Neighborhood clustering analysis to define epithelial–stromal interface for tumor infiltrating lymphocyte evaluation
Bibliographic record
Abstract
Evaluation of tumor infiltrating lymphocytes as recommended by current guidelines is largely based on stromal regions within the tumor. In the context of epithelial malignancies, the epithelial region and the epithelial-stromal interface are not assessed, because of technical difficulties in manually discerning lymphocytes when admixed with epithelial tumor cells. The inability to quantify immune cells in epithelial-associated areas may negatively impact evaluation of patient response to immune checkpoint therapies. Innovative spatial analysis techniques have emerged that can directly address challenges associated with quantification of lymphocytes in specialized regions like the interface. In this study, we apply supervised neighborhood clustering analysis (via an open-source application CytoMAP) to assess the spatial distribution of CD8+ T cells, CD8+ TIM3+ (T cell immunoglobulin and mucin-domain containing-3) exhausted T cells, and TIM3+ CD8- macrophages on a gynecological tumor microarray. Neighborhood clustering analysis is adept at objectively mapping the epithelial-stromal interface alongside the epithelial and stromal region of each tumor under a three-compartment model. When tumors are partitioned by the conventional two-compartment model (epithelial and stromal region only), the highest density of total CD8+ T cells is found in the stromal region in a slight majority of tumors. In contrast, the interface region surpasses both the epithelial and stromal region in holding the highest density of CD8+ T cells when this unique region is incorporated into the three-compartment model. Further subset analysis shows higher proportion of CD8+ TIM3+ exhausted T cells within the interface and epithelial region, as compared to CD8+ TIM3- T cells which span from the stroma to the interface. These results highlight the utility of implementing quantitative spatial technique and immune subset analysis in the assessment of tumor infiltrating lymphocytes, and underscore the potential significance of the under-reported tumor epithelial-stromal interface.
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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 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.002 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 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".