Changes in the synovial cell proteome induced by hypoxia
Bibliographic record
Abstract
FLS were isolated from rheumatoid arthritis and osteoarthritis synovia obtained at the time of joint arthroplasty. Cells from passages 2–4 were cultured under normoxic and hypoxic conditions for variable time points prior to analysis. Total proteins found in whole-cell FLS lysates were separated on immobilized pH-gradient two-dimensional (2D) PAGE and stained with Coomassie blue. To date, the in-gel digests of > 300 protein spots have been analyzed using matrix-assisted laser desorption/ionization time of flight mass spectrometry. Spectra were analyzed using the Knexus automation client and the Profound search engine (Proteometrics Canada, Winnipeg, Manitoba, Canada). 2D gels from hypoxic and normoxic FLS were superimposed using image analysis software and were compared. Differences were identified, and were related to differences in the expressed genome demonstrated in a microarray experiment using the same cell lines and conditions. Under normoxic conditions, more than 300 proteins were fully characterized in the FLS lines. Of particular note, FLS intensely expressed uridine diphosphoglucose dehydrogenase, which is an enzyme needed for the synthesis of hyaluronic acid. Other proteins identified fell into the following groups: enzymatic, transcription and cell-cycle regulation, protein binding, cytoskeletal, extracellular matrix, heat shock, protein synthesis and assembly, and membrane channel. In comparing the proteome expressed under hypoxic conditions, most of the apparent differences were quantitative, with shifts in position suggestive of phosphorylation and glycosylation. The microarray data demonstrated a spectrum of known, as well as novel, hypothetical proteins that were regulated by hypoxia. Identification of these proteins in the 2D gels is currently underway. We demonstrate techniques used in the detailed exploration of the synovial proteome. These techniques are applied to the examination of the effects of hypoxic stimulation on FLS. Comparisons between the expressed proteome and genome provide novel insights into the response of FLS to hypoxia
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
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 teacher head, 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".