Amirata Saei Dibavar

RESEARCH, TEACHING, or OTHER INTERESTS

Cancer Research, Drug Discovery, Biochemistry, Pharmaceutical Science

Scopus Publications

The role of protein corona in advancing plasma proteomics
Amir Ata Saei, Liangliang Sun, and Morteza Mahmoudi
Wiley
AbstractThe protein corona, a layer of biomolecules forming around nanoparticles in biological environments, critically influences nanoparticle interactions with biosystems, affecting pharmacokinetics and biological outcomes. Initially, the protein corona presented challenges for nanomedicine and nanotoxicology, such as nutrient depletion in cell cultures and masking of nanoparticle‐targeting species. However, recent advancements have highlighted its potential in environmental toxicity, proteomics, and immunology. This viewpoint focuses on leveraging the protein corona to enhance the depth of plasma proteome analysis, addressing challenges posed by the high dynamic range of protein concentrations in plasma. The protein corona simplifies sample preparation, enriches low‐abundance proteins, and improves proteome coverage. Innovations include using diverse nanoparticles and spiking small molecules to increase the number of quantified proteins. Reproducibility issues across core facilities necessitate standardized protocols. Moreover, top‐down proteomics enables proteoform‐specific measurements, providing deeper insights into protein corona composition. Future research should aim at improving top‐down proteomics techniques and integrating protein corona studies and proteomics for personalized medicine and advanced diagnostics.


One-Pot Time-Induced Proteome Integral Solubility Alteration Assay for Automated and Sensitive Drug-Target Identification
Zhaowei Meng, Amir Ata Saei, Hezheng Lyu, Massimiliano Gaetani, and Roman A. Zubarev
American Chemical Society (ACS)



Small molecule modulation of protein corona for deep plasma proteome profiling
Ali Akbar Ashkarran, Hassan Gharibi, Seyed Amirhossein Sadeghi, Seyed Majed Modaresi, Qianyi Wang, Teng-Jui Lin, Ghafar Yerima, Ali Tamadon, Maryam Sayadi, Maryam Jafari,et al.
Springer Science and Business Media LLC
AbstractThe protein corona formed on nanoparticles (NPs) has potential as a valuable diagnostic tool for improving plasma proteome coverage. Here, we show that spiking small molecules, including metabolites, lipids, vitamins, and nutrients into plasma can induce diverse protein corona patterns on otherwise identical NPs, significantly enhancing the depth of plasma proteome profiling. The protein coronas on polystyrene NPs when exposed to plasma treated with an array of small molecules allows for the detection of 1793 proteins marking an 8.25-fold increase in the number of quantified proteins compared to plasma alone (218 proteins) and a 2.63-fold increase relative to the untreated protein corona (681 proteins). Furthermore, we discovered that adding 1000 µg/ml phosphatidylcholine could singularly enable the detection of 897 proteins. At this specific concentration, phosphatidylcholine selectively depletes the four most abundant plasma proteins, including albumin, thus reducing the dynamic range of plasma proteome and enabling the detection of proteins with lower abundance. Employing an optimized data-independent acquisition approach, the inclusion of phosphatidylcholine leads to the detection of 1436 proteins in a single plasma sample. Our molecular dynamics results reveal that phosphatidylcholine interacts with albumin via hydrophobic interactions, H-bonds, and water bridges. The addition of phosphatidylcholine also enables the detection of 337 additional proteoforms compared to untreated protein corona using a top-down proteomics approach. Given the critical role of plasma proteomics in biomarker discovery and disease monitoring, we anticipate the widespread adoption of this methodology for the identification and clinical translation of biomarkers.


A uniform data processing pipeline enables harmonized nanoparticle protein corona analysis across proteomics core facilities
Hassan Gharibi, Ali Akbar Ashkarran, Maryam Jafari, Elizabeth Voke, Markita P. Landry, Amir Ata Saei, and Morteza Mahmoudi
Springer Science and Business Media LLC
AbstractProtein corona, a layer of biomolecules primarily comprising proteins, forms dynamically on nanoparticles in biological fluids and is crucial for predicting nanomedicine safety and efficacy. The protein composition of the corona layer is typically analyzed using liquid chromatography-mass spectrometry (LC-MS/MS). Our recent study, involving identical samples analyzed by 17 proteomics facilities, highlighted significant data variability, with only 1.8% of proteins consistently identified across these centers. Here, we implement an aggregated database search unifying parameters such as variable modifications, enzyme specificity, number of allowed missed cleavages and a stringent 1% false discovery rate at the protein and peptide levels. Such uniform search dramatically harmonizes the proteomics data, increasing the reproducibility and the percentage of consistency-identified unique proteins across distinct cores. Specifically, out of the 717 quantified proteins, 253 (35.3%) are shared among the top 5 facilities (and 16.2% among top 11 facilities). Furthermore, we note that reduction and alkylation are important steps in protein corona sample processing and as expected, omitting these steps reduces the number of total quantified peptides by around 20%. These findings underscore the need for standardized procedures in protein corona analysis, which is vital for advancing clinical applications of nanoscale biotechnologies.


Multifaceted Proteome Analysis at Solubility, Redox, and Expression Dimensions for Target Identification
Amir A. Saei, Albin Lundin, Hezheng Lyu, Hassan Gharibi, Huqiao Luo, Jaakko Teppo, Xuepei Zhang, Massimiliano Gaetani, Ákos Végvári, Rikard Holmdahl,et al.
Wiley
AbstractMultifaceted interrogation of the proteome deepens the system‐wide understanding of biological systems; however, mapping the redox changes in the proteome has so far been significantly more challenging than expression and solubility/stability analyses. Here, the first high‐throughput redox proteomics approach integrated with expression analysis (REX) is devised and combined with the Proteome Integral Solubility Alteration (PISA) assay. The whole PISA‐REX experiment with up to four biological replicates can be multiplexed into a single tandem mass tag TMTpro set. For benchmarking this compact tool, HCT116 cells treated with auranofin are analyzed, showing great improvement compared with previous studies. PISA‐REX is then applied to study proteome remodeling upon stimulation of human monocytes by interferon α (IFN‐α). Applying this tool to study the proteome changes in plasmacytoid dendritic cells (pDCs) isolated from wild‐type versus Ncf1‐mutant mice treated with interferon α, shows that NCF1 deficiency enhances the STAT1 pathway and modulates the expression, solubility, and redox state of interferon‐induced proteins. Providing comprehensive multifaceted information on the proteome, the compact PISA‐REX has the potential to become an industry standard in proteomics and to open new windows into the biology of health and disease.


Standardizing Protein Corona Characterization in Nanomedicine: A Multicenter Study to Enhance Reproducibility and Data Homogeneity
Ali Akbar Ashkarran, Hassan Gharibi, Seyed Majed Modaresi, Amir Ata Saei, and Morteza Mahmoudi
American Chemical Society (ACS)
Our recent findings reveal substantial variability in the characterization of identical protein corona across different proteomics facilities, demonstrating that protein corona datasets are not easily comparable between independent studies. We have shown that heterogeneity in the final composition of the identical protein corona mainly originates from variations in sample preparation protocols, liquid chromatography mass spectrometry (LC-MS) workflows, and raw data processing. Here, to address this issue, we developed standardized protocols and unified sample preparation workflows, and distributed identical protein corona digests to several proteomics centers that performed better in our previous study. Additionally, we examined the influence of using similar mass spectrometry instruments on data homogeneity. Furthermore, we evaluated whether standardizing database search parameters and data processing workflows could enhance data uniformity. More specifically, our new findings reveal a remarkable, stepwise improvement in protein corona data consistency across various proteomics facilities. Streamlining the whole workflow results in a dramatic increase in protein ID overlaps from 11% for good centers to 40% across core facilities that utilized similar instruments and were subjected to a uniform database search. This comprehensive analysis identifies key factors contributing to data heterogeneity in mass spectrometry-based proteomics of protein corona and plasma-related samples. By streamlining these processes, our findings significantly advance the potential for consistent and reliable nanomedicine-based diagnostics and therapeutics across different studies.


Adding Color to Mass Spectra of Biopolymers: Charge Determination Analysis (CHARDA) Assigns Charge State to Every Ion Peak
Yaroslav Lyutvinskiy, Konstantin O. Nagornov, Anton N. Kozhinov, Natalia Gasilova, Laure Menin, Zhaowei Meng, Xuepei Zhang, Amir Ata Saei, Tingting Fu, Julia Chamot-Rooke,et al.
American Chemical Society (ACS)
Traditionally, mass spectrometry (MS) output is the ion abundance plotted versus the ionic mass-to-charge ratio m/z. While employing only commercially available equipment, Charge Determination Analysis (CHARDA) adds a third dimension to MS, estimating for individual peaks their charge states z starting from z = 1 and color coding z in m/z spectra. CHARDA combines the analysis of ion signal decay rates in the time-domain data (transients) in Fourier transform (FT) MS with the interrogation of mass defects (fractional mass) of biopolymers. Being applied to individual isotopic peaks in a complex protein tandem (MS/MS) data set, CHARDA aids peptide mass spectra interpretation by facilitating charge-state deconvolution of large ionic species in crowded regions, estimating z even in the absence of an isotopic distribution (e.g., for monoisotopic mass spectra). CHARDA is fast, robust, and consistent with conventional FTMS and FTMS/MS data acquisition procedures. An effective charge-state resolution Rz ≥ 6 is obtained with the potential for further improvements.


Chemical Proteomics Reveals that the Anticancer Drug Everolimus Affects the Ubiquitin-Proteasome System
Anna A. Lobas, Amir Ata Saei, Hezheng Lyu, Roman A. Zubarev, and Mikhail V. Gorshkov
American Chemical Society (ACS)



Ultralight Ultrafast Enzymes**
Xuepei Zhang, Zhaowei Meng, Christian M. Beusch, Hassan Gharibi, Qing Cheng, Hezheng Lyu, Luciano Di Stefano, Jijing Wang, Amir A. Saei, Ákos Végvári,et al.
Wiley
AbstractInorganic materials depleted of heavy stable isotopes are known to deviate strongly in some physicochemical properties from their isotopically natural counterparts. Here we explored for the first time the effect of simultaneous depletion of the heavy carbon, hydrogen, oxygen and nitrogen isotopes on the bacterium E. coli and the enzymes expressed in it. Bacteria showed faster growth, with most proteins exhibiting higher thermal stability, while for recombinant enzymes expressed in depleted media, faster kinetics was discovered. At room temperature, luciferase, thioredoxin and dihydrofolate reductase and Pfu DNA polymerase showed up to a 250 % increase in activity compared to the native counterparts, with an additional ∼50 % increase at 10 °C. Diminished conformational and vibrational entropy is hypothesized to be the cause of the accelerated kinetics. Ultralight enzymes may find an application where extreme reaction rates are required.


Gel-Assisted Proteome Position Integral Shift Assay Returns Molecular Weight to Shotgun Proteomics and Identifies Caspase 3 Substrates
Zhaowei Meng, Amir Ata Saei, Hassan Gharibi, Xuepei Zhang, Hezheng Lyu, Susanna L. Lundström, Ákos Végvári, Massimiliano Gaetani, and Roman A. Zubarev
American Chemical Society (ACS)
Here, we present a high-throughput virtual top-down proteomics approach that restores the molecular weight (MW) information in shotgun proteomics and demonstrates its utility in studying proteolytic events in programmed cell death. With gel-assisted proteome position integral shift (GAPPIS), we quantified over 7000 proteins in staurosporine-induced apoptotic HeLa cells and identified 84 proteins exhibiting in a statistically significant manner at least two of the following features: (i) a negative MW shift; (ii) an elevated ratio in a pair of a semitryptic and tryptic peptide, (iii) a negative shift in the standard deviation of MW estimated for different peptides, and (iv) a negative shift in skewness of the same data. Of these proteins, 58 molecules were previously unreported caspase 3 substrates. Further analysis identified the preferred cleavage sites consistent with the known caspase cleavages after the DXXD motif. As a powerful tool for high-throughput MW analysis simultaneously with the conventional expression analysis, the GAPPIS assay can prove useful in studying a broad range of biological processes involving proteolytic events.


Multi-omics exploration of biomolecular corona in nanomedicine therapeutics and diagnostics
Amir Ata Saei and Morteza Mahmoudi
Informa UK Limited



Massive Solubility Changes in Neuronal Proteins upon Simulated Traumatic Brain Injury Reveal the Role of Shockwaves in Irreversible Damage
Amir Ata Saei, Hassan Gharibi, Hezheng Lyu, Brady Nilsson, Maryam Jafari, Hans Von Holst, and Roman A. Zubarev
MDPI AG
We investigated the immediate molecular consequences of traumatic brain injuries (TBIs) using a novel proteomics approach. We simulated TBIs using an innovative laboratory apparatus that employed a 5.1 kg dummy head that held neuronal cells and generated a ≤4000 g-force acceleration upon impact. A Proteome Integral Solubility Alteration (PISA) assay was then employed to monitor protein solubility changes in a system-wide manner. Dynamic impacts led to both a reduction in neuron viability and massive solubility changes in the proteome. The affected proteins mapped not only to the expected pathways, such as those of cell adhesion, collagen, and laminin structures, as well as the response to stress, but also to other dense protein networks, such as immune response, complement, and coagulation cascades. The cellular effects were found to be mainly due to the shockwave rather than the g-force acceleration. Soft materials could reduce the impact’s severity only until they were fully compressed. This study shows a way of developing a proteome-based meter for measuring irreversible shockwave-induced cell damage and provides a resource for identifying protein biomarkers of TBIs and potential drug targets for the development of products aimed at primary prevention and intervention.


Sex-Specific Silica Nanoparticle Protein Corona Compositions Exposed to Male and Female BALB/c Mice Plasmas
Ali Akbar Ashkarran, Hassan Gharibi, Jason W. Grunberger, Amir Ata Saei, Nitish Khurana, Raziye Mohammadpour, Hamidreza Ghandehari, and Morteza Mahmoudi
American Chemical Society (ACS)
As various nanoparticles (NPs) are increasingly being used in nanomedicine products for more effective and less toxic therapy and diagnosis of diseases, there is a growing need to understand their biological fate in different sexes. Herein, we report a proof-of-concept result of sex-specific protein corona compositions on the surface of silica NPs as a function of their size and porosity upon incubation with plasma proteins of female and male BALB/c mice. Our results demonstrate substantial differences between male and female protein corona profiles on the surface of silica nanoparticles. By comparing protein abundances between male and female protein coronas of mesoporous silica nanoparticles and Stöber silica nanoparticles of ∼100, 50, and 100 nm in diameter, respectively, we detected 17, 4, and 4 distinct proteins, respectively, that were found at significantly different concentrations for these constructs. These initial findings demonstrate that animal sex can influence protein corona formation on silica NPs as a function of the physicochemical properties. A more thorough consideration of the role of plasma sex would enable nanomedicine community to design and develop safer and more efficient diagnostic and therapeutic nanomedicine products for both sexes.


Multi-omics analysis of magnetically levitated plasma biomolecules
Ali Akbar Ashkarran, Hassan Gharibi, Dalia Abou Zeki, Irina Radu, Farnaz Khalighinejad, Kiandokht Keyhanian, Christoffer K. Abrahamsson, Carolina Ionete, Amir Ata Saei, and Morteza Mahmoudi
Elsevier BV



NCF1-dependent production of ROS protects against lupus by regulating plasmacytoid dendritic cell development and functions
Huqiao Luo, Vilma Urbonaviciute, Amir Ata Saei, Hezheng Lyu, Massimiliano Gaetani, Ákos Végvári, Yanpeng Li, Roman A. Zubarev, and Rikard Holmdahl
American Society for Clinical Investigation
Low capacity to produce ROS because of mutations in neutrophil cytosolic factor 1 (NCF1/p47phox), a component of NADPH oxidase 2 (NOX2) complex, is strongly associated with systemic lupus erythematosus in both humans and mouse models. Here, we aimed to identify the key immune cell type(s) and cellular mechanisms driving lupus pathogenesis under the condition of NCF1-dependent ROS deficiency. Using cell-specific Cre-deleter, human NCF1-339 variant knockin, and transgenic mouse strains, we show that low ROS production in plasmacytoid dendritic cells (pDCs) exacerbated both pristane-induced lupus and a potentially new Y-linked autoimmune accelerating locus–related spontaneous model by promoting pDC accumulation in multiple organs during lupus development, accompanied by elevated IFN-α levels and expression of IFN-stimulated genes. Mechanistic studies revealed that ROS deficiency enhanced pDC generation through the AKT/mTOR pathway and CCR2-mediated migration to tissues, which together with hyperactivation of the redox-sensitive stimulator of interferon genes/IFN-α/JAK1/STAT1 cascade further augmented type I IFN responses. More importantly, by suppressing these pathways, restoration of NOX2-derived ROS specifically in pDCs protected against lupus. These discoveries explain the causative effect of dysfunctional NCF1 in lupus and demonstrate the protective role of pDC-derived ROS in disease development driven by NCF1-dependent ROS deficiency.


Measurements of heterogeneity in proteomics analysis of the nanoparticle protein corona across core facilities
Ali Akbar Ashkarran, Hassan Gharibi, Elizabeth Voke, Markita P. Landry, Amir Ata Saei, and Morteza Mahmoudi
Springer Science and Business Media LLC
AbstractRobust characterization of the protein corona—the layer of proteins that spontaneously forms on the surface of nanoparticles immersed in biological fluids—is vital for prediction of the safety, biodistribution, and diagnostic/therapeutic efficacy of nanomedicines. Protein corona identity and abundance characterization is entirely dependent on liquid chromatography coupled to mass spectroscopy (LC-MS/MS), though the variability of this technique for the purpose of protein corona characterization remains poorly understood. Here we investigate the variability of LC-MS/MS workflows in analysis of identical aliquots of protein coronas by sending them to different proteomics core-facilities and analyzing the retrieved datasets. While the shared data between the cores correlate well, there is considerable heterogeneity in the data retrieved from different cores. Specifically, out of 4022 identified unique proteins, only 73 (1.8%) are shared across the core facilities providing semiquantitative analysis. These findings suggest that protein corona datasets cannot be easily compared across independent studies and more broadly compromise the interpretation of protein corona research, with implications in biomarker discovery as well as the safety and efficacy of our nanoscale biotechnologies.


Proteomics-Compatible Fourier Transform Isotopic Ratio Mass Spectrometry of Polypeptides
Hassan Gharibi, Alexey L. Chernobrovkin, Amir Ata Saei, Xuepei Zhang, Massimiliano Gaetani, Alexander A. Makarov, and Roman A. Zubarev
American Chemical Society (ACS)
Measuring the relative abundances of heavy stable isotopes of the elements C, H, N, and O in proteins is of interest in environmental science, archeology, zoology, medicine, and other fields. The isotopic abundance measurements of the fine structure of immonium ions with ultrahigh resolution mass spectrometry obtained in gas-phase fragmentation of polypeptides have previously uncovered anomalous deuterium enrichment in (hydroxy)proline of bone collagen in marine mammals. Here, we provide a detailed description and validation of this approach and demonstrate per mil-range precision of isotopic ratio measurements in aliphatic residues from proteins and cell lysates. The analysis consists of proteomics-type experiment demanding sub-microgram amounts of a protein sample and providing concomitantly protein sequence data allowing one to verify sample purity and establish its identity. A novel software tool protein amino acid-resolved isotopic ratio mass spectrometry (PAIR-MS) is presented for extracting isotopic ratio data from the raw data files acquired on an Orbitrap mass spectrometer.


First Experimental Evidence for Reversibility of Ammonia Loss from Asparagine
Jijing Wang, Sergey Rodin, Amir Ata Saei, Xuepei Zhang, and Roman A. Zubarev
MDPI AG
Ammonia loss from L-asparaginyls is a nonenzymatic reaction spontaneously occurring in all proteins and eventually resulting in damaging isoaspartate residues that hamper protein function and induce proteinopathy related to aging. Here, we discuss theoretical considerations supporting the possibility of a full repair reaction and present the first experimental evidence of its existence. If confirmed, the true repair of L-asparaginyl deamidation could open new avenues for preventing aging and neurodegenerative diseases.


Mass Spectrometry, Structural Analysis, and Anti-Inflammatory Properties of Photo-Cross-Linked Human Albumin Hydrogels
Shahriar Sharifi, Amir Ata Saei, Hassan Gharibi, Nouf N. Mahmoud, Shannon Harkins, Naruphorn Dararatana, Erika M. Lisabeth, Vahid Serpooshan, Ákos Végvári, Anna Moore,et al.
American Chemical Society (ACS)
Albumin-based hydrogels offer unique benefits such as biodegradability and high binding affinity to various biomolecules, which make them suitable candidates for biomedical applications. Here, we report a non-immunogenic photocurable human serum-based (HSA) hydrogel synthesized by methacryloylation of human serum albumin by methacrylic anhydride (MAA). We used matrix-assisted laser desorption ionization-time-of-flight mass spectrometry, liquid chromatography-tandem mass spectrometry, as well as size exclusion chromatography to evaluate the extent of modification, hydrolytic and enzymatic degradation of methacrylated albumin macromer and its cross-linked hydrogels. The impacts of methacryloylation and cross-linking on alteration of inflammatory response and toxicity were evaluated in vitro using brain-derived HMC3 macrophages and Ex-Ovo chick chorioallantoic membrane assay. Results revealed that the lysines in HSA were the primary targets reacting with MAA, though modification of cysteine, threonine, serine, and tyrosine, with MAA was also confirmed. Both methacrylated HSA and its derived hydrogels were nontoxic and did not induce inflammatory pathways, while significantly reducing macrophage adhesion to the hydrogels; one of the key steps in the process of foreign body reaction to biomaterials. Cytokine and growth factor analysis showed that albumin-based hydrogels demonstrated anti-inflammatory response modulating cellular events in HMC3 macrophages. Ex-Ovo results also confirmed the biocompatibility of HSA macromer and hydrogels along with slight angiogenesis-modulating effects. Photocurable albumin hydrogels may be used as a non-immunogenic platform for various biomedical applications including passivation coatings.


Redox regulation of PTPN22 affects the severity of T-cell-dependent autoimmune inflammation
Jaime James, Yifei Chen, Clara M Hernandez, Florian Forster, Markus Dagnell, Qing Cheng, Amir A Saei, Hassan Gharibi, Gonzalo Fernandez Lahore, Annika Åstrand,et al.
eLife Sciences Publications, Ltd
Chronic autoimmune diseases are associated with mutations in PTPN22, a modifier of T cell receptor (TCR) signaling. As with all protein tyrosine phosphatases, the activity of PTPN22 is redox regulated, but if or how such regulation can modulate inflammatory pathways in vivo is not known. To determine this, we created a mouse with a cysteine-to-serine mutation at position 129 in PTPN22 (C129S), a residue proposed to alter the redox regulatory properties of PTPN22 by forming a disulfide with the catalytic C227 residue. The C129S mutant mouse showed a stronger T-cell-dependent inflammatory response and development of T-cell-dependent autoimmune arthritis due to enhanced TCR signaling and activation of T cells, an effect neutralized by a mutation in Ncf1, a component of the NOX2 complex. Activity assays with purified proteins suggest that the functional results can be explained by an increased sensitivity to oxidation of the C129S mutated PTPN22 protein. We also observed that the disulfide of native PTPN22 can be directly reduced by the thioredoxin system, while the C129S mutant lacking this disulfide was less amenable to reductive reactivation. In conclusion, we show that PTPN22 functionally interacts with Ncf1 and is regulated by oxidation via the noncatalytic C129 residue and oxidation-prone PTPN22 leads to increased severity in the development of T-cell-dependent autoimmunity.


Abnormal (Hydroxy)proline Deuterium Content Redefines Hydrogen Chemical Mass
Hassan Gharibi, Alexey L. Chernobrovkin, Gunilla Eriksson, Amir Ata Saei, Zena Timmons, Andrew C. Kitchener, Daniela C. Kalthoff, Kerstin Lidén, Alexander A. Makarov, and Roman A. Zubarev
American Chemical Society (ACS)
Analysing the δ2H in individual amino acids of proteins extracted from vertebrates, we unexpectedly found in some samples, notably bone collagen from seals, more than twice as much deuterium in proline and hydroxyproline residues than in seawater. This corresponds to at least four times higher δ2H than in any previously reported biogenic sample. We ruled out diet as a plausible mechanism for such anomalous enrichment. This finding puts into question the old adage that you are what you eat. SUMMARY The chemical mass of hydrogen is defined as an interval from the lowest to the highest content of deuterium 2H, hydrogen’s heavy stable isotope. Measurements of the deviations δ2H in the deuterium content from the standard (ocean water, δ2H = 0‰) are used to characterise biological samples, such as animal bone collagen. The results are often interpreted in terms of the trophic level and diet of the animal as well as prevailing climate during its lifetime. The majority of the published bone collagen δ2H data fall into a narrow δ2H range limited to ±100‰. Using novel analysis method, we unexpectedly found greatly higher δ2H values, up to 1500‰, in seal bone collagen. Such anomalous deuterium enrichment is detected only in two amino acid residues, proline and its derivative hydroxyproline, while other residues show much smaller δ2H values. Anomalously high δ2H values, albeit of lower magnitudes, are also found for these residues in other biological sources. This finding substantially expands the upper bound of the hydrogen chemical mass for biogenic sources. Since neither diet nor environment explain these mysteriously high enrichment levels amounting to more than twice deuterium content in sea water, our understanding of stable isotopes in nature, as well as the old adage “you are what you eat”, are put in question.


Breathomics: Review of Sample Collection and Analysis, Data Modeling and Clinical Applications
Maryam Khoubnasabjafari, Mohamad Reza Afshar Mogaddam, Elaheh Rahimpour, Jafar Soleymani, Amir Ata Saei, and Abolghasem Jouyban
Informa UK Limited
Abstract Metabolomics research is rapidly gaining momentum in disease diagnosis, on top of other Omics technologies. Breathomics, as a branch of metabolomics is developing in various frontiers, for early and noninvasive monitoring of disease. This review starts with a brief introduction to metabolomics and breathomics. A number of important technical issues in exhaled breath collection and factors affecting the sampling procedures are presented. We review the recent progress in metabolomics approaches and a summary of their applications on the respiratory and non-respiratory diseases investigated by breath analysis. Recent reports on breathomics studies retrieved from Scopus and Pubmed were reviewed in this work. We conclude that analyzing breath metabolites (both volatile and nonvolatile) is valuable in disease diagnoses, and therefore believe that breathomics will turn into a promising noninvasive discipline in biomarker discovery and early disease detection in personalized medicine. The problem of wide variations in the reported metabolite concentrations from breathomics studies should be tackled by developing more accurate analytical methods and sophisticated numerical analytical alogorithms.


An integrative proteomics method identifies a regulator of translation during stem cell maintenance and differentiation
Pierre Sabatier, Christian M. Beusch, Amir A. Saei, Mike Aoun, Noah Moruzzi, Ana Coelho, Niels Leijten, Magnus Nordenskjöld, Patrick Micke, Diana Maltseva,et al.
Springer Science and Business Media LLC
AbstractDetailed characterization of cell type transitions is essential for cell biology in general and particularly for the development of stem cell-based therapies in regenerative medicine. To systematically study such transitions, we introduce a method that simultaneously measures protein expression and thermal stability changes in cells and provide the web-based visualization tool ProteoTracker. We apply our method to study differences between human pluripotent stem cells and several cell types including their parental cell line and differentiated progeny. We detect alterations of protein properties in numerous cellular pathways and components including ribosome biogenesis and demonstrate that modulation of ribosome maturation through SBDS protein can be helpful for manipulating cell stemness in vitro. Using our integrative proteomics approach and the web-based tool, we uncover a molecular basis for the uncoupling of robust transcription from parsimonious translation in stem cells and propose a method for maintaining pluripotency in vitro.


System-wide identification and prioritization of enzyme substrates by thermal analysis
Amir Ata Saei, Christian M. Beusch, Pierre Sabatier, Juan Astorga Wells, Hassan Gharibi, Zhaowei Meng, Alexey Chernobrovkin, Sergey Rodin, Katja Näreoja, Ann-Gerd Thorsell,et al.
Springer Science and Business Media LLC
AbstractDespite the immense importance of enzyme–substrate reactions, there is a lack of general and unbiased tools for identifying and prioritizing substrate proteins that are modified by the enzyme on the structural level. Here we describe a high-throughput unbiased proteomics method called System-wide Identification and prioritization of Enzyme Substrates by Thermal Analysis (SIESTA). The approach assumes that the enzymatic post-translational modification of substrate proteins is likely to change their thermal stability. In our proof-of-concept studies, SIESTA successfully identifies several known and novel substrate candidates for selenoprotein thioredoxin reductase 1, protein kinase B (AKT1) and poly-(ADP-ribose) polymerase-10 systems. Wider application of SIESTA can enhance our understanding of the role of enzymes in homeostasis and disease, opening opportunities to investigate the effect of post-translational modifications on signal transduction and facilitate drug discovery.


Nanotechnology for Targeted Detection and Removal of Bacteria: Opportunities and Challenges
Mohammad J. Hajipour, Amir Ata Saei, Edward D. Walker, Brian Conley, Yadollah Omidi, Ki‐Bum Lee, and Morteza Mahmoudi
Wiley
AbstractThe emergence of nanotechnology has created unprecedented hopes for addressing several unmet industrial and clinical issues, including the growing threat so‐termed “antibiotic resistance” in medicine. Over the last decade, nanotechnologies have demonstrated promising applications in the identification, discrimination, and removal of a wide range of pathogens. Here, recent insights into the field of bacterial nanotechnology are examined that can substantially improve the fundamental understanding of nanoparticle and bacteria interactions. A wide range of developed nanotechnology‐based approaches for bacterial detection and removal together with biofilm eradication are summarized. The challenging effects of nanotechnologies on beneficial bacteria in the human body and environment and the mechanisms of bacterial resistance to nanotherapeutics are also reviewed.

RECENT SCHOLAR PUBLICATIONS

Ai-driven prediction of cardio-oncology biomarkers through protein corona analysis
A Guha, SA Sadeghi, HH Kunhiraman, F Fang, Q Wang, A Rafieioskouei, ...
Chemical Engineering Journal, 161134 2025



The role of protein corona in advancing plasma proteomics
AA Saei, L Sun, M Mahmoudi
Proteomics 25 (1-2), 2400028 2025



Mapping the GALNT1 substrate landscape with versatile proteomics tools
AA Saei, SL Lundstrm, H Lyu, H Gharibi, W Lu, P Fang, X Zhang, Z Meng, ...
bioRxiv, 2022.08. 24.505189 2024



One-Pot Time-Induced Proteome Integral Solubility Alteration Assay for Automated and Sensitive Drug–Target Identification
Z Meng, AA Saei, H Lyu, M Gaetani, RA Zubarev
Analytical Chemistry 96 (48), 18917-18921 2024



Exploring mechanisms of action in combinatorial therapies through solubility alterations: Advancing AML treatment
E Gholizadeh, E Zangene, U Vadadokhau, D Ritz, JJ Miettinen, ...
bioRxiv, 2024.11. 08.618644 2024



Small molecule modulation of protein corona for deep plasma proteome profiling
AA Ashkarran, H Gharibi, SA Sadeghi, SM Modaresi, Q Wang, TJ Lin, ...
Nature communications 15 (1), 9638 2024



Causality analysis of protein corona composition: phosphatidylcholine-enhances plasma proteome profiling by proteomics
A Rafieioskouei, K Rogale, AA Saei, M Mahmoudi, B Bonakdarpour
bioRxiv, 2024.09. 10.612356 2024



Multifaceted proteome analysis at solubility, redox, and expression dimensions for target identification
AA Saei, A Lundin, H Lyu, H Gharibi, H Luo, J Teppo, X Zhang, M Gaetani, ...
Advanced Science, 2401502 2024



Monitoring Functional Post-Translational Modifications Using a Data-Driven Proteome Informatic Pipeline
P Nickchi, M Mirzaie, M Baumann, AA Saei, M Jafari
2024



Gel-Assisted Proteome Position Integral Shift Assay Returns Molecular Weight to Shotgun Proteomics and Identifies Caspase 3 Substrates
Z Meng, AA Saei, H Gharibi, X Zhang, H Lyu, SL Lundström, Vgvri, ...
Analytical Chemistry 96 (33), 13533-13541 2024



ThermoTargetMiner as a proteome integral solubility alteration target database for prospective drugs against lung cancer
H Lyu, H Gharibi, B Sokolova, A Voiland, B Nilsson, Z Meng, M Gaetani, ...
bioRxiv, 2024.08. 06.606599 2024



Standardizing protein corona characterization in nanomedicine: a multicenter study to enhance reproducibility and data homogeneity
AA Ashkarran, H Gharibi, SM Modaresi, AA Saei, M Mahmoudi
Nano Letters 24 (32), 9874-9881 2024



Multi-omics exploration of biomolecular corona in nanomedicine therapeutics and diagnostics
AA Saei, M Mahmoudi
Nanomedicine 19 (14), 1223-1226 2024



Adding Color to Mass Spectra of Biopolymers: Charge Determination Analysis (CHARDA) Assigns Charge State to Every Ion Peak
Y Lyutvinskiy, KO Nagornov, AN Kozhinov, N Gasilova, L Menin, Z Meng, ...
Journal of the American Society for Mass Spectrometry 35 (5), 902-911 2024



Do light eaters live shorter lives? The case of ultralight Caenorhabditis elegans
X Zhang, H Gharibi, CM Beusch, Z Meng, AA Saei, M Gaetani, ...
bioRxiv, 2024.02. 13.580069 2024



Chemical Proteomics Reveals that the Anticancer Drug Everolimus Affects the Ubiquitin–Proteasome System
AA Lobas, AA Saei, H Lyu, RA Zubarev, MV Gorshkov
ACS Pharmacology & Translational Science 2024



Ultralight ultrafast enzymes
X Zhang, Z Meng, C Beusch, H Gharibi, Q Cheng, H Lyu, L Di Stefano, ...
Angewandte Chemie, e202316488 2024



A uniform data processing pipeline enables harmonized nanoparticle protein corona analysis across proteomics core facilities
H Gharibi, AA Ashkarran, M Jafari, E Voke, MP Landry, AA Saei, ...
Nature Communications 15 (1), 342 2024



Antibiotics that Kill Gram-negative Bacteria by Restructuring the Outer Membrane Protein BamA
SM Modaresi, R Sugiyama, NDT Tram, RP Jakob, CS Phan, AA Saei, ...
bioRxiv, 2024.12. 16.628070 2024



DORSSAA: Drug-target interactOmics Resource based on Stability/Solubility Alteration Assay
E Zangene, E Gholizadeh, AA Saei, M Wilhelm, M Jafari
bioRxiv, 2023.12. 29.573639 2023

MOST CITED SCHOLAR PUBLICATIONS

Superparamagnetic iron oxide nanoparticles for delivery of therapeutic agents: opportunities and challenges
S Laurent, AA Saei, S Behzadi, A Panahifar, M Mahmoudi
Expert opinion on drug delivery 11 (9), 1449-1470 2014
Citations: 529



Proteome integral solubility alteration: a high-throughput proteomics assay for target deconvolution
M Gaetani, P Sabatier, AA Saei, CM Beusch, Z Yang, SL Lundström, ...
Journal of proteome research 18 (11), 4027-4037 2019
Citations: 233



Targeted superparamagnetic iron oxide nanoparticles for early detection of cancer: Possibilities and challenges
Z Bakhtiary, AA Saei, MJ Hajipour, M Raoufi, O Vermesh, M Mahmoudi
Nanomedicine: Nanotechnology, Biology and Medicine 12 (2), 287-307 2016
Citations: 217



Electrochemical biosensors for glucose based on metal nanoparticles
AA Saei, JE NazhadDolatabadi, P Najafi-Marandi, A Abhari, M Guardia
TrAC Trends in Analytical Chemistry 2013
Citations: 207



Theranostic MUC-1 aptamer targeted gold coated superparamagnetic iron oxide nanoparticles for magnetic resonance imaging and photothermal therapy of colon cancer
M Azhdarzadeh, F Atyabi, AA Saei, BS Varnamkhasti, Y Omidi, M Fateh, ...
Colloids and Surfaces B: Biointerfaces 143, 224-232 2016
Citations: 165



Repurposing of auranofin: Thioredoxin reductase remains a primary target of the drug
X Zhang, K Selvaraju, AA Saei, P D'Arcy, RA Zubarev, ESJ Arnr, ...
Biochimie 162, 46-54 2019
Citations: 159



Superparamagnetic iron oxide nanoparticles for in vivo molecular and cellular imaging
S Sharifi, H Seyednejad, S Laurent, F Atyabi, AA Saei, M Mahmoudi
Contrast media & molecular imaging 10 (5), 329-355 2015
Citations: 151



Microparticles containing erlotinib-loaded solid lipid nanoparticles for treatment of non-small cell lung cancer
Z Bakhtiary, J Barar, A Aghanejad, AA Saei, E Nemati, ...
Drug development and industrial pharmacy 43 (8), 1244-1253 2017
Citations: 143



Nanoparticle surface functionality dictates cellular and systemic toxicity
AA Saei, M Yazdani, SE Lohse, Z Bakhtiary, V Serpooshan, M Ghavami, ...
Chemistry of Materials 29 (16), 6578-6595 2017
Citations: 116



Cellular toxicity of nanogenomedicine in MCF-7 cell line: MTT assay
S Ahmadian, J Barar, AA Saei, MAA Fakhree, Y Omidi
Journal of visualized experiments: JoVE, 1191 2009
Citations: 108



Nanotoxicology: advances and pitfalls in research methodology
M Azhdarzadeh, AA Saei, S Sharifi, MJ Hajipour, AM Alkilany, ...
Nanomedicine 10 (18), 2931-2952 2015
Citations: 98



Comprehensive chemical proteomics for target deconvolution of the redox active drug auranofin
AA Saei, H Gullberg, P Sabatier, CM Beusch, K Johansson, B Lundgren, ...
Redox biology 32, 101491 2020
Citations: 89



An update to space biomedical research: tissue engineering in microgravity bioreactors
A Barzegari, AA Saei
BioImpacts: BI 2 (1), 23 2012
Citations: 87



ProTargetMiner as a proteome signature library of anticancer molecules for functional discovery
AA Saei, CM Beusch, A Chernobrovkin, P Sabatier, B Zhang, G Tokat, ...
Nature communications 10 (1), 5715 2019
Citations: 75



The Microbiome: The Forgotten Organ of the Astronaut‘s Body–Probiotics beyond Terrestrial Limits
AA Saei, A Barzegari
Future microbiology 7 (9), 1037-1046 2012
Citations: 69



Nanotechnology for targeted detection and removal of bacteria: opportunities and challenges
MJ Hajipour, AA Saei, ED Walker, B Conley, Y Omidi, KB Lee, ...
Advanced Science 8 (21), 2100556 2021
Citations: 68



System-wide identification and prioritization of enzyme substrates by thermal analysis
AA Saei, CM Beusch, P Sabatier, JA Wells, H Gharibi, Z Meng, ...
Nature communications 12 (1), 1296 2021
Citations: 64



Inhibition of survivin restores the sensitivity of breast cancer cells to docetaxel and vinblastine
P Ghanbari, M Mohseni, M Tabasinezhad, B Yousefi, AA Saei, S Sharifi, ...
Applied biochemistry and biotechnology 174, 667-681 2014
Citations: 62



Sphingosin 1-phosphate contributes in tumor progression
M Tabasinezhad, N Samadi, P Ghanbari, M Mohseni, AA Saei, S Sharifi, ...
Journal of cancer research and therapeutics 9 (4), 556-563 2013
Citations: 60



Measurements of heterogeneity in proteomics analysis of the nanoparticle protein corona across core facilities
AA Ashkarran, H Gharibi, E Voke, MP Landry, AA Saei, M Mahmoudi
Nature Communications 13 (1), 6610 2022
Citations: 52