A simple, time- and cost-effective, high-throughput depletion strategy for deep plasma proteomics

We introduce a cost-effective, robust high-throughput-compatible plasma depletion method enabling in-depth profiling of plasma that detects >1300 proteins per run with a throughput of 60 samples per day. The method has been fully validated by processing >3000 samples with no apparent batch effect at a cost for the depletion step of ~$2.5 per sample.

Using CSF Proteomics to Investigate Herpesvirus Infections of the Central Nervous System

Herpesviruses have complex mechanisms enabling infection of the human CNS and evasion of the immune system, allowing for indefinite latency in the host. Herpesvirus infections can cause severe complications of the central nervous system (CNS). Here, we provide a novel characterization of cerebrospinal fluid (CSF) proteomes from patients with meningitis or encephalitis caused by human herpes simplex virus 1 (HSV-1), which is the most prevalent human herpesvirus associated with the most severe morbidity. The CSF proteome was compared with those from patients with meningitis or encephalitis due to human herpes simplex virus 2 (HSV-2) or varicella-zoster virus (VZV, also known as human herpesvirus 3) infections. Virus-specific differences in CSF proteomes, most notably elevated 14-3-3 family proteins and calprotectin (i.e., S100-A8 and S100-A9), were observed in HSV-1 compared to HSV-2 and VZV samples, while metabolic pathways related to cellular and small molecule metabolism were downregulated in HSV-1 infection. Our analyses show the feasibility of developing CNS proteomic signatures of the host response in alpha herpes infections, which is paramount for targeted studies investigating the pathophysiology driving virus-associated neurological disorders, developing biomarkers of morbidity, and generating personalized therapeutic strategies.

A Parallelization Strategy for the Time Efficient Analysis of Thousands of LC/MS Runs in High-Performance Computing Environment

Combining robust proteomics instrumentation with high-throughput enabling liquid chromatography (LC) systems (e.g., timsTOF Pro and the Evosep One system, respectively) enabled mapping the proteomes of 1000s of samples. Fragpipe is one of the few computational protein identification and quantification frameworks that allows for the time-efficient analysis of such large data sets. However, it requires large amounts of computational power and data storage space that leave even state-of-the-art workstations underpowered when it comes to the analysis of proteomics data sets with 1000s of LC mass spectrometry runs. To address this issue, we developed and optimized a Fragpipe-based analysis strategy for a high-performance computing environment and analyzed 3348 plasma samples (6.4 TB) that were longitudinally collected from hospitalized COVID-19 patients under the auspice of the Immunophenotyping Assessment in a COVID-19 Cohort (IMPACC) study. Our parallelization strategy reduced the total runtime by ∼90% from 116 (theoretical) days to just 9 days in the high-performance computing environment. All code is open-source and can be deployed in any Simple Linux Utility for Resource Management (SLURM) high-performance computing environment, enabling the analysis of large-scale high-throughput proteomics studies.

Using plasma proteomics to investigate viral infections of the central nervous system including patients with HIV-associated neurocognitive disorders

State-of-the-art liquid chromatography/mass spectrometry (LC/MS)-based proteomic technologies, using microliter amounts of patient plasma, can detect and quantify several hundred plasma proteins in a high throughput fashion, allowing for the discovery of clinically relevant protein biomarkers and insights into the underlying pathobiological processes. Using such an in-house developed high throughput plasma proteomics allowed us to identify and quantify > 400 plasmas proteins in 15 min per sample, i.e., a throughput of 100 samples/day. We demonstrated the clinical applicability of our method in this pilot study by mapping the plasma proteomes from patients infected with human immunodeficiency virus (HIV) or herpes virus, both groups with involvement of the central nervous system (CNS). We found significant disease-specific differences in the plasma proteomes. The most notable difference was a decrease in the levels of several coagulation-associated proteins in HIV vs. herpes virus, among other dysregulated biological pathways providing insight into the differential pathophysiology of HIV compared to herpes virus infection. In a subsequent analysis, we found several plasma proteins associated with immunity and metabolism to differentiate patients with HIV-associated neurocognitive disorders (HAND) compared to cognitively normal people with HIV (PWH), suggesting the presence of plasma-based biomarkers to distinguishing HAND from cognitively normal PWH. Overall, our high-throughput plasma proteomics pipeline enables the identification of distinct proteomic signatures of HIV and herpes virus, which may help illuminate divergent pathophysiology behind virus-associated neurological disorders.

Thyrotoxic periodic paralysis associated with Graves’ disease: a case series

Summary

Thyrotoxic periodic paralysis (TPP) is a rare condition characterised by acute onset hypokalaemia and paralysis which most commonly affects men of Asian descent between the ages of 20 and 40 years (1, 2). It has been reported in approximately 2% of patients with thyrotoxicosis in China and Japan (1, 2, 3). Hypokalaemia in TPP results from a massive intracellular shift of potassium induced by the thyroid hormone sensitisation of Na⁺/K⁺-ATPase (4). Treatment of TPP includes prevention of this shift by using beta-blockade, rapid potassium replacement and treatment of the underlying hyperthyroidism. We present two cases of TPP with differing outcomes. In the first case, a 33-year-old Filipino gentleman presented to our emergency department (ED) with a 3-month history of recurrent proximal lower limb weakness. Serum potassium was 2.2 mmol/L (3.3–5.1) and he was given i.v. potassium replacement. Thyroid function tests (TFTs) and thyroid antibodies were consistent with Graves thyrotoxicosis. He was discharged home on carbimazole and remains well controlled on long-term medical therapy. In the second case, a 22-year-old Malaysian gentleman presented to our ED with new-onset bilateral lower limb painless paralysis. Serum potassium was 1.9 mmol/L with TFTs demonstrating Graves thyrotoxicosis. He was treated with i.v. potassium replacement and discharged home on carbimazole and propranolol. He represented to the hospital on two further occasions with TPP and was advised to consider total thyroidectomy given his refractory Graves’ disease. These cases highlight the importance of prompt recognition of this rare life-threatening complication of Graves’ disease, especially in patients of Asian descent.

Learning points

FHL2 anchors mitochondria to actin and adapts mitochondrial dynamics to glucose supply

Mitochondrial movement and distribution are fundamental to their function. Here we report a mechanism that regulates mitochondrial movement by anchoring mitochondria to the F-actin cytoskeleton. This mechanism is activated by an increase in glucose influx and the consequent O-GlcNAcylation of TRAK (Milton), a component of the mitochondrial motor-adaptor complex. The protein four and a half LIM domains protein 2 (FHL2) serves as the anchor. FHL2 associates with O-GlcNAcylated TRAK and is both necessary and sufficient to drive the accumulation of F-actin around mitochondria and to arrest mitochondrial movement by anchoring to F-actin. Disruption of F-actin restores mitochondrial movement that had been arrested by either TRAK O-GlcNAcylation or forced direction of FHL2 to mitochondria. This pathway for mitochondrial immobilization is present in both neurons and non-neuronal cells and can thereby adapt mitochondrial dynamics to changes in glucose availability.

Phosphorylation-dependent control of Activity-regulated cytoskeleton-associated protein (Arc) protein by TNIK

Activity-regulated cytoskeleton-associated protein (Arc) is an immediate early gene product that support neuroplastic changes important for cognitive function and memory formation. As a protein with homology to the retroviral Gag protein, a particular characteristic of Arc is its capacity to self-assemble into virus-like capsids that can package mRNAs and transfer those transcripts to other cells. Although a lot has been uncovered about the contributions of Arc to neuron biology and behavior, very little is known about how different functions of Arc are coordinately regulated both temporally and spatially in neurons. The answer to this question we hypothesized must involve the occurrence of different protein post-translational modifications acting to confer specificity. In this study, we used mass spectrometry and sequence prediction strategies to map novel Arc phosphorylation sites. Our approach led us to recognize serine 67 (S67) and threonine 278 (T278) as residues that can be modified by TNIK, which is a kinase abundantly expressed in neurons that shares many functional overlaps with Arc and has, along with its interacting proteins such as the NMDA receptor, and been implicated as a risk factor for psychiatric disorders. Furthermore, characterization of each residue using site-directed mutagenesis to create S67 and T278 mutant variants revealed that TNIK action at those amino acids can strongly influence Arc's subcellular distribution and self-assembly as capsids. Together, our findings reveal an unsuspected connection between Arc and TNIK. Better understanding of the interplay between these two proteins in neuronal cells could lead to new insights about apparition and progression of psychiatric disorders. Cover Image for this issue: https://doi.org/10.1111/jnc.15077.

Phosphorylation-dependent control of Activity-regulated cytoskeleton-associated protein (Arc) protein by TNIK

Activity-regulated cytoskeleton-associated protein (Arc) is an immediate early gene product that support neuroplastic changes important for cognitive function and memory formation. As a protein with homology to the retroviral Gag protein, a particular characteristic of Arc is its capacity to self-assemble into virus-like capsids that can package mRNAs and transfer those transcripts to other cells. Although a lot has been uncovered about the contributions of Arc to neuron biology and behavior, very little is known about how different functions of Arc are coordinately regulated both temporally and spatially in neurons. The answer to this question we hypothesized must involve the occurrence of different protein post-translational modifications acting to confer specificity. In this study, we used mass spectrometry and sequence prediction strategies to map novel Arc phosphorylation sites. Our approach led us to recognize serine 67 (S67) and threonine 278 (T278) as residues that can be modified by TNIK, which is a kinase abundantly expressed in neurons that shares many functional overlaps with Arc and has, along with its interacting proteins such as the NMDA receptor, and been implicated as a risk factor for psychiatric disorders. Furthermore, characterization of each residue using site-directed mutagenesis to create S67 and T278 mutant variants revealed that TNIK action at those amino acids can strongly influence Arc's subcellular distribution and self-assembly as capsids. Together, our findings reveal an unsuspected connection between Arc and TNIK. Better understanding of the interplay between these two proteins in neuronal cells could lead to new insights about apparition and progression of psychiatric disorders.

IgG1 antibodies against phosphorylcholine are associated with protection in SLE and atherosclerosis: potential underlying mechanisms

Background

The risk of cardiovascular disease (CVD) and atherosclerosis is very high in SLE. This is a clinical problem, and could also shed light on immunity and atherosclerosis in general. IgM antibodies against phosphorylcholine (anti-PC) may be protective in atherosclerosis, cardiovascular disease (CVD) and systemic lupus erythematosus (SLE). We here study IgG1 and IgG2 anti-PC, with focus on atherosclerosis and SLE.

Methods

We determined anti-PC by ELISA in 116 SLE-patients and 110 age- and sex-matched controls. For functional studies, we used three in-house generated, fully human monoclonal IgG1 anti-PC (A01, D05, E01). Apoptosis was induced in Jurkat T-cells and pre-incubated with A01, D05, E01 or isotype control IgG1 and effects on efferocytosis by human macrophages studied. Anti-PC peptide/protein characterization was determined using a proteomics de novo sequencing approach.

Results

IgG1 but not IgG2 anti-PC levels were higher among SLE patients (p=0.02). IgG1 anti-PC was negatively associated with SLICC and SLEDAI (OR: 2,978 CI: 0.876–10.098, OR: 5.108 CI 1.3 20.067 respectively) and negatively associated with CVD, atherosclerotic plaques and echolucent (potentially vulnerable plaques) but the association for the two former was not significant after controlling for confounders. D05 had maximum effect on macrophage efferocytosis efficiency, followed by A01 and E01. The monoclonal antibodies showed differential binding specificity to PC and PC associated neo-epitopes. Peptide analysis showed difference in the CDR3 region of the three anti-PC IgG1 clones which are crucial for recognition of PC on apoptotic cell surface and other neo-epitopes.

Conclusion

Anti-PC IgG1 is negatively associated with disease activity, and disease damage in SLE, but the negative association with CVD is also dependent on confounding risk factors. One potential underlying mechanism could be increased clearance of dead cells.

Funding Acknowledgement

Type of funding source: Public grant(s) – National budget only. Main funding source(s): Swedish Heart and Lung Foundation, Reumatikerfonden

THU0230 IGG1 ANTIBODIES AGAINST PHOSPHORYLCHOLINE ARE NEGATIVELY ASSOCIATED WITH DISEASE ACTIVITY, DISEASE DAMAGE, CARDIOVASCULAR DISEASE AND ATHEROSCLEROSIS IN SLE: POTENTIAL UNDERLYING MECHANISMS

Background:

Phosphorylcholine (PC) is an important component in cellular membranes and in lipoproteins that is exposed and recognized by the immune system, when cells undergo apoptosis or lipoproteins like LDL undergo oxidation. PC is also exposed in some microorganisms including nematodes and bacteria (non-self). We reported that IgM anti-PC is associated with protection in atherosclerosis, SLE, RA and other chronic inflammatory conditions.1We also reported potential underlying protective mechanisms: 1: increase in clearance of human dead cells,22: inhibition of uptake of oxLDL in macrophages, 3: inhibition of cell death.14: anti-inflammatory; 5: promotion of polarization of T regulatory cells in SLE-patients´ T cells from a low level and also in plaque T cells.3We generated in-house fully human IgG1 anti-PC clones for experimental studies to study anti-PC properties in humans. In contrast to mice, anti-PC are not germ-line encoded with a dominant clone.4

Objectives:

We here study IgG1 and IgG2 anti-PC, with focus on atherosclerosis and SLE and properties of fully human IgG1 clones, in relation to SLE.

Methods:

We determined anti-PC by ELISA in 116 SLE-patients and 110 age- and sex-matched controls. For functional studies, we used three in-house generated, fully human monoclonal IgG1 anti-PC (A01, D05, E01). Apoptosis was induced in Jurkat T-cells and pre-incubated with A01, D05, E01 or isotype control IgG1 and effects on efferocytosis by human macrophages studied. Anti-PC peptide/protein characterization was determined using a proteomics de novo sequencing approach.

Results:

IgG1 but not IgG2 anti-PC levels were higher among SLE patients (p=0.02). IgG1 anti-PC was negatively associated with SLICC and SLEDAI (OR: 2,978 CI: 0.876-10.098, OR: 5.108 CI 1.3 20.067 respectively) and negatively associated with CVD, atherosclerotic plaques and echolucent (potentially vulnerable plaques) but the association for the two former was not significant after controlling for confounders. D05 had maximum effect on macrophage efferocytosis efficiency, followed by A01 and E01. The monoclonal antibodies showed differential binding specificity to PC and PC associated neo-epitopes. Peptide analysis showed difference in the CDR3 region of the three anti-PC IgG1 clones which are crucial for recognition of PC on apoptotic cell surface and other neo-epitopes.

Conclusion:

Anti-PC IgG1 is negatively associated with disease activity, and disease damage in SLE, but the negative association with CVD is also dependent on confounding risk factors. One potential underlying mechanism could be increased clearance of dead cells.

References:

[1]Frostegard J. Immunity, atherosclerosis and cardiovascular disease.BMC Med. 2013;11:117.

[2]Rahman M, Sing S, Golabkesh Z, Fiskesund R, Gustafsson T, Jogestrand T, Frostegard AG, Hafstrom I, Liu A and Frostegard J. IgM antibodies against malondialdehyde and phosphorylcholine are together strong protection markers for atherosclerosis in systemic lupus erythematosus: Regulation and underlying mechanisms.Clin Immunol. 2016;166-167:27-37.

[3]Sun J, Lundstrom SL, Zhang B, Zubarev RA, Steuer J, Gillgren P, Rahman M, Ajeganova S, Liu A and Frostegard J. IgM antibodies against phosphorylcholine promote polarization of T regulatory cells from patients with atherosclerotic plaques, systemic lupus erythematosus and healthy donors.Atherosclerosis. 2018;268:36-48.

[4]Fiskesund R, Steen J, Amara K, Murray F, Szwajda A, Liu A, Douagi I, Malmstrom V and Frostegard J. Naturally occurring human phosphorylcholine antibodies are predominantly products of affinity-matured B cells in the adult.J Immunol. 2014;192:4551-9.

Disclosure of Interests: :

Divya Thiagarajan: None declared, Roland Fiskesund: None declared, Johanna Steen: None declared, Mizanur Rahman: None declared, Susanna Lundström: None declared, Johan Frostegård Grant/research support from: Unconditional competitive grant from Amgen, related only to PCSK9, not the topic of this abstract

Immunoglobulin G1 Antibodies Against Phosphorylcholine Are Associated With Protection in Systemic Lupus Erythematosus and Atherosclerosis: Potential Underlying Mechanisms

OBJECTIVE

Immunoglobulin M antibodies against phosphorylcholine (anti-PCs) may be protective in atherosclerosis, cardiovascular disease (CVD), and systemic lupus erythematosus (SLE). We study immunoglobulin G1 (IgG1) and immunoglobulin G2 (IgG2) anti-PCs, with a focus on atherosclerosis and SLE.

METHODS

We determined anti-PCs by using the enzyme-linked immunosorbent assay in 116 patients with SLE and 110 age- and sex-matched controls. For functional studies, we used three in-house-generated, fully human monoclonal IgG1 anti-PCs (A01, D05, and E01). Apoptosis was induced in Jurkat T cells and preincubated with A01, D05, E01, or IgG1 isotype control, and effects on efferocytosis by human macrophages were studied. Anti-PC peptide/protein characterization was determined using a proteomics de novo sequencing approach.

RESULTS

IgG1, but not IgG2, anti-PC levels were higher among patients with SLE (P = 0.02). IgG1 anti-PCs were negatively associated with Systemic Lupus International Collaborating Clinics (SLICC) damage index and Systemic Lupus Erythematosus Disease Activity Index (SLEDAI) scores (odds ratio [OR]: 2.978 [confidence interval (CI): 0.876-10.098] and OR: 5.108 [CI 1.3-20.067], respectively) and negatively associated with CVD, atherosclerotic plaques, and echolucent plaques (potentially vulnerable plaques), but the association for the two former was not significant after controlling for confounders. D05 had a maximum effect on macrophage efferocytosis efficiency, followed by A01 and E01. The monoclonal antibodies showed differential binding specificity to PC and PC-associated neoepitopes. A peptide analysis showed a difference in the complementarity-determining region 3 of the three IgG1 anti-PC clones that are crucial for recognition of PC on apoptotic cell surfaces and other neoepitopes.

CONCLUSION

IgG1 anti-PCs are negatively associated with disease activity and disease damage in SLE, but the negative association with CVD is also dependent on confounding risk factors. One potential underlying mechanism could be increased clearance of dead cells.

A Cost-Effective High-Throughput Plasma and Serum Proteomics Workflow Enables Mapping of the Molecular Impact of Total Pancreatectomy with Islet Autotransplantation

Blood is an ideal body fluid for the discovery or monitoring of diagnostic and prognostic protein biomarkers. However, discovering robust biomarkers requires the analysis of large numbers of samples to appropriately represent interindividual variability. To address this analytical challenge, we established a high-throughput and cost-effective proteomics workflow for accurate and comprehensive proteomics at an analytical depth applicable for clinical studies. For validation, we processed 1 μL each from 62 plasma samples in 96-well plates and analyzed the product by quantitative data-independent acquisition liquid chromatography/mass spectrometry; the data were queried using feature quantification with Spectronaut. To show the applicability of our workflow to serum, we analyzed a unique set of samples from 48 chronic pancreatitis patients, pre and post total pancreatectomy with islet autotransplantation (TPIAT) surgery. We identified 16 serum proteins with statistically significant abundance alterations, which represent a molecular signature distinct from that of chronic pancreatitis. In summary, we established a cost-efficient high-throughput workflow for comprehensive proteomics using PVDF-membrane-based digestion that is robust, automatable, and applicable to small plasma and serum volumes, e.g., finger stick. Application of this plasma/serum proteomics workflow resulted in the first mapping of the molecular implications of TPIAT on the serum proteome.

Proteomics in India: A Report on a Brainstorming Meeting at Hyderabad, India

The Centre for Cellular and Molecular Biology, Hyderabad, India, was host for an international forum, or "brainstorming meeting," on proteomics held in November 2014, which provided the opportunity to showcase proteomic science in India and to allow discussions between Indian scientists and students and several international visitors. This provided an amalgamation of speakers and participants whose interests lay mainly in developing and using mass-spectrometry-based proteomics to advance their research work. A week-long workshop with hands-on training in proteomic methodology followed the meeting.

f-divergence cutoff index to simultaneously identify differential expression in the integrated transcriptome and proteome

The ability to integrate ‘omics’ (i.e. transcriptomics and proteomics) is becoming increasingly important to the understanding of regulatory mechanisms. There are currently no tools available to identify differentially expressed genes (DEGs) across different ‘omics’ data types or multi-dimensional data including time courses. We present fCI (f-divergence Cut-out Index), a model capable of simultaneously identifying DEGs from continuous and discrete transcriptomic, proteomic and integrated proteogenomic data. We show that fCI can be used across multiple diverse sets of data and can unambiguously find genes that show functional modulation, developmental changes or misregulation. Applying fCI to several proteogenomics datasets, we identified a number of important genes that showed distinctive regulation patterns. The package fCI is available at R Bioconductor and http://software.steenlab.org/fCI/.

MStern Blotting-High Throughput Polyvinylidene Fluoride (PVDF) Membrane-Based Proteomic Sample Preparation for 96-Well Plates

We describe a 96-well plate compatible membrane-based proteomic sample processing method, which enables the complete processing of 96 samples (or multiples thereof) within a single workday. This method uses a large-pore hydrophobic PVDF membrane that efficiently adsorbs proteins, resulting in fast liquid transfer through the membrane and significantly reduced sample processing times. Low liquid transfer speeds have prevented the useful 96-well plate implementation of FASP as a widely used membrane-based proteomic sample processing method. We validated our approach on whole-cell lysate and urine and cerebrospinal fluid as clinically relevant body fluids. Without compromising peptide and protein identification, our method uses a vacuum manifold and circumvents the need for digest desalting, making our processing method compatible with standard liquid handling robots. In summary, our new method maintains the strengths of FASP and simultaneously overcomes one of the major limitations of FASP without compromising protein identification and quantification.

Casein kinase 1δ-dependent Wee1 protein degradation

Eukaryotic mitotic entry is controlled by Cdk1, which is activated by the Cdc25 phosphatase and inhibited by Wee1 tyrosine kinase, a target of the ubiquitin proteasome pathway. Here we use a reporter of Wee1 degradation, K328M-Wee1-luciferase, to screen a kinase-directed chemical library. Hit profiling identified CK1δ-dependent Wee1 degradation. Small-molecule CK1δ inhibitors specifically disrupted Wee1 destruction and arrested HeLa cell proliferation. Pharmacological inhibition, siRNA knockdown, or conditional deletion of CK1δ also reduced Wee1 turnover. Thus, these studies define a previously unappreciated role for CK1δ in controlling the cell cycle.

PINK1 and Parkin target Miro for phosphorylation and degradation to arrest mitochondrial motility

Cells keep their energy balance and avoid oxidative stress by regulating mitochondrial movement, distribution, and clearance. We report here that two Parkinson's disease proteins, the Ser/Thr kinase PINK1 and ubiquitin ligase Parkin, participate in this regulation by arresting mitochondrial movement. PINK1 phosphorylates Miro, a component of the primary motor/adaptor complex that anchors kinesin to the mitochondrial surface. The phosphorylation of Miro activates proteasomal degradation of Miro in a Parkin-dependent manner. Removal of Miro from the mitochondrion also detaches kinesin from its surface. By preventing mitochondrial movement, the PINK1/Parkin pathway may quarantine damaged mitochondria prior to their clearance. PINK1 has been shown to act upstream of Parkin, but the mechanism corresponding to this relationship has not been known. We propose that PINK1 phosphorylation of substrates triggers the subsequent action of Parkin and the proteasome.

The Angelman Syndrome protein Ube3A regulates synapse development by ubiquitinating arc

Angelman Syndrome is a debilitating neurological disorder caused by mutation of the E3 ubiquitin ligase Ube3A, a gene whose mutation has also recently been associated with autism spectrum disorders (ASDs). The function of Ube3A during nervous system development and how Ube3A mutations give rise to cognitive impairment in individuals with Angleman Syndrome and ASDs are not clear. We report here that experience-driven neuronal activity induces Ube3A transcription and that Ube3A then regulates excitatory synapse development by controlling the degradation of Arc, a synaptic protein that promotes the internalization of the AMPA subtype of glutamate receptors. We find that disruption of Ube3A function in neurons leads to an increase in Arc expression and a concomitant decrease in the number of AMPA receptors at excitatory synapses. We propose that this deregulation of AMPA receptor expression at synapses may contribute to the cognitive dysfunction that occurs in Angelman Syndrome and possibly other ASDs.

FLEXIQuant: a novel tool for the absolute quantification of proteins, and the simultaneous identification and quantification of potentially modified peptides

Measurements of protein abundance and quantitative assessment of multiple post-translational modifications (PTMs) within a single protein are increasingly used to understand the control of protein activity, particularly in metazoan cells. General methods of wide applicability and precision/accuracy for quantitative estimation of protein post-translational regulation are lacking. Protein mass spectrometry has evolved from a high-throughput qualitative technique to a potentially general quantitative tool, but there are still serious limitations in dynamic range and coverage. To address some of these limitations, we introduce a novel MS-based quantitative strategy, FLEXIQuant, (Full-Length Expressed Stable Isotope-labeled Proteins for Quantification), which can track changes in relative peptide abundances as a function of PTM, and determine absolute quantity of a protein from its lysate. We examined two subunits of the anaphase-promoting complex, CDC27 and APC5, as a test of our ability to monitor quantitatively, the PTM status of several peptides over time. We find evidence of differential regulation at different sites, a phenomenon we believe will be very widespread. FLEXIQuant proved itself to be capable of serving as a general quantitative tool.

Steroid hormone receptors and long term survival in invasive ovarian cancer

BACKGROUND

Steroid hormone receptors are important determinants of prognosis and predictive behavior in tumor tissues of several origins. Since their role in ovarian cancer is still controversial, we investigated the prevalence and prognostic impact of the estrogen (ER) and progesterone (PR) receptors and combinations (ER+PR+, ER+PR-, ER-PR+, and ER-PR-) in a comparably large number of patients with a long clinical follow-up.

METHODS

The present analysis included 186 patients with invasive ovarian carcinomas treated at the Department of Obstetrics and Gynecology of the Justus-Liebig-University Giessen between 1982 and 1996, the follow-up lasting up to 15.8 years (median 2.4 yrs). The expression of ER and PR was assessed by immunohistochemistry using alkaline phosphatase antialkaline phosphatase in microwave pretreated, formalin fixed, and paraffin embedded specimens of the primary tumors and was evaluated semiquantitatively using a standardized immunoreactive scoring system. Receptor expression and combinations were compared to clinical, histologic and prognostic factors, the tumor proliferation, and the clinical outcome.

RESULTS

Kaplan-Meier survival analyses supported the favorable prognostic value of PR and its level of expression in ovarian carcinomas. Especially the ER-PR+ combination, which accounted for 10.2% of all tumors, showed a significantly superior prognosis when compared with all other combinations (survivors 15 of 19 vs. 67 of 167, log rank P = 0.009) and was associated with early stage, low ascites quantity, and higher tumor differentiation. Five-year survival rates were 13/16 (81.3%) for ER-PR+ tumors versus 58/128 (45.3%) for all other steroid hormone receptor combinations. Residual analysis proved the results.

CONCLUSIONS

The determination of steroid hormone receptor status offers additional prognostic information in ovarian carcinomas. Especially the ER-PR+ phenotype predicts a favorable tumor biology and long term survival, probably reflecting functional effects on tumor proliferation, differentiation, and cellular apoptosis.

[Hereditary diseases and abnormalities as cause of death during the first 2 years of life among 7 groups of Oslo children. A comparison between Norwegian and Pakistani children]

Perinatal and infant death are important indicators of community health. We examined the rate of stillbirth and death before the age of two years among 36,700 children with Norwegian and 2,750 children with Pakistani background. There was no difference in the rate of stillbirth and death during the second year of life, but a 2.5-3 times higher death rate during the first year of life among the Pakistani children, compared with the Norwegian children. When deaths due to single gene disorders and congenital malformations were excluded, the death rate during the first year of life was similar in the two groups. The Pakistani children had an 18 times higher death rate from autosomal recessive disorders and a ten times higher death rate from malformations of the central nervous system. The difference in death rate between the two groups was probably due to the high rate of consanguinity among the Pakistani parents.

Turning data into dialogue

Health visitors often see resource management as threatening, so changing their attitude is no easy task. But one training scheme did just that, as Joyce Steen and Marie Thistleton explain.

[Hearing loss among children in Oslo]

The study concerns children born the years 1975-84. Only children in need of hearing aids are taken into account. The incidense was 1.08 per 1,000 live born children. The prevalens in January 1988 was 1.57 per 1,000 children, including 18 children moving into the city. The etiology among 75 children was 47% prenatal, 16% perinatal, 11% postnatal defects and further 26% of unknown neurogenic origin. Among the 63 impaired children living in Oslo 1988 15 or 24% had multiple handicaps. Identification of hearing loss before one year of age increased from 23% for children born 1975/79 to near 60% for children born 1980/84. At risk children should be tested before leaving hospital after delivery.

Variations in the release of the NH2-terminal fragment of gastrin-17 in the course of duodenal ulcer disease

Fasting and meal-stimulated NH2-terminal gastrin concentrations in serum were significantly higher in patients with active duodenal ulcer than in control subjects and in patients with inactive duodenal ulcer (p less than 0.05). In contrast, the COOH-terminal gastrin concentrations (the bioactive gastrins) did not differ among the groups. Parallel variation in the NH2- and COOH-terminal gastrin concentrations occurred both during meal stimulation and as response to adrenaline or secretin infusion. In a longitudinal study of duodenal ulcer patients, higher NH2- than COOH-terminal gastrin concentrations were associated with the active phase of the disease, whereas this seldom occurred during the inactive phase (p less than 0.001). These data suggest that abnormally large amounts of the NH2-terminal fragment of gastrin-17 are released to the circulation during the active phase of duodenal ulcer.

Gastrin and gastrointestinal dyspepsia in pregnancy

Fasting serum gastrin (SG) concentration and the SG response to a standard protein meal were investigated in 8 women with upper gastrointestinal dyspepsia in the 36th week of pregnancy and again 8 weeks after parturition, when the dyspepsia had disappeared. The fasting SG concentration was significantly higher (p less than 0.05) during pregnancy than post partum, whereas no statistically significant difference was found between the SG response to a protein meal stimulation during pregnancy vs. post partum. The demonstrated variations in gastrin secretion during and after pregnancy offer no explanation for the upper gastrointestinal dyspepsia of our patients.

Relationship between basal serum gastrin concentrations and gastric acid secretion in peptic ulcer disease

In large groups of control subjects and gastric, prepyloric, and duodenal ulcer patients basal gastrin concentration as basal and maximal acid output was measured. All groups had equal basal gastrin concentrations, except gastric ulcer patients, who had higher values (p less than 0.001). A significant negative correlation was found between acid output and basal gastrin in controls and prepyloric ulcer patients. In duodenal ulcer a similar correlation was seen only after exclusion of gastrin and basal acid hypersecretors, and in gastric ulcer no correlation could be found. The characteristic pattern for gastrin and acid secretion was in prepyloric ulcer patients almost like that in controls, whereas gastric ulcer patients seemed more heterogeneous. In duodenal ulcer differences may be explained by a defective feedback inhibition of acid.

The effect of calcium on hyperoxaluria following jejunoileal bypass in morbid obesity

In order to investigate the effect on urinary oxalic acid excretion, ten patients with jejunoileostomy for morbid obesity were treated with oral calcium. We found a statistically significant decrease. The investigation suggests that the oral administration of calcium alone is not sufficient, in a dosage of 900 mg daily, to normalize the urinary oxalate excretion. The indications for calcium therapy in this group of patients is discussed.