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Niche engineering drives early passage through an immune bottleneck in progression to colorectal cancer

https://doi.org/10.1101/623959
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What this work says

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

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Current Protocols in Bioinformatics
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Evolution of cancer of the colon and rectum
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The evolution of cancer of the colon and rectum
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Roles of neutrophils in cancer growth and progression
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KAZE Features
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Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma
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High Prevalence of Activated Intraepithelial Cytotoxic T Lymphocytes and Increased Neoplastic Cell Apoptosis in Colorectal Carcinomas with Microsatellite Instability
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Smad4 signalling in T cells is required for suppression of gastrointestinal cancer
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Analysis of protein-coding genetic variation in 60,706 humans
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A neoantigen fitness model predicts tumour response to checkpoint blockade immunotherapy
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Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes
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A Big Bang model of human colorectal tumor growth
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Identification of neutral tumor evolution across cancer types
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Cancer immunoediting: from immunosurveillance to tumor escape
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Natural selection of tumor variants in the generation of “tumor escape” phenotypes
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Neutrophils in cancer: neutral no more
inferredcites →https://doi.org/10.1038/nrc3670openalex-snapshot
Tumour antigens recognized by T lymphocytes: at the core of cancer immunotherapy
inferredcites →https://doi.org/10.1038/s41551-018-0254-6openalex-snapshot
A designer self-assembled supramolecule amplifies macrophage immune responses against aggressive cancer
inferredcites →https://doi.org/10.1038/s41559-018-0642-zopenalex-snapshot
The evolutionary landscape of colorectal tumorigenesis
inferredcites →https://doi.org/10.1038/s41588-018-0128-6openalex-snapshot
Quantification of subclonal selection in cancer from bulk sequencing data
inferredcites →https://doi.org/10.1038/sj.bjc.6602889openalex-snapshot
A multiplex PCR predictor for aCGH success of FFPE samples
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Much of the Genetic Risk of Colorectal Cancer Is Likely to Be Mediated Through Susceptibility to Adenomas
inferredcites →https://doi.org/10.1056/nejmoa051424openalex-snapshot
Effector Memory T Cells, Early Metastasis, and Survival in Colorectal Cancer
inferredcites →https://doi.org/10.1056/nejmoa1100370openalex-snapshot
Colonoscopic Polypectomy and Long-Term Prevention of Colorectal-Cancer Deaths
inferredcites →https://doi.org/10.1056/nejmoa1500596openalex-snapshot
PD-1 Blockade in Tumors with Mismatch-Repair Deficiency
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btp698openalex-snapshot
Fast and accurate long-read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/nar/gkq603openalex-snapshot
ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
inferredcites →https://doi.org/10.1093/nar/gkv135openalex-snapshot
multiSNV: a probabilistic approach for improving detection of somatic point mutations from multiple related tumour samples
inferredcites →https://doi.org/10.1097/ogx.0b013e31825bc1f5openalex-snapshot
Colonoscopic Polypectomy and Long-Term Prevention of Colorectal Cancer Deaths
inferredcites →https://doi.org/10.1109/tbme.2014.2303294openalex-snapshot
A Nonlinear Mapping Approach to Stain Normalization in Digital Histopathology Images Using Image-Specific Color Deconvolution
inferredcites →https://doi.org/10.1109/tpami.2008.113openalex-snapshot
Parametric Image Alignment Using Enhanced Correlation Coefficient Maximization
inferredcites →https://doi.org/10.1111/ecog.01892openalex-snapshot
A network approach for inferring species associations from co‐occurrence data
inferredcites →https://doi.org/10.1111/j.1442-9993.2001.01070.pp.xopenalex-snapshot
A new method for non‐parametric multivariate analysis of variance
inferredcites →https://doi.org/10.1111/j.1541-0420.2005.00440.xopenalex-snapshot
Distance‐Based Tests for Homogeneity of Multivariate Dispersions
inferredcites →https://doi.org/10.1126/science.1129139openalex-snapshot
Type, Density, and Location of Immune Cells Within Human Colorectal Tumors Predict Clinical Outcome
inferredcites →https://doi.org/10.1126/science.1203486openalex-snapshot
Cancer Immunoediting: Integrating Immunity’s Roles in Cancer Suppression and Promotion
inferredcites →https://doi.org/10.1136/gut.39.3.449openalex-snapshot
Growth of colorectal polyps: redetection and evaluation of unresected polyps for a period of three years.
inferredcites →https://doi.org/10.1136/gutjnl-2011-300843openalex-snapshot
Outcomes of the Bowel Cancer Screening Programme (BCSP) in England after the first 1 million tests
inferredcites →https://doi.org/10.1155/2014/271940openalex-snapshot
Macrophages, Neutrophils, and Cancer: A Double Edged Sword
inferredcites →https://doi.org/10.1155/2016/6058147openalex-snapshot
Tumor-Associated Macrophages and Neutrophils in Tumor Microenvironment
inferredcites →https://doi.org/10.1158/0008-5472.can-11-0096openalex-snapshot
Anti-TIM3 Antibody Promotes T Cell IFN-γ–Mediated Antitumor Immunity and Suppresses Established Tumors
inferredcites →https://doi.org/10.1158/1078-0432.ccr-10-1966openalex-snapshot
Simultaneous Blockade of Multiple Immune System Inhibitory Checkpoints Enhances Antitumor Activity Mediated by Interleukin-15 in a Murine Metastatic Colon Carcinoma Model
inferredcites →https://doi.org/10.1158/1078-0432.ccr-16-3122openalex-snapshot
The Promise of Targeting Macrophages in Cancer Therapy
inferredcites →https://doi.org/10.1158/2159-8290.cd-17-1327openalex-snapshot
Genetic Mechanisms of Immune Evasion in Colorectal Cancer
inferredcites →https://doi.org/10.1186/s12859-019-2876-4openalex-snapshot
NeoPredPipe: high-throughput neoantigen prediction and recognition potential pipeline
inferredcites →https://doi.org/10.1186/s13059-015-0620-6openalex-snapshot
Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy
inferredcites →https://doi.org/10.1200/jco.2008.19.6147openalex-snapshot
In Situ Cytotoxic and Memory T Cells Predict Outcome in Patients With Early-Stage Colorectal Cancer
inferredcites →https://doi.org/10.1534/g3.111.000406openalex-snapshot
Mutation Rate Inferred From Synonymous Substitutions in a Long-Term Evolution Experiment With Escherichia coli
inferredcites →https://doi.org/10.18637/jss.v028.i08openalex-snapshot
Implementing a Class of Permutation Tests: The coin Package
inferredcites →https://doi.org/10.1890/0012-9658(2003)084[0511:caopca]2.0.co;2openalex-snapshot
CANONICAL ANALYSIS OF PRINCIPAL COORDINATES: A USEFUL METHOD OF CONSTRAINED ORDINATION FOR ECOLOGY
inferredcites →https://doi.org/10.1890/08-1823.1openalex-snapshot
Associations between species and groups of sites: indices and statistical inference
inferredcites →https://doi.org/10.21037/jgo.2018.01.17openalex-snapshot
Updates on immunotherapy for colorectal cancer
inferredcites →https://doi.org/10.32614/cran.package.clinfunopenalex-snapshot
clinfun: Clinical Trial Design and Data Analysis Functions
inferredcites →https://doi.org/10.32614/cran.package.conover.testopenalex-snapshot
conover.test: Conover-Iman Test of Multiple Comparisons Using Rank Sums
inferredcites →https://doi.org/10.32614/cran.package.netassocopenalex-snapshot
netassoc: Inference of Species Associations from Co-Occurrence Data
inferredcites →https://doi.org/10.32614/cran.package.veganopenalex-snapshot
vegan: Community Ecology Package
inferredcites →https://doi.org/10.3389/fimmu.2017.00828openalex-snapshot
Reprogramming of Tumor-Associated Macrophages with Anticancer Therapies: Radiotherapy versus Chemo- and Immunotherapies
inferredcites →https://doi.org/10.3390/ijms18061324openalex-snapshot
Immune Checkpoints as a Target for Colorectal Cancer Treatment
inferredcites →https://doi.org/10.4049/jimmunol.1700893openalex-snapshot
NetMHCpan-4.0: Improved Peptide–MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data
inferredcites →https://doi.org/10.48550/arxiv.1201.0490openalex-snapshot
Scikit-learn: Machine Learning in Python
inferredcites →https://doi.org/10.57938/c0ee7f19-2729-4685-ae7c-42e7462affc3openalex-snapshot
Implementing a class of permutation tests: The coin package
inferredcites →https://doi.org/10.7717/peerj.453openalex-snapshot
scikit-image: image processing in Python

What points at this work

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

inferred← citeshttps://doi.org/10.1007/s11538-019-00675-0openalex-snapshot
Mix and Match: Phenotypic Coexistence as a Key Facilitator of Cancer Invasion
inferred← citeshttps://doi.org/10.1038/s41467-023-40218-9openalex-snapshot
Virtual alignment of pathology image series for multi-gigapixel whole slide images
inferred← citeshttps://doi.org/10.1186/s12859-019-3173-yopenalex-snapshot
EvoFreq: visualization of the Evolutionary Frequencies of sequence and model data
inferred← citeshttps://doi.org/10.3390/cancers13122908openalex-snapshot
Predicting Colorectal Cancer Occurrence in IBD
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