Identification of immune-related genes prognostic index for predicting survival and immunotherapy in colorectal carcinoma
Notice bibliographique
Résumé
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.
Récupéré en direct depuis OpenAlex et désinversé. Les résumés ne sont pas conservés dans cette base de données : les index inversés représentent 8,6 Go des 9,3 Go de texte de la base, et le serveur dispose de 13 Go libres.
Comment cette classification a été obtenuedéplier
Prédiction machine sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Le volet Gemma est une étiquette directe du modèle pour chaque travail de la base, lue sur la notice réduite au titre. Le volet Codex est un classifieur appris des 10 348 étiquettes directes de Codex et calibré sur les taux pondérés de l'échantillon; les champs sans appui suffisant ne portent aucun appel Codex. Le mode candidate est l'union des deux volets; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont pas des étiquettes humaines.
Scores du classifieur distillé par catégorie (deux têtes)
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,000 | 0,001 |
| Méta-épidémiologie (sens strict) | 0,000 | 0,000 |
| Méta-épidémiologie (sens large) | 0,000 | 0,000 |
| Bibliométrie | 0,002 | 0,002 |
| Études des sciences et des technologies | 0,000 | 0,000 |
| Communication savante | 0,001 | 0,000 |
| Science ouverte | 0,000 | 0,000 |
| Intégrité de la recherche | 0,000 | 0,000 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,006 | 0,001 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule source (Gemma direct ou Codex distillé), pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».