Additional file 2 of tRF3008A suppresses the progression and metastasis of colorectal cancer by destabilizing FOXK1 in an AGO-dependent manner
Bibliographic record
Abstract
Additional file 2: Figure S1. Genome-wide profiling of tRFs in colorectal cancer. (A) Summary of the tRFs number which expressed in both of two groups and the tRFs number specifically expressed in one group. (B) RT-qPCR to validate the differential expression of top 3 differentially expressed tRFs in 10 pairs of CRC and adjacent non-tumorous tissues. (C) The expression level of tRNAVal and tRF3008A in 7 CRC cell lines and human colon epithelial cell line using northern blot. (D) The expression level of tRNAVal and tRF3008A in various groups using northern blot. Statistical significance is measured using a Student’s t test.**: P < 0.01, ***: P < 0.001. Figure S2. tRF3008A inhibits colorectal cancer growth and migration in vitro: HCT116 cells were transfected with scrambled tRF mimetic control or tRF3008A mimetic, and HT29 cells were transfected with scrambled LNA control or tRF3008A-LNA. (A) Line graph showing the quantification of relative Edu incorporation in different groups. (B) Active caspase-3 was analyzed by immunostaining (red). (C) qRT-PCR was performed to validate the expression of tRF3008A in subcutaneous tumors. (D&E) The TUNEL assay for apoptosis detection in subcutaneously implanted tumors with different tRF3008A expression levels. Data are presented as the means ± S.D. Statistical significance is measured using a Student’s t test. *: P < 0.05, **: P < 0.01, **: P < 0.01. Figure S3. (A&B). qPCR was performed to evaluate the expression correlation between tRF3008A and its potential targets (DDA1 and HOXC13) in CRC tissues. (n = 45); Spearman’s rank correlation test was used. Figure S4. tRF3008A inhibits the growth and EMT of CRC cells through the FOXK1/Wnt pathway. HCT116 were co-transfected with tRF3008A mimetic and sh-FOXK1 or co-treated with Wnt pathway activator (Wnt agonist 1); HT29 cells were co-transfected with tRF3008A-LNA and OE-FOXK1 or co-treated with Wnt pathway inhibitor (IWR-1-endo). (A) qPCR was performed to evaluate the related mRNA levels of Wnt/β-Catenin signaling molecules (C-Jun、c-Myc and CCND1). (B) Active caspase-3 was analyzed by immunostaining (red). (C & D) Cell migration and invasion abilities were evaluated by transwell migration and matrigel invasion assay. Data were represented as means ± SD from at least three independent experiments. *: P < 0.05, **: P < 0.01, ***: P < 0.001. Figure S5. tRF3008A modulates FOXK1 in an AGO-dependent manner. tRF3008A affinity purification Mass spectrometry assay was performed: (A). The ThermoFisher Scientific 1200 liquid phase system and Q Exactive mass spectrometer were used for the analysis and identification of the samples, the quality spectrum results showed that there was a mass spectrum peak. (B) STRINGdb protein-protein interaction analysis in tRF3008A related proteins.
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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 | 0.002 | 0.016 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.002 | 0.003 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.002 | 0.001 |
| Insufficient payload (model declined to judge) | 0.865 | 0.156 |
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".