An Easy, Cost-Effective, and Scalable Method to Deplete Human Ribosomal RNA for RNA-seq

RNA sequencing (RNA-seq) is a powerful and increasingly prevalent method to characterize and quantify the transcriptome. Ribosomes are extremely abundant, however, and approximately 80% of total RNA is ribosomal RNA (rRNA). Therefore, to detect and quantify less abundant yet biologically important transcripts such as messenger RNA (mRNA) and long noncoding RNAs (lncRNA), it is essential to minimize the rRNA being sequenced. Although commercial methods exist to deplete rRNA from total RNA samples before sequencing, they are expensive and require specific amounts of input RNA, and the most commonly used kit is no longer available as a stand-alone product. Here, we present an optimized rRNA depletion protocol using RNase H and DNA oligonucleotides complementary to human rRNA transcripts. This protocol includes guidelines for DNA oligo preparation, RNA:DNA hybridization, RNase H cleavage and RNA cleanup, and benchmarking of rRNA depletion. The method is flexible because the user can include additional complementary DNA oligos directed against any abundant transcript in their particular system. Furthermore, the performance of this rRNA depletion approach is comparable to or better than that of commercial kits, at a fraction of the cost and across a wide range of input RNA amounts. © 2021 Wiley Periodicals LLC. Basic Protocol: Specific depletion of rRNA transcripts from human total RNA Support Protocol: Preparation of the rRNA depletion DNA oligonucleotide pool.

A Case of Pseudo-pneumothorax with Complications

Pseudo-pneumothorax occurs after inappropriately diagnosing a pneumothorax based on a chest X-ray. This can be attributed to skin folds, bed sheets, previous pneumothorax, heating blankets, clothes, and other circumstances that may mimic the radiographic findings of a pneumothorax. We present a case where a patient underwent a tube thoracostomy due to the diagnosis of a pneumothorax that was not, in fact, present. The unnecessary intervention was complicated by hemoptysis and cardiac arrest.

ASC acts in a caspase-1-independent manner to worsen acute pneumonia caused by Pseudomonas aeruginosa

PURPOSE

Pseudomonas aeruginosa expresses a type III secretion system (T3SS) that activates the host inflammasome-mediated immune response. We examined the role of inflammasome activation in severe infection outcomes.

METHODS

We infected C57BL/6 (B6) mice lacking inflammasome components ASC or caspase-1/11 with a highly virulent strain of P. aeruginosa, PSE9, using a mouse model of pneumonia. We evaluated inflammasome activation in vitro by infecting bone marrow-derived macrophages (BMDMs) with PSE9 and measuring cell death and release of inflammasome-dependent cytokines IL-18 and IL-1β. A bioluminescent reporter assay was used to detect activity of caspase-1 and caspase-3/7 in BMDMs from B6 and ASC-deficient mice.Results/Key Findings. ASC^-/- mice exhibited significantly improved survival relative to caspase-1/11^-/- mice and B6 mice, demonstrating that ASC and caspase-1/11 play differential roles in P. aeruginosa infection. We found that ASC^-/- BMDMs exhibited significantly reduced cell death relative to B6 BMDMs, while caspase-1/11^-/- BMDMs were resistant to cell death. IL-18 and IL-1β were both detected from supernatants of infected B6 BMDMs, but cytokine release was abrogated in both ASC^-/- and caspase-1/11^-/- BMDMs. We detected a 2.5-fold increase in the activation of caspase-3/7 in PSE9-infected B6 BMDMs, but no increase in infected ASC^-/- BMDMs. Cell death, cytokine release and caspase-3/7 activity were dependent on a functional T3SS.

CONCLUSIONS

Collectively, these results are consistent with a model whereby the T3SS apparatus of P. aeruginosa activates the caspase-1-dependent inflammasome and caspase-3/7 through an ASC-dependent mechanism. This activation may have implications for the outcomes of P. aeruginosa infections.

Bivalent Chromatin Domains in Glioblastoma Reveal a Subtype-Specific Signature of Glioma Stem Cells

Glioblastoma multiforme (GBM) can be clustered by gene expression into four main subtypes associated with prognosis and survival, but enhancers and other gene-regulatory elements have not yet been identified in primary tumors. Here, we profiled six histone modifications and CTCF binding as well as gene expression in primary gliomas and identified chromatin states that define distinct regulatory elements across the tumor genome. Enhancers in mesenchymal and classical tumor subtypes drove gene expression associated with cell migration and invasion, whereas enhancers in proneural tumors controlled genes associated with a less aggressive phenotype in GBM. We identified bivalent domains marked by activating and repressive chromatin modifications. Interestingly, the gene interaction network from common (subtype-independent) bivalent domains was highly enriched for homeobox genes and transcription factors and dominated by SHH and Wnt signaling pathways. This subtype-independent signature of early neural development may be indicative of poised dedifferentiation capacity in glioblastoma and could provide potential targets for therapy.Significance: Enhancers and bivalent domains in glioblastoma are regulated in a subtype-specific manner that resembles gene regulation in glioma stem cells. Cancer Res; 78(10); 2463-74. ©2018 AACR.

Simultaneous mapping of transcript ends at single-nucleotide resolution and identification of widespread promoter-associated non-coding RNA governed by TATA elements

Understanding the relationships between regulatory factor binding, chromatin structure, cis-regulatory elements and RNA-regulation mechanisms relies on accurate information about transcription start sites (TSS) and polyadenylation sites (PAS). Although several approaches have identified transcript ends in yeast, limitations of resolution and coverage have remained, and definitive identification of TSS and PAS with single-nucleotide resolution has not yet been achieved. We developed SMORE-seq (simultaneous mapping of RNA ends by sequencing) and used it to simultaneously identify the strongest TSS for 5207 (90%) genes and PAS for 5277 (91%) genes. The new transcript annotations identified by SMORE-seq showed improved distance relationships with TATA-like regulatory elements, nucleosome positions and active RNA polymerase. We found 150 genes whose TSS were downstream of the annotated start codon, and additional analysis of evolutionary conservation and ribosome footprinting suggests that these protein-coding sequences are likely to be mis-annotated. SMORE-seq detected short non-coding RNAs transcribed divergently from more than a thousand promoters in wild-type cells under normal conditions. These divergent non-coding RNAs were less evident at promoters containing canonical TATA boxes, suggesting a model where transcription initiation at promoters by RNAPII is bidirectional, with TATA elements serving to constrain the directionality of initiation.

Alternative cleavage and polyadenylation during colorectal cancer development

PURPOSE

Alternative cleavage and polyadenylation (APA) of mRNAs is a phenomenon that alters 3'-untranslated region length leading to altered posttranscriptional regulation of gene expression. Changing APA patterns have been shown to result in misregulation of genes involved in carcinogenesis; therefore, we hypothesized that altered APA contributes to progression of colorectal cancer, and that measurement of APA may lead to discovery of novel biomarkers.

EXPERIMENTAL DESIGN

We used next-generation sequencing to directly measure global patterns of APA changes during colorectal carcinoma progression in 15 human patient samples. Results were validated in a larger cohort of 50 patients, including 5 normal/carcinoma pairs from individuals.

RESULTS

We discovered numerous genes presenting progressive changes in APA. Genes undergoing untranslated region (3'UTR) shortening were enriched for functional groups such as cell-cycle and nucleic acid-binding and processing factors, and those undergoing 3'UTR lengthening or alternative 3'UTR usage were enriched for categories such as cell-cell adhesion and extracellular matrix. We found indications that APA changes result from differential processing of transcripts because of increased expression of cleavage and polyadenylation factors. Quantitative PCR analysis in a larger series of human patient samples, including matched pairs, confirmed APA changes in DMKN, PDXK, and PPIE genes.

CONCLUSIONS

Our results suggest that genes undergoing altered APA during human cancer progression may be useful novel biomarkers and potentially targeted for disease prevention and treatment. We propose that the strategy presented here may be broadly useful in discovery of novel biomarkers for other types of cancer and human disease.

Systematic analysis of posttranscriptional gene expression

Recent systems studies of gene expression have begun to dissect the layers of regulation that underlie the eukaryotic transcriptome, the combined consequence of transcriptional and posttranscriptional events. Among the regulatory layers of the transcriptome are those of the ribonome, a highly dynamic environment of ribonucleoproteins in which RNA-binding proteins (RBPs), noncoding regulatory RNAs (ncRNAs) and messenger RNAs (mRNAs) interact. While multiple mRNAs are coordinated together in groups within the ribonome of a eukaryotic cell, each individual type of mRNA consists of multiple copies, each of which has an opportunity to be a member of more than one modular group termed a posttranscriptional RNA operon or regulon (PTRO). The mRNAs associated with each PTRO encode functionally related proteins and are coordinated at the levels of RNA stability and translation by the actions of the specific RBPs and noncoding regulatory RNAs. This article examines the methods that led to the elucidation of PTROs and the coordinating mechanisms that appear to regulate the RNA components of PTROs. Moreover, the article considers the characteristics of the dynamic systems that drive PTROs and how mRNA components are bound collectively in physical 'states' to respond to cellular perturbations and diseases. In conclusion, these studies have challenged the extent to which cellular mRNA abundance can inform investigators of the functional status of a biological system. We argue that understanding the ribonome has greater potential for illuminating the underlying coordination principles of growth, differentiation, and disease.

A flexible loop in tyrosine hydroxylase controls coupling of amino acid hydroxylation to tetrahydropterin oxidation

The role of a polypeptide loop in tyrosine hydroxylase (TyrH) whose homolog in phenylalanine hydroxylase (PheH) takes on a different conformation when substrates are bound has been studied using site-directed mutagenesis. The loop spans positions 177 to 191; alanine was introduced into those positions, introducing one alanine substitution per TyrH variant. Mutagenesis of residues in the center of the loop resulted in alterations in the KM values for substrates, the Vmax value for dihydroxyphenylalanine (DOPA) synthesis, and the coupling of tetrahydropterin oxidation to tyrosine hydroxylation. The variant with the most altered KM value for 6-methyltetrahydropterin was TyrH F184A. The variants with the most affected K(tyr) values were those with substitutions in the center of the loop, TyrH K183A, F184A, D185A, P186A and D187A. These five variants also had the most reduced Vmax values for DOPA synthesis. Alanine substitution in positions 182-186 resulted in lowered ratios of tyrosine hydroxylation to tetrahydropterin oxidation. TyrH F184Y and PheH Y138F, variants with the residue at the center of the loop substituted with the residue present at the homologous position in the other hydroxylase, were also studied. The V/K(tyr) to V/K(phe) ratios for these variants were altered significantly, but the results did not suggest that F184 of TyrH or Y138 of PheH plays a dominant role in determining amino acid substrate specificity.

The Contiform incontinence device ? efficacy and patient acceptability

A consecutive series of 59 women with urodynamic stress incontinence but no prolapse were offered treatment with Contiform (available in small/medium/large sizes). The 24-h pad test was the primary outcome measure. Of the 59 enrolled women, 41 (69%) completed the trial protocol. Median use was 21 days (IQR 10-24.5). Two severity groups were categorized based on pretreatment pad testing (mild <30 g/day n=24 patients, 59%) and moderate/severe >30 g/day, n= 17(41%). Overall, loss was reduced by a median of 72% (5-92), p<0.0001, with the greatest reduction seen in the moderate/severe group of 85% (75-100) p<0.0001. No significant benefit on pad testing was noted in the mild group. Both groups showed significant benefit on the Incontinence Impact Questionnaire. The insertion technique was quickly learnt and the device well tolerated. A medium-sized Contiform was used by 33 (80%) women. No serious adverse events occurred.

Prawn sandwiches, red herrings and abdominal pregnancy

An unusual presentation of abdominal pregnancy is reported. The difficulty in diagnosis of this form of ectopic pregnancy, and the potential risks of delayed intervention are highlighted. The association with uterine anomaly, in this case uterus didelphys, is discussed.

A detailed study of the effect of videoframe rates of 25, 30 and 60 Hertz on human sperm movement characteristics

A comparison was made of the movement characteristics of human spermatozoa analysed at three videoframe rates (25, 30 and 60 Hz) using two computerized motility analysers from Hamilton-Thorn Research (the HTM-2030 and the IVOS) operating at 25 and 30 Hz respectively. Analysis at 30 and 60 Hz was performed on the IVOS. The use of uncapacitated, capacitated and pentoxifylline-stimulated spermatozoa ensured a full range of movement characteristics was analysed. The velocity parameters curvilinear velocity and average path velocity were highly frame-rate dependent, and mean values increased with videoframe rate. An interaction of framing rate and time of data collection resulted in an increase in straight-line velocity with framing rate. Mean lateral head displacement and linearity were similar at 25 or 30 Hz but significantly depressed at 60 Hz. Beat-cross frequency increased by 74% when analysed at 60 rather than 30 Hz. The following criteria: curvilinear velocity > 100 microns/s, linearity < 65% and lateral head displacement > 7.5 microns, were used to define hyperactivated spermatozoa. Significantly more hyperactivated cells were identified at 30 Hz than 25 Hz (1-10%) but not at 60 Hz. A different population of cells is likely to have been identified as hyperactivated at 60 Hz due to alterations in component movement parameters from which the definition of hyperactivation was derived. In conclusion, direct comparisons should not be drawn between data analysed at 25 and 30 Hz. Analysis at 60 Hz introduced complex alterations which made simple comparisons with 30 Hz data invalid.

In vitro release of ACTH from dispersed rat pars intermedia cells. II. Effect of neurotransmitter substances

Studies were carried out to test the responsiveness of dispersed pars intermedia (PI) cells to a number of neurotransmitter substances known to be present in the PI. These substances were tested over an extended dose range. The catecholamines, adrenaline, noradrenaline, and dopamine inactivated PI ACTH at high concentrations; at lower concentrations, they were without effect. Histamine and carbachol had no effect on ACTH release. 5-hydroxytryptamine stimulated ACTH release in a dose-related manner, from 10(-6) to 10(-3)M, while having no effect on ACTH release from the pars distalis (PD). We conclude that the release of ACTH from the PI may be controlled by direct serotonergic innervation.

In vitro release of ACTH from dispersed rat pars intermedia cells. I. Effect of secretagogues

Studies were made to test the responsiveness of dispersed pars intermedia (PI) cells to a number of secretagogues, that are known to alter ACTH release from the pars distalis (PD) in vitro. In summary, (a) incubation in high (K+), which will increase ACTH release from the PD, did not alter ACTH release from the PI; (b) a crude extract of rat hypothalamus (HE) increased ACTH release from PD and PI; (c) the effect of HE was not due to its vasopression content, since pretreatment of the extract with thioglycolic acid did not modify its ACTH-releasing activity and neither lysine nor arginine vasopressin stimulated ACTH release from the PI; and (d) a partially purified CRF preparation, which will stimulate ACTH release from the PD, did not alter ACTH release from the PI. We conclude that the hypothalamus contains a substance(s) that will stimulate ACTH release from the PI and that the 'secretagogue' is neither vasopressin nor the same CRF that will stimulate ACTH release from the PD.