Epigenomic analysis of primary human T cells reveals enhancers associated with TH2 memory cell differentiation and asthma susceptibility.

A characteristic feature of asthma is the aberrant accumulation, differentiation or function of memory CD4(+) T cells that produce type 2 cytokines (TH2 cells). By mapping genome-wide histone modification profiles for subsets of T cells isolated from peripheral blood of healthy and asthmatic individuals, we identified enhancers with known and potential roles in the normal differentiation of human TH1 cells and TH2 cells. We discovered disease-specific enhancers in T cells that differ between healthy and asthmatic individuals. Enhancers that gained the histone H3 Lys4 dimethyl (H3K4me2) mark during TH2 cell development showed the highest enrichment for asthma-associated single nucleotide polymorphisms (SNPs), which supported a pathogenic role for TH2 cells in asthma. In silico analysis of cell-specific enhancers revealed transcription factors, microRNAs and genes potentially linked to human TH2 cell differentiation. Our results establish the feasibility and utility of enhancer profiling in well-defined populations of specialized cell types involved in disease pathogenesis.

The promises and challenges of early non-small cell lung cancer detection: patient perceptions, low-dose CT screening, bronchoscopy and biomarkers.

Lung cancer survival statistics are sobering with survival ranking among the poorest of all cancers despite the addition of targeted therapies and immunotherapies. However, improvements in tools for early detection hold promise. The Nederlands-Leuvens Longkanker Screenings Onderzoek (NELSON) trial recently corroborated the findings from the previous National Lung Screening Trial low-dose Computerised Tomography (NLST) screening trial in reducing lung cancer mortality. Biomarker research and development is increasing at pace as the molecular life histories of lung cancers become further unravelled. Low-dose CT screening (LDCT) is effective but targets only those at the highest risk and is burdensome on healthcare. An optimally designed CT screening programme at best will only detect a low proportion of overall lung cancers as only those at very high-risk meet screening criteria. Biomarkers that help risk stratify suitable patients for LDCT screening, and those that assist in determining which LDCT detected nodules are likely to represent malignant disease are needed. Some biomarkers have been proposed as standalone lung cancer diagnosis tools. Bronchoscopy technology is improving, with better capacity to identify and obtain samples from early lung cancers. Clinicians need to be aware of each early lung cancer detection method's inherent limitations. We anticipate that the future of early lung cancer diagnosis will involve a synergistic, multimodal approach, combining several early detection methods.

Immune Surveillance in Clinical Regression of Preinvasive Squamous Cell Lung Cancer.

Before squamous cell lung cancer develops, precancerous lesions can be found in the airways. From longitudinal monitoring, we know that only half of such lesions become cancer, whereas a third spontaneously regress. Although recent studies have described the presence of an active immune response in high-grade lesions, the mechanisms underpinning clinical regression of precancerous lesions remain unknown. Here, we show that host immune surveillance is strongly implicated in lesion regression. Using bronchoscopic biopsies from human subjects, we find that regressive carcinoma in situ lesions harbor more infiltrating immune cells than those that progress to cancer. Moreover, molecular profiling of these lesions identifies potential immune escape mechanisms specifically in those that progress to cancer: antigen presentation is impaired by genomic and epigenetic changes, CCL27-CCR10 signaling is upregulated, and the immunomodulator TNFSF9 is downregulated. Changes appear intrinsic to the carcinoma in situ lesions, as the adjacent stroma of progressive and regressive lesions are transcriptomically similar. SIGNIFICANCE: Immune evasion is a hallmark of cancer. For the first time, this study identifies mechanisms by which precancerous lesions evade immune detection during the earliest stages of carcinogenesis and forms a basis for new therapeutic strategies that treat or prevent early-stage lung cancer.See related commentary by Krysan et al., p. 1442.This article is highlighted in the In This Issue feature, p. 1426.

A cholestatic diagnostic dilemma.

A 28-year-old man with hereditary spherocytosis presented with abdominal pain and jaundice. He had severe, mainly conjugated (642 µmol/l), hyperbilirubinaemia (1033 µmol/l), with elevated liver enzymes: alkaline phosphatase (ALP) (163 IU/l), γ-glutamyltransferase (gGT) (277 IU/l) and aspartate transaminase (AST) (358 IU/l). Abdominal ultrasound and magnetic resonance cholangiopancreatography (MRCP) showed gallstones in the gallbladder but an absence of biliary duct dilation. Liver biopsy was consistent with cholestasis but showed no large duct obstruction. The cause of the cholestasis was unclear, was it a primary intrahepatic pathology or secondary to a posthepatic cause? He presented with similar symptoms days later with gallstones in the bile duct (choledocholithiasis) and underwent endoscopic retrograde cholangiopancreatography (ERCP) and cholecystectomy. This report guides one through the assessment of jaundice and serves as an example whereby the diagnosis of a common cause of illness is blurred by an atypical clinical presentation and relevant comorbidities. A diagnosis of benign recurrent intrahepatic cholestasis (BRIC) is also considered.

An integrated nano-scale approach to profile miRNAs in limited clinical samples.

Profiling miRNA expression in cells that directly contribute to human disease pathogenesis is likely to aid the discovery of novel drug targets and biomarkers. However, tissue heterogeneity and the limited amount of human diseased tissue available for research purposes present fundamental difficulties that often constrain the scope and potential of such studies. We established a flow cytometry-based method for isolating pure populations of pathogenic T cells from bronchial biopsy samples of asthma patients, and optimized a high-throughput nano-scale qRT-PCR method capable of accurately measuring 96 miRNAs in as little as 100 cells. Comparison of circulating and airway T cells from healthy and asthmatic subjects revealed asthma-associated and tissue-specific miRNA expression patterns. These results establish the feasibility and utility of investigating miRNA expression in small populations of cells involved in asthma pathogenesis, and set a precedent for application of our nano-scale approach in other human diseases. The microarray data from this study (Figure 7) has been submitted to the NCBI Gene Expression Omnibus (GEO; http://ncbi.nlm.nih.gov/geo) under accession no. GSE31030.