Deleterious iron-mediated oxidation of biomolecules

Iron is an essential metal for most biological organisms. However, if not tightly controlled, iron can mediate the deleterious oxidation of biomolecules. This review focuses on the current understanding of the role of iron in the deleterious oxidation of various biomolecules, including DNA, protein, lipid, and small molecules, e.g., ascorbate and biogenic amines. The effect of chelation on the reactivity of iron is also addressed, in addition to iron-associated toxicities. The roles of the iron storage protein ferritin as both a source of iron for iron-mediated oxidations and as a mechanism to safely store iron in cells is also addressed.

Cleavage of poly(A)-binding protein by poliovirus 3C protease inhibits host cell translation: a novel mechanism for host translation shutoff

Cleavage of eukaryotic translation initiation factor 4GI (eIF4GI) by viral 2A protease (2Apro) has been proposed to cause severe translation inhibition in poliovirus-infected cells. However, infections containing 1 mM guanidine-HCl result in eIF4GI cleavage but only partial translation shutoff, indicating eIF4GI cleavage is insufficient for drastic translation inhibition. Viral 3C protease (3Cpro) cleaves poly(A)-binding protein (PABP) and removes the C-terminal domain (CTD) that interacts with several translation factors. In HeLa cell translation extracts that exhibit cap-poly(A) synergy, partial cleavage of PABP by 3Cpro inhibited translation of endogenous mRNAs and reporter RNA as effectively as complete cleavage of eIF4GI and eIF4GII by 2Apro. 3Cpro-mediated translation inhibition was poly(A) dependent, and addition of PABP to extracts restored translation. Expression of 3Cpro in HeLa cells resulted in partial PABP cleavage and similar inhibition of translation. PABP cleavage did not affect eIF4GI-PABP interactions, and the results of kinetics experiments suggest that 3Cpro might inhibit late steps in translation or ribosome recycling. The data illustrate the importance of the CTD of PABP in poly(A)-dependent translation in mammalian cells. We propose that enteroviruses use a dual strategy for host translation shutoff, requiring cleavage of PABP by 3Cpro and of eIF4G by 2Apro.

Demonstrating internal ribosome entry sites in eukaryotic mRNAs using stringent RNA test procedures

The dicistronic assay for internal ribosome entry site (IRES) activity is the most widely used method for testing putative sequences that may drive cap-independent translation initiation. This assay typically involves the transfection of cells with dicistronic DNA test constructs. Many of the reports describing eukaryotic IRES elements have been criticized for the use of inadequate methods for the detection of aberrant RNAs that may form in transfected cells using this assay. Here we propose the combined use of a new RNAi-based method together with RT-PCR to effectively identify aberrant RNAs. We illustrate the use of these methods for analysis of RNAs generated in cells transfected with dicistronic test DNAs containing either the hepatitis C virus (HCV) IRES or the X-linked inhibitor of apoptosis (XIAP) cellular IRES. Both analyses indicated aberrantly spliced transcripts occurred in cells transfected with the XIAP dicistronic DNA construct. This contributed to the unusually high levels of apparent IRES activity exhibited by the XIAP 5' UTR in vivo. Cells transfected directly with dicistronic RNA exhibited much lower levels of XIAP IRES activity, resembling the lower levels observed after translation of dicistronic RNA in rabbit reticulocyte lysates. No aberrantly spliced transcripts could be detected following direct RNA transfection of cells. Interestingly, transfection of dicistronic DNA or RNA containing the HCV IRES did not form aberrantly spliced transcripts. These observations stress the importance of using alternative test procedures (e.g., direct RNA transfection) in conjunction with a combination of sensitive RNA analyses for discerning IRES-containing sequences in eukaryotic mRNAs.

BCL-2 translation is mediated via internal ribosome entry during cell stress

The cellular response to stress involves a rapid inhibition of cap-dependent translation via multiple mechanisms, yet some translation persists. This residual translation may include proteins critical to the cellular stress response. BCL-2 is a key inhibitor of intrinsic apoptotic signaling. Its primary transcript contains a 1.45-kb 5'-untranslated region (UTR) including 10 upstream AUGs that may restrict translation initiation via cap-dependent ribosome scanning. Thus, we hypothesized that this 5'-UTR may contain an internal ribosome entry site (IRES) that facilitates BCL-2 translation, particularly during cell stress. Here we show that the BCL-2 5'-UTR demonstrated IRES activity both when translated in vitro and also when m(7)G-capped and polyadenylated mRNA was transiently transfected into 293T cells. The activity of this IRES in unstressed cells was approximately 6% the strength of the hepatitis C virus IRES but was induced 3-6-fold in a dose-dependent manner following short term treatment with either etoposide or sodium arsenite. Thus, the IRES-mediated translation of BCL-2 may enable the cell to replenish levels of this critical protein during cell stress, when cap-dependent translation is repressed, thereby maintaining the balance between pro- and anti-apoptotic BCL-2 family members in the cell and preventing unwarranted induction of apoptosis.

Robust single-cell DNA methylome profiling with snmC-seq2

Single-cell DNA methylome profiling has enabled the study of epigenomic heterogeneity in complex tissues and during cellular reprogramming. However, broader applications of the method have been impeded by the modest quality of sequencing libraries. Here we report snmC-seq2, which provides improved read mapping, reduced artifactual reads, enhanced throughput, as well as increased library complexity and coverage uniformity compared to snmC-seq. snmC-seq2 is an efficient strategy suited for large-scale single-cell epigenomic studies.

Translation of cellular inhibitor of apoptosis protein 1 (c-IAP1) mRNA is IRES mediated and regulated during cell stress

Cellular inhibitor of apoptosis protein 1 (c-IAP1) can regulate apoptosis through its interaction with downstream TNF receptor effectors (TRAF1 and TRAF2), by binding to and inhibiting certain caspases, and by controlling the levels of specific proapoptotic stimuli (e.g., Smac/DIABLO) within the cell. Studies involving the expression of c-IAP1 mRNA and protein in cells and tissues have provided evidence suggesting c-IAP1 expression may be posttranscriptionally controlled. Because the 5'-UTR of c-IAP1 mRNA is unusually long, contains multiple upstream AUG codons, and has the potential to form thermodynamically stable secondary structures, we investigated the possibility it contained an internal ribosome entry site (IRES) that may regulate its expression. In the present study, the c-IAP1 5'-UTR exhibited IRES activity when dicistronic RNA constructs were translated in rabbit reticulocyte lysate (RRL) and in transiently transfected cells. IRES-mediated translation was similar to that exhibited by the hepatitis C virus IRES but varied significantly in RRL and in HeLa, HepG2, and 293T cells, indicating the c-IAP1 IRES was system and cell type specific. IRES-mediated translation was maintained in mono- and dicistronic constructs in which the UTR was inserted downstream from a stable hairpin that prevented cap-dependent ribosome scanning. In cells, the presence or absence of a methylated cap did not significantly affect the translation of polyadenylated, monocistronic RNAs containing the c-IAP1 5'-UTR. IRES-mediated translation was stimulated in transfected cells treated with low doses of pro-apoptotic stimuli (i.e., etoposide and sodium arsenite) that inhibited endogenous cellular translation.

The canine skin and ear microbiome: A comprehensive survey of pathogens implicated in canine skin and ear infections using a novel next-generation-sequencing-based assay

This study analyzed the complex bacterial and fungal microbiota of healthy and clinically affected canine ear and skin samples. A total of 589 canine samples were included: 257 ear swab samples (128 healthy vs. 129 clinically affected) and 332 skin swab samples (172 healthy vs. 160 clinically affected) were analyzed using next-generation sequencing (NGS) to determine both relative and absolute abundances of bacteria and fungi present in the samples. This study highlighted the canine microbiota of clinically affected cases was characterized by an overall loss of microbial diversity, high microbial biomass, with overgrowth of certain members of the microbiota. The observed phenotype of these samples was best described by the combination of both relative and absolute microbial abundances. Compared to healthy samples, 78.3% of the clinically affected ear samples had microbial overgrowth; 69.8% bacterial overgrowth, 16.3% fungal overgrowth, and 7.0% had both bacterial and fungal overgrowth. The most important microbial taxa enriched in clinically affected ears were Malassezia pachydermatis, Staphylococcus pseudintermedius, Staphylococcus schleiferi, and a few anaerobic bacteria such as Finegoldia magna, Peptostreptococcus canis, and Porphyromonas cangingivalis. The anaerobic microbes identified here were previously not commonly recognized as pathogens in canine ear infections. Similar observations were found for skin samples, but yeasts and anaerobes were less abundant when compared to clinically affected cases. Results highlighted herein, signify the potential of NGS-based methods for the accurate quantification and identification of bacterial and fungal populations in diagnosing canine skin and ear infections, and highlight the limitations of traditional culture-based testing.

Abstract 4230: A novel method for sequence- and strand-specific, genome-wide 5-hmC profiling

5-Hydroxymethylcytosine (5-hmC) is a new epigenetic hallmark rapidly getting much interest as the subject of mapping and sequencing work. While the exact function of 5-hmC is not fully understood, it is likely to regulate gene expression via active DNA de-methylation. Previous studies have shown it may play an important role in cell differentiation and carcinogenesis. Cells that are more stem- and progenitor-like have greatly reduced levels of 5-hmC compared with more differentiated cells. Similarly, tumor cells display less 5-hmC than their normal counterparts. This was not associated with either grade or stage, suggesting that global loss of 5-hmC may be an early event in carcinogenesis. To date, several methods have been developed to profile 5-hmC at the genomic level: most are enrichment-based and utilize antibodies to 5-hmC or its modified forms or make use of bioorthogonal labeling and pull-down of glycosylated 5-hmC. The caveat is that these approaches are low resolution and that they require large amounts of input genomic DNA. Initial efforts for detection of 5-hmC at single-base resolution require several micrograms of DNA, require parallel or subtractive sequencing, and employ successive chemical treatments that can degrade DNA and hinder sequencing. Here we report on a new method that by combining modification-sensitive restriction enzymes with massively parallel (“next-generation”) sequencing approaches, genome-wide 5-hmC can be mapped at single site resolution from low (100 ng) DNA inputs. Importantly, this method can be used for strand-specific localization of 5-hmC as well as direct identification of single nucleotide polymorphisms (SNPs) within the sequencing reads. Data can also be compared directly with single-base resolution DNA methylation data from reduced-representation bisulfite sequencing (RRBS) for simultaneous 5-mC and 5-hmC profiling from the same sample. 5-mC and 5-hmC of human brain DNA using this combined method indicates unique distributions of the 5-hmC modification. This new method should provide a unique tool in enhancing our understanding of the interplay of genetic and epigenetic regulations in carcinogenesis.

Citation Format: XueGuang Sun, Adam Petterson, Hunter Chung, Xi Yu Jia, Marc E. Van Eden. A novel method for sequence- and strand-specific, genome-wide 5-hmC profiling. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4230. doi:10.1158/1538-7445.AM2013-4230

Abstract 3006: A novel method for locus specific detection of 5-hydroxymethylcytosine

Epigenetic mis-regulation leading to diseases such as cancer is classically understood in terms of aberrant DNA methylation patterns. For decades, 5-methylcytosine (5-mC) has been the focus of epigenetic DNA modification studies. But recently, a novel epigenetic DNA modification, 5-hydroxymethylcytosine (5-hmC), has been shown to be present in mammalian brain and ES cells. Current tools available to map DNA methylation (e.g. bisulfite conversion) cannot distinguish between 5-mC and 5-hmC. Here we describe a new method for locus specific interrogation of 5-hmC within DNA.

Treatment of DNA with a 5-hmC glucosyltransferase enzyme specifically adds a glucose moiety onto preexisting 5-hmC residues, yielding glucosyl-5-hydroxymethylcytosine (glu-5-hmC). Subsequent digestion of DNA with glu-5-hmC sensitive restriction endonucleases effectively cleaves DNA with cytosine, 5-mC, or 5-hmC within their recognition site. But when glu-5-hmC is present, DNA is not able to be cleaved. Exploiting this difference in “cleavability”, 5-hmC can be detected at loci of interest using qPCR.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3006. doi:10.1158/1538-7445.AM2011-3006

Abstract 4026: Epigenetic biomarker discovery and validation for diagnosis and therapeutic intervention for hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is one of the most common and lethal malignancies worldwide, accounting for approximately half a million annual deaths globally. HCC is completely asymptomatic in the early stages of the disease; therefore, early detection of HCC in afflicted patients is vital to receive therapeutic benefits from curative surgery. The standard diagnosis of HCC relies upon detection of the serum alpha-fetoprotein (AFP) level in at-risk subjects followed by hepatic ultrasonography to identify suspicious nodules. Accurate levels of AFP are often difficult to detect, and the imaging method to identify nodules is both operator-sensitive and subject to a high false-negative rate. While it is known that hepatocellular carcinoma is a multi-step process that requires altered expression of multiple genes, recent evidence has indicated that epigenetic abnormalities also play an important role in hepatocarcinogenesis. The discovery of reliable and accurate epigenetic biomarkers may open up new avenues for the development of novel diagnostic tools and provide new target for therapeutic interventions. Combining Next Generation Sequencing methods with well-established bisulfite conversation chemistry, a unique genome-wide epigenetic profile for HCC was done in liver tumor and normal tissues. Hypermethylated and hypomethylated gene regions from the genome-wide epigenetic profile were then validated for percent methylation in liver tumor and normal tissues using a streamlined system of methylation-sensitive restriction enzyme (MSRE) digestion combined with real-time PCR. Serum circulated genomic DNA from liver cancer patients were also examined to look for potential epigenetic markers for clinical diagnostic applications. More than one hundred gene loci were identified at differentially methylated regions (DMRs) by comparing several different stage liver tumors with their correspondent normal tissue by the genome wide epigenetic profile. Calculated CT values from combined MSRE digestion and real-time PCR quantitation indicated that percent methylation of the CpG island in the gene ADAM8 was highest in stage IV liver tumor tissue, while percent methylation of the CpG island in CSMD3 was lowest in stage IV tissue compared to normal adjacent tissue. Percent methylation of the CpG island in ZNF783 was high in all stages of HCC tumor liver tissue compared to normal adjacent tissue. Epigenomic profiling and screening with MSRE digestion and real-time PCR identified and validated differences in the CpG island methylation status of three gene loci in different stages of HCC liver tissue and normal tissue. Extensive validation of these gene specific loci in larger numbers of HCC samples is necessary before they can be considered possible epigenetic biomarkers for novel diagnostic tools and therapeutic interventions for HCC.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4026. doi:1538-7445.AM2012-4026

Abstract 2956: A targeted bisulfite sequencing method combining microfluidics-based PCR with Next-Gen sequencing

DNA methylation plays an important role in normal organismal development and in cellular differentiation in higher organisms. Changes in DNA methylation have been shown to correlate with disease risk, response to therapy and survival in a wide range of clinical conditions such as cancer and autoinflammatory diseases. Recent advances in next-generation sequencing and microarray technology have made it possible to map DNA methylation genome-wide, at a high resolution. However, these genomic assays tend to be costly, labor-intensive and impractical in the clinic. Thus, DNA methylation assays that measure a small number of genomic regions in large cohorts are needed for validating biomarker candidates discovered from genomic studies. For this reason, we have developed a targeted bisulfite sequencing platform for simultaneously measuring DNA methylation in multiple loci with multiple samples by combining microfluidics-based technology with next generation sequencing. First, post-bisulfite PCR primers for each target region were designed using our proprietary program Bisulfite Primer Seeker, and then experimentally validated using a standard genomic control. Primers which pass the validation were used for the subsequent target amplification. Target amplification were performed using Fluidigm Access Array 48.48 which allows parallel PCR reactions for 48 samples by 48 single-plex assays. An attractive aspect of this platform is that relatively small quantities of template are required (∼50 ng/sample). Assays can also be multiplexed to improve throughput. Furthermore, as with many targeted approaches, index or barcoding tags can be incorporated into the universal adapter regions of the PCR product enabling the pooling of samples before direct sequencing. Using this platform we have evaluated 9 genomic loci with 9 artificial mixed samples containing different methylation levels. Results showed the target bisulfite sequencing platform to be robust and reproducible. The methylation value between the technical replicates were highly correlated. Each of the amplicons was covered by a thousand or more reads, making the detection sensitivity reach down to the low methylation levels. Compared with other target bisulfite sequencing methods, our assay has several advantages. First, it uses relatively small amounts of gDNA as input, making it practical for most clinical samples. Secondly the workflow is simple, straightforward and can be automated. Finally, it avoids the complexity and difficulties of multiplex PCR by utilizing microfluidics-based single-plex PCR. All these features make it an ideal platform for DNA methylation biomarker validation.

Citation Format: Emily Putnam, Lam Nguyen, Hunter Chung, Peisheng Shi, Xueguang Sun, Marc E. Van Eden, Xi-Yu Jia. A targeted bisulfite sequencing method combining microfluidics-based PCR with Next-Gen sequencing. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2956. doi:10.1158/1538-7445.AM2015-2956