Large-scale pathway specific polygenic risk and transcriptomic community network analysis identifies novel functional pathways in Parkinson disease

Polygenic inheritance plays a central role in Parkinson disease (PD). A priority in elucidating PD etiology lies in defining the biological basis of genetic risk. Unraveling how risk leads to disruption will yield disease-modifying therapeutic targets that may be effective. Here, we utilized a high-throughput and hypothesis-free approach to determine biological processes underlying PD using the largest currently available cohorts of genetic and gene expression data from International Parkinson's Disease Genetics Consortium (IPDGC) and the Accelerating Medicines Partnership-Parkinson's disease initiative (AMP-PD), among other sources. We applied large-scale gene-set specific polygenic risk score (PRS) analyses to assess the role of common variation on PD risk focusing on publicly annotated gene sets representative of curated pathways. We nominated specific molecular sub-processes underlying protein misfolding and aggregation, post-translational protein modification, immune response, membrane and intracellular trafficking, lipid and vitamin metabolism, synaptic transmission, endosomal-lysosomal dysfunction, chromatin remodeling and apoptosis mediated by caspases among the main contributors to PD etiology. We assessed the impact of rare variation on PD risk in an independent cohort of whole-genome sequencing data and found evidence for a burden of rare damaging alleles in a range of processes, including neuronal transmission-related pathways and immune response. We explored enrichment linked to expression cell specificity patterns using single-cell gene expression data and demonstrated a significant risk pattern for dopaminergic neurons, serotonergic neurons, hypothalamic GABAergic neurons, and neural progenitors. Subsequently, we created a novel way of building de novo pathways by constructing a network expression community map using transcriptomic data derived from the blood of PD patients, which revealed functional enrichment in inflammatory signaling pathways, cell death machinery related processes, and dysregulation of mitochondrial homeostasis. Our analyses highlight several specific promising pathways and genes for functional prioritization and provide a cellular context in which such work should be done.

International Nosocomial Infection Control Consortium (INICC) report, data summary of 45 countries for 2012-2017: Device-associated module

BACKGROUND

We report the results of International Nosocomial Infection Control Consortium (INICC) surveillance study from January 2012 to December 2017 in 523 intensive care units (ICUs) in 45 countries from Latin America, Europe, Eastern Mediterranean, Southeast Asia, and Western Pacific.

METHODS

During the 6-year study period, prospective data from 532,483 ICU patients hospitalized in 242 hospitals, for an aggregate of 2,197,304 patient days, were collected through the INICC Surveillance Online System (ISOS). The Centers for Disease Control and Prevention-National Healthcare Safety Network (CDC-NHSN) definitions for device-associated health care-associated infection (DA-HAI) were applied.

RESULTS

Although device use in INICC ICUs was similar to that reported from CDC-NHSN ICUs, DA-HAI rates were higher in the INICC ICUs: in the medical-surgical ICUs, the pooled central line-associated bloodstream infection rate was higher (5.05 vs 0.8 per 1,000 central line-days); the ventilator-associated pneumonia rate was also higher (14.1 vs 0.9 per 1,000 ventilator-days,), as well as the rate of catheter-associated urinary tract infection (5.1 vs 1.7 per 1,000 catheter-days). From blood cultures samples, frequencies of resistance, such as of Pseudomonas aeruginosa to piperacillin-tazobactam (33.0% vs 18.3%), were also higher.

CONCLUSIONS

Despite a significant trend toward the reduction in INICC ICUs, DA-HAI rates are still much higher compared with CDC-NHSN's ICUs representing the developed world. It is INICC's main goal to provide basic and cost-effective resources, through the INICC Surveillance Online System to tackle the burden of DA-HAIs effectively.

Mechanical thrombectomy with a novel stent retriever with multifunctional zones: Initial clinical experience with the NeVa™ thrombectomy device

BACKGROUND AND PURPOSE

The NeVa™ (Vesalio, Nashville, Tennessee) thrombectomy device is a CE-approved novel hybrid-cell stent retriever with offset enlarged openings coupled with functional zones and a closed distal end. The device was designed to incorporate and trap resistant emboli. The purpose was to determine the safety and efficacy of the NeVa™ stent.

METHODS

Prospective data was collected on the first thirty consecutive patients treated at four stroke centers with NeVa™ as first line treatment between December 2017 and May 2018. Clinical outcome measures included re-perfusion scores after each pass, complications (per-procedural complications, device related adverse events, all intracerebral hemorrhage (ICH) and symptomatic ICH (sICH) on follow up imaging), 24 hour NIHSS, mRS at discharge and 90 days. Baseline data as well as treatment parameters were documented.

RESULTS

Mean presenting NIHSS was 16. Sites of primary occlusion were 10 ICA, 16 M1-MCA, 3 M2-MCA and one basilar. There were five tandem occlusions. Reperfusion outcomes after each NeVa pass; TICI ≥ 2b after first pass 63%, after 1 or 2 passes 83%, after 1 to 3 passes 90%. TICI 2c-3 after first pass 47%, after 1-2 passes 57%, after 1-3 passes 60%. TICI ≥ 2b after final pass 93%; TICI 2c-3, 63%. There were no device related serious averse events and no sICH. Clot material was partially or completely incorporated into the device after 70% passes. The mean 24 hour NIHSS was 7 and the 90 day mRS was 0-2 in 53%.

CONCLUSIONS

The NeVa™ device demonstrated a high rate of first pass complete reperfusion effect, a good safety profile and favorable 90 day clinical outcomes in this initial clinical experience.

Regulation of drug metabolizing enzymes in the leukaemic bone marrow microenvironment

The bone marrow (BM) microenvironment contributes to drug resistance in acute myeloid leukaemia (AML) and multiple myeloma (MM). We have shown that the critical drug metabolizing enzymes cytochrome P450 (CYP) 3A4 and cytidine deaminase (CDA) are highly expressed by BM stroma, and play an important role in this resistance to chemotherapy. However, what factors influence the chemoprotective capacity of the BM microenvironment, specifically related to CYP3A4 and CDA expression, are unknown. In this study, we found that the presence of AML cells decreases BM stromal expression of CYP3A4 and CDA, and this effect appears to be at least partially the result of cytokines secreted by AML cells. We also observed that stromal CYP3A4 expression is up‐regulated by drugs commonly used in AML induction therapy, cytarabine, etoposide and daunorubicin, resulting in cross‐resistance. Cytarabine also up‐regulated CDA expression. The up‐regulation of CYP3A4 associated with disease control was reversed by clarithromycin, a potent inhibitor of CYP3A4. Our data suggest that minimal residual disease states are characterized by high levels of stromal drug metabolizing enzymes and thus, strong microenvironment‐mediated drug resistance. These results further suggest a potential role for clinically targeting drug metabolizing enzymes in the microenvironment.

SEIS: Insight's Seismic Experiment for Internal Structure of Mars

By the end of 2018, 42 years after the landing of the two Viking seismometers on Mars, InSight will deploy onto Mars' surface the SEIS (Seismic Experiment for Internal Structure) instrument; a six-axes seismometer equipped with both a long-period three-axes Very Broad Band (VBB) instrument and a three-axes short-period (SP) instrument. These six sensors will cover a broad range of the seismic bandwidth, from 0.01 Hz to 50 Hz, with possible extension to longer periods. Data will be transmitted in the form of three continuous VBB components at 2 sample per second (sps), an estimation of the short period energy content from the SP at 1 sps and a continuous compound VBB/SP vertical axis at 10 sps. The continuous streams will be augmented by requested event data with sample rates from 20 to 100 sps. SEIS will improve upon the existing resolution of Viking's Mars seismic monitoring by a factor of ∼ 2500 at 1 Hz and ∼ 200 000 at 0.1 Hz. An additional major improvement is that, contrary to Viking, the seismometers will be deployed via a robotic arm directly onto Mars' surface and will be protected against temperature and wind by highly efficient thermal and wind shielding. Based on existing knowledge of Mars, it is reasonable to infer a moment magnitude detection threshold of M w ∼ 3 at 40 ∘ epicentral distance and a potential to detect several tens of quakes and about five impacts per year. In this paper, we first describe the science goals of the experiment and the rationale used to define its requirements. We then provide a detailed description of the hardware, from the sensors to the deployment system and associated performance, including transfer functions of the seismic sensors and temperature sensors. We conclude by describing the experiment ground segment, including data processing services, outreach and education networks and provide a description of the format to be used for future data distribution.

ELECTRONIC SUPPLEMENTARY MATERIAL

The online version of this article (10.1007/s11214-018-0574-6) contains supplementary material, which is available to authorized users.

Whole-exome sequencing of the BDR cohort: evidence to support the role of the PILRA gene in Alzheimer's disease

AIM

Late-onset Alzheimer's disease (LOAD) accounts for 95% of all Alzheimer's cases and is genetically complex in nature. Overlapping clinical and neuropathological features between AD, FTD and Parkinson's disease highlight the potential role of genetic pleiotropy across diseases. Recent genome-wide association studies (GWASs) have uncovered 20 new loci for AD risk; however, these exhibit small effect sizes. Using NGS, here we perform association analyses using exome-wide and candidate-gene-driven approaches.

METHODS

Whole-exome sequencing was performed on 132 AD cases and 53 control samples. Exome-wide single-variant association and gene burden tests were performed for 76 640 nonsingleton variants. Samples were also screened for known causative mutations in familial genes in AD and other dementias. Single-variant association and burden analysis was also carried out on variants in known AD and other neurological dementia genes.

RESULTS

Tentative single-variant and burden associations were seen in several genes with kinase and protease activity. Exome-wide burden analysis also revealed significant burden of variants in PILRA (P = 3.4 × 10^-5 ), which has previously been linked to AD via GWAS, hit ZCWPW1. Screening for causative mutations in familial AD and other dementia genes revealed no pathogenic variants. Variants identified in ABCA7, SLC24A4, CD33 and LRRK2 were nominally associated with disease (P < 0.05) but did not withstand correction for multiple testing. APOE (P = 0.02) and CLU (P = 0.04) variants showed significant burden on AD.

CONCLUSIONS

In addition, polygenic risk scores (PRS) were able to distinguish between cases and controls with 83.8% accuracy using 3268 variants, sex, age at death and APOE ε4 and ε2 status as predictors.

Cabozantinib is well tolerated in acute myeloid leukemia and effectively inhibits the resistance-conferring FLT3/tyrosine kinase domain/F691 mutation

BACKGROUND

Cabozantinib, a tyrosine kinase inhibitor of FMS-like tyrosine kinase 3 (FLT3), MET, AXL, vascular endothelial growth factor receptor, and KIT, is approved for use in multiple malignancies. We assessed the safety and tolerability of cabozantinib in AML, given up-regulation of multiple relevant pathways.

METHODS

Adults were eligible if they were 18 years old or older with relapsed/refractory AML or if they were 70 years old or older with newly diagnosed AML but were ineligible for conventional therapy. Cabozantinib was administered in 28-day cycles, and dose escalation occurred via cohorts. A pharmacodynamic evaluation of serial plasma samples via a plasma inhibitory assay (PIA) was used to assess FLT3-inhibitory activity in FLT3-mutant cell lines.

RESULTS

Among 18 patients enrolled, 5 were found to harbor FLT3/ITD mutations. Sixteen patients (89%) had relapsed/refractory AML, and most were treated with 2 or more lines of prior treatment. No dose-limiting toxicities (DLTs) were detected at the first dose level (40 mg daily), but 2 patients experienced DLTs at the next level (60 mg daily). The remaining patients were then dosed at 40 mg daily, the maximum tolerated dose (MTD). Additional grade 2 or higher toxicities, possibly/probably related to cabozantinib, included fatigue, nausea, transaminitis, and electrolyte imbalance. No patients had a marrow response according to formal criteria, but 4 had peripheral blast reductions; 2 of these 4 patients transiently cleared circulating blasts. One patient experienced a reduction in marrow blasts, and 1 had stable disease. The FLT3-inhibitory activity of plasma samples, as assessed with the PIA, revealed potent and sustained inhibition in FLT3/ITD and, notably, F691 tyrosine kinase domain (TKD)-mutant cells.

CONCLUSIONS

Cabozantinib is well tolerated in AML patients at an MTD of 40 mg daily and is a potent inhibitor of FLT3/ITD- and F691 TKD-altered tyrosine kinases. Cancer 2018;124:306-14. © 2017 American Cancer Society.

Genetics of Hereditary Ataxia in Scottish Terriers

BACKGROUND

Scottish Terriers have a high incidence of juvenile onset hereditary ataxia primarily affecting the Purkinje neuron of the cerebellar cortex and causing slowly progressive cerebellar dysfunction.

OBJECTIVE

To identify chromosomal regions associated with hereditary ataxia in Scottish Terriers.

ANIMALS

One hundred and fifty-three Scottish Terriers were recruited through the Scottish Terrier Club of America.

MATERIALS AND METHODS

Prospective study. Dogs were classified as affected if they had slowly progressive cerebellar signs. When possible, magnetic resonance imaging and histopathological evaluation of the brain were completed as diagnostic aids. To identify genomic regions connected with the disease, genome-wide mapping was performed using both linkage- and association-based approaches. Pedigree evaluation and homozygosity mapping were also performed to examine mode of inheritance and to investigate the region of interest, respectively.

RESULTS

Linkage and genome-wide association studies in a cohort of Scottish Terriers both identified a region on CFA X strongly associated with the disease trait. Homozygosity mapping revealed a 4 Mb region of interest. Pedigree evaluation failed to identify the possible mode of inheritance due to the lack of complete litter information.

CONCLUSION AND CLINICAL IMPORTANCE

This finding suggests that further genetic investigation of the potential region of interest on CFA X should be considered in order to identify the causal mutation as well as develop a genetic test to eliminate the disease from this breed.

Neurocognitive profile of patients with early stages of HIV infection

HIV-associated neurocognitive disorders (HAND) may include neurological disorders of various severities such as AIDS dementia complex (ADC) also known as HIV dementia and HIV-associated dementia (HAD), HIV encephalopathy, and Mild Neurocognitive Disorder (MND). As it seems HIV-associated neurocognitive disorders are associated with a metabolic encephalopathy induced by HIV infection and fueled by immune activation of macrophages and microglia. Despite of a group, evidences have described presence of cognitive alterations in HIV patients at different stages of HIV infection so far; little is known about the neurocognitive state of patients at very early stages of HIV infection. Here, we explored the neurocognitive profile of a group of cases of HIV patients at very early stages of HIV infection. We have analyzed of three groups of subjects, thus, we have studied a group of patients with early HIV infection, a healthy control group and a group of patients with mild cognitive impairment due to neurodegenerative causes. Our results suggested that cognitive processes are sensitive to very early neuropathological changes in HIV infection. Noteworthy, our results also showed that neurocognitive profile of HIV patients differs from those cognitive alterations in patients with mild cognitive disorders associated to primary neurodegeneration. Together, our results point out that HIV infection generates neural changes even at early stages of infection. Furthermore, our results highlight the importance of a deep neurocognitive exploration at very early stages of HIV infection as this approach allow improve the accompaniment, clinical attachment and interventions.

Disclosure of interest

The authors have not supplied their declaration of competing interest.

Asociación de los alelos del gen BoLA-DRB3 con la infección natural de Babesia spp en el ganado criollo Hartón del Valle

En 191 individuos de la raza bovina criolla Hartón del Valle, se evaluó la infección por los protozoarios Babesia bovis y Babesia bigemina mediante PCR convencional, los polimorfismos del gen BoLA-DRB3,2* mediante PCR-SBT y la asociación entre ambos (Odds Ratio, OR). Los alelos fueron categorizados según su asociación en resistentes (R), susceptibles (S) o neutrales (N) a la infección y los individuos genotipados según la clasificación de sus alelos como: N/N, N/R, N/S, R/R, R/S y S/S. Ningún animal fue positivo a la infección por B. bovis y por tanto no se realizaron estimaciones de asociación. La infección con B. bigemina fue del 13,1%. Se encontraron 36 alelos BoLA-DRB3,2, los más frecuentes fueron el *1101 (0,196), *20012 (0,097), *2006 (0,053) y *2703 (0,053). Se encontró una asociación positiva (p