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Sanz-Martinez P, Tascher G, Cano-Franco S, Cabrerizo-Poveda P, Münch C, Homan EJ, Stolz A. GPCR Function in Autophagy Control: A Systematic Approach of Chemical Intervention. J Mol Biol 2024; 436:168643. [PMID: 38848865 DOI: 10.1016/j.jmb.2024.168643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 05/10/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024]
Abstract
Autophagy facilitates the degradation of cellular content via the lysosome and is involved in cellular homeostasis and stress response pathways. As such, malfunction of autophagy is linked to a variety of diseases ranging from organ-specific illnesses like cardiomyopathy to systemic illnesses such as cancer or metabolic syndromes. Given the variety of autophagic functions within a cell and tissue, regulation of autophagy is complex and contains numerous positive and negative feedback loops. While our knowledge of mechanisms for cargo selectivity has significantly improved over the last decade, our understanding of signaling routes activating individual autophagy pathways remains rather sparse. In this resource study, we report on a well-characterized chemical library containing 77 GPCR-targeting ligands that was used to systematically analyze LC3B-based autophagy as well as ER-phagy flux upon compound treatment. Upon others, compounds TC-G 1004, BAY 60-6583, PSNCBAM-1, TC-G 1008, LPA2 Antagonist 1, ML-154, JTC-801 and ML-290 targeting adenosine receptor A2a (ADORA2A), adenosine receptor A2b (ADORA2B), cannabinoid receptor 1 (CNR1), G-protein coupled receptor 39 (GPR39), lysophosphatidic acid receptor 2 (LPAR2), neuropeptide S receptor 1 (NPSR1), opioid related nociceptin receptor 1 (OPRL1), and relaxin receptor 1 (RXFP1), respectively, were hit compounds for general autophagy flux. From these compounds, only JTC-801 markly increased ER-phagy flux. In addition, the global impact of these selected hit compounds were analyzed by TMT-based mass spectrometry and demonstrated the differential impact of targeting GPCRs on autophagy-associated proteins. This chemical screening exercise indicates to a significant cross-talk between GPCR signaling and regulation of autophagy pathways.
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Affiliation(s)
- Pablo Sanz-Martinez
- Institute of Biochemistry II (IBC2), Faculty of Medicine, Goethe University, Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Frankfurt am Main, Germany
| | - Georg Tascher
- Institute of Biochemistry II (IBC2), Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Sara Cano-Franco
- Institute of Biochemistry II (IBC2), Faculty of Medicine, Goethe University, Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Frankfurt am Main, Germany
| | - Paloma Cabrerizo-Poveda
- Institute of Biochemistry II (IBC2), Faculty of Medicine, Goethe University, Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Frankfurt am Main, Germany
| | - Christian Münch
- Institute of Biochemistry II (IBC2), Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Evert J Homan
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institute, Solna, Sweden.
| | - Alexandra Stolz
- Institute of Biochemistry II (IBC2), Faculty of Medicine, Goethe University, Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Frankfurt am Main, Germany.
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Chambers TL, Dimet-Wiley A, Keeble AR, Haghani A, Lo WJ, Kang G, Brooke R, Horvath S, Fry CS, Watowich SJ, Wen Y, Murach KA. Methylome-proteome integration after late-life voluntary exercise training reveals regulation and target information for improved skeletal muscle health. J Physiol 2024. [PMID: 39058663 DOI: 10.1113/jp286681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024] Open
Abstract
Exercise is a potent stimulus for combatting skeletal muscle ageing. To study the effects of exercise on muscle in a preclinical setting, we developed a combined endurance-resistance training stimulus for mice called progressive weighted wheel running (PoWeR). PoWeR improves molecular, biochemical, cellular and functional characteristics of skeletal muscle and promotes aspects of partial epigenetic reprogramming when performed late in life (22-24 months of age). In this investigation, we leveraged pan-mammalian DNA methylome arrays and tandem mass-spectrometry proteomics in skeletal muscle to provide detailed information on late-life PoWeR adaptations in female mice relative to age-matched sedentary controls (n = 7-10 per group). Differential CpG methylation at conserved promoter sites was related to transcriptional regulation genes as well as Nr4a3, Hes1 and Hox genes after PoWeR. Using a holistic method of -omics integration called binding and expression target analysis (BETA), methylome changes were associated with upregulated proteins related to global and mitochondrial translation after PoWeR (P = 0.03). Specifically, BETA implicated methylation control of ribosomal, mitoribosomal, and mitochondrial complex I protein abundance after training. DNA methylation may also influence LACTB, MIB1 and UBR4 protein induction with exercise - all are mechanistically linked to muscle health. Computational cistrome analysis predicted several transcription factors including MYC as regulators of the exercise trained methylome-proteome landscape, corroborating prior late-life PoWeR transcriptome data. Correlating the proteome to muscle mass and fatigue resistance revealed positive relationships with VPS13A and NPL levels, respectively. Our findings expose differential epigenetic and proteomic adaptations associated with translational regulation after PoWeR that could influence skeletal muscle mass and function in aged mice. KEY POINTS: Late-life combined endurance-resistance exercise training from 22-24 months of age in mice is shown to improve molecular, biochemical, cellular and in vivo functional characteristics of skeletal muscle and promote aspects of partial epigenetic reprogramming and epigenetic age mitigation. Integration of DNA CpG 36k methylation arrays using conserved sites (which also contain methylation ageing clock sites) with exploratory proteomics in skeletal muscle extends our prior work and reveals coordinated and widespread regulation of ribosomal, translation initiation, mitochondrial ribosomal (mitoribosomal) and complex I proteins after combined voluntary exercise training in a sizeable cohort of female mice (n = 7-10 per group and analysis). Multi-omics integration predicted epigenetic regulation of serine β-lactamase-like protein (LACTB - linked to tumour resistance in muscle), mind bomb 1 (MIB1 - linked to satellite cell and type 2 fibre maintenance) and ubiquitin protein ligase E3 component N-recognin 4 (UBR4 - linked to muscle protein quality control) after training. Computational cistrome analysis identified MYC as a regulator of the late-life training proteome, in agreement with prior transcriptional analyses. Vacuolar protein sorting 13 homolog A (VPS13A) was positively correlated to muscle mass, and the glycoprotein/glycolipid associated sialylation enzyme N-acetylneuraminate pyruvate lyase (NPL) was associated to in vivo muscle fatigue resistance.
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Affiliation(s)
- Toby L Chambers
- Exercise Science Research Center, Molecular Muscle Mass Regulation Laboratory, Department of Health, Human Performance, and Recreation, University of Arkansas, Fayetteville, AR, USA
| | | | - Alexander R Keeble
- University of Kentucky Center for Muscle Biology, Lexington, KY, USA
- Department of Athletic Training and Clinical Nutrition, University of Kentucky, Lexington, KY, USA
| | - Amin Haghani
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Wen-Juo Lo
- Department of Educational Statistics and Research Methods, University of Arkansas, Fayetteville, AR, USA
| | - Gyumin Kang
- University of Kentucky Center for Muscle Biology, Lexington, KY, USA
- Department of Physiology, University of Kentucky, Lexington, KY, USA
- Division of Biomedical Informatics, Department of Internal Medicine, University of Kentucky, Lexington, KY, USA
| | - Robert Brooke
- Epigenetic Clock Development Foundation, Los Angeles, CA, USA
| | - Steve Horvath
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
- Epigenetic Clock Development Foundation, Los Angeles, CA, USA
| | - Christopher S Fry
- University of Kentucky Center for Muscle Biology, Lexington, KY, USA
- Department of Athletic Training and Clinical Nutrition, University of Kentucky, Lexington, KY, USA
| | - Stanley J Watowich
- Ridgeline Therapeutics, Houston, TX, USA
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Yuan Wen
- University of Kentucky Center for Muscle Biology, Lexington, KY, USA
- Department of Physiology, University of Kentucky, Lexington, KY, USA
- Division of Biomedical Informatics, Department of Internal Medicine, University of Kentucky, Lexington, KY, USA
| | - Kevin A Murach
- Exercise Science Research Center, Molecular Muscle Mass Regulation Laboratory, Department of Health, Human Performance, and Recreation, University of Arkansas, Fayetteville, AR, USA
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3
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Costacurta M, Sandow JJ, Maher B, Susanto O, Vervoort SJ, Devlin JR, Garama D, Condina MR, Steele JR, Kahrood HV, Gough D, Johnstone RW, Shortt J. Mapping the IMiD-dependent cereblon interactome using BioID-proximity labelling. FEBS J 2024. [PMID: 38975872 DOI: 10.1111/febs.17196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 04/17/2024] [Accepted: 05/24/2024] [Indexed: 07/09/2024]
Abstract
Immunomodulatory imide drugs (IMiDs) are central components of therapy for multiple myeloma (MM). IMiDs bind cereblon (CRBN), an adaptor for the CUL4-DDB1-RBX1 E3 ligase to change its substrate specificity and induce degradation of 'neosubstrate' transcription factors that are essential to MM cells. Mechanistic studies to date have largely focussed on mediators of therapeutic activity and insight into clinical IMiD toxicities is less developed. We adopted BioID2-dependent proximity labelling (BioID2-CRBN) to characterise the CRBN interactome in the presence and absence of various IMiDs and the proteasome inhibitor, bortezomib. We aimed to leverage this technology to further map CRBN interactions beyond what has been achieved by conventional proteomic techniques. In support of this approach, analysis of cells expressing BioID2-CRBN following IMiD treatment displayed biotinylation of known CRBN interactors and neosubstrates. We observed that bortezomib alone significantly modifies the CRBN interactome. Proximity labelling also suggested that IMiDs augment the interaction between CRBN and proteins that are not degraded, thus designating 'neointeractors' distinct from previously disclosed 'neosubstrates'. Here we identify Non-Muscle Myosin Heavy Chain IIA (MYH9) as a putative CRBN neointeractor that may contribute to the haematological toxicity of IMiDs. These studies provide proof of concept for proximity labelling technologies in the mechanistic profiling of IMiDs and related E3-ligase-modulating drugs.
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Affiliation(s)
- Matteo Costacurta
- Monash Haematology, Monash Health, Clayton, Australia
- Blood Cancer Therapeutics Laboratory, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
| | - Jarrod J Sandow
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Belinda Maher
- Monash Haematology, Monash Health, Clayton, Australia
- Blood Cancer Therapeutics Laboratory, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
| | - Olivia Susanto
- Monash Haematology, Monash Health, Clayton, Australia
- Blood Cancer Therapeutics Laboratory, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
| | - Stephin J Vervoort
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Jennifer R Devlin
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Australia
| | - Daniel Garama
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Australia
| | - Mark R Condina
- Mass Dynamics, Melbourne, Australia
- Clinical & Health Sciences, University of South Australia, Adelaide, Australia
| | - Joel R Steele
- Monash Proteomics and Metabolomics Platform, Monash Biomedicine Discovery Institute, Monash University, Clayton, Australia
- Monash Bioinformatics Platform, Monash Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Hossein V Kahrood
- Monash Proteomics and Metabolomics Platform, Monash Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Daniel Gough
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Australia
| | - Ricky W Johnstone
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Australia
| | - Jake Shortt
- Monash Haematology, Monash Health, Clayton, Australia
- Blood Cancer Therapeutics Laboratory, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Australia
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Harkness BM, Chen S, Kim K, Reddy AP, McFarland TJ, Hegarty DM, Everist SJ, Saugstad JA, Lapidus J, Galor A, Aicher SA. Tear Proteins Altered in Patients with Persistent Eye Pain after Refractive Surgery: Biomarker Candidate Discovery. J Proteome Res 2024; 23:2629-2640. [PMID: 38885176 DOI: 10.1021/acs.jproteome.4c00339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Some patients develop persistent eye pain after refractive surgery, but factors that cause or sustain pain are unknown. We tested whether tear proteins of patients with pain 3 months after surgery differ from those of patients without pain. Patients undergoing refractive surgery (laser in situ keratomileusis or photorefractive keratectomy ) were recruited from 2 clinics, and tears were collected 3 months after surgery. Participants rated their eye pain using a numerical rating scale (NRS, 0-10; no pain-worst pain) at baseline, 1 day, and 3 months after surgery. Using tandem mass tag proteomic analysis, we examined tears from patients with pain [NRS ≥ 3 at 3 months (n = 16)] and patients with no pain [NRS ≤ 1 at 3 months (n = 32)] after surgery. A subset of proteins (83 of 2748 detected, 3.0%) were associated with pain 3 months after surgery. High-dimensional statistical models showed that the magnitude of differential expression was not the only important factor in classifying tear samples from pain patients. Models utilizing 3 or 4 proteins had better classification performance than single proteins and represented differences in both directions (higher or lower in pain). Thus, patterns of protein differences may serve as biomarkers of postsurgical eye pain as well as potential therapeutic targets.
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Affiliation(s)
- Brooke M Harkness
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon 97239-4197, United States
| | - Siting Chen
- School of Public Health, Oregon Health & Science University-Portland State University, Portland, Oregon 97239-4197, United States
- Biostatistics & Design Program, Oregon Health & Science University, Portland, Oregon 97239-4197, United States
| | - Kilsun Kim
- Proteomics Shared Resource, Oregon Health & Science University, Portland, Oregon 97239-4197, United States
| | - Ashok P Reddy
- Proteomics Shared Resource, Oregon Health & Science University, Portland, Oregon 97239-4197, United States
| | - Trevor J McFarland
- Department of Anesthesiology & Perioperative Medicine, Oregon Health & Science University, Portland, Oregon 97239-4197, United States
| | - Deborah M Hegarty
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, Oregon 97239-4197, United States
| | - Steven J Everist
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, Oregon 97239-4197, United States
| | - Julie A Saugstad
- Department of Anesthesiology & Perioperative Medicine, Oregon Health & Science University, Portland, Oregon 97239-4197, United States
| | - Jodi Lapidus
- School of Public Health, Oregon Health & Science University-Portland State University, Portland, Oregon 97239-4197, United States
- Biostatistics & Design Program, Oregon Health & Science University, Portland, Oregon 97239-4197, United States
| | - Anat Galor
- Bascom Palmer Eye Institute, University of Miami Health System, Miami, Florida 33146, United States
- Miami Veterans Affairs Hospital, Miami, Florida 33125-1624, United States
| | - Sue A Aicher
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, Oregon 97239-4197, United States
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5
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Dimet-Wiley AL, Latham CM, Brightwell CR, Neelakantan H, Keeble AR, Thomas NT, Noehren H, Fry CS, Watowich SJ. Nicotinamide N-methyltransferase inhibition mimics and boosts exercise-mediated improvements in muscle function in aged mice. Sci Rep 2024; 14:15554. [PMID: 38969654 PMCID: PMC11226645 DOI: 10.1038/s41598-024-66034-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 06/26/2024] [Indexed: 07/07/2024] Open
Abstract
Human hallmarks of sarcopenia include muscle weakness and a blunted response to exercise. Nicotinamide N-methyltransferase inhibitors (NNMTis) increase strength and promote the regenerative capacity of aged muscle, thus offering a promising treatment for sarcopenia. Since human hallmarks of sarcopenia are recapitulated in aged (24-month-old) mice, we treated mice from 22 to 24 months of age with NNMTi, intensive exercise, or a combination of both, and compared skeletal muscle adaptations, including grip strength, longitudinal running capacity, plantarflexor peak torque, fatigue, and muscle mass, fiber type, cross-sectional area, and intramyocellular lipid (IMCL) content. Exhaustive proteome and metabolome analyses were completed to identify the molecular mechanisms underlying the measured changes in skeletal muscle pathophysiology. Remarkably, NNMTi-treated aged sedentary mice showed ~ 40% greater grip strength than sedentary controls, while aged exercised mice only showed a 20% increase relative to controls. Importantly, the grip strength improvements resulting from NNMTi treatment and exercise were additive, with NNMTi-treated exercised mice developing a 60% increase in grip strength relative to sedentary controls. NNMTi treatment also promoted quantifiable improvements in IMCL content and, in combination with exercise, significantly increased gastrocnemius fiber CSA. Detailed skeletal muscle proteome and metabolome analyses revealed unique molecular mechanisms associated with NNMTi treatment and distinct molecular mechanisms and cellular processes arising from a combination of NNMTi and exercise relative to those given a single intervention. These studies suggest that NNMTi-based drugs, either alone or combined with exercise, will be beneficial in treating sarcopenia and a wide range of age-related myopathies.
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Affiliation(s)
| | - Christine M Latham
- Center for Muscle Biology, College of Health Sciences, University of Kentucky, Lexington, KY, USA
| | - Camille R Brightwell
- Center for Muscle Biology, College of Health Sciences, University of Kentucky, Lexington, KY, USA
| | | | - Alexander R Keeble
- Center for Muscle Biology, College of Health Sciences, University of Kentucky, Lexington, KY, USA
| | - Nicholas T Thomas
- Center for Muscle Biology, College of Health Sciences, University of Kentucky, Lexington, KY, USA
| | - Haley Noehren
- Center for Muscle Biology, College of Health Sciences, University of Kentucky, Lexington, KY, USA
| | - Christopher S Fry
- Center for Muscle Biology, College of Health Sciences, University of Kentucky, Lexington, KY, USA
| | - Stanley J Watowich
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
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Kopij G, Kiezun M, Gudelska M, Dobrzyn K, Zarzecka B, Rytelewska E, Zaobidna E, Swiderska B, Malinowska A, Rak A, Kaminski T, Smolinska N. Visfatin impact on the proteome of porcine luteal cells during implantation. Sci Rep 2024; 14:14625. [PMID: 38918475 PMCID: PMC11199572 DOI: 10.1038/s41598-024-65577-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 06/21/2024] [Indexed: 06/27/2024] Open
Abstract
Visfatin (VIS) is a hormone belonging to the adipokines' group secreted mainly by the adipose tissue. VIS plays a crucial role in the control of energy homeostasis, inflammation, cell differentiation, and angiogenesis. VIS expression was confirmed in the hypothalamic-pituitary-gonadal (HPG) axis structures, as well as in the uterus, placenta, and conceptuses. We hypothesised that VIS may affect the abundance of proteins involved in the regulation of key processes occurring in the corpus luteum (CL) during the implantation process in pigs. In the present study, we performed the high-throughput proteomic analysis (liquid chromatography with tandem mass spectrometry, LC-MS/MS) to examine the in vitro influence of VIS (100 ng/mL) on differentially regulated proteins (DRPs) in the porcine luteal cells (LCs) on days 15-16 of pregnancy (implantation period). We have identified 511 DRPs, 276 of them were up-regulated, and 235 down-regulated in the presence of VIS. Revealed DRPs were assigned to 162 gene ontology terms. Western blot analysis of five chosen DRPs, ADAM metallopeptidase with thrombospondin type 1 motif 1 (ADAMTS1), lanosterol 14-α demethylase (CYP51A1), inhibin subunit beta A (INHBA), notch receptor 3 (NOTCH3), and prostaglandin E synthase 2 (mPGES2) confirmed the veracity and accuracy of LC-MS/MS method. We indicated that VIS modulates the expression of proteins connected with the regulation of lipogenesis and cholesterologenesis, and, in consequence, may be involved in the synthesis of steroid hormones, as well as prostaglandins' metabolism. Moreover, we revealed that VIS affects the abundance of protein associated with ovarian cell proliferation, differentiation, and apoptosis, as well as CL new vessel formation and tissue remodelling. Our results suggest important roles for VIS in the regulation of ovarian functions during the peri-implantation period.
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Affiliation(s)
- Grzegorz Kopij
- Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Marta Kiezun
- Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Marlena Gudelska
- School of Medicine, Collegium Medicum, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Kamil Dobrzyn
- Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Barbara Zarzecka
- Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Edyta Rytelewska
- Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Ewa Zaobidna
- Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Bianka Swiderska
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics PAS in Warsaw, Warsaw, Poland
| | - Agata Malinowska
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics PAS in Warsaw, Warsaw, Poland
| | - Agnieszka Rak
- Institute of Zoology and Biomedical Research, Jagiellonian University in Krakow, Kraków, Poland
| | - Tadeusz Kaminski
- Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Nina Smolinska
- Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland.
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Duffus BLM, Haggerty DL, Doud EH, Mosley AL, Yamamoto BK, Atwood BK. The impact of abstinence from chronic alcohol consumption on the mouse striatal proteome: sex and subregion-specific differences. Front Pharmacol 2024; 15:1405446. [PMID: 38887549 PMCID: PMC11180734 DOI: 10.3389/fphar.2024.1405446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 05/13/2024] [Indexed: 06/20/2024] Open
Abstract
Alcohol misuse is the third leading preventable cause of death in the world. The World Health Organization currently estimates that 1 in 20 deaths are directly alcohol related. One of the ways in which consuming excessive levels of alcohol can both directly and indirectly affect human mortality and morbidity, is through chronic inflammation. Recently, studies have suggested a link between increased alcohol use and the incidence of neuroinflammatory-related diseases. However, the mechanism in which alcohol potentially influences neuroinflammatory processes is still being uncovered. We implemented an unbiased proteomics exploration of alcohol-induced changes in the striatum, with a specific emphasis on proteins related to inflammation. The striatum is a brain region that is critically involved with the progression of alcohol use disorder. Using mass spectrometry following voluntary alcohol self-administration in mice, we show that distinct protein abundances and signaling pathways in different subregions of the striatum are disrupted by chronic exposure to alcohol compared to water drinking control mice. Further, in mice that were allowed to experience abstinence from alcohol compared to mice that were non-abstinent, the overall proteome and signaling pathways showed additional differences, suggesting that the responses evoked by chronic alcohol exposure are dependent on alcohol use history. To our surprise we did not find that chronic alcohol drinking or abstinence altered protein abundance or pathways associated with inflammation, but rather affected proteins and pathways associated with neurodegeneration and metabolic, cellular organization, protein translation, and molecular transport processes. These outcomes suggest that in this drinking model, alcohol-induced neuroinflammation in the striatum is not a primary outcome controlling altered neurobehavioral function, but these changes are rather mediated by altered striatal neuronal structure and cellular health.
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Affiliation(s)
- Brittnie-lee M. Duffus
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - David L. Haggerty
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Emma H. Doud
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Amber L. Mosley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Bryan K. Yamamoto
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, United States
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De Silva S, Alli-Shaik A, Gunaratne J. FlexStat: combinatory differentially expressed protein extraction. BIOINFORMATICS ADVANCES 2024; 4:vbae056. [PMID: 38681522 PMCID: PMC11055397 DOI: 10.1093/bioadv/vbae056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/25/2024] [Accepted: 04/10/2024] [Indexed: 05/01/2024]
Abstract
Motivation Mass spectrometry-based system proteomics allows identification of dysregulated protein hubs and associated disease-related features. Obtaining differentially expressed proteins (DEPs) is the most important step of downstream bioinformatics analysis. However, the extraction of statistically significant DEPs from datasets with multiple experimental conditions or disease types through currently available tools remains a laborious task. More often such an analysis requires considerable bioinformatics expertise, making it inaccessible to researchers with limited computational analytics experience. Results To uncover the differences among the many conditions within the data in a user-friendly manner, here we introduce FlexStat, a web-based interface that extracts DEPs through combinatory analysis. This tool accepts a protein expression matrix as input and systematically generates DEP results for every conceivable combination of various experimental conditions or disease types. FlexStat includes a suite of robust statistical tools for data preprocessing, in addition to DEP extraction, and publication-ready visualization, which are built on established R scientific libraries in an automated manner. This analytics suite was validated in diverse public proteomic datasets to showcase its high performance of rapid and simultaneous pairwise comparisons of comprehensive datasets. Availability and implementation FlexStat is implemented in R and is freely available at https://jglab.shinyapps.io/flexstatv1-pipeline-only/. The source code is accessible at https://github.com/kts-desilva/FlexStat/tree/main.
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Affiliation(s)
- Senuri De Silva
- Translational Biomedical Proteomics Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117594, Singapore
| | - Asfa Alli-Shaik
- Translational Biomedical Proteomics Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
| | - Jayantha Gunaratne
- Translational Biomedical Proteomics Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117594, Singapore
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9
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Kraus F, He Y, Swarup S, Overmyer KA, Jiang Y, Brenner J, Capitanio C, Bieber A, Jen A, Nightingale NM, Anderson BJ, Lee C, Paulo JA, Smith IR, Plitzko JM, Schulman BA, Wilfling F, Coon JJ, Wade Harper J. Lysosomal storage disease proteo/lipidomic profiling using nMOST links ferritinophagy with mitochondrial iron deficiencies in cells lacking NPC2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586828. [PMID: 38585873 PMCID: PMC10996675 DOI: 10.1101/2024.03.26.586828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Lysosomal storage diseases (LSDs) comprised ~50 monogenic diseases characterized by the accumulation of cellular material in lysosomes and associated defects in lysosomal function, but systematic molecular phenotyping is lacking. Here, we develop a nanoflow-based multi-omic single-shot technology (nMOST) workflow allowing simultaneously quantify HeLa cell proteomes and lipidomes from more than two dozen LSD mutants, revealing diverse molecular phenotypes. Defects in delivery of ferritin and its autophagic receptor NCOA4 to lysosomes (ferritinophagy) were pronounced in NPC2-/- cells, which correlated with increased lyso-phosphatidylcholine species and multi-lamellar membrane structures visualized by cryo-electron-tomography. Ferritinophagy defects correlated with loss of mitochondrial cristae, MICOS-complex components, and electron transport chain complexes rich in iron-sulfur cluster proteins. Strikingly, mitochondrial defects were alleviated when iron was provided through the transferrin system. This resource reveals how defects in lysosomal function can impact mitochondrial homeostasis in trans and highlights nMOST as a discovery tool for illuminating molecular phenotypes across LSDs.
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Affiliation(s)
- Felix Kraus
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- equal contribution
| | - Yuchen He
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- equal contribution
| | - Sharan Swarup
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- equal contribution
| | - Katherine A Overmyer
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yizhi Jiang
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Johann Brenner
- Mechanisms of Cellular Quality Control, Max Planck Institute of Biophysics, Frankfurt, Germany
- CryoEM Technology, Max Planck Institute of Biochemistry, Munich, Germany
| | - Cristina Capitanio
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Anna Bieber
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Annie Jen
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Nicole M Nightingale
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Benton J Anderson
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Chan Lee
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Joao A Paulo
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Ian R Smith
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jürgen M Plitzko
- CryoEM Technology, Max Planck Institute of Biochemistry, Munich, Germany
| | - Brenda A Schulman
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Florian Wilfling
- Mechanisms of Cellular Quality Control, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Joshua J Coon
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - J Wade Harper
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
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10
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Yang Y, Pan X, Chen S. Effect of Semaglutide and Empagliflozin on Pulmonary Structure and Proteomics in Obese Mice. Diabetes Metab Syndr Obes 2024; 17:1217-1233. [PMID: 38496002 PMCID: PMC10942255 DOI: 10.2147/dmso.s456336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/28/2024] [Indexed: 03/19/2024] Open
Abstract
Objective This study utilized proteomics to investigate changes in protein expression associated with lung health in obese mice exposed to semaglutide and empagliflozin through a high-fat diet. Methods Twenty-eight male C57BL/6JC mice were randomly assigned to two groups: a control diet group (n = 7) and a high-fat diet group (n = 21). The HFD group was further divided into three groups: HFD group (n = 7), Sema group (n = 7), and Empa group (n = 7). Post-treatment, mice underwent assessments including glucose tolerance, lipids, oxidative stress markers, body weight, lung weight, and structure. Proteomics identified differentially expressed proteins (DEPs) in lung tissue, and bioinformatics analyzed the biological processes and functions of these proteins. Results Semaglutide and empagliflozin significantly attenuated obesity-induced hyperglycemia, abnormal lipid metabolism, oxidative stress response, and can decrease alveolar wall thickness, enlarge alveolar lumen, and reduce collagen content in lung tissue. Both medications also attenuated lung elastic fibre cracking and disintegration. In the HFD/NCD group, there were 66 DEPs, comprising 30 proteins that were increased and 36 that were decreased. Twenty-three DEPs overlapped between Sema/HFD and Empa/HFD, with 11 up-regulated and 12 down-regulated simultaneously. After analysing DEPs in different groups, four proteins - LYVE1, BRAF, RGCC, and CHMP5 - were all downregulated in the HFD group and upregulated by semaglutide and empagliflozin treatment. Conclusion This study demonstrates that obesity induced by a high-fat diet causes a reduction in the expression of LYVE1, BRAF, RGCC, and CHMP5 proteins, potentially affecting lung function and structure in mice. Significantly, the administration of semaglutide and empagliflozin elevates the levels of these proteins, potentially offering therapeutic benefits against lung injury caused by obesity. Merging semaglutide with empagliflozin may exert a more pronounced impact.
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Affiliation(s)
- Yu Yang
- Department of Internal Medicine, Hebei Medical University, Shijiazhuang, People’s Republic of China
- Department of Pharmacy, The Second Hospital of Hebei Medical University, Shijiazhuang, People’s Republic of China
| | - Xiaoyu Pan
- Department of Internal Medicine, Hebei Medical University, Shijiazhuang, People’s Republic of China
- Department of Endocrinology, Hebei General Hospital, Shijiazhuang, People’s Republic of China
| | - Shuchun Chen
- Department of Internal Medicine, Hebei Medical University, Shijiazhuang, People’s Republic of China
- Department of Endocrinology, Hebei General Hospital, Shijiazhuang, People’s Republic of China
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11
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Hoyer MJ, Capitanio C, Smith IR, Paoli JC, Bieber A, Jiang Y, Paulo JA, Gonzalez-Lozano MA, Baumeister W, Wilfling F, Schulman BA, Harper JW. Combinatorial selective ER-phagy remodels the ER during neurogenesis. Nat Cell Biol 2024; 26:378-392. [PMID: 38429475 PMCID: PMC10940164 DOI: 10.1038/s41556-024-01356-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 01/11/2024] [Indexed: 03/03/2024]
Abstract
The endoplasmic reticulum (ER) employs a diverse proteome landscape to orchestrate many cellular functions, ranging from protein and lipid synthesis to calcium ion flux and inter-organelle communication. A case in point concerns the process of neurogenesis, where a refined tubular ER network is assembled via ER shaping proteins into the newly formed neuronal projections to create highly polarized dendrites and axons. Previous studies have suggested a role for autophagy in ER remodelling, as autophagy-deficient neurons in vivo display axonal ER accumulation within synaptic boutons, and the membrane-embedded ER-phagy receptor FAM134B has been genetically linked with human sensory and autonomic neuropathy. However, our understanding of the mechanisms underlying selective removal of the ER and the role of individual ER-phagy receptors is limited. Here we combine a genetically tractable induced neuron (iNeuron) system for monitoring ER remodelling during in vitro differentiation with proteomic and computational tools to create a quantitative landscape of ER proteome remodelling via selective autophagy. Through analysis of single and combinatorial ER-phagy receptor mutants, we delineate the extent to which each receptor contributes to both the magnitude and selectivity of ER protein clearance. We define specific subsets of ER membrane or lumenal proteins as preferred clients for distinct receptors. Using spatial sensors and flux reporters, we demonstrate receptor-specific autophagic capture of ER in axons, and directly visualize tubular ER membranes within autophagosomes in neuronal projections by cryo-electron tomography. This molecular inventory of ER proteome remodelling and versatile genetic toolkit provide a quantitative framework for understanding the contributions of individual ER-phagy receptors for reshaping ER during cell state transitions.
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Affiliation(s)
- Melissa J Hoyer
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Cristina Capitanio
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ian R Smith
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Velia Therapeutics, San Diego, CA, USA
| | - Julia C Paoli
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Anna Bieber
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Yizhi Jiang
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Miguel A Gonzalez-Lozano
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Wolfgang Baumeister
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Florian Wilfling
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
- Mechanisms of Cellular Quality Control, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Brenda A Schulman
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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12
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Woo DU, Lee Y, Min CW, Kim ST, Kang YJ. RiceProteomeDB (RPDB): a user-friendly database for proteomics data storage, retrieval, and analysis. Sci Rep 2024; 14:3671. [PMID: 38351208 PMCID: PMC10864295 DOI: 10.1038/s41598-024-54151-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/08/2024] [Indexed: 02/16/2024] Open
Abstract
Rice, feeding a significant portion of the world, poses unique proteomic challenges critical to agricultural research and global food security. The complexity of the rice proteome, influenced by various genetic and environmental factors, demands specialized analytical approaches for effective study. The central challenges in rice proteomics lie in developing custom methods suited to the unique aspects of rice biology. These include data preprocessing, method selection, and result validation, all of which are essential for advancing rice research. Our aim is to decode these proteomic intricacies to facilitate breakthroughs in strain improvement, disease resistance, and yield optimization, all vital for combating global food insecurity. To achieve this, we have created the RiceProteomeDB (RPDB), a React + Django database, offering a streamlined and comprehensive platform for the analysis of rice proteomics data. RiceProteomeDB (RPDB) simplifies proteomics data management and analysis. It offers features for data organization, preprocessing, method selection, result validation, and data sharing. Researchers can access processed rice proteomics data, conduct analyses, and explore experimental conditions. The user-friendly web interface enhances navigation and interaction. RPDB fosters collaboration by enabling data sharing and proper acknowledgment of sources, contributing to proteomics research and knowledge dissemination. Availability and implementation: Web application: http://riceproteome.plantprofile.net/ . The web application's source code, user's manual, and sample data: https://github.com/dongu7610/Riceproteome .
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Affiliation(s)
- Dong U Woo
- Division of Bio & Medical Bigdata Department (BK4 Program), Gyeongsang National University, 501, Jinju-daero, Jinju-si, Gyeongsangnam-do, 52828, Republic of Korea
| | - Yejin Lee
- Division of Bio & Medical Bigdata Department (BK4 Program), Gyeongsang National University, 501, Jinju-daero, Jinju-si, Gyeongsangnam-do, 52828, Republic of Korea
| | - Cheol Woo Min
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Milyang, 50463, Republic of Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Milyang, 50463, Republic of Korea
| | - Yang Jae Kang
- Division of Bio & Medical Bigdata Department (BK4 Program), Gyeongsang National University, 501, Jinju-daero, Jinju-si, Gyeongsangnam-do, 52828, Republic of Korea.
- Division of Life Science Department, Gyeongsang National University, Jinju, 52828, Republic of Korea.
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13
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Fangrui L, Jiaoli Z, Schunter C, Lin W, Yongzheng T, Zhiqiang H, Bin K. How Oratosquilla oratoria compound eye response to the polarization of light: In the perspective of vision genes and related proteins. Int J Biol Macromol 2024; 259:129053. [PMID: 38161015 DOI: 10.1016/j.ijbiomac.2023.129053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/23/2023] [Accepted: 12/24/2023] [Indexed: 01/03/2024]
Abstract
The special rhabdom structure of the mid-band ommatidium in compound eye contributes to the mantis shrimp being the only animal species known to science that can recognize circularly polarized light (CPL). Although the number of mid-band ommatidium of Oratosquilla oratoria is reduced, the mid-band ommatidium still has orthogonal geometric interleaved rhabdom and short oval distal rhabdom, which may mean that the O. oratoria has weakened circular polarized light vision (CPLV). Here we explored the molecular mechanisms of how O. oratoria response to the polarization of light. Based on the specific expression patterns of vision-related functional genes and proteins, we suggest that the order of light response by O. oratoria compound eye was first natural light, then left-circularly polarized light (LCPL), linearly polarized light, right-circularly polarized light (RCPL) and dark. Meanwhile, we found that the expression levels of vision-related functional genes and proteins in O. oratoria compound eye under RCPL were not significantly different from those in DL, which may imply that O. oratoria cannot respond to RCPL. Furthermore, the response of LCPL is likely facilitated by the differential expression of opsin and microvilli - related functional genes and proteins (arrestin and sodium-coupled neutral amino acid transporter). In conclusion, this study systematically illustrated for the first time how O. oratoria compound eye response to the polarization of light at the genetic level, and it can improve the visual ecological theory behind polarized light vision evolution.
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Affiliation(s)
- Lou Fangrui
- School of Ocean, Yantai University, Yantai, Shandong 264005, China
| | - Zhou Jiaoli
- School of Ocean, Yantai University, Yantai, Shandong 264005, China
| | - Celia Schunter
- Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong Hong Kong SAR, China
| | - Wang Lin
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China
| | - Tang Yongzheng
- School of Ocean, Yantai University, Yantai, Shandong 264005, China
| | - Han Zhiqiang
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China.
| | - Kang Bin
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China.
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14
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Watkins JM, Montes C, Clark NM, Song G, Oliveira CC, Mishra B, Brachova L, Seifert CM, Mitchell MS, Yang J, Braga Dos Reis PA, Urano D, Muktar MS, Walley JW, Jones AM. Phosphorylation Dynamics in a flg22-Induced, G Protein-Dependent Network Reveals the AtRGS1 Phosphatase. Mol Cell Proteomics 2024; 23:100705. [PMID: 38135118 PMCID: PMC10837098 DOI: 10.1016/j.mcpro.2023.100705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 11/22/2023] [Accepted: 12/19/2023] [Indexed: 12/24/2023] Open
Abstract
The microbe-associated molecular pattern flg22 is recognized in a flagellin-sensitive 2-dependent manner in root tip cells. Here, we show a rapid and massive change in protein abundance and phosphorylation state of the Arabidopsis root cell proteome in WT and a mutant deficient in heterotrimeric G-protein-coupled signaling. flg22-induced changes fall on proteins comprising a subset of this proteome, the heterotrimeric G protein interactome, and on highly-populated hubs of the immunity network. Approximately 95% of the phosphorylation changes in the heterotrimeric G-protein interactome depend, at least partially, on a functional G protein complex. One member of this interactome is ATBα, a substrate-recognition subunit of a protein phosphatase 2A complex and an interactor to Arabidopsis thaliana Regulator of G Signaling 1 protein (AtRGS1), a flg22-phosphorylated, 7-transmembrane spanning modulator of the nucleotide-binding state of the core G-protein complex. A null mutation of ATBα strongly increases basal endocytosis of AtRGS1. AtRGS1 steady-state protein level is lower in the atbα mutant in a proteasome-dependent manner. We propose that phosphorylation-dependent endocytosis of AtRGS1 is part of the mechanism to degrade AtRGS1, thus sustaining activation of the heterotrimeric G protein complex required for the regulation of system dynamics in innate immunity. The PP2A(ATBα) complex is a critical regulator of this signaling pathway.
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Affiliation(s)
- Justin M Watkins
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Christian Montes
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA
| | - Natalie M Clark
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA
| | - Gaoyuan Song
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA
| | - Celio Cabral Oliveira
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Biochemistry and Molecular Biology/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Bharat Mishra
- Department of Biology, University of Alabama-Birmingham, Birmingham, Alabama, USA
| | - Libuse Brachova
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Clara M Seifert
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Malek S Mitchell
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jing Yang
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Daisuke Urano
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - M Shahid Muktar
- Department of Biology, University of Alabama-Birmingham, Birmingham, Alabama, USA
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA.
| | - Alan M Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
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15
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Jhelum H, Čerina D, Harbort CJ, Lindner A, Hanitsch LG, Leistner R, Schröder JT, von Bernuth H, Stegemann MS, Schürmann M, Zychlinsky A, Krüger R, Marsman G. Panton-Valentine leukocidin-induced neutrophil extracellular traps lack antimicrobial activity and are readily induced in patients with recurrent PVL + -Staphylococcus aureus infections. J Leukoc Biol 2024; 115:222-234. [PMID: 37943843 DOI: 10.1093/jleuko/qiad137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 10/04/2023] [Accepted: 10/09/2023] [Indexed: 11/12/2023] Open
Abstract
Staphylococcus aureus strains that produce the toxin Panton-Valentine leukocidin (PVL-SA) frequently cause recurrent skin and soft tissue infections. PVL binds to and kills human neutrophils, resulting in the formation of neutrophil extracellular traps (NETs), but the pathomechanism has not been extensively studied. Furthermore, it is unclear why some individuals colonized with PVL-SA experience recurring infections whereas others are asymptomatic. We thus aimed to (1) investigate how PVL exerts its pathogenicity on neutrophils and (2) identify factors that could help to explain the predisposition of patients with recurring infections. We provide genetic and pharmacological evidence that PVL-induced NET formation is independent of NADPH oxidase and reactive oxygen species production. Moreover, through NET proteome analysis we identified that the protein content of PVL-induced NETs is different from NETs induced by mitogen or the microbial toxin nigericin. The abundance of the proteins cathelicidin (CAMP), elastase (NE), and proteinase 3 (PRTN3) was lower on PVL-induced NETs, and as such they were unable to kill S. aureus. Furthermore, we found that neutrophils from affected patients express higher levels of CD45, one of the PVL receptors, and are more susceptible to be killed at a low PVL concentration than control neutrophils. Neutrophils from patients that experience recurring PVL-positive infections may thus be more sensitive to PVL-induced NET formation, which might impair their ability to combat the infection.
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Affiliation(s)
- Hina Jhelum
- Department of Cellular Microbiology, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117, Berlin, Germany
| | - Dora Čerina
- Department of Cellular Microbiology, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117, Berlin, Germany
| | - C J Harbort
- Department of Cellular Microbiology, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117, Berlin, Germany
| | - Andreas Lindner
- Institute of Tropical Medicine and International Health, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Leif Gunnar Hanitsch
- Department of Medical Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Rasmus Leistner
- Institute of Hygiene and Environmental Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Jennyver-Tabea Schröder
- Department of Pediatric Surgery, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Horst von Bernuth
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
- Department of Immunology, Labor Berlin GmbH, Sylter Straße 2, 13353, Berlin, Germany
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Miriam Songa Stegemann
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Mariana Schürmann
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Arturo Zychlinsky
- Department of Cellular Microbiology, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117, Berlin, Germany
| | - Renate Krüger
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Gerben Marsman
- Department of Cellular Microbiology, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117, Berlin, Germany
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16
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Liu Y, Li Z, Li W, Chen X, Yang L, Lu S, Zhou S, Li M, Xiong W, Zhang X, Liu Y, Zhou J. Discovery of β-sitosterol's effects on molecular changes in rat diabetic wounds and its impact on angiogenesis and macrophages. Int Immunopharmacol 2024; 126:111283. [PMID: 38035407 DOI: 10.1016/j.intimp.2023.111283] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/03/2023] [Accepted: 11/21/2023] [Indexed: 12/02/2023]
Abstract
Diabetes care, particularly for diabetic foot ulcers (DFUs)-related complications, increases treatment costs substantially. Failure to provide timely and appropriate treatment for severe DFUs significantly increases amputation risk. Neovascularization and macrophage polarization play an important role in diabetic wound healing during different stages of the wound repair process. Therefore, a new treatment method that promotes neovascularization and macrophage polarization may accelerate diabetic wound healing. β-sitosterol possesses anti-inflammatory, lipid-lowering, and antidiabetic properties. However, its therapeutic potential in diabetic wound healing remains underexplored. This study evaluated the healing effects of β-sitosterol on diabetic ulcer wounds in rats. We found that β-sitosterol can promote angiogenesis, alternatively activated macrophages (M2 macrophage) proliferation, and collagen synthesis in diabetic wounds. Transcriptomics analysis and proteomics analysis revealed that MAPK, mTOR and VEGF signaling pathways were enriched in β-sitosterol-treated wounds. Molecular docking revealed Ndufb5 maybe the target of β-sitosterol-treated wounds. Our findings confirm the significant diabetic wound healing effects of β-sitosterol in a rat model. β-sitosterol treatment to diabetic wounds accelerates wound healing through promoting M2 macrophage proliferation and angiogenesis. Interestingly, we also found that the process of M2 macrophage proliferation accompanies angiogenesis. Thus, β-sitosterol may be a promising therapeutic approach to enhance diabetic wound healing and reduce amputation in diabetes.
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Affiliation(s)
- Yang Liu
- Department of Plastic Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, China
| | - Zenan Li
- Department of Plastic Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, China
| | - Weidong Li
- Department of Plastic Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, China
| | - Xuan Chen
- Department of Plastic Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, China
| | - Liping Yang
- Inner Mongolia Medical University, Hohhot, Inner Mongolia Autonomous Region 010107, China
| | - Shengli Lu
- Department of Plastic Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, China
| | - Shuai Zhou
- Inner Mongolia Medical University, Hohhot, Inner Mongolia Autonomous Region 010107, China
| | - Meng Li
- Inner Mongolia Medical University, Hohhot, Inner Mongolia Autonomous Region 010107, China
| | - Wu Xiong
- Department of Burns and Plastic Surgery, The First Hospital of Hunan University of Chinese Medicine, Changsha 410007, China
| | - Xi Zhang
- Hunan Brain Hospital, Clinical Medical School of Hunan University of Chinese Medicine, Changsha 410007, China
| | - Yu Liu
- Hunan University of Chinese Medicine, College of Integrated Chinese and Western Medicine, Changsha 410007, China; Inner Mongolia Medical University, Hohhot, Inner Mongolia Autonomous Region 010107, China.
| | - Jianda Zhou
- Department of Plastic Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, China.
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17
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Tijms BM, Vromen EM, Mjaavatten O, Holstege H, Reus LM, van der Lee S, Wesenhagen KEJ, Lorenzini L, Vermunt L, Venkatraghavan V, Tesi N, Tomassen J, den Braber A, Goossens J, Vanmechelen E, Barkhof F, Pijnenburg YAL, van der Flier WM, Teunissen CE, Berven FS, Visser PJ. Cerebrospinal fluid proteomics in patients with Alzheimer's disease reveals five molecular subtypes with distinct genetic risk profiles. NATURE AGING 2024; 4:33-47. [PMID: 38195725 PMCID: PMC10798889 DOI: 10.1038/s43587-023-00550-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/29/2023] [Indexed: 01/11/2024]
Abstract
Alzheimer's disease (AD) is heterogenous at the molecular level. Understanding this heterogeneity is critical for AD drug development. Here we define AD molecular subtypes using mass spectrometry proteomics in cerebrospinal fluid, based on 1,058 proteins, with different levels in individuals with AD (n = 419) compared to controls (n = 187). These AD subtypes had alterations in protein levels that were associated with distinct molecular processes: subtype 1 was characterized by proteins related to neuronal hyperplasticity; subtype 2 by innate immune activation; subtype 3 by RNA dysregulation; subtype 4 by choroid plexus dysfunction; and subtype 5 by blood-brain barrier impairment. Each subtype was related to specific AD genetic risk variants, for example, subtype 1 was enriched with TREM2 R47H. Subtypes also differed in clinical outcomes, survival times and anatomical patterns of brain atrophy. These results indicate molecular heterogeneity in AD and highlight the need for personalized medicine.
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Affiliation(s)
- Betty M Tijms
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands.
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands.
| | - Ellen M Vromen
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
| | - Olav Mjaavatten
- Proteomics Unit at the University of Bergen, Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Henne Holstege
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Department of Clinical Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
| | - Lianne M Reus
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sven van der Lee
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Genomics of Neurodegenerative Diseases and Aging, Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
| | - Kirsten E J Wesenhagen
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
| | - Luigi Lorenzini
- Department of Radiology and Nuclear Medicine, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neuroimaging, Amsterdam, the Netherlands
| | - Lisa Vermunt
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Neurochemistry Laboratory, Department of Laboratory Medicine, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
| | - Vikram Venkatraghavan
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
| | - Niccoló Tesi
- Genomics of Neurodegenerative Diseases and Aging, Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands
| | - Jori Tomassen
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
| | - Anouk den Braber
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | | | | | - Frederik Barkhof
- Department of Radiology and Nuclear Medicine, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Queen Square Institute of Neurology and Centre for Medical Image Computing, University College London, London, UK
| | - Yolande A L Pijnenburg
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
| | - Wiesje M van der Flier
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Epidemiology & Data Science, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
| | - Charlotte E Teunissen
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Neurochemistry Laboratory, Department of Laboratory Medicine, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
| | - Frode S Berven
- Proteomics Unit at the University of Bergen, Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Pieter Jelle Visser
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Alzheimer Center Limburg, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, Stockholm, Sweden
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18
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Gheinani AH, Sack BS, Bigger-Allen A, Thaker H, Atta H, Lambrinos G, Costa K, Doyle C, Gharaee-Kermani M, Patalano S, Piper M, Cotellessa JF, Vitko D, Li H, Prabhakaran MK, Cristofaro V, Froehlich J, Lee RS, Yang W, Sullivan MP, Macoska JA, Adam RM. Integrated omics analysis unveils a DNA damage response to neurogenic injury. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.10.571015. [PMID: 38106029 PMCID: PMC10723451 DOI: 10.1101/2023.12.10.571015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Spinal cord injury (SCI) evokes profound bladder dysfunction. Current treatments are limited by a lack of molecular data to inform novel therapeutic avenues. Previously, we showed systemic inosine treatment improved bladder function following SCI in rats. Here, we applied multi-omics analysis to explore molecular alterations in the bladder and their sensitivity to inosine following SCI. Canonical pathways regulated by SCI included those associated with protein synthesis, neuroplasticity, wound healing, and neurotransmitter degradation. Upstream regulator analysis identified MYC as a key regulator, whereas causal network analysis predicted multiple regulators of DNA damage response signaling following injury, including PARP-1. Staining for both DNA damage (γH2AX) and PARP activity (poly-ADP-ribose) markers in the bladder was increased following SCI, and attenuated in inosine-treated tissues. Proteomics analysis suggested that SCI induced changes in protein synthesis-, neuroplasticity-, and oxidative stress-associated pathways, a subset of which were shown in transcriptomics data to be inosine-sensitive. These findings provide novel insights into the molecular landscape of the bladder following SCI, and highlight a potential role for PARP inhibition to treat neurogenic bladder dysfunction.
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Affiliation(s)
- Ali Hashemi Gheinani
- Urological Diseases Research Center, Boston Children's Hospital, Boston, MA, USA
- Functional Urology Research Group, Department for BioMedical Research DBMR, University of Bern, Switzerland
- Department of Urology, Inselspital University Hospital, 3010 Bern, Switzerland
- Department of Surgery, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bryan S Sack
- Urological Diseases Research Center, Boston Children's Hospital, Boston, MA, USA
- Functional Urology Research Group, Department for BioMedical Research DBMR, University of Bern, Switzerland
| | - Alex Bigger-Allen
- Urological Diseases Research Center, Boston Children's Hospital, Boston, MA, USA
- Department of Surgery, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Biological & Biomedical Sciences Graduate Program, Division of Medical Sciences, Harvard Medical School, Boston, MA
| | - Hatim Thaker
- Urological Diseases Research Center, Boston Children's Hospital, Boston, MA, USA
- Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Hussein Atta
- Urological Diseases Research Center, Boston Children's Hospital, Boston, MA, USA
- Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - George Lambrinos
- Urological Diseases Research Center, Boston Children's Hospital, Boston, MA, USA
- Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Kyle Costa
- Urological Diseases Research Center, Boston Children's Hospital, Boston, MA, USA
| | - Claire Doyle
- Urological Diseases Research Center, Boston Children's Hospital, Boston, MA, USA
- Department of Surgery, Harvard Medical School, Boston, MA, USA
| | | | | | - Mary Piper
- Harvard Chan Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Justin F Cotellessa
- Departments of Surgery and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Dijana Vitko
- Urological Diseases Research Center, Boston Children's Hospital, Boston, MA, USA
- Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Haiying Li
- Urological Diseases Research Center, Boston Children's Hospital, Boston, MA, USA
- Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Manubhai Kadayil Prabhakaran
- Urological Diseases Research Center, Boston Children's Hospital, Boston, MA, USA
- Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Vivian Cristofaro
- Division of Urology, VA Boston Healthcare System, Boston, MA, USA
- University of Massachusetts, Boston, MA, USA
| | - John Froehlich
- Urological Diseases Research Center, Boston Children's Hospital, Boston, MA, USA
- Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Richard S Lee
- Urological Diseases Research Center, Boston Children's Hospital, Boston, MA, USA
- Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Wei Yang
- Departments of Surgery and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Maryrose P Sullivan
- Division of Urology, VA Boston Healthcare System, Boston, MA, USA
- University of Massachusetts, Boston, MA, USA
| | | | - Rosalyn M Adam
- Urological Diseases Research Center, Boston Children's Hospital, Boston, MA, USA
- Department of Urology, Inselspital University Hospital, 3010 Bern, Switzerland
- Department of Surgery, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
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19
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Eszlinger M, Stephenson A, Mirhadi S, Patyra K, Moran MF, Khalil M, Kero J, Paschke R. Activation of mitogen-activated protein kinase signaling and development of papillary thyroid carcinoma in thyroid-stimulating hormone receptor D633H knockin mice. Eur Thyroid J 2023; 12:e230049. [PMID: 37855416 PMCID: PMC10563634 DOI: 10.1530/etj-23-0049] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 08/30/2023] [Indexed: 09/02/2023] Open
Abstract
Objective Nonautoimmune hyperthyroidism (NAH) is rare and occurs due to a constitutively activating thyroid stimulating hormone receptor (TSHR) mutation. In contrast to other thyroid nodules, no further evaluation for malignancy is recommended for hot thyroid nodules. In the first model for NAH in mice nearly all homozygous mice had developed papillary thyroid cancer by 12 months of age. Methods To further evaluate these mice, whole exome sequencing and phosphoproteome analysis were employed in a further generation of mice to identify any other mutations potentially responsible and to identify the pathways involved in thyroid carcinoma development. Results Only three genes (Nrg1, Rrs1, Rasal2) were mutated in all mice examined, none of which were known primary drivers of papillary thyroid cancer development. Wild-type and homozygous TSHR D633H knockin mice showed distinct phosphoproteome profiles with an enrichment of altered phosphosites found in ERK/mitogen-activated protein kinase (MAPK) signaling. Most importantly, phosphosites with known downstream effects included BRAF p.S766, which forms an inhibitory site: a decrease of phosphorylation at this site suggests an increase in MEK/ERK pathway activation. The decreased phosphorylation at BRAF p.S766 would suggest decreased AMP-activated protein kinase (AMPK) signaling, which is supported by the decreased phosphorylation of STIM1 p.S257, a downstream AMPK target. Conclusion The modified phosphoproteome profile of the homozygous mice in combination with human literature suggests a potential signaling pathway from constitutive TSHR signaling and cAMP activation to the activation of ERK/MAPK signaling. This is the first time that a specific mechanism has been identified for a possible involvement of TSH signaling in thyroid carcinoma development.
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Affiliation(s)
- Markus Eszlinger
- Department of Oncology and Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Heritage Medical Research Building, Calgary, Alberta, Canada, and Institute of Pathology, University Hospital Halle, Halle, Germany
| | - Alexandra Stephenson
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Heritage Medical Research Building, Calgary, Alberta, Canada
| | - Shideh Mirhadi
- Program in Cell Biology, Hospital for Sick Children, and Department of Molecular Genetics, University of Toronto, Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Konrad Patyra
- Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Michael F Moran
- Program in Cell Biology, Hospital for Sick Children, and Department of Molecular Genetics, University of Toronto, Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Moosa Khalil
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Jukka Kero
- Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, Turku, Finland
- Department of Pediatrics, Turku University Hospital, Turku, Finland
| | - Ralf Paschke
- Department of Oncology and Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Heritage Medical Research Building, Calgary, Alberta, Canada, and Institute of Pathology, University Hospital Halle, Halle, Germany
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Heritage Medical Research Building, Calgary, Alberta, Canada
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Medicine, Cumming School of Medicine, University of Calgary, Heritage Medical Research Building, Calgary, Alberta, Canada
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20
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Vcelkova T, Reiter W, Zylka M, Hollenstein D, Schuckert S, Hartl M, Seiser C. GSE1 links the HDAC1/CoREST co-repressor complex to DNA damage. Nucleic Acids Res 2023; 51:11748-11769. [PMID: 37878419 PMCID: PMC10681733 DOI: 10.1093/nar/gkad911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 10/27/2023] Open
Abstract
Post-translational modifications of histones are important regulators of the DNA damage response (DDR). By using affinity purification mass spectrometry (AP-MS) we discovered that genetic suppressor element 1 (GSE1) forms a complex with the HDAC1/CoREST deacetylase/demethylase co-repressor complex. In-depth phosphorylome analysis revealed that loss of GSE1 results in impaired DDR, ATR signalling and γH2AX formation upon DNA damage induction. Altered profiles of ATR target serine-glutamine motifs (SQ) on DDR-related hallmark proteins point to a defect in DNA damage sensing. In addition, GSE1 knock-out cells show hampered DNA damage-induced phosphorylation on SQ motifs of regulators of histone post-translational modifications, suggesting altered histone modification. While loss of GSE1 does not affect the histone deacetylation activity of CoREST, GSE1 appears to be essential for binding of the deubiquitinase USP22 to CoREST and for the deubiquitination of H2B K120 in response to DNA damage. The combination of deacetylase, demethylase, and deubiquitinase activity makes the USP22-GSE1-CoREST subcomplex a multi-enzymatic eraser that seems to play an important role during DDR. Since GSE1 has been previously associated with cancer progression and survival our findings are potentially of high medical relevance.
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Affiliation(s)
- Terezia Vcelkova
- Center for Anatomy and Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Wolfgang Reiter
- Mass Spectrometry Facility, Max Perutz Labs, Vienna BioCenter, 1030 Vienna, Austria
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Martha Zylka
- Center for Anatomy and Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - David M Hollenstein
- Mass Spectrometry Facility, Max Perutz Labs, Vienna BioCenter, 1030 Vienna, Austria
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Stefan Schuckert
- Center for Anatomy and Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Markus Hartl
- Mass Spectrometry Facility, Max Perutz Labs, Vienna BioCenter, 1030 Vienna, Austria
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Christian Seiser
- Center for Anatomy and Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
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21
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Zhang P, Zhang B, Fu Y, Li P, Zhang H. Cloning and functional characterization of porcine AACS revealing the regulative roles for fat deposition in pigs. PeerJ 2023; 11:e16406. [PMID: 38025737 PMCID: PMC10666648 DOI: 10.7717/peerj.16406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/13/2023] [Indexed: 12/01/2023] Open
Abstract
Fat deposition is a quantitative trait controlled by multiple genes in pigs. Using transcriptome sequencing, we previously reported that AACS is differentially expressed in the subcutaneous fat tissue of Dingyuan pigs with divergent backfat thickness. Therefore, with the aim of further characterizing this gene and its protein, we cloned the entire 3286-bp mRNA sequence of the porcine AACS, and the encoded AACS protein is a hydrophilic protein without a signal peptide or transmembrane sequence. Our findings suggested that among various tissues and pig breeds, AACS was highly expressed in subcutaneous fat. We have identified three completely linked SNP loci in the AACS gene: A-1759C, C-1683T, and A-1664G. The double luciferase activity test in the 5' flanking region indicated that the flanking region of AACS contained several active regulatory elements. The three linked SNPs that were identified in one of the critical active elements, and might serve as important molecular markers regulating backfat thickness. Finally, we observed that AACS overexpression inhibited the proliferation and differentiation of subcutaneous preadipocytes. Collectively, our results suggest that AACS inhibits subcutaneous fat deposition in pigs. This study provides a new molecular marker for understanding the mechanism of porcine fat deposition.
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Affiliation(s)
- Pan Zhang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, China
- Beijing Academy of Science and Technology, Beijing Milu Ecological Research Center, Beijing, China
| | - Bo Zhang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, China
| | - Yu Fu
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, China
| | - Pan Li
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, China
| | - Hao Zhang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, China
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22
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Mucha O, Myszka M, Podkalicka P, Świderska B, Malinowska A, Dulak J, Łoboda A. Proteome Profiling of the Dystrophic mdx Mice Diaphragm. Biomolecules 2023; 13:1648. [PMID: 38002330 PMCID: PMC10669179 DOI: 10.3390/biom13111648] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/02/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Mdx mice with a spontaneous mutation in exon 23 of the Dmd gene represent the most common model to investigate the pathophysiology of Duchenne muscular dystrophy (DMD). The disease, caused by the lack of functional dystrophin, is characterized by irreversible impairment of muscle functions, with the diaphragm affected earlier and more severely than other skeletal muscles. We applied a label-free (LF) method and the more thorough tandem mass tag (TMT)-based method to analyze differentially expressed proteins in the diaphragm of 6-week-old mdx mice. The comparison of both methods revealed 88 commonly changed proteins. A more in-depth analysis of the TMT-based method showed 953 significantly changed proteins, with 867 increased and 86 decreased in dystrophic animals (q-value < 0.05, fold-change threshold: 1.5). Consequently, several dysregulated processes were demonstrated, including the immune response, fibrosis, translation, and programmed cell death. Interestingly, in the dystrophic diaphragm, we found a significant decrease in the expression of enzymes generating hydrogen sulfide (H2S), suggesting that alterations in the metabolism of this gaseous mediator could modulate DMD progression, which could be a potential target for pharmacological intervention.
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Affiliation(s)
- Olga Mucha
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, Gronostajowa 7 Street, 30-387 Kraków, Poland; (O.M.); (M.M.); (P.P.); (J.D.)
| | - Małgorzata Myszka
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, Gronostajowa 7 Street, 30-387 Kraków, Poland; (O.M.); (M.M.); (P.P.); (J.D.)
- Doctoral School of Exact and Natural Sciences, Łojasiewicza 11 Street, 30-348 Kraków, Poland
| | - Paulina Podkalicka
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, Gronostajowa 7 Street, 30-387 Kraków, Poland; (O.M.); (M.M.); (P.P.); (J.D.)
| | - Bianka Świderska
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a Street, 02-106 Warsaw, Poland; (B.Ś.); (A.M.)
| | - Agata Malinowska
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a Street, 02-106 Warsaw, Poland; (B.Ś.); (A.M.)
| | - Józef Dulak
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, Gronostajowa 7 Street, 30-387 Kraków, Poland; (O.M.); (M.M.); (P.P.); (J.D.)
| | - Agnieszka Łoboda
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, Gronostajowa 7 Street, 30-387 Kraków, Poland; (O.M.); (M.M.); (P.P.); (J.D.)
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23
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Hoyer MJ, Capitanio C, Smith IR, Paoli JC, Bieber A, Jiang Y, Paulo JA, Gonzalez-Lozano MA, Baumeister W, Wilfling F, Schulman BA, Harper JW. Combinatorial selective ER-phagy remodels the ER during neurogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546565. [PMID: 37425907 PMCID: PMC10326971 DOI: 10.1101/2023.06.26.546565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The endoplasmic reticulum (ER) employs a diverse proteome landscape to orchestrate many cellular functions ranging from protein and lipid synthesis to calcium ion flux and inter-organelle communication. A case in point concerns the process of neurogenesis: a refined tubular ER network is assembled via ER shaping proteins into the newly formed neuronal projections to create highly polarized dendrites and axons. Previous studies have suggested a role for autophagy in ER remodeling, as autophagy-deficient neurons in vivo display axonal ER accumulation within synaptic boutons, and the membrane-embedded ER-phagy receptor FAM134B has been genetically linked with human sensory and autonomic neuropathy. However, our understanding of the mechanisms underlying selective removal of ER and the role of individual ER-phagy receptors is limited. Here, we combine a genetically tractable induced neuron (iNeuron) system for monitoring ER remodeling during in vitro differentiation with proteomic and computational tools to create a quantitative landscape of ER proteome remodeling via selective autophagy. Through analysis of single and combinatorial ER-phagy receptor mutants, we delineate the extent to which each receptor contributes to both magnitude and selectivity of ER protein clearance. We define specific subsets of ER membrane or lumenal proteins as preferred clients for distinct receptors. Using spatial sensors and flux reporters, we demonstrate receptor-specific autophagic capture of ER in axons, and directly visualize tubular ER membranes within autophagosomes in neuronal projections by cryo-electron tomography. This molecular inventory of ER proteome remodeling and versatile genetic toolkit provides a quantitative framework for understanding contributions of individual ER-phagy receptors for reshaping ER during cell state transitions.
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He A, Zheng S, Luan W, Wang L, Qian L, Qi F, Feng Z. Antiphotoaging Effect of Micronized Fat in Ultraviolet B-Induced Human Dermal Fibroblasts. Plast Reconstr Surg 2023; 152:1023-1033. [PMID: 36988447 DOI: 10.1097/prs.0000000000010458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
BACKGROUND Adipose-derived stromal vascular fraction (SVF) and mesenchymal stem cells have been proven to reduce the effects of skin photoaging. However, there is no standardized protocol for their preparation. This study aimed to investigate the skin rejuvenation potential of micronized fat, obtained using a novel device attached with a trifoliate blade, in the ultraviolet B (UV-B)-induced human dermal fibroblast model. METHODS Micronized fat was prepared to obtain adipose-derived SVF, and the adipose-derived mesenchymal stem cell-to-SVF ratio was determined by flow cytometry. The UV-B-induced human dermal fibroblasts model was constructed to identify the characteristics of the human dermal fibroblasts using vimentin and S-100 immunostaining, observe their morphology, and measure the levels of photoaging-related factors. After the previous steps were completed, different cell groups were co-cultured with UV-B-induced human dermal fibroblasts, and the extent of improvement of photoaging was evaluated. RESULTS Micronized fat had a higher adipose-derived mesenchymal stem cell-to-SVF ratio than the control fat preparations. The UV-B-induced human dermal fibroblasts model showed lowered levels of type I collagen and transforming growth factor-β and increased expression of matrix metalloproteinases (MMPs), which are the characteristics of photoaging in normal human dermal fibroblasts. Compared with different cell groups co-cultured with UV-B-induced human dermal fibroblasts, micronized fat could lower the expression of MMPs and increase the level of type I collagen but lower the level of transforming growth factor-β. CONCLUSIONS Obtaining micronized fat is more effortless and clinically safer. Micronized fat has an antiphotoaging effect by inhibiting the expression of MMPs by means of the mitogen-activated protein kinases signaling pathway. CLINICAL RELEVANCE STATEMENT The authors' work has potential clinical applications in fat grafting for facial rejuvenation.
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Affiliation(s)
- Anqi He
- From the Department of Plastic Surgery, Zhongshan Hospital (Xiamen), Fudan University
| | - Shaoluan Zheng
- From the Department of Plastic Surgery, Zhongshan Hospital (Xiamen), Fudan University
| | - Wenjie Luan
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University
| | - Lu Wang
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University
| | - Leqi Qian
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University
| | - Fazhi Qi
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University
| | - Zihao Feng
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University
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25
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Hickey KL, Swarup S, Smith IR, Paoli JC, Miguel Whelan E, Paulo JA, Harper JW. Proteome census upon nutrient stress reveals Golgiphagy membrane receptors. Nature 2023; 623:167-174. [PMID: 37757899 PMCID: PMC10620096 DOI: 10.1038/s41586-023-06657-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 09/20/2023] [Indexed: 09/29/2023]
Abstract
During nutrient stress, macroautophagy degrades cellular macromolecules, thereby providing biosynthetic building blocks while simultaneously remodelling the proteome1,2. Although the machinery responsible for initiation of macroautophagy has been well characterized3,4, our understanding of the extent to which individual proteins, protein complexes and organelles are selected for autophagic degradation, and the underlying targeting mechanisms, is limited. Here we use orthogonal proteomic strategies to provide a spatial proteome census of autophagic cargo during nutrient stress in mammalian cells. We find that macroautophagy has selectivity for recycling membrane-bound organelles (principally Golgi and endoplasmic reticulum). Through autophagic cargo prioritization, we identify a complex of membrane-embedded proteins, YIPF3 and YIPF4, as receptors for Golgiphagy. During nutrient stress, YIPF3 and YIPF4 interact with ATG8 proteins through LIR motifs and are mobilized into autophagosomes that traffic to lysosomes in a process that requires the canonical autophagic machinery. Cells lacking YIPF3 or YIPF4 are selectively defective in elimination of a specific cohort of Golgi membrane proteins during nutrient stress. Moreover, YIPF3 and YIPF4 play an analogous role in Golgi remodelling during programmed conversion of stem cells to the neuronal lineage in vitro. Collectively, the findings of this study reveal prioritization of membrane protein cargo during nutrient-stress-dependent proteome remodelling and identify a Golgi remodelling pathway that requires membrane-embedded receptors.
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Affiliation(s)
- Kelsey L Hickey
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Sharan Swarup
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Casma Therapeutics, Cambridge, MA, USA
| | - Ian R Smith
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Velia Therapeutics, San Diego, CA, USA
| | - Julia C Paoli
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | | | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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26
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Mulholland PJ, Berto S, Wilmarth PA, McMahan C, Ball LE, Woodward JJ. Adaptor protein complex 2 in the orbitofrontal cortex predicts alcohol use disorder. Mol Psychiatry 2023; 28:4766-4776. [PMID: 37679472 PMCID: PMC10918038 DOI: 10.1038/s41380-023-02236-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/17/2023] [Accepted: 08/23/2023] [Indexed: 09/09/2023]
Abstract
Alcohol use disorder (AUD) is a life-threatening disease characterized by compulsive drinking, cognitive deficits, and social impairment that continue despite negative consequences. The inability of individuals with AUD to regulate drinking may involve functional deficits in cortical areas that normally balance actions that have aspects of both reward and risk. Among these, the orbitofrontal cortex (OFC) is critically involved in goal-directed behavior and is thought to maintain a representation of reward value that guides decision making. In the present study, we analyzed post-mortem OFC brain samples collected from age- and sex-matched control subjects and those with AUD using proteomics, bioinformatics, machine learning, and reverse genetics approaches. Of the 4,500+ total unique proteins identified in the proteomics screen, there were 47 proteins that differed significantly by sex that were enriched in processes regulating extracellular matrix and axonal structure. Gene ontology enrichment analysis revealed that proteins differentially expressed in AUD cases were involved in synaptic and mitochondrial function, as well as transmembrane transporter activity. Alcohol-sensitive OFC proteins also mapped to abnormal social behaviors and social interactions. Machine learning analysis of the post-mortem OFC proteome revealed dysregulation of presynaptic (e.g., AP2A1) and mitochondrial proteins that predicted the occurrence and severity of AUD. Using a reverse genetics approach to validate a target protein, we found that prefrontal Ap2a1 expression significantly correlated with voluntary alcohol drinking in male and female genetically diverse mouse strains. Moreover, recombinant inbred strains that inherited the C57BL/6J allele at the Ap2a1 interval consumed higher amounts of alcohol than those that inherited the DBA/2J allele. Together, these findings highlight the impact of excessive alcohol consumption on the human OFC proteome and identify important cross-species cortical mechanisms and proteins that control drinking in individuals with AUD.
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Affiliation(s)
- Patrick J Mulholland
- Department of Neuroscience, Medical University of South Carolina, Charleston, SC, 29425, USA.
- Charleston Alcohol Research Center, Medical University of South Carolina, Charleston, SC, 29425, USA.
| | - Stefano Berto
- Department of Neuroscience, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Phillip A Wilmarth
- Proteomics Shared Resource, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239, USA
| | - Christopher McMahan
- School of Mathematical and Statistical Sciences, Clemson-MUSC Artificial Intelligence Hub, Clemson University, Clemson, SC, 29634-0975, USA
| | - Lauren E Ball
- Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - John J Woodward
- Department of Neuroscience, Medical University of South Carolina, Charleston, SC, 29425, USA
- Charleston Alcohol Research Center, Medical University of South Carolina, Charleston, SC, 29425, USA
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27
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Deleeuw V, Carlson E, Renard M, Zientek KD, Wilmarth PA, Reddy AP, Manalo EC, Tufa SF, Keene DR, Olbinado M, Stampanoni M, Kanki S, Yanagisawa H, Mosquera LM, Sips P, De Backer J, Sakai LY. Unraveling the role of TGFβ signaling in thoracic aortic aneurysm and dissection using Fbn1 mutant mouse models. Matrix Biol 2023; 123:17-33. [PMID: 37683955 DOI: 10.1016/j.matbio.2023.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 08/23/2023] [Accepted: 09/05/2023] [Indexed: 09/10/2023]
Abstract
Although abnormal TGFβ signaling is observed in several heritable forms of thoracic aortic aneurysms and dissections including Marfan syndrome, its precise role in aortic disease progression is still disputed. Using a mouse genetic approach and quantitative isobaric labeling proteomics, we sought to elucidate the role of TGFβ signaling in three Fbn1 mutant mouse models representing a range of aortic disease from microdissection (without aneurysm) to aneurysm (without rupture) to aneurysm and rupture. Results indicated that reduced TGFβ signaling and increased mast cell proteases were associated with microdissection. In contrast, increased abundance of extracellular matrix proteins, which could be reporters for positive TGFβ signaling, were associated with aneurysm. Marked reductions in collagens and fibrillins, and increased TGFβ signaling, were associated with aortic rupture. Our data indicate that TGFβ signaling performs context-dependent roles in the pathogenesis of thoracic aortic disease.
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Affiliation(s)
- Violette Deleeuw
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent B-9000, Belgium
| | - Eric Carlson
- Department of Molecular & Medical Genetics, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, United States
| | - Marjolijn Renard
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent B-9000, Belgium; Shriners Children's Hospital, 3101 SW Sam Jackson Park Road, Portland, OR 97239, United States
| | - Keith D Zientek
- Proteomics Shared Resource, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, OR 97239, United States
| | - Phillip A Wilmarth
- Proteomics Shared Resource, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, OR 97239, United States
| | - Ashok P Reddy
- Proteomics Shared Resource, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, OR 97239, United States
| | - Elise C Manalo
- Shriners Children's Hospital, 3101 SW Sam Jackson Park Road, Portland, OR 97239, United States
| | - Sara F Tufa
- Shriners Children's Hospital, 3101 SW Sam Jackson Park Road, Portland, OR 97239, United States
| | - Douglas R Keene
- Shriners Children's Hospital, 3101 SW Sam Jackson Park Road, Portland, OR 97239, United States
| | - Margie Olbinado
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Marco Stampanoni
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Sachiko Kanki
- Department of Thoracic and Cardiovascular Surgery, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki, Osaka 569-0801 Japan
| | - Hiromi Yanagisawa
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, The University of Tsukuba, Tsukuba, Ibaraki 305-8577 Japan
| | - Laura Muiño Mosquera
- Department of Pediatrics, Division of Pediatric Cardiology, Ghent University Hospital, Corneel Heymanslaan 10, Ghent B-9000, Belgium
| | - Patrick Sips
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent B-9000, Belgium
| | - Julie De Backer
- Department of Cardiology, Ghent University Hospital, Corneel Heymanslaan 10, Ghent B-9000, Belgium
| | - Lynn Y Sakai
- Department of Molecular & Medical Genetics, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, United States.
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28
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Tsumagari K, Sato Y, Aoyagi H, Okano H, Kuromitsu J. Proteomic characterization of aging-driven changes in the mouse brain by co-expression network analysis. Sci Rep 2023; 13:18191. [PMID: 37875604 PMCID: PMC10598061 DOI: 10.1038/s41598-023-45570-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 10/20/2023] [Indexed: 10/26/2023] Open
Abstract
Brain aging causes a progressive decline in functional capacity and is a strong risk factor for dementias such as Alzheimer's disease. To characterize age-related proteomic changes in the brain, we used quantitative proteomics to examine brain tissues, cortex and hippocampus, of mice at three age points (3, 15, and 24 months old), and quantified more than 7000 proteins in total with high reproducibility. We found that many of the proteins upregulated with age were extracellular proteins, such as extracellular matrix proteins and secreted proteins, associated with glial cells. On the other hand, many of the significantly downregulated proteins were associated with synapses, particularly postsynaptic density, specifically in the cortex but not in the hippocampus. Our datasets will be helpful as resources for understanding the molecular basis of brain aging.
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Affiliation(s)
- Kazuya Tsumagari
- Center for Integrated Medical Research, Keio University School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan.
- Proteome Homeostasis Research Unit, RIKEN Center for Integrative Medical Sciences, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
- Laboratory for Integrative Genomics, Proteome Homeostasis Research Unit, RIKEN Center for Integrative Medical Sciences, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
| | - Yoshiaki Sato
- Eisai-Keio Innovation Laboratory for Dementia, Human Biology Integration Foundation, Eisai Co., Ltd., Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Hirofumi Aoyagi
- Eisai-Keio Innovation Laboratory for Dementia, Human Biology Integration Foundation, Eisai Co., Ltd., Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Junro Kuromitsu
- Eisai-Keio Innovation Laboratory for Dementia, Human Biology Integration Foundation, Eisai Co., Ltd., Shinjuku-ku, Tokyo, 160-8582, Japan.
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29
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Hutchings C, Dawson CS, Krueger T, Lilley KS, Breckels LM. A Bioconductor workflow for processing, evaluating, and interpreting expression proteomics data. F1000Res 2023; 12:1402. [PMID: 38021401 PMCID: PMC10683783 DOI: 10.12688/f1000research.139116.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/15/2023] [Indexed: 12/01/2023] Open
Abstract
Background: Expression proteomics involves the global evaluation of protein abundances within a system. In turn, differential expression analysis can be used to investigate changes in protein abundance upon perturbation to such a system. Methods: Here, we provide a workflow for the processing, analysis and interpretation of quantitative mass spectrometry-based expression proteomics data. This workflow utilizes open-source R software packages from the Bioconductor project and guides users end-to-end and step-by-step through every stage of the analyses. As a use-case we generated expression proteomics data from HEK293 cells with and without a treatment. Of note, the experiment included cellular proteins labelled using tandem mass tag (TMT) technology and secreted proteins quantified using label-free quantitation (LFQ). Results: The workflow explains the software infrastructure before focusing on data import, pre-processing and quality control. This is done individually for TMT and LFQ datasets. The application of statistical differential expression analysis is demonstrated, followed by interpretation via gene ontology enrichment analysis. Conclusions: A comprehensive workflow for the processing, analysis and interpretation of expression proteomics is presented. The workflow is a valuable resource for the proteomics community and specifically beginners who are at least familiar with R who wish to understand and make data-driven decisions with regards to their analyses.
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Affiliation(s)
- Charlotte Hutchings
- Cambridge Centre for Proteomics, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Charlotte S. Dawson
- Cambridge Centre for Proteomics, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Thomas Krueger
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Kathryn S. Lilley
- Cambridge Centre for Proteomics, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Lisa M. Breckels
- Cambridge Centre for Proteomics, University of Cambridge, Cambridge, CB2 1QR, UK
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30
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Shorey-Kendrick LE, Crosland BA, Spindel ER, McEvoy CT, Wilmarth PA, Reddy AP, Zientek KD, Roberts VHJ, D'Mello RJ, Ryan KS, Olyaei AF, Hagen OL, Drake MG, McCarty OJT, Scottoline BP, Lo JO. The amniotic fluid proteome changes across gestation in humans and rhesus macaques. Sci Rep 2023; 13:17039. [PMID: 37814009 PMCID: PMC10562452 DOI: 10.1038/s41598-023-44125-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/04/2023] [Indexed: 10/11/2023] Open
Abstract
Amniotic fluid is a complex biological medium that offers protection to the fetus and plays a key role in normal fetal nutrition, organogenesis, and potentially fetal programming. Amniotic fluid is also critically involved in longitudinally shaping the in utero milieu during pregnancy. Yet, the molecular mechanism(s) of action by which amniotic fluid regulates fetal development is ill-defined partly due to an incomplete understanding of the evolving composition of the amniotic fluid proteome. Prior research consisting of cross-sectional studies suggests that the amniotic fluid proteome changes as pregnancy advances, yet longitudinal alterations have not been confirmed because repeated sampling is prohibitive in humans. We therefore performed serial amniocenteses at early, mid, and late gestational time-points within the same pregnancies in a rhesus macaque model. Longitudinally-collected rhesus amniotic fluid samples were paired with gestational-age matched cross-sectional human samples. Utilizing LC-MS/MS isobaric labeling quantitative proteomics, we demonstrate considerable cross-species similarity between the amniotic fluid proteomes and large scale gestational-age associated changes in protein content throughout pregnancy. This is the first study to compare human and rhesus amniotic fluid proteomic profiles across gestation and establishes a reference amniotic fluid proteome. The non-human primate model holds promise as a translational platform for amniotic fluid studies.
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Affiliation(s)
- Lyndsey E Shorey-Kendrick
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - B Adam Crosland
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Eliot R Spindel
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Cindy T McEvoy
- Division of Neonatology. Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA
| | - Phillip A Wilmarth
- Proteomics Shared Resources, Oregon Health & Science University, Portland, OR, USA
| | - Ashok P Reddy
- Proteomics Shared Resources, Oregon Health & Science University, Portland, OR, USA
| | - Keith D Zientek
- Proteomics Shared Resources, Oregon Health & Science University, Portland, OR, USA
| | - Victoria H J Roberts
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Rahul J D'Mello
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Kimberly S Ryan
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Amy F Olyaei
- Division of Neonatology. Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA
| | - Olivia L Hagen
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Matthew G Drake
- Division of Pulmonary and Critical Care Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Owen J T McCarty
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
| | - Brian P Scottoline
- Division of Neonatology. Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Jamie O Lo
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR, 97239, USA.
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA.
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31
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Jacques M, Landen S, Romero JA, Hiam D, Schittenhelm RB, Hanchapola I, Shah AD, Voisin S, Eynon N. Methylome and proteome integration in human skeletal muscle uncover group and individual responses to high-intensity interval training. FASEB J 2023; 37:e23184. [PMID: 37698381 DOI: 10.1096/fj.202300840rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 08/17/2023] [Accepted: 08/24/2023] [Indexed: 09/13/2023]
Abstract
Exercise is a major beneficial contributor to muscle metabolism, and health benefits acquired by exercise are a result of molecular shifts occurring across multiple molecular layers (i.e., epigenome, transcriptome, and proteome). Identifying robust, across-molecular level targets associated with exercise response, at both group and individual levels, is paramount to develop health guidelines and targeted health interventions. Sixteen, apparently healthy, moderately trained (VO2 max = 51.0 ± 10.6 mL min-1 kg-1 ) males (age range = 18-45 years) from the Gene SMART (Skeletal Muscle Adaptive Responses to Training) study completed a longitudinal study composed of 12-week high-intensity interval training (HIIT) intervention. Vastus lateralis muscle biopsies were collected at baseline and after 4, 8, and 12 weeks of HIIT. DNA methylation (~850 CpG sites) and proteomic (~3000 proteins) analyses were conducted at all time points. Mixed models were applied to estimate group and individual changes, and methylome and proteome integration was conducted using a holistic multilevel approach with the mixOmics package. A total of 461 proteins significantly changed over time (at 4, 8, and 12 weeks), whilst methylome overall shifted with training only one differentially methylated position (DMP) was significant (adj.p-value < .05). K-means analysis revealed cumulative protein changes by clusters of proteins that presented similar changes over time. Individual responses to training were observed in 101 proteins. Seven proteins had large effect-sizes >0.5, among them are two novel exercise-related proteins, LYRM7 and EPN1. Integration analysis showed bidirectional relationships between the methylome and proteome. We showed a significant influence of HIIT on the epigenome and more so on the proteome in human muscle, and uncovered groups of proteins clustering according to similar patterns across the exercise intervention. Individual responses to exercise were observed in the proteome with novel mitochondrial and metabolic proteins consistently changed across individuals. Future work is required to elucidate the role of these proteins in response to exercise.
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Affiliation(s)
- Macsue Jacques
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Victoria, Australia
| | - Shanie Landen
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Victoria, Australia
| | - Javier Alvarez Romero
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Victoria, Australia
| | - Danielle Hiam
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Victoria, Australia
- Institute of Nutrition and Health Sciences, Deakin University, Melbourne, Victoria, Australia
| | - Ralf B Schittenhelm
- Monash Proteomics & Metabolomics Facility, Monash University, Melbourne, Victoria, Australia
| | - Iresha Hanchapola
- Monash Proteomics & Metabolomics Facility, Monash University, Melbourne, Victoria, Australia
| | - Anup D Shah
- Monash Proteomics & Metabolomics Facility, Monash University, Melbourne, Victoria, Australia
| | - Sarah Voisin
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Victoria, Australia
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nir Eynon
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
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32
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Arumugam TV, Alli-Shaik A, Liehn EA, Selvaraji S, Poh L, Rajeev V, Cho Y, Cho Y, Kim J, Kim J, Swa HLF, Hao DTZ, Rattanasopa C, Fann DYW, Mayan DC, Ng GYQ, Baik SH, Mallilankaraman K, Gelderblom M, Drummond GR, Sobey CG, Kennedy BK, Singaraja RR, Mattson MP, Jo DG, Gunaratne J. Multiomics analyses reveal dynamic bioenergetic pathways and functional remodeling of the heart during intermittent fasting. eLife 2023; 12:RP89214. [PMID: 37769126 PMCID: PMC10538958 DOI: 10.7554/elife.89214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023] Open
Abstract
Intermittent fasting (IF) has been shown to reduce cardiovascular risk factors in both animals and humans, and can protect the heart against ischemic injury in models of myocardial infarction. However, the underlying molecular mechanisms behind these effects remain unclear. To shed light on the molecular and cellular adaptations of the heart to IF, we conducted comprehensive system-wide analyses of the proteome, phosphoproteome, and transcriptome, followed by functional analysis. Using advanced mass spectrometry, we profiled the proteome and phosphoproteome of heart tissues obtained from mice that were maintained on daily 12- or 16 hr fasting, every-other-day fasting, or ad libitum control feeding regimens for 6 months. We also performed RNA sequencing to evaluate whether the observed molecular responses to IF occur at the transcriptional or post-transcriptional levels. Our analyses revealed that IF significantly affected pathways that regulate cyclic GMP signaling, lipid and amino acid metabolism, cell adhesion, cell death, and inflammation. Furthermore, we found that the impact of IF on different metabolic processes varied depending on the length of the fasting regimen. Short IF regimens showed a higher correlation of pathway alteration, while longer IF regimens had an inverse correlation of metabolic processes such as fatty acid oxidation and immune processes. Additionally, functional echocardiographic analyses demonstrated that IF enhances stress-induced cardiac performance. Our systematic multi-omics study provides a molecular framework for understanding how IF impacts the heart's function and its vulnerability to injury and disease.
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Affiliation(s)
- Thiruma V Arumugam
- Centre for Cardiovascular Biology and Disease Research, Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe UniversityMelbourneAustralia
- Department of Physiology, Yong Loo Lin School Medicine, National University of SingaporeSingaporeSingapore
- School of Pharmacy, Sungkyunkwan UniversitySuwonRepublic of Korea
| | - Asfa Alli-Shaik
- Translational Biomedical Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and ResearchSingaporeSingapore
| | - Elisa A Liehn
- National Heart Research Institute, National Heart Centre SingaporeSingaporeSingapore
- Institute for Molecular Medicine, University of Southern DenmarkOdenseDenmark
- National Institute of Pathology "Victor Babes"BucharestRomania
| | - Sharmelee Selvaraji
- Department of Physiology, Yong Loo Lin School Medicine, National University of SingaporeSingaporeSingapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of SingaporeSingaporeSingapore
| | - Luting Poh
- Department of Physiology, Yong Loo Lin School Medicine, National University of SingaporeSingaporeSingapore
| | - Vismitha Rajeev
- Department of Physiology, Yong Loo Lin School Medicine, National University of SingaporeSingaporeSingapore
| | - Yoonsuk Cho
- School of Pharmacy, Sungkyunkwan UniversitySuwonRepublic of Korea
| | - Yongeun Cho
- School of Pharmacy, Sungkyunkwan UniversitySuwonRepublic of Korea
| | - Jongho Kim
- School of Pharmacy, Sungkyunkwan UniversitySuwonRepublic of Korea
| | - Joonki Kim
- Department of Physiology, Yong Loo Lin School Medicine, National University of SingaporeSingaporeSingapore
- Natural Products Research Center, Korea Institute of Science and TechnologyGangneungRepublic of Korea
| | - Hannah LF Swa
- Translational Biomedical Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and ResearchSingaporeSingapore
| | - David Tan Zhi Hao
- Department of Physiology, Yong Loo Lin School Medicine, National University of SingaporeSingaporeSingapore
| | - Chutima Rattanasopa
- Translational Laboratories in Genetic Medicine, Agency for Science, Technology and ResearchSingaporeSingapore
- Cardiovascular and Metabolic Disorders Program, Duke-National University of SingaporeSingaporeSingapore
| | - David Yang-Wei Fann
- Department of Physiology, Yong Loo Lin School Medicine, National University of SingaporeSingaporeSingapore
| | - David Castano Mayan
- Translational Laboratories in Genetic Medicine, Agency for Science, Technology and ResearchSingaporeSingapore
| | - Gavin Yong-Quan Ng
- Department of Physiology, Yong Loo Lin School Medicine, National University of SingaporeSingaporeSingapore
| | - Sang-Ha Baik
- Department of Physiology, Yong Loo Lin School Medicine, National University of SingaporeSingaporeSingapore
| | - Karthik Mallilankaraman
- Department of Physiology, Yong Loo Lin School Medicine, National University of SingaporeSingaporeSingapore
| | - Mathias Gelderblom
- Department of Neurology, University Medical Center Hamburg-EppendorfHamburgGermany
| | - Grant R Drummond
- Centre for Cardiovascular Biology and Disease Research, Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe UniversityMelbourneAustralia
| | - Christopher G Sobey
- Centre for Cardiovascular Biology and Disease Research, Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe UniversityMelbourneAustralia
| | - Brian K Kennedy
- Department of Physiology, Yong Loo Lin School Medicine, National University of SingaporeSingaporeSingapore
- Department of Biochemistry, Yong Loo Lin School Medicine, National University of SingaporeSingaporeSingapore
| | - Roshni R Singaraja
- Department of Medicine, Yong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
| | - Mark P Mattson
- Department of Neuroscience, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Dong-Gyu Jo
- School of Pharmacy, Sungkyunkwan UniversitySuwonRepublic of Korea
| | - Jayantha Gunaratne
- Translational Biomedical Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and ResearchSingaporeSingapore
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
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Uoselis L, Lindblom R, Lam WK, Küng CJ, Skulsuppaisarn M, Khuu G, Nguyen TN, Rudler DL, Filipovska A, Schittenhelm RB, Lazarou M. Temporal landscape of mitochondrial proteostasis governed by the UPR mt. SCIENCE ADVANCES 2023; 9:eadh8228. [PMID: 37738349 PMCID: PMC10516501 DOI: 10.1126/sciadv.adh8228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 08/24/2023] [Indexed: 09/24/2023]
Abstract
Breakdown of mitochondrial proteostasis activates quality control pathways including the mitochondrial unfolded protein response (UPRmt) and PINK1/Parkin mitophagy. However, beyond the up-regulation of chaperones and proteases, we have a limited understanding of how the UPRmt remodels and restores damaged mitochondrial proteomes. Here, we have developed a functional proteomics framework, termed MitoPQ (Mitochondrial Proteostasis Quantification), to dissect the UPRmt's role in maintaining proteostasis during stress. We find essential roles for the UPRmt in both protecting and repairing proteostasis, with oxidative phosphorylation metabolism being a central target of the UPRmt. Transcriptome analyses together with MitoPQ reveal that UPRmt transcription factors drive independent signaling arms that act in concert to maintain proteostasis. Unidirectional interplay between the UPRmt and PINK1/Parkin mitophagy was found to promote oxidative phosphorylation recovery when the UPRmt failed. Collectively, this study defines the network of proteostasis mediated by the UPRmt and highlights the value of functional proteomics in decoding stressed proteomes.
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Affiliation(s)
- Louise Uoselis
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD 20185, USA
| | - Runa Lindblom
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD 20185, USA
| | - Wai Kit Lam
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD 20185, USA
| | - Catharina J. Küng
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Marvin Skulsuppaisarn
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Grace Khuu
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD 20185, USA
| | - Thanh N. Nguyen
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD 20185, USA
| | - Danielle L. Rudler
- Harry Perkins Institute of Medical Research and ARC Centre of Excellence in Synthetic Biology, Nedlands, Western Australia, Australia
- Telethon Kids Institute, Northern Entrance, Perth Children’s Hospital, Nedlands, Western Australia, Australia
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research and ARC Centre of Excellence in Synthetic Biology, Nedlands, Western Australia, Australia
- Telethon Kids Institute, Northern Entrance, Perth Children’s Hospital, Nedlands, Western Australia, Australia
| | - Ralf B. Schittenhelm
- Monash Proteomics and Metabolomics Facility, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Michael Lazarou
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD 20185, USA
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
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Landen S, Jacques M, Hiam D, Alvarez-Romero J, Schittenhelm RB, Shah AD, Huang C, Steele JR, Harvey NR, Haupt LM, Griffiths LR, Ashton KJ, Lamon S, Voisin S, Eynon N. Sex differences in muscle protein expression and DNA methylation in response to exercise training. Biol Sex Differ 2023; 14:56. [PMID: 37670389 PMCID: PMC10478435 DOI: 10.1186/s13293-023-00539-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 08/18/2023] [Indexed: 09/07/2023] Open
Abstract
BACKGROUND Exercise training elicits changes in muscle physiology, epigenomics, transcriptomics, and proteomics, with males and females exhibiting differing physiological responses to exercise training. However, the molecular mechanisms contributing to the differing adaptations between the sexes are poorly understood. METHODS We performed a meta-analysis for sex differences in skeletal muscle DNA methylation following an endurance training intervention (Gene SMART cohort and E-MTAB-11282 cohort). We investigated for sex differences in the skeletal muscle proteome following an endurance training intervention (Gene SMART cohort). Lastly, we investigated whether the methylome and proteome are associated with baseline cardiorespiratory fitness (maximal oxygen consumption; VO2max) in a sex-specific manner. RESULTS Here, we investigated for the first time, DNA methylome and proteome sex differences in response to exercise training in human skeletal muscle (n = 78; 50 males, 28 females). We identified 92 DNA methylation sites (CpGs) associated with exercise training; however, no CpGs changed in a sex-dependent manner. In contrast, we identified 189 proteins that are differentially expressed between the sexes following training, with 82 proteins differentially expressed between the sexes at baseline. Proteins showing the most robust sex-specific response to exercise include SIRT3, MRPL41, and MBP. Irrespective of sex, cardiorespiratory fitness was associated with robust methylome changes (19,257 CpGs) and no proteomic changes. We did not observe sex differences in the association between cardiorespiratory fitness and the DNA methylome. Integrative multi-omic analysis identified sex-specific mitochondrial metabolism pathways associated with exercise responses. Lastly, exercise training and cardiorespiratory fitness shifted the DNA methylomes to be more similar between the sexes. CONCLUSIONS We identified sex differences in protein expression changes, but not DNA methylation changes, following an endurance exercise training intervention; whereas we identified no sex differences in the DNA methylome or proteome response to lifelong training. Given the delicate interaction between sex and training as well as the limitations of the current study, more studies are required to elucidate whether there is a sex-specific training effect on the DNA methylome. We found that genes involved in mitochondrial metabolism pathways are differentially modulated between the sexes following endurance exercise training. These results shed light on sex differences in molecular adaptations to exercise training in skeletal muscle.
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Affiliation(s)
- Shanie Landen
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Australia
- Centre for Endocrinology and Metabolism, Hudson Institute of Medical Research, Melbourne, VIC, Australia
| | - Macsue Jacques
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Australia
| | - Danielle Hiam
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Australia
- Institute for Physical Activity and Nutrition, School of Exercise and Nutrition Sciences, Deakin University, Geelong, Australia
| | | | - Ralf B Schittenhelm
- Monash Proteomics and Metabolomics Facility, Monash University, Melbourne, Australia
| | - Anup D Shah
- Monash Proteomics and Metabolomics Facility, Monash University, Melbourne, Australia
| | - Cheng Huang
- Monash Proteomics and Metabolomics Facility, Monash University, Melbourne, Australia
| | - Joel R Steele
- Monash Proteomics and Metabolomics Facility, Monash University, Melbourne, Australia
| | - Nicholas R Harvey
- Faculty of Health Sciences and Medicine, Bond University, Gold Coast, QLD, 4226, Australia
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Queensland University of Technology (QUT), 60 Musk Ave., Kelvin Grove, QLD, 4059, Australia
| | - Larisa M Haupt
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Queensland University of Technology (QUT), 60 Musk Ave., Kelvin Grove, QLD, 4059, Australia
| | - Lyn R Griffiths
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Queensland University of Technology (QUT), 60 Musk Ave., Kelvin Grove, QLD, 4059, Australia
| | - Kevin J Ashton
- Faculty of Health Sciences and Medicine, Bond University, Gold Coast, QLD, 4226, Australia
| | - Séverine Lamon
- Institute for Physical Activity and Nutrition, School of Exercise and Nutrition Sciences, Deakin University, Geelong, Australia
| | - Sarah Voisin
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Australia
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nir Eynon
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Australia.
- Australian Regenerative Medicine Institute (ARMI), Monash University, Clayton, VIC, 3800, Australia.
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35
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Rivolta AA, Bujold AR, Wilmarth PA, Phinney BS, Navelski JP, Horohov DW, Sanz MG. Comparison of the broncoalveolar lavage fluid proteomics between foals and adult horses. PLoS One 2023; 18:e0290778. [PMID: 37669266 PMCID: PMC10479908 DOI: 10.1371/journal.pone.0290778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 08/15/2023] [Indexed: 09/07/2023] Open
Abstract
Neonates have different cellular composition in their bronchoalveolar lavage fluid (BALF) when compared to foals and adult horses; however, little is known about the non-cellular components of BALF. The objective of this study was to determine the proteomic composition of BALF in neonatal horses and to compare it to that of foals and adult horses. Bronchoalveolar lavage fluid samples of seven neonates (< 1 week age), four 5 to 7-week-old foals, and six adult horses were collected. Quantitative proteomics of the fluid was performed using tandem mass tag labeling followed by high resolution liquid chromatography tandem mass spectrometry and protein relative abundances were compared between groups using exact text. A total of 704 proteins were identified with gene ontology terms and were classified. Of these, 332 proteins were related to the immune system in neonates, foals, and adult horses. The most frequent molecular functions identified were binding and catalytic activity and the most common biological processes were cellular process, metabolic process, and biological regulation. There was a significant difference in the proteome of neonates when compared to foals and to adult horses. Neonates had less relative expression (FDR < 0.01) of many immune-related proteins, including immunoglobulins, proteins involved in the complement cascade, ferritin, BPI fold-containing family B member 1, and macrophage receptor MARCO. This is the first report of equine neonate BALF proteomics and reveals differential abundance of proteins when compared to BALF from adult horses. The lower relative abundance of immune-related proteins in neonates could contribute to their susceptibility to pulmonary infections.
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Affiliation(s)
- Alejandra A. Rivolta
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Adina R. Bujold
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
| | - Phillip A. Wilmarth
- Proteomic Shared Resource, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Brett S. Phinney
- Genome Center Proteomics Core Facility, UC Davis, Davis, California, United States of America
| | - Joseph P. Navelski
- School of Economic Sciences, Washington State University, Pullman, Washington, United States of America
| | - David W. Horohov
- Gluck Equine Research Center, University of Kentucky, Lexington, Kentucky, United States of America
| | - Macarena G. Sanz
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
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Kapp KL, Ji Choi M, Bai K, Du L, Yende S, Kellum JA, Angus DC, Peck-Palmer OM, Robinson RAS. PATHWAYS ASSOCIATED WITH POSITIVE SEPSIS SURVIVAL OUTCOMES IN AFRICAN AMERICAN/BLACK AND NON-HISPANIC WHITE PATIENTS WITH URINARY TRACT INFECTION. Shock 2023; 60:362-372. [PMID: 37493584 PMCID: PMC10527228 DOI: 10.1097/shk.0000000000002176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
ABSTRACT Urinary tract infections (UTIs) are a common cause of sepsis worldwide. Annually, more than 60,000 US deaths can be attributed to sepsis secondary to UTIs, and African American/Black adults have higher incidence and case-fatality rates than non-Hispanic White adults. Molecular-level factors that may help partially explain differences in sepsis survival outcomes between African American/Black and Non-Hispanic White adults are not clear. In this study, patient samples (N = 166) from the Protocolized Care for Early Septic Shock cohort were analyzed using discovery-based plasma proteomics. Patients had sepsis secondary to UTIs and were stratified according to self-identified racial background and sepsis survival outcomes. Proteomics results suggest patient heterogeneity across mechanisms driving survival from sepsis secondary to UTIs. Differentially expressed proteins (n = 122, false discovery rate-adjusted P < 0.05) in Non-Hispanic White sepsis survivors were primarily in immune system pathways, while differentially expressed proteins (n = 47, false discovery rate-adjusted P < 0.05) in African American/Black patients were mostly in metabolic pathways. However, in all patients, regardless of racial background, there were 16 differentially expressed proteins in sepsis survivors involved in translation initiation and shutdown pathways. These pathways are potential targets for prognostic intervention. Overall, this study provides information about molecular factors that may help explain disparities in sepsis survival outcomes among African American/Black and Non-Hispanic White patients with primary UTIs.
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Affiliation(s)
- Kathryn L. Kapp
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
- The Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 32732, USA
| | - Min Ji Choi
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
| | - Kun Bai
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37203, USA
| | - Liping Du
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37203, USA
- Vanderbilt Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Sachin Yende
- The Clinical Research, Investigation, and Systems Modeling of Acute Illnesses (CRISMA) Center, University of Pittsburgh, Pittsburgh, PA, 15213, USA
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- Department of Clinical and Translational Science, University of Pittsburgh, PA, 15261, USA
| | - John A. Kellum
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Derek C. Angus
- The Clinical Research, Investigation, and Systems Modeling of Acute Illnesses (CRISMA) Center, University of Pittsburgh, Pittsburgh, PA, 15213, USA
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- Department of Clinical and Translational Science, University of Pittsburgh, PA, 15261, USA
| | - Octavia M. Peck-Palmer
- The Clinical Research, Investigation, and Systems Modeling of Acute Illnesses (CRISMA) Center, University of Pittsburgh, Pittsburgh, PA, 15213, USA
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- Department of Clinical and Translational Science, University of Pittsburgh, PA, 15261, USA
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Renã A. S. Robinson
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
- The Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 32732, USA
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Chen L, Zhou M, Li H, Liu D, Liao P, Zong Y, Zhang C, Zou W, Gao J. Mitochondrial heterogeneity in diseases. Signal Transduct Target Ther 2023; 8:311. [PMID: 37607925 PMCID: PMC10444818 DOI: 10.1038/s41392-023-01546-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 02/21/2023] [Accepted: 06/13/2023] [Indexed: 08/24/2023] Open
Abstract
As key organelles involved in cellular metabolism, mitochondria frequently undergo adaptive changes in morphology, components and functions in response to various environmental stresses and cellular demands. Previous studies of mitochondria research have gradually evolved, from focusing on morphological change analysis to systematic multiomics, thereby revealing the mitochondrial variation between cells or within the mitochondrial population within a single cell. The phenomenon of mitochondrial variation features is defined as mitochondrial heterogeneity. Moreover, mitochondrial heterogeneity has been reported to influence a variety of physiological processes, including tissue homeostasis, tissue repair, immunoregulation, and tumor progression. Here, we comprehensively review the mitochondrial heterogeneity in different tissues under pathological states, involving variant features of mitochondrial DNA, RNA, protein and lipid components. Then, the mechanisms that contribute to mitochondrial heterogeneity are also summarized, such as the mutation of the mitochondrial genome and the import of mitochondrial proteins that result in the heterogeneity of mitochondrial DNA and protein components. Additionally, multiple perspectives are investigated to better comprehend the mysteries of mitochondrial heterogeneity between cells. Finally, we summarize the prospective mitochondrial heterogeneity-targeting therapies in terms of alleviating mitochondrial oxidative damage, reducing mitochondrial carbon stress and enhancing mitochondrial biogenesis to relieve various pathological conditions. The possibility of recent technological advances in targeted mitochondrial gene editing is also discussed.
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Affiliation(s)
- Long Chen
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Sciences, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Mengnan Zhou
- Department of Pathogenic Biology, School of Basic Medical Science, China Medical University, Shenyang, 110001, China
| | - Hao Li
- Department of Orthopaedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
| | - Delin Liu
- Department of Orthopaedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
| | - Peng Liao
- Department of Orthopaedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
| | - Yao Zong
- Centre for Orthopaedic Research, Medical School, The University of Western Australia, Nedlands, WA, 6009, Australia
| | - Changqing Zhang
- Department of Orthopaedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China.
| | - Weiguo Zou
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Sciences, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China.
- Institute of Microsurgery on Extremities, and Department of Orthopedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China.
| | - Junjie Gao
- Department of Orthopaedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China.
- Institute of Microsurgery on Extremities, and Department of Orthopedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China.
- Shanghai Sixth People's Hospital Fujian, No. 16, Luoshan Section, Jinguang Road, Luoshan Street, Jinjiang City, Quanzhou, Fujian, China.
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38
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Mulholland PJ, Berto S, Wilmarth PA, McMahan C, Ball LE, Woodward JJ. Adaptor protein complex 2 in the orbitofrontal cortex predicts alcohol use disorder. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.28.542637. [PMID: 37398482 PMCID: PMC10312445 DOI: 10.1101/2023.05.28.542637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Alcohol use disorder (AUD) is a life-threatening disease characterized by compulsive drinking, cognitive deficits, and social impairment that continue despite negative consequences. The inability of individuals with AUD to regulate drinking may involve functional deficits in cortical areas that normally balance actions that have aspects of both reward and risk. Among these, the orbitofrontal cortex (OFC) is critically involved in goal-directed behavior and is thought to maintain a representation of reward value that guides decision making. In the present study, we analyzed post-mortem OFC brain samples collected from age- and sex-matched control subjects and those with AUD using proteomics, bioinformatics, machine learning, and reverse genetics approaches. Of the 4,500+ total unique proteins identified in the proteomics screen, there were 47 proteins that differed significantly by sex that were enriched in processes regulating extracellular matrix and axonal structure. Gene ontology enrichment analysis revealed that proteins differentially expressed in AUD cases were involved in synaptic and mitochondrial function, as well as transmembrane transporter activity. Alcohol-sensitive OFC proteins also mapped to abnormal social behaviors and social interactions. Machine learning analysis of the post-mortem OFC proteome revealed dysregulation of presynaptic (e.g., AP2A1) and mitochondrial proteins that predicted the occurrence and severity of AUD. Using a reverse genetics approach to validate a target protein, we found that prefrontal Ap2a1 expression significantly correlated with voluntary alcohol drinking in male and female genetically diverse mouse strains. Moreover, recombinant inbred strains that inherited the C57BL/6J allele at the Ap2a1 interval consumed higher amounts of alcohol than those that inherited the DBA/2J allele. Together, these findings highlight the impact of excessive alcohol consumption on the human OFC proteome and identify important cross-species cortical mechanisms and proteins that control drinking in individuals with AUD.
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39
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Huang T, Staniak M, da Veiga Leprevost F, Figueroa-Navedo AM, Ivanov AR, Nesvizhskii AI, Choi M, Vitek O. Statistical Detection of Differentially Abundant Proteins in Experiments with Repeated Measures Designs and Isobaric Labeling. J Proteome Res 2023; 22:2641-2659. [PMID: 37467362 PMCID: PMC11090052 DOI: 10.1021/acs.jproteome.3c00155] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Repeated measures experimental designs, which quantify proteins in biological subjects repeatedly over multiple experimental conditions or times, are commonly used in mass spectrometry-based proteomics. Such designs distinguish the biological variation within and between the subjects and increase the statistical power of detecting within-subject changes in protein abundance. Meanwhile, proteomics experiments increasingly incorporate tandem mass tag (TMT) labeling, a multiplexing strategy that gains both relative protein quantification accuracy and sample throughput. However, combining repeated measures and TMT multiplexing in a large-scale investigation presents statistical challenges due to unique interplays of between-mixture, within-mixture, between-subject, and within-subject variation. This manuscript proposes a family of linear mixed-effects models for differential analysis of proteomics experiments with repeated measures and TMT multiplexing. These models decompose the variation in the data into the contributions from its sources as appropriate for the specifics of each experiment, enable statistical inference of differential protein abundance, and recognize a difference in the uncertainty of between-subject versus within-subject comparisons. The proposed family of models is implemented in the R/Bioconductor package MSstatsTMT v2.2.0. Evaluations of four simulated datasets and four investigations answering diverse biological questions demonstrated the value of this approach as compared to the existing general-purpose approaches and implementations.
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Affiliation(s)
- Ting Huang
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Mateusz Staniak
- Institute of Mathematics, University of Wrocław, Wrocław, Poland
| | | | - Amanda M. Figueroa-Navedo
- Department of Chemistry and Chemical Biology, Barnett Institute of Biological and Chemical Analysis, Northeastern University, Boston, MA, USA
| | - Alexander R. Ivanov
- Department of Chemistry and Chemical Biology, Barnett Institute of Biological and Chemical Analysis, Northeastern University, Boston, MA, USA
| | | | - Meena Choi
- Departments of Microchemistry, Proteomics & Lipidomics, Genentech, South San Francisco, CA, USA
| | - Olga Vitek
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
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40
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Quanrud GM, Lyu Z, Balamurugan SV, Canizal C, Wu HT, Genereux JC. Cellular Exposure to Chloroacetanilide Herbicides Induces Distinct Protein Destabilization Profiles. ACS Chem Biol 2023; 18:1661-1676. [PMID: 37427419 PMCID: PMC10367052 DOI: 10.1021/acschembio.3c00338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 06/23/2023] [Indexed: 07/11/2023]
Abstract
Herbicides in the widely used chloroacetanilide class harbor a potent electrophilic moiety, which can damage proteins through nucleophilic substitution. In general, damaged proteins are subject to misfolding. Accumulation of misfolded proteins compromises cellular integrity by disrupting cellular proteostasis networks, which can further destabilize the cellular proteome. While direct conjugation targets can be discovered through affinity-based protein profiling, there are few approaches to probe how cellular exposure to toxicants impacts the stability of the proteome. We apply a quantitative proteomics methodology to identify chloroacetanilide-destabilized proteins in HEK293T cells based on their binding to the H31Q mutant of the human Hsp40 chaperone DNAJB8. We find that a brief cellular exposure to the chloroacetanilides acetochlor, alachlor, and propachlor induces misfolding of dozens of cellular proteins. These herbicides feature distinct but overlapping profiles of protein destabilization, highly concentrated in proteins with reactive cysteine residues. Consistent with the recent literature from the pharmacology field, reactivity is driven by neither inherent nucleophilic nor electrophilic reactivity but is idiosyncratic. We discover that propachlor induces a general increase in protein aggregation and selectively targets GAPDH and PARK7, leading to a decrease in their cellular activities. Hsp40 affinity profiling identifies a majority of propachlor targets identified by competitive activity-based protein profiling (ABPP), but ABPP can only identify about 10% of protein targets identified by Hsp40 affinity profiling. GAPDH is primarily modified by the direct conjugation of propachlor at a catalytic cysteine residue, leading to global destabilization of the protein. The Hsp40 affinity strategy is an effective technique to profile cellular proteins that are destabilized by cellular toxin exposure. Raw proteomics data is available through the PRIDE Archive at PXD030635.
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Affiliation(s)
- Guy M. Quanrud
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Ziqi Lyu
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Sunil V. Balamurugan
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Carolina Canizal
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Hoi-Ting Wu
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Joseph C. Genereux
- Department of Chemistry, University of California, Riverside, California 92521, United States
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41
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Song G, Chen J, Deng Y, Sun L, Yan Y. TMT Labeling Reveals the Effects of Exercises on the Proteomic Characteristics of the Subcutaneous Adipose Tissue of Growing High-Fat-Diet-Fed Rats. ACS OMEGA 2023; 8:23484-23500. [PMID: 37426235 PMCID: PMC10324099 DOI: 10.1021/acsomega.3c00627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/24/2023] [Indexed: 07/11/2023]
Abstract
Aim: Growing period is an important period for fat remodeling. High-fat diet and exercise are reasons for adipose tissue (AT) remodeling, but existing evidence is not enough. Therefore, the effects of moderate-intensity continuous training (MICT) and high-intensity interval training (HIIT) on the proteomic characteristics of the subcutaneous AT of growing rats on normal diet or high-fat diet (HFD) were determined. Methods: Four-week-old male Sprague-Dawley rats (n = 48) were subdivided into six groups: normal diet control group, normal diet-MICT group, normal diet-HIIT group, HFD control group, HFD-MICT group, and HFD-HIIT group. Rats in the training group ran on a treadmill 5 days a week for 8 weeks (MICT: 50 min at 60-70% VO2max intensity; HIIT: 7 min of warm-up and recovery at 70% VO2max intensity, 6 sets of 3 min of 30% VO2max followed by 3 min 90% VO2max). Following physical assessment, inguinal subcutaneous adipose tissue (sWAT) was collected for proteome analysis using tandem mass tag labeling. Results: MICT and HIIT attenuated body fat mass and lean body mass but did not affect weight gain. Proteomics revealed the impact of exercise on ribosome, spliceosome, and the pentose phosphate pathway. However, the effect was reversed on HFD and normal diet. The differentially expressed proteins (DEPs) affected by MICT were related to oxygen transport, ribosome, and spliceosome. In comparison, the DEPs affected by HIIT were related to oxygen transport, mitochondrial electron transport, and mitochondrion protein. In HFD, HIIT was more likely to cause changes in immune proteins than MICT. However, exercise did not seem to reverse the protein effects of HFD. Conclusion: The exercise stress response in the growing period was stronger but increased the energy metabolism and metabolism. MICT and HIIT can reduce fat, increase muscle percentage, and improve maximum oxygen uptake in rats fed with HFD. However, in rats with normal diet, MICT and HIIT triggered more immune responses of sWAT, especially HIIT. In addition, spliceosomes may be the key factors in AT remodeling triggered by exercise and diet.
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Affiliation(s)
- Ge Song
- Department
of Sport Biochemistry, School of Sport Science, Beijing Sport University, Beijing 100084, China
| | - Junying Chen
- Department
of Sport Biochemistry, School of Sport Science, Beijing Sport University, Beijing 100084, China
- Guangdong
Ersha Sports Training Center, Guangzhou 510105, China
| | - Yimin Deng
- Department
of Sport Biochemistry, School of Sport Science, Beijing Sport University, Beijing 100084, China
- Fuzhou
Medical College of Nanchang University, Fuzhou 344000, China
| | - Lingyu Sun
- Department
of Sport Biochemistry, School of Sport Science, Beijing Sport University, Beijing 100084, China
| | - Yi Yan
- Department
of Sport Biochemistry, School of Sport Science, Beijing Sport University, Beijing 100084, China
- Laboratory
of Sports Stress and Adaptation of General Administration of Sport, Beijing100084, China
- Laboratory
of Physical Fitness and Exercise, Ministry
of Education, Beijing Sport University, Beijing 100084, China
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42
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Mangalaparthi KK, Patel K, Khan AA, Nair B, Kumar RV, Prasad TSK, Sidransky D, Chatterjee A, Pandey A, Gowda H. Molecular Characterization of Esophageal Squamous Cell Carcinoma Using Quantitative Proteomics. Cancers (Basel) 2023; 15:3302. [PMID: 37444412 DOI: 10.3390/cancers15133302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/26/2023] [Accepted: 05/03/2023] [Indexed: 07/15/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is a heterogeneous cancer associated with a poor prognosis in advanced stages. In India, it is the sixth most common cause of cancer-related mortality. In this study, we employed high-resolution mass spectrometry-based quantitative proteomics to characterize the differential protein expression pattern associated with ESCC. We identified several differentially expressed proteins including PDPN, TOP2A, POSTN and MMP2 that were overexpressed in ESCC. In addition, we identified downregulation of esophagus tissue-enriched proteins such as SLURP1, PADI1, CSTA, small proline-rich proteins such as SPRR3, SPRR2A, SPRR1A, KRT4, and KRT13, involved in squamous cell differentiation. We identified several overexpressed proteins mapped to the 3q24-29 chromosomal region, aligning with CNV alterations in this region reported in several published studies. Among these, we identified overexpression of SOX2, TP63, IGF2BP2 and RNF13 that are encoded by genes in the 3q26 region. Functional enrichment analysis revealed proteins involved in cell cycle pathways, DNA replication, spliceosome, and DNA repair pathways. We identified the overexpression of multiple proteins that play a major role in alleviating ER stress, including SYVN1 and SEL1L. The SYVN1/SEL1L complex is an essential part of the ER quality control machinery clearing misfolded proteins from the ER. SYVN1 is an E3 ubiquitin ligase that ubiquitinates ER-resident proteins. Interestingly, there are also other non-canonical substrates of SYVN1 which are known to play a crucial role in tumor progression. Thus, SYVN1 could be a potential therapeutic target in ESCC.
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Affiliation(s)
- Kiran K Mangalaparthi
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 691001, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Krishna Patel
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 691001, India
| | - Aafaque Ahmad Khan
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Bipin Nair
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 691001, India
| | - Rekha V Kumar
- Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore 560066, India
| | - Thottethodi Subrahmanya Keshav Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 691001, India
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - David Sidransky
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Otolaryngology and Head & Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Aditi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 691001, India
- Manipal Academy of Higher Education, Manipal 576104, India
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
- Manipal Academy of Higher Education, Manipal 576104, India
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences, Hosur Road, Bangalore 560029, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 691001, India
- Manipal Academy of Higher Education, Manipal 576104, India
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Kraus F, Goodall EA, Smith IR, Jiang Y, Paoli JC, Adolf F, Zhang J, Paulo JA, Schulman BA, Harper JW. PARK15/FBXO7 is dispensable for PINK1/Parkin mitophagy in iNeurons and HeLa cell systems. EMBO Rep 2023:e56399. [PMID: 37334901 PMCID: PMC10398645 DOI: 10.15252/embr.202256399] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 05/16/2023] [Accepted: 06/01/2023] [Indexed: 06/21/2023] Open
Abstract
The protein kinase PINK1 and ubiquitin ligase Parkin promote removal of damaged mitochondria via a feed-forward mechanism involving ubiquitin (Ub) phosphorylation (pUb), Parkin activation, and ubiquitylation of mitochondrial outer membrane proteins to support the recruitment of mitophagy receptors. The ubiquitin ligase substrate receptor FBXO7/PARK15 is mutated in an early-onset parkinsonian-pyramidal syndrome. Previous studies have proposed a role for FBXO7 in promoting Parkin-dependent mitophagy. Here, we systematically examine the involvement of FBXO7 in depolarization and mt UPR-dependent mitophagy in the well-established HeLa and induced-neurons cell systems. We find that FBXO7-/- cells have no demonstrable defect in: (i) kinetics of pUb accumulation, (ii) pUb puncta on mitochondria by super-resolution imaging, (iii) recruitment of Parkin and autophagy machinery to damaged mitochondria, (iv) mitophagic flux, and (v) mitochondrial clearance as quantified by global proteomics. Moreover, global proteomics of neurogenesis in the absence of FBXO7 reveals no obvious alterations in mitochondria or other organelles. These results argue against a general role for FBXO7 in Parkin-dependent mitophagy and point to the need for additional studies to define how FBXO7 mutations promote parkinsonian-pyramidal syndrome.
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Affiliation(s)
- Felix Kraus
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Ellen A Goodall
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Ian R Smith
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Yizhi Jiang
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Julia C Paoli
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Frank Adolf
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jiuchun Zhang
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Joao A Paulo
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Brenda A Schulman
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - J Wade Harper
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
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Edwards W, Greco TM, Miner GE, Barker NK, Herring L, Cohen S, Cristea IM, Conlon FL. Quantitative proteomic profiling identifies global protein network dynamics in murine embryonic heart development. Dev Cell 2023; 58:1087-1105.e4. [PMID: 37148880 PMCID: PMC10330608 DOI: 10.1016/j.devcel.2023.04.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 01/27/2023] [Accepted: 04/14/2023] [Indexed: 05/08/2023]
Abstract
Defining the mechanisms that govern heart development is essential for identifying the etiology of congenital heart disease. Here, quantitative proteomics was used to measure temporal changes in the proteome at critical stages of murine embryonic heart development. Global temporal profiles of the over 7,300 proteins uncovered signature cardiac protein interaction networks that linked protein dynamics with molecular pathways. Using this integrated dataset, we identified and demonstrated a functional role for the mevalonate pathway in regulating the cell cycle of embryonic cardiomyocytes. Overall, our proteomic datasets are a resource for studying events that regulate embryonic heart development and contribute to congenital heart disease.
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Affiliation(s)
- Whitney Edwards
- Department of Biology and Genetics, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA; Integrative Program for Biological and Genome Sciences, UNC-Chapel Hill, Chapel Hill, NC, 27599 USA
| | - Todd M Greco
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Gregory E Miner
- Department of Cell Biology and Physiology, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Natalie K Barker
- Department of Pharmacology, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Laura Herring
- Department of Pharmacology, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sarah Cohen
- Department of Cell Biology and Physiology, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Frank L Conlon
- Department of Biology and Genetics, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, UNC-Chapel Hill, Chapel Hill, NC 27599, USA; Integrative Program for Biological and Genome Sciences, UNC-Chapel Hill, Chapel Hill, NC, 27599 USA.
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45
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Krivinko JM, DeChellis-Marks MR, Zeng L, Fan P, Lopez OL, Ding Y, Wang L, Kofler J, MacDonald ML, Sweet RA. Targeting the post-synaptic proteome has therapeutic potential for psychosis in Alzheimer Disease. Commun Biol 2023; 6:598. [PMID: 37268664 PMCID: PMC10238472 DOI: 10.1038/s42003-023-04961-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/20/2023] [Indexed: 06/04/2023] Open
Abstract
Individuals with Alzheimer Disease who develop psychotic symptoms (AD + P) experience more rapid cognitive decline and have reduced indices of synaptic integrity relative to those without psychosis (AD-P). We sought to determine whether the postsynaptic density (PSD) proteome is altered in AD + P relative to AD-P, analyzing PSDs from dorsolateral prefrontal cortex of AD + P, AD-P, and a reference group of cognitively normal elderly subjects. The PSD proteome of AD + P showed a global shift towards lower levels of all proteins relative to AD-P, enriched for kinases, proteins regulating Rho GTPases, and other regulators of the actin cytoskeleton. We computationally identified potential novel therapies predicted to reverse the PSD protein signature of AD + P. Five days of administration of one of these drugs, the C-C Motif Chemokine Receptor 5 inhibitor, maraviroc, led to a net reversal of the PSD protein signature in adult mice, nominating it as a novel potential treatment for AD + P.
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Affiliation(s)
- J M Krivinko
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - M R DeChellis-Marks
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - L Zeng
- Department of Biostatistics, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
| | - P Fan
- Department of Pharmaceutical Sciences, Computational Chemical Genomics Screening Center, University of Pittsburgh School of Pharmacy, Pittsburgh, PA, USA
| | - O L Lopez
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Y Ding
- Department of Biostatistics, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
| | - L Wang
- Department of Pharmaceutical Sciences, Computational Chemical Genomics Screening Center, University of Pittsburgh School of Pharmacy, Pittsburgh, PA, USA
| | - J Kofler
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - M L MacDonald
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - R A Sweet
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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Liu Y, Zhang X, Yang L, Zhou S, Li Y, Shen Y, Lu S, Zhou J, Liu Y. Proteomics and transcriptomics explore the effect of mixture of herbal extract on diabetic wound healing process. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 116:154892. [PMID: 37267693 DOI: 10.1016/j.phymed.2023.154892] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/28/2023] [Accepted: 05/16/2023] [Indexed: 06/04/2023]
Abstract
BACKGROUND The annual incidence of diabetic foot ulcers (DFUs) has been reported to vary from 0.2% to 11% in diabetes-specific clinical settings and less than 0.1% to 8% in community- and population-based cohorts. According to the International Diabetes Foundation, approximately 40 million to 60 million people worldwide are affected by DFUs, and a recent meta-analysis indicates a global prevalence of 6.3% among adults with diabetes, or about 33 million individuals. The cost of diabetes care is significant, amounting to $273 billion in direct and $90 billion in indirect expenses annually, in America. Foot complications in diabetes care excess annual expenditures ranging from 50% to 200% above the baseline cost of diabetes-related care. The cost of advanced-stage ulcers can be more than $50,000 per wound episode, and the direct expenses of major amputation are even higher. DFUs can be treated using various methods, including wound dressings, antibiotics, pressure-off loading, skin substitutes, stem cells, debridement, topical oxygen therapy, gene therapy and growth factors. For severe DFUs patients are at risk of amputation if treatment is not timely or appropriate. Amputating limbs not only causes physical pain to patients, but also brings economic burden due to lost productivity, and decreased employment linked to DFUs. Currently, long-term use of local antibiotics in clinical practice is prone to induce drug resistance, while growth factors do not effectively inhibit bacterial growth and control inflammation in wounds. Stem cell and gene therapies are still in the experimental stage. The method of local debridement combined with negative pressure therapy is expensive. Therefore, we urgently need an affordable, non-surgical method to treat diabetic ulcers. Extracts of bark of Bauhinia purpurea, Paeoniae rubrae, Angelica dahurica (Hoffm.) Benth. & Hook.f. ex Franch. & Sav. (Hoffm.) Benth. & Hook.f. ex Franch. & Sav., Acorus calamus L, and Radix Angelicae biseratae have been used as traditional remedies to treat inflammation-related diseases and cutaneous wounds due to their anti-inflammatory properties and their ability to promote vascular renewal. However, there have been few studies on the mixture of these five herbal extracts on diabetic wound healing. PURPOSE This study was designed to assess the healing effect of a mixture of five aforementioned herbal extracts on diabetic ulcer wounds in rats, and to reveal the potential mechanisms behind any potential wound healing using transcriptomics and proteomics. STUDY DESIGN We designed the experiment to explore the effects of five herbal extracts on diabetic wound healing process through in vivo experiments and to investigate the underlying mechanisms through proteomics and transcriptomics. METHODS We used a mixture of five aforementioned herbal extract to treat rat model of diabetic established by intraperitoneal injection of streptozotocin, and a 2 × 2 cm round full-thickness skin defect was created on the back of the rat. Staphylococcus aureus (1 ml of 1.5 × 109 cfu/ml) was evenly applied to the wound. The wound was then observed for 72 h. The infected ulcer model of diabetic rats was considered to be successfully established if the wound was found to be infected with S. aureus. According to different medications, the rats were divided into three groups, namely mixture of herbal extract (MHE), Kangfuxin solution (KFS) and control (Ctrl). The effects of the medicine on wound healing were observed. HE staining and Masson staining were performed to evaluate the histopathological changes and collagen synthesis. IHC staining was used to assess the neovascularization, and M2 macrophage proliferation was determined by immunofluorescence staining. Proteomic and transcriptomic studies were performed to explore potential mechanism of five herbal extracts to promote wound healing. UHPLC-QE-MS was performed to identify the chemical composition of mixture of herbal extract. RESULTS The study show that the mixed herbal extract promotes angiogenesis, proliferation of M2 macrophages, and collagen synthesis. Transcriptomics showed that rno-miR-1298, rno-miR-144-5p, and rno-miR-92a-1-5p are vital miRNAs which also play a significant role in role in regulating wound healing. Proteomics results showed that the following proteins were important in wounds treated with MHE: Rack1, LOC100362366, Cops2, Cops6, Eif4e, Eif3c, Rpl12, Srp54, Rpl13 and Lsm7. Autophagy, PI3-Akt and mTOR signaling pathways were enriched after treatment with MHE compared to other groups. CONCLUSION Herein, we have shown that MHE containing extracts of bark of Bauhinia purpurea, P. rubrae, A. dahurica (Hoffm.) Benth. & Hook.f. ex Franch. & Sav., A. calamus L, and R. A. biseratae has significant wound healing effects in the diabetic ulcer wound rat model. These results suggest that local application of MHE in diabetic wounds can accelerate the wound healing process. Moreover, in vivo experiments revealed that the diabetic wound healing process was primarily mediated by angiogenesis and M2 macrophage transition. Therefore, this study may provide a promising and non-surgical therapeutic strategy to accelerate diabetic wound healing, thereby decreasing the number of limb amputations in diabetic patients.
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Affiliation(s)
- Yang Liu
- Inner Mongolia Medical University, Hohhot, Inner Mongolia Autonomous Region, 010107, China; Department of Plastic Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan, 410013, China
| | - Xi Zhang
- The First Affiliated Hospital of Hunan University of Chinese Medicine, Changsha, 410007, China
| | - Liping Yang
- Inner Mongolia Medical University, Hohhot, Inner Mongolia Autonomous Region, 010107, China
| | - Shuai Zhou
- Inner Mongolia Medical University, Hohhot, Inner Mongolia Autonomous Region, 010107, China
| | - Yuewei Li
- Inner Mongolia Medical University, Hohhot, Inner Mongolia Autonomous Region, 010107, China
| | - Yiyu Shen
- Department of Plastic Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan, 410013, China
| | - Shengli Lu
- Department of Plastic Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan, 410013, China
| | - Jianda Zhou
- Department of Plastic Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan, 410013, China.
| | - Yu Liu
- Inner Mongolia Medical University, Hohhot, Inner Mongolia Autonomous Region, 010107, China; Hunan University of Chinese Medicine, Changsha, 410007, China.
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Yin K, Wu R. Investigation of cellular response to the HSP90 inhibition in human cells through thermal proteome profiling. Mol Cell Proteomics 2023; 22:100560. [PMID: 37119972 DOI: 10.1016/j.mcpro.2023.100560] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 03/31/2023] [Accepted: 04/24/2023] [Indexed: 05/01/2023] Open
Abstract
Heat shock proteins are chaperones and they are responsible for protein folding in cells. HSP90 is one of the most important chaperones in human cells, and its inhibition is promising for cancer therapy. However, despite the development of multiple HSP90 inhibitors, none of them has been approved for disease treatment due to unexpected cellular toxicity and side-effects. Hence, a more comprehensive investigation of cellular response to HSP90 inhibitors can aid in a better understanding of the molecular mechanisms of the cytotoxicity and side effects of these inhibitors. The thermal stability shifts of proteins, which represent protein structure and interaction alterations, can provide valuable information complementary to the results obtained from commonly used abundance-based proteomics analysis. Here, we systematically investigated cell response to different HSP90 inhibitors through global quantification of protein thermal stability changes using thermal proteome profiling, together with measurement of protein abundance changes. Besides the targets and potential off-targets of the drugs, proteins with significant thermal stability changes under the HSP90 inhibition are found to be involved in cell stress responses and the translation process. Moreover, proteins with thermal stability shifts under the inhibition are upstream of those with altered expression. These findings indicate that the HSP90 inhibition perturbs cell transcription and translation processes. The current study provides a different perspective for achieving a better understanding of cellular response to the chaperone inhibition.
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Affiliation(s)
- Kejun Yin
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.
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48
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Auf der Maur P, Trefny MP, Baumann Z, Vulin M, Correia AL, Diepenbruck M, Kramer N, Volkmann K, Preca BT, Ramos P, Leroy C, Eichlisberger T, Buczak K, Zilli F, Okamoto R, Rad R, Jensen MR, Fritsch C, Zippelius A, Stadler MB, Bentires-Alj M. N-acetylcysteine overcomes NF1 loss-driven resistance to PI3Kα inhibition in breast cancer. Cell Rep Med 2023; 4:101002. [PMID: 37044095 PMCID: PMC10140479 DOI: 10.1016/j.xcrm.2023.101002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 01/14/2023] [Accepted: 03/16/2023] [Indexed: 04/14/2023]
Abstract
A genome-wide PiggyBac transposon-mediated screen and a resistance screen in a PIK3CAH1047R-mutated murine tumor model reveal NF1 loss in mammary tumors resistant to the phosphatidylinositol 3-kinase α (PI3Kα)-selective inhibitor alpelisib. Depletion of NF1 in PIK3CAH1047R breast cancer cell lines and a patient-derived organoid model shows that NF1 loss reduces sensitivity to PI3Kα inhibition and correlates with enhanced glycolysis and lower levels of reactive oxygen species (ROS). Unexpectedly, the antioxidant N-acetylcysteine (NAC) sensitizes NF1 knockout cells to PI3Kα inhibition and reverts their glycolytic phenotype. Global phospho-proteomics indicates that combination with NAC enhances the inhibitory effect of alpelisib on mTOR signaling. In public datasets of human breast cancer, we find that NF1 is frequently mutated and that such mutations are enriched in metastases, an indication for which use of PI3Kα inhibitors has been approved. Our results raise the attractive possibility of combining PI3Kα inhibition with NAC supplementation, especially in patients with drug-resistant metastases associated with NF1 loss.
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Affiliation(s)
- Priska Auf der Maur
- Tumor Heterogeneity Metastasis and Resistance, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland.
| | - Marcel P Trefny
- Cancer Immunology, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Zora Baumann
- Tumor Heterogeneity Metastasis and Resistance, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Milica Vulin
- Tumor Heterogeneity Metastasis and Resistance, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Ana Luisa Correia
- Tumor Heterogeneity Metastasis and Resistance, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Maren Diepenbruck
- Tumor Heterogeneity Metastasis and Resistance, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Nicolas Kramer
- Tumor Heterogeneity Metastasis and Resistance, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Katrin Volkmann
- Tumor Heterogeneity Metastasis and Resistance, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Bogdan-Tiberius Preca
- Tumor Heterogeneity Metastasis and Resistance, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Pedro Ramos
- Oncology Research, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Cedric Leroy
- Oncology Research, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | | | - Katarzyna Buczak
- Proteomics Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Federica Zilli
- Tumor Heterogeneity Metastasis and Resistance, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Ryoko Okamoto
- Tumor Heterogeneity Metastasis and Resistance, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technische Universität München, München, Germany; Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technische Universität München, München, Germany; Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, München, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Christine Fritsch
- Oncology Research, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Alfred Zippelius
- Cancer Immunology, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Michael B Stadler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; Swiss Institute of Bioinformatics, Basel, Switzerland; Faculty of Science, University of Basel, Basel, Switzerland
| | - Mohamed Bentires-Alj
- Tumor Heterogeneity Metastasis and Resistance, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
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49
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Harkness BM, Hegarty DM, Saugstad JA, Behrens H, Betz J, David LL, Lapidus JA, Chen S, Stutzman R, Chamberlain W, Perez-Blanco M, Galor A, Aicher SA. Experimental design considerations for studies of human tear proteins. Ocul Surf 2023; 28:58-78. [PMID: 36764654 PMCID: PMC10409878 DOI: 10.1016/j.jtos.2023.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023]
Abstract
PURPOSE Human tears contain abundant, diverse sets of proteins that may serve as biomarkers of ocular surface health. There is a need for reproducible methods that consider multiple factors influencing the tear proteome, in addition to the variable of interest. Here we examined a workflow for proteomic analysis of tear proteins without the need to pool tear samples from multiple individuals, thus allowing for analyses based on individual factors, and increasing opportunities for protein biomarker discovery. METHODS Tears were collected by Schirmer strip following topical ocular anesthetic application then individually stored at -80 °C prior to processing for proteomics. Tear proteins were extracted from Schirmer strips, digested using suspension trapping spin columns (S-Trap), and labeled with high multiplicity tandem mass tags (TMT). Peptide digests were then extensively fractionated by two-dimensional chromatography and analyzed by mass spectrometry to identify and measure changes in protein abundance in each sample. Analysis of select samples was performed to test protocols and to compare the impact of clinically relevant parameters. To facilitate comparison of separate TMT experiments, common pool samples were included in each TMT instrument run and internal reference scaling (IRS) was performed. RESULTS Differences in subsets of tear proteins were noted for: geographic site of tear collection, contact lens use, and differences in tear fluid volume among individuals. CONCLUSION These findings demonstrate that proteomic analysis of human tear proteins can be performed without the need to pool samples, and that development of analytic workflows must consider factors that may affect outcomes in studies focused on diverse clinical samples.
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Affiliation(s)
- Brooke M Harkness
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA
| | - Deborah M Hegarty
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR, USA
| | - Julie A Saugstad
- Department of Anesthesiology & Perioperative Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Hannah Behrens
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR, USA
| | - Jason Betz
- Bascom Palmer Eye Institute, University of Miami, Miami, FL, USA
| | - Larry L David
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA; Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR, USA
| | - Jodi A Lapidus
- Biostatistics and Design Program, Oregon Health & Science University, USA; Oregon Health & Science University-Portland State University School of Public Health, USA
| | - Siting Chen
- Biostatistics and Design Program, Oregon Health & Science University, USA
| | - Richard Stutzman
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA
| | | | - Maricarmen Perez-Blanco
- Bascom Palmer Eye Institute, University of Miami, Miami, FL, USA; Surgical Services, Miami Veterans Administration Medical Center, Miami, FL, USA
| | - Anat Galor
- Bascom Palmer Eye Institute, University of Miami, Miami, FL, USA; Surgical Services, Miami Veterans Administration Medical Center, Miami, FL, USA
| | - Sue A Aicher
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR, USA.
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50
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Tuomivaara ST, Teo CF, Jan YN, Jan LY, Wiita AP. SLAPSHOT reveals rapid dynamics of extracellularly exposed proteome in response to calcium-activated plasma membrane phospholipid scrambling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.26.534250. [PMID: 36993417 PMCID: PMC10055316 DOI: 10.1101/2023.03.26.534250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
To facilitate our understanding of the often rapid and nuanced dynamics of extracellularly exposed proteomes during signaling events, it is important to devise robust workflows affording fast time resolution without biases and confounding factors. Here, we present Surface-exposed protein Labeling using PeroxidaSe, H2O2, and Tyramide-derivative (SLAPSHOT), to label extracellularly exposed proteins in a rapid, sensitive, and specific manner, while preserving cellular integrity. This experimentally simple and flexible method utilizes recombinant soluble APEX2 peroxidase that is applied to cells, thus circumventing biological perturbations, tedious engineering of tools and cells, and labeling biases. APEX2 neither requires metal cations for activity nor contains disulfide bonds, conferring versatility for a wide spectrum of experimental setups. We applied SLAPSHOT followed by quantitative mass spectrometry-based proteomics analysis to examine the immediate and extensive cell surface expansion and ensuing restorative membrane shedding upon the activation of Scott syndrome-linked TMEM16F, a ubiquitously expressed calcium-dependent phospholipid scramblase and ion channel. Time-course data ranging from one to thirty minutes of calcium stimulation using wild-type and TMEM16F deficient cells revealed intricate co-regulation of known protein families, including those in the integrin and ICAM families. Crucially, we identified proteins that are known to reside in intracellular organelles, including ER, as occupants of the freshly deposited membrane, and mitovesicles as an abundant component and contributor to the extracellularly exposed proteome. Our study not only provides the first accounts of the immediate consequences of calcium signaling on the extracellularly exposed proteome, but also presents a blueprint for the application of SLAPSHOT as a general approach for monitoring extracellularly exposed protein dynamics.
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Affiliation(s)
- Sami T. Tuomivaara
- Department of Laboratory Medicine, University of California, San Francisco, CA
| | - Chin Fen Teo
- Howard Hughes Medical Institute, University of California, San Francisco, CA
| | - Yuh Nung Jan
- Howard Hughes Medical Institute, University of California, San Francisco, CA
- Department of Physiology, University of California, San Francisco, CA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA
| | - Lily Y. Jan
- Howard Hughes Medical Institute, University of California, San Francisco, CA
- Department of Physiology, University of California, San Francisco, CA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA
| | - Arun P. Wiita
- Department of Laboratory Medicine, University of California, San Francisco, CA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA
- Chan Zuckerberg Biohub, San Francisco, CA
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