Clonal relatedness in tumour pairs of breast cancer patients

Analysis of Shared Variants between Cancer Biospecimens

PURPOSE

Mutational data from multiple solid and liquid biospecimens of a single patient are often integrated to track cancer evolution. However, there is no accepted framework to resolve if individual samples from the same individual share variants due to common identity versus coincidence.

EXPERIMENTAL DESIGN

Utilizing 8,000 patient tumors from The Cancer Genome Atlas across 33 cancer types, we estimated the background rates of co-occurrence of mutations between discrete pairs of samples across cancers and by cancer type. We developed a mutational profile similarity (MPS) score that uses a large background database to produce confidence estimates that two tumors share a unique, related molecular profile. The MPS algorithm was applied to randomly paired tumor profiles, including patients who underwent repeat solid tumor biopsies sequenced with Memorial Sloan Kettering-IMPACT (n = 53,113). We also evaluated the MPS in sample pairs from single patients with multiple cancers (n = 2,012), as well as patients with plasma and solid tumor variant profiles (n = 884 patients).

RESULTS

In unrelated tumors, nucleotide-specific variants are shared in 1.3% (cancer-type agnostic) and in 10% to 13% (cancer-type specific) of cases. The MPS method contextualized shared variants to specify whether patients had a single cancer versus multiple distinct cancers. When multiple tumors were compared from the same patient and an initial clinicopathologic diagnosis was discordant with molecular findings, the MPS anticipated future diagnosis changes in 28% of examined cases.

CONCLUSIONS

The use of a novel shared variant framework can provide information to clarify the molecular relationship between compared biospecimens with minimal required input.

The role of 18F-FDG PET/CT in detecting synchronous regional and distant metastatic disease in patients with an in-breast tumour recurrence

BACKGROUND

In line with the trend towards minimally invasive, patient-tailored treatment, a selected group of patients with an in-breast tumour recurrence (IBTR) is treated by repeat breast-conserving treatment (BCT). To select eligible patients for repeat BCT, a reliable pre-operative work-up is essential. This study reports on the role of 18F-FDG PET/CT in detecting synchronous regional and distant metastases in patients with IBTR.

PATIENTS AND METHODS

A nation-wide data query was sent out to all Dutch hospitals offering breast cancer treatment. Breast cancer surgeons from 34 hospitals participated, filling electronic case report forms (eCRFs) on 549 patients treated for IBTR from 2016 to 2017.

RESULTS

Of the 549 included patients, 297 were screened using 18F-FDG PET/CT for the presence of distant metastases. Forty of them (13.5 %) presented with synchronous distant metastatic disease. In 168 clinically node-negative patients who underwent 18F-FDG PET/CT, a suspect regional lymph node was found in 18 (10.7 %). Final pathology of these lymph nodes yielded a positive lymph node in 12 patients (7.1 %). Positive predictive value (PPV) of 18F-FDG PET/CT in clinically node-negative patients was 66.7 % and negative predictive value (NPV) was 85.3 %.

CONCLUSION

The clinically relevant percentage of synchronous distant metastatic disease justifies the use of 18F-FDG PET/CT in the workup of patients with an IBTR. Furthermore, 18F-FDG PET/CT can assist in detecting regional axillary lymph node metastases, but requires histopathological confirmation given the moderate PPV, before clinical decisions can be made.

Misclassification of second primary and recurrent breast cancer in the surveillance epidemiology and end results registry

The Surveillance Epidemiology and End Results (SEER) registry incorporates laterality, histology, latency, and topography to identify second primary breast cancers. Contralateral tumors are classified as second primaries, but ipsilaterals are subject to additional inclusion criteria that increase specificity but may induce biases. It is important to understand how classification methods affect accuracy of second tumor classification. We collected estrogen, progesterone, and human epidermal growth factor receptor 2 (ER, PR, Her2) status for 11,838 contralateral and 5,371 ipsilateral metachronous secondary tumors and estimated concordance odds ratios (cORs) to evaluate receptor dependence (the tendency for tumors to share receptor status) by laterality. If only second primaries are included, receptor dependence should be similar for contralateral and ipsilateral tumors. Thus, we compared ratios of cORs as a measure of inaccuracy. Cases who met ipsilateral second primary criteria were younger and had less aggressive primary tumor characteristics compared to contralateral tumors. Time to secondary tumors was (by definition) longer for ipsilaterals than contralaterals, especially among ER + primaries. Overall and in multiple strata, ipsilateral tumors showed higher receptor dependence than contralateral tumors (ratios of cORs > 1), suggesting some SEER-included ipsilaterals are recurrences. SEER multiple primary criteria increase specificity, but remain inaccurate and may lack sensitivity. The dearth of early occurring ipsilateral tumors (by definition), coupled with high observed receptor dependence among ipsilaterals, suggests important inaccuracies. Datasets that allow comparison of pathologist- and SEER-classification to true multi-marker genomic dependence are needed to understand inaccuracies induced by SEER definitions.

Single Cell Expression Analysis of Ductal Carcinoma in Situ Identifies Complex Genotypic-Phenotypic Relationships Altering Epithelial Composition

To identify mechanisms underlying the growth of ductal carcinoma in situ (DCIS) and properties that lead to progression to invasive cancer, we performed single-cell RNA-sequencing (scRNA-seq) on DCIS lesions and matched synchronous normal breast tissue. Using inferred copy number variations (CNV), we identified neoplastic epithelial cells from the clinical specimens which contained a mixture of DCIS and normal ducts. Phylogenetic analysis based on the CNVs demonstrated intratumoral clonal heterogeneity was associated with significant gene expression differences. We also classified epithelial cells into mammary cell states and found that individual genetic clones contained a mixture of cell states suggesting an ongoing pattern of differentiation after neoplastic transformation. Cell state proportions were significantly different based on estrogen receptor (ER) expression with ER-DCIS more closely resembling the distribution in the normal breast, particularly with respect to cells with basal characteristics. Using deconvolution from bulk RNA-seq in archival DCIS specimens, we show that specific alterations in cell state proportions are associated with progression to invasive cancer. Loss of an intact basement membrane (BM) is the functional definition of invasive breast cancer (IBC) and scRNA-seq data demonstrated that ongoing transcription of key BM genes occurs in specific subsets of epithelial cell states. Examining BM in archival microinvasive breast cancers and an in vitro model of invasion, we found that passive loss of BM gene expression due to cell state proportion alterations is associated with loss of the structural integrity of the duct leading to an invasive phenotype. Our analyses provide detailed insight into DCIS biology.

SIGNIFICANCE

Single cell analysis reveals that preinvasive breast cancer is comprised of multiple genetic clones and there is substantial phenotypic diversity both within and between these clones. Ductal carcinoma in situ (DCIS) of the breast is a non-invasive condition commonly identified through mammographic screening. A primary diagnosis of DCIS carries little mortality risk on its own, but its presence is a risk factor for subsequent clonally related invasive breast cancer (IBC) (1-5).

Computational Methods Summarizing Mutational Patterns in Cancer: Promise and Limitations for Clinical Applications

Since the rise of next-generation sequencing technologies, the catalogue of mutations in cancer has been continuously expanding. To address the complexity of the cancer-genomic landscape and extract meaningful insights, numerous computational approaches have been developed over the last two decades. In this review, we survey the current leading computational methods to derive intricate mutational patterns in the context of clinical relevance. We begin with mutation signatures, explaining first how mutation signatures were developed and then examining the utility of studies using mutation signatures to correlate environmental effects on the cancer genome. Next, we examine current clinical research that employs mutation signatures and discuss the potential use cases and challenges of mutation signatures in clinical decision-making. We then examine computational studies developing tools to investigate complex patterns of mutations beyond the context of mutational signatures. We survey methods to identify cancer-driver genes, from single-driver studies to pathway and network analyses. In addition, we review methods inferring complex combinations of mutations for clinical tasks and using mutations integrated with multi-omics data to better predict cancer phenotypes. We examine the use of these tools for either discovery or prediction, including prediction of tumor origin, treatment outcomes, prognosis, and cancer typing. We further discuss the main limitations preventing widespread clinical integration of computational tools for the diagnosis and treatment of cancer. We end by proposing solutions to address these challenges using recent advances in machine learning.

Genomic analysis defines clonal relationships of ductal carcinoma in situ and recurrent invasive breast cancer

Ductal carcinoma in situ (DCIS) is the most common form of preinvasive breast cancer and, despite treatment, a small fraction (5-10%) of DCIS patients develop subsequent invasive disease. A fundamental biologic question is whether the invasive disease arises from tumor cells in the initial DCIS or represents new unrelated disease. To address this question, we performed genomic analyses on the initial DCIS lesion and paired invasive recurrent tumors in 95 patients together with single-cell DNA sequencing in a subset of cases. Our data show that in 75% of cases the invasive recurrence was clonally related to the initial DCIS, suggesting that tumor cells were not eliminated during the initial treatment. Surprisingly, however, 18% were clonally unrelated to the DCIS, representing new independent lineages and 7% of cases were ambiguous. This knowledge is essential for accurate risk evaluation of DCIS, treatment de-escalation strategies and the identification of predictive biomarkers.

Evaluating statistical approaches to define clonal origin of tumours using bulk DNA sequencing: context is everything

Clonal analysis of tumour sequencing data enables the evaluation of the relationship of histologically distinct synchronous lesions, such as co-existing benign areas, and temporally distinct tumours, such as primary-recurrence comparisons. In this review, we summarise statistical approaches that are commonly employed to define tumour clonal relatedness using data from bulk DNA technologies. We discuss approaches using total copy number, allele-specific copy number and mutation data, and the relative genomic resolution required for analysis and summarise some of the current tools for inferring clonal relationships. We argue that the impact of the biological context is critical in selecting any particular approach, such as the relative genomic complexity of the lesions being compared, and we recommend considering this context before employing any method to a new dataset.

Histologic Discordance Between Primary Tumor and Nodal Metastasis in Breast Cancer: Solving a Clinical Conundrum in the Era of Genomics

Next-generation sequencing (NGS) technologies have become increasingly used for managing breast cancer. In addition to the conventional use of NGS for predicting recurrence risk and identifying potential actionable mutations, NGS can also serve as a powerful tool to understand clonal origin and evolution of tumor pairs and play a unique role in clarifying complex clinical presentations. We report an unusual case of early-stage breast cancer in which the primary tumor and draining axillary node were histologically discordant. The primary tumor was invasive lobular carcinoma, whereas the nodal metastasis was invasive ductal carcinoma. This discordance led us to question whether the tumors had the same origin. NGS performed on both specimens identified no overlapping variants, leading us to conclude that the patient had two separate primary breast cancers, with the nodal tumor representing metastasis from an occult breast cancer. DNA sequencing of the primary tumor and the nodal metastasis allowed us to predict the patient's recurrence risk, and we initiated adjuvant chemotherapy and hormonal therapy based on these results. This case illustrates the utility of NGS for successfully managing a rare and challenging case. KEY POINTS: A degree of molecular concordance is expected for tumors originating from a common stem or progenitor cell. Histological discordance and absence of any genomic overlap should raise suspicion for two separate primary tumors. Paired DNA sequencing of the primary tumor and nodal metastasis can inform clinical decisions when primary breast tumor and axillary metastasis are histologically discordant. Molecular/Precision Oncology Tumor Board is the best setting to facilitate such decisions in these challenging cases. Paired DNA sequencing under these rare circumstances may suggest an occult breast tumor.

Genetic alterations associated with multiple primary malignancies

Breast cancer (BC) patients are frequently at risk of developing other malignancies following treatment. Although studies have been conducted to elucidate the etiology of multiple primary malignancies (MPM) after a BC diagnosis, few studies have investigated other previously diagnosed primary malignancies (OPPM) before BC. Here, genome‐wide profiling was used to identify potential driver DNA copy number alterations and somatic mutations that promote the development of MPMs. To compare the genomic profiles for two primary tumors (BC and OPPM) from the same patient, tumor pairs from 26 young women (≤50 years) diagnosed with one or more primary malignancies before breast cancer were analyzed. Malignant melanoma was the most frequent OPPM, followed by gynecologic‐ and hematologic malignancies. However, significantly more genetic alterations were detected in BC compared to the OPPM. BC also showed more genetic similarity as a group than the tumor pairs. Clonality testing showed that genetic alterations on chromosomes 1, 3, 16, and 19 were concordant in both tumors in 13 patients. TP53 mutations were also found to be prevalent in BC, MM, and HM. Although all samples were classified as genetically unstable, chromothripsis‐like patterns were primarily observed in BC. Taken together, few recurrent genetic alterations were identified in both tumor pairs that can explain the development of MPMs in the same patient. However, larger studies are warranted to further investigate key driver mutations associated with MPMs.

Mitochondrial DNA analysis efficiently contributes to the identification of metastatic contralateral breast cancers

Purpose

In daily practice, a contralateral breast cancer (CBC) is usually considered as a new independent tumor despite the indications of several studies showing that the second neoplasia may be a metastatic spread of the primary tumor. Recognition of clonal masses in the context of multiple synchronous or metachronous tumors is crucial for correct prognosis, therapeutic choice, and patient management. Mitochondrial DNA (mtDNA) sequencing shows high informative potential in the diagnosis of synchronous neoplasms, based on the fact that somatic mtDNA mutations are non-recurrent events, whereas tumors sharing them have a common origin. We here applied this technique to reveal clonality of the CBC with respect to the first tumor.

Methods

We analyzed 30 sample pairs of primary breast cancers and synchronous or metachronous CBCs with detailed clinical information available and compared standard clinico-pathological criteria with mtDNA sequencing to reveal the metastatic nature of CBCs.

Results

MtDNA analysis was informative in 23% of the cases, for which it confirmed a clonal origin of the second tumor. In addition, it allowed to solve two ambiguous cases where histopathological criteria had failed to be conclusive and to suggest a clonal origin for two additional cases that had been classified as independent by pathologists.

Conclusion

Overall, the mtDNA-based classification showed a more accurate predictive power than standard histopathology in identifying cases of metastatic rather than bilateral breast cancers in our cohort, suggesting that mtDNA sequencing may be a more precise and easy-to-use method to be introduced in daily routine to support and improve histopathological diagnoses.

Multicentric breast cancer with heterogeneous histopathology: a multidisciplinary review

Multiple synchronous (multifocal or multicentric) ipsilateral breast cancers with heterogeneous histopathology are a rare clinical occurrence, however, their incidence is increasing due to the use of MRI for breast cancer screening and staging. Some studies have demonstrated poorer clinical outcomes for this pattern of breast cancer, but there is no evidence to guide clinical practice. In this multidisciplinary review, we reflect on pathology and molecular characteristics, imaging findings, surgical management including conservation and reconstructive options and approach to the axilla, and the role of chemotherapy and radiotherapy. Multidisciplinary discussions appear decisive in planning an appropriate surgical choice and defining the correct systemic treatment tailored to each clinical condition.

Analysis of Copy-Number Variations and Feline Mammary Carcinoma Survival

Feline mammary carcinomas (FMCs) are highly malignant. As the disease-free survival (DFS) and overall survival (OS) are short, prognostication is crucial. Copy-number variations (CNVs) analysis by next-generation sequencing serves to identify critical cancer-related genomic regions. Thirty-three female cats with FMCs were followed during two years after surgery. Tumours represented tubulopapillary and solid carcinomas encompassing six molecular subtypes. Regardless of the histopathological diagnosis, molecular subtypes showed important differences in survival. Luminal A tumours exhibited the highest DFS (p = 0.002) and cancer-specific OS (p = 0.001), and the lowest amount of CNVs (p = 0.0001). In contrast, basal-like triple-negative FMCs had the worst outcome (DFS, p < 0.0001; and OS, p < 0.00001) and were the most aberrant (p = 0.05). In the multivariate analysis, copy-number losses (CNLs) in chromosome B1 (1-23 Mb) harbouring several tumour-repressors (e.g. CSMD1, MTUS1, MSR1, DBC2, and TUSC3) negatively influenced DFS. Whereas, copy-number gains (CNGs) in B4 (1-29 Mb) and F2 (64-82.3 Mb) comprising epithelial to mesenchymal transition genes and metastasis-promoting transcription factors (e.g. GATA3, VIM, ZEB1, and MYC) negatively influenced DFS and cancer-specific OS. These data evidence an association between specific CNVs in chromosomes B1, B4 and F2, and poor prognosis in FMCs.

Systemic investigations into the molecular features of bilateral breast cancer for diagnostic purposes

Introduction: Many breast cancer (BC) patients develop the disease bilaterally. The emergence of two tumors in the same host is unlikely to be a random co-incidence: bilateral BC (biBC) patients are enriched by women who are susceptible to this disease due to genetic or non-genetic factors.Areas covered: Data on molecular pathogenesis and translational aspects of biBC research are summarized.Expert opinion: Studies on concordant and discordant molecular events occurring in paired tumors resemble twin studies, as they help to reveal core components of BC pathogenesis and to analyze interactions between host factors and tumor phenotype. Mutation profiling of biBC pairs suggested that most biBCs are clonally independent malignancies, although some instances of presumably contralateral metastatic spread were shown as well. Many biBCs, especially synchronous ones, demonstrate the similarity of essential tumor characteristics, which can be explained by sharing of genetic background, hormonal milieu, metabolic environment, and external exposures. biBC is strongly associated with BC-predisposing germline mutations; therefore, clinical management of biBC patients must include comprehensive genetic testing. Some contralateral metachronous BCs demonstrate high-level microsatellite instability (MSI-H). MSI-H is sometimes observed in radiation- and chemotherapy-induced tumors; therefore, it is possible that some second BCs are causally related to the therapy applied for the first cancer. MSI-H tumors are responsive to immune checkpoint blockade; hence, MSI-H analysis is advisable for biBC molecular testing. Systematic cataloging of biBC molecular portraits is likely to provide valuable information on fundamental aspects of cancer pathogenesis.

Characterization of Recurrences Following Second Breast-Conserving Surgery with Intraoperative Radiotherapy

BACKGROUND

Breast-conserving surgery with breast re-irradiation is an emerging technique in the treatment of selected cases of locally recurrent breast cancer. Further information is needed to characterize factors that may select for an appropriate patient population for this treatment approach.

METHODS

We report herein a single-institution retrospective analysis of patients with ipsilateral breast cancer recurrence treated with a second breast-conserving therapy with intraoperative radiotherapy. Patient records were reviewed to analyze toxicity, further recurrence, and characteristics of recurrent patients following this treatment approach.

RESULTS

We included 57 patients in the analysis. At median follow-up of 24.5 months, ipsilateral breast tumor recurrence occurred in six patients (11%), four of which localized to the quadrant of the initial recurrent disease and two of which recurred elsewhere in the treated breast. Locoregional control was 89%, and disease-free survival was 81%. Only one patient was found to have grade 3 or greater toxicity.

CONCLUSION

A second breast-conserving surgery with intraoperative radiotherapy is tolerable with acceptable toxicity for patients with locally recurrent disease refusing mastectomy. Prospective clinical trials are needed to define the subset of patients who may be appropriate for this treatment approach as an alternative to mastectomy.

[Clinical challenges and implications of intratumor heterogeneity]

Tumors display a high, albeit variable, grade of intratumor heterogeneity, both from a clinical and a morphological viewpoint. Furthermore, recent methods of large-scale molecular analysis demonstrate to what extent tumors can also be heterogeneous from a molecular perspective. This is of paramount importance for patients as it has a great impact on the success of so-called precision therapies and explains the reason for a significant number of therapeutic failures in modern oncology. We present an up-to-date review of the latest findings in a group of tumors with a high social impact, commonly seen in the daily routine of the pathology laboratory.

Repeat breast-conserving therapy for ipsilateral breast cancer recurrence: A systematic review

The standard of care for patients with an ipsilateral breast tumour recurrence (IBTR) after breast-conserving therapy (BCT) is a salvage mastectomy. However, there is growing interest in the feasibility of repeat BCT for these patients. This systematic review contains the latest insights on BCT options for patients with an IBTR after initial BCT. A PubMed literature search was performed for articles on BCT options for IBTR after primary lumpectomy followed by radiotherapy. Weighted estimates were calculated for 5- and 10-year local control, distant metastasis-free and overall survival rates. Secondary outcomes were toxicity, cosmesis and quality of life. In total, 34 studies were eligible for analysis, of which 5 reported on repeat breast-conserving surgery (BCS) alone, 10 with mixed populations (BCS ± RT and/or mastectomy), 18 on repeat BCS followed by re-irradiation (whole-breast or partial) and one on quality of life. The weighted estimates for 5-year overall survival for repeat BCS and repeat BCS followed by reirradiation were 77% and 87%, respectively. Five-year local control was 76% for repeat BCS alone and 89% for repeat BCS followed by re-irradiation. Grade III-IV toxicity rates after re-irradiation varied from 0 to 21%, whereas the cosmesis was excellent-good in 29-100% of patients and unacceptable in 0-18%. Repeat BCS followed by re-irradiation, with either whole breast or partial breast re-irradiation, seems a feasible alternative to mastectomy in case of IBTR, in selected patients. Toxicity rates are low and the cosmetic outcome is good, but the size and follow-up of the published patient series is limited.