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Yaghjyan L, Mai V, Darville LNF, Cline J, Wang X, Ukhanova M, Tagliamonte MS, Martinez YC, Rich SN, Koomen JM, Egan KM. Associations of gut microbiome with endogenous estrogen levels in healthy postmenopausal women. Cancer Causes Control 2023; 34:873-881. [PMID: 37286847 DOI: 10.1007/s10552-023-01728-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/23/2023] [Indexed: 06/09/2023]
Abstract
PURPOSE The gut microbiome is a potentially important contributor to endogenous estrogen levels after menopause. In healthy postmenopausal women, we examined associations of fecal microbiome composition with levels of urinary estrogens, their metabolites, and relevant metabolic pathway ratios implicated in breast cancer risk. METHODS Eligible postmenopausal women (n = 164) had a body mass index (BMI) ≤ 35 kg/m2 and no history of hormone use (previous 6 months) or cancer/metabolic disorders. Estrogens were quantified in spot urine samples with liquid chromatography-high resolution mass spectrometry (corrected for creatinine). Bacterial DNA was isolated from fecal samples and the V1-V2 hypervariable regions of 16S rRNA were sequenced on the Illumina MiSeq platform. We examined associations of gut microbiome's indices of within-sample (alpha) diversity (i.e., Shannon, Chao1, and Inverse Simpson), phylogenetic diversity, and the ratio of the two main phyla (Firmicutes and Bacteroidetes; F/B ratio) with individual estrogens and metabolic ratios, adjusted for age and BMI. RESULTS In this sample of 164 healthy postmenopausal women, the mean age was 62.9 years (range 47.0-86.0). We found significant inverse associations of observed species with 4-pathway:total estrogens (p = 0.04) and 4-pathway:2-pathway (p = 0.01). Shannon index was positively associated with 2-catechols: methylated 2-catechols (p = 0.04). Chao1 was inversely associated with E1:total estrogens (p = 0.04), and 4-pathway:2-pathway (p = 0.02) and positively associated with 2-pathway:parent estrogens (p = 0.01). Phylogenetic diversity was inversely associated with 4-pathway:total estrogens (p = 0.02), 4-pathway:parent estrogens (p = 0.03), 4-pathway:2-pathway (p = 0.01), and 4-pathway:16-pathway (p = 0.03) and positively associated with 2-pathway:parent estrogens (p = 0.01). F/B ratio was not associated with any of the estrogen measures. CONCLUSION Microbial diversity was associated with several estrogen metabolism ratios implicated in breast cancer risk. Further studies are warranted to confirm these findings in a larger and more representative sample of postmenopausal women, particularly with enrichment of minority participants.
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Affiliation(s)
- Lusine Yaghjyan
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, 2004 Mowry Rd, Gainesville, FL, 32610, USA.
| | - Volker Mai
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, 2004 Mowry Rd, Gainesville, FL, 32610, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | | | | | | | - Maria Ukhanova
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Massimiliano S Tagliamonte
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | | | - Shannan N Rich
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, 2004 Mowry Rd, Gainesville, FL, 32610, USA
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Mooradian MJ, Cleary JM, Giobbie-Hurder A, Darville LNF, Parikh A, Buchbinder EI, Cohen JV, Lawrence DP, Shapiro GI, Keer H, Chen HX, Ivy SP, Smalley KSM, Koomen JM, Sullivan RJ. Dose-escalation trial of combination dabrafenib, trametinib, and AT13387 in patients with BRAF-mutant solid tumors. Cancer 2023; 129:1904-1918. [PMID: 37042037 PMCID: PMC10793106 DOI: 10.1002/cncr.34730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 12/27/2022] [Accepted: 01/04/2023] [Indexed: 04/13/2023]
Abstract
BACKGROUND Combination BRAF and MEK inhibitor therapy is an active regimen in patients who have BRAF V600E-mutated tumors; however, the clinical efficacy of this therapy is limited by resistance. Preclinically, the addition of heat shock protein 90 (HSP90) inhibition improves the efficacy of BRAF inhibitor therapy in both BRAF inhibitor-sensitive and BRAF inhibitor-resistant mutant cell lines. METHODS Cancer Therapy Evaluation Program study 9557 (ClinicalTrials.gov identifier NCT02097225) is a phase 1 study that was designed to assess the safety and efficacy of the small-molecule HSP90 inhibitor, AT13387, in combination with dabrafenib and trametinib in BRAF V600E/K-mutant solid tumors. Correlative analyses evaluated the expression of HSP90 client proteins and chaperones. RESULTS Twenty-two patients with metastatic, BRAF V600E-mutant solid tumors were enrolled using a 3 + 3 design at four dose levels, and 21 patients were evaluable for efficacy assessment. The most common tumor type was colorectal cancer (N = 12). Dose-limiting toxicities occurred in one patient at dose level 3 and in one patient at dose level 4; specifically, myelosuppression and fatigue, respectively. The maximum tolerated dose was oral dabafenib 150 mg twice daily, oral trametinib 2 mg once daily, and intravenous AT13387 260 mg/m2 on days 1, 8, and 15. The best response was a partial response in two patients and stable disease in eight patients, with an overall response rate of 9.5% (90% exact confidence interval [CI], 2%-27%), a disease control rate of 47.6% (90% CI, 29%-67%), and a median overall survival of 5.1 months (90% CI, 3.4-7.6 months). There were no consistent proteomic changes associated with response or resistance, although responders did have reductions in BRAF expression, and epidermal growth factor receptor downregulation using HSP90 inhibition was observed in one patient who had colorectal cancer. CONCLUSIONS HSP90 inhibition combined with BRAF/MEK inhibition was safe and produced evidence of modest disease control in a heavily pretreated population. Additional translational work may identify tumor types and resistance mechanisms that are most sensitive to this approach.
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Affiliation(s)
- Meghan J. Mooradian
- Division of Medical Oncology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - James M. Cleary
- Harvard Medical School, Boston, Massachusetts, USA
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Anita Giobbie-Hurder
- Division of Biostatistics, Departments of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Lancia N. F. Darville
- Department of Proteomics and Metabolomics Core, Moffitt Cancer Center, Tampa, Florida, USA
| | - Aparna Parikh
- Division of Medical Oncology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Elizabeth I. Buchbinder
- Harvard Medical School, Boston, Massachusetts, USA
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Justine V. Cohen
- Division of Medical Oncology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Donald P. Lawrence
- Division of Medical Oncology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Geoffrey I. Shapiro
- Harvard Medical School, Boston, Massachusetts, USA
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Harold Keer
- Astex Pharmaceuticals Inc., Pleasanton, California, USA
| | - Helen X. Chen
- Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland, USA
| | - Susan Percy Ivy
- Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland, USA
| | | | - John M. Koomen
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Ryan J. Sullivan
- Division of Medical Oncology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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Ampomah PB, Cai B, Sukka SR, Gerlach BD, Yurdagul A, Wang X, Kuriakose G, Darville LNF, Sun Y, Sidoli S, Koomen JM, Tall AR, Tabas I. Macrophages use apoptotic cell-derived methionine and DNMT3A during efferocytosis to promote tissue resolution. Nat Metab 2022; 4:444-457. [PMID: 35361955 PMCID: PMC9050866 DOI: 10.1038/s42255-022-00551-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 02/11/2022] [Indexed: 12/19/2022]
Abstract
Efferocytosis, the clearance of apoptotic cells (ACs) by macrophages, is critical for tissue resolution, with defects driving many diseases. Mechanisms of efferocytosis-mediated resolution are incompletely understood. Here, we show that AC-derived methionine regulates resolution through epigenetic repression of the extracellular signal-regulated kinase 1/2 (ERK1/2) phosphatase Dusp4. We focus on two key efferocytosis-induced pro-resolving mediators, prostaglandin E2 (PGE2) and transforming growth factor beta 1 (TGF-β1), and show that efferocytosis induces prostaglandin-endoperoxide synthase 2/cyclooxygenase 2 (Ptgs2/COX2), leading to PGE2 synthesis and PGE2-mediated induction of TGF-β1. ERK1/2 phosphorylation/activation by AC-activated CD36 is necessary for Ptgs2 induction, but this is insufficient owing to an ERK-DUSP4 negative feedback pathway that lowers phospho-ERK. However, subsequent AC engulfment and phagolysosomal degradation lead to Dusp4 repression, enabling enhanced p-ERK and induction of the Ptgs2-PGE2-TGF-β1 pathway. Mechanistically, AC-derived methionine is converted to S-adenosylmethionine, which is used by DNA methyltransferase-3A (DNMT3A) to methylate Dusp4. Bone-marrow DNMT3A deletion in mice blocks COX2/PGE2, TGF-β1, and resolution in sterile peritonitis, apoptosis-induced thymus injury and atherosclerosis. Knowledge of how macrophages use AC-cargo and epigenetics to induce resolution provides mechanistic insight and therapeutic options for diseases driven by impaired resolution.
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Affiliation(s)
- Patrick B Ampomah
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA.
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA.
| | - Bishuang Cai
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Santosh R Sukka
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | | | - Arif Yurdagul
- Department of Molecular and Cellular Physiology, LSU Health Shreveport, Shreveport, LA, USA
| | - Xiaobo Wang
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - George Kuriakose
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Lancia N F Darville
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Yan Sun
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - John M Koomen
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Alan R Tall
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Ira Tabas
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Physiology, Columbia University Irving Medical Center, New York, NY, USA.
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Darville LNF, Cline JK, Rozmeski C, Martinez YC, Rich S, Eschrich SA, Egan KM, Yaghjyan L, Koomen JM. LC-HRMS of derivatized urinary estrogens and estrogen metabolites in postmenopausal women. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1154:122288. [PMID: 32769047 DOI: 10.1016/j.jchromb.2020.122288] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 07/01/2020] [Accepted: 07/25/2020] [Indexed: 12/21/2022]
Abstract
In order to undertake an epidemiologic study relating levels of parent estrogens (estrone and estradiol) and estrogen metabolites (EMs) to other breast cancer risk factors, we have optimized methods for EM quantification with ultra high performance liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS). A two-step approach was adopted; the first step comprised method development and evaluation of the method performance. The second step consisted of applying this method to quantify estrogens in postmenopausal women and determine if the observed patterns are consistent with the existing literature and prior knowledge of estrogen metabolism. First, 1-methylimidazole-2-sulfonyl chloride (MIS) was used to derivatize endogenous estrogens and estrogen metabolites in urine from study participants. Since C18 reversed phase columns have not been able to separate all the structurally related EMs, we used a C18-pentafluorophenyl (PFP) column. The parent estrogens and EMs were baseline resolved with distinct retention times on this C18-PFP column using a 30 min gradient. This method was used to quantify the parent estrogens and 13 EMs in urine samples collected in an initial pilot study involving males as well as pre- and peri-menopausal females to assess a range of EM levels in urine samples and enable comparison to the previous literature for assay evaluation. Detection limits ranged from 1 - 20 pg/mL depending on the EM. We evaluated matrix effects and interference as well as the intra- and inter-batch reproducibility including hydrolysis, extraction, derivatization and LC-MS analysis using charcoal-stripped human urine as a matrix. Methods were then applied to the measurement of estrogens in urine samples from 169 postmenopausal women enrolled in an epidemiological study to examine relationships between breast cancer risk, the intestinal microbiome, and urinary EMs. The results from our cohort are comparable to previous reports on urinary EMs in postmenopausal women and enabled thorough evaluation of the method.
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Affiliation(s)
- Lancia N F Darville
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, United States.
| | - Jayden K Cline
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, United States
| | - Carrie Rozmeski
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, United States
| | - Yessica C Martinez
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, United States
| | - Shannan Rich
- University of Florida, Gainesville, FL, United States
| | - Steven A Eschrich
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, United States
| | - Kathleen M Egan
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, United States.
| | | | - John M Koomen
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, United States
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Darville LNF, Sokolowski BHA. Label-free quantitative mass spectrometry analysis of differential protein expression in the developing cochlear sensory epithelium. Proteome Sci 2018; 16:15. [PMID: 30127667 PMCID: PMC6091194 DOI: 10.1186/s12953-018-0144-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 07/26/2018] [Indexed: 12/27/2022] Open
Abstract
Background The sensory epithelium of the inner ear converts the mechanical energy of sound to electro-chemical energy recognized by the central nervous system. This process is mediated by receptor cells known as hair cells that express proteins in a timely fashion with the onset of hearing. Methods The proteomes of 3, 14, and 30 day-old mice cochlear sensory epithelia were revealed, using label-free quantitative mass spectrometry (LTQ-Orbitrap). Statistical analysis using a one-way ANOVA followed by Bonferroni’s post-hoc test was used to show significant differences in protein expression. Ingenuity Pathway Analysis was used to observe networks of differentially expressed proteins, their biological processes, and associated diseases, while Cytoscape software was used to determine putative interactions with select biomarker proteins. These candidate biomarkers were further verified using Western blotting, while coimmunoprecipitation was used to verify putative partners determined using bioinformatics. Results We show that a comparison across all three proteomes shows that there are 447 differentially expressed proteins, with 387 differentially expressed between postnatal day 3 and 30. Ingenuity Pathway Analysis revealed ~ 62% of postnatal day 3 downregulated proteins are involved in neurological diseases. Several proteins are expressed exclusively on P3, including Parvin α, Drebrin1 (Drb1), Secreted protein acidic and cysteine rich (SPARC), Transmembrane emp24 domain-containing protein 10 (Tmed10). Coimmunoprecipitations showed that Parvin and SPARC interact with integrin-linked protein kinase and the large conductance calcium-activated potassium channel, respectively. Conclusions Quantitative mass spectrometry revealed the identification of numerous differentially regulated proteins over three days of postnatal development. These data provide insights into functional pathways regulating normal sensory and supporting cell development in the cochlea that include potential biomarkers. Interacting partners of two of these markers suggest the importance of these complexes in regulating cellular structure and synapse development. Electronic supplementary material The online version of this article (10.1186/s12953-018-0144-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lancia N F Darville
- Morsani College of Medicine, Department of Otolaryngology-HNS, University of South Florida, 12901 Bruce B. Downs Blvd, Tampa, FL 33612 USA
| | - Bernd H A Sokolowski
- Morsani College of Medicine, Department of Otolaryngology-HNS, University of South Florida, 12901 Bruce B. Downs Blvd, Tampa, FL 33612 USA
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Eroglu Z, Chen YA, Gibney GT, Weber JS, Kudchadkar RR, Khushalani NI, Markowitz J, Brohl AS, Tetteh LF, Ramadan H, Arnone G, Li J, Zhao X, Sharma R, Darville LNF, Fang B, Smalley I, Messina JL, Koomen JM, Sondak VK, Smalley KSM. Combined BRAF and HSP90 Inhibition in Patients with Unresectable BRAF V600E-Mutant Melanoma. Clin Cancer Res 2018; 24:5516-5524. [PMID: 29674508 DOI: 10.1158/1078-0432.ccr-18-0565] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 03/20/2018] [Accepted: 04/17/2018] [Indexed: 12/16/2022]
Abstract
Purpose: BRAF inhibitors are clinically active in patients with advanced BRAFV600-mutant melanoma, although acquired resistance remains common. Preclinical studies demonstrated that resistance could be overcome using concurrent treatment with the HSP90 inhibitor XL888.Patients and Methods: Vemurafenib (960 mg p.o. b.i.d.) combined with escalating doses of XL888 (30, 45, 90, or 135 mg p.o. twice weekly) was investigated in 21 patients with advanced BRAFV600-mutant melanoma. Primary endpoints were safety and determination of a maximum tolerated dose. Correlative proteomic studies were performed to confirm HSP inhibitor activity.Results: Objective responses were observed in 15 of 20 evaluable patients [75%; 95% confidence interval (CI), 51%-91%], with 3 complete and 12 partial responses. Median progression-free survival and overall survival were 9.2 months (95% CI, 3.8-not reached) and 34.6 months (6.2-not reached), respectively. The most common grade 3/4 toxicities were skin toxicities, such as rash (n = 4, 19%) and cutaneous squamous cell carcinomas (n = 3, 14%), along with diarrhea (n = 3, 14%). Pharmacodynamic analysis of patients' peripheral blood mononuclear cells (PBMC) showed increased day 8 HSP70 expression compared with baseline in the three cohorts with XL888 doses ≥45 mg. Diverse effects of vemurafenib-XL888 upon intratumoral HSP client protein expression were noted, with the expression of multiple proteins (including ERBB3 and BAD) modulated on therapy.Conclusions: XL888 in combination with vemurafenib has clinical activity in patients with advanced BRAFV600-mutant melanoma, with a tolerable side-effect profile. HSP90 inhibitors warrant further evaluation in combination with current standard-of-care BRAF plus MEK inhibitors in BRAFV600-mutant melanoma. Clin Cancer Res; 24(22); 5516-24. ©2018 AACR See related commentary by Sullivan, p. 5496.
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Affiliation(s)
- Zeynep Eroglu
- Department of Cutaneous Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Y Ann Chen
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida
| | - Geoffrey T Gibney
- Georgetown Lombardi Comprehensive Cancer Center, Washington, District of Columbia
| | | | - Ragini R Kudchadkar
- Winship Cancer Institute of Emory University School of Medicine, Atlanta, Georgia
| | | | - Joseph Markowitz
- Department of Cutaneous Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Andrew S Brohl
- Department of Cutaneous Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Leticia F Tetteh
- Department of Cutaneous Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Howida Ramadan
- Department of Cutaneous Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Gina Arnone
- Department of Cutaneous Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Jiannong Li
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida
| | - Xiuhua Zhao
- Department of Cutaneous Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Ritin Sharma
- Department of Tumor Biology, Moffitt Cancer Center, Tampa, Florida
| | | | - Bin Fang
- Department of Proteomics, Moffitt Cancer Center, Tampa, Florida
| | - Inna Smalley
- Department of Tumor Biology, Moffitt Cancer Center, Tampa, Florida
| | - Jane L Messina
- Department of Cutaneous Oncology, Moffitt Cancer Center, Tampa, Florida
| | - John M Koomen
- Molecular Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Vernon K Sondak
- Department of Cutaneous Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Keiran S M Smalley
- Department of Cutaneous Oncology, Moffitt Cancer Center, Tampa, Florida. .,Department of Tumor Biology, Moffitt Cancer Center, Tampa, Florida
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Abstract
Proteomics is a commonly used approach that can provide insights into complex biological systems. The cochlear sensory epithelium contains receptors that transduce the mechanical energy of sound into an electro-chemical energy processed by the peripheral and central nervous systems. Several proteomic techniques have been developed to study the cochlear inner ear, such as two-dimensional difference gel electrophoresis (2D-DIGE), antibody microarray, and mass spectrometry (MS). MS is the most comprehensive and versatile tool in proteomics and in conjunction with separation methods can provide an in-depth proteome of biological samples. Separation methods combined with MS has the ability to enrich protein samples, detect low molecular weight and hydrophobic proteins, and identify low abundant proteins by reducing the proteome dynamic range. Different digestion strategies can be applied to whole lysate or to fractionated protein lysate to enhance peptide and protein sequence coverage. Utilization of different separation techniques, including strong cation exchange (SCX), reversed-phase (RP), and gel-eluted liquid fraction entrapment electrophoresis (GELFrEE) can be applied to reduce sample complexity prior to MS analysis for protein identification.
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Affiliation(s)
- Lancia N F Darville
- Department of Otolaryngology, Morsani College of Medicine, University of South Florida
| | - Bernd H A Sokolowski
- Department of Otolaryngology, Morsani College of Medicine, University of South Florida;
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Darville LNF, Merchant ME, Maccha V, Siddavarapu VR, Hasan A, Murray KK. Isolation and determination of the primary structure of a lectin protein from the serum of the American alligator (Alligator mississippiensis). Comp Biochem Physiol B Biochem Mol Biol 2011; 161:161-9. [PMID: 22085437 DOI: 10.1016/j.cbpb.2011.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 11/01/2011] [Accepted: 11/02/2011] [Indexed: 10/15/2022]
Abstract
Mass spectrometry in conjunction with de novo sequencing was used to determine the amino acid sequence of a 35kDa lectin protein isolated from the serum of the American alligator that exhibits binding to mannose. The protein N-terminal sequence was determined using Edman degradation and enzymatic digestion with different proteases was used to generate peptide fragments for analysis by liquid chromatography tandem mass spectrometry (LC MS/MS). Separate analysis of the protein digests with multiple enzymes enhanced the protein sequence coverage. De novo sequencing was accomplished using MASCOT Distiller and PEAKS software and the sequences were searched against the NCBI database using MASCOT and BLAST to identify homologous peptides. MS analysis of the intact protein indicated that it is present primarily as monomer and dimer in vitro. The isolated 35kDa protein was ~98% sequenced and found to have 313 amino acids and nine cysteine residues and was identified as an alligator lectin. The alligator lectin sequence was aligned with other lectin sequences using DIALIGN and ClustalW software and was found to exhibit 58% and 59% similarity to both human and mouse intelectin-1. The alligator lectin exhibited strong binding affinities toward mannan and mannose as compared to other tested carbohydrates.
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Affiliation(s)
- Lancia N F Darville
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
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Darville LNF, Merchant ME, Hasan A, Murray KK. Proteome analysis of the leukocytes from the American alligator (Alligator mississippiensis) using mass spectrometry. Comp Biochem Physiol Part D Genomics Proteomics 2010; 5:308-16. [PMID: 20920849 DOI: 10.1016/j.cbd.2010.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Revised: 09/08/2010] [Accepted: 09/08/2010] [Indexed: 01/03/2023]
Abstract
Mass spectrometry was used in conjunction with gel electrophoresis and liquid chromatography, to determine peptide sequences from American alligator (Alligator mississippiensis) leukocytes and to identify similar proteins based on homology. The goal of the study was to generate an initial database of proteins related to the alligator immune system. We have adopted a typical proteomics approach for this study. Proteins from leukocyte extracts were separated using two-dimensional gel electrophoresis and the major bands were excised, digested and analyzed by on-line nano-LC MS/MS to generate peptide sequences. The sequences generated were used to identify proteins and characterize their functions. The protein identity and characterization of the protein function were based on matching two or more peptides to the same protein by searching against the NCBI database using MASCOT and Basic Local Alignment Search Tool (BLAST). For those proteins with only one peptide matching, the phylum of the matched protein was considered. Forty-three proteins were identified that exhibit sequence similarities to proteins from other vertebrates. Proteins related to the cytoskeletal system were the most abundant proteins identified. These proteins are known to regulate cell mobility and phagocytosis. Several other peptides were matched to proteins that potentially have immune-related function.
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Affiliation(s)
- Lancia N F Darville
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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