A Single-Cell Atlas of Liver Metastases of Colorectal Cancer Reveals the Reprogramming of the Tumor Microenvironment in Response to Preoperative Chemotherapy
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE178318 | GEO | 2021/09/10
REPOSITORIES: GEO
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Project description:The purpose of this study is to identify miRNAs involved in the pathology of colorectal cancer (CRC) liver metastasis and investigate their underlying mechanisms. A total of 39 miRNAs were identified to be differentially expressed between 16 primary CRC tissues with liver metastases and 16 CRC tissues without liver metastases from 32 patients by Affymetric miRNA microarrays. 16 coloretcal cancer tissues with liver metastasis and 16 colorectal cancer tissues without liver metastasis were included in this study for RNA extraction and hybridization on Affymetrix microarrays. We sought to identify the differentially expressed miRNAs between colorectal cancer tissues with and without liver metastasis.
2013-12-10 | E-GEOD-53159 | biostudies-arrayexpress
Project description:Colorectal cancer (CRC) patients suffer from the second highest mortality among all cancer entities. In half of all CRC patients, colorectal cancer liver metastases (CRLM) can be observed. Metastatic colorectal cancer is associated with poor overall survival and limited treatment options. Even after successful surgical resection of the primary tumor, metachronous liver metastases occur in one out of eight cases. The only available curative intended treatment is hepatic resection, but metachronous CRLM frequently recur after approximately one year. In this study, we performed a proteome analysis of three recurrent liver metastases of a single CRC patient by mass spectrometry. Despite surgical resection of the primary CRC and adjuvant chemotherapy plus cetuximab treatment, the patient developed three metachronous CRLM which occurred consecutively after 9, 21 and 31 months. We identified a set of 1,132 proteins expressed in the three metachronous CRLM, of which 481 were differentially regulated, including 81 proteins that were associated with the extracellular matrix (ECM). 56 ECM associated proteins were identified as upregulated in the third metastasis, 26 (46%) of which were previously described as negative prognostic markers in CRC, including tenascin C, nidogen 1, fibulin1 and vinculin. These data may reflect an ascending trend of malignancy from the first to the third metachronous colorectal cancer liver metastasis. Additionally, the results indicate different ECM phenotypes for recurrent metachronous metastasis, associated with different grades of malignancy and highlights the importance of individual analysis of molecular features in different, consecutive metastatic events in a single patient.
2021-09-09 | PXD020109 | Pride
Project description:The role of different cells in the tumor microenvironment (TME) is critical to the metastatic process. Phenotypic transformation of the liver cells is one of the most important stages of hepatic metastasis progression of colorectal cancer (CRC). Our aim was to identify the major molecules (i.e. genes, miRNAs and proteins) involved in this process. We isolated and performed whole genome analysis of gene, miRNA and proteins expression in three types of liver cells (Ito cells, Kupffer cells and liver sinusoidal endothelial cells) from the TME of a murine model of CRC liver metastasis. We selected the statistically significant differentially expressed molecules using the Student's t-test with Benjamini-Hochberg correction. and performed functional statistically-significant enrichment analysis of differentially expressed molecules with hypergeometric distribution using the curated collection of molecular signatures, MSigDB. To build a gene-miRNA-protein networks centered in Brca1, we developed software that collects miRNA targets from the union of the TargetScan, MicroCosm, mirTarBase and miRWalk databases. This was used to select miRNAs targeting Brca1. We validated the most relevant miRNAs with real-time quantitative PCR. To investigate BRCA1 protein expression, we built tissue microarrays (TMAs) from hepatic metastases of 34 CRC patients. Using integrated omics analyses we observed that Brca1 gene is among the twenty transcripts simultaneously up-regulated in all three types of TME liver cells during metastasis. Further analysis revealed that Brca1 is the last BRCA1-associated genome surveillance complex (BASC) gene activated in the TME. We confirmed this finding in human reanalyzing transcriptomics datasets from 184 patients from non-tumor colorectal tissue, primary colorectal tumor and colorectal liver metastasis of the GEO database. We found that the sequence of cell activation during metastasis is Endothelial->Ito->Kupffer. Immunohistochemical analysis of human liver metastases showed BRCA1 protein was co-localized in Ito, Kupffer and endothelial cells in 81.8% of early or synchronous metastases. However, in the greater part of the metachronous liver metastases this protein was not expressed in any of these TME cells. These results suggest a possible role of the co-expression of BRCA1 in Ito, Kupffer and sinusoidal endothelial cells in the early occurrence of CRC liver metastases, and point to BRCA1 as a potential TME biomarker. Animals: Balb/c mice (6- to 8-week-old males) were obtained from Charles River Laboratories Spain SA (Barcelona, Spain). All procedures were approved by the Ethical Committee for Animal Experimentation of the University of the Basque Country (EHU/UPV) in accordance with institutional, national and international guidelines regarding the protection and care of animal use for scientific purposes. Mice were kept in the animal facility of EHU/UPV and had access to standard chow and water ad libitum. Colorectal cancer cells: Murine CRC C26 cells (ATCC, Manassas, VA) syngeneic with Balb/c mice were grown under standard conditions in RPMI medium (Sigma-Aldrich, St. Louis, MO, USA) supplemented with 10% fetal bovine serum (FBS), penicillin (100 U/ml), streptomycin (100 mg/ml) and amphotericin B (0.25 mg/ml), all purchased from Life technologies, Carlsbad, CA. Control and tumor-activated hepatic cell isolation and culture: Control and tumor-activated primary cultures of hepatic cells, LSECs, Ito cells and Kupffer cells were isolated from livers with CRC metastasis, or from healthy controls. Balb/c mice were anesthetized with isofluorano and underwent surgical incisions on their left broadside. Mice were inoculated into the spleen at the incision sites using 2x106 of C26 colon carcinoma cells. Control mice were inoculated with PBS. Fourteen days later, all mice were sacrificed and the liver cells removed and purified by differential centrifugation. In brief, the mice were perfused with Clostridium histolyticum collagenase P (Sigma-Aldrich, St. Louis, MO, USA) through the cava vein and the obtained cell suspension twice centrifuged resulting in a parenchymal (PC)-enriched pellet and a non-PC-enriched supernatant. The non-PC-enriched supernatant was layered on Percoll gradients (25% on top of 50% w/v) to obtain LSECs and on Percoll gradients (33% on top of 50% w/v) to obtain Ito cells. After centrifugation the interphase between the two density cushions was collected and contained purified non-PC enriched LSECs in the first gradient and Ito cells in the second one. Both solutions contained Kupffer cells which were further separated by adherence assays. All cell fractions were washed and cultured with RPMI 1640 medium (Sigma-Aldrich, St. Louis, MO, USA) supplemented with 10% FBS and used in different experiments a maximum of 24 hours after isolation (Life technologies, Carlsbad, CA). miRNA microarray analysis : The purified total RNA was analysed using Agilent mouse miRNA microarrays. Release 18.0, 8x60K (v18) microarray slides (Agilent Technologies, USA), with 1,200 mouse miRNAs represented, were used. Briefly, 100 ng of total RNA was labelled and hybridized following the standard Agilent Protocol for the miRNA Microarray System with a miRNA Complete Labelling and Hybridization Kit, including Agilent miRNA Spike-ins, and the results were scanned using an Agilent Microarray Scanner G2565CA (Agilent Technologies, USA). The scanned TIFF image files were processed using Agilent Feature Extraction Software vs 10.7.3.1 to extract raw data and obtain QC reports. The microarray raw data were normalized using the quantile method.
2020-11-02 | GSE156430 | GEO
Project description:The role of different cells in the tumor microenvironment (TME) is critical to the metastatic process. Phenotypic transformation of the liver cells is one of the most important stages of hepatic metastasis progression of colorectal cancer (CRC). Our aim was to identify the major molecules (i.e. genes, miRNAs and proteins) involved in this process. We isolated and performed whole genome analysis of gene, miRNA and proteins expression in three types of liver cells (Ito cells, Kupffer cells and liver sinusoidal endothelial cells) from the TME of a murine model of CRC liver metastasis. We selected the statistically significant differentially expressed molecules using the Student's t-test with Benjamini-Hochberg correction. and performed functional statistically-significant enrichment analysis of differentially expressed molecules with hypergeometric distribution using the curated collection of molecular signatures, MSigDB. To build a gene-miRNA-protein networks centered in Brca1, we developed software that collects miRNA targets from the union of the TargetScan, MicroCosm, mirTarBase and miRWalk databases. This was used to select miRNAs targeting Brca1. We validated the most relevant miRNAs with real-time quantitative PCR. To investigate BRCA1 protein expression, we built tissue microarrays (TMAs) from hepatic metastases of 34 CRC patients. Using integrated omics analyses we observed that Brca1 gene is among the twenty transcripts simultaneously up-regulated in all three types of TME liver cells during metastasis. Further analysis revealed that Brca1 is the last BRCA1-associated genome surveillance complex (BASC) gene activated in the TME. We confirmed this finding in human reanalyzing transcriptomics datasets from 184 patients from non-tumor colorectal tissue, primary colorectal tumor and colorectal liver metastasis of the GEO database. We found that the sequence of cell activation during metastasis is Endothelial->Ito->Kupffer. Immunohistochemical analysis of human liver metastases showed BRCA1 protein was co-localized in Ito, Kupffer and endothelial cells in 81.8% of early or synchronous metastases. However, in the greater part of the metachronous liver metastases this protein was not expressed in any of these TME cells. These results suggest a possible role of the co-expression of BRCA1 in Ito, Kupffer and sinusoidal endothelial cells in the early occurrence of CRC liver metastases, and point to BRCA1 as a potential TME biomarker. Animals: Balb/c mice (6- to 8-week-old males) were obtained from Charles River Laboratories Spain SA (Barcelona, Spain). All procedures were approved by the Ethical Committee for Animal Experimentation of the University of the Basque Country (EHU/UPV) in accordance with institutional, national and international guidelines regarding the protection and care of animal use for scientific purposes. Mice were kept in the animal facility of EHU/UPV and had access to standard chow and water ad libitum. Colorectal cancer cells: Murine CRC C26 cells (ATCC, Manassas, VA) syngeneic with Balb/c mice were grown under standard conditions in RPMI medium (Sigma-Aldrich, St. Louis, MO, USA) supplemented with 10% fetal bovine serum (FBS), penicillin (100 U/ml), streptomycin (100 mg/ml) and amphotericin B (0.25 mg/ml), all purchased from Life technologies, Carlsbad, CA. Control and tumor-activated hepatic cell isolation and culture: Control and tumor-activated primary cultures of hepatic cells, LSECs, Ito cells and Kupffer cells were isolated from livers with CRC metastasis, or from healthy controls. Balb/c mice were anesthetized with isofluorano and underwent surgical incisions on their left broadside. Mice were inoculated into the spleen at the incision sites using 2x106 of C26 colon carcinoma cells. Control mice were inoculated with PBS. Fourteen days later, all mice were sacrificed and the liver cells removed and purified by differential centrifugation. In brief, the mice were perfused with Clostridium histolyticum collagenase P (Sigma-Aldrich, St. Louis, MO, USA) through the cava vein and the obtained cell suspension twice centrifuged resulting in a parenchymal (PC)-enriched pellet and a non-PC-enriched supernatant. The non-PC-enriched supernatant was layered on Percoll gradients (25% on top of 50% w/v) to obtain LSECs and on Percoll gradients (33% on top of 50% w/v) to obtain Ito cells. After centrifugation the interphase between the two density cushions was collected and contained purified non-PC enriched LSECs in the first gradient and Ito cells in the second one. Both solutions contained Kupffer cells which were further separated by adherence assays. All cell fractions were washed and cultured with RPMI 1640 medium (Sigma-Aldrich, St. Louis, MO, USA) supplemented with 10% FBS and used in different experiments a maximum of 24 hours after isolation (Life technologies, Carlsbad, CA). Omics analysis: 100ng of total RNA from each fraction was labeled and hybridized onto Agilent mouse RNA and miRNA microarrays, Release 18.0 (Agilent Technologies, USA) following the standard Agilent Protocol with RNA and miRNA Complete Labelling and Hybridization Kits, including Agilent RNA Spike-ins. Results were scanned using an Agilent Microarray Scanner G2565CA. Scanned TIFF image files were processed using Agilent Feature Extraction Software (v10.7.3.1) to extract the raw data. All omics data were normalized with the quantile method.
2020-11-02 | GSE156429 | GEO
Project description:The purpose of this study is to identify miRNAs involved in the pathology of colorectal cancer (CRC) liver metastasis and investigate their underlying mechanisms. A total of 39 miRNAs were identified to be differentially expressed between 16 primary CRC tissues with liver metastases and 16 CRC tissues without liver metastases from 32 patients by Affymetric miRNA microarrays.
2013-12-10 | GSE53159 | GEO
Project description:The purpose of this study is to identify lncRNAs involved in the pathology of colorectal cancer (CRC) liver metastasis and investigate their underlying mechanisms. A total of 439 miRNAs were identified to be differentially expressed between 7 primary CRC tissues with liver metastases and 8 CRC tissues without liver metastases from 15 patients by Arraystar lncRNA microarrays
2017-02-28 | GSE95423 | GEO
Project description:Peritoneal carcinomatosis (PC) originating from colorectal cancer (CRC) is associated with a poor prognosis and rapid disease progression. Metastasis is the major cause of death in patients with CRC whereas primary locoregionally circumscribed tumors are mostly curable. Due to the lack of appropriate and realistic mouse models for metastasis of CRC until recently, the research about metastasis of these tumors and possible therapeutic options is still in its infancy. With the establishment of murine CRC tumor organoids, mouse models were established which realistically mimic the process of tumor cell metastasis to the liver and the lung. However, to date no appropriate model for PC is described. Here, we establish a realistic model for peritoneal metastasis of colorectal cancer upon surgical transplantation of tumor organoids into the cecum wall. This mouse model for PC recapitulates human PC which makes it an ideal model for research of the biology of metastasis of colorectal cancer to the peritoneal cavity and for its usage for preclinical drug screening as well as for the evaluation of new therapeutic approaches which are highly needed in clinical reality.
2022-06-27 | GSE202454 | GEO
Project description:Integrative analysis of colorectal cancer (CRC) whole genomes and matched transcriptomes revealed that somatic promoter mutations are associated with increased Chromodomain helicase DNA-binding protein 2 (CHD2) levels. In both primary and metastatic CRC patients, elevated CHD2 levels are associated with worse prognosis and overall survival. We find that CHD2 increases promoter-transcription start site-chromatin accessibility and transcriptional upregulation of multiple oncogenes. In vitro, elevated CHD2 promoted CRC cell proliferation, migration and growth. In orthotopic xenografts, CHD2 promoted higher tumor burden and abdominal metastases, most prominently to the liver. FTD/TPI is an FDA approved chemotherapy for advanced chemo-refractory CRC. In orthotopic CRC models, FTD/TPI was highly effective in reducing metastases and prolonging survival for CHD2 high expressing CRCs. Thus, high CHD2 expression may be a potential CRC chemopredictive biomarker for FTD/TPI. Overall, these results provide new insights into the role of non-coding mutations and CHD2 levels to promote CRC growth and metastasis.
2021-02-12 | GSE146398 | GEO
Project description:About 50% of colorectal cancer patients develop liver metastases. Patients with metastatic colorectal cancer have 5-year survival rates below 20% despite new therapeutic regimens. Tumor heterogeneity has been linked with poor clinical outcome, but was so far mainly studied via bulk genomic analyses. In this study we performed spatial proteomics via MALDI mass spectrometry imaging on six patient matched CRC primary tumor and liver metastases to characterize interpatient, intertumor and intratumor hetereogeneity. We found several peptide features that were enriched in vital tumor areas of primary tumors and liver metastasis and tentatively derived from tumor cell specific proteins such as annexin A4 and prelamin A/C. Liver metastases of colorectal cancer showed higher heterogeneity between patients than primary tumors while within patients both entities show similar intratumor heterogeneity sometimes organized in zonal pattern. Together our findings give new insights into the spatial proteomic heterogeneity of primary CRC and patient matched liver metastases.
2023-02-17 | PXD039409 | Pride
Project description:Background & Aims: The metastatic process is complex and remains a major obstacle in the management of colorectal cancer (CRC). To gain a better insight into the biologic events driving the metastatic process we investigated genomic aberrations in a large cohort of matched CRC primaries and distant metastases from various sites. Methods: In total, 62 primary colorectal cancers, 62 matched normal specimens, and 68 matched metastases (from liver, lung, ovary, omentum, and distant lymph nodes) were analyzed by high resolution array comparative genomic hybridization (array CGH) for DNA copy number changes. Findings were validated using a publicly available dataset consisting of 21 primary tumors and matched liver metastases. Fluorescence in situ hybridization (FISH) was used to confirm some of the DNA copy number changes observed. Results: Overall patterns of DNA copy number aberrations were highly similar between primary tumors and their metastases, confirming clonality. Additional copy number aberrations in metastasis are rare and rather than recurrent they were sporadic for individual patients. The only recurrent differences between primary tumors and their metastases were two chromosomal regions, 6q21 and 8q24.21 encompassing the MYC oncogene, that coamplified in three metastases of two patients (3.2%). FISH analysis confirmed the high level co-amplification in the metastasis, which were not detected in their primary tumors. Conclusions: Primary CRC and their metastases show highly similar patterns of DNA copy number changes, additional copy number aberrations in metastasis are rare and recurrences exceptional. These observations are consistent with the hypothesis that the metastatic potential is predestined early in the development of the primary tumor. In total, 62 primary colorectal cancers, 62 matched normal specimens, and 68 matched metastases (liver, lung, ovarian, omentum and distant lymph nodes) were analyzed by high resolution array comparative genomic hybridization (array CGH).
2014-02-10 | E-GEOD-38479 | biostudies-arrayexpress