Single-cell sequencing of colorectal cancer liver metastases
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA666199 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12734302.fastq.gz | Fastqsanger.gz | |||
| SRR12734303.fastq.gz | Fastqsanger.gz | |||
| SRR12734304.fastq.gz | Fastqsanger.gz | |||
| SRR12734305.fastq.gz | Fastqsanger.gz | |||
| SRR12734306.fastq.gz | Fastqsanger.gz |
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Project description:Colorectal cancer (CRC) is the third most common and second most deadly cancer worldwide. Treatments for metastatic CRC (mCRC) are still largely based on toxic chemotherapy regimens, but important insights into tumor biology enabled the development of targeted cancer therapies. Here, we describe a proteogenomic analysis of CRC liver metastases (metastatic CRC, mCRC), an ideal setting to analyze therapeutic resistance which occurs in a short time frame. We selected liver metastases from two CRC patients on both of which we performed deep proteome profiling and WES and RNAseq-directed database searches, identifying 10 predicted muttaions, one of which was KRAS G12V. finding we generated targeted parallel reaction monitoring (PRM) assays using stable isotope labelled standard (SIS) peptides to quantify the actual concentration (fmol per µg of total protein) of the mutated and canonical (wildtype) protein variants for 8 different mutations. We demonstrate on a total of 8 tumor and 6 paired healthy tissue samples (7 and 6 out of these KRASG12V) that PRM allows quantifying the actual mutation rate on the protein level from as little 10 µg of total protein starting amount and within a single 1 hour nano-LC-MS/MS run.
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Project description:Comparison of genomic alterations of primary colorectal cancers with liver metastases of the same patient Keywords: array CGH, colorectal cancer, colon cancer, liver metastasis 21 primary colorectal cancers and 21 matched liver metastases hybridized against sex-matched control pools
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