Native Protein Complexes in the Cytoplasm of Red Blood Cells

Genetic architecture of the red blood cell proteome in genetically diverse mice reveals central role of hemoglobin beta cysteine redox status in maintaining circulating glutathione pools

Red blood cells (RBCs) transport oxygen but accumulate oxidative damage over time, reducing function in vivo and during storage-critical for transfusions. To explore genetic influences on RBC resilience, we profiled proteins, metabolites, and lipids from fresh and stored RBCs obtained from 350 genetically diverse mice. Our analysis identified over 6,000 quantitative trait loci (QTL). Compared to other tissues, prevalence of trans genetic effects over cis reflects the absence of de novo protein synthesis in anucleated RBCs. QTL hotspots at Hbb, Hba, Mon1a, and storage-specific Steap3 linked ferroptosis to hemolysis. Proteasome components clustered at multiple loci, underscoring the importance of degrading oxidized proteins. Post-translational modifications (PTMs) mapped predominantly to hemoglobins, particularly cysteine residues. Loss of reactive C93 in humanized mice (HBB C93A) disrupted redox balance, affecting glutathione pools, protein glutathionylation, and redox PTMs. These findings highlight genetic regulation of RBC oxidation, with implications for transfusion biology and oxidative stress-dependent hemolytic disorders.

RBC-GEM: A genome-scale metabolic model for systems biology of the human red blood cell

Advancements with cost-effective, high-throughput omics technologies have had a transformative effect on both fundamental and translational research in the medical sciences. These advancements have facilitated a departure from the traditional view of human red blood cells (RBCs) as mere carriers of hemoglobin, devoid of significant biological complexity. Over the past decade, proteomic analyses have identified a growing number of different proteins present within RBCs, enabling systems biology analysis of their physiological functions. Here, we introduce RBC-GEM, one of the most comprehensive, curated genome-scale metabolic reconstructions of a specific human cell type to-date. It was developed through meta-analysis of proteomic data from 29 studies published over the past two decades resulting in an RBC proteome composed of more than 4,600 distinct proteins. Through workflow-guided manual curation, we have compiled the metabolic reactions carried out by this proteome to form a genome-scale metabolic model (GEM) of the RBC. RBC-GEM is hosted on a version-controlled GitHub repository, ensuring adherence to the standardized protocols for metabolic reconstruction quality control and data stewardship principles. RBC-GEM represents a metabolic network is a consisting of 820 genes encoding proteins acting on 1,685 unique metabolites through 2,723 biochemical reactions: a 740% size expansion over its predecessor. We demonstrated the utility of RBC-GEM by creating context-specific proteome-constrained models derived from proteomic data of stored RBCs for 616 blood donors, and classified reactions based on their simulated abundance dependence. This reconstruction as an up-to-date curated GEM can be used for contextualization of data and for the construction of a computational whole-cell models of the human RBC.

Red Blood Cell Extracellular Vesicle-Based Drug Delivery: Challenges and Opportunities

Recently, red blood cell-derived extracellular vesicles (RBCEVs) have attracted attention for clinical applications because of their safety and biocompatibility. RBCEVs can escape macrophages through the binding of CD47 to inhibitory receptor signal regulatory protein α. Furthermore, genetic materials such as siRNA, miRNA, mRNA, or single-stranded RNA can be encapsulated within RBCEVs and then released into target cells for precise treatment. However, their side effects, half-lives, target cell specificity, and limited large-scale production under good manufacturing practice remain challenging. In this review, we summarized the biogenesis and composition of RBCEVs, discussed the advantages and disadvantages of RBCEVs for drug delivery compared with synthetic nanovesicles and non-red blood cell-derived EVs, and provided perspectives for overcoming current limitations to the use of RBCEVs for clinical applications.

Protein-L-isoaspartate O-methyltransferase is required for <i>in vivo</i> control of oxidative damage in red blood cells

Red blood cells (RBC) have the special challenge of a large amount of reactive oxygen species (from their substantial iron load and Fenton reactions) combined with the inability to synthesize new gene products. Considerable progress has been made in elucidating the multiple pathways by which RBC neutralize reactive oxygen species via NADPH driven redox reactions. However, far less is known about how RBC repair the inevitable damage that does occur when reactive oxygen species break through anti-oxidant defenses. When structural and functional proteins become oxidized, the only remedy available to RBC is direct repair of the damaged molecules, as RBC cannot synthesize new proteins. Amongst the most common amino acid targets of oxidative damage is the conversion of asparagine and aspartate side chains into a succinimidyl group through deamidation or dehydration, respectively. RBC express an L-isoaspartyl methyltransferase (PIMT, gene name PCMT1) that can convert succinimidyl groups back to an aspartate. Herein, we report that deletion of PCMT1 significantly alters RBC metabolism in a healthy state, but does not impair the circulatory lifespan of RBC. Through a combination of genetic ablation, bone marrow transplantation and oxidant stimulation with phenylhydrazine in vivo or blood storage ex vivo, we use omics approaches to show that, when animals are exposed to oxidative stress, RBC from PCMT1 knockout undergo significant metabolic reprogramming and increased hemolysis. This is the first report of an essential role of PCMT1 for normal RBC circulation during oxidative stress.

Irreversible alterations in the hemoglobin structure affect oxygen binding in human packed red blood cells

The ability of hemoglobin (Hb) to transport respiratory gases is directly linked to its quaternary structure properties and reversible changes between T (tense) and R (relax) state. In this study we demonstrated that packed red blood cells (pRBCs) storage resulted in a gradual increase in the irreversible changes in the secondary and quaternary structures of Hb, with subsequent impairment of the T↔R transition. Such alteration was associated with the presence of irreversibly settled in the relaxed form, quaternary structure of Hb, which we termed R'. On the secondary structure level, disordered protein organization involved formation of β-sheets and a decrease in α-helices related to the aggregation process stabilized by strong intermolecular hydrogen bonding. Compensatory changes in RBCs metabolism launched to preserve reductive microenvironment were disclosed as an activation of nicotinamide adenine dinucleotide phosphate (NADPH) production and increased reduced to oxidized glutathione (GSH/GSSG) ratio. For the first time we showed the relationship between secondary structure changes and the occurrence of newly discovered R', which through an artificial increase in oxyhemoglobin level altered Hb ability to bind and release oxygen.

From omics technologies to personalized transfusion medicine

INTRODUCTION

Blood transfusion is the single most frequent in-hospital medical procedure, a life-saving intervention for millions of recipients worldwide every year. Storage in the blood bank is an enabling strategy for this critical procedure, as it logistically solves the issue of making ~110 million units available for transfusion every year. Unfortunately, storage in the blood bank promotes a series of biochemical and morphological changes to the red blood cell that compromise the integrity and functionality of the erythrocyte in vitro and in animal models, and could negatively impact transfusion outcomes in the recipient. Areas covered: While commenting on the clinical relevance of the storage lesion is beyond the scope of this manuscript, here we will review recent advancements in our understanding of the storage lesion as gleaned through omics technologies. We will focus on how the omics-scale appreciation of the biological variability at the donor and recipient level is impacting our understanding of red blood cell storage biology. Expert commentary: Omics technologies are paving the way for personalized transfusion medicine, a discipline that promises to revolutionize a critical field in medical practice. The era of recipient-tailored additives, processing, and storage strategies may not be too far distant in the future.

Repository of Enriched Structures of Proteins Involved in the Red Blood Cell Environment (RESPIRE)

The Red Blood Cell (RBC) is a metabolically-driven cell vital for processes such a gas transport and homeostasis. RBC possesses at its surface exposing antigens proteins that are critical in blood transfusion. Due to their importance, numerous studies address the cell function as a whole but more and more details of RBC structure and protein content are now studied using massive state-of-the art characterisation techniques. Yet, the resulting information is frequently scattered in many scientific articles, in many databases and specialized web servers. To provide a more compendious view of erythrocytes and of their protein content, we developed a dedicated database called RESPIRE that aims at gathering a comprehensive and coherent ensemble of information and data about proteins in RBC. This cell-driven database lists proteins found in erythrocytes. For a given protein entry, initial data are processed from external portals and enriched by using state-of-the-art bioinformatics methods. As structural information is extremely useful to understand protein function and predict the impact of mutations, a strong effort has been put on the prediction of protein structures with a special treatment for membrane proteins. Browsing the database is available through text search for reference gene names or protein identifiers, through pre-defined queries or via hyperlinks. The RESPIRE database provides valuable information and unique annotations that should be useful to a wide audience of biologists, clinicians and structural biologists.

Database URL:http://www.dsimb.inserm.fr/respire

Numerical Investigation of the Effects of Red Blood Cell Cytoplasmic Viscosity Contrasts on Single Cell and Bulk Transport Behaviour

In-silico cellular models of blood are invaluable to gain understanding about the many interesting properties that blood exhibits. However, numerical investigations that focus on the effects of cytoplasmic viscosity in these models are not very prevalent. We present a parallelised method to implement cytoplasmic viscosity for HemoCell, an open-source cellular model based on immersed boundary lattice Boltzmann methods, using an efficient ray-casting algorithm. The effects of the implementation are investigated with single-cell simulations focusing on the deformation in shear flow, the migration due to wall induced lift forces, the characteristic response time in periodic stretching and pair collisions between red blood cells and platelets. Collective transport phenomena are also investigated in many-cell simulations in a pressure driven channel flow. The simulations indicate that the addition of a viscosity contrast between internal and external fluids significantly affects the deformability of a red blood cell, which is most pronounced during very short time-scale events. Therefore, modelling the cytoplasmic viscosity contrast is important in scenarios with high velocity deformation, typically high shear rate flows.

Protein-Protein Interaction Probed by Label-free Second Harmonic Light Scattering: Hemoglobin Adsorption on Spectrin Surface as a Case Study

In this article, we have studied the binding of different naturally occurring hemoglobin (Hb) variants on erythrocyte skeletal protein, spectrin surface using the label free nondestructive second harmonic light scattering (SHLS) technique in aqueous buffer. Hemoglobin variants like sickle hemoglobin (HbS) and hemoglobin E (HbE) were chosen as they associate with sickle cell disease and HbEβ-thalassemia, respectively, and their interaction with spectrin is compared with normal adult hemoglobin (HbA). The concentration dependent change in the second harmonic light intensity from nanomolar spectrin solution has been measured after addition of small aliquots of hemoglobins. From the second harmonic titration data, the binding constant is calculated using a modified Langmuir adsorption model of hemoglobin binding to the spectrin surface. Interestingly, it is found that the binding constant for HbE (13.8 × 10⁸ M^-1) is 1 order of magnitude higher than that of HbS (1.6 × 10⁸ M^-1) or HbA (2.1 × 10⁸ M^-1) which indicates higher affinity of HbE for spectrin compared to HbA and HbS. The number of the Hb molecules bound to the spectrin surface was estimated to be of the order of hundred's which is determined for the first time.

Integration of microRNAome, proteomics and metabolomics to analyze arsenic-induced malignant cell transformation

Long-term exposure to arsenic has been linked to tumorigenesis in different organs and tissues, such as skin; however, the detailed mechanism remains unclear. In this present study, we integrated “omics” including microRNAome, proteomics and metabolomics to investigate the potential molecular mechanisms. Compared with non-malignant human keratinocytes (HaCaT), twenty-six miRNAs were significantly altered in arsenic-induced transformed cells. Among these miRNAs, the differential expression of six miRNAs was confirmed using Q-RT-PCR, representing potential oxidative stress genes. Two-dimensional gel electrophoresis (2D-PAGE) and mass spectrometry (MS) were performed to identify the differential expression of proteins in arsenic-induced transformed cells, and twelve proteins were significantly changed. Several proteins were associated with oxidative stress and carcinogenesis including heat shock protein beta-1 (HSPB1), peroxiredoxin-2 (PRDX2). Using ultra-performance liquid chromatography and Q-TOF mass spectrometry (UPLC/Q-TOF MS), 68 metabolites including glutathione, fumaric acid, citric acid, phenylalanine, and tyrosine, related to redox metabolism, glutathione metabolism, citrate cycle, met cycle, phenylalanine and tyrosine metabolism were identified and quantified. Taken together, these results indicated that arsenic-induced transformed cells exhibit alterations in miRNA, protein and metabolite profiles providing novel insights into arsenic-induced cell malignant transformation and identifying early potential biomarkers for cutaneous squamous cell carcinoma induced by arsenic.

Proteomic analysis of red blood cells and the potential for the clinic: what have we learned so far?

INTRODUCTION

Red blood cells (RBC) are the most abundant host cells in the human body. Mature erythrocytes are devoid of nuclei and organelles and have always been regarded as circulating 'bags of hemoglobin'. The advent of proteomics has challenged this assumption, revealing unanticipated complexity and novel roles for RBCs not just in gas transport, but also in systemic metabolic homeostasis in health and disease. Areas covered: In this review we will summarize the main advancements in the field of discovery mode and redox/quantitative proteomics with respect to RBC biology. We thus focus on translational/clinical applications, such as transfusion medicine, hematology (e.g. hemoglobinopathies) and personalized medicine. Synergy of omics technologies - especially proteomics and metabolomics - are highlighted as a hallmark of clinical metabolomics applications for the foreseeable future. Expert commentary: The introduction of advanced proteomics technologies, especially quantitative and redox proteomics, and the integration of proteomics data with omics information gathered through orthogonal technologies (especially metabolomics) promise to revolutionize many biomedical areas, from hematology and transfusion medicine to personalized medicine and clinical biochemistry.

The Proteome of the Red Blood Cell: An Auspicious Source of New Insights into Membrane-Centered Regulation of Homeostasis

During the past decade, the hand-in-hand development of biotechnology and bioinformatics has enabled a view of the function of the red blood cell that surpasses the supply of oxygen and removal of carbon dioxide. Comparative proteomic inventories have yielded new clues to the processes that regulate membrane-cytoskeleton interactions in health and disease, and to the ways by which red blood cells communicate with their environment. In addition, proteomic data have revealed the possibility that many, hitherto unsuspected, metabolic processes are active in the red blood cell cytoplasm. Recent metabolomic studies have confirmed and expanded this notion. Taken together, the presently available data point towards the red blood cell membrane as the hub at which all regulatory processes come together. Thus, alterations in the association of regulatory proteins with the cell membrane may be a sine qua non for the functional relevance of any postulated molecular mechanism. From this perspective, comparative proteomics centered on the red blood cell membrane constitute a powerful tool for the identification and elucidation of the physiologically and pathologically relevant pathways that regulate red blood cell homeostasis. Additionally, this perspective provides a focus for the interpretation of metabolomic studies, especially in the development of biomarkers in the blood.

The involvement of erythrocyte metabolism in organismal homeostasis in health and disease

Historically, study of erythrocyte homeostasis has focussed on the survival of erythrocytes in the blood bank and, especially in pathological circumstances, on the mechanisms leading to accelerated aging and removal from the circulation. Recent proteomic and metabolomic data suggest that erythrocyte metabolism involves more than ATP production and transport of oxygen and carbondioxide; is subject to regulation; and is likely to reflect organismal metabolism. Also, it has become clear that systemic diseases affect erythrocyte homeostasis. The perspectives emerging from these data include new possibilities to manipulate erythrocyte function and survival in vivo, and thereby organismal homeostasis.

Supernatant protein biomarkers of red blood cell storage hemolysis as determined through an absolute quantification proteomics technology

BACKGROUND

Laboratory technologies have highlighted the progressive accumulation of the so-called "storage lesion," a wide series of alterations to stored red blood cells (RBCs) that may affect the safety and effectiveness of the transfusion therapy. New improvements in the field are awaited to ameliorate this lesion, such as the introduction of washing technologies in the cell processing pipeline. Laboratory studies that have tested such technologies so far rely on observational qualitative or semiquantitative techniques.

STUDY DESIGN AND METHODS

A state-of-the-art quantitative proteomics approach utilizing quantitative concatamers (QconCAT) was used to simultaneously monitor fluctuations in the abundance of 114 proteins in AS-3 RBC supernatants (n = 5; 11 time points, including before and after leukoreduction, at 3 hours, on Days 1 and 2, and weekly sampling from Day 7 through Day 42).

RESULTS

Leukoreduction-dependent depletion of plasma proteins was observed at the earliest time points. A subset of proteins showed very high linear correlation (r(2)  > 0.9) not only with storage time, but also with absolute levels of hemoglobin α1 and β, a proxy for RBC hemolysis and vesiculation. Linear regression was performed to describe the temporal relationship between these proteins. Our findings suggest a role for supernatant glyceraldehyde-3-phosphate dehydrogenase; peroxiredoxin-1, -2, and -6; carbonic anhydrase-1 and -2; selenium binding protein-1; biliverdin reductase; aminolevulinate dehydratase; and catalase as potential biomarkers of RBC quality during storage.

CONCLUSION

A targeted proteomics technology revealed novel biomarkers of the RBC storage lesion and promises to become a key analytical readout for the development and testing of alternative cell processing strategies.

Expression and characterization of a new isoform of the 9 kDa allergenic lipid transfer protein from tomato (variety San Marzano)

Lipid transfer proteins (LTPs) are food allergens found first in fruits of the Rosaceae family and later identified in other food plants. Their high structural stability causes them to behave as allergens in cooked and processed foods. Allergenic LTPs have been identified in tomato fruits as well, but studies of their thermal stability and structural characteristics are limited. In this article we report the identification of the coding region for a novel 9 kDa LTP isoform in the tomato variety San Marzano, together with the expression of the recombinant mature protein. The purified recombinant protein was further characterized for its thermal stability and was found to bind 1-palmitoil-2-lysophosphatidylcholine (Lyso-C16) after thermal treatments up to 105 °C. Analysis of a modeling derived structure of the protein allowed the identification of possible epitope regions on the molecular surface.

Red blood cell storage affects the stability of cytosolic native protein complexes

BACKGROUND

Refrigerated storage of red blood cell (RBC) units promotes the progressive accumulation of the so-called storage lesions, a widespread series of alterations to morphology, metabolism, and proteome integrity of stored RBCs. However, while storage lesions targeting the RBC membrane fraction have been widely documented, the cytosolic fraction is as yet an underinvestigated cause of the technical inconveniences related to the high abundance of hemoglobin.

STUDY DESIGN AND METHODS

By exploiting a recently ideated preparative two-dimensional clear native electrophoresis, followed by mass spectrometry analysis, we could monitor the changes of soluble multiprotein complexes (MPCs) in RBCs after 0, 21, and 35 days of storage under standard blood banking conditions.

RESULTS

Data indicate a substantial storage-dependent alteration of RBC MPCs, particularly of those involved in energy and redox metabolism, confirming previous evidence about the progressive dysregulation of these pathways in long-stored units.

CONCLUSION

The use of native gel-based proteomics to investigate MPCs present in the RBC cytosolic fraction proved to be a powerful tool. Results collected represent a preliminary advance in the knowledge of the key role of native cytosolic MPCs in context of RBC storage lesion. Multiprotein organization and interacting partners of some key enzymes have been found to change during storage duration, suggesting that future studies will be needed to assess whether such alterations could influence their activity and efficiency.

Metabolomics of AS-5 RBC supernatants following routine storage

BACKGROUND AND OBJECTIVES

The safety and efficacy of stored red blood cells (RBCs) transfusion has been long debated due to retrospective clinical evidence and laboratory results, indicating a potential correlation between increased morbidity and mortality following transfusion of RBC units stored longer than 14 days. We hypothesize that storage in Optisol additive solution-5 leads to a unique metabolomics profile in the supernatant of stored RBCs.

MATERIALS AND METHODS

Whole blood was drawn from five healthy donors, RBC units were manufactured, and prestorage leucoreduced by filtration. Samples were taken on days 1 and 42, the cells removed, and mass spectrometry-based metabolomics was performed.

RESULTS

The results confirmed the progressive impairment of RBC energy metabolism by day 42 with indirect markers of a parallel alteration of glutathione and NADPH homeostasis. Moreover, oxidized pro-inflammatory lipids accumulated by the end of storage.

CONCLUSION

The supernatants from stored RBCs may represent a burden to the transfused recipients from a metabolomics standpoint.

Hydrogen peroxide metabolism and sensing in human erythrocytes: a validated kinetic model and reappraisal of the role of peroxiredoxin II

Hydrogen peroxide (H2O2) metabolism in human erythrocytes has been thoroughly investigated, but unclear points persist. By integrating the available data into a mathematical model that accurately represents the current understanding and comparing computational predictions to observations we sought to (a) identify inconsistencies in present knowledge, (b) propose resolutions, and (c) examine their functional implications. The systematic confrontation of computational predictions with experimental observations of the responses of intact erythrocytes highlighted the following important discrepancy. The high rate constant (10(7)-10(8) M(-1) s(-1)) for H2O2 reduction determined for purified peroxiredoxin II (Prx2) and the high abundance of this protein indicate that under physiological conditions it consumes practically all the H2O2. However, this is inconsistent with extensive evidence that Prx2's contribution to H2O2 elimination is comparable to that of catalase. Models modified such that Prx2's effective peroxidase activity is just 10(5) M(-1) s(-1) agree near quantitatively with extensive experimental observations. This low effective activity is probably due to a strong but readily reversible inhibition of Prx2's peroxidatic activity in intact cells, implying that the main role of Prx2 in human erythrocytes is not to eliminate peroxide substrates. Simulations of the responses to physiological H2O2 stimuli highlight that a design combining abundant Prx2 with a low effective peroxidase activity spares NADPH while improving potential signaling properties of the Prx2/thioredoxin/thioredoxin reductase system.

Identification of oxidized protein hydrolase as a potential prodrug target in prostate cancer

Background

Esterases are often overexpressed in cancer cells and can have chiral specificities different from that of the corresponding normal tissues. For this reason, ester prodrugs could be a promising approach in chemotherapy. In this study, we focused on the identification and characterization of differentially expressed esterases between non-tumorigenic and tumorigenic prostate epithelial cells.

Methods

Cellular lysates from LNCaP, DU 145, and PC3 prostate cancer cell lines, tumorigenic RWPE-2 prostate epithelial cells, and non-tumorigenic RWPE-1 prostate epithelial cells were separated by native polyacrylamide gel electrophoresis (n-PAGE) and the esterase activity bands visualized using α-naphthyl acetate or α-naphthyl-N-acetylalaninate (ANAA) chiral esters and Fast Blue RR salt. The esterases were identified using nanospray LC/MS-MS tandem mass spectrometry and confirmed by Western blotting, native electroblotting, inhibition assays, and activity towards a known specific substrate. The serine protease/esterase oxidized protein hydrolase (OPH) was overexpressed in COS-7 cells to verify our results.

Results

The major esterase observed with the ANAA substrates within the n-PAGE activity bands was identified as OPH. OPH (EC 3.4.19.1) is a serine protease/esterase and a member of the prolyl oligopeptidase family. We found that LNCaP lysates contained approximately 40% more OPH compared to RWPE-1 lysates. RWPE-2, DU145 and PC3 cell lysates had similar levels of OPH activity. OPH within all of the cell lysates tested had a chiral preference for the S-isomer of ANAA. LNCaP cells were stained more intensely with ANAA substrates than RWPE-1 cells and COS-7 cells overexpressing OPH were found to have a higher activity towards the ANAA and AcApNA than parent COS-7 cells.

Conclusions

These data suggest that prodrug derivatives of ANAA and AcApNA could have potential as chemotherapeutic agents for the treatment of prostate cancer tumors that overexpress OPH.