A non-coding RNA balancing act: miR-346-induced DNA damage is limited by the long non-coding RNA NORAD in prostate cancer.

BACKGROUND: miR-346 was identified as an activator of Androgen Receptor (AR) signalling that associates with DNA damage response (DDR)-linked transcripts in prostate cancer (PC). We sought to delineate the impact of miR-346 on DNA damage, and its potential as a therapeutic agent. METHODS: RNA-IP, RNA-seq, RNA-ISH, DNA fibre assays, in vivo xenograft studies and bioinformatics approaches were used alongside a novel method for amplification-free, single nucleotide-resolution genome-wide mapping of DNA breaks (INDUCE-seq). RESULTS: miR-346 induces rapid and extensive DNA damage in PC cells - the first report of microRNA-induced DNA damage. Mechanistically, this is achieved through transcriptional hyperactivation, R-loop formation and replication stress, leading to checkpoint activation and cell cycle arrest. miR-346 also interacts with genome-protective lncRNA NORAD to disrupt its interaction with PUM2, leading to PUM2 stabilisation and its increased turnover of DNA damage response (DDR) transcripts. Confirming clinical relevance, NORAD expression and activity strongly correlate with poor PC clinical outcomes and increased DDR in biopsy RNA-seq studies. In contrast, miR-346 is associated with improved PC survival. INDUCE-seq reveals that miR-346-induced DSBs occur preferentially at binding sites of the most highly-transcriptionally active transcription factors in PC cells, including c-Myc, FOXA1, HOXB13, NKX3.1, and importantly, AR, resulting in target transcript downregulation. Further, RNA-seq reveals widespread miR-346 and shNORAD dysregulation of DNA damage, replication and cell cycle processes. NORAD drives target-directed miR decay (TDMD) of miR-346 as a novel genome protection mechanism: NORAD silencing increases mature miR-346 levels by several thousand-fold, and WT but not TDMD-mutant NORAD rescues miR-346-induced DNA damage. Importantly, miR-346 sensitises PC cells to DNA-damaging drugs including PARP inhibitor and chemotherapy, and induces tumour regression as a monotherapy in vivo, indicating that targeting miR-346:NORAD balance is a valid therapeutic strategy. CONCLUSIONS: A balancing act between miR-346 and NORAD regulates DNA damage and repair in PC. miR-346 may be particularly effective as a therapeutic in the context of decreased NORAD observed in advanced PC, and in transcriptionally-hyperactive cancer cells.

Martius labial fat pad graft (use in rectovaginal fistula repair).

INTRODUCTION AND HYPOTHESIS: The objective is to demonstrate the utility of the Martius labial fat pad graft in pelvic fistula repair. METHODS: An incision is made over the labium majus from the level of the clitoral hood superiorly and extending inferiorly to the level of the labiocrural fold. The fibrofatty graft is then mobilized from the adjacent labium majus. The flap can be divided either at its anterior or at its posterior pedicle. A subepithelial defect is created through which the flap will be passed. The flap is sewn into place by attaching it to the underlying rectovaginal fascia without associated tensioning. Next, the posterior vaginal wall is closed over the graft with a series of everting subepithelial mattress sutures followed by a reinforcing layer of interrupted #1 Vicryl through the vaginal epithelium. CONCLUSIONS: The advantages of the Martius flap in fistula repair include low morbidity, lack of a cosmetic defect, and the need for only a single surgical field. Its prominent fibrous component makes it a stronger graft than adipose tissue from other areas and its abundant blood supply promotes rapid neovascularization and lends itself well to many surgical modifications that can be utilized in even the most difficult of fistula repairs.

Implementation of a clinical prediction tool for pulmonary embolism diagnosis in a tertiary teaching hospital reduces the number of computed tomography pulmonary angiograms performed.

AIM: To evaluate the effect of implementing the Wells score clinical prediction tool (CPT) on rationalising the use of computed tomography pulmonary angiography (CTPA) for diagnosing pulmonary embolism (PE). METHODS: Within a tertiary teaching hospital, a retrospective study was conducted applying Wells score to all CTPA ordered in the first quarter of 2007. Subsequently, an algorithm including Wells score and d-dimer assay was developed to assist clinicians in rationalising their ordering of CTPA. A prospective study was performed from February to August 2009 to assess the impact of this algorithm. CTPA results, d-dimer levels, referral sources and dates were recorded. The number of CTPA performed over a 7-month period following implementation of the algorithm was compared with the same period during the previous year. PE prevalence within each risk category was compared with the published literature. RESULTS: Three hundred and thirty-three patients were investigated with CTPA in the prospective study period. Two hundred and sixty-eight patients (80.4% of cases) had complete data. The prevalence of PE in the present study was 13.8% with 57 (21.2%) patients stratified to low risk, 169 (63.0%) to intermediate risk and 42 (15.6%) to high risk. Subgroup prevalence was 8.8%, 11.8% and 23.8% respectively. Compared with the same period in 2008, 121 (26.6%) less CTPA were performed. CONCLUSION: Institutional implementation of a clinical prediction tool into the decision-making process is feasible and significantly reduces the number of CTPA being performed, with substantial cost savings and patient benefits.

Apoptosis-modulatory miR-361-3p as a novel treatment target in endocrine-responsive and endocrine-resistant breast cancer.

Breast cancer (BC) is the most diagnosed cancer in women worldwide. In estrogen receptor (ER)-positive disease, anti-estrogens and aromatase inhibitors (AI) improve patient survival; however, many patients develop resistance. Dysregulation of apoptosis is a common resistance mechanism; thus, agents that can reinstate the activity of apoptotic pathways represent promising therapeutics for advanced drug-resistant disease. Emerging targets in this scenario include microRNAs (miRs). To identify miRs modulating apoptosis in drug-responsive and -resistant BC, a high-throughput miR inhibitor screen was performed, followed by high-content screening microscopy for apoptotic markers. Validation demonstrated that miR-361-3p inhibitor significantly increases early apoptosis and reduces proliferation of drug-responsive (MCF7), plus AI-/antiestrogen-resistant derivatives (LTED, TamR, FulvR), and ER- cells (MDA-MB-231). Importantly, proliferation-inhibitory effects were observed in vivo in a xenograft model, indicating the potential clinical application of miR-361-3p inhibition. RNA-seq of tumour xenografts identified FANCA as a direct miR-361-3p target, and validation suggested miR-361-3p inhibitor effects might be mediated in part through FANCA modulation. Moreover, miR-361-3p inhibition resulted in p53-mediated G1 cell cycle arrest through activation of p21 and reduced BC invasion. Analysis of publicly available datasets showed miR-361-3p expression is significantly higher in primary breast tumours vspaired normal tissue and is associated with decreased overall survival. In addition, miR-361-3p inhibitor treatment of BC patient explants decreased levels of miR-361-3p and proliferation marker, Ki67. Finally, miR-361-3p inhibitor showed synergistic effects on BC growth when combined with PARP inhibitor, Olaparib. Together, these studies identify miR-361-3p inhibitor as a potential new treatment for drug-responsive and -resistant advanced BC.

The antiandrogen enzalutamide downregulates TMPRSS2 and reduces cellular entry of SARS-CoV-2 in human lung cells.

SARS-CoV-2 attacks various organs, most destructively the lung, and cellular entry requires two host cell surface proteins: ACE2 and TMPRSS2. Downregulation of one or both of these is thus a potential therapeutic approach for COVID-19. TMPRSS2 is a known target of the androgen receptor, a ligand-activated transcription factor; androgen receptor activation increases TMPRSS2 levels in various tissues, most notably prostate. We show here that treatment with the antiandrogen enzalutamide-a well-tolerated drug widely used in advanced prostate cancer-reduces TMPRSS2 levels in human lung cells and in mouse lung. Importantly, antiandrogens significantly reduced SARS-CoV-2 entry and infection in lung cells. In support of this experimental data, analysis of existing datasets shows striking co-expression of AR and TMPRSS2, including in specific lung cell types targeted by SARS-CoV-2. Together, the data presented provides strong evidence to support clinical trials to assess the efficacy of antiandrogens as a treatment option for COVID-19.

Evaluation of a biological risk management tool on large western United States dairies.

Critical to changing biosecurity practices on the farm is an individual assessment of those practices contributing to disease transmission. The purpose of this project was to assess, implement, and refine a biological risk management survey for use on large western United States dairy farms. Assessment tools developed by Iowa State University Center for Food Security and Public Health (Ames, IA) were refined using a focus group process and by testing them on 40 dairy herds in California. Each question was evaluated using standard criteria and producer responses. Some survey questions required refinement for clarity and others were considered unnecessary. New questions were added based on a biosecurity literature review, resulting in a new set of questions that can be used by extension educators and food animal veterinarians to help identify disease risk areas and educate dairy producers.

Postoperative Opioid Prescribing Following Gynecologic Surgery for Pelvic Organ Prolapse.

OBJECTIVES: The aim of this study was to evaluate postoperative pain scores, quantity of prescribed opioids at hospital discharge, and need for additional opioid prescriptions among women undergoing surgical treatment of pelvic organ prolapse. METHODS: Institutional billing data were used to identify all patients undergoing pelvic reconstructive surgery between January 1, 2012, and May 30, 2017. Inpatient records were utilized to obtain prescription data (reported in oral morphine equivalents for standardization) and pain scores. The cohort was organized by surgical approach (open, endoscopic, vaginal), number of concomitant procedures, and patient age stratified by decade. These factors were then matched to postoperative pain scores, amount of opioid prescribed at discharge, and number of subsequent opioid refills. Pain scores and opioid use were also compared for correlation. RESULTS: One thousand eight hundred thirty patients underwent surgical treatment of pelvic organ prolapse and met criteria for study participation. A significant decrease in pain scores, mean oral morphine equivalents prescribed, and opioid refill rates was seen with increasing patient age by decade regardless of surgical approach. Pain scores were significantly different only between patients undergoing vaginal surgery with 0 concomitant procedures versus 1 or more concomitant procedures. Finally, pain scores were directly correlated to the amount of opioid prescribed. CONCLUSIONS: Pain scores, opioid prescription amounts, and refills varied by patient age and surgical approach but were unaffected by concomitant procedures. Further work in correlating pain scores to opioid utilization is needed to ensure appropriate prescribing patterns and reduce risks of opioid dependence and diversion.

Enhancement of antitumor immunity by CTLA-4 blockade.

One reason for the poor immunogenicity of many tumors may be that they cannot provide signals for CD28-mediated costimulation necessary to fully activate T cells. It has recently become apparent that CTLA-4, a second counterreceptor for the B7 family of costimulatory molecules, is a negative regulator of T cell activation. Here, in vivo administration of antibodies to CTLA-4 resulted in the rejection of tumors, including preestablished tumors. Furthermore, this rejection resulted in immunity to a secondary exposure to tumor cells. These results suggest that blockade of the inhibitory effects of CTLA-4 can allow for, and potentiate, effective immune responses against tumor cells.

Changing education to improve patient care.

Health professionals need competencies in improvement skills if they are to contribute usefully to improving patient care. Medical education programmes in the USA have not systematically taught improvement skills to residents (registrars in the UK). The Accreditation Council for Graduate Medical Education (ACGME) has recently developed and begun to deploy a competency based model for accreditation that may encourage the development of improvement skills by the 100 000 residents in accredited programmes. Six competencies have been identified for all physicians, independent of specialty, and measurement tools for these competencies have been described. This model may be applicable to other healthcare professions. This paper explores patterns that inhibit efforts to change practice and proposes an educational model to provide changes in management skills based on trainees' analysis of their own work.

Manipulation of costimulatory signals to enhance antitumor T-cell responses.

One of the major goals of tumor immunotherapy is the induction of tumor-specific T-cell responses that will be effective in eradicating disseminated tumors. Emerging information on the role of costimulatory molecules in T-cell activation offers several new strategies for enhancing antitumor responses, including the induction of expression of costimulatory molecules on tumor cells, enhancement of the presentation of transferred tumor antigen by host antigen-presenting cells, and ex vivo antigen priming of autologous antigen-presenting cells.

The roles of mutS, sbcCD and recA in the propagation of TGG repeats in Escherichia coli.

A 24 triplet TGG.CCA repeat array shows length- and orientation-dependent propagation when present in the plasmid pUC18. When TGG(24) is present as template for leading-strand synthesis, plasmid recovery is normal in all strains tested. However, when it acts as template for lagging-strand synthesis, plasmid propagation is seriously compromised. Plasmids carrying deletions in the 5' side of this sequence can be isolated and products carrying 15 TGG triplets do not significantly interfere with plasmid propagation. Mutations in sbcCD, mutS and recA significantly improve the recovery of plasmids with TGG(24) on the lagging-strand template. These findings suggest that TGG(24) can fold into a structure that can interfere with DNA replication in vivo but that TGG(15) cannot. Furthermore, since the presence of the MutS and SbcCD proteins are required for propagation interference, it is likely that stabilisation of mismatched base pairs and secondary structure cleavage are implicated. In contrast, there is no correlation of triplet repeat expansion and deletion instability with predicted DNA folding. These results argue for a dissociation of the factors affecting DNA fragility from those affecting trinucleotide repeat expansion-contraction instability.

DNA palindromes adopt a methylation-resistant conformation that is consistent with DNA cruciform or hairpin formation in vivo.

Long DNA palindromes present a threat to genomic stability and are not tolerated in Escherichia coli. It has been suggested that this is a consequence of cruciform or hairpin formation by palindromic sequences. This work describes a methylation inhibition assay for unusual DNA secondary structure in vivo that is both internally controlled and non-invasive. If a palindrome with a central GATC target site for Dam methylase assumes a cruciform or hairpin conformation in vivo, then the GATC sequence will be located in a single-stranded loop and will consequently not be modified. The centre of a long perfect palindrome located in bacteriophage lambda is shown to be methylation-resistant in vivo. Changes to the central sequence and insertions of 10 base-pairs of asymmetric sequence do not alter the degree of under-methylation, but insertions of 20 base-pairs or more of asymmetric sequence reduce the under-methylation of the palindrome centre. We also show that the centres of long palindromes are more under-methylated than equivalent sequences in a non-palindromic context. These results are consistent with an unusual secondary structure, such as DNA cruciform or hairpin, and indicate that the formation pathway of the structure detected is independent of the composition and symmetry of the central 10 base-pairs of the palindrome.

Secondary structures in d(CGG) and d(CCG) repeat tracts.

Several studies have been made to elucidate the nature of secondary structures in the single strands of d(CGG).d(CCG) repeat tracts but with conflicting conclusions. Here, we review this work and attempt to come towards consensus. Some investigators find that the G-rich strand forms hairpins. Of these, some conclude that pairing is in the alignment d(GGC).d(GGC) with two Watson-Crick bonds and one G.G bond per duplex repeat, others conclude that the alignment is d(GCG).d(GCG) with two G.G bonds and one C.C bond per duplex repeat. Others find quadruplex formation and conclude that this is in the latter alignment with two G4-quartets per quadruplex repeat and C.C bonds. We investigate why these different results were obtained and conclude that quadruplexes are likely to form under physiological conditions. We argue that they are probably bonded in the alignment d(GGC).d(GGC) with one G4-quartet and two C.G.C.G. quartets per quadruplex repeat. The C-rich strand does not appear to form quadruplexes under physiological conditions but forms hairpins. Apparently, short hairpins adopt the alignment d(CCG).d(CCG) with mismatched cytosine residues stacked into the helix but with 15 or more repeat units, the dominant form is a distorted hairpin aligned as d(GCC).d(GCC) with unpaired cytosine residues possibly turned outwards and stacked in the minor groove.

Evidence for two preferred hairpin folding patterns in d(CGG).d(CCG) repeat tracts in vivo.

Unusual DNA secondary structures have been implicated in the expansion of trinucleotide repeat tracts that has been found to be responsible for a growing number of human inherited disorders and folate-sensitive fragile chromosome sites. By inserting trinucleotide repeat sequences into a palindromic clamp in lambda phage we are able to investigate their tendencies to form hairpins in vivo in any particular alignment and with odd or even numbers of repeat units in the hairpin. We previously showed that with d(CAG).d(CTG) repeat tracts there was a markedly greater tendency to form hairpins with even numbers of repeat units than with odd numbers, whereas d(GAC).d(GTC) repeats showed no such alternation despite having the same base composition. We expected that d(CGG).d(CCG) repeats, might show the same pattern as d(CAG).(CTG) repeats since they are also involved in trinucleotide repeat expansion disorders. The pattern was not so clear and we wondered whether this might be because d(CGG).d(CCG) repeats have more than one possible alignment in which they could self-anneal. We now present results for all three alignments, which suggest that while even-membered hairpins are preferred in the frame d(CGG).d(CCG), hairpins with odd numbers of trinucleotides are more stable in the frame d(GGC).d(GCC). In both cases the base-pair predicted to close the terminal loop of unpaired bases is 5'C.3'G which has previously been found to be a favoured loop-closing pair.

Slow replication of palindrome-containing DNA.

Lambda red gam phage carrying a 571 base-pair palindrome are unviable in wild-type Escherichia coli hosts. By using de-methylation to study the fate of DNA strands introduced into E. coli, we have demonstrated that a decrease in the yield of palindrome-containing molecules with two newly synthesized strands can occur without any concomitant loss of replicated molecules containing input strands. This implies that the palindrome-containing DNA is not being destroyed even as a consequence of replication, but rather that its replication rate is reduced. These results demonstrate that a palindrome can mediate unviability without directing cleavage of its carrier replicon.

The effects of trinucleotide repeats found in human inherited disorders on palindrome inviability in Escherichia coli suggest hairpin folding preferences in vivo.

Unusual DNA secondary structures have been implicated in the expansion of trinucleotide repeat tracts that are associated with several human inherited disorders. We present evidence consistent with the folding of these trinucleotide repeats into hairpin loops at the center of a long DNA palindrome in vivo. Our assay utilizes a palindrome in bacteriophage lambda, the center of which determines its ability to inhibit plaque formation in a manner that is consistent with folding into a hairpin or cruciform structure. We show that central inserts of even numbers of d(CAG).d(CTG) repeats inhibit plaque formation more than do odd numbers. Both d(CAG)2.d(CTG)2 and d(CGG)2.d(CCG)2 central sequences behave like DNA sequences known to form two-base loops in vitro, suggesting that they may also form compact and stable loops. By contrast, repeats of d(GAC).d(GTC) do not show any evidence consistent with unusual loop stability. These results agree with in vitro evidence that the unstable repeats can form hairpin secondary structures and suggest a favored position of folding. We discuss the potential roles of secondary structures, DNA replication and recombination in models of repeat tract expansion.

The effects of nucleotide sequence changes on DNA secondary structure formation in Escherichia coli are consistent with cruciform extrusion in vivo.

The construction in bacteriophage lambda of a set of long DNA palindromes with paired changes in the central sequence is described. Identical palindrome centers were previously used by others to test the S-type model for cruciform extrusion in vitro. Long DNA palindromes prevent the propagation of carrier phage lambda on a wild-type host, and the sbcC mutation is sufficient to almost fully alleviate this inviability. The plaque areas produced by the palindrome containing phages were compared on an Escherichia coli sbcC lawn. Central sequence changes had a greater effect upon the plaque area than peripheral changes, implying that the residual palindrome-mediated inviability in E. coli sbcC is center-dependent and could be due to the formation of a cruciform structure. The results argue strongly that intrastrand pairing within palindromes is critical in determining their effects in vivo. In addition, the same data suggests that DNA loops in vivo may sometimes contain two bases only.

Action of a transposable element in coding sequence fusions.

The original Casadaban technique for isolating fused cistrons encoding hybrid beta-galactosidase proteins used a Mucts62 prophage to align the upstream coding sequence and lacZ prior to selection. Kinetic analysis of araB-lacZ fusion colony emergence indicated that the required DNA rearrangements were regulated and responsive to conditions on selection plates. This has been cited as an example of "directed mutation." Here we show genetically that the MuA and integration host factor (IHF) transposition functions are involved in the formation of hybrid araB-lacZ cistrons and propose a molecular model for how fusions can form from the initial strand-transfer complex. These results confirm earlier indications of direct Mu involvement in the fusion process. The proposed model explains how rearranged Mu sequences come to be found as interdomain linkers in certain hybrid cistrons and indicates that the fusion process involves a spatially and temporally coordinated sequence of biochemical reactions.

The effects of central asymmetry on the propagation of palindromic DNA in bacteriophage lambda are consistent with cruciform extrusion in vivo.

The propagation of lambda phages carrying long perfect palindromes has been compared with that of phages carrying imperfect palindromes with small regions of central asymmetry. The perfect palindromes confer a more deleterious phenotype than those with central asymmetry and the severity of the phenotype declines with the length of asymmetry in the range from O to 27 base pairs. These results argue that a center-dependent reaction is involved in the phenotypic effects of palindromic DNA sequences, consistent with the idea that cruciform extrusion occurs in vivo.

The interaction of cos with Chi is separable from DNA packaging in recA-recBC-mediated recombination of bacteriophage lambda.

Chi (5'-GCTGGTGG) is a recombinator in RecA-RecBC-mediated recombination in Escherichia coli. In bacteriophage lambda vegetative recombination, Chi is fully active only when it is correctly oriented with respect to cos, the site that defines the ends of the packaged chromosome. Here we demonstrate that packaging from cos is not necessary for this cos-Chi interaction. Our evidence suggests that correctly oriented cos is an activator of Chi. cos, as an activator, is (1) dominant over cos-, (2) active opposite an extensive heterology, (3) able to interact with Chi only when on the same (cis) chromosome, and (4) able to interact with Chi at distances as far as greater than or equal to 20 kb. Thus, cos and Chi form a two-component recombinator system for general recombination. cos may serve as an asymmetric entry site for a recombination enzyme that recognizes Chi in an asymmetric way.