Clinicopathologic and Genomic Features in Triple-Negative Breast Cancer Between Special and No-Special Morphologic Pattern

Abstract

Background: Triple-negative breast cancer (TNBC) is refractory and heterogeneous, comprising various entities with divergent phenotype, biology, and clinical presentation. As an aggressive subtype, Chinese TNBC patients with special morphologic patterns (STs) were restricted to its incidence of 10-15% in total TNBC population.

Methods: We recruited 89 patients with TNBC at Guangdong Provincial People's Hospital (GDPH) from October 2014 to May 2021, comprising 72 cases of invasive ductal carcinoma of no-special type (NSTs) and 17 cases of STs. The clinical data of these patients was collected and statistically analyzed. Formalin-fixed, paraffin-embedded (FFPE) tumor tissues and matched blood samples were collected for targeted next-generation sequencing (NGS) with cancer-related, 520- or 33-gene assay. Immunohistochemical analysis of FFPE tissue sections was performed using anti-programmed cell death-ligand 1(PD-L1) and anti-androgen receptor antibodies.

Results: Cases with NSTs presented with higher histologic grade and Ki-67 index rate than ST patients (NSTs to STs: grade I/II/III 1.4%, 16.7%,81.9% vs 0%, 29.4%, 58.8%; p<0.05; Ki-67 ≥30%: 83.3% vs. 58.8%, p<0.05), while androgen receptor (AR) and PD-L1 positive (combined positive score≥10) rates were lower than of STs cases (AR: 11.1% vs. 47.1%; PD-L1: 9.6% vs. 33.3%, p<0.05). The most commonly altered genes were TP53 (88.7%), PIK3CA (26.8%), MYC (18.3%) in NSTs, and TP53 (68.8%), PIK3CA (50%), JAK3 (18.8%), KMT2C (18.8%) in STs respectively. Compared with NSTs, PIK3CA and TP53 mutation frequency showed difference in STs (47.1% vs 19.4%, p=0.039; 64.7% vs 87.5%, p=0.035).

Conclusions: In TNBC patients with STs, decrease in histologic grade and ki-67 index, as well as increase in PD-L1 and AR expression were observed when compared to those with NSTs, suggesting that TNBC patients with STs may better benefit from immune checkpoint inhibitors and/or AR inhibitors. Additionally, lower TP53 and higher PIK3CA mutation rates were also found in STs patients, providing genetic evidence for deciphering at least partly potential mechanism of action.

Keywords: Chinese breast cancer; PD-L1 (22C3); mutation landscape; special type; triple negative breast cancer.

Figure 1

Invasive ductal carcinoma of no-special type and special morphologic pattern of triple negative breast cancers. (A) Invasive ductal carcinoma; (B) Apocrine carcinoma (Carcinoma with apocrine differentiation); (C) Metaplastic breast carcinoma; (D) Medullary carcinoma; (E) Glycogen-rich clear cell carcinoma; (F) Mixed type.

Figure 2

The landscape of genetic alterations in TNBC. Top 50 genomic alterations are shown in the Oncoprint. Different colors denote different types of alterations and different clinicopathologic features. (A) Summary of the features of the genomic alteration of the 89 patients with TNBC. Tumor samples were grouped according to histologic types as: no-special type (NSTs, n = 72) and special type (STs, n = 17). The top bar shows the histologic type of each patient; the side bar (rows) summarizes the percentage of tumors with alterations in each gene (left) and alteration composition for each gene in the entire cohort (right). (B) Summary of the features of the genomic mutation of the 89 patients with TNBC. Tumor samples were grouped according to histologic types as: no-special type (NSTs, n = 72) and special type (STs, n = 17). The top bar shows the histologic type of each patient; the side bar (rows) summarizes the percentage of tumors with mutations in each gene (left), and the mutation composition for each gene in the entire cohort (right). (C) Summary of copy number variations and Fusion in the 45 patients with TNBC who carry copy number variations. Tumor samples were grouped according to histologic types as: no-special type (NSTs, n = 38) and special type (STs, n = 7). The top bar shows each patient’s histologic type; the side bar (rows) summarizes the percentage of tumors with variation in each gene (left) and alteration composition for each gene (right), in the entire cohort. (D) Summary of germline mutation of the 62 patients with TNBC. Tumor samples were grouped according to histologic types as: no-special type (NSTs, n = 48) and special type (STs, n = 14). The side bar (rows) summarizes the percentage of tumors with mutation in each gene (left) and alteration composition for each gene (right), in the entire cohort. TNBC, triple-negative breast cancer; NST, no-special type; ST, special type; indel, insertions or deletions; LGR, large genomic rearrangement; CN_amp, copy number amplification; CN_del, copy number deletion.

Figure 3

(A) Summary of genomic features of the 72 NST cases of TNBC patients. (B) Summary of genomic features of the 17 ST cases of TNBC patients. (C) Differentially mutated genes between NSTs and STs TNBC patients. The X-axis represents the specific genes. The Y-axis represents the percentage of samples with mutations in a specific gene. * indicated p values <0.05. TNBC, triple-negative breast cancer; NST, no-special type; ST, special type.

Figure 4

Lollipop diagram of the TP53 and PIK3CA domains with the mutation location identified in TNBC patients. Different types of mutations were colored by different colored dots, and each colored dot represents one mutation. The length of the lollipop represents the number of patients harboring a specific variant. (A) The type and location of TP53 mutation in NST patients. (B) The type and location of TP53 mutation in ST patients. (C) The type and location of PIK3CA mutation in NST patients. (D) The type and location of PIK3CA mutation in ST patients. TNBC, triple-negative breast cancer; NST, no-special type; ST, special type.

Figure 5

Kyoto Encyclopedia of Genes and Genomes analysis reveals distinct pathways in NSTs and STs tumors of TNBC. In total, 36.2% of the NSTs patients and 78.6% of the STs patients had at least one clinically relevant genomic alteration in genes involved in the PI3K-AKT signaling pathways, respectively. (A) Summary of the features of the PI3K-AKT signaling pathways genomic alteration of the 32 patients with TNBC. Tumor samples were grouped according to histologic types as: no-special type (IDC-NSTs, n=21) and special type (STs, n=11). (B) Comparison of the features of the PI3K-AKT signaling pathways genomic alteration between NSTs and STs TNBC patients. (C) Comparison of the features of the PI3K-AKT signaling pathways genomic alteration among STs TNBC patients. TNBC, triple-negative breast cancer; NST, no-special type; ST, special type; TMB, tumor mutation burden.