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Article
Open AccessAuthor Correction: Pathway level subty** identifies a slow-cycling biological phenotype associated with poor clinical outcomes in colorectal cancer
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Article
Open AccessPathway level subty** identifies a slow-cycling biological phenotype associated with poor clinical outcomes in colorectal cancer
Molecular stratification using gene-level transcriptional data has identified subtypes with distinctive genotypic and phenotypic traits, as exemplified by the consensus molecular subtypes (CMS) in colorectal c...
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Article
Open AccessMulti-label transcriptional classification of colorectal cancer reflects tumor cell population heterogeneity
Transcriptional classification has been used to stratify colorectal cancer (CRC) into molecular subtypes with distinct biological and clinical features. However, it is not clear whether such subtypes represent...
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Article
Open AccessThe neuronal protein Neuroligin 1 promotes colorectal cancer progression by modulating the APC/β-catenin pathway
Colorectal cancer (CRC) remains largely incurable when diagnosed at the metastatic stage. Despite some advances in precision medicine for this disease in recent years, new molecular targets, as well as prognos...
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Article
Open AccessA non-dividing cell population with high pyruvate dehydrogenase kinase activity regulates metabolic heterogeneity and tumorigenesis in the intestine
Although reprogramming of cellular metabolism is a hallmark of cancer, little is known about how metabolic reprogramming contributes to early stages of transformation. Here, we show that the histone deacetylas...
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Article
Open AccessThe EurOPDX Data Portal: an open platform for patient-derived cancer xenograft data sharing and visualization
Patient-derived xenografts (PDX) mice models play an important role in preclinical trials and personalized medicine. Sharing data on the models is highly valuable for numerous reasons – ethical, economical, re...
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Article
Open AccessAuthor Correction: Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts
A Correction to this paper has been published: https://doi.org/10.1038/s41588-021-00811-4.
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Article
Open AccessConservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts
Patient-derived xenografts (PDXs) are resected human tumors engrafted into mice for preclinical studies and therapeutic testing. It has been proposed that the mouse host affects tumor evolution during PDX engr...
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Article
Open AccessMachine learning for RNA sequencing-based intrinsic subty** of breast cancer
Stratification of breast cancer (BC) into molecular subtypes by multigene expression assays is of demonstrated clinical utility. In principle, global RNA-sequencing (RNA-seq) should enable reconstructing exist...
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Chapter
Genomics in Pseudomyxoma Peritonei
Pseudomyxoma peritonei (PMP) syndrome from appendiceal mucinous tumors generically shows a favorable biologic behavior. Cytoreductive surgery plus Hyperthermic IntraPEritoneal Chemotherapy (CRS + HIPEC) is con...
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Article
Open AccessEvolving neoantigen profiles in colorectal cancers with DNA repair defects
Neoantigens that arise as a consequence of tumor-specific mutations can be recognized by T lymphocytes leading to effective immune surveillance. In colorectal cancer (CRC) and other tumor types, a high number ...
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Article
Open AccessFOXA1 and AR in invasive breast cancer: new findings on their co-expression and impact on prognosis in ER-positive patients
The role of forkhead-box A1 (FOXA1) and Androgen receptor (AR) in breast cancer (BC) has been extensively studied. However, the prognostic role of their co-expression in Estrogen receptor positive (ER+) BC has...
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Article
Open AccessSelective analysis of cancer-cell intrinsic transcriptional traits defines novel clinically relevant subtypes of colorectal cancer
Stromal content heavily impacts the transcriptional classification of colorectal cancer (CRC), with clinical and biological implications. Lineage-dependent stromal transcriptional components could therefore do...
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Article
Correction: Corrigendum: Stromal contribution to the colorectal cancer transcriptome
Nat. Genet. 47, 312–319 (2015); published online 23 February 2015; corrected after print 29 August 2016 In the version of this article initially published, an affiliation for author Zsolt Fekete was incorrectl...
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Article
Open AccessMicroRNA–mRNA interactions underlying colorectal cancer molecular subtypes
Colorectal cancer (CRC) transcriptional subtypes have been recently identified by gene expression profiling. Here we describe an analytical pipeline, microRNA master regulator analysis (MMRA), developed to sea...
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Article
The molecular landscape of colorectal cancer cell lines unveils clinically actionable kinase targets
The development of molecularly targeted anticancer agents relies on large panels of tumour-specific preclinical models closely recapitulating the molecular heterogeneity observed in patients. Here we describe ...
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Article
Stromal contribution to the colorectal cancer transcriptome
Claudio Isella and colleagues report an analysis of colorectal cancer (CRC) gene expression data from patient-derived xenografts, which they use to reconcile three commonly used CRC classification systems. The...
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Article
Open AccessMulcom: a multiple comparison statistical test for microarray data in Bioconductor
Many microarray experiments search for genes with differential expression between a common "reference" group and multiple "test" groups. In such cases currently employed statistical approaches based on t-tests or...
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Article
A molecular signature for Epithelial to Mesenchymal transition in a human colon cancer cell system is revealed by large-scale microarray analysis
Sporadic colorectal cancer is a major cause of death worldwide. Development takes place in a sequential manner from benign adenomas leading to carcinomas. In 90% of tumours bearing a Ras mutation it is Ki-Ras ...
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Paraptotic Cell Death Induced by the Thioxotriazole Copper Complex A0: A New Tool to Kill Apoptosis-Resistant Cancer Cells
The copper(II) complex A0 induces non-apoptotic programmed cell death in human HT1080 fibrosarcoma cells but not in normal fibroblasts (J Med Chem, 50(8):1916–1924, 2007). While typical apoptotic features, such a...
