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Hayashi SY, Craddock BP, Miller WT. Effects of heterologous kinase domains on growth factor receptor specificity. Cell Signal 2024; 122:111307. [PMID: 39048037 DOI: 10.1016/j.cellsig.2024.111307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 07/02/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024]
Abstract
The kinase domains of receptor tyrosine kinases (RTKs) are highly conserved, yet they are able to discriminate among potential substrates to selectively activate downstream signaling pathways. In this study, we tested the importance of catalytic domain specificity by creating two series of chimeric RTKs. In one set, the kinase domain of insulin-like growth factor I receptor (IGF1R) was replaced by the kinase domains from insulin receptor (IR), macrophage stimulating protein 1 receptor/Ron (Ron) or Src. In the other set of chimeras, the kinase domain of epidermal growth factor receptor (EGFR) was similarly replaced by the kinase domains of IR, Ron, or Src. We expressed the wild-type and chimeric forms of the receptors in mammalian cells. For some signaling events, such as recognition of IRS1, the identity of the tyrosine kinase catalytic domain did not appear to be crucial. In contrast, recognition of some sites, such as the C-terminal autophosphorylation sites on EGFR, did depend on the identity of the kinase domain. Our data also showed that ligand dependence was lost when the native kinase domains were replaced by Src, suggesting that the identity of the kinase domains could be important for proper receptor regulation. Overall, the results are consistent with the idea that the fidelity of RTK signaling depends on co-localization and targeting with substrates, as well as on the intrinsic specificity of the kinase domain.
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Affiliation(s)
- Samantha Y Hayashi
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY, USA 11794
| | - Barbara P Craddock
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY, USA 11794
| | - W Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY, USA 11794; Department of Veterans Affairs Medical Center, Northport, NY 11768, USA.
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Tirado TC, Machado KC, Shigunov P, Batista M, Figueiredo FB. A peptide dataset for target analysis of human complement system proteins. Data Brief 2024; 53:110217. [PMID: 38445196 PMCID: PMC10912339 DOI: 10.1016/j.dib.2024.110217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/15/2024] [Accepted: 02/15/2024] [Indexed: 03/07/2024] Open
Abstract
The targeted LC-MS/MS method has been widely applied for peptide quantification, offering sensibility, specificity, and reproducibility to the analysis. However, it requires the prior selection of targets, including the construction of a spectral library. Here, we present a dataset comprising peptide mass spectra for targeted LC-MS/MS method setup, applied to a set of human complement system proteins. Additionally, we selected a group of peptides and demonstrated their stability and reproducibility in quantification. This dataset is invaluable for studies aiming at the quantification of the complement system proteins by targeted LC-MS/MS, as it provides data for spectral library construction and a list of selected peptides.
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Affiliation(s)
- Thais Cristina Tirado
- Laboratório de Biologia Celular, Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCruz), Curitiba, Paraná, Brazil
- Laboratório de Referência em Leishmanioses, Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCruz), Curitiba, Paraná, Brazil
| | - Kelly Cavalcanti Machado
- Plataforma de Espectrometria de Massas RPT02H, Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCruz), Curitiba, Paraná, Brazil
| | - Patrícia Shigunov
- Laboratório de Biologia Básica de Células-Tronco, Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCruz), Curitiba, Paraná, Brazil
| | - Michel Batista
- Plataforma de Espectrometria de Massas RPT02H, Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCruz), Curitiba, Paraná, Brazil
| | - Fabiano Borges Figueiredo
- Laboratório de Biologia Celular, Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCruz), Curitiba, Paraná, Brazil
- Laboratório de Referência em Leishmanioses, Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCruz), Curitiba, Paraná, Brazil
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Schwaner C, Barbosa M, Haley J, Pales Espinosa E, Allam B. Transcriptomics, proteomics, and physiological assays reveal immunosuppression in the eastern oyster Crassostrea virginica exposed to acidification stress. FISH & SHELLFISH IMMUNOLOGY 2024; 146:109366. [PMID: 38218419 DOI: 10.1016/j.fsi.2024.109366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 01/15/2024]
Abstract
Ocean acidification (OA) is recognized as a major stressor for a broad range of marine organisms, particularly shell-building invertebrates. OA can cause alterations in various physiological processes such as growth and metabolism, although its effect on host-pathogen interactions remains largely unexplored. In this study, we used transcriptomics, proteomics, and physiological assays to evaluate changes in immunity of the eastern oyster Crassostrea virginica exposed to OA conditions (pH = 7.5 vs pH = 7.9) at various life stages. The susceptibility of oyster larvae to Vibrio infection increased significantly (131 % increase in mortality) under OA conditions, and was associated with significant changes in their transcriptomes. The significantly higher mortality of larvae exposed to pathogens and acidification stress could be the outcome of an increased metabolic demand to cope with acidification stress (as seen by upregulation of metabolic genes) at the cost of immune function (downregulation of immune genes). While larvae were particularly vulnerable, juveniles appeared more robust to the stressors and there were no differences in mortality after pathogen (Aliiroseovarius crassostrea and Vibrio spp.) exposure. Proteomic investigations in adult oysters revealed that acidification stress resulted in a significant downregulation of mucosal immune proteins including those involved in pathogen recognition and microbe neutralization, suggesting weakened mucosal immunity. Hemocyte function in adults was also impaired by high pCO2, with a marked reduction in phagocytosis (67 % decrease in phagocytosis) in OA conditions. Together, results suggest that OA impairs immune function in the eastern oyster making them more susceptible to pathogen-induced mortality outbreaks. Understanding the effect of multiple stressors such as OA and disease is important for accurate predictions of how oysters will respond to future climate regimes.
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Affiliation(s)
- Caroline Schwaner
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook NY, 11790, USA
| | - Michelle Barbosa
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook NY, 11790, USA
| | - John Haley
- Stony Brook University, Biological Mass Spectrometry Center, Stony Brook Medicine, Stony Brook, NY, 11790, USA
| | | | - Bassem Allam
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook NY, 11790, USA.
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Proteomic and Transcriptomic Responses Enable Clams to Correct the pH of Calcifying Fluids and Sustain Biomineralization in Acidified Environments. Int J Mol Sci 2022; 23:ijms232416066. [PMID: 36555707 PMCID: PMC9781830 DOI: 10.3390/ijms232416066] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/09/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Seawater pH and carbonate saturation are predicted to decrease dramatically by the end of the century. This process, designated ocean acidification (OA), threatens economically and ecologically important marine calcifiers, including the northern quahog (Mercenaria mercenaria). While many studies have demonstrated the adverse impacts of OA on bivalves, much less is known about mechanisms of resilience and adaptive strategies. Here, we examined clam responses to OA by evaluating cellular (hemocyte activities) and molecular (high-throughput proteomics, RNASeq) changes in hemolymph and extrapallial fluid (EPF-the site of biomineralization located between the mantle and the shell) in M. mercenaria continuously exposed to acidified (pH ~7.3; pCO2 ~2700 ppm) and normal conditions (pH ~8.1; pCO2 ~600 ppm) for one year. The extracellular pH of EPF and hemolymph (~7.5) was significantly higher than that of the external acidified seawater (~7.3). Under OA conditions, granulocytes (a sub-population of hemocytes important for biomineralization) were able to increase intracellular pH (by 54% in EPF and 79% in hemolymph) and calcium content (by 56% in hemolymph). The increased pH of EPF and hemolymph from clams exposed to high pCO2 was associated with the overexpression of genes (at both the mRNA and protein levels) related to biomineralization, acid-base balance, and calcium homeostasis, suggesting that clams can use corrective mechanisms to mitigate the negative impact of OA.
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Alvarez FA, Kaddour H, Lyu Y, Preece C, Cohen J, Baer L, Stopeck AT, Thompson P, Okeoma CM. Blood plasma derived extracellular vesicles (BEVs): particle purification liquid chromatography (PPLC) and proteomic analysis reveals BEVs as a potential minimally invasive tool for predicting response to breast cancer treatment. Breast Cancer Res Treat 2022; 196:423-437. [PMID: 36114323 PMCID: PMC10560447 DOI: 10.1007/s10549-022-06733-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 08/28/2022] [Indexed: 11/02/2022]
Abstract
PURPOSE Circulating blood plasma derived extracellular vesicles (BEVs) containing proteins hold promise for their use as minimally invasive biomarkers for predicting response to cancer therapy. The main goal of this study was to establish the efficiency and utility of the particle purification liquid chromatography (PPLC) BEV isolation method and evaluate the role of BEVs in predicting breast cancer (BC) patient response to neoadjuvant chemotherapy (NAC). METHODS PPLC isolation was used to separate BEVs from non-EV contaminants and characterize BEVs from 17 BC patients scheduled to receive NAC. Using LC-MS/MS, we compared the proteome of PPLC-isolated BEVs from patients (n = 7) that achieved a pathological complete response (pCR) after NAC (responders [R]) to patients (n = 10) who did not achieve pCR (non-responders [NR]). Luminal MCF7 and basaloid MDA-MB-231 BC cells were treated with isolated BEVs and evaluated for metabolic activity by MTT assay. RESULTS NR had elevated BEV concentrations and negative zeta potential (ζ-potential) prior to receipt of NAC. Eight proteins were enriched in BEVs of NR. GP1BA (CD42b), PECAM-1 (CD31), CAPN1, HSPB1 (HSP27), and ANXA5 were validated using western blot. MTT assay revealed BEVs from R and NR patients increased metabolic activity of MCF7 and MDA-MB-231 BC cells and the magnitude was highest in MCF7s treated with NR BEVs. CONCLUSION PPLC-based EV isolation provides a preanalytical separation process for BEVs devoid of most contaminants. Our findings suggest that PPLC-isolated BEVs and the five associated proteins may be established as predictors of chemoresistance, and thus serve to identify NR to spare them the toxic effects of NAC.
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Affiliation(s)
- Folnetti A Alvarez
- Department of Pharmacology, Stony Brook University Renaissance School of Medicine, Stony Brook, NY, 11794-8651, USA
| | - Hussein Kaddour
- Department of Pharmacology, Stony Brook University Renaissance School of Medicine, Stony Brook, NY, 11794-8651, USA
- Regeneron Pharmaceuticals, Inc, Tarrytown, NY, 10591, USA
| | - Yuan Lyu
- Department of Pharmacology, Stony Brook University Renaissance School of Medicine, Stony Brook, NY, 11794-8651, USA
- Medical Research Center, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Christina Preece
- Department of Pathology, Stony Brook University Renaissance School of Medicine, Stony Brook, NY, 11794-8651, USA
- Department of Medicine, Cedars Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Jules Cohen
- Department of Medicine, Division of Hematology and Medical Oncology, Stony Brook University, Stony Brook, NY, 11794-8651, USA
- Stony Brook University Cancer Center, Stony Brook, NY, 11794-8651, USA
| | - Lea Baer
- Department of Medicine, Division of Hematology and Medical Oncology, Stony Brook University, Stony Brook, NY, 11794-8651, USA
- Stony Brook University Cancer Center, Stony Brook, NY, 11794-8651, USA
| | - Alison T Stopeck
- Department of Medicine, Division of Hematology and Medical Oncology, Stony Brook University, Stony Brook, NY, 11794-8651, USA
- Stony Brook University Cancer Center, Stony Brook, NY, 11794-8651, USA
| | - Patricia Thompson
- Department of Pathology, Stony Brook University Renaissance School of Medicine, Stony Brook, NY, 11794-8651, USA
- Stony Brook University Cancer Center, Stony Brook, NY, 11794-8651, USA
| | - Chioma M Okeoma
- Department of Pharmacology, Stony Brook University Renaissance School of Medicine, Stony Brook, NY, 11794-8651, USA.
- Department of Pathology, Microbiology, and Immunology, New York Medical College, Valhalla, NY, 10595-1524, USA.
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Schwaner C, Farhat S, Haley J, Pales Espinosa E, Allam B. Transcriptomic, Proteomic, and Functional Assays Underline the Dual Role of Extrapallial Hemocytes in Immunity and Biomineralization in the Hard Clam Mercenaria mercenaria. Front Immunol 2022; 13:838530. [PMID: 35273613 PMCID: PMC8902148 DOI: 10.3389/fimmu.2022.838530] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/28/2022] [Indexed: 12/13/2022] Open
Abstract
Circulating hemocytes in the hemolymph represent the backbone of innate immunity in bivalves. Hemocytes are also found in the extrapallial fluid (EPF), the space delimited between the shell and the mantle, which is the site of shell biomineralization. This study investigated the transcriptome, proteome, and function of EPF and hemolymph in the hard clam Mercenaria mercenaria. Total and differential hemocyte counts were similar between EPF and hemolymph. Overexpressed genes in the EPF were found to have domains previously identified as being part of the "biomineralization toolkit" and involved in bivalve shell formation. Biomineralization related genes included chitin-metabolism genes, carbonic anhydrase, perlucin, and insoluble shell matrix protein genes. Overexpressed genes in the EPF encoded proteins present at higher abundances in the EPF proteome, specifically those related to shell formation such as carbonic anhydrase and insoluble shell matrix proteins. Genes coding for bicarbonate and ion transporters were also overexpressed, suggesting that EPF hemocytes are involved in regulating the availability of ions critical for biomineralization. Functional assays also showed that Ca2+ content of hemocytes in the EPF were significantly higher than those in hemolymph, supporting the idea that hemocytes serve as a source of Ca2+ during biomineralization. Overexpressed genes and proteins also contained domains such as C1q that have dual functions in biomineralization and immune response. The percent of phagocytic granulocytes was not significantly different between EPF and hemolymph. Together, these findings suggest that hemocytes in EPF play a central role in both biomineralization and immunity.
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Affiliation(s)
- Caroline Schwaner
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States
| | - Sarah Farhat
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States
| | - John Haley
- Stony Brook University Biological Mass Spectrometry Center, Stony Brook Medicine, Stony Brook, NY, United States
| | | | - Bassem Allam
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States
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