Fibroblast growth factor 21 (FGF21) therapy attenuates left ventricular dysfunction and metabolic disturbance by improving FGF21 sensitivity, cardiac mitochondrial redox homoeostasis and structural changes in pre-diabetic rats

AIMS

Fibroblast growth factor 21 (FGF21) acts as a metabolic regulator and exerts cardioprotective effects. However, the effects of long-term FGF21 administration on the heart under the FGF21-resistant condition in obese, insulin-resistant rats have not been investigated. We hypothesized that long-term FGF21 administration reduces FGF21 resistance and insulin resistance and attenuates cardiac dysfunction in obese, insulin-resistant rats.

METHODS

Eighteen rats were fed on either a normal diet (n = 6) or a high-fat diet (HFD; n = 12) for 12 weeks. Then, rats in the HFD group were divided into two subgroups (n = 6 per subgroup) and received either the vehicle (HFV) or recombinant human FGF21 (rhFGF21, 0.1 mg kg(-1)  day(-1) ; HFF) injected intraperitoneally for 28 days. The metabolic parameters, inflammation, malondialdehyde (MDA), heart rate variability (HRV), left ventricular (LV) function, cardiac mitochondrial redox homoeostasis, cardiac mitochondrial fatty acid β-oxidation (FAO) and anti-apoptotic signalling pathways were determined.

RESULTS

HFV rats had increased dyslipidaemia, insulin resistance, plasma FGF21 levels, TNF-α, adiponectin and MDA, depressed HRV, and impaired LV and mitochondrial function. HFV rats also had decreased cardiac Bcl-2, cardiac PGC-1α and CPT-1 protein expression. However, FGF21 restored metabolic parameters, decreased TNF-α and MDA, increased serum adiponectin, and improved HRV, cardiac mitochondrial and LV function in HFF rats. Moreover, HFF rats had increased cardiac Bcl-2, cardiac PGC-1α and CPT-1 protein expression.

CONCLUSION

Long-term FGF21 therapy attenuates FGF21 resistance and insulin resistance and exerts cardioprotection by improving cardiometabolic regulation via activating anti-apoptotic and cardiac mitochondrial FAO signalling pathways in obese, insulin-resistant rats.

Molecular cloning and expression analysis of Fem1b from oriental river prawn Macrobrachium nipponense

Feminization-1 homolog b (Fem1b) is one of the genes essential for male development and play central roles in sex determination of Caenorhabditis elegans. In this study, we cloned and characterized the full-length Fem1b cDNA from the freshwater prawn Macrobrachium nipponense (MnFem1b) in different tissues and at different developmental stages. Real-time quantitative reverse polymerase chain reaction (RT-qPCR) showed that the MnFem1b gene was expressed in all investigated tissues, with the highest expression level found in the testes. The results revealed that the MnFem1b gene might play roles in aspects of development of the male prawn phenotype. The RT-qPCR also revealed that MnFem1b mRNA expression was significantly increased at 10 days after metamorphosis. The expression levels in all investigated tissues showed a certain degree of sexually dimorphism, the expression levels in males were significantly higher than those in females (P < 0.05). Notably, the highest expression of MnFem1b was found in the testes. The expression of MnFem1b in different tissues indicates that it plays multiple biological functions in M. nipponense.

DNMT3B isoforms without catalytic activity stimulate gene body methylation as accessory proteins in somatic cells

Promoter DNA methylation is a key epigenetic mechanism for stable gene silencing, but is correlated with expression when located in gene bodies. Maintenance and de novo DNA methylation by catalytically active DNA methyltransferases (DNMT1 and DNMT3A/B) require accessory proteins such as UHRF1 and DNMT3L. DNMT3B isoforms are widely expressed, although some do not have active catalytic domains and their expression can be altered during cell development and tumourigenesis, questioning their biological roles. Here, we show that DNMT3B isoforms stimulate gene body methylation and re-methylation after methylation-inhibitor treatment. This occurs independently of the isoforms' catalytic activity, demonstrating a similar functional role to the accessory protein DNMT3L, which is only expressed in undifferentiated cells and recruits DNMT3A to initiate DNA methylation. This unexpected role for DNMT3B suggests that it might substitute for the absent accessory protein DNMT3L to recruit DNMT3A in somatic cells.

A reactor-like spinneret used in 3D printing alginate hollow fiber: a numerical study of morphological evolution

In this paper, a reactor-like spinneret is proposed to generate a continuous hollow hydrogel fiber. In order to reliably control the deforming dynamics, the components of the spinneret are standardized in order to ease the online observation of morphological evolution. We found that not only did a co-flow occur in the tubular space, but a relatively large shrinkage of the shell layer at the outlet also occurred. Whereupon a weak coupling of the velocity field and diffusion-reacting co-flow was developed to describe the monitored co-flow morphology and to simulate the intermediate state of the concentration field, as well as to calculate the shrinkage profile with an integral formula. And a critical isogram [G]cri was determined to correspond to the morphological segmental feature, to trigger gelation and shrinkage as a threshold of solubility and the integral upper limit of the shrinkage region. Experimental evidence indicates that: the simulation is able to effectively predict the inner diameter of the hollow fiber; the transient inner diameter of the fiber at the outlet is expanded by approximately 70 μm (co-flow distance = 15 mm) as compared to the initial fluid dynamics value, and that the relative mean error of the simulated inner diameter was less than 8%. The proposed study provides deeper insight into the printing of hollow fibers and other gelling processes which utilize a reactor-like spinneret.

Abstract B02: The role of chromatin remodeler protein ARID1a in ovarian clear cell carcinoma

Ovarian cancer is the fifth leading cause of cancer death among women in the United States and ovarian clear cell carcinoma (OCCC) is an aggressive subtype of epithelial ovarian cancer. Recent whole genome and whole exome sequencing studies have revealed that the chromatin remodeler protein AT-Rich Interactive Domain 1a (ARID1a) is frequently mutated in OCCC. ARID1a loss is also often observed in endometriosis which is strongly associated with OCCC. Consequently, we hypothesize that loss of ARID1a is an early step in transformation of endometriosis into OCCC. Here, we show that knocking down ARID1a in an immortalized endometriosis line, promotes greater invasion of basement membrane in vitro, and higher efficiency of anchorage-independent growth. Using two independent genome wide approaches to assay chromatin accessibility and DNA methylation, we demonstrate that the loss of ARID1a does not significantly alter global chromatin accessibility and DNA methylation with the exception of the genomic regions containing late replicating domains. Our findings do however indicate that the loss of ARID1a contributes to altered distribution of H3K27me3 and H3K27ac marks. Specifically we find an increased deposit of the polycomb repressive mark in the knock-down line outside of promoters. Interestingly, we also find the knock-down line has a higher level of the active mark H3K27ac at the promoters and a lower level at the enhancers relative to the scrambled control. Moreover, many of the genes differentially expressed upon ARID1a knock-down are consistent with the changes of H3K27ac at the respective gene promoter. We therefore conclude that loss of ARID1a expression contributes to cellular transformation through deregulation of gene expression primarily through alteration of histone marks.

Citation Format: Ranjani Lakshminarasimhan, Claudia Andreu-Vieyra, Kate Lawrenson, Simon A. Gayther, Peter A. Jones, Gangning Liang. The role of chromatin remodeler protein ARID1a in ovarian clear cell carcinoma. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr B02.

Abstract B03: Identification of epigenetic regulated genes through simultaneous analysis of DNA methylation and chromatin structure in uncultured tumors

The contribution of promoter DNA methylation to the alteration of caner related gene expression has been well studied, however, these genes can also potentially be altered by chromatin accessibility without involvement of DNA methylation and can be epigenetically inherited. In this study, we used an assay developed in our laboratory (AcceSssIble) that can simultaneously interrogate DNA methylation and chromatin accessibility allowing us to investigate the epigenetic changes in uncultured clear cell renal cell carcinoma (ccRCC) tumors and normal tissue to uncover genes that contribute to ccRCC tumorigenesis. AcceSssIble is both cost-effective and easily analyzed using simple and straightforward computational analysis. Our study revealed significant changes to the epigenome of ccRCC, especially identifying epigenetically up- (160) or down-regulated genes (180), which are dependent on accessibility changes with (30%) or without (70%) DNA methylation involvement, and which were validated by a cross-correlation of the identified genes with RNA-seq and DNA methylation data from larger cohorts of ccRCC samples from The Cancer Genome Atlas (TCGA). In addition, our findings also revealed these sets of genes not found to be commonly mutated in ccRCC and undergo epigenetic changes at higher frequencies than common ccRCC mutations. In addition, pathway analysis suggests that genetic and epigenetic alterations are independent events, and one such example includes a set of changes in HIF1α signaling pathway genes that are independent of the Von Hippel-Lindau (VHL) status. This suggests a novel epigenetic basis for HIF1αs role during tumorigenesis that may be a common occurrence in ccRCC. Thus, the AcceSssIble analysis on ccRCC samples revealed novel candidates for epigenetic driver genes which were previously undetectable by widely used methylation studies. Overall, this study provides a novel approach that can help identify new epigenetic therapeutic targets and treatment strategies complementing current approaches based primarily on the genetic makeup of primary tumors.

Citation Format: Elinne Becket, Sameer Chopra, Christopher Duymich, Lin J. Justin, Jueng Soo You, Kurinji Pandiyan, Peter W. Nichols, Kimberly D. Siegmund, Peter A. Jones, Gangning Liang. Identification of epigenetic regulated genes through simultaneous analysis of DNA methylation and chromatin structure in uncultured tumors. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr B03.

Identification of DNA Methylation-Independent Epigenetic Events Underlying Clear Cell Renal Cell Carcinoma

Alterations in chromatin accessibility independent of DNA methylation can affect cancer-related gene expression, but are often overlooked in conventional epigenomic profiling approaches. In this study, we describe a cost-effective and computationally simple assay called AcceSssIble to simultaneously interrogate DNA methylation and chromatin accessibility alterations in primary human clear cell renal cell carcinomas (ccRCC). Our study revealed significant perturbations to the ccRCC epigenome and identified gene expression changes that were specifically attributed to the chromatin accessibility status whether or not DNA methylation was involved. Compared with commonly mutated genes in ccRCC, such as the von Hippel-Lindau (VHL) tumor suppressor, the genes identified by AcceSssIble comprised distinct pathways and more frequently underwent epigenetic changes, suggesting that genetic and epigenetic alterations could be independent events in ccRCC. Specifically, we found unique DNA methylation-independent promoter accessibility alterations in pathways mimicking VHL deficiency. Overall, this study provides a novel approach for identifying new epigenetic-based therapeutic targets, previously undetectable by DNA methylation studies alone, that may complement current genetic-based treatment strategies. Cancer Res; 76(7); 1954-64. ©2016 AACR.

Draft Genome Sequence of "Candidatus Liberibacter asiaticus" from a Citrus Tree in San Gabriel, California

The draft genome sequence of "Candidatus Liberibacter asiaticus" strain SGCA5 from an orange citrus tree in San Gabriel, California, is reported here. SGCA5 has a genome size of 1,201,445 bp, a G+C content of 36.4%, 1,152 predicted open reading frames (ORFs), and 42 RNA genes.

De Novo Genome Sequence of "Candidatus Liberibacter solanacearum" from a Single Potato Psyllid in California

The draft genome sequence of "Candidatus Liberibacter solanacearum" strain RSTM from a potato psyllid (Bactericera cockerelli) in California is reported here. The RSTM strain has a genome size of 1,286,787 bp, a G+C content of 35.1%, 1,211 predicted open reading frames (ORFs), and 43 RNA genes.

DNA-Demethylating Agents Target Colorectal Cancer Cells by Inducing Viral Mimicry by Endogenous Transcripts

DNA-demethylating agents have shown clinical anti-tumor efficacy via an unknown mechanism of action. Using a combination of experimental and bioinformatics analyses in colorectal cancer cells, we demonstrate that low-dose 5-AZA-CdR targets colorectal cancer-initiating cells (CICs) by inducing viral mimicry. This is associated with induction of dsRNAs derived at least in part from endogenous retroviral elements, activation of the MDA5/MAVS RNA recognition pathway, and downstream activation of IRF7. Indeed, disruption of virus recognition pathways, by individually knocking down MDA5, MAVS, or IRF7, inhibits the ability of 5-AZA-CdR to target colorectal CICs and significantly decreases 5-AZA-CdR long-term growth effects. Moreover, transfection of dsRNA into CICs can mimic the effects of 5-AZA-CdR. Together, our results represent a major shift in understanding the anti-tumor mechanisms of DNA-demethylating agents and highlight the MDA5/MAVS/IRF7 pathway as a potentially druggable target against CICs.

Linker histone H1.2 establishes chromatin compaction and gene silencing through recognition of H3K27me3

Linker histone H1 is a protein component of chromatin and has been linked to higher-order chromatin compaction and global gene silencing. However, a growing body of evidence suggests that H1 plays a gene-specific role, regulating a relatively small number of genes. Here we show that H1.2, one of the H1 subtypes, is overexpressed in cancer cells and contributes to gene silencing. H1.2 gets recruited to distinct chromatin regions in a manner dependent on EZH2-mediated H3K27me3, and inhibits transcription of multiple growth suppressive genes via modulation of chromatin architecture. The C-terminal tail of H1.2 is critical for the observed effects, because mutations of three H1.2-specific amino acids in this domain abrogate the ability of H1.2 to bind H3K27me3 nucleosomes and inactivate target genes. Collectively, these results provide a molecular explanation for H1.2 functions in the regulation of chromatin folding and indicate that H3K27me3 is a key mechanism governing the recruitment and activity of H1.2 at target loci.

Abstract A1-05: Elucidation of epigenetic driver genes in clear cell renal cell carcinoma using a newly developed assay, AcceSssIble

Background: While many studies have uncovered genetic mutations that drive tumorigenesis, far fewer have described epigenetic changes, such as nucleosome positioning and DNA methylation, which lead to the development of cancer. Therefore, accurately mapping these changes between normal and tumor tissue will provide novel information to identify genes that undergo epigenetic changes that drive tumorigenesis (“epigenetic driver genes”). In this study, we used an assay developed in our laboratory to investigate the epigenetic changes between clear cell renal cell carcinoma (ccRCC, the most common subtype of renal carcinoma) tumors and normal tissue to uncover genes that contribute to ccRCC tumorigenesis.

Methods: Current methods to investigate epigenomic changes in clinical samples are expensive and require abundant biological sample material for analysis. We have developed a novel assay (“AcceSssIble”) to simultaneously determine DNA methylation and chromatin accessibility in clinical samples. It is rapid and cost-effective, only requiring 20 mg of tissue, the Infinium HumanMethylation450 BeadChip platform, and the CpG methyltransferase M.SssI. We used this method to measure the changes in DNA methylation and chromatin accessibility in 9 matched pairs of ccRCC tumors and adjacent normal tissue from different patients, and intersected this data with RNA-seq data of 72 matched ccRCC samples and DNA methylation data of 160 matched ccRCC samples from The Cancer Genome Atlas (TCGA). Genes that were revealed to have the most changes in chromatin structure and expression were then targeted by siRNA knockdown for functional validation in ccRCC.

Results: From the AcceSssIble assay on 9 pairs of ccRCC patient tumor/normal samples, we uncovered 438 genes whose promoters change in chromatin accessibility in at least 2 ccRCC samples, both dependent and independent of DNA methylation changes, and have an accompanying change in gene expression in TCGA RNA-seq data. The results produce a striking figure in which chromatin accessibility changes are inversely correlated with DNA methylation but directly correlated with gene expression changes. Interestingly, loss of (DNA methylation change-dependent) accessibility preferentially occurred within CpG islands, while gain of (DNA methylation change-dependent) accessibility was strongly biased towards non-CpG islands. Meanwhile, chromatin accessibility changes independent of DNA methylation changes do not show preference in CpG content. Furthermore, pathway analyses reveal involvement of HIF1α signaling, cAMP-mediated signaling, and G-protein Coupled Receptor Signaling in the development of ccRCC. Lastly, we performed siRNA knockdown experiments on several top genes most changing in expression and accessibility, which revealed two genes, encoding type IV collagen and an RNA-binding protein, whose knockdown resulted in a significant increase in proliferation in normal kidney epithelial cells.

Conclusions: Our study revealed a vast number of chromatin accessibility and accompanying gene expression changes that occur in gene promoters in the development of ccRCC, both dependent and independent of DNA methylation changes. Each individual tumor has a unique profile of epigenetic alterations. Moreover, almost none of the genes that were found to undergo epigenetic and resulting gene expression changes overlap with TCGA's findings of commonly mutated genes in ccRCC. Overall, these studies represent novel approaches that can help identify new therapeutic target genes and treatment strategies for ccRCC, including personalized approaches.

Citation Format: Elinne Coral Becket, Christopher Duymich, Yin-Wei Chang, Kurinji Pandiyan, Peter Nichols, Peter Jones, Inderbir Gill, Gangning Liang. Elucidation of epigenetic driver genes in clear cell renal cell carcinoma using a newly developed assay, AcceSssIble. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A1-05.

Hypermethylation of the VTRNA1-3 Promoter is Associated with Poor Outcome in Lower Risk Myelodysplastic Syndrome Patients

Myelodysplastic syndrome (MDS) is a heterogeneous group of clonal hematopoietic disorders. MDS is frequently associated with deletions on chromosome 5q as well as aberrant DNA methylation patterns including hypermethylation of key tumor suppressors. We have previously shown that hypermethylation and silencing of the non-coding RNA VTRNA2-1 are correlated with poor outcomes in acute myeloid leukemia patients. In this study, we find that VTRNA1-2 and VTRNA1-3, both located on chromosome 5q, can be regulated and silenced by promoter DNA methylation, and that the hypomethylating agent 5-aza-2-deoxycytidine causes reactivation these genes. In normal hematopoiesis, we find that vault RNAs (vtRNAs) show differential methylation between various hematopoietic cell populations, indicating that allele-specific methylation events may occur during hematopoiesis. In addition, we show that VTRNA1-3 promoter hypermethylation is frequent in lower risk MDS patients and is associated with a decreased overall survival.

Outlining the limits of partial nephrectomy

Amongst nephron-sparing modalities, partial nephrectomy (PN) is the standard of care in the treatment of renal cell carcinoma (RCC). Despite the increasing utilization of PN, particularly propagated by robot-assisted, minimally invasive approaches for small renal masses (SRMs), the limits of PN appear to be also evolving. In this review, we sought to address the tumour stage beyond which PN may be oncologically perilous. While the evidence supports PN in the treatment of tumours < pT2a, PN may have a role in advanced or metastatic RCC. Other scenarios wherein PN has limited utility are also explored, including anatomical or surgical factors that dictate the difficulty of the case, such as prior renal surgery. Lastly, we discuss the emerging role of molecular biomarkers, specifically epigenetics, to aid in the risk stratification of SRMs and to select tumours optimally suited for PN.

Prognosis of small cell lung cancer patients with diabetes treated with metformin

BACKGROUNDS

It has been reported that metformin has an anticancer impact in various solid tumors, but its role in small cell lung cancer (SCLC) remains unclear. This study aimed to investigate the effect of metformin on survival in diabetic SCLC patients.

METHODS

A total of 79 SCLC patients with diabetes treated in our hospital between 2000 and 2010 were enrolled. The clinicopathological data and survival time were collected and evaluated. Univariate and multivariate analyses were used to investigate the association between metformin use and the survival of SCLC.

RESULTS

Among the 79 diabetic patients, 36 patients took metformin. The median OS and DFS were significantly better in the metformin group compared to non-metformin group (OS 18.0 vs 11.5 months, p < 0.001; DFS 10.8 vs 6.5 months, p < 0.001). Multivariate Cox analysis indicated that metformin use was an independent prognostic factor for long-term outcome (HR = 0.549, 95 % CI 0.198-0.978, p = 0.001).

CONCLUSIONS

The prognosis of SCLC patients with diabetes treated with metformin was improved, which might be considered a potential useful anticancer drug in treating SCLC patients.

Epigenetic alterations and microRNA misexpression in cancer and autoimmune diseases: a critical review

Epigenetic markers such as DNA methylation and histone modifications around promoter regions modify chromatin structure and regulate expression of downstream genes. In fact, aberrant epigenetic modifications are common events in human disease including tumorigenesis and autoimmunity. Small non-coding RNAs named microRNAs (miRNAs) are modulators of gene expression and play critical roles in various cellular processes. Several miRNAs have been characterized as tumor suppressors or oncogenes in cancer, and recent reports implicate certain miRNAs in the pathogenesis of autoimmune diseases. Epigenetic investigations have shown that distinct miRNAs are directly regulated by DNA methylation and histone modifications at their promoters. Moreover, miRNAs themselves are key participants in regulating the chromatin modifying machinery. Chromatin-modifying drugs such as DNA methylation inhibitors and histone deacetylase inhibitors have shown efficacy in human malignancies and there is some evidence that these drugs may be useful in autoimmune disease. The benefits of these drugs are at least partially mediated by restoring expression of epigenetically silenced tumor suppressor genes, including miRNAs. The complex layers regulating gene expression have yet to be fully elucidated, but it is clear that epigenetic alterations and miRNA misexpression are essential events in pathologic processes, especially cancer and autoimmune disease, and represent promising therapeutic targets.

Mycophenolic acid upregulates miR-142-3P/5P and miR-146a in lupus CD4+T cells

BACKGROUND

Mycophenolic acid (MPA), the active metabolite of mycophenolate mofetil (MMF), is a noncompetitive inhibitor of inosine monophosphate dehydrogenase, and is now widely used for the treatment of systemic lupus erythematosus (SLE). Dysregulated expression of microRNA has been reported to be associated with the pathogenesis of SLE. However, it is unexplored whether altering microRNA expression in SLE patients is one of the therapeutic effects of MPA.

OBJECTIVES

This study thus aims to investigate the effect of MPA on microRNAs expression in lupus CD4(+)T cells and its underlying mechanisms.

RESULTS

According to our microarray data, 101 upregulated microRNAs and 77 downregulated microRNAs were identified in MPA-treated lupus CD4(+)T cells. Among these microRNAs, miR-142-3p/5p and miR-146a expression was found to be significantly increased in MPA-treated lupus CD4(+)T cells compared to untreated controls. Furthermore, we observed that MPA-treated CD4(+)T cells from patients with SLE showed enriched levels of H4 acetylation in the putative miRNA-142 regulatory region and enhanced levels of H3 acetylation in the putative miRNA-146a regulatory region compared to untreated cells.

CONCLUSION

Data from this study suggest that MPA activates miR-142 and miR-146a expression through histone modification at the promoter region, which may partially explain the pharmacological mechanisms of MPA for SLE.