Distinct IDH1/2-associated Methylation Profile and Enrichment of TP53 and TERT Mutations Distinguish Dedifferentiated Chondrosarcoma from Conventional Chondrosarcoma

Dedifferentiated chondrosarcoma (DDCS) is a rare high-grade chondrosarcoma characterized by a well-differentiated chondrosarcoma (WDCS) component that abruptly transitions to a high-grade, noncartilaginous sarcomatous component. To date, the molecular pathogenesis of DDCS and its distinction from conventional chondrosarcoma remain poorly understood. By targeted sequencing, we examined the mutational and copy-number profiles of 18 DDCS, including macrodissected WDCS components, compared with 55 clinically sequenced conventional chondrosarcomas. In conjunction with publicly available external data, we analyzed the methylation and expression profiles of 34 DDCS and 94 conventional chondrosarcomas. Isocitrate dehydrogenase 1/isocitrate dehydrogenase 2 (IDH1/IDH2) mutations were present in 36% conventional chondrosarcomas and 71% DDCS. Compared with conventional chondrosarcomas, DDCS had higher frequencies of TP53 and TERT promoter mutations and CDKN2A/B copy-number losses. Paired analysis of macrodissected WDCS and the high-grade components revealed TERT promoter mutations as early events. Despite phenotypic similarities, the percentage of genome with copy-number alterations in DDCS was significantly lower than that in other high-grade sarcomas. Differential methylation analysis revealed reduction of IDH1/IDH2-associated global hypermethylation characteristically seen in conventional chondrosarcoma and a distinct methylation profile in DDCS. The WDCS and high-grade components in DDCS showed similar methylation profiles. These CpG sites were associated with upregulated expression of genes involved in G2-M checkpoints and E2F targets. Genomic profiling revealed enrichment of TP53, TERT promoter, and CDKN2A/B alterations in DDCS. Integrated methylation and gene expression analysis revealed distinct IDH1/IDH2-associated methylation and transcriptional profiles as early events in DDCS, which may underlie the pathogenesis of dedifferentiation in chondrosarcomas.

Significance

DDCS is a rare, high-grade chondrosarcoma with a dismal prognosis. About 50%-80% of DDCS harbor IDH1/IDH2 mutations. We uncover a significant alteration of IDH-associated methylation profile in DDCS, which we propose is key to the progression to dedifferentiation. In this context, the potential effect of the use of IDH inhibitors is unclear but important to address, as clinical trials of selective IDH1 inhibitors showed worse outcome in DDCS.

Malignancies in Pleural, Peritoneal, and Pericardial Effusions

CONTEXT.—

The incidence and types of malignancies in effusion cytology are largely limited to studies performed in the 1970s through the 1990s.

OBJECTIVE.—

To examine how the incidence of different types of malignancies in effusions has changed with time.

DESIGN.—

A computerized search for fluid cytology from 2000 through 2016 (database included age, gender, cytologic diagnosis, and type of malignancy) was performed, and all cases were reviewed.

RESULTS.—

Of 30 085 effusion specimens, 3285 (11%) were positive for malignancy (2175 pleural, 955 peritoneal, and 155 pericardial). Of those, 1023 (31%) had known primary sites (648 pleural, 267 peritoneal, and 108 pericardial). Malignancy was more common in females than males in both pleural (15% versus 9%) and peritoneal (14% versus 5%) effusions (P < .001). The most common metastatic tumors in pleural fluid were lung for males and breast for females; in peritoneal fluid, hematolymphoid for males and Müllerian tumors for females; in pericardial fluid, lung for both genders. Among invasive mammary carcinomas, lobular carcinoma tended to metastasize to peritoneal fluid, whereas ductal carcinoma tended to metastasize to pleural fluid (P < .001). Plasma cell neoplasms metastasized to pleural and pericardial but not peritoneal fluid (P = .002).

CONCLUSIONS.—

Although pulmonary and Müllerian tumors continue to be the most common origin of metastasis in pleural and peritoneal fluid for males and females, respectively, the frequencies for other malignancies have changed. Familiarity with the more common sites of metastasis in effusion cytology is important, especially in patients with unknown primary, as this will be valuable in judicious triaging of specimens for ancillary studies.

Ovarian Torsion in an Adolescent with Beckwith-Wiedemann Syndrome and Unilateral Tubo-ovarian Hyperplasia

BACKGROUND

Beckwith-Wiedemann syndrome (BWS) is the most common pediatric overgrowth syndrome. BWS has a broad phenotypic presentation along with an increased propensity to develop various embryonal tumors. There are very few reported cases of gonadal hyperplasia in BWS patients in the existing literature.

CASE

We describe a 13-year-old girl with BWS who presented with an episode of abdominal pain and was found to have torsion and necrosis of a markedly hyperplastic right ovary and fallopian tube. We present a brief literature review on ovarian hyperplasia in BWS patients for which we used an online search of the databases PubMed, Embase, Ovid Medline, and Cochrane.

RESULTS AND CONCLUSION

Through an extensive literature search, we only found 3 previous reports of ovarian hyperplasia in BWS patients, all in postmortem specimens. Our case highlights a potentially important aspect of visceral organ hyperplasia in patients with BWS that could remain indolent until adolescence and might present as an abrupt-onset abdominopelvic catastrophe.

Candida pneumonia with severe clinical course, recovery with antifungal therapy and unusual pathologic findings: A case report

BACKGROUND

Candida is frequently isolated from the respiratory tract and usually reflects airway colonization. True Candida pneumonia is rare. Our aim is to document a case of Candida pneumonia confirmed by cultures, molecular techniques, and surgical lung biopsy, and to highlight a previously unreported pathologic manifestation of this infection.

CASE SUMMARY

A 59-year-old man with a history of chronic obstructive pulmonary disease (COPD) presented with dry cough, low-grade fever, and progressive dyspnea. He was eventually diagnosed with sarcoidosis based on bilateral lung infiltrates and granulomas in a transbronchial biopsy. His condition worsened after immunosuppression, prompting surgical lung biopsy, which revealed suppurative granulomas containing Candida albicans, confirmed by cultures and polymerase chain reaction. Despite multiple episodes of respiratory failure and a prolonged course in intensive care, he recovered fully after antifungal therapy and is currently alive with COPD-related dyspnea 3 years after his initial presentation.

CONCLUSION

Candida can rarely cause clinically significant pneumonia in adults, and should be considered in the differential diagnosis of suppurative granulomas in the lung.

Hypoxia sensing through -adrenergic receptors

Life-sustaining responses to low oxygen, or hypoxia, depend on signal transduction by HIFs, but the underlying mechanisms by which cells sense hypoxia are not completely understood. Based on prior studies suggesting a link between the β-adrenergic receptor (β-AR) and hypoxia responses, we hypothesized that the β-AR mediates hypoxia sensing and is necessary for HIF-1α accumulation. Beta blocker treatment of mice suppressed hypoxia induction of renal HIF-1α accumulation, erythropoietin production, and erythropoiesis in vivo. Likewise, beta blocker treatment of primary human endothelial cells in vitro decreased hypoxia-mediated HIF-1α accumulation and binding to target genes and the downstream hypoxia-inducible gene expression. In mechanistic studies, cAMP-activated PKA and/or GPCR kinases (GRK), which both participate in β-AR signal transduction, were investigated. Direct activation of cAMP/PKA pathways did not induce HIF-1α accumulation, and inhibition of PKA did not blunt HIF-1α induction by hypoxia. In contrast, pharmacological inhibition of GRK, or expression of a GRK phosphorylation-deficient β-AR mutant in cells, blocked hypoxia-mediated HIF-1α accumulation. Mass spectrometry-based quantitative analyses revealed a hypoxia-mediated β-AR phosphorylation barcode that was different from the classical agonist phosphorylation barcode. These findings indicate that the β-AR is fundamental to the molecular and physiological responses to hypoxia.

Pharmacological Targeting of the Histone Chaperone Complex FACT Preferentially Eliminates Glioblastoma Stem Cells and Prolongs Survival in Preclinical Models

The nearly universal recurrence of glioblastoma (GBM) is driven in part by a treatment-resistant subpopulation of GBM stem cells (GSC). To identify improved therapeutic possibilities, we combined the EGFR/HER2 inhibitor lapatinib with a novel small molecule, CBL0137, which inhibits FACT (facilitates chromatin transcription), a histone chaperone complex predominantly expressed in undifferentiated cells. Lapatinib and CBL0137 synergistically inhibited the proliferation of patient-derived GBM cells. Compared with non-stem tumor cells (NSTC) enriched from the same specimens, the GSCs were extremely sensitive to CBL0137 monotherapy or FACT knockdown. FACT expression was elevated in GSCs compared with matched NSTCs and decreased in GSCs upon differentiation. Acute exposure of GSCs to CBL0137 increased asymmetric cell division, decreased GSC marker expression, and decreased the capacity of GSCs to form tumor spheres in vitro and to initiate tumors in vivo Oral administration of CBL0137 to mice bearing orthotopic GBM prolonged their survival. Knockdown of FACT reduced the expression of genes encoding several core stem cell transcription factors (SOX2, OCT4, NANOG, and OLIG2), and FACT occupied the promoters of these genes. FACT expression was elevated in GBM tumors compared with non-neoplastic brain tissues, portended a worse prognosis, and positively correlated with GSC markers and stem cell gene expression signatures. Preferential targeting of GSCs by CBL0137 and synergy with EGFR inhibitors support the development of clinical trials combining these two agents in GBM. Cancer Res; 76(8); 2432-42. ©2016 AACR.

Quinacrine overcomes resistance to erlotinib by inhibiting FACT, NF-κB, and cell-cycle progression in non-small cell lung cancer

Erlotinib is a tyrosine kinase inhibitor approved for the treatment of patients with advanced non-small cell lung cancer (NSCLC). In these patients, erlotinib prolongs survival but its benefit remains modest because many tumors express wild-type (wt) EGFR or develop a second-site EGFR mutation. To test drug combinations that could improve the efficacy of erlotinib, we combined erlotinib with quinacrine, which inhibits the FACT (facilitates chromatin transcription) complex that is required for NF-κB transcriptional activity. In A549 (wtEGFR), H1975 (EGFR-L858R/T790M), and H1993 (MET amplification) NSCLC cells, this drug combination was highly synergistic, as quantified by Chou-Talalay combination indices, and slowed xenograft tumor growth. At a sub-IC50 but more clinically attainable concentration of erlotinib, quinacrine, alone or in combination with erlotinib, significantly inhibited colony formation and induced cell-cycle arrest and apoptosis. Quinacrine decreased the level of active FACT subunit SSRP1 and suppressed NF-κB-dependent luciferase activity. Knockdown of SSRP1 decreased cell growth and sensitized cells to erlotinib. Moreover, transcriptomic profiling showed that quinacrine or combination treatment significantly affected cell-cycle-related genes that contain binding sites for transcription factors that regulate SSRP1 target genes. As potential biomarkers of drug combination efficacy, we identified genes that were more strongly suppressed by the combination than by single treatment, and whose increased expression predicted poorer survival in patients with lung adenocarcinoma. This preclinical study shows that quinacrine overcomes erlotinib resistance by inhibiting FACT and cell-cycle progression, and supports a clinical trial testing erlotinib alone versus this combination in advanced NSCLC.

Abstract A263: Combination of quinacrine and erlotinib overcomes resistance to erlotinib in non-small cell lung cancer

The epidermal growth factor receptor (EGFR) inhibitor erlotinib is highly effective in non-small cell lung cancer (NSCLC) patients whose tumors express EGFR mutations, e.g., EGFR-L858R or EGFR exon 19 del. However, the efficacy of erlotinib is limited by either primary or secondary resistance, i.e., in patients whose tumors express wild-type EGFR (wtEGFR), or in initially sensitive patients whose tumors develop the second-site mutation EGFR-L858R/T790M or Met amplification after 10-14 months of erlotinib treatment. To improve treatment with erlotinib, we combined it with quinacrine in several erlotinib-resistant NSCLC cells. Quinacrine is a 9-aminoacridine derivative that suppresses nuclear factor-kappa B (NF-κB) by causing chromatin trapping of the FACT (facilitates chromatin transcription) complex. In A549 (wtEGFR), H1975 (EGFR-L858R/T790M), and H1993 (Met amplification) cells, the combination of erlotinib and quinacrine at 5 to 1 or 10 to 1 fixed ratios was highly synergistic, as quantified by the Chou-Talalay combination indices [ED50: 0.61 (0.42-0.81); ED75: 0.53 (0.40-0.67); ED90: 0.63 (0.54-0.71)]. Addition of quinacrine to erlotinib treatment inhibited colony formation and induced significant cell cycle arrest and apoptosis in A549 and H1975 cells. Upon quinacrine treatment, the FACT subunit SSRP1 disappeared from the soluble protein fraction, and NF-κB-dependent luciferase activity was decreased. Knockdown of SSRP1 decreased cell viability and colony formation, and sensitized the cells to erlotinib treatment. Moreover, microarray analysis of A549 and H1975 cells treated with erlotinib only, quinacrine only, or both, showed that quinacrine or combination treatment significantly affected genes involved in cell cycle progression or nucleotide metabolism, and many of these genes contain binding sites for transcription factors that regulate SSRP1-enriched genes. These data support a Phase I/II clinical trial (NCT01839955) that is just beginning, combining erlotinib and quinacrine in wtEGFR NSCLC patients after first-line chemotherapy. To assess synergistic effects in this clinical trial, we identified genes from the microarray analysis that were more significantly suppressed by combination treatment than by either single treatment. We further narrowed them down to those whose increased expression is associated with poorer survival in lung adenocarcinoma patients (HR ranges from 1.58-2.92) as potential biomarkers of drug synergy for the clinical trial. These genes, most of which are involved in various cell cycle processes, included BIRC5, DLGAP5, FOSL1, FOXM1, HIST1H2AK, HIST1H2BM, KIFC1, MKI67, PBK, PLK1, TOP2A, and ZWILCH. We conclude that the combination of quinacrine and erlotinib helps overcome erlotinib resistance in NSCLC, potentially by targeting FACT and suppressing cell cycle progression.

Citation Information: Mol Cancer Ther 2013;12(11 Suppl):A263.

Citation Format: Josephine Kam Tai Dermawan, Katerina Gurova, John Pink, Afshin Dowlati, Sarmishtha De, Goutham Narla, Neelesh Sharma, George Stark. Combination of quinacrine and erlotinib overcomes resistance to erlotinib in non-small cell lung cancer. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr A263.