Epigenetic Alterations in Bone and Soft Tissue Tumors

Genetic and environmental reprogramming of the sarcoma epigenome

Sarcomas are rare and heterogenous mesenchymal tumors occurring in soft tissue and bone. The World Health Organization Classification of sarcomas comprises more than hundred different entities which are very diverse in their molecular, genetic and epigenetic signatures as they are in their clinical presentations and behaviors. While sarcomas can be associated with an underlying hereditary cancer predisposition, most sarcomas developed sporadically without identifiable cause. Sarcoma oncogenesis involves complex interactions between genetic, epigenetic and environmental factors which are intimately related and intensively studied. Several molecular discoveries have been made over the last decades leading to the development of new therapeutic avenues. Sarcoma research continues its effort toward a more specific and personalized approach to all sarcoma sub-types to improve patient outcomes and this through world-wide collaboration. This chapter on "Genetic and Environmental Reprogramming of the Sarcoma Epigenome" provides a comprehensive review of general concepts and epidemiology of sarcoma as well as a detailed description of the genetic, molecular and epigenetic alterations seen in sarcomas, their therapeutic implications and ongoing research. This review also presents evidenced-based data on the environmental and occupational factors possibly involved in the etiology of sarcomas and a brief discussion on the role of the microbiome in sarcoma.

Endometrial Stem/Progenitor cell (ES/PC) Marker Expression Profile in Adenosarcoma and Endometrial Stromal Sarcoma

BACKGROUND

The uterus is one of the most dynamic organs in the human body, and this dynamic homeostasis is supported by endometrial stem/progenitor cells (ES/PCs), which are heterogeneous in their phenotype and degree of differentiation. ES/PCs are generally localized in the endometrial stroma, the site of origin for adenosarcoma and endometrial stromal sarcoma (ESS). Subsets of ESSs and adenosarcomas harbor SUZ12 or DICER1 gene alterations, two genes with roles in embryonic stem cell biology. However, the possible contribution of ES/PCs to tumorigenesis is unexplored.

METHOD

We examined the expression of eleven ES/PC markers, along with three proteins expressed in the mature endometrial stroma (ER, PR and CD10) in 60 uterine tumors (24 low-, 11 high-grade ESS, 25 adenosarcomas). Protein expression profiles were assessed by unsupervised hierarchical clustering. miRNA expression profiles were examined in a subset of adenosarcoma with/without DICER1 mutations, using the NanoString platform.

RESULTS

ES/PC markers were variably expressed, and the tumors exhibited limited immunophenotypic resemblance to different ES/PCs. Within the ESSs, the ES/PC marker clustering pattern was prognostic for both overall and disease-free survival. Comparing adenosarcomas and ESSs, most high-grade ESSs clustered with one another, while low-grade ESSs and adenosarcomas tended to cluster with one another. Among the adenosarcomas, the miRNA expression profiles were varied with respect to the DICER1 mutation status, with pathway analysis pointing to dysregulated signal transduction and stem cell biology.

CONCLUSIONS

ESSs and adenosarcomas exhibit varying immunophenotypic resemblance to ES/PCs. These expression profiles have prognostic implications and may be genetically driven.

Histone Mutations and Bone Cancers

Primary bone tumors are rare cancers that cause significant morbidity and mortality. The recent identification of recurrent mutations in histone genes H3F3A and H3F3B within specific bone cancers, namely, chondroblastomas and giant cell tumors of bone (GCTB), has provided insights into the cellular and molecular origins of these neoplasms and enhanced understanding of how histone variants control chromatin function. Somatic mutations in H3F3A and H3F3B produce oncohistones, H3.3G34W and H3.3K36M, in more than nine of ten GCTB and chondroblastomas, respectively. Incorporation of the mutant histones into nucleosomes inhibits histone methyltransferases NSD2 and SETD2 to alter the chromatin landscape and change gene expression patterns that control cell proliferation, survival, and differentiation, as well as DNA repair and chromosome stability. The discovery of these histone mutations has facilitated more accurate diagnoses of these diseases and stratification of malignant tumors from benign tumors so that appropriate care can be delivered. The broad-scale epigenomic and transcriptomic changes that arise from incorporation of mutant histones into chromatin provide opportunities to develop new and disease-specific therapies. In this chapter, we review how mutant histones inhibit SETD2 and NSD2 function in bone tumors and discuss how this information could lead to better treatments for these cancers.

Locally Aggressive Giant Cell Tumor of Bone With Pulmonary Distant Metastasis and Extrapulmonary Seeding in Pregnancy

Giant cell tumor of bone (GCTB) is a locally aggressive benign neoplasm that is associated with a large biological spectrum ranging from latent benign to highly recurrent and occasionally metastatic tumor. In this article, we present a case of a 26-year-old woman who presented with swelling at the left lower ribs during pregnancy. Surgical excision was done, and histopathology showed tumor with features consistent with GCTB. MRI preformed after delivery revealed recurrence of the mass with extensive growth reaching 17 cm with two subcutaneous satellite nodules in the adjacent abdominal wall. positron emission tomography-computed tomography (PET-CT) scan revealed bilateral fluorodeoxyglucose (FDG)-avid lung nodules. Surgical resection was done, and histopathology showed no evidence of malignant transformation. Few months later, the tumor recurred again, with peritoneal deposits. The patient underwent wide massive resection of the recurrent mass and then started on denosumab therapy. Molecular analysis of the tumor detected H3F3A G34W mutation with no copy number alterations. We are presenting this case of GCTB with pulmonary distant metastasis and extrapulmonary seeding to upsurge awareness among clinicians about the possible extreme aggressive biological behavior of GCTB that can mimic the presentation of malignant bone tumor and also to discuss the possible predictive factors of such aggressive behavior.

Proteomic approaches for cancer epigenetics research

Introduction: Epigenetic dysregulation drives or supports numerous human cancers. The chromatin landscape in cancer cells is often marked by abnormal histone post-translational modification (PTM) patterns and by aberrant assembly and recruitment of protein complexes to specific genomic loci. Mass spectrometry-based proteomic analyses can support the discovery and characterization of both phenomena. Areas covered: We broadly divide this literature into two parts: 'modification-centric' analyses that link histone PTMs to cancer biology; and 'complex-centric' analyses that examine protein-protein interactions that occur de novo as a result of oncogenic mutations. We also discuss proteomic studies of oncohistones. We highlight relevant examples, discuss limitations, and speculate about forthcoming innovations regarding each application. Expert commentary: 'Modification-centric' analyses have been used to further understanding of cancer's histone code and to identify associated therapeutic vulnerabilities. 'Complex-centric' analyses have likewise revealed insights into mechanisms of oncogenesis and suggested potential therapeutic targets, particularly in MLL-associated leukemia. Proteomic experiments have also supported some of the pioneering studies of oncohistone-mediated tumorigenesis. Additional applications of proteomics that may benefit cancer epigenetics research include middle-down and top-down histone PTM analysis, chromatin reader profiling, and genomic locus-specific protein identification. In the coming years, proteomic approaches will remain powerful ways to interrogate the biology of cancer.