A microRNA expression and regulatory element activity atlas of the mouse immune system

To better define the control of immune system regulation, we generated an atlas of microRNA (miRNA) expression from 63 mouse immune cell populations and connected these signatures with assay for transposase-accessible chromatin using sequencing (ATAC-seq), chromatin immunoprecipitation followed by sequencing (ChIP-seq) and nascent RNA profiles to establish a map of miRNA promoter and enhancer usage in immune cells. miRNA complexity was relatively low, with >90% of the miRNA compartment of each population comprising <75 miRNAs; however, each cell type had a unique miRNA signature. Integration of miRNA expression with chromatin accessibility revealed putative regulatory elements for differentially expressed miRNAs, including miR-21a, miR-146a and miR-223. The integrated maps suggest that many miRNAs utilize multiple promoters to reach high abundance and identified dominant and divergent miRNA regulatory elements between lineages and during development that may be used by clustered miRNAs, such as miR-99a/let-7c/miR-125b, to achieve distinct expression. These studies, with web-accessible data, help delineate the cis-regulatory elements controlling miRNA signatures of the immune system.

Multicenter Evaluation of Independent High-Throughput and RT-qPCR Technologies for the Development of Analytical Workflows for Circulating miRNA Analysis

Background: Among emerging circulating biomarkers, miRNA has the potential to detect lung cancer and follow the course of the disease. However, miRNA analysis deserves further standardization before implementation into clinical trials or practice. Here, we performed international ring experiments to explore (pre)-analytical factors relevant to the outcome of miRNA blood tests in the context of the EU network CANCER-ID. Methods: Cell-free (cfmiRNA) and extracellular vesicle-derived miRNA (EVmiRNA) were extracted using the miRNeasy Serum/Plasma Advanced, and the ExoRNeasy Maxi kit, respectively, in a plasma cohort of 27 NSCLC patients and 20 healthy individuals. Extracted miRNA was investigated using small RNA sequencing and hybridization platforms. Validation of the identified miRNA candidates was performed using quantitative PCR. Results: We demonstrate the highest read counts in healthy individuals and NSCLC patients using QIAseq. Moreover, QIAseq showed 15.9% and 162.9% more cfmiRNA and EVmiRNA miRNA counts, respectively, in NSCLC patients compared to healthy control samples. However, a systematic comparison of selected miRNAs revealed little agreement between high-throughput platforms, thus some miRNAs are detected with one technology, but not with the other. Adding to this, 35% (9 of 26) of selected miRNAs in the cfmiRNA and 42% (11 of 26) in the EVmiRNA fraction were differentially expressed by at least one qPCR platform; about half of the miRNAs (54%) were concordant for both platforms. Conclusions: Changing of (pre)-analytical methods of miRNA analysis has a significant impact on blood test results and is therefore a major confounding factor. In addition, to confirm miRNA biomarker candidates screening studies should be followed by targeted validation using an independent platform or technology.

Systematic assessment of commercially available low-input miRNA library preparation kits

High-throughput sequencing is increasingly favoured to assay the presence and abundance of microRNAs (miRNAs) in biological samples, even from low RNA amounts, and a number of commercial vendors now offer kits that allow miRNA sequencing from sub-nanogram (ng) inputs. Although biases introduced during library preparation have been documented, the relative performance of current reagent kits has not been investigated in detail. Here, six commercial kits capable of handling <100ng total RNA input were used for library preparation, performed by kit manufactures, on synthetic miRNAs of known quantities and human total RNA samples. We compared the performance of miRNA detection sensitivity, reliability, titration response and the ability to detect differentially expressed miRNAs. In addition, we assessed the use of unique molecular identifiers (UMI) sequence tags in one kit. We observed differences in detection sensitivity and ability to identify differentially expressed miRNAs between the kits, but none were able to detect the full repertoire of synthetic miRNAs. The reliability within the replicates of all kits was good, while larger differences were observed between the kits, although none could accurately quantify the relative levels of the majority of miRNAs. UMI tags, at least within the input ranges tested, offered little advantage to improve data utility. In conclusion, biases in miRNA abundance are heavily influenced by the kit used for library preparation, suggesting that comparisons of datasets prepared by different procedures should be made with caution. This article is intended to assist researchers select the most appropriate kit for their experimental conditions.

Multicenter Evaluation of Circulating Plasma MicroRNA Extraction Technologies for the Development of Clinically Feasible Reverse Transcription Quantitative PCR and Next-Generation Sequencing Analytical Work Flows

BACKGROUND

In human body fluids, microRNA (miRNA) can be found as circulating cell-free miRNA (cfmiRNA), as well as secreted into extracellular vesicles (EVmiRNA). miRNAs are being intensively evaluated as minimally invasive liquid biopsy biomarkers in patients with cancer. The growing interest in developing clinical assays for circulating miRNA necessitates careful consideration of confounding effects of preanalytical and analytical parameters.

METHODS

By using reverse transcription quantitative real-time PCR and next-generation sequencing (NGS), we compared extraction efficiencies of 5 different protocols for cfmiRNA and 2 protocols for EVmiRNA isolation in a multicentric manner. The efficiency of the different extraction methods was evaluated by measuring exogenously spiked cel-miR-39 and 6 targeted miRNAs in plasma from 20 healthy individuals.

RESULTS

There were significant differences between the tested methods. Although column-based extraction methods were highly effective for the isolation of endogenous miRNA, phenol extraction combined with column-based miRNA purification and ultracentrifugation resulted in lower quality and quantity of isolated miRNA. Among all extraction methods, the ubiquitously expressed miR-16 was represented with high abundance when compared with other targeted miRNAs. In addition, the use of miR-16 as an endogenous control for normalization of quantification cycle values resulted in a decreased variability of column-based cfmiRNA extraction methods. Cluster analysis of normalized NGS counts clearly indicated a method-dependent bias.

CONCLUSIONS

The choice of plasma miRNA extraction methods affects the selection of potential miRNA marker candidates and mechanistic interpretation of results, which should be done with caution, particularly across studies using different protocols.

Abstract 1593: Multicenter evaluation of miRNA extraction technologies for the development of a clinically relevant miRNA analysis workflow

MicroRNAs (miRNAs) are small noncoding RNAs that interfere with and regulate different biological pathways. Therefore, dysregulation of miRNAs could lead to disease initiation and progression, particularly in various types of cancer. In human body fluids, miRNAs can be found as circulating cell-free miRNAs (cfmiRNAs, often associated with RNA-binding proteins) as well as exosomal miRNAs (exomiRNAs), both serving as potentially valuable biomarkers to evaluate patient's disease progression, or to monitor treatment efficacy. Various methods for the extraction and analysis of miRNAs, cfmiRNAs or exomiRNAs, are commercially available. Here, we describe the efforts of the Innovative Medicines Initiative (IMI) consortium CANCER-ID (www.cancer-id.eu), a public-private partnership of experts from academia, biotech and pharmaceutical industry, in generating comparative data using different RNA/miRNA extraction technologies in a multicenter ring study.

To address clinical relevance in a later stage of the project, K2EDTA plasma samples from 20 healthy donors were collected in a centralized way with respective informed consent. Five different RNA/miRNA extraction methods and two extraction methods specific for exomiRNAs were selected for comparison: mirVana (ThermoFisher Scientific), miRCURY RNA Isolation Kit (Exiqon), miRNeasy Serum/Plasma kit (QIAGEN), miRNeasy Advanced Serum/Plasma kit (QIAGEN), Plasma/Serum RNA Purification mini kit (Norgen), exoRNeasy Serum/Plasma (QIAGEN) and ultracentrifugation. The eluates were sent to one CANCER-ID partner, centrally performing RT-qPCR analysis on six miRNAs, as well as miRNA massive parallel sequencing.

After extraction using the miRCURY RNA isolation kit and miRNeasy Advanced Serum/Plasma kit, highest miRNA-seq calls (mean: 2x10^6) and lowest RT-qPCR Cq-values (mean: 26.6) for six miRNAs were observed with both extraction methods. Samples from patients and healthy volunteers, respectively, were collected under signed informed consent.

Based on the results of the evaluation of the different miRNA extraction technologies a single extraction technology will be selected for the next iteration of ring studies, the comparison of different analysis platforms and the integration of downstream workflows. First results of these ring studies will be presented.

This work is supported by IMI JU & EFPIA (grand no. 115749).

Citation Format: Martin H. Neumann, Francesca Di Pasquale, Markus Sprenger-Haussels, Jonathan M. Shaffer, Martin Schlumpberger, Fay Betsou, Wim Ammerlaan, Taija af Hallström, Evi Lianidou, Robert Sjöback, Sebastian Bender, Thomas Schlange. Multicenter evaluation of miRNA extraction technologies for the development of a clinically relevant miRNA analysis workflow [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1593.

Alternative RISC assembly: binding and repression of microRNA-mRNA duplexes by human Ago proteins

MicroRNAs (miRNAs) are small noncoding RNAs that post-transcriptionally regulate protein output from the majority of human mRNAs. In contrast to the consensus view that all miRNAs are associated with Argonaute (Ago) proteins, we determine that miRNAs are expressed in a 13-fold excess relative to Agos in HeLa cells and that miRNAs are bound to mRNAs in a sevenfold excess relative to Agos, implying the existence of miRNA-mRNA duplexes not stoichiometrically bound by Agos. We show that all four human Agos can repress miRNA-mRNA duplexes, but only Ago2 can cleave small interfering RNA-mRNA duplexes in vitro. We visualize direct Ago binding to miRNA-mRNA duplexes in live cells using fluorescence lifetime imaging microscopy. In contrast to the consensus view that Agos bind miRNA duplexes, these data demonstrate that Agos can bind and repress miRNA-mRNA duplexes and support a model of catalytic Ago function in translational repression.

Abstract 149: DNA methylation biomarker discovery using the Methyl-Profiler PCR Array System

Histone modifications and DNA methylation are epigenetic events that can modulate gene expression patterns associated with normal development and disease pathology. Epigenetic alterations are clearly involved in breast cancer initiation and progression, as they silence tumor suppressor genes and activate proto-oncogenes. As a result, the profiling of gene promoter DNA methylation status can lead to the identification of novel biomarkers which can aid in the development and improvement of diagnostic, prognostic, and therapeutic treatments. The Methyl-Profiler PCR Array System proves to be quite useful for these purposes.

The Methyl-Profiler DNA Methylation technology method is designed for semi high-throughput gene/target-specific DNA methylation profiling. The method involves the selective digestion of sample DNA with methylation-specific restriction enzymes, followed by precise quantization of intact remaining target DNA by real-time PCR using assays specially designed and validated for high G/C content amplicons. Attesting to the power of this method, as little as one µg of genomic DNA can be used to profile the methylation status of up to 96 gene/target assays, and as low as five % hyper-methylated DNA copies can be reliably detected in a heterogeneous sample. In short, this technology yields quantitative data comparable to bisulfite sequencing, but without the need for bisulfite conversion.

Using the Methyl-Profiler assay, the methylation status of highly relevant methylation targets in breast cancer cell lines was profiled in an effort to discover novel DNA methylation biomarkers. Several putative markers were identified and compared with results as generated by Illumina® Infinium® Methylation Assay platform, demonstrating the viability of the Methyl-Profiler method in discovering DNA methylation biomarkers. In three short procedural steps, the Methyl-Profiler PCR System can efficiently and reproducible identify novel methylation-related targets that may prove to be valuable in developing breast cancer preventative and therapeutic strategies.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 149.

Bimolecular fluorescence complementation demonstrates that the c-Fes protein-tyrosine kinase forms constitutive oligomers in living cells

The c-fes proto-oncogene encodes a unique nonreceptor protein-tyrosine kinase (c-Fes) that contributes to the differentiation of myeloid hematopoietic, vascular endothelial, and some neuronal cell types. Although originally identified as the normal cellular homologue of the oncoproteins encoded by avian and feline transforming retroviruses, c-Fes has recently been implicated as a tumor suppressor in breast and colonic epithelial cells. Structurally, c-Fes consists of a unique N-terminal region harboring an FCH domain, two coiled-coil motifs, a central SH2 domain, and a C-terminal kinase domain. In living cells, c-Fes kinase activity is tightly regulated by a mechanism that remains unclear. Previous studies have established that c-Fes forms high molecular weight oligomers in vitro, suggesting that the dual coiled-coil motifs may regulate the interconversion of inactive monomeric and active oligomeric states. Here we show for the first time that c-Fes forms oligomers in live cells independently of its activation status using a YFP bimolecular fluorescence complementation assay. We also demonstrate that both N-terminal coiled-coil regions are essential for c-Fes oligomerization in transfected COS-7 cells as well as HCT 116 colorectal cancer and K-562 myeloid leukemia cell lines. Together, these data provide the first evidence that c-Fes, unlike c-Src, c-Abl, and other nonreceptor tyrosine kinases, is constitutively oligomeric in both its repressed and active states. This finding suggests that conformational changes, rather than oligomerization, may govern its kinase activity in vivo.

Promoter methylation blocks FES protein-tyrosine kinase gene expression in colorectal cancer

The FES locus encodes a unique nonreceptor protein-tyrosine kinase (FES) traditionally viewed as a proto-oncogene but more recently implicated as a tumor suppressor in colorectal cancer (CRC). Recent studies have demonstrated that while FES is expressed in normal colonic epithelium, expression is lost in tumor tissue and colorectal cancer cell lines, a finding common among tumor suppressors. Here we provide compelling evidence that promoter methylation is an important mechanism responsible for downregulation of FES gene expression in colorectal cancer cells. Treatment with the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine resulted in the expression of functional FES transcripts in all CRC cell lines examined, including Caco-2, COLO 320, DLD-1, HCT 116, SNU-1040, SW-480, and HT-29. Bisulfite sequencing of genomic DNA isolated from 5-aza-2'-deoxycytidine-treated HT-29 cells identified methylated CpG dinucleotides immediately upstream from the FES transcription initiation sites. In contrast, this region of the FES promoter was hypomethylated in genomic DNA from normal colonic epithelium. In addition, methylation completely blocked the activity of the FES promoter in reporter gene assays. Promoter methylation is a previously unrecognized mechanism by which FES expression is suppressed in CRC cell lines, and is consistent with a tumor suppressor role for FES in this tumor site despite its tyrosine kinase activity.

The flanking region sequences of the 15-kDa lipoprotein gene differentiate pathogenic treponemes

The species Treponema pallidum includes three subspecies (pallidum, pertenue, and endemicum) that cause syphilis, yaws, and bejel, respectively. A closely related species, Treponema paraluiscuniculi, is the etiologic agent of venereal syphilis in rabbits but does not infect humans. Although these treponemes cause distinct diseases, no laboratory method for differentiation has been reported. Genetic signatures were defined in the 5' and 3' flanking regions of the 15-kDa lipoprotein gene (tpp15) that distinguish the human pathogens and T. paraluiscuniculi, as well as distinguishing T. pallidum subsp. pallidum from the causes of human nonvenereal treponematoses. A single Eco47III restriction site in the 5' flanking region differentiates T. pallidum subsp. pallidum from the other subspecies and species, and an XcmI site in the 3' flanking region differentiates T. paraluiscuniculi from the human pathogens. Polymerase chain reaction methods and restriction polymorphism were used to analyze 27 strains of pathogenic Treponema species.

Identification of the Treponema pallidum subsp. pallidum glycerophosphodiester phosphodiesterase homologue

To identify potential opsonic targets of Treponema pallidum subsp. pallidum, a treponemal genomic expression library was constructed and differentially screened with opsonic and non-opsonic T. pallidum antisera. This method identified an immunoreactive clone containing an open reading frame encoding a 356 residue protein. Nucleotide sequence analysis demonstrated the translated protein to be a homologue of glycerophosphodiester phosphodiesterase, a glycerol metabolizing enzyme previously identified in Haemophilus influenzae, Escherichia coli, Bacillus subtilis and Borrelia hermsii. Sequence alignment analyses revealed the T. pallidum and H. influenzae enzymes share a high degree of amino acid sequence similarity (72%), suggesting that in T. pallidum this molecule may be surface exposed and involved in IgD binding as is the case with its counterpart in H. influenzae.

Detection of Treponema pallidum by a sensitive reverse transcriptase PCR

Syphilis is diagnosed by serologic testing or by identification of the causative agent, Treponema pallidum. The bacterium has historically been detected in clinical specimens by dark-field microscopy, immunostaining with polyclonal or monoclonal antibodies, or the rabbit inoculation test (RIT). RIT is considered to be very sensitive and specific, although it is available only in research settings and is not clinically useful due to the length of time required to obtain a result. In recent years, several PCR methods have been developed for the detection of T. pallidum, but none of these has shown a clear advantage in sensitivity over RIT. We have developed a specific and highly sensitive reverse transcriptase PCR (RT-PCR) that targets a 366 bp region of the 16S rRNA of T. pallidum. This RT-PCR can detect a single organism by Southern analysis when whole organisms are diluted and 10(-2) to 10(-3) T. pallidum organisms when RNA equivalents are used to make cDNA. The test was demonstrated to detect 10(-2) T. pallidum RNA equivalents in cerebrospinal fluid. Twenty different strains of T. pallidum, isolated from cerebrospinal fluids, aqueous humor, blood, and chancres, were shown to be detectable by this test. This efficient and sensitive technique could be more useful than existing methods for detecting very low numbers of organisms in clinical samples.

Conservation of the 15-kilodalton lipoprotein among Treponema pallidum subspecies and strains and other pathogenic treponemes: genetic and antigenic analyses

The 15-kDa lipoprotein of Treponema pallidum is a major immunogen during natural syphilis infection in humans and experimental infection in other hosts. The humoral and cellular immune responses to this molecule appear late in infection as resistance to reinfection is developing. One therefore might hypothesize that this antigen is important for protective immunity. This possibility is explored by using both genetic and antigenic approaches. Limited or no cross-protection has been demonstrated between the T. pallidum subspecies and strains or between Treponema species. We therefore hypothesized that if the 15-kDa antigen was of major importance in protective immunity, it might be a likely site of antigenic diversity. To explore this possibility, the sequences of the open reading frames of the 15-kDa gene have been determined for Treponema pallidum subsp. pallidum (Nichols and Bal-3 strains), T. pallidum subsp. pertenue (Gauthier strain), T. pallidum subsp. endemicum (Bosnia strain), Treponema paraluiscuniculi (Cuniculi A, H, and K strains), and a little-characterized simian isolate of Treponema sp. (Fribourg-Blanc strain). No significant differences in DNA sequences of the genes for the coding region of the 15-kDa antigen were found among the different species and subspecies studied. In addition, all organisms showed expression of the 15-kDa antigen as determined by monoclonal antibody staining. The role of the 15-kDa antigen in protection against homologous infection with T. pallidum subsp. pallidum Nichols was examined in rabbits immunized with a purified recombinant 15-kDa fusion protein. No alteration in chancre development was observed in immunized, compared to unimmunized, rabbits, and the antisera induced by the immunization failed to enhance phagocytosis of T. pallidum subsp. pallidum by macrophages in vitro. These results do not support a major role for this antigen in protection against syphilis infection.

VDRL antibodies enhance phagocytosis of Treponema pallidum by macrophages

Although reactivity in nontreponemal tests develops in patients with untreated syphilis, no immunologic function has been ascribed to these antibodies. This study demonstrates that rabbit antibodies induced by immunization with VDRL antigen and VDRL antibodies affinity-purified from syphilitic rabbit serum enhance phagocytosis of Treponema pallidum. The proportion of macrophages ingesting treponemes in the presence of these antisera was 45% +/- 5% and 27% +/- 4%, respectively, versus 14% +/- 3% for normal serum (P < .001 and P < .01). Both IgG and IgM fractions contained opsonic activity. Absorption of VDRL antibodies from syphilitic serum diminished but did not eliminate opsonization, suggesting at least two classes of target molecules. Despite opsonic capacity, VDRL antibodies fail to facilitate macrophage-mediated killing of T. pallidum. Nevertheless, VDRL-immunized rabbits are partially protected against T. pallidum infection, developing fewer lesions (delayed and smaller) than do unimmunized controls. These results suggest a heretofore unrecognized functional role for VDRL antibodies in syphilis infection.

Characterization of the serum requirement for macrophage-mediated killing of Treponema pallidum ssp. pallidum: relationship to the development of opsonizing antibodies

Serum pools were collected from rabbits bled at various times after intra-testicular infection with Treponema pallidum ssp. pallidum. These were tested for their ability to opsonize T. pallidum and promote killing of the organisms by macrophages. Compared to normal sera, significant opsonization was first seen on day 10 of infection as measured by both ingestion (P < 0.001) and macrophage-mediated killing (P = 0.006); significant levels of functional antibodies persisted through 300 days of infection. Although opsonic activity peaked early in infection, antibodies that promoted optimal macrophage-mediated killing developed much later, suggesting that these two functions may represent activities of antibodies with differing specificities or affinities. The initial development of antibodies that augment both phagocytosis and killing corresponds with the in vivo clearance of treponemes from the primary site of infection. These observations support the hypothesis that macrophages are the major effector mechanism for elimination of T. pallidum during early syphilis infection.

Opsonization of Treponema pallidum is mediated by immunoglobulin G antibodies induced only by pathogenic treponemes

Rabbit antisera to Leptospira interrogans, Borrelia hermsii, and Treponema phagedenis biotype Reiter, reactive to shared spirochetal antigens, failed to enhance phagocytosis of Treponema pallidum by macrophages, while immunoglobulin G to Treponema pallidum subsp. pertenue and Treponema paraluiscuniculi promoted phagocytosis. Opsonic antibodies are directed to pathogen-restricted, not shared spirochetal, antigens.

A subpopulation of Treponema pallidum is resistant to phagocytosis: possible mechanism of persistence

While untreated syphilis infection is characterized by spontaneous resolution of early lesions, a few organisms evade the host immune response and persist for many years. Macrophages are generally recognized as the effector cell responsible for bacterial clearance, and phagocytosis is enhanced by immune serum. This study examined the susceptibility of Treponema pallidum isolated at various stages of lesion resolution to opsonization and phagocytosis by macrophages in vitro. Findings suggest that the population of organisms remaining after the majority of bacteria have been cleared in vivo is resistant to phagocytosis. This may provide a mechanism for the persistence of T. pallidum in the face of an otherwise active immune response.