Plasma proteomic associations with genetics and health in the UK Biobank

The Pharma Proteomics Project is a precompetitive biopharmaceutical consortium characterizing the plasma proteomic profiles of 54,219 UK Biobank participants. Here we provide a detailed summary of this initiative, including technical and biological validations, insights into proteomic disease signatures, and prediction modelling for various demographic and health indicators. We present comprehensive protein quantitative trait locus (pQTL) mapping of 2,923 proteins that identifies 14,287 primary genetic associations, of which 81% are previously undescribed, alongside ancestry-specific pQTL mapping in non-European individuals. The study provides an updated characterization of the genetic architecture of the plasma proteome, contextualized with projected pQTL discovery rates as sample sizes and proteomic assay coverages increase over time. We offer extensive insights into trans pQTLs across multiple biological domains, highlight genetic influences on ligand-receptor interactions and pathway perturbations across a diverse collection of cytokines and complement networks, and illustrate long-range epistatic effects of ABO blood group and FUT2 secretor status on proteins with gastrointestinal tissue-enriched expression. We demonstrate the utility of these data for drug discovery by extending the genetic proxied effects of protein targets, such as PCSK9, on additional endpoints, and disentangle specific genes and proteins perturbed at loci associated with COVID-19 susceptibility. This public-private partnership provides the scientific community with an open-access proteomics resource of considerable breadth and depth to help to elucidate the biological mechanisms underlying proteo-genomic discoveries and accelerate the development of biomarkers, predictive models and therapeutics1.

Characterization and translational development of IOA-289, a novel autotaxin inhibitor for the treatment of solid tumors

Background

Autotaxin-lysophosphatidic acid (ATX-LPA) signaling has a predominant role in immunological and fibrotic processes, including cancer. Several ATX inhibitors and LPA receptor antagonists have been clinically evaluated, but none in patients with solid tumors. Many cancers are burdened with a high degree of fibrosis and an immune desert phenotype (so-called 'cold' tumors). In these cold tumors, the fibrotic stroma provides an intrinsic cancer-supporting mechanism. Furthermore, the stroma prevents penetration and limits the effectiveness of existing therapies. IOA-289 is a novel ATX inhibitor with a unique chemical structure, excellent potency and an attractive safety profile.

Materials and methods

In vitro and in vivo pharmacology studies have been carried out to elucidate the pharmaceutical properties and mechanism of action of IOA-289. A phase I clinical study in healthy volunteers was carried out to determine the pharmacokinetics and pharmacodynamics of IOA-289 following a single oral dose.

Results

In vitro and in vivo studies showed that IOA-289 is a potent inhibitor of ATX and, as a monotherapy, is able to slow progression of lung fibrosis and tumor growth in mouse models. In a clinical study, IOA-289 showed a dose-dependent increase in plasma exposure levels and a corresponding decrease in circulating LPA.

Conclusions

Our data show that IOA-289 is a novel ATX inhibitor with a unique chemical structure, excellent potency and an attractive safety profile. Our data support the further development of IOA-289 as a novel therapeutic approach for the treatment of cancer, particularly those with a high fibrotic and immunologically cold phenotype.

Dissociating Representations of Time and Number in Reinforcement-Rate Learning by Deletion of the GluA1 AMPA Receptor Subunit in Mice

Theories of learning differ in whether they assume that learning reflects the strength of an association between memories or symbolic encoding of the statistical properties of events. We provide novel evidence for symbolic encoding of informational variables by demonstrating that sensitivity to time and number in learning is dissociable. Whereas responding in normal mice was dependent on reinforcement rate, responding in mice that lacked the GluA1 AMPA receptor subunit was insensitive to reinforcement rate and, instead, dependent on the number of times a cue had been paired with reinforcement. This suggests that GluA1 is necessary for weighting numeric information by temporal information in order to calculate reinforcement rate. Sample sizes per genotype varied between seven and 23 across six experiments and consisted of both male and female mice. The results provide evidence for explicit encoding of variables by animals rather than implicit encoding via variations in associative strength.

Period-Prevalence and Risk Factors for Delirium in a Tertiary Referral ICU: A prospective cohort study

BACKGROUND

Delirium is common in intensive care and leads to increases in morbidity, mortality, Intensive Care Unit (ICU) length of stay, and hospital length of stay. Certain risk factors predict the appearance of delirium.

STUDY OBJECTIVES

To determine the rates of delirium, the rate of risk factors, and their relationship to the occurrence of delirium in an adult ICU.

METHODS

Single-centre, prospective, observational study. Demographic and treatment data were collected. The Confusion Assessment Method for ICU (CAM-ICU) was performed twice daily to assess for delirium continuously during a 3-week period. Statistical analysis was used to determine the relationship between risk factors and the occurrence of delirium.

RESULTS

86 patients were screened, 44 patients were included, and 260 patient-days were analyzed. The incidence of delirium was 42.9%, the prevalence of delirium in ICU was 50%. Urinary catheters and use of opioids were the most common factors with a positive association for occurrence of delirium. Exposure to daylight and sleeping for more than 4 hours at night were the factors most commonly associated with a lack of delirium.

CONCLUSION

The rates of delirium in ICU were high and risk factors occurred frequently. Addressing modifiable risk factors, including the promotion of adequate sleep, could improve outcomes.

Weekly paclitaxel, carboplatin, cetuximab, and cetuximab, docetaxel, cisplatin, and fluorouracil, followed by local therapy in previously untreated, locally advanced head and neck squamous cell carcinoma

BACKGROUND

The survival advantage of induction chemotherapy (IC) followed by locoregional treatment is controversial in locally advanced head and neck squamous cell carcinoma (LAHNSCC). We previously showed feasibility and safety of cetuximab-based IC (paclitaxel/carboplatin/cetuximab-PCC, and docetaxel/cisplatin/5-fluorouracil/cetuximab-C-TPF) followed by local therapy in LAHNSCC. The primary end point of this phase II clinical trial with randomization to PCC and C-TPF followed by combined local therapy in patients with LAHNSCC stratified by human papillomavirus (HPV) status and T-stage was 2-year progression-free survival (PFS) compared with historical control.

PATIENTS AND METHODS

Eligible patients were ≥18 years with squamous cell carcinoma of the oropharynx, oral cavity, nasopharynx, hypopharynx, or larynx with measurable stage IV (T0-4N2b-2c/3M0) and known HPV by p16 status. Stratification was by HPV and T-stage into one of the two risk groups: (i) low-risk: HPV-positive and T0-3 or HPV-negative and T0-2; (ii) intermediate/high-risk: HPV-positive and T4 or HPV-negative and T3-4. Patient reported outcomes were carried out.

RESULTS

A total of 136 patients were randomized in the study, 68 to each arm. With a median follow up of 3.2 years, the 2-year PFS in the PCC arm was 89% in the overall, 96% in the low-risk and 67% in the intermediate/high-risk groups; in the C-TPF arm 2-year PFS was 88% in the overall, 88% in the low-risk and 89% in the intermediate/high-risk groups.

CONCLUSION

The observed 2-year PFS of PCC in the low-risk group and of C-TPF in the intermediate/high-risk group showed a 20% improvement compared with the historical control derived from RTOG-0129, therefore reaching the primary end point of the trial.

The magnitude of Yo-Yo test improvements following an aerobic training intervention are associated with total genotype score

Recent research has demonstrated that there is considerable inter-individual variation in the response to aerobic training, and that this variation is partially mediated by genetic factors. As such, we aimed to investigate if a genetic based algorithm successfully predicted the magnitude of improvements following eight-weeks of aerobic training in youth soccer players. A genetic test was utilised to examine five single nucleotide polymorphisms (VEGF rs2010963, ADRB2 rs1042713 and rs1042714, CRP rs1205 & PPARGC1A rs8192678), whose occurrence is believed to impact aerobic training adaptations. 42 male soccer players (17.0 ± 1y, 176 ± 6 cm, 69 ± 9 kg) were tested and stratified into three different Total Genotype Score groups; "low", "medium"and "high", based on the possession of favourable polymorphisms. Subjects underwent two Yo-Yo tests separated by eight-weeks of sports-specific aerobic training. Overall, there were no significant differences between the genotype groups in pre-training Yo-Yo performance, but evident between-group response differentials emerged in post-training Yo-Yo test performance. Subjects in the "high" group saw much larger improvements (58%) than those in the 'medium" (35%) and "low" (7%) groups. There were significant (p<0.05) differences between the groups in the magnitude of improvement, with athletes in the "high" and medium group having larger improvements than the "low" group (d = 2.59 "high" vs "low"; d = 1.32 "medium" vs "low"). In conclusion, the magnitude of improvements in aerobic fitness following a training intervention were associated with a genetic algorithm comprised of five single nucleotide polymorphisms. This information could lead to the development of more individualised aerobic training designs, targeting optimal fitness adaptations.

A genetic-based algorithm for personalized resistance training

Association studies have identified dozens of genetic variants linked to training responses and sport-related traits. However, no intervention studies utilizing the idea of personalised training based on athlete's genetic profile have been conducted. Here we propose an algorithm that allows achieving greater results in response to high- or low-intensity resistance training programs by predicting athlete's potential for the development of power and endurance qualities with the panel of 15 performance-associated gene polymorphisms. To develop and validate such an algorithm we performed two studies in independent cohorts of male athletes (study 1: athletes from different sports (n = 28); study 2: soccer players (n = 39)). In both studies athletes completed an eight-week high- or low-intensity resistance training program, which either matched or mismatched their individual genotype. Two variables of explosive power and aerobic fitness, as measured by the countermovement jump (CMJ) and aerobic 3-min cycle test (Aero3) were assessed pre and post 8 weeks of resistance training. In study 1, the athletes from the matched groups (i.e. high-intensity trained with power genotype or low-intensity trained with endurance genotype) significantly increased results in CMJ (P = 0.0005) and Aero3 (P = 0.0004). Whereas, athletes from the mismatched group (i.e. high-intensity trained with endurance genotype or low-intensity trained with power genotype) demonstrated non-significant improvements in CMJ (P = 0.175) and less prominent results in Aero3 (P = 0.0134). In study 2, soccer players from the matched group also demonstrated significantly greater (P < 0.0001) performance changes in both tests compared to the mismatched group. Among non- or low responders of both studies, 82% of athletes (both for CMJ and Aero3) were from the mismatched group (P < 0.0001). Our results indicate that matching the individual's genotype with the appropriate training modality leads to more effective resistance training. The developed algorithm may be used to guide individualised resistance-training interventions.

SU-E-T-261: Determination of Initial Exposure Rates and Clearance Constants in a Sequence of 165 Consecutive Thyroid Cancer Patients Undergoing NaI-131 Therapy

PURPOSE

Following surgery, papillary and follicular thyroid cancers are usually treated with oral administration of NaI-131. In order to estimate subsequent staff, family, and public exposures, it is important to measure both exposure rates as well as the time of clearance of residual activity from these individuals. There is the additional possibility that patient whole-body absorbed dose estimates may be made using the data.

METHODS

During the historical interval 2006 - 2010, a total of 165 consecutive thyroid cancer patients were assayed at the time of activity administration and over the following several days. Using a calibrated radiation detector, exposure rates at one meter from the navel were measured between 2 and 5 times before release. By using these measurements and assuming a single-exponential clearance, we were able to evaluate initial exposure rates as well as the biological rate constant [k(biol)] for clearance of I-131 from the body.

RESULTS

Regression analyses were used to fit the initial exposure [X(0)] results as a function of administered activity. By least-squares, the slope was determined to be 0.15 mR/h/mCi over a clinically determined activity range of 25 to 250 mCi. At a given activity, there was wide variation of X(0) due to individual factors such as amount of residual thyroid mass and body habitus. For example, at 150 mCi, X(0) varied from 15 to 35 mR/h at one meter with the average being 25 mR/h. For the 165 patients, the mean biological clearance constant was 0.049/h.

CONCLUSION

Average initial exposure rates at one meter from 165 NaI-131 patients have been determined. The biological clearance was seen to be much more rapid than the physical decay constant for I-131 (0.0036/h). At a given activity level, variation of exposure rates was approximately +/- 40% over the corresponding patient population.

In-Situ Ellipsometry and Light Scattering Studies of Substrate Cleaning and Initial Layer Deposition in Low Temperature CVD of Crystalline Si

The first in-situ observations of initial stages of growth during Si vapour-phase homoepitaxy are reported, using the simultaneous measurement of dual-wavelength ellipsometry (364/488nm) and diffuse light scattering (488nm). Effective medium modelling shows that initial growth is nonuniform with pits present in the first 50–200Å of growth which rapidly fill in as growth proceeds. The sizes of the ellipsometric and scattering discontinuities are dependent on the extent of pre-growth roughening associated with oxide removal and finite wavelength effects become important for growth on roughened substrates.

Sensitivity and specificity of immunohistochemical antibodies used to distinguish between benign and malignant pleural disease: a systematic review of published reports

AIMS

A systematic review of published reports that have evaluated the ability of immunohistochemistry and argyrophil nucleolar organizing region (AgNOR) staining to distinguish between benign and malignant pleural disease.

METHODS

Nineteen relevant papers published during the period 1979-2005 were identified. Individual results of immunohistochemistry for five diagnostic antibodies were extracted to calculate diagnostic sensitivity and specificity. results from five of these studies that had evaluated proliferation markers or AgNOR staining techniques were also summarized.

RESULTS

Most antibodies demonstrated poor to moderate diagnostic ability. Desmin and epithelial membrane antigen (EMA) were the most useful, with sensitivity and specificity both above 74%. The combination of EMA and AgNOR was reported as having 95% diagnostic sensitivity. A high MCM2 labelling index also differentiated between benign and malignant pleural disease.

CONCLUSIONS

Immunohistochemistry is of limited value, but newer diagnostic methods may be useful additions in this area of pathology. The diagnostic importance of histological features seen on plain tissue sections is emphasized as vital for correctly differentiating between benign pleural disease and malignant pleural mesothelioma.

Diabetic Goto-Kakizaki rats display pronounced hyperglycemia and longer-lasting cognitive impairments following ischemia induced by cortical compression

Hyperglycemia has been shown to worsen the outcome of brain ischemia in several animal models but few experimental studies have investigated impairments in cognition induced by ischemic brain lesions in hyperglycemic animals. The Goto-Kakizaki (GK) rat naturally develops type 2 diabetes characterized by mild hyperglycemia and insulin resistance. We hypothesized that GK rats would display more severe cerebral damage due to hyperglycemia-aggravated brain injury and, accordingly, more severe cognitive impairments. In this study, recovery of motor and cognitive functions of GK and healthy Wistar rats was examined following extradural compression (EC) of the sensorimotor cortex. For this purpose, tests of vestibulomotor function (beam-walking) and combined tests of motor function and learning (locomotor activity from day (D) 1 to D5, operant lever-pressing from D14 to D25) were used. EC consistently reduced cerebral blood flow in both strains. Anesthesia-challenge and EC resulted in pronounced hyperglycemia in GK but not in Wistar rats. Lower beam-walking scores, increased locomotor activity, impairments in long-term habituation and learning of operant lever-pressing were more pronounced and observed at later time-points in GK rats. Fluoro-Jade, a marker of irreversible neuronal degeneration, revealed consistent degeneration in the ipsilateral cortex, hippocampus and thalamus at 2, 7 and 14 days post-compression. The amount of degeneration in these structures was considerably higher in GK rats. Thus, GK rats exhibited marked hyperglycemia during EC, as well as longer-lasting behavioral deficits and increased neurodegeneration during recovery. The GK rat is thus an attractive model for neuropathologic and cognitive studies after ischemic brain injury in hyperglycemic rats.

Randomized trial of two physiotherapy interventions for primary care neck and back pain patients: 'McKenzie' vs brief physiotherapy pain management

OBJECTIVES

Interventions that take psychosocial factors into account are recommended for patients with persistent back or neck pain. We compared the effectiveness of a brief physiotherapy pain management approach using cognitive-behavioural principles (Solution-Finding Approach-SFA) with a commonly used method of physical therapy (McKenzie Approach-McK).

METHODS

Eligible patients referred by GPs to physiotherapy departments with neck or back pain lasting at least 2 weeks were randomized to McK (n= 161) or to SFA (n= 154). They were further randomized to receive an educational booklet or not. The primary outcome was the Tampa Scale of Kinesiophobia (TSK) (Activity-Avoidance scale used as a proxy for coping) at 6 weeks, and 6 and 12 months.

RESULTS

Of 649 patients assessed for eligibility, 315 were recruited (219 with back pain, 96 with neck pain). There were no statistically significant differences in outcomes between the groups, except that at any time point SFA patients supported by a booklet reported less reliance on health professionals (Multidimensional Health Locus of Control Powerful Others Scale), while at 6 months McK patients showed slightly more improvement on activity-avoidance (TSK). At 6 weeks, patient satisfaction was greater for McK (median 90% compared with 70% for SFA). Both interventions resulted in modest but clinically important improvements over time on the Roland Disability Questionnaire Scores and Northwick Park Neck Pain Scores.

CONCLUSIONS

The McK approach resulted in higher patient satisfaction overall but the SFA could be more cost-effective, as fewer (three vs four) sessions were needed.

Clinical effects of air filters in homes of asthmatic adults sensitized and exposed to pet allergens

BACKGROUND

Despite medical advice, many pet-allergic asthma sufferers refuse to remove the pet to which they are sensitized from their home.

OBJECTIVE

We aimed to assess the clinical effects of air cleaners in the homes of adult asthma patients sensitized and exposed to cats and/or dogs.

METHODS

We performed a randomized, parallel-group study of 30 asthmatic adults sensitized to and sharing a home with cats or dogs. The effects of placing air cleaners in the living room and bedroom for 12 months and using high efficiency particulate air filter vacuum cleaners (active group) were compared with using these vacuum cleaners alone (control group). Measures of airway responsiveness, treatment requirement, lung function, peak flow, reservoir and airborne allergen were recorded before, during and after the interventions. A beneficial clinical response was assessed in terms of a 'combined asthma outcome'. This was defined as a two or more doubling dose improvement in bronchial hyper-reactivity to histamine and/or a reduction in treatment requirement of at least one step change on the British Thoracic Society guidelines for asthma treatment.

RESULTS

A beneficial clinical response was observed in 10/15 subjects in the active group compared with 3/15 in the control group after 12 months intervention (P = 0.01). No significant differences between the active and control groups were detected for changes in measures of lung function, reservoir pet allergen and airborne pet allergen during the study.

CONCLUSION

Whilst the study design has not allowed complete exclusion of a placebo effect, we believe that this pragmatic study of adult asthmatic patients sensitized and exposed to pets resulted in a small, but significant improvement in combined asthma outcome.

A new familial 'giant platelet syndrome' with structural, metabolic and functional abnormalities of platelets due to a primary megakaryocyte defect

We have investigated platelet morphology, function and biochemistry in a family affected by dominantly inherited congenital thrombocytopenia with giant platelets. A defect of aggregation was defined with evidence of disturbed fatty acid distribution in platelet membrane phospholipids and impaired arachidonic acid mobilization. Release of 5-hydroxytryptamine was normal. Platelet ultrastructure was grossly abnormal and volume analysis revealed small as well as giant forms. Bone marrow megakaryocytes were morphologically abnormal and the distribution of mean nuclear ploidy atypical, suggesting the production of abnormal platelets due to a primary megakaryocyte disorder. The features of this condition are distinct from those previously described in familial thrombocytopenia and constitute a new "giant platelet syndrome". The qualitative and quantitative platelet defects may be secondary to a disturbance of megakaryocyte cytoplasmic fragmentation.

Changes in the factor VIII complex in diabetic ketoacidosis: evidence of endothelial cell damage?

Factor VIII-related antigen and von Willebrand factor are synthesised by and released from vascular endothelium. Acute increases in the plasma concentration of these proteins may reflect endothelial cell damage. We have thus measured the plasma concentration of factor VIII-related antigen and von Willebrand factor, together with procoagulant factor VIII, during the course of acute diabetic ketoacidosis in seven patients. In addition, evidence for qualitative changes in the factor VIII complex was sought. Plasma factor VIII-related antigen and von Willebrand factor were markedly increased (plasma factor VIII-related antigen at presentation, median 2.75 U/ml; von Willebrand factor 2.95 U/ml) and returned toward normal with clinical and biochemical resolution (plasma factor VIII-related antigen at clinical recovery, median 1.80 U/ml; von Willebrand factor 2.05 U/ml). Plasma procoagulant factor VIII followed a similar pattern, but levels were less elevated (plasma procoagulant factor VIII, at presentation, median 1.6 U/ml; at clinical recovery, 1.2 U/ml). Crossed immunoelectrophoresis and sodium dodecyl sulphate-acrylamide electrophoresis with autoradiographic identification of multimeric structure revealed no evidence of structurally abnormal factor VIII-related antigen in diabetic ketoacidosis. However, an extra peak on crossed immunoelectrophoresis ("pre-peak") was a feature in the acute phase ketoacidotic plasma in six subjects, and may represent aggregated factor VIII. Changes in plasma factor VIII are a feature of diabetic ketoacidosis and, whilst not specific to this condition, may be the result of endothelial cell damage.

The routine measurement of platelet volume: a comparison of light-scattering and aperture-impedance technologies

The effect of dipotassium ethylenediaminetetra-acetic acid (EDTA) on platelet count and mean volume (MPV) was evaluated using two routine measurement systems, a Coulter S Plus (Phase 1) (S+) and a Technicon H6000 (H6000). In normal subjects (n = 29) MPV increased by 17% during 39 h storage in EDTA when measured by the S+. In contrast MPV decreased by 22% when measured by the H6000. MPV differences of up to 40% were observed between the two systems. Concomitant platelet counts, in both systems, changed by less than 4%. A mathematical model of the variation of MPV with storage time was constructed, enabling experimental results to be extrapolated, with accuracy, to time zero (MPV0). The H6000 average MPV0 was significantly larger than the S+ average MPV0. Using the anticoagulant sodium citrate and prostaglandin E1 (NaCitrate-PGE1) there were no significant changes in MPV measured by the S+ during 7 h storage, although a linear decrease in platelet count was observed. A decrease in H6000 MPV was observed whether the blood was stored in EDTA or NaCitrate-PGE1. Methodology, anti-coagulation and storage time all influence MPV. Until these determinants are standardised the clinical value of MPV cannot be assessed.

The platelet defect in acute myeloid leukaemia

In a study of platelets from 13 patients with acute myeloid leukaemia abnormal aggregation and release reactions were found. A previously unrecognised quantitative defect of thromboxane B2 production may, at least in part, explain these findings. In contrast to a previous report, we were unable to show a convincing storage pool defect in these platelets. The platelet membrane glycoproteins were largely normal.

Mutagenicity of methyl-, ethyl-, propyl- and butylnitrosourea towards Escherichia coli WP2 strains with varying DNA repair capabilities

Methyl- (MNUA), ethyl- (ENUA), propyl- (PNUA) and butylnitrosourea (BNUA) have been tested for toxicity and mutation in a liquid suspension assay towards Escherichia coli WP2 and some of its repair deficient derivatives. A comparison of survival rates after nitrosourea exposure between WP2 and WP2 uvrA showed no difference between the two strains but a consistent difference in potency between the various nitrosoureas studied. Toxicity increased in the order MNUA less than PNUA less than ENUA less than BNUA. ENUA and PNUA induced a greater number of trp+ revertants in both strains than did MNUA and BNUA, particularly at low survival rates. None of these differences in biological potency could be accounted for by differences in rates of hydrolysis. ENUA, PNUA and BNUA were non-mutagenic towards WP2 lexA, WP2 recA and WP2 uvrA lexA, whereas MNUA did induce mutations. Ethyl methanesulphonate (EMS) was able to mutate WP2 lexA. These results are discussed in the light of current theories regarding the mechanism of action of these compounds.