Shared genetic aetiology between cognitive functions and physical and mental health in UK Biobank (N=112 151) and 24 GWAS consortia

Causes of the well-documented association between low levels of cognitive functioning and many adverse neuropsychiatric outcomes, poorer physical health and earlier death remain unknown. We used linkage disequilibrium regression and polygenic profile scoring to test for shared genetic aetiology between cognitive functions and neuropsychiatric disorders and physical health. Using information provided by many published genome-wide association study consortia, we created polygenic profile scores for 24 vascular-metabolic, neuropsychiatric, physiological-anthropometric and cognitive traits in the participants of UK Biobank, a very large population-based sample (N=112 151). Pleiotropy between cognitive and health traits was quantified by deriving genetic correlations using summary genome-wide association study statistics and to the method of linkage disequilibrium score regression. Substantial and significant genetic correlations were observed between cognitive test scores in the UK Biobank sample and many of the mental and physical health-related traits and disorders assessed here. In addition, highly significant associations were observed between the cognitive test scores in the UK Biobank sample and many polygenic profile scores, including coronary artery disease, stroke, Alzheimer's disease, schizophrenia, autism, major depressive disorder, body mass index, intracranial volume, infant head circumference and childhood cognitive ability. Where disease diagnosis was available for UK Biobank participants, we were able to show that these results were not confounded by those who had the relevant disease. These findings indicate that a substantial level of pleiotropy exists between cognitive abilities and many human mental and physical health disorders and traits and that it can be used to predict phenotypic variance across samples.

Twenty-five cases of feline bronchial disease (1995–2000)

Twenty-five cases of feline bronchial disease were identified retrospectively. The criteria for inclusion were consistent clinical signs or histopathology and no other identifiable aetiology. Patient records were analysed to determine historical, clinical, clinicopathologic and radiographic features. The main presenting complaints were coughing and dyspnoea. The most common physical finding was dyspnoea. The majority of radiographs had a bronchial pattern either as the sole change or as a component of a mixed pattern. Bronchoalveolar lavage cytology was neutrophilic or eosinophilic in the majority of cats. There was no association between age, breed, sex, clinical signs, bronchoalveolar lavage cytology or radiographic severity and disease severity.

The use of real-time PCR in the diagnosis and monitoring of Mycoplasma haemofelis copy number in a naturally infected cat

A 5-year-old male neutered cat was diagnosed with severe anaemia due to acute Mycoplasma haemofelis infection. Inflammatory respiratory disease was present concurrently. The cat was treated successfully using a fresh transfusion of whole blood and a 6 week course of doxycycline. The patient made a rapid recovery although the allergic airway disease subsequently required specific therapy consisting of inhaled fluticasone and salbutamol. Real-time quantitative PCR assays confirmed the presence of M. haemofelis DNA copies in the blood at presentation. Repeat PCR assays showed a reduction in copy number during treatment and negative PCR results were obtained both 91 and 425 days after presentation. The report describes, for the first time, the use of real-time PCR in the diagnosis and monitoring of natural M. haemofelis copy number, as well as the induction of long-term negative PCR status.

A retrospective analysis of feline bronchoalveolar lavage cytology and microbiology (1995–2000)

A retrospective study of 88 bronchoalveolar lavage specimens from 80 cats presenting to the University of Sydney Veterinary Centre between 1995 and 2000 was performed. Bronchoalveolar lavage cytology and microbiology in conjunction with other diagnostic aids and patient records were used to classify cases as lower respiratory tract infections (LTRIs), LRTI revisits, feline bronchial disease, cardiac disease, neoplastic disease and multisystemic disease. Cases for which a definitive diagnosis could not be made were classified as inconclusive. Infectious agents identified were Mycoplasma spp., Pasteurella spp., Bordetella bronchiseptica, Salmonella typhimurium, Pseudomonas sp., Cryptococcus neoformans, Aelurostrongylus abstrusus and Eucoleus aerophilus. The study highlights the importance of bronchoalveolar lavage cytology and microbiology in the evaluation of feline lower respiratory tract disease.

Abstract S4-05: Interrogating the landscape of long noncoding RNAs in breast cancer to identify predictors of tamoxifen resistance

Background: We previously performed an informatics-based analysis on RNA sequencing libraries from 7,256 tumor and normal tissue specimens to delineate the landscape of long noncoding RNAs (lncRNAs) in the human transcriptome. This analysis identified 58,648 lncRNAs, including over 45,000 novel transcripts (Iyer MK et al, Nature Genetics, 2015). We now interrogate this lncRNA compendium to identify top candidate estrogen receptor (ER)-associated lncRNAs in breast cancer and characterize their association with disease progression.

Methods: To prioritize differentially expressed lncRNAs in cancer vs normal tissue, and in ER+ vs ER- disease, we performed Sample Set Enrichment Analysis (SSEA) on >1000 RNA Seq libraries, from breast cancer and normal tissue samples from The Cancer Genome Atlas project. The effect of the top prioritized lncRNA on cancer phenotypes was studied via in vitro proliferation, colony formation, invasion and tamoxifen resistance assays in MCF7 and T47D cells, and via in vivo mouse xenograft studies and chick chorioallantoic membrane (CAM) assays. To study the mechanism by which this lncRNA promotes tumor progression, we identified its top protein interactors and subdomains responsible for function, and then studied the effects of disrupting function of this lncRNA on cancer phenotypes. Finally, in a "guilt-by-association" study, we developed a signature of 150 protein coding genes most strongly associated with our lncRNA of interest, and investigated the association of this signature with clinical outcomes using Oncomine analyses.

Results: SSEA analysis on over 1000 TCGA samples nominated Breast Cancer Associated Transcript (BRCAT 431) as the top overexpressed ER-regulated lncRNA in breast cancer. In vitro experiments demonstrate that siRNA-mediated knockdown of BRCAT431 resulted in significantly decreased proliferation, colony formation, and invasion (by >50% in most assays). Tamoxifen resistance was associated with significantly increased BRCAT431 levels in both MCF7 and T47D cells, and knockdown of BRCAT431 reversed tamoxifen resistance. In vivo xenograft and CAM studies demonstrate that knockdown of BRCAT431 also significantly decreased xenograft growth and tumor invasion by >50%. RNA pulldown followed by mass spectrometry identified the RNA binding protein hnRNPL as a key protein interacting with BRCAT431. Deletion studies identified a 27 base region of BRCAT431 necessary for its interaction with hnRNPL, and loss of this region abrogated BRCAT431- induced invasion. Finally, guilt-by-association studies demonstrate a strong association between BRCAT431 overexpression and tumor grade, recurrence, and metastases.

Conclusion: In this study, we develop the largest reported compendia of breast cancer lncRNAs. We prioritize BRCAT431 as the top lncRNA upregulated in ER-positive breast cancers, and demonstrate that it confers aggressive oncogenic phenotypes in vitro and in vivo. We identify a novel mechanism by which this lncRNA functions. Our results suggest that by promoting tamoxifen resistance, BRCAT431 increases the clinical risk of recurrence and metastases in breast cancer. Overall, this study supports the rationale for investigating lncRNAs as novel biomarkers and therapeutic targets in breast cancer.

Citation Format: Feng FY, Niknafs Y, Han S, Ma T, Speers C, Malik R, Evans J, Zhang C, Pierce LJ, Hayes DF, Rae JM, Chinnaiyan AM. Interrogating the landscape of long noncoding RNAs in breast cancer to identify predictors of tamoxifen resistance. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr S4-05.

Some pharmacokinetic indices of oral fluconazole administration to koalas (Phascolarctos cinereus) infected with cryptococcosis

Three asymptomatic koalas serologically positive for cryptococcosis and two symptomatic koalas were treated with 10 mg/kg fluconazole orally, twice daily for at least 2 weeks. The median plasma Cmax and AUC0-8 h for asymptomatic animals were 0.9 μg/mL and 4.9 μg/mL·h, respectively; and for symptomatic animals 3.2 μg/mL and 17.3 μg/mL·h, respectively. An additional symptomatic koala was treated with fluconazole (10 mg/kg twice daily) and a subcutaneous amphotericin B infusion twice weekly. After 2 weeks the fluconazole Cmax was 3.7 μg/mL and the AUC0-8 h was 25.8 μg/mL*h. An additional three koalas were treated with fluconazole 15 mg/kg twice daily for at least 2 weeks, with the same subcutaneous amphotericin protocol co-administered to two of these koalas (Cmax : 5.0 μg/mL; mean AUC0-8 h : 18.1 μg/mL*h). For all koalas, the fluconazole plasma Cmax failed to reach the MIC90 (16 μg/mL) to inhibit C. gattii. Fluconazole administered orally at either 10 or 15 mg/kg twice daily in conjunction with amphotericin is unlikely to attain therapeutic plasma concentrations. Suggestions to improve treatment of systemic cryptococcosis include testing pathogen susceptibility to fluconazole, monitoring plasma fluconazole concentrations, and administration of 20-25 mg/kg fluconazole orally, twice daily, with an amphotericin subcutaneous infusion twice weekly.

Low density lipoprotein receptor related protein 1 and 6 gene variants and ischaemic stroke risk

BACKGROUND AND PURPOSE

Low density lipoprotein receptor related proteins (LRPs) 1 and 6 have been implicated in cerebral ischaemia. In addition, genetic variation in LRP1 and LRP6 has been linked with various factors that are related to risk of ischaemic stroke. The aim of this study was to examine the association of LRP1 and LRP6 gene variants with risk of ischaemic stroke as part of the Ischemic Stroke Genetics Study (ISGS).

METHODS

A Caucasian series (434 stroke patients, 319 controls) and an African American series (161 stroke patients, 116 controls) were included. Fourteen LRP6 variants and three LRP1 variants were genotyped and assessed for association with ischaemic stroke.

RESULTS

In the Caucasian series, significant associations with ischaemic stroke were observed for LRP6 rs2075241 [odds ratio (OR) 0.42, P = 0.023], rs2302685 (OR 0.44, P = 0.049), rs7975614 (OR 0.07, P = 0.017), rs10492120 (OR 0.62, P = 0.036) and rs10743980 (OR 0.66, P = 0.037). Risk of ischaemic stroke was significantly lower for carriers of any of these five protective LRP6 variants (24.0% of subjects) compared to non-carriers (OR 0.57, P = 0.003). The protective association for LRP6 rs2075241 was observed at a similar magnitude across ischaemic stroke subtypes, whilst the effects of rs23022685, rs10492120 and rs10743980 were most apparent for cardioembolic and large vessel stroke. In the African American series, LRP1 rs11172113 was associated with an increased risk of stroke (OR 1.89, P = 0.006).

CONCLUSIONS

The results of our preliminary study provide evidence that LRP6 and LRP1 variants may be associated with risk of ischaemic stroke. Validation in larger studies is warranted.

Surgery for endometriosis-associated infertility: do we exaggerate the magnitude of effect?

OBJECTIVE

Surgery remains the mainstay in the diagnosis and management of endometriosis. The number of surgeries performed for endometriosis worldwide is ever increasing, however do we have evidence for improvement of infertility after the surgery and do we exaggerate the magnitude of effect of surgery when we counsel our patients? The management of patients who failed the surgery could be by repeat surgery or assisted reproduction. What evidence do we have for patients who fail assisted reproduction and what is their best chance for achieving pregnancy?

MATERIAL AND METHODS

In this study we reviewed the evidence-based practice pertaining to the outcome of surgery assisted infertility associated with endometriosis. Manuscripts published in PubMed and Science Direct as well as the bibliography cited in these articles were reviewed. Patients with peritoneal endometriosis with mild and severe disease were addressed separately. Patients who failed the primary surgery and managed by repeat or assisted reproduction technology were also evaluated. Patients who failed assisted reproduction and managed by surgery were also studied to determine of the best course of action.

RESULTS

In patients with minimal and mild pelvic endometriosis, excision or ablation of the peritoneal endometriosis increases the pregnancy rate. In women with severe endometriosis, controlled trials suggested an improvement of pregnancy rate. In women with ovarian endometrioma 4 cm or larger ovarian cystectomy increases the pregnancy rate, decreases the recurrence rate, but is associated with decrease in ovarian reserve. In patients who have failed the primary surgery, assisted reproduction appears to be significantly more effective than repeat surgery. In patients who failed assisted reproduction, the management remains to be extremely controversial. Surgery in expert hands might result in significant improvement in pregnancy rate.

CONCLUSION

In women with minimal and mild endometriosis, surgical excision or ablation of endometriosis is recommended as first line with doubling the pregnancy rate. In patients with moderate and severe endometriosis surgical excision also is recommended as first line. In patients who failed to conceive spontaneously after surgery, assisted reproduction is more effective than repeat surgery. Following surgery, the ovarian reserve may be reduced as determined by Anti Mullerian Hormone. The antral follicle count is not significantly reduced. In women with large endometriomas > 4 cm the ovarian endometrioma should be removed. In women who have failed assisted reproduction, further management remains controversial in the present time.

Diagnostic accuracy of common clinical tests for assessing abdominal muscle function after motor-complete spinal cord injury above T6

STUDY DESIGN

Diagnostic study.

OBJECTIVES

The objective of this study was to compare patterns of electromyography (EMG) recordings of abdominal muscle function in persons with motor-complete spinal cord injury (SCI) above T6 and in able-bodied controls, and to determine whether manual examination or ultrasound measures of muscle activation can be accurate alternatives to EMG.

SETTING

Research center focused on SCI and University laboratory, Vancouver, Canada.

METHODS

Thirteen people with SCI (11 with American Spinal Injury Association Impairment Scale (AIS) A and 2 AIS B; C4-T5), and 13 matched able-bodied participants volunteered for the study. Participants completed trunk tasks during manual examination of the abdominal muscles and then performed maximal voluntary isometric contractions, while EMG activity and muscle thickness changes were recorded. The frequency of muscle responses detected by manual examination and ultrasound were compared with detection by EMG (sensitivity and specificity).

RESULTS

All individuals with SCI were able to elicit EMG activity above resting levels in at least one abdominal muscle during one task. In general, the activation pattern was task specific, confirming voluntary control of the muscles. Ultrasound, when compared with EMG, showed low sensitivity but was highly specific in its ability to detect preserved abdominal muscle function in persons with SCI. Conversely, manual examination was more sensitive than ultrasound but showed lower specificity.

CONCLUSION

The results from this study confirm preserved voluntary abdominal muscle function in individuals classified with motor-complete SCI above T6 and highlight the need for further research in developing more accurate clinical measures to diagnose the level of trunk muscle preservation in individuals with SCI.

Frequency-resolved noise figure measurements of phase (in)sensitive fiber optical parametric amplifiers

We measure the frequency-resolved noise figure of fiber optical parametric amplifiers both in phase-insensitive and phase-sensitive modes in the frequency range from 0.03 to 3 GHz. We also measure the variation in noise figure due to the degradation in pump optical signal to noise ratio and also as a function of the input signal powers. Noise figure degradation due to stimulated Brillouin scattering is observed.