scholarly journals Pathologic evolution-related Gene Analysis based on both single-cell and bulk transcriptomics in Colorectal Cancer

2020 ◽  
Vol 11 (23) ◽  
pp. 6861-6873
Author(s):  
Jiali Li ◽  
Zihang Zeng ◽  
Jiarui Chen ◽  
Xingyu Liu ◽  
Xueping Jiang ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Single Cell ◽  
Gene Analysis ◽  
Related Gene

scholarly journals Quantifying single-cell ERK dynamics in colorectal cancer organoids reveals EGFR as an amplifier of oncogenic MAPK pathway signalling

2021 ◽  
Author(s):  
Bas Ponsioen ◽  
Jasmin B. Post ◽  
Julian R. Buissant des Amorie ◽  
Dimitrios Laskaris ◽  
Ravian L. van Ineveld ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Single Cell ◽  
Mapk Pathway

scholarly journals Colorectal Cancer Stem Cell States Uncovered by Simultaneous Single‐Cell Analysis of Transcriptome and Telomeres

2021 ◽  
Vol 8 (8) ◽  
pp. 2004320
Author(s):  
Hua Wang ◽  
Peng Gong ◽  
Tong Chen ◽  
Shan Gao ◽  
Zhenfeng Wu ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Stem Cell ◽  
Cancer Stem Cell ◽  
Single Cell ◽  
Single Cell Analysis ◽  
Cell Analysis

scholarly journals Enzyme-generated intracellular fluorescence for single-cell reporter gene analysis utilizingEscherichia coli ?-glucuronidase

Cytometry ◽  
1996 ◽  
Vol 24 (4) ◽  
pp. 321-329 ◽  
Author(s):  
Matthew Lorincz ◽  
Mario Roederer ◽  
Zhenjun Diwu ◽  
Leonard A. Herzenberg ◽  
Garry P. Nolan
Keyword(s):  
Single Cell ◽  
Reporter Gene ◽  
Gene Analysis ◽  
Reporter Gene Analysis ◽  
Intracellular Fluorescence

scholarly journals Cryopreservation of microglia enables single-cell RNA sequencing with minimal effects on disease-related gene expression patterns

iScience ◽  
2021 ◽  
Vol 24 (4) ◽  
pp. 102357
Author(s):  
Brenda Morsey ◽  
Meng Niu ◽  
Shetty Ravi Dyavar ◽  
Courtney V. Fletcher ◽  
Benjamin G. Lamberty ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Rna Sequencing ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Related Gene ◽  
Single Cell Rna Sequencing ◽  
Disease Related Gene

scholarly journals Reconstructing single-cell karyotype alterations in colorectal cancer identifies punctuated and gradual diversification patterns

2021 ◽  
Author(s):  
Yannik Bollen ◽  
Ellen Stelloo ◽  
Petra van Leenen ◽  
Myrna van den Bos ◽  
Bas Ponsioen ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Single Cell ◽  
Temporal Dynamics ◽  
De Novo ◽  
Tumor Evolution ◽  
Genome Wide ◽  
Aneuploid Tumor ◽  
Evolutionary Paths ◽  
Tumor Biopsies ◽  
Punctuated Evolution

AbstractCentral to tumor evolution is the generation of genetic diversity. However, the extent and patterns by which de novo karyotype alterations emerge and propagate within human tumors are not well understood, especially at single-cell resolution. Here, we present 3D Live-Seq—a protocol that integrates live-cell imaging of tumor organoid outgrowth and whole-genome sequencing of each imaged cell to reconstruct evolving tumor cell karyotypes across consecutive cell generations. Using patient-derived colorectal cancer organoids and fresh tumor biopsies, we demonstrate that karyotype alterations of varying complexity are prevalent and can arise within a few cell generations. Sub-chromosomal acentric fragments were prone to replication and collective missegregation across consecutive cell divisions. In contrast, gross genome-wide karyotype alterations were generated in a single erroneous cell division, providing support that aneuploid tumor genomes can evolve via punctuated evolution. Mapping the temporal dynamics and patterns of karyotype diversification in cancer enables reconstructions of evolutionary paths to malignant fitness.

Identifying an immune-related gene-pair for prognosis prediction of metastatic colorectal cancer.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. e15565-e15565
Author(s):  
Qiqi Zhu ◽  
Du Cai ◽  
Wei Wang ◽  
Min-Er Zhong ◽  
Dejun Fan ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
High Risk ◽  
Prognostic Value ◽  
Validation Cohort ◽  
Risk Group ◽  
High Risk Group ◽  
Related Gene ◽  
Training Cohort ◽  
Gene Pairs ◽  
Immune Related Gene

e15565 Background: Few robust predictive biomarkers have been applied in clinical practice due to the heterogeneity of metastatic colorectal cancer (mCRC) . Using the gene pair method, the absolute expression value of genes can be converted into the relative order of genes, which can minimize the influence of the sequencing platform difference and batch effects, and improve the robustness of the model. The main objective of this study was to establish an immune-related gene pairs signature (IRGPs) and evaluate the impact of the IRGPs in predicting the prognosis in mCRC. Methods: A total of 205 mCRC patients containing overall survival (OS) information from the training cohort ( n = 119) and validation cohort ( n = 86) were enrolled in this study. LASSO algorithm was used to select prognosis related gene pairs. Univariate and multivariate analyses were used to validate the prognostic value of the IRGPs. Gene sets enrichment analysis (GSEA) and immune infiltration analysis were used to explore the underlying biological mechanism. Results: An IRGPs signature containing 22 gene pairs was constructed, which could significantly separate patients of the training cohort ( n = 119) and validation cohort ( n = 86) into the low-risk and high-risk group with different outcomes. Multivariate analysis with clinical factors confirmed the independent prognostic value of IRGPs that higher IRGPs was associated with worse prognosis (training cohort: hazard ratio (HR) = 10.54[4.99-22.32], P < 0.001; validation cohort: HR = 3.53[1.24-10.08], P = 0.012). GSEA showed that several metastasis and immune-related pathway including angiogenesis, TGF-β-signaling, epithelial-mesenchymal transition and inflammatory response were enriched in the high-risk group. Through further analysis of the immune factors, we found that the proportions of CD4+ memory T cell, regulatory T cell, and Myeloid dendritic cell were significantly higher in the low-risk group, while the infiltrations of the Macrophage (M0) and Neutrophil were significantly higher in the high-risk group. Conclusions: The IRGPs signature could predict the prognosis of mCRC patients. Further prospective validations are needed to confirm the clinical utility of IRGPs in the treatment decision.

scholarly journals Single-Cell Analysis Reveals Characterization of Infiltrating T Cells in Moderately Differentiated Colorectal Cancer

2021 ◽  
Vol 11 ◽  
Author(s):  
Xi Yang ◽  
Quan Qi ◽  
Yuefen Pan ◽  
Qing Zhou ◽  
Yinhang Wu ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Rectal Cancer ◽  
Colon Cancer ◽  
T Cells ◽  
T Cell ◽  
Single Cell ◽  
Peripheral Blood ◽  
Strong Correlation ◽  
Tumor Tissue ◽  
Cell Populations

ObjectiveThis study aimed to characterize the tumor-infiltrating T cells in moderately differentiated colorectal cancer.MethodsUsing single-cell RNA sequencing data of isolated 1632 T cells from tumor tissue and 1252 T cells from the peripheral blood of CRC patients, unsupervised clustering analysis was performed to identify functionally distinct T cell populations, followed by correlations and ligand-receptor interactions across cell types. Finally, differential analysis of the tumor-infiltrating T cells between colon cancer and rectal cancer were carried out.ResultsA total of eight distinct T cell populations were identified from tumor tissue. Tumor-Treg showed a strong correlation with Th17 cells. CD8+TRM was positively correlated with CD8+IEL. Seven distinct T cell populations were identified from peripheral blood. There was a strong correlation between CD4+TN and CD4+blood-TCM. Colon cancer and rectal cancer showed differences in the composition of tumor-infiltrating T cell populations. Tumor-infiltrating CD8+IEL cells were found in rectal cancer but not in colon cancer, while CD8+ TN cells were found in the peripheral blood of colon cancer but not in that of rectal cancer. A larger number of tumor-infiltrating CD8+ Tex (88.94%) cells were found in the colon cancer than in the rectal cancer (11.06%). The T cells of the colon and rectal cancers showed changes in gene expression pattern.ConclusionsWe characterized the T cell populations in the CRC tumor tissue and peripheral blood.

Spatiotemporal Immune Landscape of Colorectal Cancer Liver Metastasis at Single-Cell Level

2021 ◽  
pp. candisc.0316.2021
Author(s):  
Yingcheng Wu ◽  
Shuaixi Yang ◽  
Jiaqiang Ma ◽  
Zechuan Chen ◽  
Guohe Song ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Liver Metastasis ◽  
Single Cell ◽  
Single Cell Level ◽  
Cell Level ◽  
Colorectal Cancer Liver Metastasis

scholarly journals Single‐cell immune profiling reveals new insights into colorectal cancer

2019 ◽  
Vol 97 (3) ◽  
pp. 241-243
Author(s):  
Tapio Lönnberg ◽  
Michael JT Stubbington
Keyword(s):  
Colorectal Cancer ◽  
Single Cell ◽  
Immune Profiling
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