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Lee Y, Ni J, Beretov J, Wasinger VC, Graham P, Li Y. Recent advances of small extracellular vesicle biomarkers in breast cancer diagnosis and prognosis. Mol Cancer 2023; 22:33. [PMID: 36797736 PMCID: PMC9933347 DOI: 10.1186/s12943-023-01741-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 02/06/2023] [Indexed: 02/18/2023] Open
Abstract
Current clinical tools for breast cancer (BC) diagnosis are insufficient but liquid biopsy of different bodily fluids has recently emerged as a minimally invasive strategy that provides a real-time snapshot of tumour biomarkers for early diagnosis, active surveillance of progression, and post-treatment recurrence. Extracellular vesicles (EVs) are nano-sized membranous structures 50-1000 nm in diameter that are released by cells into biological fluids. EVs contain proteins, nucleic acids, and lipids which play pivotal roles in tumourigenesis and metastasis through cell-to-cell communication. Proteins and miRNAs from small EVs (sEV), which range in size from 50-150 nm, are being investigated as a potential source for novel BC biomarkers using mass spectrometry-based proteomics and next-generation sequencing. This review covers recent developments in sEV isolation and single sEV analysis technologies and summarises the sEV protein and miRNA biomarkers identified for BC diagnosis, prognosis, and chemoresistance. The limitations of current sEV biomarker research are discussed along with future perspective applications.
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Affiliation(s)
- Yujin Lee
- grid.1005.40000 0004 4902 0432St. George and Sutherland Clinical Campuses, School of Clinical Medicine, UNSW Sydney, Kensington, NSW 2052 Australia ,grid.416398.10000 0004 0417 5393Cancer Care Centre, St. George Hospital, Kogarah, NSW 2217 Australia
| | - Jie Ni
- grid.1005.40000 0004 4902 0432St. George and Sutherland Clinical Campuses, School of Clinical Medicine, UNSW Sydney, Kensington, NSW 2052 Australia ,grid.416398.10000 0004 0417 5393Cancer Care Centre, St. George Hospital, Kogarah, NSW 2217 Australia
| | - Julia Beretov
- grid.1005.40000 0004 4902 0432St. George and Sutherland Clinical Campuses, School of Clinical Medicine, UNSW Sydney, Kensington, NSW 2052 Australia ,grid.416398.10000 0004 0417 5393Cancer Care Centre, St. George Hospital, Kogarah, NSW 2217 Australia ,grid.416398.10000 0004 0417 5393Anatomical Pathology, NSW Health Pathology, St. George Hospital, Kogarah, NSW 2217 Australia
| | - Valerie C. Wasinger
- grid.1005.40000 0004 4902 0432Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, UNSW Sydney, Kensington, NSW 2052 Australia ,grid.1005.40000 0004 4902 0432School of Medical Science, UNSW Sydney, Kensington, NSW 2052 Australia
| | - Peter Graham
- grid.1005.40000 0004 4902 0432St. George and Sutherland Clinical Campuses, School of Clinical Medicine, UNSW Sydney, Kensington, NSW 2052 Australia ,grid.416398.10000 0004 0417 5393Cancer Care Centre, St. George Hospital, Kogarah, NSW 2217 Australia
| | - Yong Li
- St. George and Sutherland Clinical Campuses, School of Clinical Medicine, UNSW Sydney, Kensington, NSW, 2052, Australia. .,Cancer Care Centre, St. George Hospital, Kogarah, NSW, 2217, Australia.
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Sowers ML, Tang H, Singh VK, Khan A, Mishra A, Restrepo BI, Jagannath C, Zhang K. Multi-OMICs analysis reveals metabolic and epigenetic changes associated with macrophage polarization. J Biol Chem 2022; 298:102418. [PMID: 36030823 PMCID: PMC9525912 DOI: 10.1016/j.jbc.2022.102418] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 12/04/2022] Open
Abstract
Macrophages (MФ) are an essential immune cell for defense and repair that travel to different tissues and adapt based on local stimuli. A critical factor that may govern their polarization is the crosstalk between metabolism and epigenetics. However, simultaneous measurements of metabolites, epigenetics, and proteins (phenotype) have been a major technical challenge. To address this, we have developed a novel triomics approach using mass spectrometry to comprehensively analyze metabolites, proteins, and histone modifications in a single sample. To demonstrate this technique, we investigated the metabolic-epigenetic-phenotype axis following polarization of human blood–derived monocytes into either ‘proinflammatory M1-’ or ‘anti-inflammatory M2-’ MФs. We report here a complex relationship between arginine, tryptophan, glucose, and the citric acid cycle metabolism, protein and histone post-translational modifications, and human macrophage polarization that was previously not described. Surprisingly, M1-MФs had globally reduced histone acetylation levels but high levels of acetylated amino acids. This suggests acetyl-CoA was diverted, in part, toward acetylated amino acids. Consistent with this, stable isotope tracing of glucose revealed reduced usage of acetyl-CoA for histone acetylation in M1-MФs. Furthermore, isotope tracing also revealed MФs uncoupled glycolysis from the tricarboxylic acid cycle, as evidenced by poor isotope enrichment of succinate. M2-MФs had high levels of kynurenine and serotonin, which are reported to have immune-suppressive effects. Kynurenine is upstream of de novo NAD+ metabolism that is a necessary cofactor for Sirtuin-type histone deacetylases. Taken together, we demonstrate a complex interplay between metabolism and epigenetics that may ultimately influence cell phenotype.
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Affiliation(s)
- Mark L Sowers
- Dept. of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX
| | - Hui Tang
- Dept. of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX
| | - Vipul K Singh
- Dept. of Pathology and Genomic Medicine, Center for Molecular and Translational Human Infectious Diseases Research Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX
| | - Arshad Khan
- Dept. of Pathology and Genomic Medicine, Center for Molecular and Translational Human Infectious Diseases Research Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX
| | - Abhishek Mishra
- Dept. of Pathology and Genomic Medicine, Center for Molecular and Translational Human Infectious Diseases Research Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX
| | | | - Chinnaswamy Jagannath
- Dept. of Pathology and Genomic Medicine, Center for Molecular and Translational Human Infectious Diseases Research Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX.
| | - Kangling Zhang
- Dept. of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX.
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Cyst stem cell lineage eIF5 non-autonomously prevents testicular germ cell tumor formation via eIF1A/eIF2γ-mediated pre-initiation complex. Stem Cell Res Ther 2022; 13:351. [PMID: 35883200 PMCID: PMC9327282 DOI: 10.1186/s13287-022-03025-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 07/02/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Stem cell niche maintains stem cell population identity and is essential for the homeostasis of self-renewal and differentiation in Drosophila testes. However, the mechanisms of CySC lineage signals-mediated soma-germline communications in response to external stimuli are unclear. METHODS Pre-initiation complex functions were evaluated by UAS-Gal4-mediated cell effects. RNA sequencing was conducted in NC and eIF5 siRNA-treated cells. Genetic interaction analysis was used to indicate the relationships between eIF5 and eIF1A/eIF2γ in Drosophila testes. RESULTS Here, we demonstrated that in CySCs, translation initiation factor eIF5 mediates cyst cell differentiation and the non-autonomously affected germ cell differentiation process. CySCs lacking eIF5 displayed unbalanced cell proliferation and apoptosis, forming testicular germ cell tumors (TGCTs) during spermatogenesis. eIF5 transcriptional regulation network analysis identified multiple metabolic processes and several key factors that might be involved in germ cell differentiation and TGCT formation. Importantly, knockdown of eIF1A and eIF2γ, key components of pre-initiation complex, mimicked the phenotype of knocking down eIF5 in the stem cell niche of Drosophila testes. Genetic interaction analysis indicated that eIF5 was sufficient to rescue the phenotype of tumorlike structures induced by down-regulating eIF1A or eIF2γ in CySCs. CONCLUSIONS These findings demonstrated that CySC lineage eIF5, together with eIF1A or eIF2γ, mediates soma-germline communications for the stem cell niche homeostasis in Drosophila testes, providing new insights for the prevention of TGCTs.
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Patil NY, Tang H, Rus I, Zhang K, Joshi AD. Decoding Cinnabarinic Acid-Specific Stanniocalcin 2 Induction by Aryl Hydrocarbon Receptor. Mol Pharmacol 2022; 101:45-55. [PMID: 34764210 PMCID: PMC8969126 DOI: 10.1124/molpharm.121.000376] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/17/2021] [Indexed: 01/03/2023] Open
Abstract
Aryl hydrocarbon receptor (AhR) is a ligand-mediated transcription factor known for regulating response to xenobiotics, including prototypical 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) through the activation of CYP1A1 expression. Upon ligand-binding, AhR translocates to the nucleus, interacts with the AhR nuclear translocator, and binds to xenobiotic response elements (XREs; GCGTG) present in the promoter region of AhR-regulated genes. Recently, we identified a novel tryptophan catabolite, cinnabarinic acid (CA), as an endogenous AhR agonist capable of activating expression of AhR target gene stanniocalcin 2 (stc2). The CA-driven stc2 induction bestowed cytoprotection against hepatotoxicity in an AhR-dependent manner. Interestingly, only CA but not TCDD was able to induce stc2 expression in liver, and CA was unable to upregulate the TCDD responsive cyp1a1 gene. In this report, we identified CA-specific histone H4 lysine 5 acetylation and H3 lysine 79 methylation at the AhR-bound stc2 promoter. Moreover, histone H4 lysine 5 acetylation writer, activating transcription factor 2 (Atf2), and H3 lysine 79 methylation writer, disruptor of telomeric silencing 1-like histone lysine methyltransferase (Dot1l), were interacting with the AhR complex at the stc2 promoter exclusively in response to CA treatment concurrent with the histone epigenetic marks. Suppressing Atf2 and Dot1l expression using RNA interference confirmed their role in stc2 expression. CRISPR/Cas9-assisted replacement of cyp1a1 promoter-encompassing XREs with stc2 promoter XREs resulted in CA-dependent induction of cyp1a1, underlining a fundamental role of quaternary structure of XRE sequence in agonist-specific gene regulation. In conclusion, CA-driven recruitment of specific chromatin regulators to the AhR complex and resulting histone epigenetic modifications may serve as a molecular basis for agonist-specific stc2 regulation by AhR. SIGNIFICANCE STATEMENT: Results reported here provide a mechanistic explanation for the agonist-specific differential gene regulation by identifying interaction of aryl hydrogen receptor with specific chromatin regulators concomitant with unique histone epigenetic marks. This study also demonstrated that the agonist-specific target-gene expression can be transferred with the gene-specific promoter xenobiotic response element-sequence in the context of chromatin architecture.
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Affiliation(s)
- Nikhil Y Patil
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma (N.Y.P., I.R., A.D.J.); and Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas (H.T., K.Z.)
| | - Hui Tang
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma (N.Y.P., I.R., A.D.J.); and Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas (H.T., K.Z.)
| | - Iulia Rus
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma (N.Y.P., I.R., A.D.J.); and Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas (H.T., K.Z.)
| | - Kangling Zhang
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma (N.Y.P., I.R., A.D.J.); and Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas (H.T., K.Z.)
| | - Aditya D Joshi
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma (N.Y.P., I.R., A.D.J.); and Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas (H.T., K.Z.)
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Yao L, Guo Y, Zhang X, Xu C, Wang Y, Liu X, Wang Y, Li Y, Qi Y, Sha J, Qin C, Yang X, Guo X. Quantitative proteomic biomarkers from extracellular vesicles of human seminal plasma in the differential diagnosis of azoospermia. Clin Transl Med 2021; 11:e423. [PMID: 34047465 PMCID: PMC8161617 DOI: 10.1002/ctm2.423] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/25/2021] [Accepted: 05/01/2021] [Indexed: 12/18/2022] Open
Affiliation(s)
- Liping Yao
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Yueshuai Guo
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Xiangzheng Zhang
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Chen Xu
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Yichun Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaofei Liu
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Yue Wang
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Yan Li
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Yaling Qi
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Jiahao Sha
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Chao Qin
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaoyu Yang
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China.,Clinical Center of Reproductive Medicine, The First Hospital of Nanjing Medical University, Nanjing, China
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
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Wang Y, Wang M, Li M, Zhao T, Zhou L. Cinnamaldehyde inhibits the growth of Phytophthora capsici through disturbing metabolic homoeostasis. PeerJ 2021; 9:e11339. [PMID: 33987017 PMCID: PMC8092109 DOI: 10.7717/peerj.11339] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/03/2021] [Indexed: 11/20/2022] Open
Abstract
Background Phytophthora capsici Leonian (P. capsici) can cause wilting and roots rotting on pepper and other cash crops. The new fungicide cinnamaldehyde (CA) has high activity against this pathogen. However, its potential mechanism is still unknown. Methods In order to gain insights into the mechanism, isobaric tags for relative and absolute quantification (iTRAQ)-based quantitative proteomics was used to analyze P. capsici treated with CA. The iTRAQ results were evaluated by parallel reaction monitoring (PRM) analysis and quantitative real-time PCR (qRT-PCR) analysis. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was used to speculate the biochemical pathways that the agent may act on. Results The results showed that 1502 differentially expressed proteins were identified, annotated and classified into 209 different terms (like metabolic process, cellular process, single-organism process) based on Gene Ontology (GO) functional enrichment analysis and nine different pathways (glyoxylate and dicarboxylate metabolism, fatty acid metabolism and so on) based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. This study suggested that CA disordered fatty acid metabolism, polysaccharide metabolism and leucine metabolism. Based on PRM analysis, five proteins including CAMK/CAMK1 protein kinase, glucan 1,3-beta-glucosidase, 1,3-beta-glucanosyltransferase, methylcrotonoyl-CoA carboxylase subunit alpha and isovaleryl-CoA dehydrogenase were down-regulated in P. capsici treated with CA. Furthermore, the qRT-PCR analysis showed that the gene expression level of the interested proteins was consistent with the protein expression level, except for CAMK/CAMK1 protein kinase, acetyl-CoA carboxylase and fatty acid synthase subunit alpha. Conclusions CA destroyed the metabolic homoeostasisof P. capsici, which led to cell death. This is the first proteomic analysis of P. capsici treated with CA, which may provide an important information for exploring the mechanism of the fungicide CA against P. capsici.
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Affiliation(s)
- Yinan Wang
- Henan Agricultural University, College of Plant Protection, Zhengzhou, Henan, China.,Henan Agricultural University, Henan Key Laboratory for Creation and Application of New Pesticides, Zhengzhou, Henan, China.,Henan Agricultural University, Henan Research Center of Green Pesticide Engineering and Technology, Zhengzhou, Henan, China
| | - Mengke Wang
- Henan Agricultural University, College of Plant Protection, Zhengzhou, Henan, China.,Henan Agricultural University, Henan Key Laboratory for Creation and Application of New Pesticides, Zhengzhou, Henan, China.,Henan Agricultural University, Henan Research Center of Green Pesticide Engineering and Technology, Zhengzhou, Henan, China
| | - Min Li
- Henan Agricultural University, College of Plant Protection, Zhengzhou, Henan, China.,Henan Agricultural University, Henan Key Laboratory for Creation and Application of New Pesticides, Zhengzhou, Henan, China.,Henan Agricultural University, Henan Research Center of Green Pesticide Engineering and Technology, Zhengzhou, Henan, China
| | - Te Zhao
- Henan Agricultural University, College of Plant Protection, Zhengzhou, Henan, China.,Henan Agricultural University, Henan Key Laboratory for Creation and Application of New Pesticides, Zhengzhou, Henan, China.,Henan Agricultural University, Henan Research Center of Green Pesticide Engineering and Technology, Zhengzhou, Henan, China
| | - Lin Zhou
- Henan Agricultural University, College of Plant Protection, Zhengzhou, Henan, China.,Henan Agricultural University, Henan Key Laboratory for Creation and Application of New Pesticides, Zhengzhou, Henan, China.,Henan Agricultural University, Henan Research Center of Green Pesticide Engineering and Technology, Zhengzhou, Henan, China
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7
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Mutation pattern and genotype-phenotype correlations of SETD2 in neurodevelopmental disorders. Eur J Med Genet 2021; 64:104200. [PMID: 33766796 DOI: 10.1016/j.ejmg.2021.104200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 10/17/2020] [Accepted: 03/16/2021] [Indexed: 11/24/2022]
Abstract
SETD2 encodes an important protein for epigenetic modification of histones which plays an essential role in early development. Variants in SETD2 have been reported in neurodevelopmental disorders including autism spectrum disorder (ASD). However, most de novo SETD2 variants were reported in different large-cohort sequencing studies, mutation pattern and comprehensive genotype-phenotype correlations for SETD2 are still lacking. We have applied target sequencing to identify rare, clinical-relevant SETD2 variants and detected two novel de novo SETD2 variants, including a de novo splicing variant (NM_014159: c.4715+1G>A) and a de novo missense variant (c.3185C>T: p.P1062L) in two individuals with a diagnosis of ASD. To analyze the correlations between SETD2 mutations and corresponding phenotypes, we systematically review the reported individuals with de novo SETD2 variants, classify the pathogenicity, and analyze the detailed phenotypes. We subsequently manually curate 17 SETD2 de novo variants in 17 individuals from published literature. Individuals with de novo SETD2 variants present common phenotypes including speech and motor delay, intellectual disability, macrocephaly, ASD, overgrowth and recurrent otitis media. Our study reveals new SETD2 mutations and provided a relatively homozygous phenotype spectrum of SETD2-related neurodevelopmental disorders which will be beneficial for disease classification and diagnosis in clinical practice.
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Koss B, Shields BD, Taylor EM, Storey AJ, Byrum SD, Gies AJ, Washam CL, Choudhury SR, Hyun Ahn J, Uryu H, Williams JB, Krager KJ, Chiang TC, Mackintosh SG, Edmondson RD, Aykin-Burns N, Gajewski TF, Wang GG, Tackett AJ. Epigenetic Control of Cdkn2a.Arf Protects Tumor-Infiltrating Lymphocytes from Metabolic Exhaustion. Cancer Res 2020; 80:4707-4719. [PMID: 33004350 PMCID: PMC7642172 DOI: 10.1158/0008-5472.can-20-0524] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/04/2020] [Accepted: 08/28/2020] [Indexed: 01/06/2023]
Abstract
T-cell exhaustion in cancer is linked to poor clinical outcomes, where evidence suggests T-cell metabolic changes precede functional exhaustion. Direct competition between tumor-infiltrating lymphocytes (TIL) and cancer cells for metabolic resources often renders T cells dysfunctional. Environmental stress produces epigenome remodeling events within TIL resulting from loss of the histone methyltransferase EZH2. Here, we report an epigenetic mechanism contributing to the development of metabolic exhaustion in TIL. A multiomics approach revealed a Cdkn2a.Arf-mediated, p53-independent mechanism by which EZH2 inhibition leads to mitochondrial dysfunction and the resultant exhaustion. Reprogramming T cells to express a gain-of-function EZH2 mutant resulted in an enhanced ability of T cells to inhibit tumor growth in vitro and in vivo. Our data suggest that manipulation of T-cell EZH2 within the context of cellular therapies may yield lymphocytes that are able to withstand harsh tumor metabolic environments and collateral pharmacologic insults. SIGNIFICANCE: These findings demonstrate that manipulation of T-cell EZH2 in cellular therapies may yield cellular products able to withstand solid tumor metabolic-deficient environments. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/80/21/4707/F1.large.jpg.
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Affiliation(s)
- Brian Koss
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Bradley D Shields
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Erin M Taylor
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Aaron J Storey
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas
- Arkansas Children's Research Institute, Little Rock, Arkansas
| | - Allen J Gies
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
- Arkansas Children's Research Institute, Little Rock, Arkansas
| | - Charity L Washam
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
- Arkansas Children's Research Institute, Little Rock, Arkansas
| | - Samrat Roy Choudhury
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Jeong Hyun Ahn
- Lineberger Comprehensive Cancer Center, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Hidetaka Uryu
- Lineberger Comprehensive Cancer Center, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Jason B Williams
- Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Kimberly J Krager
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Tung-Chin Chiang
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Rick D Edmondson
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Nukhet Aykin-Burns
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Thomas F Gajewski
- Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas.
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas
- Arkansas Children's Research Institute, Little Rock, Arkansas
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9
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Verhelst S, De Clerck L, Willems S, Van Puyvelde B, Daled S, Deforce D, Dhaenens M. Comprehensive histone epigenetics: A mass spectrometry based screening assay to measure epigenetic toxicity. MethodsX 2020; 7:101055. [PMID: 32995308 PMCID: PMC7508989 DOI: 10.1016/j.mex.2020.101055] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/02/2020] [Indexed: 01/23/2023] Open
Abstract
Evidence of the involvement of epigenetics in pathologies such as cancer, diabetes, and neurodegeneration has increased global interest in epigenetic modifications. For nearly thirty years, it has been known that cancer cells exhibit abnormal DNA methylation patterns. In contrast, the large-scale analysis of histone post-translational modifications (hPTMs) has lagged behind because classically, histone modification analysis has relied on site specific antibody-based techniques. Mass spectrometry (MS) is a technique that holds the promise to picture the histone code comprehensively in a single experiment. Therefore, we developed an MS-based method that is capable of tracking all possible hPTMs in an untargeted approach. In this way, trends in single and combinatorial hPTMs can be reported and enable prediction of the epigenetic toxicity of compounds. Moreover, this method is based on the use of human cells to provide preliminary data, thereby omitting the need to sacrifice laboratory animals. Improving the workflow and the user-friendliness in order to become a high throughput, easily applicable, toxicological screening assay is an ongoing effort. Still, this novel toxicoepigenetic assay and the data it generates holds great potential for, among others, pharmaceutical industry, food science, clinical diagnostics and, environmental toxicity screening. •There is a growing interest in epigenetic modifications, and more specifically in histone post-translational modifications (hPTMs).•We describe an MS-based workflow that is capable of tracking all possible hPTMs in an untargeted approach that makes use of human cells.•Improving the workflow and the user-friendliness in order to become a high throughput, easily applicable, toxicological screening assay is an ongoing effort.
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Key Words
- AUC, area under the curve
- DDA, data-dependent acquisition
- DIA, data-independent acquisition
- DTT, dithiothreitol
- Drug safety
- FA, formic acid
- FDR, false discovery rate
- GABA, gamma-aminobutyric acid
- GRX, gingisrex
- HAT, histone acetyltransferase
- HDACi, histone deacetylase inhibitor
- HLB, hypotonic lysis buffer
- HPLC, high-performance liquid chromatography
- Histone post-translational modifications
- K, Lysine
- LC-MS/MS
- M, Methionine
- MS, Mass spectrometry
- MS/MS, tandem mass spectrometry
- N, asparagine
- PBS, phosphate buffered saline
- Pharmacoepigenetics
- Proteomics
- Q, glutamine
- R, arginine
- RA, relative abundance
- RP, reversed phase
- RT, room temperature
- S, serine
- SWATH, sequential window acquisition of all theoretical fragment ion spectra
- T, threonine
- TEAB, triethylammonium bicarbonate
- Toxicoepigenetics
- VPA, valproic acid
- Y, tyrosine
- hESC, human embryonic stem cell
- hPTM, histone post-translational modification
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Affiliation(s)
- Sigrid Verhelst
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Laura De Clerck
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Sander Willems
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Bart Van Puyvelde
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Simon Daled
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Dieter Deforce
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Maarten Dhaenens
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
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10
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Xu L, Gimple RC, Lau WB, Lau B, Fei F, Shen Q, Liao X, Li Y, Wang W, He Y, Feng M, Bu H, Wang W, Zhou S. THE PRESENT AND FUTURE OF THE MASS SPECTROMETRY-BASED INVESTIGATION OF THE EXOSOME LANDSCAPE. MASS SPECTROMETRY REVIEWS 2020; 39:745-762. [PMID: 32469100 DOI: 10.1002/mas.21635] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/03/2020] [Accepted: 02/05/2020] [Indexed: 02/05/2023]
Abstract
Exosomes are critical intercellular messengers released upon the fusion of multivesicular bodies with the cellular plasma membrane that deliver their cargo in the form of extracellular vesicles. Containing numerous nonrandomly packed functional proteins, lipids, and RNAs, exosomes are vital intercellular messengers that contribute to the physiologic processes of the healthy organism. During the post-genome era, exosome-oriented proteomics have garnered great interest. Since its establishment, mass spectrometry (MS) has been indispensable for the field of proteomics research and has advanced rapidly to interrogate biological samples at a higher resolution and sensitivity. Driven by new methodologies and more advanced instrumentation, MS-based approaches have revolutionized our understanding of protein biology. As the access to online proteomics database platforms has blossomed, experimental data processing occurs with more speed and accuracy. Here, we review recent advances in the technological progress of MS-based proteomics and several new detection strategies for MS-based proteomics research. We also summarize the use of integrated online databases for proteomics research in the era of big data. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Lian Xu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, People's Republic of China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pathology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Ryan C Gimple
- Department of Medicine, Division of Regenerative Medicine, University of California, San Diego, La Jolla, CA.,Department of Pathology, Case Western Reserve University, Cleveland, OH
| | - Wayne Bond Lau
- Department of Emergency Medicine, Thomas Jefferson University Hospital, Philadelphia, PA
| | - Bonnie Lau
- Department of Emergency Medicine, Kaiser Permanente Santa Clara Medical Center, Affiliate of Stanford University, Stanford, CA
| | - Fan Fei
- Department of Neurosurgery, Sichuan People's Hospital, Chengdu, Sichuan, People's Republic of China
| | - Qiuhong Shen
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, People's Republic of China.,School of Biological Sciences, Chengdu Medical College, Chengdu, Sichuan, People's Republic of China
| | - Xiaolin Liao
- Department of Neurosurgery, Sichuan People's Hospital, Chengdu, Sichuan, People's Republic of China
| | - Yichen Li
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong, People's Republic of China
| | - Wei Wang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pathology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Ying He
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pathology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Min Feng
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pathology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Hong Bu
- Laboratory of Pathology, Department of Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Wei Wang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, People's Republic of China
| | - Shengtao Zhou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, People's Republic of China
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11
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Sowers ML, Tang H, Tian B, Goldblum R, Midoro-Horiuti T, Zhang K. Bisphenol A Activates an Innate Viral Immune Response Pathway. J Proteome Res 2019; 19:644-654. [PMID: 31816243 DOI: 10.1021/acs.jproteome.9b00548] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Bisphenol A (BPA) is a ubiquitous component in the manufacturing of plastic. It is commonly found in food and beverage containers. Because of its broad exposure and evidence that it may act as an estrogen-like molecule, many have studied its potential effects. For example, epidemiological studies have found an association between in utero BPA exposure and onset of childhood asthma. Our previous work suggested BPA treated mice induced asthma-like symptoms in both mothers and their pups. In order to better understand theconsequences of BPA exposure and potential mechanisms, we used a proteomics approach. Using both CD4+ T cells from an in vivo model of BPA exposure and an in vitro epithelial cell model, we identified activation of both innate and adaptive immune signaling following BPA exposure. Furthermore, our proteomic results from our multigenerational mouse model study implicates aberrant immune activation across several generations. We propose the following; BPA can active an innate viral immune response by upregulating a probable palmitoyltransferase ZDHHC1, and its binding partner stimulator of interferon-gamma (STING). It also has additional histone epigenetic perturbations, suggesting a role for epigenetic inheritance of these immune perturbations.
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12
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Thomas SP, Haws SA, Borth LE, Denu JM. A practical guide for analysis of histone post-translational modifications by mass spectrometry: Best practices and pitfalls. Methods 2019; 184:53-60. [PMID: 31816396 DOI: 10.1016/j.ymeth.2019.12.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 11/23/2019] [Accepted: 12/02/2019] [Indexed: 02/06/2023] Open
Abstract
Advances in mass spectrometry (MS) have revolutionized the ability to measure global changes in histone post-translational modifications (PTMs). The method routinely quantifies over 60 modification states in a single sample, far exceeding the capabilities of traditional western blotting. Thus, MS-based histone analysis has become an increasingly popular tool for understanding how genetic and environmental factors influence epigenetic states. However, histone proteomics experiments exhibit unique challenges, such as batch-to-batch reproducibility, accurate peak integration, and noisy data. Here, we discuss the steps of histone PTM analysis, from sample preparation and peak integration to data analysis and validation. We outline a set of best practices for ensuring data quality, accurate normalization, and robust statistics. Using these practices, we quantify histone modifications in 5 human cell lines, revealing that each cell line exhibits a unique epigenetic signature. We also provide a reproducible workflow for histone PTM analysis in the form of an R script, which is freely available at https://github.com/DenuLab/HistoneAnalysisWorkflow.
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Affiliation(s)
- Sydney P Thomas
- Wisconsin Institute for Discovery, 330 N. Orchard Street, Madison, WI, USA; Department of Biomolecular Chemistry, University of Wisconsin, Madison, 420 Henry Mall, Madison, WI, USA
| | - Spencer A Haws
- Wisconsin Institute for Discovery, 330 N. Orchard Street, Madison, WI, USA; Department of Biomolecular Chemistry, University of Wisconsin, Madison, 420 Henry Mall, Madison, WI, USA
| | - Laura E Borth
- Wisconsin Institute for Discovery, 330 N. Orchard Street, Madison, WI, USA; Department of Biomolecular Chemistry, University of Wisconsin, Madison, 420 Henry Mall, Madison, WI, USA
| | - John M Denu
- Wisconsin Institute for Discovery, 330 N. Orchard Street, Madison, WI, USA; Department of Biomolecular Chemistry, University of Wisconsin, Madison, 420 Henry Mall, Madison, WI, USA.
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13
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De Clerck L, Willems S, Noberini R, Restellini C, Van Puyvelde B, Daled S, Bonaldi T, Deforce D, Dhaenens M. hSWATH: Unlocking SWATH's Full Potential for an Untargeted Histone Perspective. J Proteome Res 2019; 18:3840-3849. [PMID: 31429292 DOI: 10.1021/acs.jproteome.9b00214] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Mass spectrometry (MS) has become the technique of choice for large-scale analysis of histone post-translational modifications (hPTMs) and their combinatorial patterns, especially in untargeted settings where novel discovery-driven hypotheses are being generated. However, MS-based histone analysis requires a distinct sample preparation, acquisition, and data analysis workflow when compared to traditional MS-based approaches. To this end, sequential window acquisition of all theoretical fragment ion spectra (SWATH) has great potential, as it allows for untargeted accurate identification and quantification of hPTMs. Here, we present a complete SWATH workflow specifically adapted for the untargeted study of histones (hSWATH). We assess its validity on a technical dataset of time-lapse deacetylation of a commercial histone extract using HDAC1, which contains a ground truth, i.e., acetylated substrate peptides reduce in intensity. We successfully apply this workflow in a biological setting and subsequently investigate the differential response to HDAC inhibition in different breast cancer cell lines.
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Affiliation(s)
- Laura De Clerck
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology , Ghent University , 9000 Ghent , Belgium
| | - Sander Willems
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology , Ghent University , 9000 Ghent , Belgium
| | - Roberta Noberini
- Department of Experimental Oncology, IEO , European Institute of Oncology IRCCS , 20141 Milan , Italy
| | - Camilla Restellini
- Department of Experimental Oncology, IEO , European Institute of Oncology IRCCS , 20141 Milan , Italy
| | - Bart Van Puyvelde
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology , Ghent University , 9000 Ghent , Belgium
| | - Simon Daled
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology , Ghent University , 9000 Ghent , Belgium
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO , European Institute of Oncology IRCCS , 20141 Milan , Italy
| | - Dieter Deforce
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology , Ghent University , 9000 Ghent , Belgium
| | - Maarten Dhaenens
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology , Ghent University , 9000 Ghent , Belgium
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14
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El Kennani S, Adrait A, Permiakova O, Hesse AM, Ialy-Radio C, Ferro M, Brun V, Cocquet J, Govin J, Pflieger D. Systematic quantitative analysis of H2A and H2B variants by targeted proteomics. Epigenetics Chromatin 2018; 11:2. [PMID: 29329550 PMCID: PMC5767011 DOI: 10.1186/s13072-017-0172-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 12/20/2017] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Histones organize DNA into chromatin through a variety of processes. Among them, a vast diversity of histone variants can be incorporated into chromatin and finely modulate its organization and functionality. Classically, the study of histone variants has largely relied on antibody-based assays. However, antibodies have a limited efficiency to discriminate between highly similar histone variants. RESULTS In this study, we established a mass spectrometry-based analysis to address this challenge. We developed a targeted proteomics method, using selected reaction monitoring or parallel reaction monitoring, to quantify a maximum number of histone variants in a single multiplexed assay, even when histones are present in a crude extract. This strategy was developed on H2A and H2B variants, using 55 peptides corresponding to 25 different histone sequences, among which a few differ by a single amino acid. The methodology was then applied to mouse testis extracts in which almost all histone variants are expressed. It confirmed the abundance profiles of several testis-specific histones during successive stages of spermatogenesis and the existence of predicted H2A.L.1 isoforms. This methodology was also used to explore the over-expression pattern of H2A.L.1 isoforms in a mouse model of male infertility. CONCLUSIONS Our results demonstrate that targeted proteomics is a powerful method to quantify highly similar histone variants and isoforms. The developed method can be easily transposed to the study of human histone variants, whose abundance can be deregulated in various diseases.
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Affiliation(s)
- Sara El Kennani
- INSERM U1038, CEA, BIG-BGE, Univ. Grenoble Alpes, Grenoble, France
| | - Annie Adrait
- INSERM U1038, CEA, BIG-BGE, Univ. Grenoble Alpes, Grenoble, France
| | - Olga Permiakova
- INSERM U1038, CEA, BIG-BGE, Univ. Grenoble Alpes, Grenoble, France
| | - Anne-Marie Hesse
- INSERM U1038, CEA, BIG-BGE, Univ. Grenoble Alpes, Grenoble, France
| | - Côme Ialy-Radio
- INSERM U1016, Institut Cochin, CNRS UMR8104, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Myriam Ferro
- INSERM U1038, CEA, BIG-BGE, Univ. Grenoble Alpes, Grenoble, France
| | - Virginie Brun
- INSERM U1038, CEA, BIG-BGE, Univ. Grenoble Alpes, Grenoble, France
| | - Julie Cocquet
- INSERM U1016, Institut Cochin, CNRS UMR8104, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Jérôme Govin
- INSERM U1038, CEA, BIG-BGE, Univ. Grenoble Alpes, Grenoble, France.
| | - Delphine Pflieger
- INSERM U1038, CEA, BIG-BGE, Univ. Grenoble Alpes, Grenoble, France. .,CNRS, FR CNRS 3425, Biosciences and Biotechnology Institute of Grenoble, Grenoble, France.
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15
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Güzel C, Govorukhina NI, Stingl C, Dekker LJM, Boichenko A, van der Zee AGJ, Bischoff RP, Luider TM. Comparison of Targeted Mass Spectrometry Techniques with an Immunoassay: A Case Study for HSP90α. Proteomics Clin Appl 2017; 12. [DOI: 10.1002/prca.201700107] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 08/31/2017] [Indexed: 01/02/2023]
Affiliation(s)
- Coşkun Güzel
- Department of Neurology; Neuro-Oncology; Clinical and Cancer Proteomics Laboratory; Erasmus University Medical Centre; Rotterdam The Netherlands
| | - Natalia I. Govorukhina
- Department of Analytical Biochemistry; Centre for Pharmacy; University of Groningen; Groningen The Netherlands
| | - Christoph Stingl
- Department of Neurology; Neuro-Oncology; Clinical and Cancer Proteomics Laboratory; Erasmus University Medical Centre; Rotterdam The Netherlands
| | - Lennard J. M. Dekker
- Department of Neurology; Neuro-Oncology; Clinical and Cancer Proteomics Laboratory; Erasmus University Medical Centre; Rotterdam The Netherlands
| | - Alexander Boichenko
- Department of Analytical Biochemistry; Centre for Pharmacy; University of Groningen; Groningen The Netherlands
| | - Ate G. J. van der Zee
- Department of Gynecology; University Medical Centre Groningen; Groningen the Netherlands
| | - Rainer P.H. Bischoff
- Department of Analytical Biochemistry; Centre for Pharmacy; University of Groningen; Groningen The Netherlands
| | - Theo M. Luider
- Department of Neurology; Neuro-Oncology; Clinical and Cancer Proteomics Laboratory; Erasmus University Medical Centre; Rotterdam The Netherlands
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16
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Zhang K, Xu P, Sowers JL, Machuca DF, Mirfattah B, Herring J, Tang H, Chen Y, Tian B, Brasier AR, Sowers LC. Proteome Analysis of Hypoxic Glioblastoma Cells Reveals Sequential Metabolic Adaptation of One-Carbon Metabolic Pathways. Mol Cell Proteomics 2017; 16:1906-1921. [PMID: 28874504 DOI: 10.1074/mcp.ra117.000154] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Indexed: 02/04/2023] Open
Abstract
Rapidly proliferating tumors are exposed to a hypoxic microenvironment because of their density, high metabolic consumption, and interruptions in blood flow because of immature angiogenesis. Cellular responses to hypoxia promote highly malignant and metastatic behavior, as well as a chemotherapy-resistant state. To better understand the complex relationships between hypoxic adaptations and cancer progression, we studied the dynamic proteome responses of glioblastoma cells exposed to hypoxia via an innovative approach: quantification of newly synthesized proteins using heavy stable-isotope arginine labeling combined with accurate assessment of cell replication by quantification of the light/heavy arginine ratio of peptides in histone H4. We found that hypoxia affects cancer cells in multiple intertwined ways: inflammation, typically with over-expressed glucose transporter (GLUT1), DUSP4/MKP2, and RelA proteins; a metabolic adaptation with overexpression of all glycolytic pathway enzymes for pyruvate/lactate synthesis; and the EMT (epithelial-mesenchymal transition) and cancer stem cell (CSC) renewal with characteristic morphological changes and mesenchymal/CSC protein expression profiles. For the first time, we identified the vitamin B12 transporter protein TCN2, which is essential for one-carbon metabolism, as being significantly downregulated. Further, we found, by knockdown and overexpression experiments, that TCN2 plays an important role in controlling cancer cell transformation toward the highly aggressive mesenchymal/CSC stage; low expression of TCN2 has an effect similar to hypoxia, whereas high expression of TCN2 can reverse it. We conclude that hypoxia induces sequential metabolic responses of one-carbon metabolism in tumor cells. Our mass spectrometry data are available via ProteomeXchange with identifiers PXD005487 (TMT-labeling) and PXD007280 (label-free).
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Affiliation(s)
- Kangling Zhang
- From the ‡Department of Pharmacology, University of Texas Medical Branch, Galveston (UTMB), Texas, 77555; .,¶Sealy Center for Molecular Medicine, UTMB, Galveston, Texas, 77555
| | - Pei Xu
- ‖Department of Neuroscience and Cell Biology, UTMB, Galveston, Texas, 77555
| | - James L Sowers
- ‖Department of Neuroscience and Cell Biology, UTMB, Galveston, Texas, 77555
| | - Daniel F Machuca
- From the ‡Department of Pharmacology, University of Texas Medical Branch, Galveston (UTMB), Texas, 77555
| | - Barsam Mirfattah
- From the ‡Department of Pharmacology, University of Texas Medical Branch, Galveston (UTMB), Texas, 77555
| | - Jason Herring
- From the ‡Department of Pharmacology, University of Texas Medical Branch, Galveston (UTMB), Texas, 77555
| | - Hui Tang
- From the ‡Department of Pharmacology, University of Texas Medical Branch, Galveston (UTMB), Texas, 77555
| | - Yan Chen
- ‖Department of Neuroscience and Cell Biology, UTMB, Galveston, Texas, 77555
| | - Bing Tian
- §Institute for Translational Sciences, UTMB, Galveston, Texas, 77555.,¶Sealy Center for Molecular Medicine, UTMB, Galveston, Texas, 77555
| | - Allan R Brasier
- §Institute for Translational Sciences, UTMB, Galveston, Texas, 77555.,¶Sealy Center for Molecular Medicine, UTMB, Galveston, Texas, 77555
| | - Lawrence C Sowers
- From the ‡Department of Pharmacology, University of Texas Medical Branch, Galveston (UTMB), Texas, 77555.,§Institute for Translational Sciences, UTMB, Galveston, Texas, 77555
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17
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Li H, Han J, Pan J, Liu T, Parker CE, Borchers CH. Current trends in quantitative proteomics - an update. JOURNAL OF MASS SPECTROMETRY : JMS 2017; 52:319-341. [PMID: 28418607 DOI: 10.1002/jms.3932] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 03/28/2017] [Accepted: 04/06/2017] [Indexed: 05/11/2023]
Abstract
Proteins can provide insights into biological processes at the functional level, so they are very promising biomarker candidates. The quantification of proteins in biological samples has been routinely used for the diagnosis of diseases and monitoring the treatment. Although large-scale protein quantification in complex samples is still a challenging task, a great amount of effort has been made to advance the technologies that enable quantitative proteomics. Seven years ago, in 2009, we wrote an article about the current trends in quantitative proteomics. In writing this current paper, we realized that, today, we have an even wider selection of potential tools for quantitative proteomics. These tools include new derivatization reagents, novel sampling formats, new types of analyzers and scanning techniques, and recently developed software to assist in assay development and data analysis. In this review article, we will discuss these innovative methods, and their current and potential applications in proteomics. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- H Li
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, V8Z 7X8, Canada
| | - J Han
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, V8Z 7X8, Canada
| | - J Pan
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, V8Z 7X8, Canada
| | - T Liu
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, V8Z 7X8, Canada
| | - C E Parker
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, V8Z 7X8, Canada
| | - C H Borchers
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, V8Z 7X8, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8P 5C2, Canada
- Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, H3T 1E2, Canada
- Gerald Bronfman Department of Oncology, Jewish General Hospital, Montreal, Quebec, H3T 1E2, Canada
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18
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Bilan V, Selevsek N, Kistemaker HAV, Abplanalp J, Feurer R, Filippov DV, Hottiger MO. New Quantitative Mass Spectrometry Approaches Reveal Different ADP-ribosylation Phases Dependent On the Levels of Oxidative Stress. Mol Cell Proteomics 2017; 16:949-958. [PMID: 28325851 DOI: 10.1074/mcp.o116.065623] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 03/20/2017] [Indexed: 11/06/2022] Open
Abstract
Oxidative stress is a potent inducer of protein ADP-ribosylation. Although individual oxidative stress-induced ADP-ribosylated proteins have been identified, it is so far not clear to which extent different degrees of stress severity quantitatively and qualitatively alter ADP-ribosylation. Here, we investigated both quantitative and qualitative changes of the hydrogen peroxide (H2O2)-induced ADP-ribosylome using a label-free shotgun quantification and a parallel reaction monitoring (PRM) mass spectrometry approach for a selected number of identified ADP-ribosylated peptides. Although the major part of the basal HeLa ADP-ribosylome remained unchanged upon all tested H2O2 concentrations, some selected peptides change the extent of ADP-ribosylation depending on the degree of the applied oxidative stress. Low oxidative stress (i.e. 4 μm and 16 μm H2O2) caused a reduction in ADP-ribosylation of modified proteins detected under untreated conditions. In contrast, mid to strong oxidative stress (62 μm to 1 mm H2O2) induced a significant increase in ADP-ribosylation of oxidative stress-targeted proteins. The application of the PRM approach to SKOV3 and A2780, ovarian cancer cells displaying different sensitivities to PARP inhibitors, revealed that the basal and the H2O2-induced ADP-ribosylomes of SKOV3 and A2780 differed significantly and that the sensitivity to PARP inhibitors correlated with the level of ARTD1 expression in these cells. Overall, this new PRM-MS approach has proven to be sensitive in monitoring alterations of the ADP-ribosylome and has revealed unexpected alterations in proteins ADP-ribosylation depending on the degree of oxidative stress.
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Affiliation(s)
- Vera Bilan
- From the ‡Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.,§Molecular Life Science (MLS) program of the Life Science Zurich Graduate School, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Nathalie Selevsek
- ¶Functional Genomics Center Zurich, University of Zurich/ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Hans A V Kistemaker
- ‖Leiden Institute of Chemistry, Department of Bio-organic Synthesis, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Jeannette Abplanalp
- From the ‡Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.,§Molecular Life Science (MLS) program of the Life Science Zurich Graduate School, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Roxane Feurer
- From the ‡Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Dmitri V Filippov
- ‖Leiden Institute of Chemistry, Department of Bio-organic Synthesis, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Michael O Hottiger
- From the ‡Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland;
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19
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Zhang C, Liu Y. Retrieving Quantitative Information of Histone PTMs by Mass Spectrometry. Methods Enzymol 2016; 586:165-191. [PMID: 28137562 DOI: 10.1016/bs.mie.2016.10.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Posttranslational modifications (PTMs) of histones are one of the main research interests in the rapidly growing field of epigenetics. Accurate and precise quantification of these highly complex histone PTMs is critical for understanding the histone code and the biological significance behind it. It nonetheless remains a major analytical challenge. Mass spectrometry (MS) has been proven as a robust tool in retrieving quantitative information of histone PTMs, and a variety of MS-based quantitative strategies have been successfully developed and employed in basic research as well as clinical studies. In this chapter, we provide an overview for quantitative analysis of histone PTMs, often highly flexible and case dependent, as a primer for future experimental designs.
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Affiliation(s)
- C Zhang
- Baylor College of Medicine, Houston, TX, United States.
| | - Y Liu
- University of Michigan, Ann Arbor, MI, United States.
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20
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Daniell H, Chan HT, Pasoreck EK. Vaccination via Chloroplast Genetics: Affordable Protein Drugs for the Prevention and Treatment of Inherited or Infectious Human Diseases. Annu Rev Genet 2016; 50:595-618. [PMID: 27893966 PMCID: PMC5496655 DOI: 10.1146/annurev-genet-120215-035349] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Plastid-made biopharmaceuticals treat major metabolic or genetic disorders, including Alzheimer's, diabetes, hypertension, hemophilia, and retinopathy. Booster vaccines made in chloroplasts prevent global infectious diseases, such as tuberculosis, malaria, cholera, and polio, and biological threats, such as anthrax and plague. Recent advances in this field include commercial-scale production of human therapeutic proteins in FDA-approved cGMP facilities, development of tags to deliver protein drugs to targeted human cells or tissues, methods to deliver precise doses, and long-term stability of protein drugs at ambient temperature, maintaining their efficacy. Codon optimization utilizing valuable information from sequenced chloroplast genomes enhanced expression of eukaryotic human or viral genes in chloroplasts and offered unique insights into translation in chloroplasts. Support from major biopharmaceutical companies, development of hydroponic production systems, and evaluation by regulatory agencies, including the CDC, FDA, and USDA, augur well for advancing this novel concept to the clinic and revolutionizing affordable healthcare.
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Affiliation(s)
- Henry Daniell
- Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104;
| | - Hui-Ting Chan
- Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104;
| | - Elise K Pasoreck
- Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104;
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21
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Tran TK, Han QQ, Shi Y, Guo L. A comparative proteomic analysis of Salmonella typhimurium under the regulation of the RstA/RstB and PhoP/PhoQ systems. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1686-1695. [PMID: 27618760 DOI: 10.1016/j.bbapap.2016.09.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 08/23/2016] [Accepted: 09/08/2016] [Indexed: 11/17/2022]
Abstract
In pathogenic bacteria, the two-component regulatory systems (TCSs) play important roles in signal transduction and regulation of their pathogenesis. Here, we used quantitative proteomic methods to comparatively analyze functional networks under the control of the RstA/RstB system versus the PhoP/PhoQ system in Salmonella typhimurium. By comparing the proteomic profile from a wild-type strain to that from a ΔrstB strain or a ΔphoPQ strain under a condition known to activate these TCSs, we found that the levels of 159 proteins representing 6.92% of the 2297 proteins identified from the ΔrstB strain and 341 proteins representing 14.9% of the 2288 proteins identified from the ΔphoPQ strain were significantly changed, respectively. Bioinformatics analysis revealed that the RstA/RstB system and the PhoP/PhoQ system coordinated with regard to the regulation of specific proteins as well as metabolic processes. Our observations suggested that the regulatory networks controlled by the PhoP/PhoQ system were much more extensive than those by the RstA/RstB system, whereas the RstA/RstB system specifically regulated expression of the constituents participating in pyrimidine metabolism and iron acquisition. Additional results also suggested that the RstA/RstB system was required for regulation of Salmonella motility and invasion.
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Affiliation(s)
- Trung-Kien Tran
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China; Hung Vuong University, Phu Tho, Vietnam
| | - Qiang-Qiang Han
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yixin Shi
- The School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA; The Center for Infectious Diseases and Vaccinology at the Biodesign Institute, Arizona State University, Tempe, AZ 85287-4501, USA.
| | - Lin Guo
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China.
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22
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Measurement of Histone Methylation Dynamics by One-Carbon Metabolic Isotope Labeling and High-energy Collisional Dissociation Methylation Signature Ion Detection. Sci Rep 2016; 6:31537. [PMID: 27530234 PMCID: PMC4987619 DOI: 10.1038/srep31537] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 07/21/2016] [Indexed: 02/07/2023] Open
Abstract
Accumulating evidence suggests that cellular metabolites and nutrition levels control epigenetic modifications, including histone methylation. However, it is not currently possible to measure the metabolic control of histone methylation. Here we report a novel detection method to monitor methyl transfer from serine to histones through the one-carbon metabolic pathway, using stable-isotope labeling and detection of lysine methylation signature ions generated in high-energy-dissociation (HCD) tandem mass spectrometry. This method is a long-needed tool to study the metabolic control of histone methylation.
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23
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Shi T, Song E, Nie S, Rodland KD, Liu T, Qian WJ, Smith RD. Advances in targeted proteomics and applications to biomedical research. Proteomics 2016; 16:2160-82. [PMID: 27302376 PMCID: PMC5051956 DOI: 10.1002/pmic.201500449] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 05/09/2016] [Accepted: 06/10/2016] [Indexed: 12/17/2022]
Abstract
Targeted proteomics technique has emerged as a powerful protein quantification tool in systems biology, biomedical research, and increasing for clinical applications. The most widely used targeted proteomics approach, selected reaction monitoring (SRM), also known as multiple reaction monitoring (MRM), can be used for quantification of cellular signaling networks and preclinical verification of candidate protein biomarkers. As an extension to our previous review on advances in SRM sensitivity (Shi et al., Proteomics, 12, 1074-1092, 2012) herein we review recent advances in the method and technology for further enhancing SRM sensitivity (from 2012 to present), and highlighting its broad biomedical applications in human bodily fluids, tissue and cell lines. Furthermore, we also review two recently introduced targeted proteomics approaches, parallel reaction monitoring (PRM) and data-independent acquisition (DIA) with targeted data extraction on fast scanning high-resolution accurate-mass (HR/AM) instruments. Such HR/AM targeted quantification with monitoring all target product ions addresses SRM limitations effectively in specificity and multiplexing; whereas when compared to SRM, PRM and DIA are still in the infancy with a limited number of applications. Thus, for HR/AM targeted quantification we focus our discussion on method development, data processing and analysis, and its advantages and limitations in targeted proteomics. Finally, general perspectives on the potential of achieving both high sensitivity and high sample throughput for large-scale quantification of hundreds of target proteins are discussed.
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Affiliation(s)
- Tujin Shi
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ehwang Song
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Song Nie
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Karin D Rodland
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Tao Liu
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Wei-Jun Qian
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Richard D Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
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24
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Rauniyar N. Parallel Reaction Monitoring: A Targeted Experiment Performed Using High Resolution and High Mass Accuracy Mass Spectrometry. Int J Mol Sci 2015; 16:28566-81. [PMID: 26633379 PMCID: PMC4691067 DOI: 10.3390/ijms161226120] [Citation(s) in RCA: 206] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 11/24/2015] [Accepted: 11/25/2015] [Indexed: 12/22/2022] Open
Abstract
The parallel reaction monitoring (PRM) assay has emerged as an alternative method of targeted quantification. The PRM assay is performed in a high resolution and high mass accuracy mode on a mass spectrometer. This review presents the features that make PRM a highly specific and selective method for targeted quantification using quadrupole-Orbitrap hybrid instruments. In addition, this review discusses the label-based and label-free methods of quantification that can be performed with the targeted approach.
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Affiliation(s)
- Navin Rauniyar
- W.M. Keck Foundation Biotechnology Resource Laboratory, School of Medicine, Yale University, 300 George Street, New Haven, CT 06511, USA.
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA.
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