Additional file 1 of TAM family receptors in conjunction with MAPK signalling are involved in acquired resistance to PI3Kα inhibition in head and neck squamous cell carcinoma
Bibliographic record
Abstract
Additional file 1. Supplemental Tables & Figures. Additional Table 1. Sources and cell culture media for established HNSCC cell lines used in this study. Additional Table 2. Short-tandem repeat (STR) profiling results confirming matching identities of primary tumor, blood, xenograft tumors and cell lines, where available. Additional Table 3. Antibodies used in this study. Additional Table 4. Clinical features of HNSCC patients used to generate PDX models of acquired drug resistance. Additional Fig. 1. (A) Schematic outlining the derivation of cell line from PDX-C. (B) Phase contrast microscopy image of PDX-C cells. (C) Flow cytometry for cell surface expression of EpCAM (CD326) in PDX-C cells. Over 99% of PDX-C cells were found to be CD326-positive. Additional Fig. 2. Schematic outlining the development of the alpelisib-resistant HNSCC cell lines. Parental cells (Cal33 and 93-VU-147T) were treated with increasing doses of alpelisib, beginning with their IC50 values (0.5 μM for Cal33, 1.7 μM for 93-VU-147T), as previously established [20]. Additional Fig. 3. Relative abundance of small, medium and large sized colonies for parental and alpelisib-resistant cell lines ((A) Cal33 cells, (B) 93-VU-147T cells) when untreated, and when treated with alpelisib. Colony counts and sizes were analyzed in ImageJ version 1.52a. Briefly, RGB images of wells were converted in binary images and analyzed using the Analyze Particles feature. Colony size cutoffs were set as follows (in pixels): Small 0–100; Medium 101–500; Large > 501. Additional Fig. 4. (A) & (B) Immunoblot of MER-TK expression in parental and alpelisib-resistant Cal33 and 93-VU-147T cells. Short and long exposures of MER-TK blot are shown. HEK293T cells served as a positive control for MER-TK expression. Additional Fig. 5. Histological comparison of PDX tissues and their corresponding primary tumors (where available), stained with H&E. Scale bar represents 50 μM. Additional Fig. 6. Representative IHC sections showing Ki67 staining PDX tissues treated with the vehicle agent (corn oil) or alpelisib (endpoint either while still responding or treated out to the emergence of resistance). Scale bar represents 100 μM. Additional Fig. 7. Representative IHC sections showing AXL staining in PDX-C and PDX-E models. Quantification completed using Fiji software is shown below. ns = not significant, unpaired Student’s t-test. Scale bars represent 100 μM. Additional Fig. 8. Immunoblot of TYRO3 and AXL expression in 25 HNSCC cell lines, ordered by sensitivity to alpelisib (IC50 values indicated).
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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 | 0.001 | 0.020 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.002 | 0.004 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.003 | 0.002 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.002 | 0.001 |
| Insufficient payload (model declined to judge) | 0.902 | 0.183 |
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".