BACKGROUND Breast cancer (BC) immune infiltrates play a critical role in tumor progression and response to treatment. Besides stromal tumor infiltrating lymphocytes (sTILs) which have recently reached level 1B evidence as a prognostic marker in triple negative BC, a plethora of methods to assess immune infiltration exists, and it is unclear how these compare to each other and if they can be used interchangeably. METHODS Two experienced pathologists scored sTIL, intra-tumoral TIL (itTIL), and 6 immune cell types (CD3+, CD4+, CD8+, CD20+, CD68+, FOXP3+) in the International Cancer Genomics Consortium breast cancer cohort using hematoxylin and eosin-stained (n = 243) and immunohistochemistry-stained tissue microarrays (n = 254) and whole slides (n = 82). The same traits were evaluated using transcriptomic- and methylomic-based deconvolution methods or signatures. RESULTS The concordance correlation coefficient (CCC) between pathologists for sTIL was very good (0.84) and for cell-specific immune infiltrates slightly lower (0.63-0.66). Comparison between tissue microarray and whole slide pathology scores revealed systematically higher values in whole slides (ratio 2.60-5.98). The Spearman correlations between microscopic sTIL and transcriptomic- or methylomic-based assessment of immune infiltrates were highly variable (r = 0.01-0.56). Similar observations were made for cell type-specific quantifications (r = 0.001-0.54). We observed a strong inter-method variability between the omics-derived estimations, which is further cell type dependent. Finally, we demonstrated that most methods more accurately identify highly infiltrated (sTIL ≥ 60%; area under the curve, AUC, 0.64-0.99) as compared to lowly infiltrated tumors (sTIL ≤ 10%; AUC 0.52-0.82). CONCLUSIONS There is a lower inter-pathologist concordance for cell-specific quantification as compared to overall infiltration quantification. Microscopic assessments are underestimated when considering small cores (tissue microarray) instead of whole slides. Results further highlight considerable differences between the microscopic-, transcriptomic-, and methylomic-based methods in the assessment of overall and cell-specific immune infiltration in BC. We therefore call for extreme caution when assessing immune infiltrates using current methods and emphasize the need for standardized immune characterization beyond TIL.

中文翻译：

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对评估乳腺癌总体和细胞特异性免疫浸润方法的综合评估。

背景技术乳腺癌（BC）免疫浸润在肿瘤进展和对治疗的反应中起关键作用。除了最近已达到三阴性BC的预后标志物的基质肿瘤浸润淋巴细胞（sTILs）达到1B证据外，还存在大量评估免疫浸润的方法，目前尚不清楚它们如何相互比较以及是否可以使用它们可以互换。方法在国际癌症基因组学联合会乳腺癌研究小组中，两名经验丰富的病理学家使用苏木精和曙红染色对sTIL，肿瘤内TIL（itTIL）和6种免疫细胞类型（CD3 +，CD4 +，CD8 +，CD20 +，CD68 +，FOXP3 +）进行了评分。 = 243）和免疫组织化学染色的组织芯片（n = 254）和整个玻片（n = 82）。使用基于转录组和基于甲基组学的反卷积方法或签名评估了相同的性状。结果sTIL的病理学家之间的一致性相关系数（CCC）非常好（0.84），而细胞特异性免疫浸润的一致性相关系数则稍低（0.63-0.66）。组织微阵列和整个玻片病理评分之间的比较显示，整个玻片的系统值较高（比率2.60-5.98）。微观sTIL与基于转录组或基于甲基组学的免疫浸润评估之间的Spearman相关性是高度可变的（r = 0.01-0.56）。对于细胞类型特异性的定量分析也得出了类似的观察结果（r = 0.001-0.54）。我们观察到在组学派生的估计之间方法之间存在很强的可变性，这进一步取决于细胞类型。最后，我们证明，与低浸润的肿瘤（sTIL≤10％； AUC 0.52-0.82）相比，大多数方法可以更准确地识别高度浸润的肿瘤（sTIL≥60％；曲线下面积，AUC，0.64-0.99）。结论与总浸润定量相比，病理学家之间对细胞特异性定量的一致性较低。当考虑小的核心（组织微阵列）而不是整个玻片时，显微镜评估被低估了。结果进一步凸显了在评估BC总体免疫和细胞特异性免疫浸润方面，基于显微镜，转录组和甲基组学的方法之间存在显着差异。因此，在使用当前方法评估免疫浸润液时，我们需要格外谨慎，并强调需要在TIL以外进行标准化的免疫表征。