Identification of immune-related genes prognostic index for predicting survival and immunotherapy in colorectal carcinoma
Bibliographic record
Abstract
1.Clinical DataTranscript data and Clinicopathological information was downloaded from The Cancer Genome Atlas (TCGA) database (https://portal.Gdc.cancer.gov/), including 41 cases of para-tumor, 473 cases of CRC tumor and 452 clinical cases. The survival and transcriptional data of 250 CRC cases were downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/). The transcript dataset GSE161158 uploaded in November 2020 by Moffitt Cancer Research Center, University of Miami was used (10). Lists of immune related genes were download from ImmPort (https://www.immport. org/home) and Innate DB (https://www.innatedb.ca/). KEGG (http://www.gsea-msigdb.org/gsea/index.jsp) gene sets and all Gene Ontology (GO) gene sets were used as Gene Symbols. Gene mutation information was downloaded from cBioPortal (http://www.cbioportal.org/). 2.Murine Data2.1 IRGPI Genes Expression in CRC Murine ModelSPF Balb/c male mice, 6 - 8 weeks old, body mass (20 ± 5) g, purchased from Huaxing Experimental Animal Farm of Huiji District (Zhengzhou City, China), experimental animal license NO. is SCXK (Yu) 2019-0002. All animal experiments was approved by the Experimental Mouse Ethics Committee of Nanjing University of Traditional Chinese Medicine (NO. 202010A026).The above mice were randomly divided into: Control group (C), CRC Model group (M)，10 per group. Five Balb/c male mice were taken as tumor-bearing mice, and 1×107 CT26 cells were subcutaneously injected into the left axilla, and sacrificed one week later. The subcutaneous tumor was removed under sterile conditions, placed in sterile PBS, and disintegrated into several 1 mm3 masses. Under sterile conditions, the two groups of mice were dissected to expose the colon, the 1 mm3 tumor mass was fixed to the colon of the CRC Model group with tissue glue, while nothing was fixed in the Control group, and then the abdomen of the two groups of mice was sutured. After 3 days of postoperative recovery, mice were weighed, and Micro-CT scans were performed on the 26th day (under the condition of isoflurane respiratory anesthesia), and on the 27th day, the mice were sacrificed after anesthesia with 2 % sodium pentobarbital. Total RNA was extracted from the colon of the Control group and the tumor tissue of the CRC Model group by FastPure Cell/Tissue Total RNA Isolation Kit (Vazyme, China, Cat#RC101-01) , and after reverse transcribed into cDNA using HiScript® Ⅲ RT SuperMix for q PCR (Vazyme, China, Cat#R323-01), Real-Time PCR was used to detect the expression of IRCPI genes in each group using BlastaqTM Green 2× qPCR MasterMix (abm, Canada, Cat#G891). The primer sequences are shown in Supplementary Table S4.2.2 Immune Infiltration in CRC murine model The liver, colon, tumor, and mesentery of paraffin-embedded mice were sectioned, and then stained with hematoxylin-eosin (HE staining), and photographed with an upright white light photographic microscope (Nikon, Japan, Eclipse Ci-L). TIME immune cells were detected by flow cytometry (FCM). PBMCs were extracted by RBC lysate (FcMACS, China, Cat#FMS-RBC500). At least 5×106 cell suspensions(100 μL) were incubated with FC blocker at 4 ℃ for 10 min, then Anti-Human/Mouse CD11b FITC Antibody (PeproTech, USA, Cat#03221-50)、PE-Cy™7 Rat Anti-Mouse CD86 Antibody (BD Pharmingen™, USA, Cat#560582) and Alexa Fluor® 488 Anti-Mouse CD206 Antibody (Biolegend, USA, Cat#141710) were used to marked Macrophages; Alexa Fluor® 488 anti-mouse CD19 Antibody (Invitrogen, USA, REF#11-0193-81) and PE/Cy7 anti-mouse/rat/human CD27 Antibody (Biolegend, USA, Cat#124216) were used to marked B cells; Anti-Mouse CD4 APC-Cyanine7 (PeproTech, USA, Cat#06122-87)、Anti-Mouse CD8a FITC Antibody (PeproTech, USA, Cat#10122-50)、Anti-Mouse CD25 APC Antibody (PeproTech, USA, Cat#07312-80) and Anti-Mouse/Rat FOXP3 PE Antibody (PeproTech, USA, Cat#83422-60) were used to marked T cells, and PBMCs monochromic tubes were made respectively. The cells were detected on the Amnis FlowSight flow cytometer (Merck Millipore, USA), and immunocyte subsets were analyzed using the IDEAS software (Merck Millipore, USA). Supplement Fig.S7 visualized the analysis strategies for IRGPI immunocyte subsets by Flow cytometry.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.002 | 0.002 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.006 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".