15 research outputs found
Adjusting Breast Cancer Patient Prognosis with Non-HER2-Gene Patterns on Chromosome 17
<div><p>Background</p><p><i>HER2</i> and <i>TOP2A</i> gene status are assessed for diagnostic and research purposes in breast cancer with fluorescence in situ hybridization (FISH). However, FISH probes do not target only the annotated gene, while chromosome 17 (chr17) is among the most unstable chromosomes in breast cancer. Here we asked whether the status of specifically targeted genes on chr17 might help in refining prognosis of early high-risk breast cancer patients.</p><p>Methods</p><p>Copy numbers (CN) for 14 genes on chr17, 4 of which were within and 10 outside the core <i>HER2</i> amplicon (HER2- and non-HER2-genes, respectively) were assessed with qPCR in 485 paraffin-embedded tumor tissue samples from breast cancer patients treated with adjuvant chemotherapy in the frame of two randomized phase III trials.</p><p>Principal Findings</p><p><i>HER2</i>-genes CN strongly correlated to each other (Spearman’s rho >0.6) and were concordant with FISH <i>HER2</i> status (Kappa 0.6697 for <i>ERBB2</i> CN). <i>TOP2A</i> CN were not concordant with <i>TOP2A</i> FISH status (Kappa 0.1154). CN hierarchical clustering revealed distinct patterns of gains, losses and complex alterations in HER2- and non-HER2-genes associated with IHC4 breast cancer subtypes. Upon multivariate analysis, non-HER2-gene gains independently predicted for shorter disease-free survival (DFS) and overall survival (OS) in patients with triple-negative cancer, as compared to luminal and HER2-positive tumors (interaction p = 0.007 for DFS and p = 0.011 for OS). Similarly, non-HER2-gene gains were associated with worse prognosis in patients who had undergone breast-conserving surgery as compared to modified radical mastectomy (p = 0.004 for both DFS and OS). Non-HER2-gene losses were unfavorable prognosticators in patients with 1–3 metastatic nodes, as compared to those with 4 or more nodes (p = 0.017 for DFS and p = 0.001 for OS).</p><p>Conclusions</p><p><i>TOP2A</i> FISH and qPCR may not identify the same pathology on chr17q. Non-HER2 chr17 CN patterns may further predict outcome in breast cancer patients with known favorable and unfavorable prognosis.</p></div
Multivariate analysis models involving the main significant non-HER2-gene CN pattern effects on patient OS.
<p>Findings as for DFS in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103707#pone-0103707-g006" target="_blank">Figure 6</a>.</p
Multiple Correspondence Analyses graphs for comparing gene copies as assessed with qPCR and FISH.
<p><b>A:</b> Correspondence of <i>HER2</i> FISH (copies) to CN variables (n = 398). <b>B:</b> Correspondence of TOP2A FISH (copies) with CN variables co-expression (n = 393). Green: normal or loss; red: gain or amplification.</p
Demographic and clinicopathological characteristics of patients and tumors from HE10/00 & HE10/97 cohorts.
<p>*according to REMARK (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103707#pone-0103707-g001" target="_blank">Figure 1</a>);</p><p>∧NOS2, ERBB2, THRA, RARA, TOP2A; MRM = modified radical mastectomy; BCS = breast conserving surgery;</p><p>**E = epirubicin; T = paclitaxel (Taxol); C = cyclophosphamide; M = methotrexate; F = fluorouracil.</p
Significant interactions between non-HER2 gene CN clusters and clinicopathologic parameters affecting patient survival.
<p>In <b>A,</b> among patients with non-TNBC tumors those with non-HER2 gene CN gains fare best; among patients with TNBC, those with non-HER2 gains fare worse. In <b>B,</b> patients with favorable nodal status (1–3 metastatic lymph nodes) and tumors with non-HER2-gene CN losses have similarly bad outcome as those with unfavorable nodal status. In <b>C,</b> non-HER2-gene CN gains strikingly confer the opposite outcome to patients who have undergone modified radical mastectomy (MRM) as compared to breast-conserving surgery (BCS).</p
Multivariate analysis models involving the main significant non-HER2-gene CN genotype effects on patient DFS.
<p>Red circles: novel findings with potentially significant clinical implications, worthy pursuing for further validation. CN gains in non-HER2 genes on chr17 confer inverse risk for relapse in patients with TNBC and non-TNBC tumors, and in those who have undergone BCS in comparison to MRM. Similarly, the favorable 1–3 nodal status confers the same risk for relapse as the unfavorable disease with >3 positive nodes, if tumors have non-HER2-gene CN losses.</p
Hierarchical clustering of log transformed qPCR copy number (CN) values for chr17 genes in association with relevant breast cancer subtypes.
<p><b>A:</b> clustering of all 14 genes was informative in 376 cases and revealed 4 main CN patterns, out of which high CN for the HER2-related genes form the HER2 cluster and are predominantly found in HER2-positive (Luminal-HER2 and HER2-enriched) tumors; gains for the HER2 gene itself (ERBB2) mostly occur in parallel with STARD3. Luminal A and B, as well as TNBC are evenly represented in the non-HER2 clusters. <b>B:</b> If analyzing CN for the 4 HER2-related genes only, 36 of 93 tumors (38.7%) have non-continuous gains for these genes (complex pattern, red cluster) while the rest exhibit continuous gains in at least two genes, predominantly STARD3 and ERBB2 (gains, green cluster). <b>C:</b> Clustering of the non-HER2-related gene CN, i.e., 10 of 14 genes excluding STARD3, ERBB2, PSMD3 and THRA, yields 3 main clusters with equal representation of all subtypes (distribution of HER2-positive tumors and TNBC is shown). Cluster legend: natural log 0.69 corresponds to 2 copies; log 1.38 to 4 copies.</p
Concordance between FISH and qPCR CN classification of chromosome 17 gene status.
<p>Non-amplified: HER2/CEP17 ratio <2.2, TOP2A/CEP17 ratio <2;</p><p>*McNemar higher P-values indicate higher agreement.</p
Correlations of log transformed copy number (CN) values.
<p><b>A:</b> correlation map (clustered). <b>B:</b> Significant Spearman’s rho (<b>i, ii, iii</b>) and TOP2A correlations (<b>iv</b>). <b>Except for those marked with a black dot in B, all other correlations yielded p values <0.0001. However, concerning the degree of correlation (rho values),</b> the most significant correlations are observed for the examined genes within the core HER2 amplicon (boxed in <b>A</b>, part <b>i</b> in <b>B</b>). NOS2 (centromerically to ERBB2), as well as RARA and IGFBP4 (telomerically to THRA) correlate with the core <i>HER2</i> amplicon status (colored stars in <b>A</b>, part <b>ii</b> in <b>B</b>). Interestingly, the CN status of the <i>TOP2A</i> gene, which is located between RARA and IGFBP4, differs from the status of these two genes (black star in <b>A</b>); <i>TOP2A</i> CN are vaguely correlated to the other genes examined (part <b>iv</b> in <b>B</b>).</p
Tumor Infiltrating Lymphocytes Affect the Outcome of Patients with Operable Triple-Negative Breast Cancer in Combination with Mutated Amino Acid Classes
<div><p>Background</p><p>Stromal tumor infiltrating lymphocytes (TILs) density is an outcome predictor in triple-negative breast cancer (TNBC). Herein we asked whether TILs are related to coding mutation load and to the chemical class of the resulting mutated amino acids, i.e., charged, polar, and hydrophobic mutations.</p><p>Methods</p><p>We examined paraffin tumors from TNBC patients who had been treated with adjuvant chemotherapy mostly within clinical trials (training cohort, N = 133; validation, N = 190) for phenotype concordance; TILs density; mutation load and types.</p><p>Results</p><p>Concordance of TNBC phenotypes was 42.1% upon local / central, and 72% upon central / central pathology assessment. TILs were not associated with mutation load, type and class of mutated amino acids. Polar and charged mutation patterns differed between TP53 and PIK3CA (p<0.001). Hydrophobic mutations predicted for early relapse in patients with high nodal burden and <50% TILs tumors (training: HR 3.03, 95%CI 1.11–8.29, p = 0.031; validation: HR 2.90, 95%CI 0.97–8.70, p = 0.057), especially if compared to patients with >50% TILs tumors (training p = 0.003; validation p = 0.015).</p><p>Conclusions</p><p>TILs density is unrelated to mutation load in TNBC, which may be regarded as an unstable phenotype. If further validated, hydrophobic mutations along with TILs density may help identifying TNBC patients in higher risk for relapse.</p></div