Primary cutaneous carcinosarcoma: insights into its clonal origin and mutational pattern expression analysis through next-generation sequencing

The Response of Triple-Negative Breast Cancer to Neoadjuvant Chemotherapy and the Epithelial–Mesenchymal Transition

It would be highly desirable to find prognostic and predictive markers for triple-negative breast cancer (TNBC), a strongly heterogeneous and invasive breast cancer subtype often characterized by a high recurrence rate and a poor outcome. Here, we investigated the prognostic and predictive capabilities of ARIADNE, a recently developed transcriptomic test focusing on the epithelial–mesenchymal transition. We first compared the stratification of TNBC patients obtained by ARIADNE with that based on other common pathological indicators, such as grade, stage and nodal status, and found that ARIADNE was more effective than the other methods in dividing patients into groups with different disease-free survival statistics. Next, we considered the response to neoadjuvant chemotherapy and found that the classification provided by ARIADNE led to statistically significant differences in the rates of pathological complete response within the groups.

Classification of triple negative breast cancer by epithelial mesenchymal transition and the tumor immune microenvironment

Triple-negative breast cancer (TNBC) accounts for about 15–20% of all breast cancers and differs from other invasive breast cancer types because it grows and spreads rapidly, it has limited treatment options and typically worse prognosis. Since TNBC does not express estrogen or progesterone receptors and little or no human epidermal growth factor receptor (HER2) proteins are present, hormone therapy and drugs targeting HER2 are not helpful, leaving chemotherapy only as the main systemic treatment option. In this context, it would be important to find molecular signatures able to stratify patients into high and low risk groups. This would allow oncologists to suggest the best therapeutic strategy in a personalized way, avoiding unnecessary toxicity and reducing the high costs of treatment. Here we compare two independent patient stratification strategies for TNBC based on gene expression data: The first is focusing on the epithelial mesenchymal transition (EMT) and the second on the tumor immune microenvironment. Our results show that the two stratification strategies are not directly related, suggesting that the aggressiveness of the tumor can be due to a multitude of unrelated factors. In particular, the EMT stratification is able to identify a high-risk population with high immune markers that is, however, not properly classified by the tumor immune microenvironment based strategy.

Classification of triple-negative breast cancers through a Boolean network model of the epithelial-mesenchymal transition

Predicting the metastasis risk in patients with a primary breast cancer tumor is of fundamental importance to decide the best therapeutic strategy in the framework of personalized medicine. Here, we present ARIADNE, a general algorithmic strategy to assess the risk of metastasis from transcriptomic data of patients with triple-negative breast cancer, a subtype of breast cancer with poorer prognosis with respect to the other subtypes. ARIADNE identifies hybrid epithelial/mesenchymal phenotypes by mapping gene expression data into the states of a Boolean network model of the epithelial-mesenchymal pathway. Using this mapping, it is possible to stratify patients according to their prognosis, as we show by validating the strategy with three independent cohorts of triple-negative breast cancer patients. Our strategy provides a prognostic tool that could be applied to other biologically relevant pathways, in order to estimate the metastatic risk for other breast cancer subtypes or other tumor types. A record of this paper's transparent peer review process is included in the supplemental information.

Trichoblastic carcinosarcoma in a 34-year-old woman with histopathologic and molecular analysis, including re-demonstration of a CDKN2A p.(R58*) mutation

Trichoblastic carcinosarcomas are rare, adnexal-type cutaneous carcinosarcomas that are thought to be related histogenetically to trichoblastomas, yet in which both the epithelial and stromal components show features of malignancy. Ten cases have been described in the literature thus far, with a predilection for the head and neck of older males. We present a case of cutaneous carcinosarcoma in sun-damaged skin of a 34-year-old woman showing features of a trichoblastic carcinosarcoma, with histopathologic analysis along with targeted next-generation sequencing of 50 cancer-associated genes. Two pathogenic variants in TP53 were identified, p.(R158C), p.(R273P), along with a likely pathogenic variant CDKN2A, p.(R58*). In particular, it is noted that the CDKN2A p.(R58*) missense mutation has been described in two previous cases of cutaneous carcinosarcomas, including a case of trichoblastic carcinosarcoma.

Cutaneous adnexal carcinosarcoma: Immunohistochemical and molecular evidence of epithelial mesenchymal transition

Cutaneous carcinosarcomas are rare biphenotypic tumors that simultaneously show epithelial and mesenchymal differentiation. The most common carcinomatous components in skin carcinosarcomas are basal cell carcinoma and squamous cell carcinoma; adnexal carcinomas are rarely encountered. We report a case of an adnexal carcinoma with ductal and squamous differentiation and spindle cell component, which is interpreted as carcinosarcoma. Loss of immunohistochemical expression of E-cadherin and β-catenin detected in the sarcomatous component suggested epithelial mesenchymal transition (EMT). RNA sequencing analysis identified several gene mutations and alterations such as translocations and upregulations/downregulations, either shared by the two components of the tumor or differentially present in the carcinoma or the sarcoma parts. Thus, mutations in genes, such as TP53, were found in both components of the tumor while mutations in PDGFRA and RB1 (a pathogenic missense mutation) were exclusively present in the sarcomatous areas, further supporting EMT. EMT is a dynamic process by which tumors acquire mesenchymal phenotype while simultaneously losing epithelial properties. Although the pathways involved in EMT have been extensively studied, this phenomenon still needs to be investigated in cutaneous tumors of adnexal origin for a better understanding of their pathogenesis. These molecular changes may represent promising targets for personalized therapies.

Pilomatrical carcinosarcoma of the temple: A case report

Pilomatrical carcinosarcoma is a very rare entity, with only six cases reported until now. This report describes the case of a 100-year-old woman with a mass on the left temple that had existed for several decades but had recently grown in size. Histology showed an asymmetric lesion composed of basaloid cells, spindle cells, and "shadow" or "ghost" cells. Cells had atypical hyperchromatic nuclei with prominent nucleoli, high mitotic activity, and atypical mitosis. In the central area, an epidermal cyst-like structure was seen. The diagnosis of pilomatrical carcinosarcoma was rendered. This case appeared to have arisen from malignant transformation of a pilomatricoma because of the long clinical history and existence of a benign epidermal cyst-like structure. In addition, the observation that the basaloid cells and spindle cells showed a gradual transition from one to the other and that both types were positive for β-catenin would seem to support a common clonal origin for the carcinomatous and sarcomatous components.

Explaining the dynamics of tumor aggressiveness: At the crossroads between biology, artificial intelligence and complex systems

Facing metastasis is the most pressing challenge of cancer research. In this review, we discuss recent advances in understanding phenotypic plasticity of cancer cells, highlighting the kinetics of cancer stem cell and the role of the epithelial mesenchymal transition for metastasis. It appears that the tumor micro-environment plays a crucial role in triggering phenotypic transitions, as we illustrate discussing the challenges posed by macrophages and cancer associated fibroblasts. To disentangle the complexity of environmentally induced phenotypic transitions, there is a growing need for novel advanced algorithms as those proposed in our recent work combining single cell data analysis and numerical simulations of gene regulatory networks. We conclude discussing recent developments in artificial intelligence and its applications to personalized cancer treatment.

Topography of epithelial-mesenchymal plasticity

The transition between epithelial and mesenchymal states has fundamental importance for embryonic development, stem cell reprogramming, and cancer progression. Here, we construct a topographic map underlying epithelial-mesenchymal transitions using a combination of numerical simulations of a Boolean network model and the analysis of bulk and single-cell gene expression data. The map reveals a multitude of metastable hybrid phenotypic states, separating stable epithelial and mesenchymal states, and is reminiscent of the free energy measured in glassy materials and disordered solids. Our work not only elucidates the nature of hybrid mesenchymal/epithelial states but also provides a general strategy to construct a topographic representation of phenotypic plasticity from gene expression data using statistical physics methods.

EMT and MET: necessary or permissive for metastasis?

Epithelial‐to‐mesenchymal transition (EMT) and its reverse mesenchymal‐to‐epithelial transition (MET) have been suggested to play crucial roles in metastatic dissemination of carcinomas. These phenotypic transitions between states are not binary. Instead, carcinoma cells often exhibit a spectrum of epithelial/mesenchymal phenotype(s). While epithelial/mesenchymal plasticity has been observed preclinically and clinically, whether any of these phenotypic transitions are indispensable for metastatic outgrowth remains an unanswered question. Here, we focus on epithelial/mesenchymal plasticity in metastatic dissemination and propose alternative mechanisms for successful dissemination and metastases beyond the traditional EMT/MET view. We highlight multiple hypotheses that can help reconcile conflicting observations, and outline the next set of key questions that can offer valuable insights into mechanisms of metastasis in multiple tumor models.

Comprehensive Genomic Profiling Aids in Distinguishing Metastatic Recurrence from Second Primary Cancers

BACKGROUND

Metastatic recurrence after treatment for locoregional cancer is a major cause of morbidity and cancer-specific mortality. Distinguishing metastatic recurrence from the development of a second primary cancer has important prognostic and therapeutic value and represents a difficult clinical scenario. Advances beyond histopathological comparison are needed. We sought to interrogate the ability of comprehensive genomic profiling (CGP) to aid in distinguishing between these clinical scenarios.

MATERIALS AND METHODS

We identified three prospective cases of recurrent tumors in patients previously treated for localized cancers in which histologic analyses suggested subsequent development of a distinct second primary. Paired samples from the original primary and recurrent tumor were subjected to hybrid capture next-generation sequencing-based CGP to identify base pair substitutions, insertions, deletions, copy number alterations (CNA), and chromosomal rearrangements. Genomic profiles between paired samples were compared using previously established statistical clonality assessment software to gauge relatedness beyond global CGP similarities.

RESULTS

A high degree of similarity was observed among genomic profiles from morphologically distinct primary and recurrent tumors. Genomic information suggested reclassification as recurrent metastatic disease, and patients received therapy for metastatic disease based on the molecular determination.

CONCLUSIONS

Our cases demonstrate an important adjunct role for CGP technologies in separating metastatic recurrence from development of a second primary cancer. Larger series are needed to confirm our observations, but comparative CGP may be considered in patients for whom distinguishing metastatic recurrence from a second primary would alter the therapeutic approach. The Oncologist 2017;22:152-157Implications for Practice: Distinguishing a metastatic recurrence from a second primary cancer can represent a difficult clinicopathologic problem but has important prognostic and therapeutic implications. Approaches to aid histologic analysis may improve clinician and pathologist confidence in this increasingly common clinical scenario. Our series provides early support for incorporating paired comprehensive genomic profiling in clinical situations in which determination of metastatic recurrence versus a distinct second primary cancer would influence patient management.

Lung Sarcomatoid Carcinoma Metastasis to Skin: A Case Report and Review of the Literature

Sarcomatoid carcinoma is a biphasic neoplasm composed of highly complex, intimately admixed malignant epithelial and mesenchymal elements. We herein report a rare case of cutaneous metastasis of pulmonary sarcomatoid carcinoma that contains liposarcomatous, rhabdosarcomatous and chondrosarcomatous heterologous differentiation, and review relevant literatures to lead to a better understanding of this rare but highly aggressive tumor.

Advances and Applications of Ion Torrent Personal Genome Machine in Cutaneous Squamous Cell Carcinoma Reveal Novel Gene Mutations

The Ion Torrent Personal Genome Machine (Ion PGM) is a semiconductor-based sequencing technology that is high quality, scalable, and economic. Its applications include genomic sequencing, drug resistance testing, microbial characterization, and targeted sequencing in cancer studies. However, little is known about the application of Ion PGM in cutaneous squamous cell carcinoma (cSCC). We therefore investigated the utility and validity of Ion PGM in cSCC and also gained a better understanding of the underlying molecular biology of cSCC. We detected novel gene mutations (KDR, FGFR2, and EGFR) in two cSCC patients. Moreover, we validated these mutations by pyrosequencing and Sanger sequencing. Our results indicated that the mutation screen using Ion PGM is consistent with traditional sequencing methods. Notably, these identified mutations were present at significantly higher rates in high-risk cSCC. Our results demonstrate a method to detect targetable genes in high-risk cSCC, and suggest that Ion PGM may enable therapeutic decision-making and future potential targets for personalized therapies in cSCC.

Significance of circulating tumor cells in soft tissue sarcoma

Circulating tumor cells can be detected from the peripheral blood of cancer patients. Their prognostic value has been established in the last 10 years for metastatic colorectal, breast, and prostate cancer. On the contrary their presence in patients affected by sarcomas has been poorly investigated. The discovery of EpCAM mRNA expression in different sarcoma cell lines and in a small cohort of metastatic sarcoma patients supports further investigations on these rare tumors to deepen the importance of CTC isolation. Although it is not clear whether EpCAM expression might be originally present on tumor sarcoma cells or acquired during the mesenchymal-epithelial transition, the discovery of EpCAM on circulating sarcoma cells opens a new scenario in CTC detection in patients affected by a rare mesenchymal tumor.

Cutaneous basal cell carcinosarcomas: evidence of clonality and recurrent chromosomal losses

Cutaneous carcinosarcomas are heterogeneous group of tumors composed of malignant epithelial and mesenchymal components. Although mutation analyses have identified clonal changes between these morphologically disparate components in some subtypes of cutaneous carcinosarcoma, few cases have been analyzed thus far. To our knowledge, copy number variations (CNVs) and copy-neutral loss of heterozygosity (CN-LOH) have not been investigated in cutaneous carcinosarcomas. We analyzed 4 carcinosarcomas with basal cell carcinoma and osteosarcomatous components for CNVs/CN-LOH by comparative genomic hybridization/single-nucleotide polymorphism array, TP53 hot spot mutations by polymerase chain reaction and Sanger sequencing, and TP53 genomic rearrangements by fluorescence in situ hybridization. All tumors displayed multiple CNV/CN-LOH events (median, 7.5 per tumor). Three of 4 tumors displayed similar CNV/CN-LOH patterns between the epithelial and mesenchymal components within each tumor, supporting a common clonal origin. Recurrent changes included allelic loss at 9p21 (CDKN2A), 9q (PTCH1), and 17p (TP53). Allelic losses of chromosome 16 including CDH1 (E-cadherin) were present in 2 tumors and were restricted to the sarcomatous component. TP53 mutation analysis revealed an R248L mutation in both epithelial and mesenchymal components of 1 tumor. No TP53 rearrangements were identified. Our findings indicate that basal cell carcinosarcomas harbor CNV/CN-LOH changes similar to conventional basal cell carcinoma, with additional changes including recurrent 9p21 losses and a relatively high burden of copy number changes. In addition, most cutaneous carcinosarcomas show evidence of clonality between epithelial and mesenchymal components.

Carcinosarcoma of the parotid: investigating its biology with morphoproteomics

Carcinosarcoma of the parotid is a rare biphasic malignant neoplasm comprised of both carcinomatous and sarcomatous components representing approximately 0.4% of all malignant salivary gland neoplasms. We report a case of a 55-year-old Caucasian man who presented with a progressively enlarging left facial mass. Histopathological evaluation of the tumoral tissue revealed a high grade, mixed epithelial and mesenchymal malignant tumor, most consistent with a carcinosarcoma of the parotid. Morphoproteomic analysis was performed and revealed expression of secreted protein acidic and rich in cysteine (SPARC); glioma-associated oncogen protein 2 (Gli2); and phosphorylated signal transducer and activator of transcription (p-STAT3 [Tyr705]) in the carcinomatous and malignant mesenchymal components. These aforementioned markers have been linked to the epithelial-mesenchymal transition in which epithelial cells lose their characteristics and phenotypically become mesenchymal cells. This finding allows us to further understand the biology of the 2 cellular components of the carcinosarcoma as having a monoclonal origin.

Epithelial cell adhesion molecule is expressed in a subset of sarcomas and correlates to the degree of cytological atypia in leiomyosarcomas

Epithelial cell adhesion molecule (EpCAM) is a protein involved in cell-to-cell attachment and is considered to be strictly expressed in epithelial tissues and epithelial-derived tumors. Furthermore, EpCAM has been shown to be a negative prognostic marker for several carcinomas. In this study, we performed a genomic meta-analysis of gene expression profiles housed in the Cancer Cell Line Encyclopedia to demonstrate that EpCAM mRNA is expressed at low to moderate levels in certain sarcoma cell lines. We utilized immunohistochemical staining to confirm that the EpCAM protein is expressed in a subset of angiosarcomas and leiomyosarcomas and in all the investigated osteosarcomas. Finally, we conducted a statistical analysis of clinical data to demonstrate that EpCAM protein expression is significantly and directly correlated with the degree of cytological atypia in leiomyosarcomas. In conclusion, this data suggests that, contrary to conventional beliefs, EpCAM is expressed in a subset of sarcomas and is a negative prognostic marker for leiomyosarcomas.