Comparison of classification methods for clonality between pairs in the PT/LR cohort.

<p><b>Cor</b> (Correspondence): correspondence number with the Bollet/Servant cohort. <b>scores</b>: scores obtained with partial identity (PIS) or methylation (MS). <b>Time</b>: time elapsed between diagnosis of the PT and diagnosis of the recurrence. <b>Classification</b>: classification of the recurrence based on copy number (PIS), methylation (MS) or clinical features (clinical). <b>Divergence</b>: which method deviated from the others.</p

Histogram of the distribution of methylome-similarity score (MS) between unrelated PT/LR pairs.

<p>MS score for matched pairs is represented by circles. The vertical dashed line corresponds to the 95% quantile of the distribution of the MS scores for the unrelated pairs, used as a threshold to define clonal pairs ().</p

Correlation between methylation and copy-number scores.

<p>The horizontal red line (resp. vertical dashed blue line) corresponds to the 95% quantile of the distribution of the methylation-scores (resp. partial identity scores) for the unrelated pairs: (resp. ). PT/AM (resp. PT/LR, resp. PT/CL) pairs are colored in yellow (resp. blue, resp. pink). The black line corresponds to the linear regression between methylation and copy-number scores for all the datasets.</p

Pairwise methylome distance for each samples.

<p>Each boxplot represents the Manhattan distance between primary tumor and an unrelated locoregional evolution, or the Manhattan distance between locoregional evolution i and an unrelated primary tumor. The black square represent the Manhattan distance between the matched primary tumor and locoregional evolution from sample . The yellow (resp. blue, resp. pink) panel represents the PT/AM (resp. PT/LR, resp. PT/CL) set. The last panel represents the distribution of distances between the healthy breast tissue and all the other healthy breast tissues from the cohort.</p

Distribution of methylation distances between different samples pairs for each groups.

<p><b>Real</b>: boxplot of methylome distances for all matched pairs that is a PT and its corresponding metastasis or recurrence. <b>Artificial</b>: boxplot of methylome distances for all unmatched pairs that is a PT and an unrelated metastasis or recurrence. <b>Primary</b>: boxplot of methylome distances to distances between two PT of two different individuals. <b>Recurrence</b>: boxplot of methylome distances between two metastasis or recurrence samples of two different individuals.</p

A Stromal Immune Module Correlated with the Response to Neoadjuvant Chemotherapy, Prognosis and Lymphocyte Infiltration in <i>HER2</i>-Positive Breast Carcinoma Is Inversely Correlated with Hormonal Pathways

<div><p>Introduction</p><p><i>HER2</i>-positive breast cancer (BC) is a heterogeneous group of aggressive breast cancers, the prognosis of which has greatly improved since the introduction of treatments targeting <i>HER2</i>. However, these tumors may display intrinsic or acquired resistance to treatment, and classifiers of <i>HER2</i>-positive tumors are required to improve the prediction of prognosis and to develop novel therapeutic interventions.</p><p>Methods</p><p>We analyzed 2893 primary human breast cancer samples from 21 publicly available datasets and developed a six-metagene signature on a training set of 448 <i>HER2</i>-positive BC. We then used external public datasets to assess the ability of these metagenes to predict the response to chemotherapy (Ignatiadis dataset), and prognosis (METABRIC dataset).</p><p>Results</p><p>We identified a six-metagene signature (138 genes) containing metagenes enriched in different gene ontologies. The gene clusters were named as follows: Immunity, Tumor suppressors/proliferation, Interferon, Signal transduction, Hormone/survival and Matrix clusters. In all datasets, the Immunity metagene was less strongly expressed in ER-positive than in ER-negative tumors, and was inversely correlated with the Hormonal/survival metagene. Within the signature, multivariate analyses showed that strong expression of the “Immunity” metagene was associated with higher pCR rates after NAC (OR = 3.71[1.28–11.91], <i>p</i> = 0.019) than weak expression, and with a better prognosis in <i>HER2</i>-positive/ER-negative breast cancers (HR = 0.58 [0.36–0.94], <i>p</i> = 0.026). Immunity metagene expression was associated with the presence of tumor-infiltrating lymphocytes (TILs).</p><p>Conclusion</p><p>The identification of a predictive and prognostic immune module in <i>HER2</i>-positive BC confirms the need for clinical testing for immune checkpoint modulators and vaccines for this specific subtype. The inverse correlation between Immunity and hormone pathways opens research perspectives and deserves further investigation.</p></div

Summarized PT/LR Clinical and histological features.

<p><b>Cor</b> (Correspondence): correspondence number with the Bollet/Servant cohort from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103986#pone.0103986-Bollet1" target="_blank">[16]</a>, <b>Type</b>: histological type of the tumor (D =  ductal, L =  lobular), <b>Grade</b>: Aggressiveness of the tumor (1 to 3), <b>ER</b>: presence of estrogen receptors, <b>PR</b>: presence of progesterone receptors, <b>HER2</b>: presence of HER2 receptors, <b>Loc</b> (Location): 1 if the recurrence was located less than 4cm from the PT.</p

Significantly differentially methylated genes between PT and AM samples.

<p><b>CpG</b>: CpG probe name. <b>Gene</b>: Associated gene. <b>Pvalue</b>: FDR corrected p-value. <b>Methylation Variation</b>: Mean variation of methylation from the primary tumor to the axillary metastasis.</p

Kaplan-Meier estimates of the metastasis-free survival between TR and NP for the different classification methods.

<p>The full black (resp. green) line corresponds to the survival for samples classified as TR (resp. NP) and the corresponding dashed lines correspond to upper and lower 95 CI. The red crosses represent censored data. Panel A (resp. B, resp. C) represent the methylation-based (resp. copy-number based, resp. clinical based) classification.</p

Summarized PT/AM Clinical and histological features.

<p><b>Age</b>: Age of the patient at diagnosis of the primary tumor in years, <b>Type</b>: histological type of the tumor (D =  ductal, L =  lobular, Meta = Metaplasia), <b>Grade</b>: Aggressiveness of the tumor (1 to 3), <b>ER</b>: presence of estrogen receptors, <b>PR</b>: presence of progesterone receptors, <b>HER2</b>: presence of HER2 receptors.</p