Metabolic memory (MM) is the phenomenon whereby diabetes complications persist and progress after glycemic recovery is achieved. Here, we present data showing that MM is heritable and that the transmission correlates with hyperglycemia-induced DNA hypomethylation and aberrant gene expression. Streptozocin was used to induce hyperglycemia in adult zebrafish, and then, following streptozocin withdrawal, a recovery phase was allowed to reestablish a euglycemic state. Blood glucose and serum insulin returned to physiological levels during the first 2 weeks of the recovery phase as a result of pancreatic β-cell regeneration. In contrast, caudal fin regeneration and skin wound healing remained impaired to the same extent as in diabetic fish, and this impairment was transmissible to daughter cell tissue. Daughter tissue that was never exposed to hyperglycemia, but was derived from tissue that was, did not accumulate AGEs or exhibit increased levels of oxidative stress. However, CpG island methylation and genome-wide microarray expression analyses revealed the persistence of hyperglycemia-induced global DNA hypomethylation that correlated with aberrant gene expression for a subset of loci in this daughter tissue. Collectively, the data presented here implicate the epigenetic mechanism of DNA methylation as a potential contributor to the MM phenomenon.

Diagnosis of Parkinson’ disease (PD) carries a high misdiagnosis rate due to failure to recognize atypical parkinsonian disorders (APD). Usually by the time of diagnosis greater than 60% of the neurons in the substantia nigra are dead. Therefore, early detection would be beneficial so that therapeutic intervention may be initiated early in the disease process. We used splice variant-specific microarrays to identify mRNAs whose expression is altered in peripheral blood of early-stage PD patients compared to healthy and neurodegenerative disease controls. Quantitative polymerase chain reaction assays were used to validate splice variant transcripts in independent sample sets. Here we report a PD signature used to classify blinded samples with 90% sensitivity and 94% specificity and an APD signature that resulted in a diagnosis with 95% sensitivity and 94% specificity. This study provides the first discriminant functions with coherent diagnostic signatures for PD and APD. Analysis of the PD biomarkers identified a regulatory network with nodes centered on the transcription factors HNF4A and TNF, which have been implicated in insulin regulation.

KRAS mutations are highly prevalent in non-small cell lung cancer (NSCLC), and tumors harboring these mutations tend to be aggressive and resistant to chemotherapy. We used next-generation sequencing technology to identify pathways that are specifically altered in lung tumors harboring a KRAS mutation. Paired-end RNA-sequencing of 15 primary lung adenocarcinoma tumors (8 harboring mutant KRAS and 7 with wild-type KRAS) were performed. Sequences were mapped to the human genome, and genomic features, including differentially expressed genes, alternate splicing isoforms and single nucleotide variants, were determined for tumors with and without KRAS mutation using a variety of computational methods. Network analysis was carried out on genes showing differential expression (374 genes), alternate splicing (259 genes), and SNV-related changes (65 genes) in NSCLC tumors harboring a KRAS mutation. Genes exhibiting two or more connections from the lung adenocarcinoma network were used to carry out integrated pathway analysis. The most significant signaling pathways identified through this analysis were the NFκB, ERK1/2, and AKT pathways. A 27 gene mutant KRAS-specific sub network was extracted based on gene–gene connections from the integrated network, and interrogated for druggable targets. Our results confirm previous evidence that mutant KRAS tumors exhibit activated NFκB, ERK1/2, and AKT pathways and may be preferentially sensitive to target therapeutics toward these pathways. In addition, our analysis indicates novel, previously unappreciated links between mutant KRAS and the TNFR and PPARγ signaling pathways, suggesting that targeted PPARγ antagonists and TNFR inhibitors may be useful therapeutic strategies for treatment of mutant KRAS lung tumors. Our study is the first to integrate genomic features from RNA-Seq data from NSCLC and to define a first draft genomic landscape model that is unique to tumors with oncogenic KRAS mutations.

MicroRNAs are involved in cell proliferation, differentiation, and apoptosis and can function as tumor suppressor genes or oncogenes. The role of microRNAs in neuroendocrine tumors such as ileal carcinoids is largely unknown. We examined the differential expression of 95 microRNAs by RT-PCR using the QuantiMir System in eight matching primary and metastatic carcinoid tumors from the ileum. All microRNAs chosen for the QuantiMir System Array were based on their potential functions related to cancer biology, cell development and apoptosis. The expression of microRNAs for the samples was normalized to microRNA-197, and the matching primary and metastatic tumors were compared. There was down-regulation of microRNA-133a, 145, 146, 222 and 10b in all samples between the primary and matching metastatic tumors and up-regulation of microRNA-183, 488 and 19a + b in six of eight metastatic carcinoids compared to the primary tumors. MicroRNA-133a was further analyzed by TaqMan Real Time RT-PCR and Northern hybridization using six additional matching primary and metastatic samples which supported the PCR Array findings. There were significant differences in microRNA-133a expression with down-regulation in the metastasis compared to the primary in the eight original cases (p<0.009) and in the six additional cases used for validation (p<0.014). Laser capture microdissection and Real Time RT-PCR analysis using normal ileum found microRNA-133a expression in normal enterochromaffin cells. In situ hybridization in normal ileum showed that some of the mucosal endocrine cells expressed microRNA-133a. Both primary and metastatic ileal carcinoid tumors expressed microRNA-133a by in situ hybridization. These results provide information about novel marker microRNAs that may be used as biomarkers and/or therapeutic targets in intestinal carcinoid tumors.

Purpose

Immunotherapeutic modalities are commonly used for treatment of patients with melanoma. The therapeutic success in pre-clinical models has not yielded the expected clinical results. To understand this discrepancy, we attempted to define immune homeostasis of 209 patients with melanoma across stages of disease relative to normal controls.

Patients and Methods

PBMC and plasma were collected from patients and healthy donors. PBMC were analyzed for frequencies of natural killer, dendritic, and T-cells, and their functional status. Matched plasma samples were analyzed for the concentrations of 27 cytokines, chemokines, and growth factors. RNA was isolated from 24 metastatic melanoma tumor biopsies and profiled by microarray analysis.

Results

The frequency of NK, T-cells, and DC in patients does not significantly change across stages of melanoma. However, plasma concentrations of Th2 cytokines (IL-4, IL-5, IL-10 and IL-13) in tumor bearing patients were significantly higher than those with resected melanoma. Expression array analysis of metastatic melanoma revealed that the malignant melanocytes were not the source of the Th2 cytokines, but did highly up-regulate VEGF transcripts, consistent with plasma VEGF concentrations. In vitro VEGF exposure of normal PBMC lead to re-polarization from Th1 to Th2 emulating the state of metastatic melanoma.

Conclusions

Patients with metastatic melanoma exist in a state of Th2 mediated “chronic inflammation” as a result of at least VEGF overproduction by malignant tumors. These data support prior observations regarding the impact of VEGF on immune cell function and suggests consideration of VEGF inhibitors in future cancer immunotherapy clinical studies in metastatic melanoma.

Context:

The signs and symptoms of Graves’ ophthalmopathy (GO) result from inflammation and increased volume of the orbital adipose tissues and extraocular muscles.

Objective:

To identify differentially regulated genes that may be involved in stimulating the orbital adipose tissue expansion seen in GO.

Design:

Gene expression profiling was used to compare genes expressed in orbital adipose tissues from GO patients and normal individuals.

Setting:

Private practice tertiary referral center.

Patients:

Orbital adipose tissues were collected at transantral orbital decompression surgery from 20 euthyroid patients undergoing this procedure for severe GO and at early autopsy from 8 normal individuals having no evidence of thyroid or ocular disease.

Results:

Of the 12,686 genes analyzed, 25 known genes were increased in expression (> 4 fold) in GO orbital tissues, while 11 genes were decreased (> 4 fold). Upregulated genes, confirmed by quantitative RT-PCR, included secreted frizzled related protein-1 (sFRP-1; 18.5 fold) and several adipocyte-related genes, including peroxisome proliferator activated receptor-γ (44.1 fold) and adiponectin (25 fold). Treatment in vitro of GO orbital preadipocytes with recombinant sFRP-1 (100 nM) significantly increased adiponectin (2.0 fold; p<.05), leptin (7 fold; p<.002), and thyrotropin receptor mRNA (13 fold; p<.003) levels, and enhanced Oil red-O staining in the cultures.

Conclusions:

These results support the concept that orbital adipogenesis is enhanced in GO, and suggest that elevated levels of sFRP-1 in the GO orbit may be involved in stimulating this pathogenic process.