Complex regulation of Eomes levels mediated through distinct functional features of the Meteor long non-coding RNA locus

Long non-coding RNAs (lncRNAs) are implicated in a plethora of cellular processes, but an in-depth understanding of their functional features or their mechanisms of action is currently lacking. Here we study Meteor, a lncRNA transcribed near the gene encoding EOMES, a pleiotropic transcription factor implicated in various processes throughout development and in adult tissues. Using a wide array of perturbation techniques, we show that transcription elongation through the Meteor locus is required for Eomes activation in mouse embryonic stem cells, with Meteor repression linked to a change in the subpopulation primed to differentiate to the mesoderm lineage. We further demonstrate that a distinct functional feature of the locus-namely, the underlying DNA element-is required for suppressing Eomes expression following neuronal differentiation. Our results demonstrate the complex regulation that can be conferred by a single locus and emphasize the importance of careful selection of perturbation techniques when studying lncRNA loci.

140 Lessons From the Front Line: Communication is Key

Introduction

As junior doctors, we very rarely receive formal teaching on communication after medical school, with telephone encounters and difficult conversations over technology being a vital yet missing part of our education. The COVID-19 pandemic has required us to adapt how we communicate with patients’ families due to hospital visiting restrictions. In an era where tragically deterioration and death have been much more commonplace, we looked to identify areas where junior doctors felt their communication skills could be improved, and implemented a teaching programme to deliver this.

Methods

Pre-teaching questionnaires were distributed to a range of grades of junior doctors working in University Hospital of Llandough, Cardiff. The questionnaires were distributed at the beginning of June 2020, after 3 months of working in pandemic conditions. A teaching session on telephone and video communication skills was delivered by a local palliative care consultant. Post-teaching, a repeat questionnaire was undertaken to assess response and identify key learning points.

Results

Pre-teaching, 100% of the 22 respondents had had to participate in difficult conversations over the phone, 82% had had no formal phone based communication skills training and 81.82% felt some form of formal teaching would be helpful. Post-teaching, 12 junior doctors provided feedback with an average 37% increase in confidence to undertake difficult conversations. Key learning points from the session highlighted the importance of preparation, regularly updating the family to build trust and rapport, and integrating family updates via tele-communication into daily ward life.

Conclusions

Education around telephone communication skills is critical to enable us to adapt our skills in accordance with the demands of the pandemic, to continue to support relatives and to engage with technology with confidence. Increased preparation is required to navigate difficult conversations via technology, and successful communication requires clinicians to take responsibility for initiating regular family updates.

141 Face Time’ for the First Time: Patients, Families and Junior Doctors

Introduction

Over the course of the COVID-19 pandemic, supporting effective communication between patients and their families has been a recognised challenge in the healthcare environment. Virtual communication via telecommunication and video-calling is more important than ever, but with minimal clinician education, preparation and relevant technological infrastructure available in the context of a global pandemic, we have recognised communication as an area for improvement as junior doctors working on a COVID-19 ward.

Methods

We interviewed via telephone 22 nominated next of kin relatives of patients admitted to a COVID-19 ward in the University Hospital of Llandough during May 2020 using a pre-prepared survey. We then provided relatives with the opportunity to engage with video-call updates from a doctor (with the patient’s permission). In appropriate scenarios, we used video calling to break bad news and to facilitate difficult communications with family members. These video calls were provided via Accurx, an NHS approved video communication system.

Results

Initial survey results showed an average understanding score of their relative’s current clinical plan of 5.5/10, with 63% of respondents saying they did not feel well informed. Nearly a quarter of respondents (22%) had received difficult news over the phone during the COVID-19 pandemic, and 86% said they would find video communication useful. Post-intervention survey results suggested a unanimous improvement in relative satisfaction, with relatives reporting an increased understanding around the admission, reassurance around the quality of care being given and less isolation from the patient.

Conclusions

The COVID-19 pandemic has provided novel communication challenges to physicians, promoting flexibility and adaptation to some of the core inter-personal skills we develop throughout training. Technology plays a huge role in this, and the use of video calling in particular can preserve non-verbal communication within the doctor-relative relationship and improve emotional connection between patients and their loved ones.

Abstract P4-15-05: The presence of one or multiple foci of microinvasion is not associated with an increased risk of local recurrence in women with ductal carcinoma in situ treated with breast conserving therapy

Background: Ductal Carcinoma in Situ (DCIS) is a non-invasive breast cancer often treated with breast-conserving surgery (BCS) with or without radiotherapy (RT). It is unclear if the presence of microinvasion (MI) (invasion ≤1mm) is associated with an increased risk of LR (DCIS or invasive) or invasive LR compared to women with pure DCIS. In addition, the impact of multiple foci (>2) of MI compared to pure DCIS is also unknown; therefore, it is unclear if some women with MI require more aggressive treatment. We evaluated the impact of the presence of MI and the number of foci of MI on the risks of any LR and invasive LR in a population of women with DCIS with and without MI treated with BCS.

Methods: The cohort includes all women diagnosed with pure DCIS or DCIS with MI in Ontario from 1994-2003 treated with BCS +/- RT. All cases had systematic pathology review to confirm the presence and number of foci of MI. Treatment and outcomes were ascertained through administrative databases and validated by chart review. Cox proportional hazards model was used to evaluate the impact of MI and the number of foci of MI (1 vs >2 foci) on the development of any LR and invasive LR compared to cases with pure DCIS. The 10-yr local recurrence-free survival (LRFS) and invasive LRFS rates were calculated using the Kaplan-Meier approach with differences compared using the log-rank test.

Results: The population cohort includes 2,988 women with DCIS treated by BCS (N=2,721 pure DCIS, N= 267 DCIS with MI). Median follow-up (12 years; p=.23) and median age at diagnosis (58 years; p=.17) were similar in both groups. RT was given in 58% of cases with MI and 51% of cases with pure DCIS (p=.03). Hormonal therapy was utilized in 7.1% of women with MI and 5.3% of women with pure DCIS (p=.22). LR developed in 59 (22.1%) cases with MI and 530 (19.6%) cases of pure DCIS. Women with MI were more likely to have high nuclear grade (p<.001), and larger tumor size (p<.001) compared to those without MI. On multivariable analyses adjusted for age, the presence of 1 focus of MI(HR=.92, 95% CI: .64-1.33) or ≥2 foci of MI (HR=1.26, 95% CI: .85-1.85) was not associated with an increased risk of any LR compared to cases with pure DCIS. Factors associated with any LR were age <50 years at diagnosis, RT, multifocality and high nuclear grade. The presence of 1 focus of MI (HR=.86, 95% CI: .52-1.40) or > 2 foci of MI (HR=1.45, 95% CI: .90-2.32) was also not associated with an increased risk of invasive LR compared to cases of pure DCIS. Among women treated with BCS alone, the 10 year LRFS rates were 80%, 75% and 73% for women with pure DCIS, 1 focus, >2 foci of MI (p=.10). The invasive LRFS rates were 89%, 91% and 85% (p=.26). Among women treated with BCS+RT, the 10 year LRFS rates were 87%, 88% and 80% (p=0.32) for women with pure DCIS, 1 focus or ≥2 foci of MI. The invasive LRFS rates were 93%, 90% and 86% (p=.44). There was no interaction between the presence of MI and RT.

Conclusions: Women with DCIS with one or multiple foci of microinvasion (<1mm) treated by breast conserving therapy do not have an increased risk of LR or invasive LR compared to women with pure DCIS.

Citation Format: Lalani N, Paszat L, Sutradhar R, Gu S, Fong C, Nofech-Mozes S, Hanna W, Tuck A, Youngson B, Miller N, Done SJ, Chang MC, Sengupta S, Elavathil L, Jani PA, Bonin M, Rakovitch E. The presence of one or multiple foci of microinvasion is not associated with an increased risk of local recurrence in women with ductal carcinoma in situ treated with breast conserving therapy [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P4-15-05.

Abstract P2-12-02: Is breast-conserving therapy effective in women with large ductal carcinoma in situ (DCIS) lesions? A population-based analysis

Background: Most women diagnosed with DCIS will be treated by breast-conserving surgery (BCS) with or without radiotherapy (RT). Data on outcomes following breast-conserving therapy are predominantly based on women with small (<25mm) lesions. The paucity of data on outcomes of women with larger (>40mm) DCIS lesions leads to uncertainty of the appropriateness of breast-conserving therapy for women with larger lesions. Specifically, it is unclear if women with large tumors experience higher risks of local recurrence (LR) and invasive LR after BCS+/-RT that would preclude recommendations of breast-conserving therapy. We report the outcomes and evaluate the impact of large tumor size (>40mm) on recurrence risk in a population of women with pure DCIS treated by BCS alone or with RT.

Methods: The cohort includes all women diagnosed with DCIS in Ontario from 1994-2003 treated with BCS +/- RT; 82% had pathology review. Treatment and outcomes were ascertained through administrative databases and validated by chart review. Cox proportional hazards model was used to evaluate the impact of tumor size (≤10mm,11-25mm, 26-39mm, ≥40mm) on the development of any LR (DCIS or invasive) and invasive LR. The 10 and 15-year LR-free survival (LRFS) and invasive LRFS rates were calculated using the Kaplan-Meier method with differences compared using the log-rank test.

Results: The cohort includes 3262 women with DCIS treated by BCS (N=1635 had RT). Median age at diagnosis was 59 years (IQR 50-68 years). Median follow-up was 13 years (IQR 8-15 years). Distribution of tumor size: 707 (22%) ≤10mm, 524 (16%) 11-25mm, 107 (3%) 26-39mm, 84 (3%) ≥40mm, unable to determine in 1840 (56%). Women with lesions ≥ 40mm were more likely to be ≤50 years of age at diagnosis (p=.02), have high nuclear grade (p<.001), multifocality (p<.001), and positive margins (p<.001) compared to women with smaller lesions. On multivariable analyses adjusted for age and year of diagnosis, tumor size ≥40mm was significantly associated with an increased risk of LR compared to size ≤10mm (HR=2.5, 95%CI:1.64-3.81). Other factors associated with LR were age <50 years (p<.001), omission of RT (p<.001), high nuclear grade (p=.002), and multifocality (p=.0008). Tumor size ≥40mm was not significantly associated with an increased risk of invasive LR (HR=1.68, 95%CI:.94-3.04). Women with tumour size ≥40mm treated with BCS alone had lower 10 and 15 year LRFS (53% and 41%) and invasive LRFS rates (78% and 75%) compared to women with smaller lesions. However, women with larger lesions treated with RT had significantly higher LRFS and invasive LRFS rates

Outcomes by tumour size for women with DCIS treated with BCS with or without RT  ≤10mm N=70711-25mm N=52426-39mm N=107≥40mm N=84p-valueBCS AloneLRFS (%)      10 yr85797053<0.001 15 yr81746741  Invasive LRFS (%)      10 yr928786780.03 15 yr89838375 BCS + RTLRFS (%)      10 yr928874850.01 15 yr86847079  Invasive LRFS (%)      10 yr959492910.27 15 yr90918789 

. There was a significant interaction between tumor size ≥40mm and RT (p=.02).

Conclusions: Women with DCIS lesions ≥40mm treated by BCS alone experience significantly higher risks of LR and invasive LR compared to smaller lesions but this risk can be mitigated with the addition of RT.

Citation Format: Lalani N, Paszat L, Nofech-Mozes S, Sutradhar R, Gu S, Hanna W, Fong C, Miller N, Youngson B, Done SJ, Tuck A, Chang MC, Sengupta S, Jani PA, Bonin M, Rakovitch E. Is breast-conserving therapy effective in women with large ductal carcinoma in situ (DCIS) lesions? A population-based analysis [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-12-02.

Abstract P3-17-01: Long-term rates of breast preservation after breast-conserving therapy for ductal carcinoma in situ

Background: Despite evidence that radiotherapy (RT) after breast-conserving surgery (BCS) for ductal carcinoma in situ (DCIS) halves the risk of recurrence, the benefit of RT in the management of DCIS continues to be a matter of controversy. One argument against the use of RT after BCS is that patients who develop ipsilateral local recurrence (LR) can be salvaged with further breast-conserving surgery such that the omission of RT will lead to high rates of breast preservation while minimizing exposure to RT. Breast preservation is an important determinant of quality of life for women with early stage breast cancer and DCIS. Yet the management of LR and the impact of RT on the resultant long-term risks of bilateral breast preservation in a population of women with DCIS are unclear. We assessed the treatment of LR, the impact of RT on the use of salvage mastectomy and the long-term risks of bilateral breast preservation achieved in a population of women with DCIS treated with BCS alone or BCS+RT.

Methods: A population-based analysis of women diagnosed with DCIS from 1994-2003 treated with BCS alone or BCS+RT with pathology review. Treatment and outcomes, including the development of LR and contralateral breast events, were determined by administrative databases with validation by review of operative or pathology reports. Median follow-up was 10.2 years for cases treated by BCS alone, 11.6 years for those treated by BCS+RT. We used a propensity-adjusted Cox proportional hazards model to evaluate factors associated with the use of salvage mastectomy for LR and to evaluate factors associated with any mastectomy. We assessed the risk of long-term breast preservation by calculating the KM 10-year risk of ipsilateral mastectomy and any mastectomy.

Results: The population cohort includes 3303 women with pure DCIS;1649 (50%) were treated by BCS alone, 1654 (50%) received BCS+RT. Women treated with RT had more high risk features of DCIS than those treated by BCS alone. LR developed in 343 (21%) women treated by BCS alone and in 257 (15.5%) women treated by BCS+RT (p<0.01). Most women who developed LR received salvage mastectomy, irrespective of age at diagnosis and histology. Salvage mastectomy was used in 57.4% (197/343) of cases that recurred after BCS alone and in 67.6% (173/257) that recurred after BCS+RT. The likelihood of receiving salvage mastectomy for LR was similar in patients initially treated by BCS+RT vs. those initially treated BCS alone. Most (90%) of mastectomies were performed for a LR. Overall, individuals initially treated by BCS+RT had a 29% lower probability of having a mastectomy at 10 years compared to those treated by BCS alone (HR=0.71, 95%CI: 0.60,0.84,p<0.0001). The 10 year mastectomy-free survival rates are 82.7% for women initially treated by BCS alone and 87.3% for those treated by BCS+RT (p=0.0096).

Conclusion: Women who received RT after BCS for DCIS experience a greater likelihood of long-term bilateral breast preservation. This is attributable to the lower risks of LR and that most local recurrences after breast-conserving therapy are treated by salvage mastectomy. Long-term breast preservation should be considered in discussions weighing the benefits and risks of RT after conservative surgery for DCIS.

Citation Format: Rakovitch E, Nofech-Mozes S, Hanna W, Gu S, Fong C, Tuck A, Sengupta S, Elavathil L, Jani P, Done S, Miller N, Youngson B, Bonin M, Chang M, Paszat L. Long-term rates of breast preservation after breast-conserving therapy for ductal carcinoma in situ [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P3-17-01.

Abstract P6-09-04: Nuclear grade has a limited role in predicting recurrence in DCIS following breast conserving surgery: A population-based study

This abstract was not presented at the symposium.

Nuclear RNA Decay Pathways Aid Rapid Remodeling of Gene Expression in Yeast

In budding yeast, the nuclear RNA surveillance system is active on all pre-mRNA transcripts and modulated by nutrient availability. To test the role of nuclear surveillance in reprogramming gene expression, we identified transcriptome-wide binding sites for RNA polymerase II and the exosome cofactors Mtr4 (TRAMP complex) and Nab3 (NNS complex) by UV crosslinking immediately following glucose withdrawal (0, 4, and 8 min). In glucose, mRNA binding by Nab3 and Mtr4 was mainly restricted to promoter-proximal sites, reflecting early transcription termination. Following glucose withdrawal, many growth-related mRNAs showed reduced transcription but increased Nab3 binding, accompanied by downstream recruitment of Mtr4, and oligo(A) tailing. We conclude that transcription termination is followed by TRAMP-mediated RNA decay. Upregulated transcripts evaded increased surveillance factor binding following glucose withdrawal. Some upregulated genes showed use of alternative transcription starts to bypass strong NNS binding sites. We conclude that nuclear surveillance pathways regulate both positive and negative responses to glucose availability.

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Changes in nuclear surveillance factor binding very rapidly follow nutritional shift

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Downregulated genes frequently show strongly increased surveillance factor binding

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Upregulated genes are protected against elevated surveillance factor binding

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The behavior of functionally related genes indicates posttranscriptional coregulation

RNA polymerase II stalling at pre-mRNA splice sites is enforced by ubiquitination of the catalytic subunit

Numerous links exist between co-transcriptional RNA processing and the transcribing RNAPII. In particular, pre-mRNA splicing was reported to be associated with slowed RNAPII elongation. Here, we identify a site of ubiquitination (K1246) in the catalytic subunit of RNAPII close to the DNA entry path. Ubiquitination was increased in the absence of the Bre5-Ubp3 ubiquitin protease complex. Bre5 binds RNA in vivo, with a preference for exon 2 regions of intron-containing pre-mRNAs and poly(A) proximal sites. Ubiquitinated RNAPII showed similar enrichment. The absence of Bre5 led to impaired splicing and defects in RNAPII elongation in vivo on a splicing reporter construct. Strains expressing RNAPII with a K₁₂₄₆R mutation showed reduced co-transcriptional splicing. We propose that ubiquinitation of RNAPII is induced by RNA processing events and linked to transcriptional pausing, which is released by Bre5-Ubp3 associated with the nascent transcript.

Strand-specific, high-resolution mapping of modified RNA polymerase II

Reversible modification of the RNAPII C‐terminal domain links transcription with RNA processing and surveillance activities. To better understand this, we mapped the location of RNAPII carrying the five types of CTD phosphorylation on the RNA transcript, providing strand‐specific, nucleotide‐resolution information, and we used a machine learning‐based approach to define RNAPII states. This revealed enrichment of Ser5P, and depletion of Tyr1P, Ser2P, Thr4P, and Ser7P in the transcription start site (TSS) proximal ~150 nt of most genes, with depletion of all modifications close to the poly(A) site. The TSS region also showed elevated RNAPII relative to regions further 3′, with high recruitment of RNA surveillance and termination factors, and correlated with the previously mapped 3′ ends of short, unstable ncRNA transcripts. A hidden Markov model identified distinct modification states associated with initiating, early elongating and later elongating RNAPII. The initiation state was enriched near the TSS of protein‐coding genes and persisted throughout exon 1 of intron‐containing genes. Notably, unstable ncRNAs apparently failed to transition into the elongation states seen on protein‐coding genes.

Evaluation of swabbing methods for estimating the prevalence of bacterial carriage in the upper respiratory tract: a cross sectional study

OBJECTIVES

Bacterial carriage in the upper respiratory tract is usually asymptomatic but can lead to respiratory tract infection (RTI), meningitis and septicaemia. We aimed to provide a baseline measure of Streptococcus pneumoniae, Moraxella catarrhalis, Pseudomonas aeruginosa, Staphylococcus aureus, Haemophilus influenzae and Neisseria meningitidis carriage within the community. Self-swabbing and healthcare professional (HCP) swabbing were compared.

DESIGN

Cross-sectional study.

SETTING

Individuals registered at 20 general practitioner practices within the Wessex Primary Care Research Network South West, UK.

PARTICIPANTS

10,448 individuals were invited to participate; 5394 within a self-swabbing group and 5054 within a HCP swabbing group. Self-swabbing invitees included 2405 individuals aged 0-4 years and 3349 individuals aged ≥5 years. HCP swabbing invitees included 1908 individuals aged 0-4 years and 3146 individuals aged ≥5 years.

RESULTS

1574 (15.1%) individuals participated, 1260 (23.4%, 95% CI 22.3% to 24.5%) undertaking self-swabbing and 314 (6.2%, 95% CI 5.5% to 6.9%) undertaking HCP-led swabbing. Participation was lower in young children and more deprived practice locations. Swab positivity rates were 34.8% (95% CI 32.2% to 37.4%) for self-taken nose swabs (NS), 19% (95% CI 16.8% to 21.2%) for self-taken whole mouth swabs (WMS), 25.2% (95% CI 20.4% to 30%) for nasopharyngeal swabs (NPS) and 33.4% (95% CI 28.2% to 38.6%) for HCP-taken WMS. Carriage rates of S. aureus were highest in NS (21.3%). S. pneumoniae carriage was highest in NS (11%) and NPS (7.4%). M. catarrhalis carriage was highest in HCP-taken WMS (28.8%). H. influenzae and P. aeruginosa carriage were similar between swab types. N. meningitidis was not detected in any swab. Age and recent RTI affected carriage of S. pneumoniae and H. influenzae. Participant costs were lower for self-swabbing (£41.21) versus HCP swabbing (£69.66).

CONCLUSIONS

Higher participation and lower costs of self-swabbing as well as sensitivity of self-swabbing favour this method for use in large population-based respiratory carriage studies.

Integrity of SRP RNA is ensured by La and the nuclear RNA quality control machinery

The RNA component of signal recognition particle (SRP) is transcribed by RNA polymerase III, and most steps in SRP biogenesis occur in the nucleolus. Here, we examine processing and quality control of the yeast SRP RNA (scR1). In common with other pol III transcripts, scR1 terminates in a U-tract, and mature scR1 retains a U_4–5 sequence at its 3′ end. In cells lacking the exonuclease Rex1, scR1 terminates in a longer U_5–6 tail that presumably represents the primary transcript. The 3′ U-tract of scR1 is protected from aberrant processing by the La homologue, Lhp1 and overexpressed Lhp1 apparently competes with both the RNA surveillance system and SRP assembly factors. Unexpectedly, the TRAMP and exosome nuclear RNA surveillance complexes are also implicated in protecting the 3′ end of scR1, which accumulates in the nucleolus of cells lacking the activities of these complexes. Misassembled scR1 has a primary degradation pathway in which Rrp6 acts early, followed by TRAMP-stimulated exonuclease degradation by the exosome. We conclude that the RNA surveillance machinery has key roles in both SRP biogenesis and quality control of the RNA, potentially facilitating the decision between these alternative fates.

Kinetic analysis of pre-ribosome structure in vivo

Pre-ribosomal particles undergo numerous structural changes during maturation, but their high complexity and short lifetimes make these changes very difficult to follow in vivo. In consequence, pre-ribosome structure and composition have largely been inferred from purified particles and analyzed in vitro. Here we describe techniques for kinetic analyses of the changes in pre-ribosome structure in living cells of Saccharomyces cerevisiae. To allow this, in vivo structure probing by DMS modification was combined with affinity purification of newly synthesized 20S pre-rRNA over a time course of metabolic labeling with 4-thiouracil. To demonstrate that this approach is generally applicable, we initially analyzed the accessibility of the region surrounding cleavage site D site at the 3' end of the mature 18S rRNA region of the pre-rRNA. This revealed a remarkably flexible structure throughout 40S subunit biogenesis, with little stable RNA-protein interaction apparent. Analysis of folding in the region of the 18S central pseudoknot was consistent with previous data showing U3 snoRNA-18S rRNA interactions. Dynamic changes in the structure of the hinge between helix 28 (H28) and H44 of pre-18S rRNA were consistent with recently reported interactions with the 3' guide region of U3 snoRNA. Finally, analysis of the H18 region indicates that the RNA structure matures early, but additional protection appears subsequently, presumably reflecting protein binding. The structural analyses described here were performed on total, affinity-purified, newly synthesized RNA, so many classes of RNA and RNA-protein complex are potentially amenable to this approach.

Transcriptome-wide analysis of exosome targets

The exosome plays major roles in RNA processing and surveillance but the in vivo target range and substrate acquisition mechanisms remain unclear. Here we apply in vivo RNA crosslinking (CRAC) to the nucleases (Rrp44, Rrp6), two structural subunits (Rrp41, Csl4) and a cofactor (Trf4) of the yeast exosome. Analysis of wild-type Rrp44 and catalytic mutants showed that both the CUT and SUT classes of non-coding RNA, snoRNAs and, most prominently, pre-tRNAs and other Pol III transcripts are targeted for oligoadenylation and exosome degradation. Unspliced pre-mRNAs were also identified as targets for Rrp44 and Rrp6. CRAC performed using cleavable proteins (split-CRAC) revealed that Rrp44 endonuclease and exonuclease activities cooperate on most substrates. Mapping oligoadenylated reads suggests that the endonuclease activity may release stalled exosome substrates. Rrp6 was preferentially associated with structured targets, which frequently did not associate with the core exosome indicating that substrates follow multiple pathways to the nucleases.

Antimicrobial susceptibility and synergy studies of cystic fibrosis sputum by direct sputum sensitivity testing

Standard disc diffusion antimicrobial susceptibility testing (C+S) on individual Pseudomonas aeruginosa colonial morphotypes cultured from cystic fibrosis (CF) sputum has questionable clinical relevance. Direct sputum sensitivity testing (DSST) is a whole-sputum susceptibility test that removes bias associated with selecting individual colonial morphotypes. We sought to determine whether, in principle, the results from DSST support the possibility of improved clinical relevance compared with C+S. Individual (DSSTi) and combination (DSST) susceptibility to gentamicin, tobramycin, ceftazidime and meropenem were determined on 130 sputum samples referred from CF subjects with antibiotic-resistant chronic Gram-negative endobronchial infection. DSSTi and concurrent C+S were compared for categorical susceptibility, synergistic combinations were evaluated and the combination DSST efficacy index (DEI) calculated. Meropenem and tobramycin were the most active individual antibiotics by DSSTi on 89 P. aeruginosa-predominant samples, with 62 % of samples sensitive to each. C+S and DSSTi showed poor agreement (κ ranging from 0.02 to 0.6), discordance ranging from 20 % (meropenem) to 49 % (tobramycin), with DSSTi demonstrating both increased susceptibility and increased resistance. The combination that most frequently had the highest DEI was tobramycin + meropenem, occurring in 76 % of samples. DSSTi appears to be reproducible, yields different antimicrobial susceptibility results from C+S without simply identifying the most resistant isolates and DSST identifies the most effective in vitro antibiotic combinations, providing preliminary proof of concept of the potentially improved clinical relevance of whole-sputum testing. Future studies will determine whether these potential theoretical advantages translate into clinical benefits.

415. Increased expression of an androgen receptor regulated gene, kit ligand, in polycystic ovaries

Polycystic ovaries (PCO) are induced by pathological or pharmacological female androgen excess, but the role of the androgen receptor (AR) in the pathogenesis of PCO is unknown. We therefore tested the hypothesis that PCO have increased expression of AR or kit ligand (KITL), a cytokine that was recently identified as a candidate AR-regulated gene in the ovary (1). Immunohistochemical analysis of AR and KITL expression was performed on archival paraffin-embedded sections of 8 morphologically normal and 8 polycystic ovaries from women under the age of 40 years. Stained sections were scanned with a NanoZoomer Digital Pathology System and immunoreactivity was qualitatively assessed using a 0-3+ scale, where 3+ represents the most intense staining. Electronic images of follicles at different stages of folliculogenesis were assessed by two independent observers who were blinded to the morphology of the source ovary. Each individual ovary contributed a minimum of 1 follicle per size class and a minimum of 10 follicles per size class were analysed. AR immunoreactivity was present in granulosa cells at all stages of folliculogenesis, in thecal cells of large antral follicles, and in the ovarian stroma. Staining intensity for AR did not differ between normal and polycystic ovaries. KITL expression, summarised in Table 1, was found to be significantly elevated in the oocytes of primordial and primary follicles and in the granulosa cells of follicles at all stages of folliculogenesis. These results show that AR expression is normal in PCO but expression of an AR-regulated gene is increased, potentially due to an excess of androgen hormone that is characteristic of women with PCO. Based on the roles of KITL established by murine studies, increased expression of KITL could explain many of the features of PCO including follicle excess, hyperthecosis and abnormal androgen secretion.

Kinetic studies on the formation of DNA triplexes containing the nucleoside analogue 2'-O-(2-aminoethyl)-5-(3-amino-1-propynyl)uridine

We have examined the kinetics of triple helix formation of oligonucleotides that contain the nucleotide analogue 2'-O-(2-aminoethyl)-5-(3-amino-1-propynyl)uridine (bis-amino-U, BAU), which forms very stable base triplets with AT. Triplex stability is determined by both the number and location of the modifications. BAU-containing oligonucleotides generate triplexes with extremely slow kinetics, as evidenced by 14 degrees C hysteresis between annealing and melting profiles even when heated at a rate as slow as 0.2 degrees C min(-1). The association kinetics were measured by analysis of the hysteresis profiles, temperature-jump relaxation and DNase I footprinting. We find that the slow kinetics are largely due to the decreased rate of dissociation; BAU modification has little effect on the association reaction. The sequence selectivity is also due to the slower dissociation of BAU from AT than other base pairs.

Chronic lymphocytic leukemia lymphocytes lack the capacity to repair UVC-induced lesions

Cells from chronic lymphocytic leukemia (CLL) patients and from healthy individuals were irradiated with UVC and incubated for varying periods of time. The number of single strand breaks and alkali-labile sites was determined by comet analysis. Unirradiated CLL and healthy cells exhibited no significant numbers of single strand breaks. The extent of DNA damage was found to increase with dose for both healthy and CLL cells. However, the CLL cells had much more extensive DNA fragmentation than healthy cells at each dose. Deoxyribonucleoside supplemented medium inhibited comet formation in both cell types. Thymidine alone produced the same effect. In healthy cells, repair of lesions was complete after 4 h of incubation as indicated by the absence of comet formation. The CLL cells exhibited no significant repair even after 48 h. CLL lymphocytes are killed by very low doses of UVC radiation. The results reported here suggest that this hypersensitivity results from the inability of CLL cells to repair UVC-induced DNA damage and a contributing factor is the low amounts of intracellular deoxyribonucleosides.

Hypersensitivity of lymphocytes from chronic lymphocytic leukemia patients to ultraviolet light-C radiation

Chronic lymphocytic leukemia (CLL) results in the accumulation of mature immunologically defective lymphocytes in GO phase. Lymphocytes from CLL patients were exposed to UVC radiation to determine whether these cells are capable of undergoing apoptosis, as a response to DNA damage. Lymphocytes from CLL patients were found to be readily killed by ultraviolet light-C (UVC) radiation. Cells from healthy donors were minimally affected by doses of UVC ten times higher then those which caused dramatic drops in the metabolism of CLL cells. At four hours after irradiation, the reduction of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) had dropped by 50% for CLL cells exposed to a dose of 10 J/m2. In contrast, there was no significant drop for healthy cells exposed to 100 J/m2. Cell death was measured by trypan blue staining, flow cytometry of Annexin V-PI stained cells, and Wright staining. By 24 hours after irradiation, significant amounts of cell death were observed in CLL cells at doses which had no significant effects on viability of healthy lymphocytes. The extreme sensitivity of CLL lymphocytes to UVC indicates that phototherapy should be explored as a potential treatment for this neoplasm.

Localization of platelet-derived growth factor beta receptor expression in the periepithelial stroma of human breast carcinoma

Platelet-derived growth factor (PDGF) BB is secreted by most human breast carcinoma cells; however, only recently have PDGF beta receptors been demonstrated in malignant breast tissue. In the present study, the tissue localization of PDGF beta receptor expression was studied in human breast carcinoma and nonmalignant breast tissues stained using both immunofluorescence and immunoperoxidase techniques. We examined a total of 29 cases of breast carcinomas, which showed both in situ and invasive components. PDGF beta receptor staining was localized in the periepithelial stroma and was particularly intense in regions immediately adjacent to carcinoma in situ components in all tumors examined. A diffuse low level of PDGF beta receptor staining was seen throughout the stroma of eight nonmalignant breast tissues as well as of nonmalignant regions of tumor tissues. Image analysis was used to assess the coincidence of staining of PDGF beta receptor with epithelial or stromal cells in 13 of the 29 tumor tissues studied. Less than 5% of malignant ductal epithelium or myoepithelium showed PDGF beta receptor staining. Analysis with stromal cell type-specific markers indicated significant localization of PDGF beta receptor primarily within alpha smooth muscle actin-staining cells (32%) and vascular endothelial cells (41%) in the periepithelial stroma. PDGF beta receptor positivity was strongly associated with periepithelial stromal cells adjacent to the basement membrane surrounding regions of carcinoma in situ but was less intense in regions of invasive carcinoma where basement membrane was degraded. The absence of PDGF beta receptors on carcinoma cells and their presence in the surrounding stroma suggest a paracrine stimulation of adjacent stromal tissue by malignant epithelial cells in human breast tumors.

Autoantibodies to endogenous growth hormone in short children (the Wessex Growth Study)

Small stature is associated with low growth hormone secretion, but in most cases the reason is unknown. The commonest cause of hormone insufficiency is autoimmunity, and autoantibodies to hormones are often found where there is autoimmune disease of the corresponding gland. Displaceable growth hormone binding by the sera of 125 short (< 3rd centile) but otherwise normal school entrants was significantly higher (P < 0.05) than by the sera of 100 age-matched children of normal height (10th-90th centile), and binding in 21 (17%) of the small children exceeded the upper limit of 95% of the normal population. Furthermore, urinary growth hormone excretion was significantly lower in the small children (total overnight output 0.6-1.7 ng) compared with controls (1.5-3.7 ng) (P < 0.05) even when corrected for body surface area. Thus, growth hormone binding and growth hormone excretion discriminated between two groups of children selected only on the basis of height. The assay used for growth hormone binding was specific for IgG, suggesting that the binding factor was antibody. Autoimmunity merits further investigation as a basis for poor growth.

A medium for the isolation, enumeration and rapid presumptive identification of injured Clostridium perfringens and Bacillus cereus

A blood-free egg yolk medium (BCP) containing pyruvate, inositol, mannitol and a bromocresol purple indicator in a nutrient agar base has been developed to initiate the growth of Clostridium perfringens. It is comparable to blood agar for the growth of normal, chilled stored vegetative cells and heat-injured spores of Cl. perfringens and Bacillus cereus. It has the advantage over blood agar in exhibiting presumptive evidence of Cl. perfringens (production of lecithinase and inositol fermentation) after an overnight incubation at 43 degrees - 45 degrees C. Pyruvate, catalase and other hydrogen peroxide degraders were found to remove toxins rapidly formed in media exposed to air and light. Free radical scavengers of superoxide, hydroxyl ions and singlet oxygen were ineffective. Without scavengers the formation of 10-20 micrograms/ml hydrogen peroxide in the exposed medium was indicated and found lethal to injured Cl. perfringens. The BCP medium has been used successfully for the rapid identification and enumeration of Cl. perfringens in foods and faeces from food poisoning outbreaks and cases of suspected infectious diarrhoea. Greater recovery of severely injured vegetative Cl. perfrigens could be obtained by pre-incubation at 37 degrees C of inoculated media for 2-4 h followed by overnight incubation at 43 degrees - 45 degrees C. Tryptose-sulphite-cycloserine and Shahidi-Ferguson-perfringens agar base were found to inhibit the growth of several strains of injured vegetative Cl. perfringens. This was not completely overcome by the addition of pyruvate. The inclusion of mannitol also allows the medium to be used for the presumptive identification of B. cereus. Growth and lecithinase activity are profuse on BCP. Heat-injured spores are recovered equally well on BCP and blood agar. A scheme for the identification of some other clostridia on BCP is presented.

An enzyme-linked immunosorbent assay (ELISA) for the measurement of serum antibodies to growth hormone. The Wessex Growth Study

A solid-phase enzyme-linked immunosorbent assay for measuring antibodies to growth hormone (GH) was developed, with occasional use and long shelf-life in mind. With coating protein concentration optimised, the standard curve was linear over a 25-fold range of concentration. The interassay coefficient of variation ranged from 14.4% to 9.3%. The specificity of the assay was confirmed by the substitution of insulin for GH as coating protein and by preabsorption of sera with GH coupled covalently to Sepharose beads. There was no binding signal with insulin and absorption was dose dependent, maximum (greater than 80% complete) with 2 x 10(4) micrograms GH/ml undiluted serum. The assay was simple to perform, cheap and reliable.

Nucleolar cycles during the fifth stadium in Manduca epidermis

The changing pattern of nucleolar structure in the epidermal cells of Manduca sexta has been correlated with hormonal changes taking place during the fifth stadium. The epidermal nucleoli show three cycles of development, the first and third of which occur at the beginnings of the intermoult and moult phases respectively and are related to larval and pupal syntheses. The second phase occurs in the middle of the stadium but prior to the onset of wandering and commitment to pupation. A phase of mitosis separates the second and third cycles. The three cycles thus correspond in time to those found in Calpodes. The three cycles of nucleolar change are superimposed over nuclear changes relating to the degree of ploidy. Each phase begins with an expansion of the condensed nucleoli to form lobed rings and then necklaces. In the first phase (day 0-3), the rings and necklaces progress to form threaded networks. Both rings and networks have many ribosomal precursor granules that are lacking in condensed nucleoli. The rings and networks are therefore presumed to be more active in rRNA synthesis than the condensed state. The first and third phases of nucleolar change occur after elevated titres of haemolymph ecdysteroid. Post-thoracic ligation of animals at ecdysis blocks nucleolar changes as well as the appearance of polyploid nuclei. Nucleolar changes may be a primary response of the epidermis to stimulation by ecdysone.