Single-cell transcriptome landscape in colorectal cancer

One tumor tissue specimen pathologically diagnosed as adenocarcinoma undergoing radical colorectal surgery without any preoperative treatment at our center was collected, and the single cell transcriptome sequencing was performed, which was consistent with the inclusion and exclusion criteria for the prospective observational clinical study.The detailed procedures of pre-processing and quality control were as follows: (1) Raw data quality control; (2) Data comparison and mapping; (3) Cell Barcode Correction; (4) UMI disaggregation; (5) Count matrix generation; (6) Quality control indicators; (7) Data standardization and normalization; (8) Identification of highly variable genes (HVGs); (9) Filtering condition settings: nCount_RNA > 1000 & nFeature_RNA < 3000 & percent.mt < 10 & nFeature_RNA > 200. The t-Distributed Stochastic Neighbor Embedding (t-SNE) algorithm was used for downscaling and cell clustering, and the "SingleR" R package was used for cell annotation. The "CellChat" and "NicheNet" R packages were used for cell communication. The "monocle2" was used for cell trajectory analysis. One tumor tissue specimen pathologically diagnosed as adenocarcinoma undergoing radical colorectal surgery without any preoperative treatment at our center was collected, and the single cell transcriptome sequencing was performed, which was consistent with the inclusion and exclusion criteria for the prospective observational clinical study.The following inclusion criteria must all be met for eligibility: (1) Age ≥18 years and ≤70 years；(2) ECOG performance status of 0 or 1; (3) Pathologically proven colorectal adenocarcinoma; (4) No family history of hereditary cancer; (5) Treated with standardized radical resection of colorectal cancer satisfying R0 resection and removal of at least 12 lymph nodes; (6) Adequate primary tumor tissues from surgery or biopsy in compliance with the sample criteria; (7) Adequate peripheral blood sample in compliance with the sample criteria; (8) Patient able and voluntary to provide legitimate informed consent for the study. The exclusion criteria included the following : (1) Currently participating in clinical trials that might interfere with treatment judgments or receiving experimental treatments; (2) Patients who present abnormalities involving heart, lung, liver, kidney, hematopoiesis, and bone marrow reserve that cannot tolerate surgical treatments and chemotherapy; (3) Any other progressive malignant disease or malignancy requiring treatment within the preceding 5 years with the exception of curative basal cell carcinoma and squamous cell carcinoma; (4) Mental illness or serious cardiovascular disease; (5) Pregnancy, breastfeeding, or planning for pregnancy within 1 year; (6) Emergency surgery for perforation, bleeding, bowel obstruction, etc. Postoperative follow-up time points for CRC patients were based on specific time points after surgery, including scheduled follow-up visits at the first, third, and sixth months after surgery and subsequent six-month or annual follow-up visits. At each follow-up visit, high-quality clinical assessment, appropriate imaging and laboratory tests, and detailed data recording and analysis played important roles in evaluating treatment outcomes, monitoring survival, and guiding subsequent treatment decisions.