Genomic, Transcriptomic, Epigenetic, and Immune Profiling of Mucinous Breast Cancer

Clinicopathological characteristics and genomic profiling of pure mucinous breast cancer

PURPOSE

Pure mucinous breast cancer (PMC) is a rare histological type with a favourable prognosis. However, cases with recurrence have been reported and diagnosed in clinical practice. The mechanisms underlying PMC recurrence remain unknown. In this study, we aimed to identify the prognostic factors associated with PMC.

MATERIALS AND METHODS

A total of 166 patients diagnosed with PMC were included. We compared the clinicopathological characteristics between patients with and without recurrence. The 21-gene assay was performed in 10 patients with recurrence and 20 TNM stage-matched patients without recurrence. Whole-exon sequencing was performed in 12 PMC primary tumours and four positive lymph nodes (LNs).

RESULTS

Tumour size, lymph node status and TNM staging differed significantly between recurrent group and non-recurrent group. And the 21-gene recurrence scores did not differ significantly between recurrent group and its TNM stage-matched non-recurrent group. The most frequently mutated genes in the primary tumours of regional LN-positive PMCs were ADCY10 (3/6) and SHANK3 (3/6), and they more recurrently harboured gains of 15q23, 17q23.2 and 20p11.21, and loss of 21p11.2. And these alterations were not detected in primary tumours of regional LN-negative PMCs.

CONCLUSION

TNM stage is an important prognostic factor in PMC. Although we revealed that regional LN-positive PMCs show increased occurrence of duplication variants at 15q23, 17q23.2 and 20p11.21, and deletion variants at 21p11.2. Further investigation, including multi-omics studies, are needed and may provide additional insights into the nature of PMC.

Molecular Classification of Breast Cancer

Breast carcinomas classified based on traditional morphologic assessment provide useful prognostic information. Although morphology is still the gold standard of classification, recent advances in molecular technologies have enabled the classification of these tumors into four distinct subtypes based on its intrinsic molecular profile that provide both predictive and prognostic information. This article describes the association between the different molecular subtypes with the histologic subtypes of breast cancer and illustrates how these subtypes may affect the appearance of tumors on imaging studies.

Spectrum of Mucin-containing Lesions of the Breast: Multimodality Imaging Review with Pathologic Correlation

Mucin-containing lesions of the breast encompass a wide range of benign and malignant processes. The spectrum of histologic findings includes incidental mucus-filled benign cysts or ducts, mucocele-like lesions (MLLs), mucin-producing ductal carcinoma in situ, and invasive mucinous carcinoma. MLL is characterized by the presence of mucin-containing cysts that are typically associated with extravasated stromal mucin. MLL is often benign but can be associated with epithelial atypia or malignancy. Mucinous carcinoma represents the malignant end of the spectrum of mucinous lesions of the breast. Evidence-based literature supports a conservative approach for benign MLLs without associated atypia or malignancy, reserving excision for those lesions exhibiting such pathologic features. The most common imaging finding for MLL is microcalcifications at mammography. No specific imaging feature is predictive of malignant outcome at surgical excision. Invasive mucinous carcinoma is a heterogeneous breast tumor subtype, as defined according to the World Health Organization criteria. Mucinous carcinomas are categorized into pure (>90% mucinous component) or mixed (10%-90% mucinous component) subtypes. Pure mucinous carcinomas are generally associated with excellent prognosis and survival, with a few exceptions. Mixed mucinous carcinomas do not have the same favorable prognosis and instead behave similarly to invasive breast carcinomas of no special type. Characteristic diagnostic imaging features can be identified for mucinous carcinoma based on its mucinous and nonmucinous contents. ©RSNA, 2023 Online supplemental material is available for this article. Quiz questions for this article are available through the Online Learning Center.

TCGA RNA-Seq and Tumor-Infiltrating Lymphocyte Imaging Data Reveal Cold Tumor Signatures of Invasive Ductal Carcinomas and Estrogen Receptor-Positive Human Breast Tumors

Comparative studies of immune-active hot and immune-deserted cold tumors are critical for identifying therapeutic targets and strategies to improve immunotherapy outcomes in cancer patients. Tumors with high tumor-infiltrating lymphocytes (TILs) are likely to respond to immunotherapy. We used the human breast cancer RNA-seq data from the cancer genome atlas (TCGA) and classified them into hot and cold tumors based on their lymphocyte infiltration scores. We compared the immune profiles of hot and cold tumors, their corresponding normal tissue adjacent to the tumor (NAT), and normal breast tissues from healthy individuals from the Genotype-Tissue Expression (GTEx) database. Cold tumors showed a significantly lower effector T cells, lower levels of antigen presentation, higher pro-tumorigenic M2 macrophages, and higher expression of extracellular matrix (ECM) stiffness-associated genes. Hot/cold dichotomy was further tested using TIL maps and H&E whole-slide pathology images from the cancer imaging archive (TCIA). Analysis of both datasets revealed that infiltrating ductal carcinoma and estrogen receptor ER-positive tumors were significantly associated with cold features. However, only TIL map analysis indicated lobular carcinomas as cold tumors and triple-negative breast cancers (TNBC) as hot tumors. Thus, RNA-seq data may be clinically relevant to tumor immune signatures when the results are supported by pathological evidence.

Mucinous carcinoma of the breast: distinctive histopathologic and genetic characteristics

Mucinous carcinoma is a rare histologic type of breast cancer that, when classified with favorable histology, can be treated with different therapeutic options. This study reviews the histologic findings of mucinous carcinoma that support or exclude favorable histology and emphasizes the necessity of an appropriate gross examination with radiologic findings for an accurate diagnosis. In addition, unusual findings such as micropapillary arrangements and lobular differentiation in mucinous carcinoma and their implications for prognosis and treatment are reviewed. Mucinous carcinoma involves upregulation of MUC2, a mucus-associated gene common in mucinous carcinoma of the breast as well as various other organs. In mucinous carcinoma, the fraction of genome altered and tumor mutation burden are lower than those of invasive carcinoma of no special type, the most common histology of breast cancer. In addition, the genetic alterations found in mucinous carcinoma are diverse, unlike the pathognomonic genetic alterations observed in other histologic types of breast cancer. These genetic features support the importance of conventional microscopic evaluations for the pathologic differential diagnosis of mucinous carcinoma of the breast in routine practice. A variety of breast lesions, including mucinous cystadenocarcinoma and mucocele-like lesions, as well as mucinous carcinoma from other organs, can mimic mucinous carcinoma of the breast. In order to obtain an accurate pathologic diagnosis, careful evaluation of the overall histopathologic characteristics and ancillary testing are required to provide information on appropriate treatment and prognosis.

Neuroendocrine tumours of the breast: a genomic comparison with mucinous breast cancers and neuroendocrine tumours of other anatomic sites

AIMS

Breast neuroendocrine tumours (NETs) constitute a rare histologic subtype of oestrogen receptor (ER)-positive breast cancer, and their definition according to the WHO classification was revised in 2019. Breast NETs display histologic and transcriptomic similarities with mucinous breast carcinomas (MuBCs). Here, we sought to compare the repertoire of genetic alterations in breast NETs with MuBCs and NETs from other anatomic origins.

METHODS

On histologic review applying the new WHO criteria, 18 breast tumours with neuroendocrine differentiation were reclassified as breast NETs (n=10) or other breast cancers with neuroendocrine differentiation (n=8). We reanalysed targeted sequencing or whole-exome sequencing data of breast NETs (n=10), MuBCs type A (n=12) and type B (n=11).

RESULTS

Breast NETs and MuBCs were found to be genetically similar, harbouring a lower frequency of PIK3CA mutations, 1q gains and 16q losses than ER-positive/HER2-negative breast cancers. 3/10 breast NETs harboured the hallmark features of ER-positive disease (ie, PIK3CA mutations and concurrent 1q gains/16q losses). Breast NETs showed an enrichment of oncogenic/likely oncogenic mutations affecting transcription factors compared with common forms of ER-positive breast cancer and with pancreatic and pulmonary NETs.

CONCLUSIONS

Breast NETs are heterogeneous and are characterised by an enrichment of mutations in transcription factors and likely constitute a spectrum of entities histologically and genomically related to MuBCs. While most breast NETs are distinct from ER-positive/HER2-negative IDC-NSTs, a subset of breast NETs appears to be genetically similar to common forms of ER-positive breast cancer, suggesting that some breast cancers may acquire neuroendocrine differentiation later in tumour evolution.

The genomic landscape of carcinomas with mucinous differentiation

Mucinous carcinomas can arise in any organ with epithelial cells that produce mucus. While mucinous tumors from different organs are histologically similar, it remains to be elucidated whether they share molecular alterations. Here we analyzed a total of 902 patients across six cancer types by comparing mucinous and non-mucinous samples, integrating text mining of pathology reports, gene expression, methylation, mutational and copy-number profiling. We found that, in addition to genes involved in mucin processing and secretion, MUC2 up-regulation is a multi-cancer biomarker of mucinous histology and is regulated by DNA methylation in colorectal, breast and stomach cancer. The majority of carcinomas with mucinous differentiation had fewer DNA copy-number alterations than non-mucinous tumors. The tumor mutational burden was lower in breast and lung with mucinous differentiation compared to their non-mucinous counterparts. We found several differences in the frequency of oncogenic gene and pathway alterations between mucinous and non-mucinous carcinomas, including a lower frequency of p53 pathway alterations in colorectal and lung cancer, and a lower frequency of PI-3-Kinase/Akt pathway alterations in breast and stomach cancer with mucinous differentiation. This study shows that carcinomas with mucinous differentiation originating from different organs share transcriptomic and genomic similarities. These results might pave the way for a more biologically relevant taxonomy for these rare cancers.

Clinicopathological and Molecular Analysis of 45 Cases of Pure Mucinous Breast Cancer

Pure mucinous breast carcinoma (PMBC) is characterized by clusters of tumor cells floating in abundant extracellular mucin and can be classified into paucicellular (Type A) and hypercellular (Type B) subtypes. However, the clinicopathological and genomic differences between these two subtypes have not been well characterized. We retrospectively investigated the clinicopathologic features of 45 cases of surgically removed PMBC (31 Type A and 14 Type B). We also performed whole-exome sequencing (WES) in eight cases of PMBC. We found that Type B PMBC occurs at an older age and shows more aggressive clinical behavior than Type A. WES analysis revealed that HYDIN was the most frequently mutated gene in both types of PMBC. Although Type B PMBC showed a tendency toward more frequent genetic alterations, there were no statistically significant differences between the two subtypes in single nucleotide variants or insertions or deletions of bases associated with moderate or high effects. Our results provide additional evidence that PMBCs are clinicopathologically and genetically heterogeneous and lack pathognomonic genetic alterations. Further, Type B PMBC is more frequently associated with lymph node metastasis than Type A.

Problematic breast tumors reassessed in light of novel molecular data

Breast cancer is a vastly heterogeneous disease encompassing a panoply of special histological subtypes. Although rare breast tumors have largely not been investigated systematically in large scale genomics series, recent studies have shed light on the genetic underpinnings of special histologic subtypes of breast cancer. Genomic analyses of estrogen receptor-positive special histologic types of breast cancer have not resulted in the identification of novel pathognomonic genetic alterations in addition to the confirmation of the presence of CDH1 loss-of-function mutations in invasive lobular carcinomas. By contrast, the analyses of triple-negative breast cancers have demonstrated that low-grade triple-negative breast cancers categorically differ from the common forms of high-grade triple-negative disease biologically and phenotypically and are underpinned by specific fusion genes or hotspot mutations. A subset of low-grade triple-negative disease has been shown to harbor highly recurrent if not pathognomonic genetic alterations, such as ETV6-NTRK3 fusion gene in secretory carcinomas, the MYB-NFIB fusion gene, MYBL1 rearrangements or MYB gene amplification in adenoid cystic carcinomas, and HRAS Q61 hotspot mutations coupled with mutations in PI3K pathway genes in estrogen receptor-negative adenomyoepitheliomas. A subset of these pathognomonic genetic alterations (e.g., NTRK1/2/3 fusion genes) now constitute an FDA approved indication for the use of TRK inhibitors in the advanced/metastatic setting. These studies have also corroborated that salivary gland-like tumors of the breast, other than acinic cell carcinomas, harbor the repertoire of somatic genetic alterations detected in their salivary gland counterparts. Reassuringly, the systematic study of special histologic types of breast cancer utilizing state-of-the-art sequencing approaches, rather than rendering pathology obsolete, has actually strengthened the importance of breast cancer histologic typing and is providing additional ancillary markers for the diagnosis of these rare but fascinating entities.

Integrative Analysis of DNA Methylation Identified 12 Signature Genes Specific to Metastatic ccRCC

Background: Abnormal epigenetic alterations can contribute to the development of human malignancies. Identification of these alterations for early screening and prognosis of clear cell renal cell carcinoma (ccRCC) has been a highly sought-after goal. Bioinformatic analysis of DNA methylation data provides broad prospects for discovery of epigenetic biomarkers. However, there is short of exploration of methylation-driven genes of ccRCC.

Methods: Gene expression data and DNA methylation data in metastatic ccRCC were sourced from the Gene Expression Omnibus (GEO) database. Differentially methylated genes (DMGs) at 5′-C-phosphate-G- 3′ (CpG) sites and differentially expressed genes (DEGs) were screened and the overlapping genes in DMGs and DEGs were then subject to gene set enrichment analysis. Next, the weighted gene co-expression network analysis (WGCNA) was used to search hub DMGs associated with ccRCC. Cox regression and ROC analyses were performed to screen potential biomarkers and develop a prognostic model based on the screened hub genes.

Results: Three hundred and fourteen overlapping DMGs were obtained from two independent GEO datasets. The turquoise module contained 79 hub DMGs, which represent the most significant module screened by WGCNA. Furthermore, a total of 12 hub genes (CETN3, DCAF7, GPX4, HNRNPA0, NUP54, SERPINB1, STARD5, TRIM52, C4orf3, C12orf51, and C17orf65) were identified in the TCGA database by multivariate Cox regression analyses. All the 12 genes were then used to generate the model for diagnosis and prognosis of ccRCC. ROC analysis showed that these genes exhibited good diagnostic efficiency for metastatic and non-metastatic ccRCC. Furthermore, the prognostic model with the 12 methylation-driven genes demonstrated a good prediction of 5-year survival rates for ccRCC patients.

Conclusion: Integrative analysis of DNA methylation data identified 12 signature genes, which could be used as epigenetic biomarkers for prognosis of metastatic ccRCC. This prognostic model has a good prediction of 5-year survival for ccRCC patients.

The genomic landscape of metastatic histologic special types of invasive breast cancer

Histologic special types of breast cancer (BC) account for ~20% of BCs. Large sequencing studies of metastatic BC have focused on invasive ductal carcinomas of no special type (IDC-NSTs). We sought to define the repertoire of somatic genetic alterations of metastatic histologic special types of BC. We reanalyzed targeted capture sequencing data of 309 special types of BC, including metastatic and primary invasive lobular carcinomas (ILCs; n = 132 and n = 127, respectively), mixed mucinous (n = 5 metastatic and n = 14 primary), micropapillary (n = 12 metastatic and n = 8 primary), and metaplastic BCs (n = 6 metastatic and n = 5 primary), and compared metastatic histologic special types of BC to metastatic IDC-NSTs matched according to clinicopathologic characteristics and to primary special type BCs. The genomic profiles of metastatic and primary special types of BC were similar. Important differences, however, were noted: metastatic ILCs harbored a higher frequency of genetic alterations in TP53, ESR1, FAT1, RFWD2, and NF1 than primary ILCs, and in CDH1, PIK3CA, ERBB2, TBX3, NCOR1, and RFWD2 than metastatic IDC-NSTs. Metastatic ILCs displayed a higher mutational burden, and more frequently dominant APOBEC mutational signatures than primary ILCs and matched metastatic IDC-NSTs. ESR1 and NCOR mutations were frequently detected in metastatic mixed mucinous BCs, whereas PIK3CA and TP53 were the most frequently altered genes in metastatic micropapillary and metaplastic BCs, respectively. Taken together, primary and metastatic BCs histologic special types have remarkably similar repertoires of somatic genetic alterations. Metastatic ILCs more frequently harbor APOBEC mutational signatures than primary ILCs and metastatic IDC-NSTs.

New Advances in Molecular Breast Cancer Pathology

Breast cancer (BC) comprises a diverse spectrum of diseases featuring distinct presentation, morphological, biological, and clinical phenotypes. BC behaviour and response to therapy also vary widely. Current evidence indicates that traditional prognostic and predictive classification systems are insufficient to reflect the biological and clinical heterogeneity of BC. Advancements in high-throughput molecular techniques and bioinformatics have contributed to the improved understanding of BC biology, refinement of molecular taxonomies and the development of novel prognostic and predictive molecular assays. Molecular testing has also become increasingly important in the diagnosis and treatment of BC in the era of precision medicine. Despite the enormous amount of research work to develop and refine BC molecular prognostic and predictive assays, it is still in evolution and proper incorporation of these molecular tests into clinical practice to guide patient's management remains a challenge. With the increasing use of more sophisticated high throughput molecular techniques, large amounts of data will continue to emerge, which could potentially lead to identification of novel therapeutic targets and allow more precise classification systems that can accurately predict outcome and response to therapy. In this review, we provide an update on the molecular classification of BC and molecular prognostic assays. Companion diagnostics, contribution of massive parallel sequencing and the use of liquid biopsy are also highlighted.

Breast Cancer: A Molecularly Heterogenous Disease Needing Subtype-Specific Treatments

Breast cancer is the most commonly occurring cancer in women. There were over two-million new cases in world in 2018. It is the second leading cause of death from cancer in western countries. At the molecular level, breast cancer is a heterogeneous disease, which is characterized by high genomic instability evidenced by somatic gene mutations, copy number alterations, and chromosome structural rearrangements. The genomic instability is caused by defects in DNA damage repair, transcription, DNA replication, telomere maintenance and mitotic chromosome segregation. According to molecular features, breast cancers are subdivided in subtypes, according to activation of hormone receptors (estrogen receptor and progesterone receptor), of human epidermal growth factors receptor 2 (HER2), and or BRCA mutations. In-depth analyses of the molecular features of primary and metastatic breast cancer have shown the great heterogeneity of genetic alterations and their clonal evolution during disease development. These studies have contributed to identify a repertoire of numerous disease-causing genes that are altered through different mutational processes. While early-stage breast cancer is a curable disease in about 70% of patients, advanced breast cancer is largely incurable. However, molecular studies have contributed to develop new therapeutic approaches targeting HER2, CDK4/6, PI3K, or involving poly(ADP-ribose) polymerase inhibitors for BRCA mutation carriers and immunotherapy.

Breast cancer histologic subtypes show excess familial clustering

BACKGROUND

The inherited predisposition to developing specific histologic subtypes of invasive breast carcinoma has been incompletely investigated. By using a large, population-based database, the authors sought to investigate familial clustering of breast cancer by histologic subtype.

METHODS

By using the Utah Population Database, which links genealogy records to the National Cancer Institute's statewide Surveillance, Epidemiology, and End Results cancer registry, the authors identified patients with breast cancer by histology and tested for evidence of shared genetic predisposition to histologic specific subtypes by examining pairwise relatedness and estimating the relative risk (RR) among first-degree, second-degree, and third-degree relatives.

RESULTS

The authors identified 23,629 individuals in the Utah Population Database who had at least 3 generations of genealogy and at least 1 primary breast cancer, 2883 (12.2%) of which were specific histologic subtypes other than invasive ductal carcinoma (including inflammatory [n = 178], lobular [n = 1688], and mucinous [n = 542]). Statistically significant excess distant relatedness was identified for the mucinous subtype (P = .011) as well as for inflammatory breast cancers (P = .024). The RR for breast cancer of any histology in second-degree relatives was significantly increased for patients with inflammatory (RR, 1.32; 95% CI, 1.02-1.68; P = .03), lobular (RR, 1.36; 95% CI, 1.25-1.47; P < .001), and mucinous (RR, 1.27; 95% CI, 1.12-1.44; P = .00021) subtypes.

CONCLUSIONS

These findings provide evidence for significant familial clustering within histological subtypes for lobular, mucinous, and inflammatory breast carcinomas. Further research is required to identify the underlying genetic variants responsible for the increased risk. Studies of high-risk pedigrees segregating a specific histologic subtype could be a powerful design for predisposition gene identification.