Recombinant human interleukin 1 alpha: purification and biological characterization

Interleukin 1 (IL 1) is a polypeptide hormone produced by activated macrophages that affects many different cell types involved in immune and inflammatory responses. The cloning and expression of a murine IL 1 cDNA in Escherichia coli encoding a polypeptide precursor of 270 amino acids has been reported, and expression of the carboxy-terminal 156 amino acids of this precursor in E. coli yields biologically active IL 1. By using the murine IL 1 cDNA as a probe, we have isolated its human homolog from cDNA generated to lipopolysaccharide-stimulated human leukocyte mRNA. Nucleotide sequence analysis of this cDNA predicts a protein of analysis of this cDNA predicts a protein of 271 amino acids (termed IL 1 alpha) which shows congruent to 61% homology to its murine counterpart but only 27% homology to a recently characterized human IL 1 precursor (IL 1 beta). We have expressed the carboxy-terminal 154 amino acids of IL 1 alpha in E. coli, purified this protein to homogeneity, and have compared it with pure recombinant murine IL 1 in several different IL 1 assays based on murine and human cells. Recombinant IL 1 is capable of stimulating T cell and fibroblast proliferation and inducing fibroblast collagenase and prostaglandin production, thus proving that a single molecule has many of the activities previously ascribed to only partially purified IL 1 preparations. Our results indicate that there exists a family of at least two human IL 1 genes (alpha and beta) whose dissimilar protein products have similar biological activities.     

Deep Brain Stimulation Imposes Complex Informational Lesions

Deep brain stimulation (DBS) therapy has become an essential tool for treating a range of brain disorders. In the resting state, DBS is known to regularize spike activity in and downstream of the stimulated brain target, which in turn has been hypothesized to create informational lesions. Here, we specifically test this hypothesis using repetitive joint articulations in two non-human Primates while recording single-unit activity in the sensorimotor globus pallidus and motor thalamus before, during, and after DBS in the globus pallidus (GP) GP-DBS resulted in: (1) stimulus-entrained firing patterns in globus pallidus, (2) a monophasic stimulus-entrained firing pattern in motor thalamus, and (3) a complete or partial loss of responsiveness to joint position, velocity, or acceleration in globus pallidus (75%, 12/16 cells) and in the pallidal receiving area of motor thalamus (ventralis lateralis pars oralis, VLo) (38%, 21/55 cells). Despite loss of kinematic tuning, cells in the globus pallidus (63%, 10/16 cells) and VLo (84%, 46/55 cells) still responded to one or more aspects of joint movement during GP-DBS. Further, modulated kinematic tuning did not always necessitate modulation in firing patterns (2/12 cells in globus pallidus; 13/23 cells in VLo), and regularized firing patterns did not always correspond to altered responses to joint articulation (3/4 cells in globus pallidus, 11/33 cells in VLo). In this context, DBS therapy appears to function as an amalgam of network modulating and network lesioning therapies.     

Protein-Based Classifier to Predict Conversion from Clinically Isolated Syndrome to Multiple Sclerosis

Multiple sclerosis is an inflammatory, demyelinating, and neurodegenerative disease of the central nervous system. In most patients, the disease initiates with an episode of neurological disturbance referred to as clinically isolated syndrome, but not all patients with this syndrome develop multiple sclerosis over time, and currently, there is no clinical test that can conclusively establish whether a patient with a clinically isolated syndrome will eventually develop clinically defined multiple sclerosis. Here, we took advantage of the capabilities of targeted mass spectrometry to establish a diagnostic molecular classifier with high sensitivity and specificity able to differentiate between clinically isolated syndrome patients with a high and a low risk of developing multiple sclerosis. Based on the combination of abundances of proteins chitinase 3-like 1 and ala-β-his-dipeptidase in cerebrospinal fluid, we built a statistical model able to assign to each patient a precise probability of conversion to clinically defined multiple sclerosis. Our results are of special relevance for patients affected by multiple sclerosis as early treatment can prevent brain damage and slow down the disease progression.Multiple sclerosis is an inflammatory, demyelinating, and neurodegenerative disease of the central nervous system, and although the etiology of the disease is not fully understood, it is probably caused by the interaction of a complex genetic architecture and environmental factors. Multiple sclerosis affects over 2 million people worldwide, and it is typically diagnosed between ages 20 and 40, thus making a significant impact on public health and its economy (1).In most patients, the disease initiates with an episode of neurological disturbance referred to as clinically isolated syndrome. However, not all patients with this syndrome develop multiple sclerosis over time (2), and currently, the magnetic resonance imaging (MRI) abnormalities and the presence of IgG oligoclonal bands in cerebrospinal fluid (CSF) are used as predictors for later conversion to clinically definite multiple sclerosis (CDMS)¹ (3–5). Although such abnormalities are considered important factors that influence the likelihood of developing CDMS, there is currently no clinical test that can conclusively establish whether a patient with a clinically isolated syndrome will eventually develop CDMS.The lack of diagnostic and prognostic biomarkers is a common problem for many diseases lacking a complete etiology, which is the case for most neurological disorders related to the central nervous system such as Parkinson''s and Alzheimer''s diseases, schizophrenia, and multiple sclerosis. In the particular case of multiple sclerosis, early treatment of patients with a clinically isolated syndrome can prevent brain damage and slow down the disease progression (6). Therefore, the availability of a diagnostic test in the initial stages of the disease is not only desirable but also of extreme relevance to attenuate the degenerative effects of the disease.Biomarker validation has traditionally been dominated by enzyme linked immuno-sorbent assays (ELISA), but recent advances in proteomics techniques have enabled the measurement of a subset of selected proteins over a large dynamic concentration range in multiple samples. Targeted mass spectrometry has thus become the method of choice when quantifying simultaneously a panel of proteins across many different biological samples (7–9). In particular, selected reaction monitoring (SRM) is the gold standard targeted mass spectrometry method for protein quantification due to its high precision, reliability, and throughput (10–13). This targeted mass spectrometry method is performed on triple quadrupole instruments, in which a predefined peptide precursor ion is first isolated, and then selected fragment ions arising from its collisional dissociation are measured over time. Each pair of precursor and fragment ion is called a transition, and multiple transitions can be coordinately measured and used to conclusively identify and quantify a peptide in a clinical complex sample.In a previous study, we used a screening mass spectrometric approach to discover potential markers for multiple sclerosis conversion in patients that initially presented a clinical isolated syndrome (14). In that discovery phase, quantitative mass spectrometry with iTRAQ labeling was used to measure protein abundances in pooled CSF samples from patients presenting a clinical isolated syndrome that either remained normal (CIS) or had eventually converted to clinically definite multiple sclerosis (CDMS) (n = 60). In the initial screening, several proteins exhibited significant differences in abundance when comparing these two groups of patients. The abundance change in one of the altered proteins, chitinase 3-like 1 (CH3L1), was confirmed by ELISA in CSF of individual patients, whereas for others, such as semaphorin 7A (SEM7A) and ala-β-his-dipeptidase (CNDP1), their abundance changes were confirmed by targeted mass spectrometry in follow-up studies with independent cohorts (15). Moreover, the levels of CH3L1 were associated with brain MRI abnormalities and disability progression during the follow-up period, as well as with shorter time to conversion to clinically definite multiple sclerosis (14).We now set out to establish a diagnostic protein classifier with high sensitivity and specificity able to differentiate between patients with a clinically isolated syndrome that have either a high or a low risk of developing clinically definite multiple sclerosis over time. For this purpose, CSF samples from an independent patient cohort from the one used in the discovery study were collected, and a set of preselected protein biomarker candidates were systematically quantified by targeted mass spectrometry (SRM) and evaluated for their classification power. Out of this study, we established a protein classifier based on the combination of abundances of proteins chitinase 3-like 1 and ala-β-his-dipeptidase, which is able to differentiate with high sensitivity and specificity between patients with a clinically isolated syndrome that have either a high or low risk of developing clinically definite multiple sclerosis. Moreover, the statistical model built around this protein classifier enables clinicians to easily assign to each patient a precise probability of conversion to clinically definite multiple sclerosis (Fig. 1).Open in a separate windowFig. 1.General workflow used in the present study. Initially, protein candidates identified in our previous discovery studies—together with several proteins described by other groups—were selected and quantified by targeted mass spectrometry (SRM) in a relatively large cohort individual patients. Protein quantities were then evaluated by their capability of classifying patients with clinical isolated syndrome, and thus, the best prognostic protein combination was identified.     

Isolation of a cDNA clone for the alpha subunit of the human GABA-A receptor

A cDNA clone of an alpha subunit of the human GABA-A receptor has been isolated. The human clone (pCLL800) contains 1055 nucleotides in an open reading frame and 260 nucleotides in the 5' non-coding region. The 351 amino acid sequence of this human alpha subunit shows 97% homology with its bovine counterpart. Hybridization of pCLL800 to Northern blots shows a 3.9/4.3 Kb RNA doublet in human cortex, rat whole brain, cortex, hippocampus, midbrain, olfactory bulb and cerebellum. Developmental studies show that the levels of the rat alpha mRNA increase between one and three weeks of age in a manner similar to the development of the benzodiazepine binding sites.     

Cupric-amyloid beta peptide complex stimulates oxidation of ascorbate and generation of hydroxyl radical

A growing body of evidence supports an important role for oxidative stress in the pathogenesis of Alzheimer's disease. Recently, a number of papers have shown a synergistic neurotoxicity of amyloid beta peptide and cupric ions. We hypothesized that complexes of cupric ions with neurotoxic amyloid beta peptides (Abeta) can stimulate copper-mediated free radical formation. We found that neurotoxic Abeta (1-42), Abeta (1-40), and Abeta (25-35) stimulated copper-mediated oxidation of ascorbate, whereas nontoxic Abeta (40-1) did not. Formation of ascorbate free radical was significantly increased by Abeta (1-42) in the presence of ceruloplasmin. Once cupric ion is reduced to cuprous ion, it can be oxidized by oxygen to generate superoxide radical or it can react with hydrogen peroxide to form hydroxyl radical. Hydrogen peroxide greatly increased the oxidation of cyclic hydroxylamines and ascorbate by cupric-amyloid beta peptide complexes, implying redox cycling of copper ions. Using the spin-trapping technique, we have shown that toxic amyloid beta peptides led to a 4-fold increase in copper-mediated hydroxyl radical formation. We conclude that toxic Abeta peptides do indeed stimulate copper-mediated oxidation of ascorbate and generation of hydroxyl radicals. Therefore, cupric-amyloid beta peptide-stimulated free radical generation may be involved in the pathogenesis of Alzheimer's disease.     

Quantitative variability of 342 plasma proteins in a human twin population

The degree and the origins of quantitative variability of most human plasma proteins are largely unknown. Because the twin study design provides a natural opportunity to estimate the relative contribution of heritability and environment to different traits in human population, we applied here the highly accurate and reproducible SWATH mass spectrometry technique to quantify 1,904 peptides defining 342 unique plasma proteins in 232 plasma samples collected longitudinally from pairs of monozygotic and dizygotic twins at intervals of 2–7 years, and proportioned the observed total quantitative variability to its root causes, genes, and environmental and longitudinal factors. The data indicate that different proteins show vastly different patterns of abundance variability among humans and that genetic control and longitudinal variation affect protein levels and biological processes to different degrees. The data further strongly suggest that the plasma concentrations of clinical biomarkers need to be calibrated against genetic and temporal factors. Moreover, we identified 13 cis‐SNPs significantly influencing the level of specific plasma proteins. These results therefore have immediate implications for the effective design of blood‐based biomarker studies.     

Extending the Limits of Quantitative Proteome Profiling with Data-Independent Acquisition and Application to Acetaminophen-Treated Three-Dimensional Liver Microtissues

The data-independent acquisition (DIA) approach has recently been introduced as a novel mass spectrometric method that promises to combine the high content aspect of shotgun proteomics with the reproducibility and precision of selected reaction monitoring. Here, we evaluate, whether SWATH-MS type DIA effectively translates into a better protein profiling as compared with the established shotgun proteomics.We implemented a novel DIA method on the widely used Orbitrap platform and used retention-time-normalized (iRT) spectral libraries for targeted data extraction using Spectronaut. We call this combination hyper reaction monitoring (HRM). Using a controlled sample set, we show that HRM outperformed shotgun proteomics both in the number of consistently identified peptides across multiple measurements and quantification of differentially abundant proteins. The reproducibility of HRM in peptide detection was above 98%, resulting in quasi complete data sets compared with 49% of shotgun proteomics.Utilizing HRM, we profiled acetaminophen (APAP)¹-treated three-dimensional human liver microtissues. An early onset of relevant proteome changes was revealed at subtoxic doses of APAP. Further, we detected and quantified for the first time human NAPQI-protein adducts that might be relevant for the toxicity of APAP. The adducts were identified on four mitochondrial oxidative stress related proteins (GATM, PARK7, PRDX6, and VDAC2) and two other proteins (ANXA2 and FTCD).Our findings imply that DIA should be the preferred method for quantitative protein profiling.Quantitative mass spectrometry is a powerful and widely used approach to identify differentially abundant proteins, e.g. for proteome profiling and biomarker discovery (1). Several tens of thousands of peptides and thousands of proteins can be routinely identified from a single sample injection in shotgun proteomics (2). Shotgun proteomics, however, is limited by low analytical reproducibility. This is due to the complexity of the samples that results in under sampling (supplemental Fig. 1) and to the fact that the acquisition of MS2 spectra is often triggered outside of the elution peak apex. As a result, only 17% of the detectable peptides are typically fragmented, and less than 60% of those are identified. This translates in reliable identification of only 10% of the detectable peptides (3). The overlap of peptide identification across technical replicates is typically 35–60% (4), which results in inconsistent peptide quantification. Alternatively to shotgun proteomics, selected reaction monitoring (SRM) enables quantification of up to 200–300 peptides at very high reproducibility, accuracy, and precision (5–8).Data-independent acquisition (DIA), a novel acquisition type, overcomes the semistochastic nature of shotgun proteomics (9–18). Spectra are acquired according to a predefined schema instead of dependent on the data. Targeted analysis of DIA data was introduced with SWATH-MS (19). For the originally published SWATH-MS, the mass spectrometer cycles through 32 predefined, contiguous, 25 Thomson wide precursor windows, and records high-resolution fragment ion spectra (19). This results in a comprehensive measurement of all detectable precursors of the selected mass range. The main novelty of SWATH-MS was in the analysis of the collected DIA data. Predefined fragment ions are extracted using precompiled spectrum libraries, which results in SRM-like data. Such targeted analyses are now enabled by several publicly available computational tools, in particular Spectronaut², Skyline (20), and OpenSWATH (21). The accuracy of peptide identification is evaluated based on the mProphet method (22).We introduce a novel SWATH-MS-type DIA workflow termed hyper reaction monitoring (HRM) (reviewed in (23)) implemented on a Thermo Scientific Q Exactive platform. It consists of comprehensive DIA acquisition and targeted data analysis with retention-time-normalized spectral libraries (24). Its high accuracy of peptide identification and quantification is due to three aspects. First, we developed a novel, improved DIA method. Second, we reimplemented the mProphet (22) approach in the software Spectronaut (www.spectronaut.org). Third, we developed large, optimized, and retention-time-normalized (iRT) spectral libraries.We compared HRM and state-of-the-art shotgun proteomics in terms of ability to discover differentially abundant proteins. For this purpose, we used a “profiling standard sample set” with 12 non-human proteins spiked at known absolute concentrations into a stable human cell line protein extract. This resulted in quasi complete data sets for HRM and the detection of a larger number of differentially abundant proteins as compared with shotgun proteomics. We utilized HRM to identify changes in the proteome in primary three-dimensional human liver microtissues after APAP exposure (25–27). These primary hepatocytes exhibit active drug metabolism. With a starting material of only 12,000 cells per sample, the abundance of 2,830 proteins was quantified over an APAP concentration range. Six novel NAPQI-cysteine proteins adducts that might be relevant for the toxicity of APAP were found and quantified mainly on mitochondrion-related proteins.     

Onobrychis dushanbensis sp. nov. endemic to Tajikistan

Onobrychis dushanbensis Ranjbar, Vitek & Karamian, a new Fabaceae species endemic to Tajikistan, is described and illustrated. The new species belongs to Onobrychis Miller subgen. Sisyrosema (Bunge) Grossheim sect. Hymenobrychis DC. It is closely related to O. chorassanica Bunge and O. seravschanica B. Fedtsch., but is easily distinguished by its purple flowers with darker venation (vs yellowish with purple venation), with wings 9–10 mm long (vs wings 4–5 mm long) and bracts 14–15 mm long (vs bracts 4–5 mm long). The relationships between the new and closely related species are discussed.     

Role of MAP1B in axonal retrograde transport of mitochondria

The MAPs (microtubule-associated proteins) MAP1B and tau are well known for binding to microtubules and stabilizing these structures. An additional role for MAPs has emerged recently where they appear to participate in the regulation of transport of cargos on the microtubules found in axons. In this role, tau has been associated with the regulation of anterograde axonal transport. We now report that MAP1B is associated with the regulation of retrograde axonal transport of mitochondria. This finding potentially provides precise control of axonal transport by MAPs at several levels: controlling the anterograde or retrograde direction of transport depending on the type of MAP involved, controlling the speed of transport and controlling the stability of the microtubule tracks upon which transport occurs.