Short Nucleotide Insertions in the MCL-1 Promoter Affect Its Gene Expression.
Bibliographic record
Abstract
Abstract We have recently reported a short nucleotide (six and eighteen) insertion (6- and 18-nt) in the MCL-1 promoter (−190bp upstream of the major transcription start site, GenBank, AN: AF198614) in B-cell chronic lymphocytic leukemia patients. These insertions were found to be polymorphisms. CD38-negative CLL patients with these promoter insertions had higher mRNA levels, poor response to standard chemotherapy and shorter survival. The aim of the present study was to test the hypothesis that these insertions directly effect MCL-1 gene expression. K562 and HeLa cells were transfected with pGL3-Basic, pGL3-Control and four reporter plasmids were constructed with a +0/0, +6/6, +18/18, and −23/23 MCL-1 promoter linked to Luciferase. Firefly activity in each transfection was normalized to Renilla Luciferase activity. At 24-hours post-transfection cells were induced with phorbol 12-myristate 13-acetate (PMA), granulocyte-macrophage colony stimulating factor (GM-CSF), both PMA and GM-CSF, or with fresh media only. At 48-hours post-transfection cells were harvested and Dual-Luciferase Assay was performed. Compared to transfection with pGL3-(+0/0) plasmid, the Luciferase PMA-stimulated activity for K562 cells transfected with pGL3-(+6/6) and pGL3-(+18/18) was 1.7 (P=0.0277) and 1.5 times higher (P=0.0067) respectively, and for pGL3-(−23/23) was 3.2 times lower (P=0.0021). The Luciferase PMA-stimulated activity for HeLa cells transfected with pGL3-(+6/6) was 3.3 times higher (P=0.0038), pGL-3-(+18/18) was 2.3 times higher (P=0.0245), and did not differ significantly for pGL3-(−23/23), compared to pGL3-(+0/0). Similar results were observed for GM-CSF-stimulated activity for HeLa cells, where activity was 3.9 times (P=0.0068) for pGL3-(+6/6) and 2.5 times (P=0.0258) higher for pGL3-(+18/18). Unstimulated Luciferase activity was also 2.5 times higher (P=0.0115) for pGL3-(+18/18) compared to pGL3-(+0/0) plasmid. These results provide experimental evidence for the positive effect of these nucleotide insertions (6- and 18-nt) on MCL-1 gene expression in both hemopoietic (K562) and epithelial (HeLa) cells.
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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 | 0.000 |
| 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 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 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".