Deciphering the genomic, epigenomic, and transcriptomic landscapes of pre-invasive lung cancer lesions

The molecular alterations that occur in cells before cancer is manifest are largely uncharted. Lung carcinoma in situ (CIS) lesions are the pre-invasive precursor to squamous cell carcinoma. Although microscopically identical, their future is in equipoise, with half progressing to invasive cancer and half regressing or remaining static. The cellular basis of this clinical observation is unknown. Here, we profile the genomic, transcriptomic, and epigenomic landscape of CIS in a unique patient cohort with longitudinally monitored pre-invasive disease. Predictive modeling identifies which lesions will progress with remarkable accuracy. We identify progression-specific methylation changes on a background of widespread heterogeneity, alongside a strong chromosomal instability signature. We observed mutations and copy number changes characteristic of cancer and chart their emergence, offering a window into early carcinogenesis. We anticipate that this new understanding of cancer precursor biology will improve early detection, reduce overtreatment, and foster preventative therapies targeting early clonal events in lung cancer.

Home Society Politics and Immigrant Political Incorporation: The Case of Greek Immigrants in New York City

This article examines the processes through which home society politics affect Greek immigrant incorporation into the host society's political structures. The argument made is that immigrant concern with the home society's territorial sovereignty prompt immigrant incorporation into the American polity. Following Turkey's invasion of Cyprus in the summer of 1974 and numerous Turkish claims on Greek islands since then, Greek and American-born activists and leaders have engaged in an “Americanization project” characterized by two levels of mobilizing activity: activists and leaders have sought to first create formal relations with local and national level American politicians and parties and second to mobilize immigrants to enter American political structures (by becoming naturalized citizens, voting and contributing funds to political campaigns) so that they may this way influence American foreign policy in the Aegean. To foster the process of “Americanization,” activists and leaders have relied on the construction of binational identities.

Well-differentiated bronchial neuroendocrine tumors: Clinical management and outcomes in 105 patients

INTRODUCTION

Bronchial neuroendocrine tumors (NETs) are rare tumors representing approximately 20%-30% of all neuroendocrine tumors and 2%-3% of all adult lung cancers. Here, they present a large case series of well-differentiated bronchial NETs with the aim of investigating the behavior of these tumors and long-term outcomes.

METHODS

A retrospective review was performed of 105 patients with bronchial NETs managed in a tertiary referral center in the period between January 1998 and January 2012.

RESULTS

Bronchial NETs are commoner in females and the commonest presenting symptoms were cough (13.9%) and dyspnoea (11.6%). Octreoscan^TM and Gallium-68 DOTATATE PET were found to have similar diagnostic sensitivity and FDG PET was more sensitive for higher-grade tumors. Over a median follow-up period of 35.5 months mortality rate was 5.7%. The 5-year survival was 76% and the 10-year survival was 62%. Female patients survived longer but this difference was not statistically significant (P = .59). Older age greater than 50 years (P = .027), higher levels of Chromogranin A (CgA) (P = .034), first-line treatment with surgery (P = .005), ki67 over 10% (P = .037), and tumor stage (P = .036) but not tumor grade (P = .22), were significantly associated with survival.

DISCUSSION

Several factors have been identified which are independently associated with survival including CgA levels greater than 100 pmol/L, tumor stage, age greater than 50, ki67 over 10% and having surgery as first-line treatment. There was no difference in survival between typical and atypical carcinoids.

Prognostic Impact of Novel Molecular Subtypes of Small Intestinal Neuroendocrine Tumor

PURPOSE

Small intestinal neuroendocrine tumors (SINET) are the commonest malignancy of the small intestine; however, underlying pathogenic mechanisms remain poorly characterized. Whole-genome and -exome sequencing has demonstrated that SINETs are mutationally quiet, with the most frequent known mutation in the cyclin-dependent kinase inhibitor 1B gene (CDKN1B) occurring in only ∼8% of tumors, suggesting that alternative mechanisms may drive tumorigenesis. The aim of this study is to perform genome-wide molecular profiling of SINETs in order to identify pathogenic drivers based on molecular profiling. This study represents the largest unbiased integrated genomic, epigenomic, and transcriptomic analysis undertaken in this tumor type.

EXPERIMENTAL DESIGN

Here, we present data from integrated molecular analysis of SINETs (n = 97), including whole-exome or targeted CDKN1B sequencing (n = 29), HumanMethylation450 BeadChip (Illumina) array profiling (n = 69), methylated DNA immunoprecipitation sequencing (n = 16), copy-number variance analysis (n = 47), and Whole-Genome DASL (Illumina) expression array profiling (n = 43).

RESULTS

Based on molecular profiling, SINETs can be classified into three groups, which demonstrate significantly different progression-free survival after resection of primary tumor (not reached at 10 years vs. 56 months vs. 21 months, P = 0.04). Epimutations were found at a recurrence rate of up to 85%, and 21 epigenetically dysregulated genes were identified, including CDX1 (86%), CELSR3 (84%), FBP1 (84%), and GIPR (74%).

CONCLUSIONS

This is the first comprehensive integrated molecular analysis of SINETs. We have demonstrated that these tumors are highly epigenetically dysregulated. Furthermore, we have identified novel molecular subtypes with significant impact on progression-free survival.

Assessment of RainDrop BS-seq as a method for large-scale, targeted bisulfite sequencing

We present a systematic assessment of RainDrop BS-seq, a novel method for large-scale, targeted bisulfite sequencing using microdroplet-based PCR amplification coupled with next-generation sequencing. We compared DNA methylation levels at 498 target loci (1001 PCR amplicons) in human whole blood, osteosarcoma cells and an archived tumor tissue sample. We assessed the ability of RainDrop BS-seq to accurately measure DNA methylation over a range of DNA quantities (from 10 to 1500 ng), both with and without whole-genome amplification (WGA) following bisulfite conversion. DNA methylation profiles generated using at least 100 ng correlated well (median R = 0.92) with those generated on Illumina Infinium HumanMethylation450 BeadChips, currently the platform of choice for epigenome-wide association studies (EWAS). WGA allowed for testing of samples with a starting DNA amount of 10 and 50 ng, although a reduced correlation was observed (median R = 0.79). We conclude that RainDrop BS-seq is suitable for measuring DNA methylation levels using nanogram quantities of DNA, and can be used to study candidate epigenetic biomarker loci in an accurate and high-throughput manner, paving the way for its application to routine clinical diagnostics.

Genome-wide DNA methylation profiling of gastrointestinal neuroendocrine tumors to identify hypermethylation of mTOR, Wnt, and Notch pathways in GI NET pathogenesis

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Background: Aberrant DNA methylation is known to play an important role in the pathogenesis of many human cancers, however little is known about its role in gastrointestinal neuroendocrine tumours (GI NET) development. We report the first unbiased genome-wide DNA methylation analysis of a large cohort of GI NETs, aiming to identify key methylation variable positions (MVPs) specific to GI NETs which may contribute to tumorigenesis and metastatic progression. Methods: Illumina Infinium Human Methylation 450 Array analysis was performed on 56 cases of GI NET DNA extracted from macrodissected tumour (n=67) and normal (n=29) specimens. Tumours were gastrointestinal primaries (n=39) or metastases (liver, mesenteric, omental or lymph node, n=28) of low (n=35), intermediate (n=17) or high grade (n=3)(unknown grade n=12). Data analysis was performed using the "ChAMP" custom pipeline and pathway analyses were performed using "GREAT," "WebGestalt," and "GSEA" web tools. A Bonferroni adjusted significance threshold value of p<0.05 was used throughout. Results: In order to identify and validate a GI NET specific methylation signature our cohort was divided into a discovery set (31 cases) and validation set (25 cases). Comparison of primary GI NET tumours with normal small bowel identified a total of 77,916 MVPs, including 1,666 sites hypermethylated by over 30% in tumour compared to normal tissue. Application of the profile to the validation set correctly identified 85% of samples. Tumours demonstrated global hypomethylation relative to normal tissue. Gene ontology analysis identified methylation of multiple cancer related pathways (including the Wnt, mTOR and Notch pathways) as a feature of hepatic metastases of GI NET primaries. Increasing RASSF1 promoter hypermethylation was associated with higher tumour grade. Conclusions: This study is the first comprehensive analysis of the epigenetic profile of GI NETs and identifies potential novel biomarkers and therapeutic targets. We are currently performing integrated analysis of epigenomic, genomic and transcriptomic data to further define the pathways involved in GI NET pathogenesis.

Somatic mutation of CDKN1B in small intestine neuroendocrine tumors

The diagnosed incidence of small intestine neuroendocrine tumors (SI-NETs) is increasing, and the underlying genomic mechanisms have not yet been defined. Using exome- and genome-sequence analysis of SI-NETs, we identified recurrent somatic mutations and deletions in CDKN1B, the cyclin-dependent kinase inhibitor gene, which encodes p27. We observed frameshift mutations of CDKN1B in 14 of 180 SI-NETs, and we detected hemizygous deletions encompassing CDKN1B in 7 out of 50 SI-NETs, nominating p27 as a tumor suppressor and implicating cell cycle dysregulation in the etiology of SI-NETs.

Neuroendocrine tumours: cracking the epigenetic code

The field of epigenetics has evolved rapidly over recent years providing insight into the tumorigenesis of many solid and haematological malignancies. Determination of epigenetic modifications in neuroendocrine tumour (NET) development is imperative if we are to improve our understanding of the biology of this heterogenous group of tumours. Epigenetic marks such as DNA methylation at RASSF1A are frequent findings in NETs of all origins and may be associated with worse prognosis. MicroRNA signatures and histone modifications have been identified which can differentiate subtypes of NET and distinguish NET from adenocarcinoma in cases of diagnostic uncertainty. Historically, candidate gene-driven approaches have yielded limited insight into the epigenetics of NET. Recent progress has been facilitated by development of high-throughput tools including second-generation sequencing and arrays for analysis of the 'epigenome' of tumour and normal tissue, permitting unbiased approaches such as exome sequencing that identified mutations of chromatin-remodelling genes ATRX/DAXX in 44% of pancreatic NETs. Epigenetic changes are reversible and therefore represent an attractive therapeutic target; to date, clinical outcomes of epigenetic therapies in solid tumours have been disappointing; however, in vitro studies on NETs are promising and further clinical trials are required to determine utility of this class of novel agents. In this review, we perform a comprehensive evaluation of epigenetic changes found in NETs to date, including rare NETs such as phaeochromocytoma and adrenocortical tumours. We suggest priorities for future research and discuss potential clinical applications and novel therapies.

Hitting the target: where do molecularly targeted therapies fit in the treatment scheduling of neuroendocrine tumours?

Neuroendocrine tumours (NETs) are a rare and heterogeneous group of tumours whose incidence is increasing and their prevalence is now greater than that of any other upper gastrointestinal tumour. Diagnosis can be challenging, and up to 25% of patients present with metastatic disease. Following the recent FDA approval of two new molecularly targeted therapies for the treatment of advanced pancreatic NETs (pNETs), the first in 25 years, we review all systemic therapies and suggest where these newer targeted therapies fit in the treatment schedule for these challenging tumours. Clinical trial data relating to the routine use of sunitinib and everolimus in low-intermediate-grade pNETs are summarised alongside newer molecularly targeted agents undergoing clinical assessment in NETs. We particularly focus on the challenge of optimal scheduling of molecularly targeted treatments around existing systemic and localised treatment such as chemotherapy or radiotargeted therapy. We also discuss application of current evidence to subgroups of patients who have not so far been directly addressed such as those with poorer performance status or patients receiving radical surgery who may benefit from adjuvant treatment.

Testicular germ cell tumors with bony metastases: Diagnosis, management, and outcomes (a case series)

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Background: Metastasis of testicular germ cell tumour (GCT) to bone is a rare event and there is little evidence on optimal curative management.

Methods: A retrospective review of case records of germ cell tumour patients within the Anglian Germ Cell Cancer Group between 10/01/2005 and 14/03/2011 was conducted.

Results: 2,550 cases of testicular germ cell tumour were reviewed and 19 patients with bone metastases were identified, median age 38yrs. Average duration of follow-up was 21.7 months. Most were NSGCT (11/19), or seminoma (3/19). Five patients were treated on the basis of markers alone. Bone metastases present at diagnosis 12/19, and diagnosed at relapse/progression in 6/19 cases. Bony metastases were most commonly found in the vertebrae (15/19), pelvis (5/19) and ribs (3/19). In 10 cases a single bone metastasis was found, in 9 cases multiple areas of bone metastasis occurred. The imaging modality diagnostic of bone metastases was most frequently CT scan (11/19), FDG-PET (4/19) or MRI (3/19). The majority of these cases received only one line of chemotherapy (13/19), others received up to a maximum of seven line of systemic treatment (Table). Six patients (31.6%) died during follow up after an average of 17.5months and 3.3 lines of systemic treatment.

Conclusions: Bone metastasis in GCT is rare, and is believed to confer poor prognosis. This series of patient outcomes following standard first-line platinum based chemotherapy is small but appears to support this conclusion.

[Table: see text]

Surgical management and palliative treatment in bronchial neuroendocrine tumours: a clinical study of 45 patients

Bronchial neuroendocrine tumours account for 1-2% of all lung cancers; they are thought to arise from the neuroendocrine cells located in the bronchial mucosa. The majority of the literature available comprises surgical series and there is a scarcity of data available for the management of patients with inoperable disease. We present a series of 45 patients referred to our institution from 1998 to 2006, with a mean follow-up of 54 months. Histological diagnosis from our department was available for 39 patients, with the remainder having had histological assessment performed previously. Typical carcinoid was present in 25 cases, atypical in 9 cases, large cell neuroendocrine carcinoma in 4 and 1 case of small cell lung carcinoma. All patients were staged at time of initial diagnosis with CT scan, in addition Octreoscans were performed when appropriate. Twenty-six of these 45 cases had unresectable disease, whilst the remainder were treated with surgical resection. Initial therapy with surgical resection was performed in 19 patients, 2 of whom had undergone neo-adjuvant chemotherapy. Recurrence occurred in 7 (36.8%), average duration of disease-free survival post-surgery was 61 months. Chemotherapy was first line therapy in five cases, four achieved disease stabilization and one case had progressive disease. Somatostatin analogues were used as first line therapy in six patients, for symptom control and anti-tumour effect. Peptide receptor radionuclide therapy, with Yttrium-90 DOTA-Octreotate, was given in two cases, both of whom achieved disease stabilization for 9-12 months respectively. There was a significant difference between Stage 4 and Stage 1 disease at presentation and survival. In conclusion curative surgical resection is treatment of choice, however, chemotherapy, somatostatin analogues and peptide receptor radionuclide therapy offers palliation improving both symptoms and mortality.