Easy and Accessible Workflow for Label-Free Single-Cell Proteomics

Single-cell proteomics (SCP) can provide information that is unattainable through either bulk-scale protein measurements or single-cell profiling of other omes. Maximizing proteome coverage often requires custom instrumentation, consumables, and reagents for sample processing and separations, which has limited the accessibility of SCP to a small number of specialized laboratories. Commercial platforms have become available for SCP cell isolation and sample preparation, but the high cost of these platforms and the technical expertise required for their operation place them out of reach of many interested laboratories. Here, we assessed the new HP D100 Single Cell Dispenser for label-free SCP. The low-cost instrument proved highly accurate and reproducible for dispensing reagents in the range from 200 nL to 2 μL. We used the HP D100 to isolate and prepare single cells for SCP within 384-well PCR plates. When the well plates were immediately centrifuged following cell dispensing and again after reagent dispensing, we found that ∼97% of wells that were identified in the instrument software as containing a single cell indeed provided the proteome coverage expected of a single cell. This commercial dispenser combined with one-step sample processing provides a very rapid and easy-to-use workflow for SCP with no reduction in proteome coverage relative to a nanowell-based workflow, and the commercial well plates also facilitate autosampling with unmodified instrumentation. Single-cell samples were analyzed using home-packed 30 μm i.d. nanoLC columns as well as commercially available 50 μm i.d. columns. The commercial columns resulted in ∼35% fewer identified proteins. However, combined with the well plate-based preparation platform, the presented workflow provides a fully commercial and relatively low-cost alternative for SCP sample preparation and separation, which should greatly broaden the accessibility of SCP to other laboratories.

Data-Dependent Acquisition with Precursor Coisolation Improves Proteome Coverage and Measurement Throughput for Label-Free Single-Cell Proteomics

We combined efficient sample preparation and ultra-low-flow liquid chromatography with a newly developed data acquisition and analysis scheme termed wide window acquisition (WWA) to quantify >3,000 proteins from single cells in rapid label-free analyses. WWA employs large isolation windows to intentionally co-isolate and co-fragment adjacent precursors along with the selected precursor. Optimized WWA increased the number of MS2-identified proteins by ≈40 % relative to standard data-dependent acquisition. For a 40-min LC gradient operated at ≈15 nL/min, we identified an average of 3,524 proteins per single-cell-sized aliquot of protein digest. Reducing the active gradient to 20 min resulted in a modest 10 % decrease in proteome coverage. Using this platform, we compared protein expression between single HeLa cells having an essential autophagy gene, atg9a, knocked out, with their isogenic WT parental line. Similar proteome coverage was observed, and 268 proteins were significantly up- or downregulated. Protein upregulation primarily related to innate immunity, vesicle trafficking and protein degradation.

Rapid, One-Step Sample Processing for Label-Free Single-Cell Proteomics

Sample preparation for single-cell proteomics is generally performed in a one-pot workflow with multiple dispensing and incubation steps. These hours-long processes can be labor intensive and lead to long sample-to-answer times. Here we report a sample preparation method that achieves cell lysis, protein denaturation, and digestion in 1 h using commercially available high-temperature-stabilized proteases with a single reagent dispensing step. Four different one-step reagent compositions were evaluated, and the mixture providing the highest proteome coverage was compared to the previously employed multistep workflow. The one-step preparation increases proteome coverage relative to the previous multistep workflow while minimizing labor input and the possibility of human error. We also compared sample recovery between previously used microfabricated glass nanowell chips and injection-molded polypropylene chips and found the polypropylene provided improved proteome coverage. Combined, the one-step sample preparation and the polypropylene substrates enabled the identification of an average of nearly 2400 proteins per cell using a standard data-dependent workflow with Orbitrap mass spectrometers. These advances greatly simplify sample preparation for single-cell proteomics and broaden accessibility with no compromise in terms of proteome coverage.

In-Depth Mass Spectrometry-Based Proteomics of Formalin-Fixed, Paraffin-Embedded Tissues with a Spatial Resolution of 50-200 μm

Formalin-fixed, paraffin-embedded (FFPE) tissues are banked in large repositories to cost-effectively preserve valuable specimens for later study. With the rapid growth of spatial proteomics, FFPE tissues can serve as a more accessible alternative to more commonly used frozen tissues. However, extracting proteins from FFPE tissues is challenging due to cross-links formed between proteins and formaldehyde. Here, we have adapted the nanoPOTS sample processing workflow, which was previously applied to single cells and fresh-frozen tissues, to profile protein expression from FFPE tissues. Following the optimization of extraction solvents, times, and temperatures, we identified an average of 1312 and 3184 high-confidence master proteins from 10 μm thick FFPE-preserved mouse liver tissue squares having lateral dimensions of 50 and 200 μm, respectively. The observed proteome coverage for FFPE tissues was on average 88% of that achieved for similar fresh-frozen tissues. We also characterized the performance of our fully automated sample preparation and analysis workflow, termed autoPOTS, for FFPE spatial proteomics. This modified nanodroplet processing in one pot for trace samples (nanoPOTS) and fully automated processing in one pot for trace sample (autoPOTS) workflows provides the greatest coverage reported to date for high-resolution spatial proteomics applied to FFPE tissues. Data are available via ProteomeXchange with identifier PXD029729.

Label-Free Profiling of up to 200 Single-Cell Proteomes per Day Using a Dual-Column Nanoflow Liquid Chromatography Platform

Single-cell proteomics (SCP) has great potential to advance biomedical research and personalized medicine. The sensitivity of such measurements increases with low-flow separations (<100 nL/min) due to improved ionization efficiency, but the time required for sample loading, column washing, and regeneration in these systems can lead to low measurement throughput and inefficient utilization of the mass spectrometer. Herein, we developed a two-column liquid chromatography (LC) system that dramatically increases the throughput of label-free SCP using two parallel subsystems to multiplex sample loading, online desalting, analysis, and column regeneration. The integration of MS1-based feature matching increased proteome coverage when short LC gradients were used. The high-throughput LC system was reproducible between the columns, with a 4% difference in median peptide abundance and a median CV of 18% across 100 replicate analyses of a single-cell-sized peptide standard. An average of 621, 774, 952, and 1622 protein groups were identified with total analysis times of 7, 10, 15, and 30 min, corresponding to a measurement throughput of 206, 144, 96, and 48 samples per day, respectively. When applied to single HeLa cells, we identified nearly 1000 protein groups per cell using 30 min cycles and 660 protein groups per cell for 15 min cycles. We explored the possibility of measuring cancer therapeutic targets with a pilot study comparing the K562 and Jurkat leukemia cell lines. This work demonstrates the feasibility of high-throughput label-free single-cell proteomics.

Features of Peptide Fragmentation Spectra in Single-Cell Proteomics

The goal of proteomics is to identify and quantify the complete set of proteins in a biological sample. Single-cell proteomics specializes in the identification and quantitation of proteins for individual cells, often used to elucidate cellular heterogeneity. The significant reduction in ions introduced into the mass spectrometer for single-cell samples could impact the features of MS2 fragmentation spectra. As all peptide identification software tools have been developed on spectra from bulk samples and the associated ion-rich spectra, the potential for spectral features to change is of great interest. We characterize the differences between single-cell spectra and bulk spectra by examining three fundamental spectral features that are likely to affect peptide identification performance. All features show significant changes in single-cell spectra, including the loss of annotated fragment ions, blurring signal and background peaks due to diminishing ion intensity, and distinct fragmentation pattern, compared to bulk spectra. As each of these features is a foundational part of peptide identification algorithms, it is critical to adjust algorithms to compensate for these losses.

Lung imaging in rodents using dual energy micro-CT

Dual energy CT imaging is expected to play a major role in the diagnostic arena as it provides material decomposition on an elemental basis. The purpose of this work is to investigate the use of dual energy micro-CT for the estimation of vascular, tissue, and air fractions in rodent lungs using a post-reconstruction three-material decomposition method. We have tested our method using both simulations and experimental work. Using simulations, we have estimated the accuracy limits of the decomposition for realistic micro-CT noise levels. Next, we performed experiments involving ex vivo lung imaging in which intact lungs were carefully removed from the thorax, were injected with an iodine-based contrast agent and inflated with air at different volume levels. Finally, we performed in vivo imaging studies in (n=5) C57BL/6 mice using fast prospective respiratory gating in end-inspiration and end-expiration for three different levels of positive end-expiratory pressure (PEEP). Prior to imaging, mice were injected with a liposomal blood pool contrast agent. The mean accuracy values were for Air (95.5%), Blood (96%), and Tissue (92.4%). The absolute accuracy in determining all fraction materials was 94.6%. The minimum difference that we could detect in material fractions was 15%. As expected, an increase in PEEP levels for the living mouse resulted in statistically significant increases in air fractions at end-expiration, but no significant changes in end-inspiration. Our method has applicability in preclinical pulmonary studies where various physiological changes can occur as a result of genetic changes, lung disease, or drug effects.

Dual-energy micro-CT of the rodent lung

The purpose of this work is to investigate the use of dual-energy micro-computed tomography (CT) for the estimation of vascular, tissue, and air fractions in rodent lungs using a postreconstruction three material decomposition method. Using simulations, we have estimated the accuracy limits of the decomposition for realistic micro-CT noise levels. Next, we performed experiments involving ex vivo lung imaging in which intact rat lungs were carefully removed from the thorax, injected with an iodine-based contrast agent, and then inflated with different volumes of air (n = 2). Finally, we performed in vivo imaging studies in C57BL/6 mice (n = 5) using fast prospective respiratory gating in end inspiration and end expiration for three different levels of positive end expiratory pressure (PEEP). Before imaging, mice were injected with a liposomal blood pool contrast agent. The three-dimensional air, tissue, and blood fraction maps were computed and analyzed. The results indicate that separation and volume estimation of the three material components of the lungs are possible. The mean accuracy values for air, blood, and tissue were 93, 93, and 90%, respectively. The absolute accuracy in determining all fraction materials was 91.6%. The coefficient of variation was small (2.5%) indicating good repeatability. The minimum difference that we could detect in material fractions was 15%. As expected, an increase in PEEP levels for the living mouse resulted in statistically significant increases in air fractions at end expiration but no significant changes at end inspiration. Our method has applicability in preclinical pulmonary studies where changes in lung structure and gas volume as a result of lung injury, environmental exposures, or drug bioactivity would have important physiological implications.

Investigations on X-ray luminescence CT for small animal imaging

X-ray Luminescence CT (XLCT) is a hybrid imaging modality combining x-ray and optical imaging in which x-ray luminescent nanophosphors (NPs) are used as emissive imaging probes. NPs are easily excited using common CT energy x-ray beams, and the NP luminescence is efficiently collected using sensitive light based detection systems. XLCT can be recognized as a close analog to fluorescence diffuse optical tomography (FDOT). However, XLCT has remarkable advantages over FDOT due to the substantial excitation penetration depths provided by x-rays relative to laser light sources, long term photo-stability of NPs, and the ability to tune NP emission within the NIR spectral window. Since XCLT uses an x-ray pencil beam excitation, the emitted light can be measured and back-projected along the x-ray path during reconstruction, where the size of the X-ray pencil beam determines the resolution for XLCT. In addition, no background signal competes with NP luminescence (i.e., no auto fluorescence) in XLCT. Currently, no small animal XLCT system has been proposed or tested. This paper investigates an XLCT system built and integrated with a dual source micro-CT system. Two novel sampling paradigms that result in more efficient scanning are proposed and tested via simulations. Our preliminary experimental results in phantoms indicate that a basic CT-like reconstruction is able to recover a map of the NP locations and differences in NP concentrations. With the proposed dual source system and faster scanning approaches, XLCT has the potential to revolutionize molecular imaging in preclinical studies.

Phase-selective image reconstruction of the lungs in small animals using Micro-CT

Gating in small animal imaging can compensate for artifacts due to physiological motion. This paper presents a strategy for sampling and image reconstruction in the rodent lung using micro-CT. The approach involves rapid sampling of free-breathing mice without any additional hardware to detect respiratory motion. The projection images are analyzed post-acquisition to derive a respiratory signal, which is used to provide weighting factors for each projection that favor a selected phase of the respiration (e.g. end-inspiration or end-expiration) for the reconstruction. Since the sampling cycle and the respiratory cycle are uncorrelated, the sets of projections corresponding to any of the selected respiratory phases do not have a regular angular distribution. This drastically affects the image quality of reconstructions based on simple filtered backprojection. To address this problem, we use an iterative reconstruction algorithm that combines the Simultaneous Algebraic Reconstruction Technique with Total Variation minimization (SART-TV). At each SART-TV iteration, backprojection is performed with a set of weighting factors that favor the desired respiratory phase. To reduce reconstruction time, the algorithm is implemented on a graphics processing unit. The performance of the proposed approach was investigated in simulations and in vivo scans of mice with primary lung cancers imaged with our in-house developed dual tube/detector micro-CT system. We note that if the ECG signal is acquired during sampling, the same approach could be used for phase-selective cardiac imaging.

Apolipoprotein(a) inhibits the conversion of Glu-plasminogen to Lys-plasminogen: a novel mechanism for lipoprotein(a)-mediated inhibition of plasminogen activation

BACKGROUND

Elevated plasma concentrations of lipoprotein(a) [Lp(a)] are associated with an increased risk for thrombotic disorders. Lp(a) is a unique lipoprotein consisting of a low-density lipoprotein-like moiety covalently linked to apolipoprotein(a) [apo(a)], a homologue of the fibrinolytic proenzyme plasminogen. Several in vitro and in vivo studies have shown that Lp(a)/apo(a) can inhibit tissue-type plasminogen activator-mediated plasminogen activation on fibrin surfaces, although the mechanism of inhibition by apo(a) remains controversial. Essential to fibrin clot lysis are a number of plasmin-dependent positive feedback reactions that enhance the efficiency of plasminogen activation, including the plasmin-mediated conversion of Glu-plasminogen to Lys-plasminogen.

OBJECTIVE

Using acid-urea gel electrophoresis to resolve the two forms of radiolabeled plasminogen, we determined whether apo(a) is able to inhibit Glu-plasminogen to Lys-plasminogen conversion.

METHODS

The assays were performed in the absence or presence of different recombinant apo(a) species, including point mutants, deletion mutants and variants that represent greater than 90% of the known apo(a) isoform sizes.

RESULTS

Apo(a) substantially suppressed Glu-plasminogen conversion. Critical roles were identified for the kringle IV types 5-9 and kringle V; contributory roles for sequences within the amino-terminal half of the molecule were also observed. Additionally, with the exception of the smallest naturally-occurring isoform of apo(a), isoform size was found not to contribute to the inhibitory capacity of apo(a).

CONCLUSION

These findings underscore a novel contribution to the understanding of Lp(a)/apo(a)-mediated inhibition of plasminogen activation: the ability of the apo(a) component of Lp(a) to inhibit the key positive feedback step of plasmin-mediated Glu-plasminogen to Lys-plasminogen conversion.

Surgical informatics on the internet: any improvement?

PURPOSE

The Internet is a popular, but ungoverned, source of medical information. This study tracked the change in performance of commonly available search engines and the quality of medical data therein over a four-year period.

METHODS

We compared the accuracy of information on a commonly performed surgical procedure (vasectomy) using six standard search engines in a four-year period and with two recently developed search engines. The top 25 ranked sites cited by each search engine were scored for description of the procedure, post-operative instructions, complications and unproven associations.

RESULTS

There was no improvement in quality of individual sites over the study period. Additionally, the hit rate of search engines remained poor with 27 sites cited (40%) in 2002 either irrelevant or unavailable.

DISCUSSION

Few useful sites with accurate information on surgical procedures are available on the Internet and simple search strategies fail to identify site quality or relevancy.

CONCLUSION

At present, the Internet cannot be recommended as a reliable resource for many aspects of health information for patients. The onus is on health-care providers to provide high quality sites and direct patients to these sources of reliable information

Changing trends in the management of gallstone disease

BACKGROUND

Day case cholecystectomy is increasingly becoming a management option for elective cases while "same admission" cholecystectomy is now considered a favorable option in the treatment of acute cholecystitis. To assess the advent of these changes in our surgical practice, a retrospective analysis of our experience is presented.

METHODS

All patients undergoing cholecystectomy between January 2000 and January 2001 were analyzed according to admission status, operation type, conversion rate, complications, and nonsurgical intervention.

RESULTS

156 patients underwent cholecystectomy and 152 charts were retrieved. Laparoscopic cholecystectomy was performed on 95% of patients with a conversion rate of 9%. Morbidity for the series was 12.5%, including one common bile duct injury (0.6%). Day case and acute cholecystectomy comprised 67% of our cholecystectomy practice.

CONCLUSIONS

Our findings suggest that there is an increasing trend toward shortening the hospital stay of patients undergoing laparoscopic cholecystectomy. This does not appear to have had a deleterious effect on outcome.

Iron deficiency enhances cholesterol gallstone formation

BACKGROUND

Cholesterol gallstones occur most commonly in multiparous women, but the causes for this phenomenon remain unclear. This same patient population is prone to chronic iron deficiency anemia. In addition, iron is known to play an important role in hepatic enzyme metabolism. Therefore, we tested the hypotheses that iron deficiency would alter hepatic cholesterol metabolism and enhance gallstone formation.

METHODS

Forty adult prairie dogs were fed either a control iron-supplemented (200 ppm), an iron-deficient (8 ppm), a 0.4% cholesterol iron-supplemented (200 ppm), or a 0.4% cholesterol iron-deficient (8 ppm) diet. After 8 weeks gallbladder bile, serum, and liver were harvested. Gallbladder bile was examined for cholesterol crystals and gallstones. Bile lipids and hepatic enzymes were measured, and a cholesterol saturation index (CSI) was calculated.

RESULTS

Animals receiving the iron-deficient diet were more likely to have cholesterol crystals in their bile than were animals on the control diet (80% vs. 20%; p < 0.05). Animals on the 0.4% cholesterol iron-deficient diet had more cholesterol crystals per high-powered field (79 +/- 10 vs. 49 +/- 9; p = 0.07), a higher molar % cholesterol (6.0 +/- 0.3 vs 4.4 +/- 0.5; p < 0.05), and a higher CSI (1.27 +/- 0.10 vs. 0.91 +/- 0.07; p < 0.05) compared to animals receiving the 0.4% cholesterol iron supplemented diet. The 7 alpha-hydroxylase levels were lower in the animals on the iron-deficient diet compared to those receiving the control diet (0.42 +/- 0.08 vs 1.17 +/- 0.40 pmol/mg per minute; p = 0.07).

CONCLUSIONS

These data suggest that an iron-deficient diet (1) alters hepatic enzyme metabolism, which, in turn, (2) increases gallbladder bile cholesterol and promotes cholesterol crystal formation. We conclude that iron deficiency plays a previously unrecognized role in the pathogenesis of cholesterol gallstone formation in women.

Comparison of pentobarbital alone and pentobarbital in combination with lidocaine for euthanasia of dogs

Pentobarbital alone, pentobarbital plus 1% lidocaine solution, pentobarbital plus 2% lidocaine solution, and pentobarbital plus 3% lidocaine solution were each used to euthanatize 6 dogs. For each dog, time between the beginning of injection of the euthanasia solution and each of the following events was recorded: collapse, onset of apnea, flat-line electrocardiogram, flat-line electroencephalogram, loss of palpable heartbeat, and loss of palpable pulse. Any signs of pain or discomfort were also recorded. There were no significant differences among groups except for time to flat-line electrocardiogram. Dogs euthanatized with pentobarbital alone had significantly longer times than did dogs euthanatized with pentobarbital in combination with any of the lidocaine concentrations. We concluded that pentobarbital in combination with lidocaine was a reasonable alternative to pentobarbital alone when euthanatizing dogs.

The microbiological contamination of equipment processed by the HSDU

The microbiological hazard to staff of used instruments and equipment when returned to the HSDU appears to be small providing reasonable precautions are taken (Parsons et al, 1985). Nevertheless, little evidence is available on the contamination of used equipment or the efficiency of cleaning and disinfection methods.

An outbreak of food-borne enterotoxigenic Escherichia coli diarrhoea in England

An outbreak of diarrhoea with abdominal pain occurred among members of the staff of a school and their guests after a social function at which a cold buffet was served. Sixty people attended the function and 43 subsequently completed questionnaires. Of these, 27 had diarrhoea. The median incubation period was 36 h and the range 12-66 h. Food history analysis showed an association between diarrhoea and eating curried turkey mayonnaise. Stool specimens from 13 of those who developed diarrhoea were examined: Escherichia coli 06.H16 (producing heat-stable and heat-labile enterotoxins) was found in nine specimens and E. coli 027.H20 (producing heat-stable enterotoxin) in 11 specimens. Eight patients had both strains and only one was negative for enterotoxigenic E. coli. Food samples were not available for examination. Enterotoxigenic E. coli should be considered as a possible cause in well-defined outbreaks of food-borne diarrhoea with abdominal pain.

Effects of long-term lithium administration on renal structure and function in rats. A distinctive tubular lesion

Because lithium salts are widely used for long-term therapy of affective disorders and have been recently implicated as a cause of tubulointerstitial renal disease, we have undertaken experiments designed to establish the site of the early and late pathologic lesions and to determine their correlation with the lithium-induced concentrating defect. Male Wistar rats given a semisynthetic diet that contained lithium carbonate, 90 mEq/kg dry weight, developed serum lithium levels in the human therapeutic range; pair-fed controls received sodium carbonate. Within 3 weeks, treated rats developed marked polyuria, with elevation of free water clearance and vasopressin-resistant diabetes insipidus. Early morphologic changes were confined to the cortical collecting tubules and, possibly, contiguous portions of distal tubules. The tubules were dilated and irregularly lined with cells that had bulging or thinned basophilic cytoplasm, enlarged nuclei, sometimes basal vacuolization, and a few mitoses. These changes were evident at 3 weeks and progressed through the end of the observation period at 18 weeks. The proliferative component of the lesion was demonstrated by the finding of a significant and specific increase in 3H-thymidine uptake by nuclei of collecting/distal tubules of lithium-treated rats. The lesion, but not the increased thymidine uptake, extended into the medullary collecting ducts at 9 and 18 weeks. Although occasional intratubular mononuclear cells were seen at 9 and 18 weeks, no interstitial inflammation or fibrosis was seen. These tubular epithelial lesions were not seen in the kidneys of Brattleboro rats or glucose-treated Wistar rats despite comparable polyuria. We suggest that this early, persistent, and reproducible lesion, characterized by reactive and proliferating tubular cells in the cortical collecting tubules, predisposes the kidney to injury from otherwise mild or insignificant insults and may explain the sporadic occurrence of serious tubulointerstitial disease in patients on long-term lithium therapy.

Lepromatous leprosy

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