Label-free Quantitative Proteomics of Mouse Cerebrospinal Fluid Detects β-Site APP Cleaving Enzyme (BACE1) Protease Substrates In Vivo

Analysis of murine cerebrospinal fluid (CSF) by quantitative mass spectrometry is challenging because of low CSF volume, low total protein concentration, and the presence of highly abundant proteins such as albumin. We demonstrate that the CSF proteome of individual mice can be analyzed in a quantitative manner to a depth of several hundred proteins in a robust and simple workflow consisting of single ultra HPLC runs on a benchtop mass spectrometer. The workflow is validated by a comparative analysis of BACE1−/− and wild-type mice using label-free quantification. The protease BACE1 cleaves the amyloid precursor protein (APP) as well as several other substrates and is a major drug target in Alzheimer''s disease. We identified a total of 715 proteins with at least 2 unique peptides and quantified 522 of those proteins in CSF from BACE1−/− and wild-type mice. Several proteins, including the known BACE1 substrates APP, APLP1, CHL1 and contactin-2 showed lower abundance in the CSF of BACE1−/− mice, demonstrating that BACE1 substrate identification is possible from CSF. Additionally, ectonucleotide pyrophosphatase 5 was identified as a novel BACE1 substrate and validated in cells using immunoblots and by an in vitro BACE1 protease assay. Likewise, receptor-type tyrosine-protein phosphatase N2 and plexin domain-containing 2 were confirmed as BACE1 substrates by in vitro assays. Taken together, our study shows the deepest characterization of the mouse CSF proteome to date and the first quantitative analysis of the CSF proteome of individual mice. The BACE1 substrates identified in CSF may serve as biomarkers to monitor BACE1 activity in Alzheimer patients treated with BACE inhibitors.Cerebrospinal fluid (CSF)¹ consists of interstitial fluid that is in continuous exchange with the central nervous system and the peripheral blood system. It represents the only body fluid in humans that is in direct contact with brain tissue and accessible in a routine clinical setting. Thus, the easy accessibility from the periphery renders CSF perfectly suited to study pathologic neurological processes (1). Human CSF has a relatively low protein content (∼ 0.4 mg/ml), but features a highly diverse proteome. It is thus increasingly studied by modern mass spectrometry based proteomics (2). The proteomic analysis of human CSF typically involves various protein concentration and fractionation steps as well as the depletion of highly abundant proteins, such as serum albumin. This allows the identification of several hundred up to 2600 proteins from several milliliters of human CSF (3).Mice are the most popular animal model in preclinical research, because of their similarity to humans in genetics and physiology, their unlimited supply and their ease of genetic engineering. The study of their CSF can provide valuable insights into disease mechanisms and biomarker discovery and may allow the rapid translation of preclinical findings into human patients. However, the proteomic study of murine CSF has been limited because of several shortcomings. The low total CSF volume of ∼30 μl and an average yield of only ∼10 μl blood-free CSF pose a challenge for various protein concentration and depletion steps that are routinely applied to human CSF, where the sample volume is up to 1,000-fold more (4, 5). One study reported the identification of 289 proteins and the quantification of 103 proteins using pooled immunodepleted CSF from 10–12 mice per sample (6). A second study reported the identification of 566 proteins in murine CSF of individual mice, relying on time consuming fractionation by two dimensional liquid chromatography tandem MS (2D-LC-MS/MS) (7).Here we show that label-free quantitative proteomics in murine CSF can be achieved in unprecedented depth in individual animals using single ultra HPLC runs on the benchtop Q Exactive mass spectrometer. We demonstrate the feasibility of our approach by comparing the CSF of BACE1 (β-site amyloid precursor protein (APP) cleaving enzyme 1) −/− mice with their wild-type littermates.BACE1 is a membrane bound aspartyl protease that is essential in the pathogenesis of Alzheimer''s disease. It is the rate-limiting enzyme in a proteolytic cascade leading to the liberation of the neurotoxic Aβ peptide from the much larger amyloid precursor protein (APP) into the extracellular space (8, 9). Inhibition of BACE1 abolishes Aβ generation, rendering BACE1 a prime drug target for the therapy of Alzheimer''s disease (10). Besides APP, BACE1 processes numerous other substrates in vivo and in vitro, which raises concerns about mechanism based side effects on the therapeutic inhibition of this protease (11). Although BACE1 expression levels are the highest in the brain, it is currently unknown whether BACE1 substrate levels besides APP can be monitored in the CSF as a read-out of BACE1 activity. This would be desirable, as it would allow the longitudinal monitoring of BACE1 substrate levels on therapeutic inhibition of BACE1 in humans and thus an effective screening for possible adverse effects.Our approach allows the accurate identification and quantification of several hundred proteins in as little as 2 μl of murine CSF in ∼4.5 h per sample, at a much greater speed and proteomic depth than in previous studies, despite using lower sample amounts (6, 7). Overall, 715 proteins were identified with at least two unique peptides and 522 proteins were quantified in at least three biological replicates of both BACE1−/− and wild-type mice. We provide evidence that BACE1 activity is reflected in the composition of the CSF, as the secreted ectodomains of well-known BACE1 substrates were reduced in BACE1−/− animals. In addition, we identified and validated a previously unknown BACE1 substrate candidate and confirmed two recently described novel BACE1 substrates. The three proteins may represent novel prognostic or diagnostic biomarkers and may aid in the development of APP-specific BACE1 inhibitors.     

Prevalence of Pulmonary Hypertension in the General Population: The Rotterdam Study

Background

Pulmonary hypertension is characterized by increased pulmonary artery pressure and carries an increased mortality. Population-based studies into pulmonary hypertension are scarce and little is known about its prevalence in the general population. We aimed to describe the distribution of echocardiographically-assessed pulmonary artery systolic pressure (ePASP) in the general population, to estimate the prevalence of pulmonary hypertension, and to identify associated factors.

Methods

Participants (n = 3381, mean age 76.4 years, 59% women) from the Rotterdam Study, a population-based cohort, underwent echocardiography. Echocardiographic pulmonary hypertension was defined as ePASP>40 mmHg.

Results

Mean ePASP was 26.3 mmHg (SD 7.0). Prevalence of echocardiographic pulmonary hypertension was 2.6% (95%CI: 2.0; 3.2). Prevalence was higher in older participants compared to younger ones (8.3% in those over 85 years versus 0.8% in those between 65 and 70), and in those with underlying disorders versus those without (5.9% in subjects with COPD versus 2.3%; 9.2% in those with left ventricular systolic dysfunction versus 2.3%; 23.1% in stages 3 or 4 left ventricular diastolic dysfunction versus 1.9% in normal or stage 1). Factors independently associated with higher ePASP were older age, higher BMI, left ventricular diastolic dysfunction, COPD and systemic hypertension.

Conclusion

In this large population-based study, we show that pulmonary hypertension as measured by echocardiography has a low prevalence in the overall general population in the Netherlands, but estimates may be higher in specific subgroups, especially in those with underlying diseases. Increased pulmonary arterial pressure is likely to gain importance in the near future due to population aging and the accompanying prevalences of underlying disorders.     

Drug-Resistant Urothelial Cancer Cell Lines Display Diverse Sensitivity Profiles to Potential Second-Line Therapeutics

Combination chemotherapy with gemcitabine and cisplatin in patients with metastatic urothelial cancer of the bladder frequently results in the development of acquired drug resistance. Availability of cell culture models with acquired resistance could help to identify candidate treatments for an efficient second-line therapy. Six cisplatin- and six gemcitabine-resistant cell lines were established. Cell viability assays were performed to evaluate the sensitivity to 16 different chemotherapeutic substances. The activity of the drug transporter ATP-binding cassette transporter, subfamily B, member 1 (ABCB1, a critical mediator of multidrug resistance in cancer) was evaluated using fluorescent ABCB1 substrates. For functional assessment, cells overexpressing ABCB1 were generated by transduction with a lentiviral vector encoding for ABCB1, while zosuquidar was used for selective inhibition. In this study, 8 of 12 gemcitabine- or cisplatin-resistant cell lines were cross-resistant to carboplatin, 5 to pemetrexed, 4 to methotrexate, 3 to oxaliplatin, 5-fluorouracil, and paclitaxel, and 2 to cabazitaxel, larotaxel, docetaxel, topotecan, doxorubicin, and mitomycin c, and 1 of 12 cell lines was cross-resistant to vinflunine and vinblastine. In one cell line with acquired resistance to gemcitabine (TCC-SUP^rGEMCI²⁰), cross-resistance seemed to be mediated by ABCB1 expression. Our model identified the vinca alkaloids vinblastine and vinflunine, in Europe an already approved second-line therapeutic for metastatic bladder cancer, as the most effective compounds in urothelial cancer cells with acquired resistance to gemcitabine or cisplatin. These results demonstrate that this in vitro model can reproduce clinically relevant results and may be suitable to identify novel substances for the treatment of metastatic bladder cancer.     

The Effectiveness of Different Interventions to Promote Poison Prevention Behaviours in Households with Children: A Network Meta-Analysis

Background

There is evidence from 2 previous meta-analyses that interventions to promote poison prevention behaviours are effective in increasing a range of poison prevention practices in households with children. The published meta-analyses compared any intervention against a “usual care or no intervention” which potentially limits the usefulness of the analysis to decision makers. We aim to use network meta-analysis to simultaneously evaluate the effectiveness of different interventions to increase prevalence of safe storage of i) Medicines only, ii) Other household products only, iii) Poisons (both medicines and non-medicines), iv) Poisonous plants; and v) Possession of poison control centre (PCC) telephone number in households with children.

Methods

Data on the effectiveness of poison prevention interventions was extracted from primary studies identified in 2 newly-undertaken systematic reviews. Effect estimates were pooled across studies using a random effects network meta-analysis model.

Results

28 of the 47 primary studies identified were included in the analysis. Compared to usual care intervention, the intervention with education and low cost/free equipment elements was most effective in promoting safe storage of medicines (odds ratio 2.51, 95% credible interval 1.01 to 6.00) while interventions with education, low cost/free equipment, home safety inspection and fitting components were most effective in promoting safe storage of other household products (2.52, 1.12 to 7.13), safe storage of poisons (11.10, 1.60 to 141.50) and possession of PCC number (38.82, 2.19 to 687.10). No one intervention package was more effective than the others in promoting safe storage of poisonous plants.

Conclusion

The most effective interventions varied by poison prevention practice, but education alone was not the most effective intervention for any poison prevention practice. Commissioners and providers of poison prevention interventions should tailor the interventions they commission or provide to the poison prevention practices they wish to promote.

Highlights

• Network meta-analysis is useful for comparing multiple injury-prevention interventions.
• More intensive poison prevention interventions were more effective than education alone.
• Education and low cost/free equipment was most effective in promoting safe storage of medicines.
• Education, low cost/free equipment, home safety inspection and fitting was most effective in promoting safe storage of household products and poisons.
• Education, low cost/free equipment and home inspection were most effective in promoting possession of a poison control centre number.
• None of the intervention packages was more effective than the others in promoting safe storage of poisonous plants.

     

<Emphasis Type="Italic">Steinmanniporella,</Emphasis> a new dasycladale genus name for “<Emphasis Type="Italic">Linoporella</Emphasis>” with two orders of laterals

After Barattolo (Abstracts of the 5th international symposium on fossil algae, 1991) and Barattolo and Romano (Bollettino della Societa Paleontologica Italiana, 44(3): 237–254, 2005) emended the diagnosis of the genus Linoporella Steinmann to include species with three orders of laterals, algae included formerly in this genus but with only two orders of laterals remained in open nomenclature. Comparisons of these algae with other Jurassic and Cretaceous dasycladaleans with two orders of laterals resulted in the introduction of the new genus Steinmanniporella.     

Somatodendritic serotonin release and re-uptake in mouse embryonic stem cell-derived serotonergic neurons

Serotonergic neurotransmission plays an important role during neural development. Serotonergic dysfunction is observed in various psychiatric disorders and many psychoactive drugs target proteins on serotonergic neurons. Serotonergic neurons are located in the raphé nuclei and densely innervate the whole brain. The low number and the intricate accessibility of these neurons do not allow to culture them and therefore to date it was impossible to study drug-target interactions on bona fide serotonergic neurons. In order to circumvent such problems we have developed a protocol that allows the rapid and efficient generation of serotonergic neurons from mouse embryonic stem cells. Neuronal precursors were obtained by neuronal stem sphere formation in floating culture in the presence of various mitogens. Differentiation into neurons was induced by withdrawal of the mitogens. About 90% of the resulting neurons exhibited a serotonergic phenotype as judged by immunostaining against serotonin, its synthesising enzyme tryptophan hydroxylase 2, the serotonin transporter as well as 5-HT1(A) and 5-HT1(B) autoreceptors. In addition, we found expression of the vesicular monoamine transporter vMAT2 and the presynaptic protein Bassoon, which is involved in organizing the assembly of the presynaptic active zone. Depolarisation-induced calcium influx was visualised by Fluo-4, and accompanying exocytotic events by FM dye staining. Proteins involved in 5-HT release and re-uptake as well as depolarisation evoked exocytosis were evenly co-distributed on neurites and cell bodies suggesting that ES cell-derived serotonergic neurons also exhibit somatodendritic release comparable to serotonergic neurons in the raphé nuclei.     

Proteomic and functional analysis of the mitotic Drosophila centrosome

Regulation of centrosome structure, duplication and segregation is integrated into cellular pathways that control cell cycle progression and growth. As part of these pathways, numerous proteins with well‐established non‐centrosomal localization and function associate with the centrosome to fulfill regulatory functions. In turn, classical centrosomal components take up functional and structural roles as part of other cellular organelles and compartments. Thus, although a comprehensive inventory of centrosome components is missing, emerging evidence indicates that its molecular composition reflects the complexity of its functions. We analysed the Drosophila embryonic centrosomal proteome using immunoisolation in combination with mass spectrometry. The 251 identified components were functionally characterized by RNA interference. Among those, a core group of 11 proteins was critical for centrosome structure maintenance. Depletion of any of these proteins in Drosophila SL2 cells resulted in centrosome disintegration, revealing a molecular dependency of centrosome structure on components of the protein translation machinery, actin‐ and RNA‐binding proteins. In total, we assigned novel centrosome‐related functions to 24 proteins and confirmed 13 of these in human cells.     

Duplex (or quadruplet) CH domain containing human multidomain proteins: an inventory

In this paper, the inventory presented for singlet CH (calponin homology/actin binding) domain containing human multidomain proteins [1] is extended to several duplex and one quadruplet CH containing forms. Invariably, the duplexes are located at the begin of the molecules. The regions connecting the two CH units suggest amino acid conservations which allows the placing of 18 duplex containing molecules into six groups wherein the gene for one member in each group created the others more recently by gene duplication. The ancient multidomain proteins, possibly, were primarily the result of an exon shuffling (transposition) mechanism that also guided the placing of the CH singlet or duplex domain at the amino end of the newly created proteins. A mechanism that creates pseudogenes could conceivably produce genes that encode multi-domain proteins. Intragenomic duplications (slippage) might have facilitated the occurrence of encoding repeats, thus allowing for the creation of multiple identical domains within one molecule. Gene duplication with subsequent modification and small domain gene recombination which formed multidomain proteins are important forces driving evolution.     

Single and multiple CH (calponin homology) domain containing multidomain proteins in <Emphasis Type="Italic">Dictyostelium discoideum</Emphasis>: an inventory

We present an inventory of single or multiple calponin homology (CH) domain containing proteins of Dictyostelium discoideum. A multiple alignment and a phylogenetic tree of all 60 CH domains found in 36 proteins showed that most CH domains can be assigned to one of 6 types. We have then distributed the proteins into several classes according to the type and arrangement of the CH domains. Most proteins belong to the class of ABD (actin-binding domain)-forming CH tandems (CH1–CH2) of the α-actinin and fimbrin families or to the class of CH3 domain-bearing proteins. There are a few examples of proteins with a single CH1 or CH2 domain, one with a CH1–CH1 doublet and a single representative of the CHe class of microtubule-binding proteins. A comparison with CH domain proteins in Homo sapiens suggests that while the individual domains are available in both species, the existence of identical multidomain proteins in toto is rare. Fimbrin 1, α-actinin and EB1 appear as perfect orthologs in both species, whereas filamin and interaptin may represent ancestral forms of human filamin and nesprins. In four more cases (NAV/Unc-53-, smoothelin-, transgelin- and Gas2-related proteins) functional data are needed in order to establish a potential relationship with a human counterpart. Although extensive data exist for a few of the D. discoideum CH proteins, most remain to be characterized and our analysis may help predicting some of their properties.