriptional regulatory interactions

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Core epithelial-to-mesenchymal transition interactome gene-expression signature is associated with claudin-low and metaplastic breast cancer subtypes

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The potential of the CMB305 vaccine regimen to target NY-ESO-1 and improve outcomes for synovial sarcoma and myxoid/round cell liposarcoma patients

inferredcites →https://doi.org/10.1080/2162402x.2018.1507600openalex-snapshot

PRAME and HLA Class I expression patterns make synovial sarcoma a suitable target for PRAME specific T-cell receptor gene therapy

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GLay: community structure analysis of biological networks

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Molecular signatures database (MSigDB) 3.0

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ContEst: estimating cross-contamination of human samples in next-generation sequencing data

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Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs

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STAR: ultrafast universal RNA-seq aligner

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Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments

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Diffusion maps for high-dimensional single-cell analysis of differentiation data

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Circular binary segmentation for the analysis of array-based DNA copy number data

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GENES AFFECTING THE REGULATION OF SUC2 GENE EXPRESSION BY GLUCOSE REPRESSION IN SACCHAROMYCES CEREVISIAE

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Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation

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JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

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inferredcites →https://doi.org/10.1097/pas.0b013e3181f7ce2copenalex-snapshot

Gene Expression Profiling of Synovial Sarcoma: Distinct Signature of Poorly Differentiated Type

inferredcites →https://doi.org/10.1101/120295openalex-snapshot

STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-Seq

inferredcites →https://doi.org/10.1101/459891openalex-snapshot

Integrative inference of brain cell similarities and differences from single-cell genomics

inferredcites →https://doi.org/10.1101/559021openalex-snapshot

High multiplex, digital spatial profiling of proteins and RNA in fixed tissue using genomic detection methods

inferredcites →https://doi.org/10.1101/gad.1899710openalex-snapshot

EWS-FLI-1 modulates miRNA145 and SOX2 expression to initiate mesenchymal stem cell reprogramming toward Ewing sarcoma cancer stem cells

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Finding and evaluating community structure in networks

inferredcites →https://doi.org/10.1111/j.2517-6161.1995.tb02031.xopenalex-snapshot

Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

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Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma

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A major chromatin regulator determines resistance of tumor cells to T cell–mediated killing

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Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq

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The SSX Family of Cancer‐Testis Antigens as Target Proteins for Tumor Therapy

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Synovial Sarcoma: Recent Discoveries as a Roadmap to New Avenues for Therapy

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Efficacy of PD-1 Blockade Is Potentiated by Metformin-Induced Reduction of Tumor Hypoxia

inferredcites →https://doi.org/10.1158/2326-6066.cir-18-0277openalex-snapshot

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inferredcites →https://doi.org/10.1186/1471-2105-12-323openalex-snapshot

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

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HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions

inferredcites →https://doi.org/10.1186/gb-2009-10-3-r25openalex-snapshot

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

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A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries

inferredcites →https://doi.org/10.1186/s13569-017-0077-3openalex-snapshot

Overexpressed PRAME is a potential immunotherapy target in sarcoma subtypes

inferredcites →https://doi.org/10.1200/jco.2012.46.0147openalex-snapshot

Chromosome Instability Accounts for Reverse Metastatic Outcomes of Pediatric and Adult Synovial Sarcomas

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iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections

inferredcites →https://doi.org/10.1371/journal.pone.0051136openalex-snapshot

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inferredcites →https://doi.org/10.1371/journal.pone.0169407openalex-snapshot

HDAC and Proteasome Inhibitors Synergize to Activate Pro-Apoptotic Factors in Synovial Sarcoma

inferredcites →https://doi.org/10.1371/journal.pone.0197702openalex-snapshot

Macrophage Migration Inhibitory Factor protects cancer cells from immunogenic cell death and impairs anti-tumor immune responses

inferredcites →https://doi.org/10.3892/or.2017.5617openalex-snapshot

Evaluation of expression of cancer stem cell markers and fusion gene in synovial sarcoma: Insights into histogenesis and pathogenesis

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CD4+ T Cell Responses to SSX-4 in Melanoma Patients

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Transcriptional Profiling of the Human Monocyte-to-Macrophage Differentiation and Polarization: New Molecules and Patterns of Gene Expression

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Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.bbcan.2021.188613openalex-snapshot

Precision medicine and phosphoproteomics for the identification of novel targeted therapeutic avenues in sarcomas

inferred← citeshttps://doi.org/10.1101/2020.08.11.245472openalex-snapshot

Mapping multicellular programs from single-cell profiles

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