Efficacy of computational predictions of the functional effect of idiosyncratic pharmacogenetic variants

Background

Pharmacogenetic variation is important to drug responses through diverse and complex mechanisms. Predictions of the functional impact of missense pharmacogenetic variants primarily rely on the degree of sequence conservation between species as a primary discriminator. However, idiosyncratic or off-target drug-variant interactions sometimes involve effects that are peripheral or accessory to the central systems in which a gene functions. Given the importance of sequence conservation to functional prediction tools-these idiosyncratic pharmacogenetic variants may violate the assumptions of predictive software commonly used to infer their effect.

Methods

Here we exhaustively assess the effectiveness of eleven missense mutation functional inference tools on all known pharmacogenetic missense variants contained in the Pharmacogenomics Knowledgebase (PharmGKB) repository. We categorize PharmGKB entries into sub-classes to catalog likely off-target interactions, such that we may compare predictions across different variant annotations.

Results

As previously demonstrated, functional inference tools perform variably across the complete set of PharmGKB variants, with large numbers of variants incorrectly classified as 'benign'. However, we find substantial differences amongst PharmGKB variant sub-classes, particularly in variants known to cause off-target, type B adverse drug reactions, that are largely unrelated to the main pharmacological action of the drug. Specifically, variants associated with off-target effects (hence referred to as off-target variants) were most often incorrectly classified as 'benign'. These results highlight the importance of understanding the underlying mechanism of pharmacogenetic variants and how variants associated with off-target effects will ultimately require new predictive algorithms.

Conclusion

In this work we demonstrate that functional inference tools perform poorly on pharmacogenetic variants, particularly on subsets enriched for variants causing off-target, type B adverse drug reactions. We describe how to identify variants associated with off-target effects within PharmGKB in order to generate a training set of variants that is needed to develop new algorithms specifically for this class of variant. Development of such tools will lead to more accurate functional predictions and pave the way for the increased wide-spread adoption of pharmacogenetics in clinical practice.

Gametic specialization of centromeric histone paralogs in Drosophila virilis

In most eukaryotes, centromeric histone (CenH3) proteins mediate mitosis and meiosis and ensure epigenetic inheritance of centromere identity. We hypothesized that disparate chromatin environments in soma versus germline might impose divergent functional requirements on single CenH3 genes, which could be ameliorated by gene duplications and subsequent specialization. Here, we analyzed the cytological localization of two recently identified CenH3 paralogs, Cid1 and Cid5, in Drosophila virilis using specific antibodies and epitope-tagged transgenic strains. We find that only ancestral Cid1 is present in somatic cells, whereas both Cid1 and Cid5 are expressed in testes and ovaries. However, Cid1 is lost in male meiosis but retained throughout oogenesis, whereas Cid5 is lost during female meiosis but retained in mature sperm. Following fertilization, only Cid1 is detectable in the early embryo, suggesting that maternally deposited Cid1 is rapidly loaded onto paternal centromeres during the protamine-to-histone transition. Our studies reveal mutually exclusive gametic specialization of divergent CenH3 paralogs. Duplication and divergence might allow essential centromeric genes to resolve an intralocus conflict between maternal and paternal centromeric requirements in many animal species.

Innovation of heterochromatin functions drives rapid evolution of essential ZAD-ZNF genes in Drosophila

Contrary to dogma, evolutionarily young and dynamic genes can encode essential functions. We find that evolutionarily dynamic ZAD-ZNF genes, which encode the most abundant class of insect transcription factors, are more likely to encode essential functions in Drosophila melanogaster than ancient, conserved ZAD-ZNF genes. We focus on the Nicknack ZAD-ZNF gene, which is evolutionarily young, poorly retained in Drosophila species, and evolves under strong positive selection. Yet we find that it is necessary for larval development in D. melanogaster. We show that Nicknack encodes a heterochromatin-localizing protein like its paralog Oddjob, also an evolutionarily dynamic yet essential ZAD-ZNF gene. We find that the divergent D. simulans Nicknack protein can still localize to D. melanogaster heterochromatin and rescue viability of female but not male Nicknack-null D. melanogaster. Our findings suggest that innovation for rapidly changing heterochromatin functions might generally explain the essentiality of many evolutionarily dynamic ZAD-ZNF genes in insects.

MHC class II transactivator CIITA induces cell resistance to Ebola virus and SARS-like coronaviruses

Recent outbreaks of Ebola virus (EBOV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have exposed our limited therapeutic options for such diseases and our poor understanding of the cellular mechanisms that block viral infections. Using a transposon-mediated gene-activation screen in human cells, we identify that the major histocompatibility complex (MHC) class II transactivator (CIITA) has antiviral activity against EBOV. CIITA induces resistance by activating expression of the p41 isoform of invariant chain CD74, which inhibits viral entry by blocking cathepsin-mediated processing of the Ebola glycoprotein. We further show that CD74 p41 can block the endosomal entry pathway of coronaviruses, including SARS-CoV-2. These data therefore implicate CIITA and CD74 in host defense against a range of viruses, and they identify an additional function of these proteins beyond their canonical roles in antigen presentation.

Categorising cancers to enable tailored care planning through a secondary analysis of cancer registration data in the UK

OBJECTIVES

The aim of this study is to categorise cancers into broad groups based on clusters of common treatment aims, experiences and outcomes to provide a numerical framework for understanding the services required to meet the needs of people with different cancers. This framework will enable a high-level overview of care and support requirements for the whole cancer population.

SETTING AND PARTICIPANTS

People in the UK with 1 of 20 common cancers; an estimated 309 000 diagnoses in 2014, 1 679 000 people diagnosed in a 20-year period and still living in 2010 and 135 000 cancer deaths in 2014.

PRIMARY AND SECONDARY OUTCOME MEASURES

Survival and stage at diagnosis data were reviewed alongside clinically led assumptions to identify commonalities and cluster cancer types into three groups. The three cancer groups were then described using incidence, prevalence and mortality data collected and reported by UK cancer registries. This was then reviewed, validated and refined following consultation.

RESULTS

Group 1 includes cancers with the highest survival; 5-year survival is over 80%. Group 3 cancers have shorter term survival. Five-year survival is not >20% for any cancer in this group and many do not survive over a year. Group 2 includes cancers where people typically live more than a year but are less likely to live >5 years. We estimate that the majority (64%) of people living with cancer (20 year prevalence) have a cancer type in group 1 'longer term survival', but significant minorities of people have cancers in group 2 'intermediate survival' (19%) and group 3 'shorter term survival' (10%).

CONCLUSIONS

Every person with cancer has unique needs shaped by a multitude of factors including comorbidities, treatment regimens, patient preferences, needs, attitudes and behaviours. However, to deliver personalised care, there needs to be a high-level view of potential care requirements to support service planning.

Using routinely collected data to stratify prostate cancer patients into phases of care in the United Kingdom: implications for resource allocation and the cancer survivorship programme

BACKGROUND

Prostate cancer is the most commonly diagnosed malignancy in British men. The increasing use of PSA screening test has resulted in many more patients being diagnosed with this condition. Advances in its treatment have improved the survival rate among these patients. By 2040, the prevalence of prostate cancer survivors is expected to reach 830 000. Many of them will require medical support for the management of their progressive disease or long-term toxicities from previous treatments. Successful implementation of the cancer survivorship programme among these patients depends on a good understanding of their demand on the health care system. The aim of this study is to segment the population of prostate cancer survivors into different needs groups and to quantify them with respect to their phase of care.

METHODS

Incidence, survival, prevalence and mortality data collected and reported by cancer registries across the United Kingdom have been used for the current study to provide indicative estimates as to the number of prostate cancer patients in each phase of the care pathway in a year.

RESULTS

The majority of prostate cancer patients are in the post-treatment monitoring phase. Around a fifth of the patients are either receiving treatment or in the recovery and readjustment phase having completed their treatment in the preceding year. Thirteen percent have not received any anticancer treatment, a further 12% (32 000) have developed metastatic disease and 4% are in the final stage of their lives.

CONCLUSION

On the basis of our estimates, patients undergoing post-treatment monitoring phase will constitute the biggest group among prostate cancer survivors. The pressure to provide adequate follow-up care to these patients will be a challenge. There is limited data available to definitively quantify the number of prostate cancer patients who follow different pathways of care, and we hope this study has highlighted the importance of collecting and reporting of such data to help future health care planning for these patients.

Pharmacokinetics of oxycodone after subcutaneous administration in a critically ill population compared with a healthy cohort

This study aimed to characterise and compare the absorption pharmacokinetics of a single subcutaneous dose of oxycodone in critically ill patients and healthy subjects. Blood samples taken at intervals from two minutes to eight hours after a subcutaneous dose of oxycodone in patients (5 mg) and healthy volunteers (10 mg) were assayed using high performance liquid chromatography. Data were analysed using a non-compartmental approach and presented as mean (SD). Parameters were corrected for dose differences between the groups assuming linear kinetics. Ten patients (eight male, two female) and seven healthy male subjects were included. Maximum venous concentration and area under the concentration curve were approximately two-fold lower in the patient group for an equivalent dose, suggesting either reduced bioavailability or increased clearance: maximum venous concentration 0.14 ± 0.06 vs 0.05 ± 0.02 µg/ml (P <0.0001); area under the concentration curve 19.50 ± 9.15 vs 9.72 ± 2.71 µg/ml/minute (P <0.001) respectively. However, time to maximum venous concentration and mean residence time were not different, suggesting similar absorption rates: time to maximum venous concentration 22.10 ± 18.0 vs 20.50 ± 16.10 minutes (P=0.81); mean residence time 353 ± 191 vs 291 ± 80 minutes (P=0.26). Kinetic parameters were less variable in patients than in volunteers. The patients therefore had reduced exposure to subcutaneous oxycodone. This warrants further model-based analysis and experimentation. Dose regimens for subcutaneous oxycodone developed in healthy volunteers cannot be directly translated to critically ill patients.

New pathways of care for cancer survivors: adding the numbers

BACKGROUND

Two million people in the UK had a cancer diagnosis at the end of 2008. Understanding the number of people diagnosed with cancer with and without health needs is valuable information that can be used to inform service planning, treatment provision and support for people at the right time in the right place as demand grows over time.

METHODS

Using available data and clinically led assumptions about patient need and outcomes, we make indicative estimates. We quantify, for three common cancers, the number of people in each of the five main identified phases of the cancer care pathway.

RESULTS

Estimates are provided for each phase of the pathway for breast, colorectal and lung cancers. We estimate that there are nearly 575,000 women a year with breast cancer in the care pathway at some point in the year, 8% are in the rehabilitation phase and 4% in the progressive illness phase. This compares to nearly 270,000 with colorectal and around 95,000 with lung cancer.

CONCLUSION

Using readily available data, we estimate the numbers of patients with different health needs. These numbers could inform the targeting of resources for service providers.

Rheumatoid arthritis (RA)-associated HLA-DR alleles form less stable complexes with class II-associated invariant chain peptide than non-RA-associated HLA-DR alleles

Certain HLA-DR alleles confer strong susceptibility to the autoimmune disease rheumatoid arthritis (RA). We compared RA-associated alleles, HLA-DR*0401, HLA-DR*0404, and HLA-DR*0405, with closely related, non-RA-associated alleles, HLA-DR*0402 and HLA-DR*0403, to determine whether they differ in their interactions with the class II chaperone, invariant chain (Ii). Ii binds to class II molecules in the endoplasmic reticulum, inhibits binding of other ligands, and directs class II-Ii complexes to endosomes, where Ii is degraded to class II-associated Ii peptide (CLIP). To evaluate the interaction of Ii and CLIP with these DR4 alleles, we introduced HLA-DR*0401, *0402, and *0404 alleles into a human B cell line that lacked endogenous HLA-DR or HLA-DM molecules. In a similar experiment, we introduced HLA-DR*0403 and *0405 into an HLA-DM-expressing B cell line, 8.1.6, and its DM-negative derivative, 9.5.3. Surface abundance of DR4-CLIP peptide complexes and their susceptibility to SDS-induced denaturation suggested that the different DR4-CLIP complexes had different stabilities. Pulse-chase experiments showed CLIP dissociated more rapidly from RA-associated DR molecules in B cell lines. In vitro assays using soluble rDR4 molecules showed that DR-CLIP complexes of DR*0401 and DR*0404 were less stable than complexes of DR*0402. Using CLIP peptide variants, we mapped the reduced CLIP interaction of RA-associated alleles to the shared epitope region. The reduced interaction of RA-associated HLA-DR4 molecules with CLIP may contribute to the pathophysiology of autoimmunity in RA.

Antidepressant interactions with warfarin

The interactions between warfarin and antidepressants can have potentially serious consequences resulting from enhanced or reduced anticoagulant activity. Information about such interactions was obtained from a Medline and hand search of the published literature, and by directly contacting manufacturers. The different classes of antidepressants are discussed in turn. The possible mechanisms are considered with particular reference to the cytochrome p450 system. From currently available data on the newer antidepressants our conclusions are that citalopram, nefazodone and sertraline may be relatively less likely to interact with warfarin. Fluoxetine, fluvoxamine, paroxetine and moclobemide appear to have the highest potential of the antidepressants for interactions. There is insufficient data on venlafaxine to make a prediction. The clinical implications of these findings are discussed and specific recommendations for International Normalized Ratio monitoring are suggested.

Charging for intensive care using direct nursing hours as the cost marker

The hypothesis that direct nursing hours correlate with the cost of a patient stay in intensive care was tested. One hundred and thirty-nine patients were studied and the data collected included: (a) direct nursing hours applied to each patient; (b) a daily TISS score: (c) a detailed costing of each patient (all costs are shown in N.Z.$). There was a strong correlation between the direct nursing hours and the total cost per patient (r2 = 0.98) (total cost = 54 x direct nursing hours + 344). Also a strong correlation existed between the total TISS scores and the total costs per patient (r2 = 0.96) (total cost = 67.13 x TISS). Direct nursing hours offer a relatively simple and logical method of allocating costs per patient.

Neuropsychiatric side effects related to treatment with felbamate

Seven patients with refractory seizure disorders and neuropsychiatric symptoms believed secondary to felbamate are presented. Five were on concomitant valproic acid (and other agents). Anergia, apathy, bradyphrenia, and increased irritability were prominent. One patient on felbamate monotherapy had a new-onset psychosis. Felbamate's NMDA receptor antagonism and GABA potentiation (perhaps enhanced by valproic acid use) are discussed as possible mechanisms of these side effects.

In situ monitoring with the Tradescantia bioassays on the genotoxicity of gaseous emissions from a closed landfill site and an incinerator

A dual monitoring system composed of the Tradescantia-Micronucleus (Trad-MCN) and Tradescantia-Stamen-Hair-Mutation (Trad-SHM) bioassays was utilized to monitor directly the genotoxicity of the gaseous emission at a closed landfill site and around an incinerator. Four of the commonly emitted gaseous agents from the landfill flare pipes, i.e. toluene, ethylbenzene, trichloroethylene and ethyltoluene were also evaluated for their genotoxicity in the laboratory. The in situ monitoring trips (360 km one way) were carried out by transporting the plant cuttings in a clean air box or in an air-tight plastic bag to the site and exposing these test cuttings for 5-7 h. The exposed plant samples were examined for micronuclei frequencies or the pink mutation rate after the appropriate recovery periods (24 h for MCN, 7-11 days for SHM). A total of 20 monitoring trips were made to the landfill, and 8 to the nearby surroundings (100-500 m from the chimney) of the incinerator site in a two year period. The major findings of the Trad-MCN test on the clastogenicity of the gaseous emission from the flare pipe of the landfill site showed positive responses or toxic effects in 6 out of 20 trips, and that from the incinerator showed positive responses in 5 out of the 8 trips. These positive responses were closely associated with the weather, i.e. low wind velocity, high temperature and relative humidity, and especially the distance from the chimney of the incinerator. The MCN frequencies and mutation rates of the Elementary School site (E. Sch) which is about 200 m from the fence of the landfill site were mostly negative, except the test results of three trips. Trad-SHM tests on the mutagenicity of gaseous emissions from the flare pipe of the landfill showed 12 positive responses out of 20 trials and 2 positives out of 4 trials from the incinerator gaseous emissions. The average mutation rate from 20 Trad-SHM monitoring trips is positive when the ANOVA and Dunnett's t-statistic were applied to the consolidated data. There is a significant (0.01) difference between the lab control and the gas exposed groups, and between the field control and gas exposed groups. Results of the Trad-SHM test at the E. Sch. site were mostly negative except for one trip. In general, micronuclei frequencies and mutation rates of the field control groups were relatively higher than those of the lab controls. The Trad-MCN test on pure gases showed positive responses in all 3 repeated tests on toluene (50-892 ppm). The test results of ethylbenzene yielded positive responses at 172 ppm/min and 1549 ppm/min dosages and exhibited toxicity at higher concentrations. Trad-MCN tests on trichloroethylene and ethyltoluene yielded positive responses at around 100-200 ppm/min level. Three repeated Trad-SHM tests on toluene yielded no positive response at low concentrations (4.3-12.9 ppm).

Characterization of major depression symptoms in multiple sclerosis patients

Retrospective review of affective disturbances in 238 patients with multiple sclerosis (MS) seen over a 6-month period revealed: 1) 51 patients (22%) received pharmacologic treatment for depressive symptoms during or within 4 years of the study period, and 17 (7%) received treatment for rapid mood swings; 2) among the 51 depressed patients, response rate to medication was extremely high; 3) relapse of depressive symptomatology after discontinuation of medication was also high (17/29); 4) first episodes of major depression frequently occurred during periods of MS progression or exacerbation, but first episodes also occurred during periods of relative clinical stability; 5) suicidal ideation was common (12 patients), but only 1 patient had a history of attempted suicide; and 6) side effects were tolerable in most patients.

Measurement of treatment response to sertraline in depressed multiple sclerosis patients using the Carroll scale

We studied 11 patients with stable multiple sclerosis (MS) with major depression in terms of response to Sertraline at 100 mg q.d. in an open label trial. Patients were evaluated with self assessment measurements (Carroll scale) prior to and during treatment. Only one patient discontinued the drug during the three month treatment trial, and this was due to perceived lack of efficacy by the patient. The remainder of the patients completed at least three months of treatment and had significant improvement in depressive symptoms by self assessment measurements. No patients experienced side effects. Sertraline appears to be well tolerated and effective in treatment of major depression in MS. The Carroll scale is an easily administered means of assessing treatment response, and correlated highly with our clinical impressions.

The improved Allium/Vicia root tip micronucleus assay for clastogenicity of environmental pollutants

The meristematic mitotic cells of plant roots are appropriate and efficient cytogenetic materials for the detection of clastogenicity of environmental pollutants, especially for in situ monitoring of water contaminants. Among several cytological endpoints in these fast dividing cells, such as chromosome/chromatid aberrations, sister-chromatid exchanges and micronuclei, the most effective and simplest indicator of cytological damage is micronucleus formation. Although the Allium cepa and Vicia faba root meristem micronucleus assays (Allium/Vicia root MCN) have been used in clastogenicity studies about 12 times by various authors in the last 25 years, there is no report on the comparison of the efficiency of these two plant systems and in different cell populations (meristem and F1) of the root tip as well as under adequate recovery duration. In order to maximize the efficiency of these bioassays, the current study was designed to compare the Allium and the Vicia root MCN assays on the basis of chromosome length, peak sensitivity of the mitotic cells, and the regions of the root tip where the MCN are formed. The total length of the 2n complement of Allium chromosomes is 14.4 microns and the total length of the 2n complement of Vicia is 9.32 microns. The peak sensitivity determined by serial fixation at 12-h intervals after 100 R of X-irradiation is 44 h. The slope of the X-ray dose-response curve of Allium roots derived from the meristematic regions was lower than that derived from cells in the F1 region. Higher efficiency was also demonstrated when the MCN frequencies were scored from the F1 cells in both Allium and Vicia treated with formaldehyde (FA), mitomycin C (MMC), and maleic hydrazide (MH). The results indicated that scoring of MCN frequencies from the F1 cell region of the root tip was more efficient than scoring from the meristematic region. The X-ray linear regression dose-response curves were established in both Allium and Vicia cell systems and the coefficients of correlations, slope values were used to verify the reliability and efficiency of these two plant cell systems. Based on the dose-response slope value of 0.894 for Allium and 0.643 for Vicia, the Allium root MCN was a more efficient test system. The greater sensitivity of the Allium roots is probably due to the greater total length of the diploid complement and the higher number of metacentric chromosomes.(ABSTRACT TRUNCATED AT 400 WORDS)

Prenuptial seizures: a report of five cases

The cases of 5 patients with seizures occurring the day of or shortly before their weddings are presented. Major life events may precipitate or exacerbate epileptic or nonepileptic seizures as a result of 1) missed medications, 2) sleep deprivation, 3) alcohol or concomitant medications, 4) hyperventilation, or 5) the emotional state directly or stress indirectly. Seizures occurring at times of psychological stress may be either neurological or psychiatric in origin. The physician treating patients with a new onset or exacerbation of seizures around a major life event must consider all of these factors in the evaluation.

Chronic low back pain patients around the world: cross-cultural similarities and differences

OBJECTIVE

The current study sought to determine whether there were any significant cross-cultural differences in medical-physical findings, or in psychosocial, behavioral, vocational, and avocational functioning, for chronic low back pain patients.

DESIGN

Partially double-blind controlled comparison of six different culture groups.

SETTING

Subjects were selected from primarily ambulatory care facilities specializing in treating chronic pain patients. PATIENTS-SUBJECTS: Subjects consisted of 63 chronic low back pain patients and 63 healthy controls. Low back pain patients were randomly selected from six different culture groups (American, Japanese, Mexican, Colombian, Italian, and New Zealander). Ten to 11 were gathered per culture from a pool of patients treated at various pain treatment programs. Likewise, 10 or 11 control group subjects were obtained from each culture from a pool of healthy support staff.

MAIN OUTCOME MEASURES

The Sickness Impact Profile and the Medical Examination and Diagnostic Information Coding System were used as primary outcome measures.

RESULTS

Findings showed that (a) low back pain subjects across all cultures had significantly more medical-physical findings and more impairment on psychosocial, behavioral, vocational, and avocational measures than controls did; (b) Mexican and New Zealander low back pain subjects had significantly fewer physical findings than other low back pain groups did; (c) the American, New Zealander, and Italian low back pain patients reported significantly more impairment in psychosocial, recreational, and/or work areas, with the Americans the most dysfunctional; and (d) findings were not a function of working class, age, sex, pain intensity, pain duration, previous surgeries, or differences in medical-physical findings.

CONCLUSIONS

It was concluded that there were important cross-cultural differences in chronic low back pain patients' self-perceived level of dysfunction, with the American patients clearly the most dysfunctional. Possible explanations included cross-cultural differences in social expectation; attention; legal-administrative requirements; financial gains; attitudes-expectations about usage, type, and availability of health care; and self-perceived ability and willingness to cope.

Catecholamine metabolism in the attention deficit disorder: implications for the use of amino acid precursor therapy

The use of catecholamine precursors and agonists in the attention deficit disorder and various biochemical studies have implicated deficient catecholamine metabolism in the pathogenesis of this illness. The amino acid L-tyrosine, a catecholamine precursor, is capable of augmenting central dopamine norepinephrine. Study of its use in the treatment of the attention deficit disorder as a safer alternative to stimulant therapy is thus warranted.

Phase separations in phospholipd membranes

Phase diagrams representing lateral phase separations in the plane of lipid bilayer membranes have been determined for binary mixtures containing dielaidoylphosphatidylcholine together with dimyristoylphosphatidylcholine, dipalmitoylphosphatidylcholine, distearoylphosphatidylcholine, dioleoylphosphatidylcholine, and dipalmitoylphosphatidylethanolamine. The phase diagrams were deduced from observations of the temperature dependence of the paramagnetic resonance spectra of low concentrations of spin-labels incorporated in these bilayer membranes. In one case, the binary mixture of dipalmitoylphosphatidylethamine and dielaidoylphosphatidylcholine, evidence has been obtained for fluid-fluid immiscibility, in specified temperature and compoistion ranges. This immiscibility could give a lateral phase separation into fluid domains in the plane of the membrane, and/or a transverse phase separation into an asymmetrical bilayer membrane, and/or possibly disco ntinuous bilayer membranes of different composition. An asymmetrical bilayer membrane can be expected on theoretical grounds to form a nonplanar membrane.