Formation of the 12q14-q15 Amplicon Precedes the Development of a Well-differentiated Liposarcoma Arising From a nonchondroid Pulmonary Hamartoma

Primary intrathoracic liposarcomas: A clinicopathologic and molecular study of 43 cases in one of the largest medical centers of China

Introduction

Primary intrathoracic liposarcoma is extremely rare, and most published series lack genetic analyses. The aim of our study is to better understand the clinicopathologic and genetic features of these rare lesions.

Materials and methods

Forty-three primary intrathoracic liposarcomas were identified and most cases were analyzed by systematic genetic studies, including fluorescence in situ hybridization (FISH), whole-exome sequencing (WES), and Sanger sequencing.

Results

This series included 27 males and 16 females (ratios, 1.68:1) aged 24-73 years (median, 53 years). Tumors mainly occurred in the mediastinum (n=23, 53.5%), followed by pleural cavity (n=16, 37.2%) and lung (n=4, 9.3%). The study included 21 well-differentiated liposarcomas (WDLs), 19 dedifferentiated liposarcomas (DDLs), 2 myxoid pleomorphic liposarcomas (MPLs) and 1 pleomorphic liposarcoma (PL), without identification of myxoid liposarcoma. FISH analysis identified MDM2 amplification in 17 of 18 WDLs (94.4%) and all DDLs (16/16, 100.0%). The MDM2-nonamplified WDL was CDK4-nonamplified but FRS2-amplified. WES and Sanger sequencing found somatic TP53 mutation in the 2 MPLs. Follow-up information was available for 33 of 38 cases (86.8%). Thirteen patients (39.4%) showed no evidence of disease, 10 patients (30.3%) were alive with disease, and 8 patients (24.2%) died of disease. Fourteen cases developed recurrence and 1 with metastasis.

Conclusions

WDL/DDL was the overwhelming subtype in this location, followed by MPL and PL. Analysis of the FRS2 gene, in combination with MDM2 and other genes of 12q13-15, may more precisely characterize WDL/DDLs. MPL is the most fatal subtype of this site. Further studies are needed to explore the role of TP53 in the pathogenesis of MPL.

An experimental model for the study of well-differentiated and dedifferentiated liposarcoma; deregulation of targetable tyrosine kinase receptors

Therapeutic progress in well-differentiated/dedifferentiated liposarcoma (WDLPS/DDLPS) is hampered by lack of relevant experimental models, thereby limiting comprehensive molecularly based investigations. Our goal is to bridge this experimental gap by establishing and characterizing an in vitro/in vivo model useful for examining WDLPS/DDLPS molecular pathogenesis and also therapeutic screening and testing. WDLPS/DDLPS cells were isolated from freshly resected human surgical specimens and were phenotypically and molecularly characterized. MDM2 amplification was determined via FISH analysis. Adipogenic differentiation was evaluated using Oil Red O staining and western blotting (WB). Tyrosine kinase receptors' (TKRs) expression in pre-adipocytes, adipocytes, WDLPS, and DDLPS cells was determined via western blot analysis. SCID mouse xenograft growth was assessed after subcutaneous and/or intraperitoneal tumor cell injection. There was enhanced proliferation, migration, invasion, survival, and pro-angiogenic capacity in DDLPS cells vs WDLPS cells. DDLPS cells formed tumors in SCID mice whereas WDLPS did not. WDLPS/DDLPS cells, especially those that exhibited baseline PPARγ expression, partially retained terminal adipogenic differentiation capacity. MDM2 amplification was found in all WDLPS/DDLPS cell strains, CDK4 overexpression was observed in LPS cells as compared with normal adipocytes, and enhanced JUN expression and phosphorylation was seen in DDLPS cells as compared with WDLPS cells. The TKRs: MET, AXL, KIT, and IGF-1R were overexpressed in LPS cells vs normal adipocytes and pre-adipocytes. In conclusion, these newly established cellular and xenograft models can facilitate investigation of liposarcomagenesis, dedifferentiation, and tumor progression. Further studies of the molecular deregulations so identified may lead to improved therapeutic strategies for patients afflicted by these unfavorable malignancies.

Latent factor analysis to discover pathway-associated putative segmental aneuploidies in human cancers

Tumor microenvironmental stresses, such as hypoxia and lactic acidosis, play important roles in tumor progression. Although gene signatures reflecting the influence of these stresses are powerful approaches to link expression with phenotypes, they do not fully reflect the complexity of human cancers. Here, we describe the use of latent factor models to further dissect the stress gene signatures in a breast cancer expression dataset. The genes in these latent factors are coordinately expressed in tumors and depict distinct, interacting components of the biological processes. The genes in several latent factors are highly enriched in chromosomal locations. When these factors are analyzed in independent datasets with gene expression and array CGH data, the expression values of these factors are highly correlated with copy number alterations (CNAs) of the corresponding BAC clones in both the cell lines and tumors. Therefore, variation in the expression of these pathway-associated factors is at least partially caused by variation in gene dosage and CNAs among breast cancers. We have also found the expression of two latent factors without any chromosomal enrichment is highly associated with 12q CNA, likely an instance of “trans”-variations in which CNA leads to the variations in gene expression outside of the CNA region. In addition, we have found that factor 26 (1q CNA) is negatively correlated with HIF-1α protein and hypoxia pathways in breast tumors and cell lines. This agrees with, and for the first time links, known good prognosis associated with both a low hypoxia signature and the presence of CNA in this region. Taken together, these results suggest the possibility that tumor segmental aneuploidy makes significant contributions to variation in the lactic acidosis/hypoxia gene signatures in human cancers and demonstrate that latent factor analysis is a powerful means to uncover such a linkage.

Gene signatures are a powerful tool to investigate biological processes in human cancer. However, it is clear that these gene signatures do not fully reflect the complexity of human cancer. Here we demonstrate how a latent factor model can improve the in vivo relevance of these pathway-associated gene signatures by dissecting them into co-regulated transcriptional components which better represent the structure in human cancer. We use this approach to analyze hypoxia and lactic acidosis gene signatures to identify latent factors that represent distinct, interacting components of the various biological processes which are in the initial gene signatures but poorly dissected. Some factors are clustered in small chromosomal regions and their expression values are highly correlated with their DNA copy number in both cancer cell lines and human tumors. Therefore, the gene dosage at the DNA levels may explain the differences in gene expression. Several factors contain genes which are known to directly modulate the hypoxia response and allow us to generate testable hypotheses regarding particular copy number changes and hypoxia signatures. Therefore, the use of latent factor analysis is a powerful means to identify pathway-associated changes in the DNA copy number and gene dosage.

Carboxypeptidase M: a biomarker for the discrimination of well-differentiated liposarcoma from lipoma

The discrimination between well-differentiated liposarcomas/atypical lipomatous tumors and lipomas can be diagnostically challenging at the histological level. However, cytogenetic identification of ring and giant rod chromosomes supports the diagnosis of well-differentiated liposarcoma/atypical lipomatous tumor. These abnormal chromosomes are mainly composed of amplified genomic sequences derived from chromosome 12q13-15, and contain several genes, including MDM2, CDK4 (SAS), TSPAN31, HMGA2, and others. MDM2 is consistently amplified in well-differentiated liposarcomas/atypical lipomatous tumors, and up to 25% in other sarcomas. As part of a large genomic study of lipomatous neoplasms, we initially found CPM to be consistently amplified in well-differentiated liposarcomas/atypical lipomatous tumors. To further explore this initial finding, we investigated the copy number status of MDM2 and CPM by fluorescent in situ hybridization (FISH) on a series of 138 tumors and 17 normal tissues, including 32 well-differentiated liposarcoma/atypical lipomatous tumors, 63 lipomas, 11 pleomorphic lipomas, 2 lipoblastomas, 30 other tumors and 17 normal fat samples. All 32 well-differentiated liposarcoma/atypical lipomatous tumors showed amplification of MDM2 and CPM, usually >20 copies per cell. The other tumors lacked MDM2 and/or CPM amplification. Chromogenic in situ hybridization confirmed the above results on a subset of these tumors (n=27). These findings suggest that identification of CPM amplification could be used as an alternative diagnostic tool for the diagnosis of well-differentiated liposarcoma/atypical lipomatous tumors.

Pseudosarcomatous fibroblastic/myofibroblastic proliferation in perinephric adipose tissue adjacent to renal cell carcinoma: a lesion mimicking well-differentiated liposarcoma

Cytologically atypical stromal cells were found in the perinephric adipose tissue, mimicking well-differentiated liposarcoma in 12 of 59 (20%) consecutive nephrectomy specimens that were resected for renal cell carcinoma. Morphologically, the atypical cells included enlarged, hyperchromatic spindle cells and floret-type multinucleate cells. Of 59, 10 (17%) renal cell carcinomas invaded through the renal capsule into the perinephric adipose tissue. Of these cases, three (30%) contained the aforementioned atypical cells. In contrast, 9 of 49 cases without extrarenal invasion (18%) contained the atypical stromal cells. Of the 12 cases with atypical stromal cells, 3 (25%) were associated with extrarenal involvement. The atypical spindle cells exhibited focal to variable positivity for smooth muscle actin and desmin in 3 of the 14 cases (including two cases from our consultation files) each. Cytokeratin AE1/AE3, cytokeratin Cam 5.2, cytokeratin 7, epithelial membrane antigen, and S-100 were negative in all cases. Amplification of MDM2 gene region, which is commonly observed in well-differentiated liposarcoma, was absent by fluorescence in situ hybridization (FISH) in the atypical stromal cells. Immunohistochemistry and FISH suggest that the atypical cells are most consistent with reactive fibroblasts/myofibroblasts. Recognition of these atypical fibroblasts/myofibroblasts may help in avoiding the potential pitfall of misdiagnosing them as well-differentiated liposarcoma.

Aggressive angiomyxoma with t(12;21) and HMGA2 rearrangement: report of a case and review of the literature

Conventional cytogenetic analysis of an aggressive angiomyxoma of the rectal wall of a 72-year-old woman revealed a translocation between the long arms of chromosomes 12 and 21, with the karyotype 46,XX,t(12;21)(q15;q21.1). Involvement of the HMGA2 gene locus (12q15) was confirmed by fluorescence in situ hybridization using an HMGA2 breakpoint flanking probe set performed on metaphase and interphase cells from an in situ culture of fresh lesional tissue. Karyotypic rearrangements of 12q13 approximately q15 are considered recurrent in aggressive angiomyxoma, although reported in only five previous cases. Translocation partner chromosome 21 is unique to the present case.

Pulmonary chondroma: a tumor associated with Carney triad and different from pulmonary hamartoma

The Carney triad is the clinical association of gastric stromal sarcomas, pulmonary cartilaginous tumors, and extra-adrenal paragangliomas. The pulmonary tumors are its second commonest component and have been misinterpreted clinically and pathologically as metastases from the gastric tumors and pulmonary cartilaginous hamartomas, respectively. They have not been previously described in detail in the pathology literature or compared with pulmonary cartilaginous hamartomas. Forty-two patients with pulmonary cartilaginous tumors as a component of Carney triad were identified. Clinical, radiographic, and pathologic findings in the cases were tabulated. Hematoxylin and eosin-stained sections of the neoplasms were evaluated for a series of histologic features. A subgroup of 41 tumors from the latter was compared with those in a group of pulmonary cartilaginous hamartomas. Patients with Carney triad group were predominantly young women. Their pulmonary neoplasm(s) were usually asymptomatic, often multiple, well circumscribed, medium-sized (mean diameter=2.8 cm), and composed almost exclusively of cartilage and bone surrounded by a fibrous pseudocapsule. The cartilage was usually myxoid, less frequently hyaline, and commonly calcified, ossified, or both. They showed no fat, smooth muscle or entrapped respiratory epithelium, tissues that were common in pulmonary hamartoma (P<0.0001). None of the tumors metastasized or was fatal. The pulmonary neoplasms in the Carney triad are well-differentiated benign cartilaginous tumors that are best designated as chondromas. They differ pathologically from pulmonary cartilaginous hamartomas on the basis of the presence of a thin fibrous pseudocapsule, frequent bone metaplasia, and calcification, and also the absence of entrapped epithelium and fat.

HMGA2 regulates transcription of the Imp2 gene via an intronic regulatory element in cooperation with nuclear factor-kappaB

IMP2 (insulin-like growth factor-II mRNA binding protein 2) is an oncofetal protein that is aberrantly expressed in several types of cancer. We recently identified the Imp2 gene as a target gene of the architectural transcription factor HMGA2 (high mobility group A2) and its tumor-specific truncated form HMGA2Tr. In this study, we investigated the mechanism via which HMGA2 regulates Imp2 gene expression. We show that HMGA2 and HMGA2Tr directly regulate transcription of the Imp2 gene by binding to an AT-rich regulatory region located in the first intron. In reporter experiments, we show that this AT-rich regulatory region mimics the response of the endogenous Imp2 gene to HMGA2 and HMGA2Tr. Furthermore, we show that a consensus nuclear factor-kappaB (NF-kappaB) binding site located immediately adjacent to the AT-rich regulatory region binds NF-kappaB and that NF-kappaB and HMGA2 cooperate to regulate Imp2 gene expression. Finally, we provide evidence that there is a strong and statistically significant correlation between HMGA2 and IMP2 gene expression in human liposarcomas.