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Alharbi M, Lai A, Godbole N, Guanzon D, Nair S, Zuñiga F, Quinn A, Yang M, Wu SY, Salomon C. Enhancing precision targeting of ovarian cancer tumor cells in vivo through extracellular vesicle engineering. Int J Cancer 2024; 155:1510-1523. [PMID: 38848494 DOI: 10.1002/ijc.35055] [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: 10/27/2023] [Revised: 04/29/2024] [Accepted: 05/15/2024] [Indexed: 06/09/2024]
Abstract
Extracellular vesicles (EVs) function as natural mediators of intercellular communication, secreted by cells to facilitate cell-cell signaling. Due to their low toxicity, immunogenicity, biodegradability, and potential to encapsulate therapeutic drugs, EVs hold significant therapeutic promise. Nevertheless, their limited targeting ability often diminishes their therapeutic impact. Therefore, enhancing EVs by incorporating targeting units onto their membranes could bolster their targeting capabilities, enabling them to accumulate in specific cells and tissues. In this study, we engineered EVs to fuse ephrin-B2 with the EV membrane protein LAMP2b. This modification aimed to direct the engineered EVs toward the ephrin-B4 receptor expressed on the surface of ovarian cancer cells. The engineered EVs retained their inherent properties, including size, expression of EV membrane proteins, and morphology, upon isolation. In vitro experiments using real-time imaging revealed that EVs engineered with the ephrin-B2 ligand exhibited substantial internalization and uptake by ovarian cancer cells, in stark contrast to native EVs. In vivo, the engineered EVs carrying the ephrin-B2 ligand effectively targeted ovarian cancer cells, surpassing the targeting efficiency of control EVs. This innovative approach establishes a novel targeting system, enhancing the uptake of EVs by ovarian cancer cells. Our findings underscore the potential of using EVs to target cancer cells, thereby enhancing the effectiveness of anti-cancer therapies while minimizing off-target effects and toxicity in normal cells and organs.
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Affiliation(s)
- Mona Alharbi
- Translational Extracellular Vesicles in Obstetrics and Gynae-Oncology Group, University of Queensland Centre for Clinical Research, Faculty of Medicine, Royal Brisbane and Women's Hospital, The University of Queensland, Brisbane, Australia
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Andrew Lai
- Translational Extracellular Vesicles in Obstetrics and Gynae-Oncology Group, University of Queensland Centre for Clinical Research, Faculty of Medicine, Royal Brisbane and Women's Hospital, The University of Queensland, Brisbane, Australia
- UQ Centre for Extracellular Vesicle Nanomedicine, The University of Queensland, Brisbane, QLD, Australia
| | - Nihar Godbole
- Translational Extracellular Vesicles in Obstetrics and Gynae-Oncology Group, University of Queensland Centre for Clinical Research, Faculty of Medicine, Royal Brisbane and Women's Hospital, The University of Queensland, Brisbane, Australia
- UQ Centre for Extracellular Vesicle Nanomedicine, The University of Queensland, Brisbane, QLD, Australia
| | - Dominic Guanzon
- Translational Extracellular Vesicles in Obstetrics and Gynae-Oncology Group, University of Queensland Centre for Clinical Research, Faculty of Medicine, Royal Brisbane and Women's Hospital, The University of Queensland, Brisbane, Australia
- UQ Centre for Extracellular Vesicle Nanomedicine, The University of Queensland, Brisbane, QLD, Australia
| | - Soumyalekshmi Nair
- Translational Extracellular Vesicles in Obstetrics and Gynae-Oncology Group, University of Queensland Centre for Clinical Research, Faculty of Medicine, Royal Brisbane and Women's Hospital, The University of Queensland, Brisbane, Australia
- UQ Centre for Extracellular Vesicle Nanomedicine, The University of Queensland, Brisbane, QLD, Australia
| | - Felipe Zuñiga
- Department of Clinical Biochemistry and Immunology, Faculty of Pharmacy, University of Concepción, Concepción, Chile
| | - Alexander Quinn
- Centre for Clinical Research, Royal Brisbane and Women's Hospital, The University of Queensland, Brisbane, Australia
| | - Mengliu Yang
- School of Biomedical Sciences, The University of Queensland, Brisbane, Australia
| | - Sherry Y Wu
- UQ Centre for Extracellular Vesicle Nanomedicine, The University of Queensland, Brisbane, QLD, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, Australia
| | - Carlos Salomon
- Translational Extracellular Vesicles in Obstetrics and Gynae-Oncology Group, University of Queensland Centre for Clinical Research, Faculty of Medicine, Royal Brisbane and Women's Hospital, The University of Queensland, Brisbane, Australia
- UQ Centre for Extracellular Vesicle Nanomedicine, The University of Queensland, Brisbane, QLD, Australia
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Zhou M, Ge X, Xu X, Sheng B, Wang H, Shi H, Liu S, Tan B, Xu K, Wang J. A hot and cold tumor‑related prognostic signature for stage II colorectal cancer. Oncol Lett 2024; 28:419. [PMID: 39006949 PMCID: PMC11240279 DOI: 10.3892/ol.2024.14552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 06/05/2024] [Indexed: 07/16/2024] Open
Abstract
Globally, colorectal cancer (CRC) is one of the most lethal and prevalent malignancies. Based on the presence of immune cell infiltration in the tumor microenvironment, CRC can be divided into immunologically 'hot' or 'cold' tumors, which in turn leads to the differential efficacy of immunotherapy. However, the immune characteristics of hot and cold CRC tumors remain largely elusive, prompting further investigation of their properties regarding the tumor microenvironment. In the present study, a predictive model was developed based on the differential expression of proteins between cold and hot CRC tumors. First, the differentially expressed proteins (DEPs) were identified using digital spatial profiling and mass spectrometry-based proteomics analysis, and the pathway features of the DEPs were analyzed using functional enrichment analysis. A novel eight-gene signature prognostic risk model was developed (IDO1, MAT1A, NPEPL1, NT5C, PTGR2, RPL29, TMEM126A and TUBB4B), which was validated using data obtained from The Cancer Genome Atlas. The results revealed that the risk score of the eight-gene signature acted as an independent prognostic indicator in patients with stage II CRC (T3-4N0M0). It was also found that a high-risk score in the eight-gene signature was associated with high immune cell infiltration in patients with CRC. Taken together, these findings revealed some of the differential immune characteristics of hot and cold CRC tumors, and an eight-gene signature prognostic risk model was developed, which may serve as an independent prognostic indicator for patients with stage II CRC (T3-4N0M0).
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Affiliation(s)
- Ming Zhou
- Department of Colorectal Surgery and Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, P.R. China
- Center for Medical Research and Innovation in Digestive System Tumors, Ministry of Education, Hangzhou, Zhejiang 310000, P.R. China
- Zhejiang Provincial Clinical Research Center for Cancer, Hangzhou, Zhejiang 310000, P.R. China
- Cancer Center of Zhejiang University, Hangzhou, Zhejiang 310000, P.R. China
| | - Xiaoxu Ge
- Department of Colorectal Surgery and Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, P.R. China
- Center for Medical Research and Innovation in Digestive System Tumors, Ministry of Education, Hangzhou, Zhejiang 310000, P.R. China
- Zhejiang Provincial Clinical Research Center for Cancer, Hangzhou, Zhejiang 310000, P.R. China
- Cancer Center of Zhejiang University, Hangzhou, Zhejiang 310000, P.R. China
| | - Xiaoming Xu
- Department of Pathology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, P.R. China
| | - Biao Sheng
- Department of Colorectal Surgery and Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, P.R. China
- Center for Medical Research and Innovation in Digestive System Tumors, Ministry of Education, Hangzhou, Zhejiang 310000, P.R. China
- Zhejiang Provincial Clinical Research Center for Cancer, Hangzhou, Zhejiang 310000, P.R. China
- Cancer Center of Zhejiang University, Hangzhou, Zhejiang 310000, P.R. China
| | - Hao Wang
- Department of Colorectal Surgery and Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, P.R. China
- Center for Medical Research and Innovation in Digestive System Tumors, Ministry of Education, Hangzhou, Zhejiang 310000, P.R. China
- Zhejiang Provincial Clinical Research Center for Cancer, Hangzhou, Zhejiang 310000, P.R. China
- Cancer Center of Zhejiang University, Hangzhou, Zhejiang 310000, P.R. China
| | - Haoyu Shi
- Department of Colorectal Surgery and Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, P.R. China
- Center for Medical Research and Innovation in Digestive System Tumors, Ministry of Education, Hangzhou, Zhejiang 310000, P.R. China
- Zhejiang Provincial Clinical Research Center for Cancer, Hangzhou, Zhejiang 310000, P.R. China
- Cancer Center of Zhejiang University, Hangzhou, Zhejiang 310000, P.R. China
| | - Sikun Liu
- Department of Colorectal Surgery and Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, P.R. China
- Center for Medical Research and Innovation in Digestive System Tumors, Ministry of Education, Hangzhou, Zhejiang 310000, P.R. China
- Zhejiang Provincial Clinical Research Center for Cancer, Hangzhou, Zhejiang 310000, P.R. China
- Cancer Center of Zhejiang University, Hangzhou, Zhejiang 310000, P.R. China
| | - Boren Tan
- Department of Colorectal Surgery and Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, P.R. China
- Center for Medical Research and Innovation in Digestive System Tumors, Ministry of Education, Hangzhou, Zhejiang 310000, P.R. China
- Zhejiang Provincial Clinical Research Center for Cancer, Hangzhou, Zhejiang 310000, P.R. China
- Cancer Center of Zhejiang University, Hangzhou, Zhejiang 310000, P.R. China
| | - Kailun Xu
- Department of Breast Surgery and Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, P.R. China
| | - Jian Wang
- Department of Colorectal Surgery and Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, P.R. China
- Center for Medical Research and Innovation in Digestive System Tumors, Ministry of Education, Hangzhou, Zhejiang 310000, P.R. China
- Zhejiang Provincial Clinical Research Center for Cancer, Hangzhou, Zhejiang 310000, P.R. China
- Cancer Center of Zhejiang University, Hangzhou, Zhejiang 310000, P.R. China
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Aumer T, Däther M, Bergmayr L, Kartika S, Zeng T, Ge Q, Giorgio G, Hess AJ, Michalakis S, Traube FR. The type of DNA damage response after decitabine treatment depends on the level of DNMT activity. Life Sci Alliance 2024; 7:e202302437. [PMID: 38906675 PMCID: PMC11192838 DOI: 10.26508/lsa.202302437] [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: 10/15/2023] [Revised: 06/08/2024] [Accepted: 06/11/2024] [Indexed: 06/23/2024] Open
Abstract
Decitabine and azacytidine are considered as epigenetic drugs that induce DNA methyltransferase (DNMT)-DNA crosslinks, resulting in DNA hypomethylation and damage. Although they are already applied against myeloid cancers, important aspects of their mode of action remain unknown, highly limiting their clinical potential. Using a combinatorial approach, we reveal that the efficacy profile of both compounds primarily depends on the level of induced DNA damage. Under low DNMT activity, only decitabine has a substantial impact. Conversely, when DNMT activity is high, toxicity and cellular response to both compounds are dramatically increased, but do not primarily depend on DNA hypomethylation or RNA-associated processes. By investigating proteome dynamics on chromatin, we show that decitabine induces a strictly DNMT-dependent multifaceted DNA damage response based on chromatin recruitment, but not expression-level changes of repair-associated proteins. The choice of DNA repair pathway hereby depends on the severity of decitabine-induced DNA lesions. Although under moderate DNMT activity, mismatch (MMR), base excision (BER), and Fanconi anaemia-dependent DNA repair combined with homologous recombination are activated in response to decitabine, high DNMT activity and therefore immense replication stress induce activation of MMR and BER followed by non-homologous end joining.
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Affiliation(s)
- Tina Aumer
- Institute of Chemical Epigenetics Munich, Department of Chemistry, University of Munich (LMU), München, Germany
- https://ror.org/02kkvpp62 TUM School of Natural Sciences, Technical University of Munich (TUM), München, Germany
| | - Maike Däther
- Institute of Chemical Epigenetics Munich, Department of Chemistry, University of Munich (LMU), München, Germany
- https://ror.org/02kkvpp62 TUM School of Natural Sciences, Technical University of Munich (TUM), München, Germany
| | - Linda Bergmayr
- https://ror.org/02kkvpp62 TUM School of Natural Sciences, Technical University of Munich (TUM), München, Germany
| | - Stephanie Kartika
- Department of Biochemistry, University of Munich (LMU), München, Germany
| | - Theodor Zeng
- https://ror.org/02kkvpp62 TUM School of Natural Sciences, Technical University of Munich (TUM), München, Germany
| | - Qingyi Ge
- https://ror.org/02kkvpp62 TUM School of Natural Sciences, Technical University of Munich (TUM), München, Germany
| | - Grazia Giorgio
- Department of Ophthalmology, University Hospital LMU Munich, München, Germany
| | - Alexander J Hess
- https://ror.org/02kkvpp62 TUM School of Natural Sciences, Technical University of Munich (TUM), München, Germany
| | | | - Franziska R Traube
- Institute of Chemical Epigenetics Munich, Department of Chemistry, University of Munich (LMU), München, Germany
- https://ror.org/02kkvpp62 TUM School of Natural Sciences, Technical University of Munich (TUM), München, Germany
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
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Wu E, Xu G, Xie D, Qiao L. Data-independent acquisition in Metaproteomics. Expert Rev Proteomics 2024. [PMID: 39152734 DOI: 10.1080/14789450.2024.2394190] [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: 03/11/2024] [Revised: 08/12/2024] [Accepted: 08/14/2024] [Indexed: 08/19/2024]
Abstract
INTRODUCTION Metaproteomics offers insights into the function of complex microbial communities while it is also capable of revealing microbe-microbe and host-microbe interactions. Data-independent acquisition (DIA) mass spectrometry is an emerging technology, which holds great potential to achieve deep and accurate metaproteomics with higher reproducibility yet still facing a series of challenges due to the inherent complexity of metaproteomics and DIA data. AREAS COVERED This review offers an overview of the DIA metaproteomics approaches, covering aspects such as database construction, search strategy, and data analysis tools. Several cases of current DIA metaproteomics studies are presented to illustrate the procedures. Important ongoing challenges are also highlighted. Future perspectives of DIA methods for metaproteomics analysis are further discussed. Cited references are searched through and collected from Google Scholar and PubMed. EXPERT OPINION Considering the inherent complexity of DIA metaproteomics data, data analysis strategies specifically designed for interpretation is imperative. From this point of view, we anticipate that deep learning methods and de novo sequencing methods will become more prevalent in the future, potentially improving protein coverage in metaproteomics. Moreover, the advancement of metaproteomics also depends on the development of sample preparation methods, data analysis strategies, etc. These factors are key to unlocking the full potential of metaproteomics.
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Affiliation(s)
- Enhui Wu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Chemistry, Fudan University, Shanghai, China
| | - Guanyang Xu
- Department of Chemistry, Fudan University, Shanghai, China
| | - Dong Xie
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Liang Qiao
- Department of Chemistry, Fudan University, Shanghai, China
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Langbøl M, Saruhanian A, Saruhanian S, Tiedemann D, Baskaran T, Vohra R, Rives AS, Prokosch V, Liu H, Lackmann JW, Müller S, Nielsen CH, Kolko M, Rovelt J. Proteomic and Cytokine Profiling in Plasma from Patients with Normal-Tension Glaucoma and Ocular Hypertension. Cell Mol Neurobiol 2024; 44:59. [PMID: 39150567 DOI: 10.1007/s10571-024-01492-3] [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: 04/16/2024] [Accepted: 08/06/2024] [Indexed: 08/17/2024]
Abstract
Primary open-angle glaucoma (POAG) is subdivided depending on eye pressure. Patients with normal-tension glaucoma (NTG) have never had high intraocular pressure (IOP) measured while patients with ocular hypertension (OHT) have high eye pressure but no signs of glaucoma. Although IOP is considered to be a risk factor for all glaucoma patients, it is reasonable to assume that other risk factors such as inflammation play a role. We aimed to characterize the proteome and cytokine profile during hypoxia in plasma from patients with NTG (n = 10), OHT (n = 10), and controls (n = 10). Participants were exposed to hypoxia for two hours, followed by 30 min of normoxia. Samples were taken before ("baseline"), during ("hypoxia"), and after hypoxia ("recovery"). Proteomics based on liquid chromatography coupled with mass spectrometry (LC-MS) was performed. Cytokines were measured by Luminex assays. Bioinformatic analyses indicated the involvement of complement and coagulation cascades in NTG and OHT. Regulation of high-density lipoprotein 3 (HDL3) apolipoproteins suggested that changes in cholesterol metabolism are related to OHT. Hypoxia decreased the level of tumor necrosis factor-α (TNF-α) in OHT patients compared to controls. Circulating levels of interleukin-1β (IL-1β) and C-reactive protein (CRP) were decreased in NTG patients compared to controls during hypoxia. After recovery, plasma interleukin-6 (IL-6) was upregulated in patients with NTG and OHT. Current results indicate an enhanced systemic immune response in patients with NTG and OHT, which correlates with pathogenic events in glaucoma. Apolipoproteins may have anti-inflammatory effects, enabling OHT patients to withstand inflammation and development of glaucoma despite high IOP.
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Affiliation(s)
- Mia Langbøl
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, Building 22, 2100, Copenhagen Ø, Denmark.
| | - Arevak Saruhanian
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, Building 22, 2100, Copenhagen Ø, Denmark
| | - Sarkis Saruhanian
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, Building 22, 2100, Copenhagen Ø, Denmark
- Department of Veterinary & Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Daniel Tiedemann
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, Building 22, 2100, Copenhagen Ø, Denmark
- Department of Ophthalmology, Copenhagen University Hospital, Rigshospitalet-Glostrup, Glostrup, Denmark
| | - Thisayini Baskaran
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, Building 22, 2100, Copenhagen Ø, Denmark
| | - Rupali Vohra
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, Building 22, 2100, Copenhagen Ø, Denmark
- Department of Ophthalmology, Copenhagen University Hospital, Rigshospitalet-Glostrup, Glostrup, Denmark
| | - Amalie Santaolalla Rives
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, Building 22, 2100, Copenhagen Ø, Denmark
| | - Verena Prokosch
- Department of Ophthalmology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50937, Cologne, Germany
| | - Hanhan Liu
- Department of Ophthalmology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50937, Cologne, Germany
| | - Jan-Wilm Lackmann
- CECAD/CMMC Proteomics Facility, CECAD Research Center, University of Cologne, Cologne, Germany
| | - Stefan Müller
- CECAD/CMMC Proteomics Facility, CECAD Research Center, University of Cologne, Cologne, Germany
| | - Claus Henrik Nielsen
- Institute for Inflammation Research, Center for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen University Hospital, 2200, Copenhagen, Denmark
- Department of Odontology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Miriam Kolko
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, Building 22, 2100, Copenhagen Ø, Denmark
- Department of Ophthalmology, Copenhagen University Hospital, Rigshospitalet-Glostrup, Glostrup, Denmark
| | - Jens Rovelt
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, Building 22, 2100, Copenhagen Ø, Denmark
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Smit ER, Romijn M, Langerhorst P, van der Zwaan C, van der Staaij H, Rotteveel J, van Kaam AH, Fustolo-Gunnink SF, Hoogendijk AJ, Onland W, Finken MJJ, van den Biggelaar M. Distinct protein patterns related to postnatal development in small for gestational age preterm infants. Pediatr Res 2024:10.1038/s41390-024-03481-0. [PMID: 39152333 DOI: 10.1038/s41390-024-03481-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 07/18/2024] [Accepted: 07/30/2024] [Indexed: 08/19/2024]
Abstract
BACKGROUND Preterm infants, especially those born small for gestational age (SGA), are at risk of short-term and long-term health complications. Characterization of changes in circulating proteins postnatally in preterm infants may provide valuable fundamental insights into this population. Here, we investigated postnatal developmental patterns in preterm infants and explored protein signatures that deviate between SGA infants and appropriate for gestational age (AGA) infants using a mass spectrometry (MS)-based proteomics workflow. METHODS Longitudinal serum samples obtained at postnatal days 0, 3, 7, 14, and 28 from 67 preterm infants were analyzed using unbiased MS-based proteomics. RESULTS 314 out of 833 quantified serum proteins change postnatally, including previously described age-related changes in immunoglobulins, hemoglobin subunits, and new developmental patterns, e.g. apolipoproteins (APOA4) and terminal complement cascade (C9) proteins. Limited differences between SGA and AGA infants were found at birth while longitudinal monitoring revealed 69 deviating proteins, including insulin-sensitizing hormone adiponectin, platelet proteins, and 24 proteins with an annotated function in the immune response. CONCLUSIONS This study shows the potential of MS-based serum profiling in defining circulating protein trajectories in the preterm infant population and its ability to identify longitudinal alterations in protein levels associated with SGA. IMPACT Postnatal changes of circulating proteins in preterm infants have not fully been elucidated but may contribute to development of health complications. Mass spectrometry-based analysis is an attractive approach to study circulating proteins in preterm infants with limited material. Longitudinal plasma profiling reveals postnatal developmental-related patterns in preterm infants (314/833 proteins) including previously described changes, but also previously unreported proteins. Longitudinal monitoring revealed an immune response signature between SGA and AGA infants. This study highlights the importance of taking postnatal changes into account for translational studies in preterm infants.
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Affiliation(s)
- Eva R Smit
- Department of Molecular Hematology, Sanquin Research, Amsterdam, the Netherlands
| | - Michelle Romijn
- Department of Neonatology, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Reproduction and Development Research Institute, Amsterdam, the Netherlands
- Department of Pediatric Endocrinology, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Pieter Langerhorst
- Department of Molecular Hematology, Sanquin Research, Amsterdam, the Netherlands
| | - Carmen van der Zwaan
- Department of Molecular Hematology, Sanquin Research, Amsterdam, the Netherlands
| | - Hilde van der Staaij
- Sanquin Research & Lab Services, Sanquin Blood Supply Foundation, Amsterdam, the Netherlands
- Department of Pediatrics, Division of Neonatology, Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, the Netherlands
- Department of Pediatric Hematology, Emma Children's Hospital, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Joost Rotteveel
- Amsterdam Reproduction and Development Research Institute, Amsterdam, the Netherlands
- Department of Pediatric Endocrinology, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Anton H van Kaam
- Department of Neonatology, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Reproduction and Development Research Institute, Amsterdam, the Netherlands
| | - Suzanne F Fustolo-Gunnink
- Sanquin Research & Lab Services, Sanquin Blood Supply Foundation, Amsterdam, the Netherlands
- Department of Pediatrics, Division of Neonatology, Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, the Netherlands
- Department of Pediatric Hematology, Emma Children's Hospital, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Arie J Hoogendijk
- Department of Molecular Hematology, Sanquin Research, Amsterdam, the Netherlands
| | - Wes Onland
- Department of Neonatology, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Reproduction and Development Research Institute, Amsterdam, the Netherlands
| | - Martijn J J Finken
- Amsterdam Reproduction and Development Research Institute, Amsterdam, the Netherlands
- Department of Pediatric Endocrinology, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
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7
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Urbauer E, Aguanno D, Mindermann N, Omer H, Metwaly A, Krammel T, Faro T, Remke M, Reitmeier S, Bärthel S, Kersting J, Huang Z, Xian F, Schmidt M, Saur D, Huber S, Stecher B, List M, Gómez-Varela D, Steiger K, Allez M, Rath E, Haller D. Mitochondrial perturbation in the intestine causes microbiota-dependent injury and gene signatures discriminative of inflammatory disease. Cell Host Microbe 2024; 32:1347-1364.e10. [PMID: 39013472 DOI: 10.1016/j.chom.2024.06.013] [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: 10/12/2023] [Revised: 05/13/2024] [Accepted: 06/20/2024] [Indexed: 07/18/2024]
Abstract
Mitochondrial dysfunction is associated with inflammatory bowel diseases (IBDs). To understand how microbial-metabolic circuits contribute to intestinal injury, we disrupt mitochondrial function in the epithelium by deleting the mitochondrial chaperone, heat shock protein 60 (Hsp60Δ/ΔIEC). This metabolic perturbation causes self-resolving tissue injury. Regeneration is disrupted in the absence of the aryl hydrocarbon receptor (Hsp60Δ/ΔIEC;AhR-/-) involved in intestinal homeostasis or inflammatory regulator interleukin (IL)-10 (Hsp60Δ/ΔIEC;Il10-/-), causing IBD-like pathology. Injury is absent in the distal colon of germ-free (GF) Hsp60Δ/ΔIEC mice, highlighting bacterial control of metabolic injury. Colonizing GF Hsp60Δ/ΔIEC mice with the synthetic community OMM12 reveals expansion of metabolically flexible Bacteroides, and B. caecimuris mono-colonization recapitulates the injury. Transcriptional profiling of the metabolically impaired epithelium reveals gene signatures involved in oxidative stress (Ido1, Nos2, Duox2). These signatures are observed in samples from Crohn's disease patients, distinguishing active from inactive inflammation. Thus, mitochondrial perturbation of the epithelium causes microbiota-dependent injury with discriminative inflammatory gene profiles relevant for IBD.
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Affiliation(s)
- Elisabeth Urbauer
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany
| | - Doriane Aguanno
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany
| | - Nora Mindermann
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany
| | - Hélène Omer
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany
| | - Amira Metwaly
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany
| | - Tina Krammel
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany
| | - Tim Faro
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, 80337 Munich, Germany
| | - Marianne Remke
- Institute of Pathology, Technical University of Munich, 81675 Munich, Germany
| | - Sandra Reitmeier
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany
| | - Stefanie Bärthel
- Division of Translational Cancer Research, German Cancer Research Center and German Cancer Consortium, 69120 Heidelberg, Germany; Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, 81675 Munich, Germany; Institute of Experimental Cancer Therapy, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Johannes Kersting
- Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof Forum 3, 85354 Freising, Germany
| | - Zihua Huang
- Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof Forum 3, 85354 Freising, Germany
| | - Feng Xian
- Systems Biology of Pain, Division of Pharmacology & Toxicology, Department of Pharmaceutical Sciences, Faculty of Life Sciences, University of Vienna, 1090 Vienna, Austria
| | - Manuela Schmidt
- Systems Biology of Pain, Division of Pharmacology & Toxicology, Department of Pharmaceutical Sciences, Faculty of Life Sciences, University of Vienna, 1090 Vienna, Austria
| | - Dieter Saur
- Division of Translational Cancer Research, German Cancer Research Center and German Cancer Consortium, 69120 Heidelberg, Germany; Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, 81675 Munich, Germany; Institute of Experimental Cancer Therapy, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Samuel Huber
- Section of Molecular Immunology and Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Bärbel Stecher
- Max von Pettenkofer-Institute for Hygiene and Clinical Microbiology, Ludwig-Maximilians University of Munich, 80336 Munich, Germany; German Center for Infection Research, Partner site LMU Munich, 80336 Munich, Germany
| | - Markus List
- Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof Forum 3, 85354 Freising, Germany; Munich Data Science Institute (MDSI), Technical University of Munich, 85748 Garching, Germany
| | - David Gómez-Varela
- Systems Biology of Pain, Division of Pharmacology & Toxicology, Department of Pharmaceutical Sciences, Faculty of Life Sciences, University of Vienna, 1090 Vienna, Austria
| | - Katja Steiger
- Institute of Pathology, Technical University of Munich, 81675 Munich, Germany
| | - Matthieu Allez
- Department of Gastroenterology, Hôpital Saint-Louis, APHP, INSERM UMRS 1160, Paris Diderot, Sorbonne Paris-Cité University, 75010 Paris, France
| | - Eva Rath
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany
| | - Dirk Haller
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany.
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8
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Lan L, He H, Zhang J. An integration of neuroimaging and serum proteomics analysis suggests immune and inflammation are associated with white matter microstructure changes in cerebral small vessel disease with depressive symptoms. J Stroke Cerebrovasc Dis 2024; 33:107921. [PMID: 39137823 DOI: 10.1016/j.jstrokecerebrovasdis.2024.107921] [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: 12/03/2023] [Revised: 08/04/2024] [Accepted: 08/08/2024] [Indexed: 08/15/2024] Open
Abstract
INTRODUCTION Depressive symptoms are a common concomitant of cerebral small vessel disease (CSVD), of which pathogenesis requires more study. White matter microstructural abnormalities and proteomic alternation have been widely reported regarding depression in the elderly with CSVD. Exploring the relationship between cerebral white matter microstructural alterations and serum proteins may complete the explanation of molecular mechanisms for the findings from neuroimaging research of CSVD combined with depressive symptoms. METHODS An untargeted proteomics approach based on mass spectrometry was used to obtain serum proteomic profiles, which were clustered into co-expression protein modules. White matter microstructural integrity was measured using the FMRIB Software Library (FSL) and MATLAB to analyze diffusion tensor imaging (DTI) data and calculate the differences in fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD), and radial diffusivity (RD) for 50 regions of interest (ROI). Integrating the proteome with the DTI results, weighted gene co-expression analysis (WGCNA) was used to identify protein modules related to white matter microstructural alterations, and the proteins of the corresponding modules were analyzed for functional enrichment through bioinformatics techniques. RESULTS DTI measurements were analCerebral small vessel disease (CSVD); Depression; Diffusion tensor imaging (DTI); Proteomics; Inflammationyzed between individuals with CSVD and depressive symptoms (CSVD+D) (n = 24) and those without depressive symptoms (CSVD-D) (n = 35). Results showed an overall increase in MD, AD, and RD within the left hemisphere of the CSVD+D group, suggesting widespread loss of white matter integrity and axonal demyelination, including left superior longitudinal fasciculus (SLF), left posterior corona radiata (PCR) and right external capsule (EC). We identified two protein modules associated with DTI diffusivity, and functional enrichment analyses revealed that complement and coagulation cascades and immune responses participate in the alternation of white matter microstructure in the CSVD+D group. CONCLUSION The results suggested immune- and inflammation-related mechanism was associated with white matter microstructure changes in CSVD with depressive symptoms.
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Affiliation(s)
- Liuyi Lan
- Department of Neurology, Zhongnan Hospital, Wuhan University, No.169, Donghu Road, Wuhan, Hubei 430071, China
| | - Haoying He
- Department of Neurology, Zhongnan Hospital, Wuhan University, No.169, Donghu Road, Wuhan, Hubei 430071, China
| | - Junjian Zhang
- Department of Neurology, Zhongnan Hospital, Wuhan University, No.169, Donghu Road, Wuhan, Hubei 430071, China.
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9
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Vieira de Souza E, L Bookout A, Barnes CA, Miller B, Machado P, Basso LA, Bizarro CV, Saghatelian A. Rp3: Ribosome profiling-assisted proteogenomics improves coverage and confidence during microprotein discovery. Nat Commun 2024; 15:6839. [PMID: 39122697 PMCID: PMC11316118 DOI: 10.1038/s41467-024-50301-4] [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: 10/10/2023] [Accepted: 07/08/2024] [Indexed: 08/12/2024] Open
Abstract
There has been a dramatic increase in the identification of non-canonical translation and a significant expansion of the protein-coding genome. Among the strategies used to identify unannotated small Open Reading Frames (smORFs) that encode microproteins, Ribosome profiling (Ribo-Seq) is the gold standard for the annotation of novel coding sequences by reporting on smORF translation. In Ribo-Seq, ribosome-protected footprints (RPFs) that map to multiple genomic sites are removed since they cannot be unambiguously assigned to a specific genomic location. Furthermore, RPFs necessarily result in short (25-34 nucleotides) reads, increasing the chance of multi-mapping alignments, such that smORFs residing in these regions cannot be identified by Ribo-Seq. Moreover, it has been challenging to identify protein evidence for Ribo-Seq. To solve this, we developed Rp3, a pipeline that integrates proteogenomics and Ribosome profiling to provide unambiguous evidence for a subset of microproteins missed by current Ribo-Seq pipelines. Here, we show that Rp3 maximizes proteomics detection and confidence of microprotein-encoding smORFs.
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Affiliation(s)
- Eduardo Vieira de Souza
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, 90616-900, Porto Alegre, Rio Grande do Sul, Brazil
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | | | - Brendan Miller
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Pablo Machado
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, 90616-900, Porto Alegre, Rio Grande do Sul, Brazil
| | - Luiz A Basso
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, 90616-900, Porto Alegre, Rio Grande do Sul, Brazil
| | - Cristiano V Bizarro
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil.
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, 90616-900, Porto Alegre, Rio Grande do Sul, Brazil.
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA.
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10
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Leduc A, Khoury L, Cantlon J, Khan S, Slavov N. Massively parallel sample preparation for multiplexed single-cell proteomics using nPOP. Nat Protoc 2024:10.1038/s41596-024-01033-8. [PMID: 39117766 DOI: 10.1038/s41596-024-01033-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 05/27/2024] [Indexed: 08/10/2024]
Abstract
Single-cell proteomics by mass spectrometry (MS) allows the quantification of proteins with high specificity and sensitivity. To increase its throughput, we developed nano-proteomic sample preparation (nPOP), a method for parallel preparation of thousands of single cells in nanoliter-volume droplets deposited on glass slides. Here, we describe its protocol with emphasis on its flexibility to prepare samples for different multiplexed MS methods. An implementation using the plexDIA MS multiplexing method, which uses non-isobaric mass tags to barcode peptides from different samples for data-independent acquisition, demonstrates accurate quantification of ~3,000-3,700 proteins per human cell. A separate implementation with isobaric mass tags and prioritized data acquisition demonstrates analysis of 1,827 single cells at a rate of >1,000 single cells per day at a depth of 800-1,200 proteins per human cell. The protocol is implemented by using a cell-dispensing and liquid-handling robot-the CellenONE instrument-and uses readily available consumables, which should facilitate broad adoption. nPOP can be applied to all samples that can be processed to a single-cell suspension. It takes 1 or 2 d to prepare >3,000 single cells. We provide metrics and software (the QuantQC R package) for quality control and data exploration. QuantQC supports the robust scaling of nPOP to higher plex reagents for achieving reliable and scalable single-cell proteomics.
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Affiliation(s)
- Andrew Leduc
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA, USA.
| | - Luke Khoury
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA, USA
| | | | - Saad Khan
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA, USA
| | - Nikolai Slavov
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA, USA.
- Parallel Squared Technology Institute, Watertown, MA, USA.
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11
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Panich J, Toppari E, Tejedor-Sanz S, Fong B, Dugan E, Chen Y, Petzold CJ, Zhao Z, Yoshikuni Y, Savage DF, Singer SW. Functional plasticity of HCO3- uptake and CO2 fixation in Cupriavidus necator H16. BIORESOURCE TECHNOLOGY 2024:131214. [PMID: 39127361 DOI: 10.1016/j.biortech.2024.131214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 08/01/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024]
Abstract
Despite its prominence, the ability to engineer Cupriavidus necator H16 for inorganic carbon uptake and fixation is underexplored. We tested the roles of endogenous and heterologous genes on C. necator inorganic carbon metabolism. Deletion of β-carbonic anhydrase can had the most deleterious effect on C. necator autotrophic growth. Replacement of this native uptake system with several classes of dissolved inorganic carbon (DIC) transporters from Cyanobacteria and chemolithoautotrophic bacteria recovered autotrophic growth and supported higher cell densities compared to wild-type (WT) C. necator in batch culture. Strains expressing Halothiobacillus neopolitanus DAB2 (hnDAB2) and diverse rubisco homologs grew in CO2 similarly to the wild-type strain. Our experiments suggest that the primary role of carbonic anhydrase during autotrophic growth is to support anaplerotic metabolism, and an array of DIC transporters can complement this function. This work demonstrates flexibility in HCO3- uptake and CO2 fixation in C. necator, providing new pathways for CO2-based biomanufacturing.
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Affiliation(s)
- Justin Panich
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Emili Toppari
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sara Tejedor-Sanz
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Advanced Biofuel and Bioproducts Process Development Unit, Lawrence Berkeley NationalLaboratory, Emeryville, CA 94608, USA
| | - Bonnie Fong
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Eli Dugan
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA, 94720, USA
| | - Yan Chen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Christopher J Petzold
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Zhiying Zhao
- The US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, CA 94720, USA
| | - Yasuo Yoshikuni
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; The US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, CA 94720, USA; Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, CA94720, USA
| | - David F Savage
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA, 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Steven W Singer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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12
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Hofer SJ, Daskalaki I, Bergmann M, Friščić J, Zimmermann A, Mueller MI, Abdellatif M, Nicastro R, Masser S, Durand S, Nartey A, Waltenstorfer M, Enzenhofer S, Faimann I, Gschiel V, Bajaj T, Niemeyer C, Gkikas I, Pein L, Cerrato G, Pan H, Liang Y, Tadic J, Jerkovic A, Aprahamian F, Robbins CE, Nirmalathasan N, Habisch H, Annerer E, Dethloff F, Stumpe M, Grundler F, Wilhelmi de Toledo F, Heinz DE, Koppold DA, Rajput Khokhar A, Michalsen A, Tripolt NJ, Sourij H, Pieber TR, de Cabo R, McCormick MA, Magnes C, Kepp O, Dengjel J, Sigrist SJ, Gassen NC, Sedej S, Madl T, De Virgilio C, Stelzl U, Hoffmann MH, Eisenberg T, Tavernarakis N, Kroemer G, Madeo F. Spermidine is essential for fasting-mediated autophagy and longevity. Nat Cell Biol 2024:10.1038/s41556-024-01468-x. [PMID: 39117797 DOI: 10.1038/s41556-024-01468-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 07/02/2024] [Indexed: 08/10/2024]
Abstract
Caloric restriction and intermittent fasting prolong the lifespan and healthspan of model organisms and improve human health. The natural polyamine spermidine has been similarly linked to autophagy enhancement, geroprotection and reduced incidence of cardiovascular and neurodegenerative diseases across species borders. Here, we asked whether the cellular and physiological consequences of caloric restriction and fasting depend on polyamine metabolism. We report that spermidine levels increased upon distinct regimens of fasting or caloric restriction in yeast, flies, mice and human volunteers. Genetic or pharmacological blockade of endogenous spermidine synthesis reduced fasting-induced autophagy in yeast, nematodes and human cells. Furthermore, perturbing the polyamine pathway in vivo abrogated the lifespan- and healthspan-extending effects, as well as the cardioprotective and anti-arthritic consequences of fasting. Mechanistically, spermidine mediated these effects via autophagy induction and hypusination of the translation regulator eIF5A. In summary, the polyamine-hypusination axis emerges as a phylogenetically conserved metabolic control hub for fasting-mediated autophagy enhancement and longevity.
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Affiliation(s)
- Sebastian J Hofer
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
- Centre de Recherche des Cordeliers, Équipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
| | - Ioanna Daskalaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece
- Department of Biology, School of Sciences and Engineering, University of Crete, Heraklion, Greece
| | - Martina Bergmann
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Jasna Friščić
- Department of Dermatology, Allergy and Venerology, University of Lübeck, Lübeck, Germany
- Institute for Systemic Inflammation Research, University of Lübeck, Lübeck, Germany
| | - Andreas Zimmermann
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
| | - Melanie I Mueller
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Mahmoud Abdellatif
- BioTechMed Graz, Graz, Austria
- Centre de Recherche des Cordeliers, Équipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
- Division of Cardiology, Medical University of Graz, Graz, Austria
| | - Raffaele Nicastro
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Sarah Masser
- BioTechMed Graz, Graz, Austria
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Graz, Austria
| | - Sylvère Durand
- Centre de Recherche des Cordeliers, Équipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
| | - Alexander Nartey
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Mara Waltenstorfer
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Sarah Enzenhofer
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Isabella Faimann
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Verena Gschiel
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Thomas Bajaj
- Neurohomeostasis Research Group, Department of Psychiatry and Psychotherapy, University Hospital Bonn, Bonn, Germany
| | - Christine Niemeyer
- Neurohomeostasis Research Group, Department of Psychiatry and Psychotherapy, University Hospital Bonn, Bonn, Germany
| | - Ilias Gkikas
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece
- Department of Biology, School of Sciences and Engineering, University of Crete, Heraklion, Greece
| | - Lukas Pein
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Giulia Cerrato
- Centre de Recherche des Cordeliers, Équipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
| | - Hui Pan
- Centre de Recherche des Cordeliers, Équipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
| | - YongTian Liang
- Institute for Biology and Genetics, Freie Universität Berlin, Berlin, Germany
- Cluster of Excellence, NeuroCure, Berlin, Germany
| | - Jelena Tadic
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
| | - Andrea Jerkovic
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Fanny Aprahamian
- Centre de Recherche des Cordeliers, Équipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
| | - Christine E Robbins
- Department of Biochemistry and Molecular Biology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Nitharsshini Nirmalathasan
- Centre de Recherche des Cordeliers, Équipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
| | - Hansjörg Habisch
- Research Unit Integrative Structural Biology, Otto Loewi Research Center, Medicinal Chemistry, Medical University of Graz, Graz, Austria
| | - Elisabeth Annerer
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Graz, Austria
| | | | - Michael Stumpe
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | | | | | - Daniel E Heinz
- Neurohomeostasis Research Group, Department of Psychiatry and Psychotherapy, University Hospital Bonn, Bonn, Germany
| | - Daniela A Koppold
- Institute of Social Medicine, Epidemiology and Health Economics, corporate member of Freie Universität Berlin and Humboldt-Universität, Charité-Universitätsmedizin, Berlin, Germany
- Department of Pediatrics, Division of Oncology and Hematology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Internal Medicine and Nature-based Therapies, Immanuel Hospital Berlin, Berlin, Germany
| | - Anika Rajput Khokhar
- Institute of Social Medicine, Epidemiology and Health Economics, corporate member of Freie Universität Berlin and Humboldt-Universität, Charité-Universitätsmedizin, Berlin, Germany
- Department of Dermatology, Venereology and Allergology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Andreas Michalsen
- Institute of Social Medicine, Epidemiology and Health Economics, corporate member of Freie Universität Berlin and Humboldt-Universität, Charité-Universitätsmedizin, Berlin, Germany
- Department of Internal Medicine and Nature-based Therapies, Immanuel Hospital Berlin, Berlin, Germany
| | - Norbert J Tripolt
- Interdisciplinary Metabolic Medicine Trials Unit, Division of Endocrinology and Diabetology, Medical University of Graz, Graz, Austria
- Division of Endocrinology and Diabetology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Harald Sourij
- Interdisciplinary Metabolic Medicine Trials Unit, Division of Endocrinology and Diabetology, Medical University of Graz, Graz, Austria
- Division of Endocrinology and Diabetology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Thomas R Pieber
- BioTechMed Graz, Graz, Austria
- Interdisciplinary Metabolic Medicine Trials Unit, Division of Endocrinology and Diabetology, Medical University of Graz, Graz, Austria
- Division of Endocrinology and Diabetology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
- HEALTH - Institute for Biomedical Research and Technologies, Joanneum Research Forschungsgesellschaft, Graz, Austria
| | - Rafael de Cabo
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Mark A McCormick
- Department of Biochemistry and Molecular Biology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Christoph Magnes
- HEALTH - Institute for Biomedical Research and Technologies, Joanneum Research Forschungsgesellschaft, Graz, Austria
| | - Oliver Kepp
- Centre de Recherche des Cordeliers, Équipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
| | - Joern Dengjel
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Stephan J Sigrist
- Institute for Biology and Genetics, Freie Universität Berlin, Berlin, Germany
- Cluster of Excellence, NeuroCure, Berlin, Germany
| | - Nils C Gassen
- Neurohomeostasis Research Group, Department of Psychiatry and Psychotherapy, University Hospital Bonn, Bonn, Germany
| | - Simon Sedej
- BioTechMed Graz, Graz, Austria
- Division of Cardiology, Medical University of Graz, Graz, Austria
- Institute of Physiology, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Tobias Madl
- BioTechMed Graz, Graz, Austria
- Research Unit Integrative Structural Biology, Otto Loewi Research Center, Medicinal Chemistry, Medical University of Graz, Graz, Austria
| | | | - Ulrich Stelzl
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Graz, Austria
| | - Markus H Hoffmann
- Department of Dermatology, Allergy and Venerology, University of Lübeck, Lübeck, Germany
- Institute for Systemic Inflammation Research, University of Lübeck, Lübeck, Germany
| | - Tobias Eisenberg
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
| | - Nektarios Tavernarakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece.
- Division of Basic Sciences, School of Medicine, University of Crete, Heraklion, Greece.
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Équipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France.
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France.
- Institut du Cancer Paris CARPEM, Department of Biology, Hôpital Européen Georges Pompidou, AP-HP, Paris, France.
| | - Frank Madeo
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria.
- Field of Excellence BioHealth, University of Graz, Graz, Austria.
- BioTechMed Graz, Graz, Austria.
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13
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Ivanov MV, Kopeykina AS, Gorshkov MV. Reanalysis of DIA Data Demonstrates the Capabilities of MS/MS-Free Proteomics to Reveal New Biological Insights in Disease-Related Samples. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1775-1785. [PMID: 38938158 DOI: 10.1021/jasms.4c00134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
Data-independent acquisition (DIA) at the shortened data acquisition time is becoming a method of choice for quantitative proteomic applications requiring high throughput analysis of large cohorts of samples. With the advent of the combination of high resolution mass spectrometry with an asymmetric track lossless analyzer, these DIA capabilities were further extended with the recent demonstration of quantitative analyses at the speed of up to hundreds of samples per day. In particular, the proteomic data for the brain samples related to multiple system atrophy disease were acquired using 7 and 28 min chromatography gradients (Guzman et al., Nat. Biotech. 2024). In this work, we applied the recently introduced DirectMS1 method to reanalysis of these data using only MS1 spectra. Both DirectMS1 and DIA results were matched against long gradient DDA analysis from the earlier study of the same sample cohort. While the quantitation efficiency of DirectMS1 was comparable with DIA on the same data sets, we found an additional five proteins of biological significance relevant to the analyzed tissue samples. Among the findings, DirectMS1 was able to detect decreased caspase activity for Vimentin protein in the multiple system atrophy samples missed by the MS/MS-based quantitation methods. Our study suggests that DirectMS1 can be an efficient MS1-only addition to the analysis of DIA data in high-throughput quantitative proteomic studies.
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Affiliation(s)
- Mark V Ivanov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Anna S Kopeykina
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Mikhail V Gorshkov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
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14
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Chen Y, Wijekoon S, Matsumoto A, Luo J, Kiriazis H, Masterman E, Yildiz G, Cross J, Parslow A, Chooi R, Sadoshima J, Greening D, Weeks K, McMullen J. Distinct functional and molecular profiles between physiological and pathological atrial enlargement offer potential new therapeutic opportunities for atrial fibrillation. Clin Sci (Lond) 2024; 138:941-962. [PMID: 39018488 PMCID: PMC11292366 DOI: 10.1042/cs20240178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 07/17/2024] [Accepted: 07/17/2024] [Indexed: 07/19/2024]
Abstract
Atrial fibrillation (AF) remains challenging to prevent and treat. A key feature of AF is atrial enlargement. However, not all atrial enlargement progresses to AF. Atrial enlargement in response to physiological stimuli such as exercise is typically benign and reversible. Understanding the differences in atrial function and molecular profile underpinning pathological and physiological atrial remodelling will be critical for identifying new strategies for AF. The discovery of molecular mechanisms responsible for pathological and physiological ventricular hypertrophy has uncovered new drug targets for heart failure. Studies in the atria have been limited in comparison. Here, we characterised mouse atria from (1) a pathological model (cardiomyocyte-specific transgenic (Tg) that develops dilated cardiomyopathy [DCM] and AF due to reduced protective signalling [PI3K]; DCM-dnPI3K), and (2) a physiological model (cardiomyocyte-specific Tg with an enlarged heart due to increased insulin-like growth factor 1 receptor; IGF1R). Both models presented with an increase in atrial mass, but displayed distinct functional, cellular, histological and molecular phenotypes. Atrial enlargement in the DCM-dnPI3K Tg, but not IGF1R Tg, was associated with atrial dysfunction, fibrosis and a heart failure gene expression pattern. Atrial proteomics identified protein networks related to cardiac contractility, sarcomere assembly, metabolism, mitochondria, and extracellular matrix which were differentially regulated in the models; many co-identified in atrial proteomics data sets from human AF. In summary, physiological and pathological atrial enlargement are associated with distinct features, and the proteomic dataset provides a resource to study potential new regulators of atrial biology and function, drug targets and biomarkers for AF.
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MESH Headings
- Atrial Fibrillation/physiopathology
- Atrial Fibrillation/metabolism
- Atrial Fibrillation/genetics
- Animals
- Heart Atria/metabolism
- Heart Atria/physiopathology
- Heart Atria/pathology
- Mice, Transgenic
- Myocytes, Cardiac/metabolism
- Myocytes, Cardiac/pathology
- Atrial Remodeling
- Receptor, IGF Type 1/metabolism
- Receptor, IGF Type 1/genetics
- Cardiomyopathy, Dilated/physiopathology
- Cardiomyopathy, Dilated/genetics
- Cardiomyopathy, Dilated/metabolism
- Cardiomyopathy, Dilated/pathology
- Disease Models, Animal
- Fibrosis
- Mice
- Humans
- Signal Transduction
- Phosphatidylinositol 3-Kinases/metabolism
- Heart Failure/physiopathology
- Heart Failure/genetics
- Heart Failure/metabolism
- Heart Failure/pathology
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Affiliation(s)
- Yi Ching Chen
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Diabetes, Central Clinical School, Monash University, Clayton, Victoria, Australia
- Baker Department of Cardiometabolic Health, The University of Melbourne, Melbourne, Victoria, Australia
- Baker Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, Victoria, Australia
| | - Seka Wijekoon
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Aya Matsumoto
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Jieting Luo
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Helen Kiriazis
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Baker Department of Cardiometabolic Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Emma Masterman
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Gunes Yildiz
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Jonathon Cross
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Adam C. Parslow
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Baker Department of Cardiometabolic Health, The University of Melbourne, Melbourne, Victoria, Australia
- Baker Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, Victoria, Australia
| | - Roger Chooi
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Junichi Sadoshima
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, NJ, U.S.A
| | - David W. Greening
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Baker Department of Cardiometabolic Health, The University of Melbourne, Melbourne, Victoria, Australia
- Baker Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, Victoria, Australia
| | - Kate L. Weeks
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Diabetes, Central Clinical School, Monash University, Clayton, Victoria, Australia
- Baker Department of Cardiometabolic Health, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Anatomy and Physiology, University of Melbourne, Melbourne, Victoria, Australia
| | - Julie R. McMullen
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Diabetes, Central Clinical School, Monash University, Clayton, Victoria, Australia
- Baker Department of Cardiometabolic Health, The University of Melbourne, Melbourne, Victoria, Australia
- Baker Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, Victoria, Australia
- Monash Alfred Baker Centre for Cardiovascular Research, Monash University, Melbourne, Victoria, Australia
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15
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Li Z, Shi B, Li N, Sun J, Zeng X, Huang R, Bok S, Chen X, Han J, Yallowitz AR, Debnath S, Cung M, Ling Z, Zhong CQ, Hong Y, Li G, Koenen M, Cohen P, Su X, Lu H, Greenblatt MB, Xu R. Bone controls browning of white adipose tissue and protects from diet-induced obesity through Schnurri-3-regulated SLIT2 secretion. Nat Commun 2024; 15:6697. [PMID: 39107299 PMCID: PMC11303806 DOI: 10.1038/s41467-024-51155-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 07/31/2024] [Indexed: 08/10/2024] Open
Abstract
The skeleton has been suggested to function as an endocrine organ controlling whole organism energy balance, however the mediators of this effect and their molecular links remain unclear. Here, utilizing Schnurri-3-/- (Shn3-/-) mice with augmented osteoblast activity, we show Shn3-/-mice display resistance against diet-induced obesity and enhanced white adipose tissue (WAT) browning. Conditional deletion of Shn3 in osteoblasts but not adipocytes recapitulates lean phenotype of Shn3-/-mice, indicating this phenotype is driven by skeleton. We further demonstrate osteoblasts lacking Shn3 can secrete cytokines to promote WAT browning. Among them, we identify a C-terminal fragment of SLIT2 (SLIT2-C), primarily secreted by osteoblasts, as a Shn3-regulated osteokine that mediates WAT browning. Lastly, AAV-mediated Shn3 silencing phenocopies the lean phenotype and augmented glucose metabolism. Altogether, our findings establish a novel bone-fat signaling axis via SHN3 regulated SLIT2-C production in osteoblasts, offering a potential therapeutic target to address both osteoporosis and metabolic syndrome.
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Affiliation(s)
- Zan Li
- State Key Laboratory of Cellular Stress Biology, Cancer Research Center, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, People's Republic of China
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Sports Medicine, Xiangya Hospital, Central South University, Changsha, People's Republic of China
- PET Center, Department of Nuclear Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Baohong Shi
- State Key Laboratory of Cellular Stress Biology, Cancer Research Center, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, People's Republic of China
- Xiamen Key Laboratory of Regeneration Medicine, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Xiamen University, Xiamen, China
| | - Na Li
- State Key Laboratory of Cellular Stress Biology, Cancer Research Center, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, People's Republic of China
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Xiamen Key Laboratory of Regeneration Medicine, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Xiamen University, Xiamen, China
| | - Jun Sun
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Xiangchen Zeng
- State Key Laboratory of Cellular Stress Biology, Cancer Research Center, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, People's Republic of China
| | - Rui Huang
- State Key Laboratory of Cellular Stress Biology, Cancer Research Center, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, People's Republic of China
| | - Seoyeon Bok
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Xiaohui Chen
- State Key Laboratory of Cellular Stress Biology, Cancer Research Center, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, People's Republic of China
- Xiamen Key Laboratory of Regeneration Medicine, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Xiamen University, Xiamen, China
| | - Jie Han
- State Key Laboratory of Cellular Stress Biology, Cancer Research Center, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, People's Republic of China
| | - Alisha R Yallowitz
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Shawon Debnath
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Michelle Cung
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Zheng Ling
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Chuan-Qi Zhong
- College of Life Science, Xiamen University, Xiamen, China
| | - Yixang Hong
- Xiamen Cardiovascular Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Gang Li
- Xiamen Cardiovascular Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Mascha Koenen
- Laboratory of Molecular Metabolism, The Rockefeller University, New York, NY, USA
| | - Paul Cohen
- Laboratory of Molecular Metabolism, The Rockefeller University, New York, NY, USA
| | - Xinhui Su
- PET Center, Department of Nuclear Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hongbin Lu
- Department of Sports Medicine, Xiangya Hospital, Central South University, Changsha, People's Republic of China.
- Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Changsha, China.
- Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.
| | - Matthew B Greenblatt
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
- Research Division, Hospital for Special Surgery, New York, NY, USA.
| | - Ren Xu
- State Key Laboratory of Cellular Stress Biology, Cancer Research Center, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, People's Republic of China.
- Xiamen Key Laboratory of Regeneration Medicine, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Xiamen University, Xiamen, China.
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16
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Humphries EM, Loudon C, Craft GE, Hains PG, Robinson PJ. Quantitative Comparison of Deparaffinization, Rehydration, and Extraction Methods for FFPE Tissue Proteomics and Phosphoproteomics. Anal Chem 2024. [PMID: 39102789 DOI: 10.1021/acs.analchem.3c04479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are suitable for proteomic and phosphoproteomic biomarker studies by data-independent acquisition mass spectrometry. The choice of the sample preparation method influences the number, intensity, and reproducibility of identifications. By comparing four deparaffinization and rehydration methods, including heptane, histolene, SubX, and xylene, we found that heptane and methanol produced the lowest coefficients of variation (CVs). Using this, five extraction methods from the literature were modified and evaluated for their performance using kidney, leg muscle, lung, and testicular rat organs. All methods performed well, except for SP3 due to insufficient tissue lysis. Heat n' Beat was the fastest and most reproducible method with the highest digestion efficiency and lowest CVs. S-Trap produced the highest peptide yield, while TFE produced the best phosphopeptide enrichment efficiency. The quantitation of FFPE-derived peptides remains an ongoing challenge with bias in UV and fluorescence assays across methods, most notably in SPEED. Functional enrichment analysis demonstrated that each method favored extracting some gene ontology cellular components over others including chromosome, cytoplasmic, cytoskeleton, endoplasmic reticulum, membrane, mitochondrion, and nucleoplasm protein groups. The outcome is a set of recommendations for choosing the most appropriate method for different settings.
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Affiliation(s)
- Erin M Humphries
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales 2145, Australia
| | - Clare Loudon
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales 2145, Australia
| | - George E Craft
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales 2145, Australia
| | - Peter G Hains
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales 2145, Australia
| | - Phillip J Robinson
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales 2145, Australia
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17
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Górska AM, Santos-García I, Eiriz I, Brüning T, Nyman T, Pahnke J. Evaluation of cerebrospinal fluid (CSF) and interstitial fluid (ISF) mouse proteomes for the validation and description of Alzheimer's disease biomarkers. J Neurosci Methods 2024:110239. [PMID: 39102902 DOI: 10.1016/j.jneumeth.2024.110239] [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: 03/26/2024] [Revised: 07/22/2024] [Accepted: 07/26/2024] [Indexed: 08/07/2024]
Abstract
BACKGROUND Mass spectrometry (MS)-based cerebrospinal fluid (CSF) proteomics is an important method for discovering biomarkers of neurodegenerative diseases. CSF serves as a reservoir for interstitial fluid (ISF), and extensive communication between the two fluid compartments helps to remove waste products from the brain. NEW METHOD We performed proteomic analyses of both CSF and ISF fluid compartments using intracerebral microdialysis to validate and detect novel biomarkers of Alzheimer's disease (AD) in APPtg and C57Bl/6J control mice. RESULTS We identified up to 625 proteins in ISF and 4,483 proteins in CSF samples. By comparing the biofluid profiles of APPtg and C57Bl/6J mice, we detected 37 and 108 significantly up- and downregulated candidates, respectively. In ISF, 7 highly regulated proteins, such as Gfap, Aldh1l1, Gstm1, and Txn, have already been implicated in AD progression, whereas in CSF, 9 out of 14 highly regulated proteins, such as Apba2, Syt12, Pgs1 and Vsnl1, have also been validated to be involved in AD pathogenesis. In addition, we also detected new interesting regulated proteins related to the control of synapses and neurotransmission (Kcna2, Cacng3, and Clcn6) whose roles as AD biomarkers should be further investigated. COMPARISON WITH EXISTING METHODS This newly established combined protocol provides better insight into the mutual communication between ISF and CSF as an analysis of tissue or CSF compartments alone. CONCLUSIONS The use of multiple fluid compartments, ISF and CSF, for the detection of their biological communication enables better detection of new promising AD biomarkers.
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Affiliation(s)
- Anna Maria Górska
- Translational Neurodegeneration Research and Neuropathology Lab, Department of Clinical Medicine (KlinMed), Medical Faculty, University of Oslo (UiO) and Section of Neuropathology Research, Department of Pathology, Clinics for Laboratory Medicine (KLM), Oslo University Hospital (OUS) Sognsvannsveien 20, NO-0372 Oslo, Norway; School of Neurobiology, Biochemistry and Biophysics, The Georg S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, IL-6997801, Israel.
| | - Irene Santos-García
- Translational Neurodegeneration Research and Neuropathology Lab, Department of Clinical Medicine (KlinMed), Medical Faculty, University of Oslo (UiO) and Section of Neuropathology Research, Department of Pathology, Clinics for Laboratory Medicine (KLM), Oslo University Hospital (OUS) Sognsvannsveien 20, NO-0372 Oslo, Norway; School of Neurobiology, Biochemistry and Biophysics, The Georg S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, IL-6997801, Israel.
| | - Ivan Eiriz
- Translational Neurodegeneration Research and Neuropathology Lab, Department of Clinical Medicine (KlinMed), Medical Faculty, University of Oslo (UiO) and Section of Neuropathology Research, Department of Pathology, Clinics for Laboratory Medicine (KLM), Oslo University Hospital (OUS) Sognsvannsveien 20, NO-0372 Oslo, Norway; School of Neurobiology, Biochemistry and Biophysics, The Georg S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, IL-6997801, Israel.
| | - Thomas Brüning
- Translational Neurodegeneration Research and Neuropathology Lab, Department of Clinical Medicine (KlinMed), Medical Faculty, University of Oslo (UiO) and Section of Neuropathology Research, Department of Pathology, Clinics for Laboratory Medicine (KLM), Oslo University Hospital (OUS) Sognsvannsveien 20, NO-0372 Oslo, Norway; School of Neurobiology, Biochemistry and Biophysics, The Georg S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, IL-6997801, Israel.
| | - Tuula Nyman
- Proteomics Core Facility, Department of Immunology, Oslo University Hospital (OUS) and University of Oslo (UiO), Faculty of Medicine, Sognsvannsveien 20, NO-0372 Oslo, Norway; School of Neurobiology, Biochemistry and Biophysics, The Georg S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, IL-6997801, Israel.
| | - Jens Pahnke
- Translational Neurodegeneration Research and Neuropathology Lab, Department of Clinical Medicine (KlinMed), Medical Faculty, University of Oslo (UiO) and Section of Neuropathology Research, Department of Pathology, Clinics for Laboratory Medicine (KLM), Oslo University Hospital (OUS) Sognsvannsveien 20, NO-0372 Oslo, Norway; Proteomics Core Facility, Department of Immunology, Oslo University Hospital (OUS) and University of Oslo (UiO), Faculty of Medicine, Sognsvannsveien 20, NO-0372 Oslo, Norway; Institute of Nutritional Medicine (INUM) and Lübeck Institute of Dermatology (LIED), University of Lübeck (UzL) and University Medical Center Schleswig-Holstein (UKSH), Ratzeburger Allee 160, D-23538 Lübeck, Germany; Department of Pharmacology, Faculty of Medicine and Life Sciences, University of Latvia, Jelgavas iela 3, LV-1004 Rīga, Latvia; School of Neurobiology, Biochemistry and Biophysics, The Georg S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, IL-6997801, Israel.
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18
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Bayne EF, Buck KM, Towler AG, Zhu Y, Pergande MR, Zhou T, Price S, Rossler KJ, Morales-Tirado V, Lloyd S, Wang F, He Y, Tian Y, Ge Y. High-Throughput Extracellular Matrix Proteomics of Human Lungs Enabled by Photocleavable Surfactant and diaPASEF. J Proteome Res 2024; 23:2908-2918. [PMID: 38315831 DOI: 10.1021/acs.jproteome.3c00532] [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] [Indexed: 02/07/2024]
Abstract
The extracellular matrix (ECM) is a complex assembly of proteins that provide interstitial scaffolding and elastic recoil for human lungs. The pulmonary extracellular matrix is increasingly recognized as an independent bioactive entity, by creating biochemical and mechanical signals that influence disease pathogenesis, making it an attractive therapeutic target. However, the pulmonary ECM proteome ("matrisome") remains challenging to analyze by mass spectrometry due to its inherent biophysical properties and relatively low abundance. Here, we introduce a strategy designed for rapid and efficient characterization of the human pulmonary ECM using the photocleavable surfactant Azo. We coupled this approach with trapped ion mobility MS with diaPASEF to maximize the depth of matrisome coverage. Using this strategy, we identify nearly 400 unique matrisome proteins with excellent reproducibility that are known to be important in lung biology, including key core matrisome proteins.
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Affiliation(s)
- Elizabeth F Bayne
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kevin M Buck
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Anna G Towler
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Yanlong Zhu
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Melissa R Pergande
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Tianhua Zhou
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Scott Price
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Kalina J Rossler
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Vanessa Morales-Tirado
- Discovery Immunology, Pharmacology and Pathology, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States
| | - Sarah Lloyd
- Discovery Immunology, Pharmacology and Pathology, AbbVie, Inc., North Chicago, Illinois 60064, United States
| | - Fei Wang
- Quantitative Translational & ADME Science, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States
| | - Yupeng He
- Discovery Immunology, Pharmacology and Pathology, AbbVie, Inc., North Chicago, Illinois 60064, United States
| | - Yu Tian
- Quantitative Translational & ADME Science, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
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19
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Liu Z, Yuan H, Wang Y, Li K, Suo C, Jin L, Ding C, Chen X. Proteogenomic Analysis Identifies a Causal Association between Plasma Apolipoprotein B Levels and Liver Cancer Risk. J Proteome Res 2024. [PMID: 39091241 DOI: 10.1021/acs.jproteome.4c00397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Liver oncogenesis is accompanied by discernible protein changes in the bloodstream. By employing plasma proteomic profiling, we can delve into the molecular mechanisms of liver cancer and pinpoint potential biomarkers. In this nested case-control study, we applied liquid chromatography-tandem mass spectrometry for proteome profiling in baseline plasma samples. Differential protein expression was determined and was subjected to functional enrichment, network, and Mendelian randomization (MR) analyses. We identified 193 proteins with notable differential levels between the groups. Of these proteins, MR analysis offered a compelling negative association between apolipoprotein B (APOB) and liver cancer. This association was further corroborated in the UK Biobank cohort: genetically predicted APOB levels were associated with a 31% (95% CI 19-42%) decreased risk of liver cancer; and phenotypic analysis indicated an 11% (95% CI 8-14%) decreased liver cancer risk for every 0.1 g/L increase of circulating APOB levels. Multivariable MR analysis suggested that the hepatic fat content might fully mediate the APOB-liver cancer connection. In summary, we identified some plasma proteins, particularly APOB, as potential biomarkers of liver cancer. Our findings underscore the intricate link between lipid metabolism and liver cancer, offering hints for targeted prophylactic strategies and early detection.
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Affiliation(s)
- Zhenqiu Liu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, Shanghai 200438, China
- Fudan University Taizhou Institute of Health Sciences, Taizhou 225316, China
| | - Huangbo Yuan
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, Shanghai 200438, China
- Fudan University Taizhou Institute of Health Sciences, Taizhou 225316, China
| | - Yunzhi Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Kai Li
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Chen Suo
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai 200032, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, Shanghai 200438, China
- Fudan University Taizhou Institute of Health Sciences, Taizhou 225316, China
| | - Chen Ding
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xingdong Chen
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Zhongshan Hospital, Fudan University, Shanghai 200433, China
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20
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Stefanakis K, Samiotaki M, Papaevangelou V, Valenzuela-Vallejo L, Giannoukakis N, Mantzoros CS. Longitudinal proteomics of leptin treatment in humans with acute and chronic energy deficiency-induced hypoleptinemia reveal novel, mainly immune-related, pleiotropic effects. Metabolism 2024; 159:155984. [PMID: 39097160 DOI: 10.1016/j.metabol.2024.155984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 07/26/2024] [Accepted: 07/29/2024] [Indexed: 08/05/2024]
Abstract
BACKGROUND Leptin is known for its metabolic, immunomodulatory and neuroendocrine properties, but the full spectrum of molecules downstream of leptin and relevant underlying mechanisms remain to be fully clarified. Our objective was to identify proteins and pathways influenced by leptin through untargeted proteomics in two clinical trials involving leptin administration in lean individuals. METHODS We performed untargeted liquid chromatography-tandem mass spectrometry serum proteomics across two studies a) Short-term randomized controlled crossover study of lean male and female humans undergoing a 72-h fast with concurrent administration of either placebo or high-dose leptin; b) Long-term (36-week) randomized controlled trial of leptin replacement therapy in human females with acquired relative energy deficiency and hypoleptinemia. We explored longitudinal proteomic changes and run adjusted mixed models followed by post-hoc tests. We further attempted to identify ontological pathways modulated during each experimental condition and/or comparison, through integrated qualitative pathway and enrichment analyses. We also explored dynamic longitudinal relationships between the circulating proteome with clinical and hormonal outcomes. RESULTS 289 and 357 unique proteins were identified per each respective study. Short-term leptin administration during fasting markedly upregulated several proinflammatory molecules, notably C-reactive protein (CRP) and cluster of differentiation (CD) 14, and downregulated lecithin cholesterol acyltransferase and several immunoglobulin variable chains, in contrast with placebo, which produced minimal changes. Quantitative pathway enrichment further indicated an upregulation of the acute phase response and downregulation of immunoglobulin- and B cell-mediated immunity by leptin. These changes were independent of participants' biological sex. In the long term study, leptin likewise robustly and persistently upregulated proteins of the acute phase response, and downregulated immunoglobulin-mediated immunity. Leptin also significantly and differentially affected a wide array of proteins related to immune function, defense response, coagulation, and inflammation compared with placebo. These changes were more notable at the 24-week visit, coinciding with the highest measured levels of serum leptin. We further identified distinct co-regulated clusters of proteins and clinical features during leptin administration indicating robust longitudinal correlations between the regulation of immunoglobulins, immune-related molecules, serpins (including cortisol and thyroxine-binding globulins), lipid transport molecules and growth factors, in contrast with placebo, which did not produce similar associations. CONCLUSIONS These high-throughput longitudinal results provide unique functional insights into leptin physiology, and pave the way for affinity-based proteomic analyses measuring several thousands of molecules, that will confirm these data and may fully delineate underlying mechanisms.
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Affiliation(s)
- Konstantinos Stefanakis
- Department of Internal Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
| | - Martina Samiotaki
- Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", Fleming 34, 166 72 Vari, Greece
| | - Vassiliki Papaevangelou
- Third Department of Paediatrics, Attikon University Hospital, National and Kapodistrian University of Athens, Greece
| | - Laura Valenzuela-Vallejo
- Department of Internal Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Nick Giannoukakis
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Christos S Mantzoros
- Department of Internal Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
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21
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Ahola S, Pazurek LA, Mayer F, Lampe P, Hermans S, Becker L, Amarie OV, Fuchs H, Gailus-Durner V, de Angelis MH, Riedel D, Nolte H, Langer T. Opa1 processing is dispensable in mouse development but is protective in mitochondrial cardiomyopathy. SCIENCE ADVANCES 2024; 10:eadp0443. [PMID: 39093974 PMCID: PMC11296347 DOI: 10.1126/sciadv.adp0443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 06/28/2024] [Indexed: 08/04/2024]
Abstract
Mitochondrial fusion and fission accompany adaptive responses to stress and altered metabolic demands. Inner membrane fusion and cristae morphogenesis depends on optic atrophy 1 (Opa1), which is expressed in different isoforms and is cleaved from a membrane-bound, long to a soluble, short form. Here, we have analyzed the physiological role of Opa1 isoforms and Opa1 processing by generating mouse lines expressing only one cleavable Opa1 isoform or a non-cleavable variant thereof. Our results show that expression of a single cleavable or non-cleavable Opa1 isoform preserves embryonic development and the health of adult mice. Opa1 processing is dispensable under metabolic and thermal stress but prolongs life span and protects against mitochondrial cardiomyopathy in OXPHOS-deficient Cox10-/- mice. Mechanistically, loss of Opa1 processing disturbs the balance between mitochondrial biogenesis and mitophagy, suppressing cardiac hypertrophic growth in Cox10-/- hearts. Our results highlight the critical regulatory role of Opa1 processing, mitochondrial dynamics, and metabolism for cardiac hypertrophy.
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Affiliation(s)
- Sofia Ahola
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Fiona Mayer
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Philipp Lampe
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Steffen Hermans
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Lore Becker
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Oana V Amarie
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Helmut Fuchs
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Valerie Gailus-Durner
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Martin Hrabe de Angelis
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Experimental Genetics, TUM School of Life Sciences, Technische Universität München, Freising, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg
| | - Dietmar Riedel
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Hendrik Nolte
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Thomas Langer
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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22
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Pergande MR, Osterbauer KJ, Buck KM, Roberts DS, Wood NN, Balasubramanian P, Mann MW, Rossler KJ, Diffee GM, Colman RJ, Anderson RM, Ge Y. Mass Spectrometry-Based Multiomics Identifies Metabolic Signatures of Sarcopenia in Rhesus Monkey Skeletal Muscle. J Proteome Res 2024; 23:2845-2856. [PMID: 37991985 PMCID: PMC11109024 DOI: 10.1021/acs.jproteome.3c00474] [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: 11/24/2023]
Abstract
Sarcopenia is a progressive disorder characterized by age-related loss of skeletal muscle mass and function. Although significant progress has been made over the years to identify the molecular determinants of sarcopenia, the precise mechanisms underlying the age-related loss of contractile function remains unclear. Advances in "omics" technologies, including mass spectrometry-based proteomic and metabolomic analyses, offer great opportunities to better understand sarcopenia. Herein, we performed mass spectrometry-based analyses of the vastus lateralis from young, middle-aged, and older rhesus monkeys to identify molecular signatures of sarcopenia. In our proteomic analysis, we identified proteins that change with age, including those involved in adenosine triphosphate and adenosine monophosphate metabolism as well as fatty acid beta oxidation. In our untargeted metabolomic analysis, we identified metabolites that changed with age largely related to energy metabolism including fatty acid beta oxidation. Pathway analysis of age-responsive proteins and metabolites revealed changes in muscle structure and contraction as well as lipid, carbohydrate, and purine metabolism. Together, this study discovers new metabolic signatures and offers new insights into the molecular mechanisms underlying sarcopenia for the evaluation and monitoring of a therapeutic treatment of sarcopenia.
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Affiliation(s)
- Melissa R. Pergande
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Katie J. Osterbauer
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Kevin M. Buck
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - David S. Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Nina N. Wood
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | | | - Morgan W. Mann
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Kalina J. Rossler
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Gary M. Diffee
- Department of Kinesiology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ricki J. Colman
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Rozalyn M. Anderson
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
- Geriatric Research Education and Clinical Center, William S. Middleton Memorial Veterans Hospital, Madison, WI 53705, USA
| | - Ying Ge
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
- Human Proteomics Program, University of Wisconsin-Madison, Madison, WI 53705, USA
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23
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Reis-de-Oliveira G, Carregari VC, Sousa GRDRD, Martins-de-Souza D. OmicScope unravels systems-level insights from quantitative proteomics data. Nat Commun 2024; 15:6510. [PMID: 39095347 PMCID: PMC11297029 DOI: 10.1038/s41467-024-50875-z] [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: 02/13/2024] [Accepted: 07/13/2024] [Indexed: 08/04/2024] Open
Abstract
Shotgun proteomics analysis presents multifaceted challenges, demanding diverse tool integration for insights. Addressing this complexity, OmicScope emerges as an innovative solution for quantitative proteomics data analysis. Engineered to handle various data formats, it performs data pre-processing - including joining replicates, normalization, data imputation - and conducts differential proteomics analysis for both static and longitudinal experimental designs. Empowered by Enrichr with over 224 databases, OmicScope performs Over Representation Analysis (ORA) and Gene Set Enrichment Analysis (GSEA). Additionally, its Nebula module facilitates meta-analysis from independent datasets, providing a systems biology approach for enriched insights. Complete with a data visualization toolkit and accessible as Python package and a web application, OmicScope democratizes proteomics analysis, offering an efficient and high-quality pipeline for researchers.
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Affiliation(s)
- Guilherme Reis-de-Oliveira
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil.
- Research Center, Boldrini Children's Hospital, Campinas, SP, Brazil.
| | - Victor Corasolla Carregari
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | | | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil.
- University of Campinas (UNICAMP), Campinas, SP, Brazil.
- Instituto Nacional de Biomarcadores Em Neuropsiquiatria (INBION) Conselho Nacional de Desenvolvimento Científico E Tecnológico, São Paulo, Brazil.
- Experimental Medicine Research Cluster (EMRC), University of Campinas, Campinas, SP, Brazil.
- D'Or Institute for Research and Education (IDOR), São Paulo, Brazil.
- INCT in Modelling Human Complex Diseases with 3D Platforms (Model3D), São Paulo, Brazil.
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24
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Skawinski CLS, Shah PS. I'm Walking into Spiderwebs: Making Sense of Protein-Protein Interaction Data. J Proteome Res 2024; 23:2723-2732. [PMID: 38556766 PMCID: PMC11296932 DOI: 10.1021/acs.jproteome.3c00892] [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: 04/02/2024]
Abstract
Protein-protein interactions (PPIs) are at the heart of the molecular landscape permeating life. Proteomics studies can explore this protein interaction landscape using mass spectrometry (MS). Thanks to their high sensitivity, mass spectrometers can easily identify thousands of proteins within a single sample, but that same sensitivity generates tangled spiderwebs of data that hide biologically relevant findings. So, what does a researcher do when she finds herself walking into spiderwebs? In a field focused on discovery, MS data require rigor in their analysis, experimental validation, or a combination of both. In this Review, we provide a brief primer on MS-based experimental methods to identify PPIs. We discuss approaches to analyze the resulting data and remove the proteomic background. We consider the advantages between comprehensive and targeted studies. We also discuss how scoring might be improved through AI-based protein structure information. Women have been essential to the development of proteomics, so we will specifically highlight work by women that has made this field thrive in recent years.
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Affiliation(s)
| | - Priya S. Shah
- Department of Chemical Engineering, University of California – Davis, California
- Department of Microbiology and Molecular Genetics, University of California – Davis, California
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25
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Gu K, Kumabe H, Yamamoto T, Tashiro N, Masuda T, Ito S, Ohtsuki S. Improving Proteomic Identification Using Narrow Isolation Windows with Zeno SWATH Data-Independent Acquisition. J Proteome Res 2024; 23:3484-3495. [PMID: 38978496 DOI: 10.1021/acs.jproteome.4c00149] [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] [Indexed: 07/10/2024]
Abstract
Data-independent acquisition (DIA) techniques such as sequential window acquisition of all theoretical mass spectra (SWATH) acquisition have emerged as the preferred strategies for proteomic analyses. Our study optimized the SWATH-DIA method using a narrow isolation window placement approach, improving its proteomic performance. We optimized the acquisition parameter combinations of narrow isolation windows with different widths (1.9 and 2.9 Da) on a ZenoTOF 7600 (Sciex); the acquired data were analyzed using DIA-NN (version 1.8.1). Narrow SWATH (nSWATH) identified 5916 and 7719 protein groups on the digested peptides, corresponding to 400 ng of protein from mouse liver and HEK293T cells, respectively, improving identification by 7.52 and 4.99%, respectively, compared to conventional SWATH. The median coefficient of variation of the quantified values was less than 6%. We further analyzed 200 ng of benchmark samples comprising peptides from known ratios ofEscherichia coli, yeast, and human peptides using nSWATH. Consequently, it achieved accuracy and precision comparable to those of conventional SWATH, identifying an average of 95,456 precursors and 9342 protein groups across three benchmark samples, representing 12.6 and 9.63% improved identification compared to conventional SWATH. The nSWATH method improved identification at various loading amounts of benchmark samples, identifying 40.7% more protein groups at 25 ng. These results demonstrate the improved performance of nSWATH, contributing to the acquisition of deeper proteomic data from complex biological samples.
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Affiliation(s)
- Kongxin Gu
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Haruka Kumabe
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Takumi Yamamoto
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Naoto Tashiro
- Department of Pharmaceutical Microbiology, School of Pharmacy, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Takeshi Masuda
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
- Department of Pharmaceutical Microbiology, School of Pharmacy, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Daihoji, Tsuruoka, Yamagata 997-0017, Japan
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Shingo Ito
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
- Department of Pharmaceutical Microbiology, School of Pharmacy, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Sumio Ohtsuki
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
- Department of Pharmaceutical Microbiology, School of Pharmacy, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
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26
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Rogers ZJ, Colombani T, Khan S, Bhatt K, Nukovic A, Zhou G, Woolston BM, Taylor CT, Gilkes DM, Slavov N, Bencherif SA. Controlling Pericellular Oxygen Tension in Cell Culture Reveals Distinct Breast Cancer Responses to Low Oxygen Tensions. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2402557. [PMID: 38874400 PMCID: PMC11321643 DOI: 10.1002/advs.202402557] [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: 03/14/2024] [Revised: 04/11/2024] [Indexed: 06/15/2024]
Abstract
In oxygen (O2)-controlled cell culture, an indispensable tool in biological research, it is presumed that the incubator setpoint equals the O2 tension experienced by cells (i.e., pericellular O2). However, it is discovered that physioxic (5% O2) and hypoxic (1% O2) setpoints regularly induce anoxic (0% O2) pericellular tensions in both adherent and suspension cell cultures. Electron transport chain inhibition ablates this effect, indicating that cellular O2 consumption is the driving factor. RNA-seq analysis revealed that primary human hepatocytes cultured in physioxia experience ischemia-reperfusion injury due to cellular O2 consumption. A reaction-diffusion model is developed to predict pericellular O2 tension a priori, demonstrating that the effect of cellular O2 consumption has the greatest impact in smaller volume culture vessels. By controlling pericellular O2 tension in cell culture, it is found that hypoxia vs. anoxia induce distinct breast cancer transcriptomic and translational responses, including modulation of the hypoxia-inducible factor (HIF) pathway and metabolic reprogramming. Collectively, these findings indicate that breast cancer cells respond non-monotonically to low O2, suggesting that anoxic cell culture is not suitable for modeling hypoxia. Furthermore, it is shown that controlling atmospheric O2 tension in cell culture incubators is insufficient to regulate O2 in cell culture, thus introducing the concept of pericellular O2-controlled cell culture.
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Affiliation(s)
- Zachary J. Rogers
- Department of Chemical EngineeringNortheastern UniversityBostonMA02115USA
| | - Thibault Colombani
- Department of Chemical EngineeringNortheastern UniversityBostonMA02115USA
| | - Saad Khan
- Department of BioengineeringNortheastern UniversityBostonMA02115USA
| | - Khushbu Bhatt
- Department of Pharmaceutical SciencesNortheastern UniversityBostonMA02115USA
| | - Alexandra Nukovic
- Department of Chemical EngineeringNortheastern UniversityBostonMA02115USA
| | - Guanyu Zhou
- Department of Chemical EngineeringNortheastern UniversityBostonMA02115USA
| | | | - Cormac T. Taylor
- Conway Institute of Biomolecular and Biomedical Research and School of MedicineUniversity College DublinBelfieldDublinD04 V1W8Ireland
| | - Daniele M. Gilkes
- Department of OncologyThe Sidney Kimmel Comprehensive Cancer CenterThe Johns Hopkins University School of MedicineBaltimoreMD21321USA
- Cellular and Molecular Medicine ProgramThe Johns Hopkins University School of MedicineBaltimoreMD21321USA
- Department of Chemical and Biomolecular EngineeringThe Johns Hopkins UniversityBaltimoreMD21218USA
- Johns Hopkins Institute for NanoBioTechnologyThe Johns Hopkins UniversityBaltimoreMD21218USA
| | - Nikolai Slavov
- Department of BioengineeringNortheastern UniversityBostonMA02115USA
- Departments of BioengineeringBiologyChemistry and Chemical BiologySingle Cell Center and Barnett InstituteNortheastern UniversityBostonMA02115USA
- Parallel Squared Technology InstituteWatertownMA02472USA
| | - Sidi A. Bencherif
- Department of Chemical EngineeringNortheastern UniversityBostonMA02115USA
- Department of BioengineeringNortheastern UniversityBostonMA02115USA
- Harvard John A. Paulson School of Engineering and Applied SciencesHarvard UniversityCambridgeMA02138USA
- Biomechanics and Bioengineering (BMBI)UTC CNRS UMR 7338University of Technology of CompiègneSorbonne UniversityCompiègne60203France
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27
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Iruzubieta P, Damborenea A, Ioghen M, Bajew S, Fernandez-Torrón R, Töpf A, Herrero-Reiriz Á, Epure D, Vill K, Hernández-Laín A, Manterola M, Azkargorta M, Pikatza-Menoio O, Pérez-Fernandez L, García-Puga M, Gaina G, Bastian A, Streata I, Walter MC, Müller-Felber W, Thiele S, Moragón S, Bastida-Lertxundi N, López-Cortajarena A, Elortza F, Gereñu G, Alonso-Martin S, Straub V, de Sancho D, Teleanu R, López de Munain A, Blázquez L. Biallelic variants in SNUPN cause a limb girdle muscular dystrophy with myofibrillar-like features. Brain 2024; 147:2867-2883. [PMID: 38366623 PMCID: PMC11292911 DOI: 10.1093/brain/awae046] [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: 09/08/2023] [Revised: 01/20/2024] [Accepted: 01/26/2024] [Indexed: 02/18/2024] Open
Abstract
Alterations in RNA-splicing are a molecular hallmark of several neurological diseases, including muscular dystrophies, where mutations in genes involved in RNA metabolism or characterized by alterations in RNA splicing have been described. Here, we present five patients from two unrelated families with a limb-girdle muscular dystrophy (LGMD) phenotype carrying a biallelic variant in SNUPN gene. Snurportin-1, the protein encoded by SNUPN, plays an important role in the nuclear transport of small nuclear ribonucleoproteins (snRNPs), essential components of the spliceosome. We combine deep phenotyping, including clinical features, histopathology and muscle MRI, with functional studies in patient-derived cells and muscle biopsies to demonstrate that variants in SNUPN are the cause of a new type of LGMD according to current definition. Moreover, an in vivo model in Drosophila melanogaster further supports the relevance of Snurportin-1 in muscle. SNUPN patients show a similar phenotype characterized by proximal weakness starting in childhood, restrictive respiratory dysfunction and prominent contractures, although inter-individual variability in terms of severity even in individuals from the same family was found. Muscle biopsy showed myofibrillar-like features consisting of myotilin deposits and Z-disc disorganization. MRI showed predominant impairment of paravertebral, vasti, sartorius, gracilis, peroneal and medial gastrocnemius muscles. Conservation and structural analyses of Snurportin-1 p.Ile309Ser variant suggest an effect in nuclear-cytosol snRNP trafficking. In patient-derived fibroblasts and muscle, cytoplasmic accumulation of snRNP components is observed, while total expression of Snurportin-1 and snRNPs remains unchanged, which demonstrates a functional impact of SNUPN variant in snRNP metabolism. Furthermore, RNA-splicing analysis in patients' muscle showed widespread splicing deregulation, in particular in genes relevant for muscle development and splicing factors that participate in the early steps of spliceosome assembly. In conclusion, we report that SNUPN variants are a new cause of limb girdle muscular dystrophy with specific clinical, histopathological and imaging features, supporting SNUPN as a new gene to be included in genetic testing of myopathies. These results further support the relevance of splicing-related proteins in muscle disorders.
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Affiliation(s)
- Pablo Iruzubieta
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastián, Spain
- Department of Neurology, Donostia University Hospital, Osakidetza Basque Health Service, 20014 San Sebastián, Spain
- CIBERNED, ISCIII (CIBER, Carlos III Institute, Spanish Ministry of Sciences and Innovation), 28031, Madrid, Spain
| | - Alberto Damborenea
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastián, Spain
| | - Mihaela Ioghen
- Clinical Neurosciences Department, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, Paediatric Neurology, 020021 Bucharest, Romania
| | - Simon Bajew
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastián, Spain
| | - Roberto Fernandez-Torrón
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastián, Spain
- Department of Neurology, Donostia University Hospital, Osakidetza Basque Health Service, 20014 San Sebastián, Spain
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trust, NE4 5NR Newcastle Upon Tyne, UK
| | - Álvaro Herrero-Reiriz
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastián, Spain
| | - Diana Epure
- Department of Paediatric Neurology, Doctor Victor Gomoiu Children’s Hospital, 022102 Bucharest, Romania
| | - Katharina Vill
- Department of Pediatric Neurology and Developmental Medicine and LMU Center for Children with Medical Complexity, Dr. von Hauner Children’s Hospital, LMU University Hospital, Ludwig-Maximilians-University Munich, 80539 Munich, Germany
- Institute of Human Genetics, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Aurelio Hernández-Laín
- Neuropathology Unit, Department of Pathology, 12 de Octubre University Hospital, 28041 Madrid, Spain
- Department of Neuro-oncology, Instituto de Investigación Sanitaria imas12, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
- Universidad Complutense de Madrid, Facultad de Medicina, 28040 Madrid, Spain
| | - María Manterola
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastián, Spain
| | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain
- Centre for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Oihane Pikatza-Menoio
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastián, Spain
- CIBERNED, ISCIII (CIBER, Carlos III Institute, Spanish Ministry of Sciences and Innovation), 28031, Madrid, Spain
| | - Laura Pérez-Fernandez
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastián, Spain
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), 20014 San Sebastián, Spain
| | - Mikel García-Puga
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastián, Spain
- CIBERNED, ISCIII (CIBER, Carlos III Institute, Spanish Ministry of Sciences and Innovation), 28031, Madrid, Spain
| | - Gisela Gaina
- Department of Cell Biology, Neurosciences and Experimental Myology, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania
| | - Alexandra Bastian
- Department of Pathology, Colentina Clinical Hospital, 020125 Bucharest, Romania
| | - Ioana Streata
- Human Genomics Laboratory, Regional Centre of Medical Genetics, Craiova University of Medicine and Pharmacy, 200349 Dolj, Romania
| | - Maggie C Walter
- Friedrich Baur Institute at the Department of Neurology, LMU University Hospital, Ludwig-Maximilians-University Munich, 80539 Munich, Germany
| | - Wolfgang Müller-Felber
- Institute of Human Genetics, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Simone Thiele
- Friedrich Baur Institute at the Department of Neurology, LMU University Hospital, Ludwig-Maximilians-University Munich, 80539 Munich, Germany
| | - Saioa Moragón
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastián, Spain
| | - Nerea Bastida-Lertxundi
- Department of Clinical Genetics, Donostia University Hospital, Osakidetza Basque Health Service, 20014 San Sebastián, Spain
| | - Aitziber López-Cortajarena
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), 20014 San Sebastián, Spain
- Ikerbasque, Basque Foundation for Science, 48009 Bilbao, Spain
| | - Felix Elortza
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain
- Centre for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Gorka Gereñu
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastián, Spain
- CIBERNED, ISCIII (CIBER, Carlos III Institute, Spanish Ministry of Sciences and Innovation), 28031, Madrid, Spain
- Ikerbasque, Basque Foundation for Science, 48009 Bilbao, Spain
| | - Sonia Alonso-Martin
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastián, Spain
- CIBERNED, ISCIII (CIBER, Carlos III Institute, Spanish Ministry of Sciences and Innovation), 28031, Madrid, Spain
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trust, NE4 5NR Newcastle Upon Tyne, UK
| | - David de Sancho
- Donostia International Physics Center, 20018 San Sebastián, Spain
- Faculty of Chemistry, University of the Basque Country, 20018 San Sebastián, Spain
| | - Raluca Teleanu
- Clinical Neurosciences Department, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, Paediatric Neurology, 020021 Bucharest, Romania
| | - Adolfo López de Munain
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastián, Spain
- Department of Neurology, Donostia University Hospital, Osakidetza Basque Health Service, 20014 San Sebastián, Spain
- CIBERNED, ISCIII (CIBER, Carlos III Institute, Spanish Ministry of Sciences and Innovation), 28031, Madrid, Spain
- Faculty of Medicine, University of the Basque Country, 20014 San Sebastián, Spain
- Faculty of Medicine, University of Deusto, 48007 Bilbao, Spain
| | - Lorea Blázquez
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastián, Spain
- CIBERNED, ISCIII (CIBER, Carlos III Institute, Spanish Ministry of Sciences and Innovation), 28031, Madrid, Spain
- Ikerbasque, Basque Foundation for Science, 48009 Bilbao, Spain
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Oliinyk D, Will A, Schneidmadel FR, Böhme M, Rinke J, Hochhaus A, Ernst T, Hahn N, Geis C, Lubeck M, Raether O, Humphrey SJ, Meier F. µPhos: a scalable and sensitive platform for high-dimensional phosphoproteomics. Mol Syst Biol 2024; 20:972-995. [PMID: 38907068 PMCID: PMC11297287 DOI: 10.1038/s44320-024-00050-9] [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: 08/25/2023] [Revised: 06/06/2024] [Accepted: 06/11/2024] [Indexed: 06/23/2024] Open
Abstract
Mass spectrometry has revolutionized cell signaling research by vastly simplifying the analysis of many thousands of phosphorylation sites in the human proteome. Defining the cellular response to perturbations is crucial for further illuminating the functionality of the phosphoproteome. Here we describe µPhos ('microPhos'), an accessible phosphoproteomics platform that permits phosphopeptide enrichment from 96-well cell culture and small tissue amounts in <8 h total processing time. By greatly minimizing transfer steps and liquid volumes, we demonstrate increased sensitivity, >90% selectivity, and excellent quantitative reproducibility. Employing highly sensitive trapped ion mobility mass spectrometry, we quantify ~17,000 Class I phosphosites in a human cancer cell line using 20 µg starting material, and confidently localize ~6200 phosphosites from 1 µg. This depth covers key signaling pathways, rendering sample-limited applications and perturbation experiments with hundreds of samples viable. We employ µPhos to study drug- and time-dependent response signatures in a leukemia cell line, and by quantifying 30,000 Class I phosphosites in the mouse brain we reveal distinct spatial kinase activities in subregions of the hippocampal formation.
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Affiliation(s)
- Denys Oliinyk
- Functional Proteomics, Jena University Hospital, 07747, Jena, Germany
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
| | - Andreas Will
- Functional Proteomics, Jena University Hospital, 07747, Jena, Germany
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
| | - Felix R Schneidmadel
- Functional Proteomics, Jena University Hospital, 07747, Jena, Germany
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
| | - Maximilian Böhme
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
- Klinik für Innere Medizin II, Jena University Hospital, 07747, Jena, Germany
| | - Jenny Rinke
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
- Klinik für Innere Medizin II, Jena University Hospital, 07747, Jena, Germany
| | - Andreas Hochhaus
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
- Klinik für Innere Medizin II, Jena University Hospital, 07747, Jena, Germany
| | - Thomas Ernst
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
- Klinik für Innere Medizin II, Jena University Hospital, 07747, Jena, Germany
| | - Nina Hahn
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, 07747, Jena, Germany
- Center for Sepsis Control and Care, Jena University Hospital, 07747, Jena, Germany
| | - Christian Geis
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, 07747, Jena, Germany
- Center for Sepsis Control and Care, Jena University Hospital, 07747, Jena, Germany
| | - Markus Lubeck
- Bruker Daltonics GmbH & Co. KG, 28359, Bremen, Germany
| | | | - Sean J Humphrey
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, 3052, Victoria, Australia.
| | - Florian Meier
- Functional Proteomics, Jena University Hospital, 07747, Jena, Germany.
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany.
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29
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Chen K, Sun R, Guan Y, Fang T, Tao J, Li Z, Zhang B, Yu Z, Tian J, Teng Z, Wang J. Manganese-induced Photothermal-Ferroptosis for Synergistic Tumor Therapy. J Control Release 2024; 372:386-402. [PMID: 38909699 DOI: 10.1016/j.jconrel.2024.06.053] [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: 02/12/2024] [Revised: 06/10/2024] [Accepted: 06/20/2024] [Indexed: 06/25/2024]
Abstract
Ferroptosis-related tumor therapy based on nanomedicines has recently gained significant attention. However, the therapeutic performance is still hindered by the tumor's physical barriers such as the fibrotic tumor matrix and elevated interstitial fluid pressure, as well as chemical barriers like glutathione (GSH) overabundance. These physicochemical barriers impede the bioavailability of nanomedicines and compromise the therapeutic efficacy of lipid reactive oxygen species (ROS). Thus, this study pioneers a manganese-mediated overcoming of physicochemical barriers in the tumor microenvironment using organosilica-based nanomedicine (MMONs), which bolsters the synergy of photothermal-ferroptosis treatment. The MMONs display commendable proficiency in overcoming tumor physical barriers, due to their MnO2-mediated shape-morphing and softness-transformation ability, which facilitates augmented cellular internalization, enhanced tumor accumulation, and superior drug penetration. Also, the MMONs possess excellent capability in chemical barrier overcoming, including MnO2-mediated dual GSH clearance and enhanced ROS generation, which facilitates ferroptosis and heat shock protein inhibition. Notably, the resulting integration of physical and chemical barrier overcoming leads to amplified photothermal-ferroptosis synergistic tumor therapy both in vitro and in vivo. Accordingly, the comparative proteomic analysis has identified promoted ferroptosis with a transient inhibitory response observed in the mitochondria. This research aims to improve treatment strategies to better fight the complex defenses of tumors.
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Affiliation(s)
- Kun Chen
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening & Guangdong-Hongkong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Rui Sun
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening & Guangdong-Hongkong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China; Department of Laboratory Medicine, Dongguan Institute of Clinical Cancer Research, The Tenth Affiliated Hospital of Southern Medical University (Dongguan People's Hospital), Dongguan 523018, China
| | - Yudong Guan
- Department of Urology, Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong 518020, China
| | - Tao Fang
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening & Guangdong-Hongkong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jun Tao
- Key Laboratory for Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, Jiangsu National Synergetic Innovation Centre for Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Zhijie Li
- Department of Urology, Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong 518020, China.
| | - Bingchen Zhang
- Department of Laboratory Medicine, Dongguan Institute of Clinical Cancer Research, The Tenth Affiliated Hospital of Southern Medical University (Dongguan People's Hospital), Dongguan 523018, China
| | - Zhiqiang Yu
- Department of Laboratory Medicine, Dongguan Institute of Clinical Cancer Research, The Tenth Affiliated Hospital of Southern Medical University (Dongguan People's Hospital), Dongguan 523018, China.
| | - Jiahang Tian
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening & Guangdong-Hongkong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Zhaogang Teng
- Key Laboratory for Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, Jiangsu National Synergetic Innovation Centre for Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing 210023, China.
| | - Jigang Wang
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening & Guangdong-Hongkong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China; Department of Urology, Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong 518020, China; State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; State Key Laboratory of Antiviral Drugs, School of Pharmacy, Henan University, Kaifeng 475004, PR China.
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30
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Veronese M, Kallabis S, Kaczmarek AT, Das A, Robers L, Schumacher S, Lofrano A, Brodesser S, Müller S, Hofmann K, Krüger M, Rugarli EI. ERLIN1/2 scaffolds bridge TMUB1 and RNF170 and restrict cholesterol esterification to regulate the secretory pathway. Life Sci Alliance 2024; 7:e202402620. [PMID: 38782601 PMCID: PMC11116810 DOI: 10.26508/lsa.202402620] [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: 01/25/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
Complexes of ERLIN1 and ERLIN2 (ER lipid raft-associated 1 and 2) form large ring-like cup-shaped structures on the endoplasmic reticulum (ER) membrane and serve as platforms to bind cholesterol and E3 ubiquitin ligases, potentially defining functional nanodomains. Here, we show that ERLIN scaffolds mediate the interaction between the full-length isoform of TMUB1 (transmembrane and ubiquitin-like domain-containing 1) and RNF170 (RING finger protein 170). We identify a luminal N-terminal conserved region in TMUB1 and RNF170, which is required for this interaction. Three-dimensional modelling shows that this conserved motif binds the stomatin/prohibitin/flotillin/HflKC domain of two adjacent ERLIN subunits at different interfaces. Protein variants that preclude these interactions have been previously linked to hereditary spastic paraplegia. Using omics-based approaches in combination with phenotypic characterization of HeLa cells lacking both ERLINs, we demonstrate a role of ERLIN scaffolds in limiting cholesterol esterification, thereby favouring cholesterol transport from the ER to the Golgi apparatus and regulating Golgi morphology and the secretory pathway.
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Affiliation(s)
- Matteo Veronese
- https://ror.org/00rcxh774 Institute for Genetics, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Sebastian Kallabis
- https://ror.org/00rcxh774 Institute for Genetics, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Alexander Tobias Kaczmarek
- https://ror.org/00rcxh774 Institute for Genetics, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Anushka Das
- https://ror.org/00rcxh774 Institute for Genetics, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Lennart Robers
- https://ror.org/00rcxh774 Institute for Genetics, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Simon Schumacher
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
- Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Alessia Lofrano
- https://ror.org/00rcxh774 Institute for Genetics, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Susanne Brodesser
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
- Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Stefan Müller
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Kay Hofmann
- https://ror.org/00rcxh774 Institute for Genetics, University of Cologne, Cologne, Germany
| | - Marcus Krüger
- https://ror.org/00rcxh774 Institute for Genetics, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
- https://ror.org/00rcxh774 Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Elena I Rugarli
- https://ror.org/00rcxh774 Institute for Genetics, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
- https://ror.org/00rcxh774 Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
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31
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Díaz Ludovico I, Powell SM, Many G, Bramer L, Sarkar S, Stratton K, Liu T, Shi T, Qian WJ, Burnum-Johnson KE, Melchior JT, Nakayasu ES. A fast and sensitive size-exclusion chromatography method for plasma extracellular vesicle proteomic analysis. Proteomics 2024; 24:e2400025. [PMID: 38895962 DOI: 10.1002/pmic.202400025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024]
Abstract
Extracellular vesicles (EVs) carry diverse biomolecules derived from their parental cells, making their components excellent biomarker candidates. However, purifying EVs is a major hurdle in biomarker discovery since current methods require large amounts of samples, are time-consuming and typically have poor reproducibility. Here we describe a simple, fast, and sensitive EV fractionation method using size exclusion chromatography (SEC) on a fast protein liquid chromatography (FPLC) system. Our method uses a Superose 6 Increase 5/150, which has a bed volume of 2.9 mL. The FPLC system and small column size enable reproducible separation of only 50 µL of human plasma in 15 min. To demonstrate the utility of our method, we used longitudinal samples from a group of individuals who underwent intense exercise. A total of 838 proteins were identified, of which, 261 were previously characterized as EV proteins, including classical markers, such as cluster of differentiation (CD)9 and CD81. Quantitative analysis showed low technical variability with correlation coefficients greater than 0.9 between replicates. The analysis captured differences in relevant EV proteins involved in response to physical activity. Our method enables fast and sensitive fractionation of plasma EVs with low variability, which will facilitate biomarker studies in large clinical cohorts.
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Affiliation(s)
- Ivo Díaz Ludovico
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Samantha M Powell
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Gina Many
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Lisa Bramer
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Soumyadeep Sarkar
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Kelly Stratton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Kristin E Burnum-Johnson
- Environmental and Molecular Science Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - John T Melchior
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
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32
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Demirci H, Popovic S, Dittmayer C, Yilmaz DE, El-Shimy IA, Mülleder M, Hinze C, Su M, Mertins P, Kirchner M, Osmanodja B, Paliege A, Budde K, Amann K, Persson PB, Mutig K, Bachmann S. Immunosuppression with cyclosporine versus tacrolimus shows distinctive nephrotoxicity profiles within renal compartments. Acta Physiol (Oxf) 2024; 240:e14190. [PMID: 38884453 DOI: 10.1111/apha.14190] [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: 04/15/2024] [Revised: 05/18/2024] [Accepted: 06/04/2024] [Indexed: 06/18/2024]
Abstract
AIM Calcineurin inhibitors (CNIs) are the backbone for immunosuppression after solid organ transplantation. Although successful in preventing kidney transplant rejection, their nephrotoxic side effects contribute to allograft injury. Renal parenchymal lesions occur for cyclosporine A (CsA) as well as for the currently favored tacrolimus (Tac). We aimed to study whether chronic CsA and Tac exposures, before reaching irreversible nephrotoxic damage, affect renal compartments differentially and whether related pathogenic mechanisms can be identified. METHODS CsA and Tac were administered chronically in wild type Wistar rats using osmotic minipumps over 4 weeks. Functional parameters were controlled. Electron microscopy, confocal, and 3D-structured illumination microscopy were used for histopathology. Clinical translatability was tested in human renal biopsies. Standard biochemical, RNA-seq, and proteomic technologies were applied to identify implicated molecular pathways. RESULTS Both drugs caused significant albeit differential damage in vasculature and nephron. The glomerular filtration barrier was more affected by Tac than by CsA, showing prominent deteriorations in endothelium and podocytes along with impaired VEGF/VEGFR2 signaling and podocyte-specific gene expression. By contrast, proximal tubule epithelia were more severely affected by CsA than by Tac, revealing lysosomal dysfunction, enhanced apoptosis, impaired proteostasis and oxidative stress. Lesion characteristics were confirmed in human renal biopsies. CONCLUSION We conclude that pathogenetic alterations in the renal compartments are specific for either treatment. Considering translation to the clinical setting, CNI choice should reflect individual risk factors for renal vasculature and tubular epithelia. As a step in this direction, we share protein signatures identified from multiomics with potential pathognomonic relevance.
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Affiliation(s)
- Hasan Demirci
- Institute of Functional Anatomy, Charité, Universitätsmedizin Berlin, Berlin, Germany
- Department of Cell- and Neurobiology, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Suncica Popovic
- Institute of Functional Anatomy, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Carsten Dittmayer
- Department of Neuropathology, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Duygu Elif Yilmaz
- Institute of Functional Anatomy, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Ismail Amr El-Shimy
- Molecular Epidemiology Unit, Berlin Institute of Health, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Michael Mülleder
- Core Facility-High-Throughput Mass Spectrometry, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Christian Hinze
- Department of Nephrology and Hypertension, Hannover Medical School, Hannover, Germany
| | - Mingzhen Su
- Department of Cell- and Neurobiology, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Philipp Mertins
- Core Unit Proteomics, Berlin Institute of Health at Charité, Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Marieluise Kirchner
- Core Unit Proteomics, Berlin Institute of Health at Charité, Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Bilgin Osmanodja
- Department of Nephrology and Medical Intensive Care, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Alexander Paliege
- Department of Nephrology, Universitätsklinikum Carl Gustav Carus Dresden, Dresden, Germany
| | - Klemens Budde
- Department of Nephrology and Medical Intensive Care, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Kerstin Amann
- Department of Nephropathology, Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Pontus B Persson
- Department of Translational Physiology, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Kerim Mutig
- Department of Translational Physiology, Charité, Universitätsmedizin Berlin, Berlin, Germany
- Department of Pharmacology, Institute of Pharmacy, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Sebastian Bachmann
- Institute of Functional Anatomy, Charité, Universitätsmedizin Berlin, Berlin, Germany
- Department of Cell- and Neurobiology, Charité, Universitätsmedizin Berlin, Berlin, Germany
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33
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Diaz-Vegas A, Cooke KC, Cutler HB, Yau B, Masson SWC, Harney D, Fuller OK, Potter M, Madsen S, Craw NR, Zhang Y, Moreno CL, Kebede MA, Neely GG, Stöckli J, Burchfield JG, James DE. Deletion of miPEP in adipocytes protects against obesity and insulin resistance by boosting muscle metabolism. Mol Metab 2024; 86:101983. [PMID: 38960128 PMCID: PMC11292358 DOI: 10.1016/j.molmet.2024.101983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 06/24/2024] [Accepted: 06/27/2024] [Indexed: 07/05/2024] Open
Abstract
Mitochondria facilitate thousands of biochemical reactions, covering a broad spectrum of anabolic and catabolic processes. Here we demonstrate that the adipocyte mitochondrial proteome is markedly altered across multiple models of insulin resistance and reveal a consistent decrease in the level of the mitochondrial processing peptidase miPEP. OBJECTIVE To determine the role of miPEP in insulin resistance. METHODS To experimentally test this observation, we generated adipocyte-specific miPEP knockout mice to interrogate its role in the aetiology of insulin resistance. RESULTS We observed a strong phenotype characterised by enhanced insulin sensitivity and reduced adiposity, despite normal food intake and physical activity. Strikingly, these phenotypes vanished when mice were housed at thermoneutrality, suggesting that metabolic protection conferred by miPEP deletion hinges upon a thermoregulatory process. Tissue specific analysis of miPEP deficient mice revealed an increment in muscle metabolism, and upregulation of the protein FBP2 that is involved in ATP hydrolysis in the gluconeogenic pathway. CONCLUSION These findings suggest that miPEP deletion initiates a compensatory increase in skeletal muscle metabolism acting as a protective mechanism against diet-induced obesity and insulin resistance.
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Affiliation(s)
- Alexis Diaz-Vegas
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia.
| | - Kristen C Cooke
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Harry B Cutler
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Belinda Yau
- School of Medical Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Stewart W C Masson
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Dylan Harney
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Oliver K Fuller
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Meg Potter
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Søren Madsen
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Niamh R Craw
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Yiju Zhang
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Cesar L Moreno
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Melkam A Kebede
- School of Medical Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - G Gregory Neely
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Jacqueline Stöckli
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - James G Burchfield
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - David E James
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia; School of Medical Sciences, University of Sydney, Camperdown, New South Wales, Australia.
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Li Q, Feng H, Tian Q, Xiang Y, Wang X, He YX, Zhu K. Discovery of antibacterial diketones against gram-positive bacteria. Cell Chem Biol 2024:S2451-9456(24)00277-0. [PMID: 39089260 DOI: 10.1016/j.chembiol.2024.06.017] [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: 10/23/2023] [Revised: 04/21/2024] [Accepted: 06/28/2024] [Indexed: 08/03/2024]
Abstract
The rapid rise of antibiotic resistance calls for the discovery of new antibiotics with distinct antibacterial mechanisms. New target mining is indispensable for developing antibiotics. Plant-microbial antibiotics are appealing to underexplored sources due to a dearth of comprehensive understanding of antibacterial activity and the excavation of new targets. Here, a series of phloroglucinol derivatives of plant-root-associated Pseudomonas fluorescens were synthesized for structure-activity relationship analysis. Notably, 2,4-diproylphloroglucinol (DPPG) displayed efficient bactericidal activity against a wide range of gram-positive bacteria. Importantly, mechanistic study exhibits that DPPG binds to type II NADH dehydrogenase (NDH-2), an essential enzyme catalyzing the transfer of electrons from NADH to quinones in the electron transport chain (ETC), blocking electron transfer in S. aureus. Last, we validated the efficacy of DPPG in vivo through animal infection models. Our findings not only provide a distinct antibiotic lead to treat multidrug resistant pathogens but also identify a promising antibacterial target.
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Affiliation(s)
- Qian Li
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Hanzhong Feng
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Qiong Tian
- State Key Laboratory of Applied Organic Chemistry, Department of Chemistry and School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Yun Xiang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Xiaolei Wang
- State Key Laboratory of Applied Organic Chemistry, Department of Chemistry and School of Pharmacy, Lanzhou University, Lanzhou 730000, China.
| | - Yong-Xing He
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China; State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China.
| | - Kui Zhu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
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Ni M, Wan D, Wu J, Gong W, Wang J, Zheng Z. Candidate prognostic biomarkers and prediction models for high-grade serous ovarian cancer from urinary proteomics. J Proteomics 2024; 304:105234. [PMID: 38925351 DOI: 10.1016/j.jprot.2024.105234] [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: 04/09/2024] [Revised: 06/22/2024] [Accepted: 06/22/2024] [Indexed: 06/28/2024]
Abstract
High-grade serous ovarian cancer (HGSOC) is one of the most common histologic types of ovarian cancer. The purpose of this study was to identify potential prognostic biomarkers in urine specimens from patients with HGSOC. First, 56 urine samples with information on relapse-free survival (RFS) months were collected and classified into good prognosis (RFS ≥ 12 months) and poor prognosis (RFS < 12 months) groups. Next, data-independent acquisition (DIA)-based mass spectrometry (MS) analysis was combined with MSFragger-DIA workflow to identify potential prognostic biomarkers in a discovery set (n = 31). With the aid of parallel reaction monitoring (PRM) analysis, four candidate biomarkers (ANXA1, G6PI, SPB3, and SPRR3) were finally validated in both the discovery set and an independent validation set (n = 25). Subsequent RFS and Cox regression analyses confirmed the utility of these candidate biomarkers as independent prognostic factors affecting RFS in patients with HGSOC. Regression models were constructed to predict the 12-month RFS rate, with area under the receiver operating characteristic curve (AUC) values ranging from 0.847 to 0.905. Overall, candidate prognostic biomarkers were identified in urine specimens from patients with HGSOC and prediction models for the 12-month RFS rate constructed. SIGNIFICANCE: OC is one of the leading causes of death due to gynecological malignancies. HGSOC constitutes one of the most common histologic types of OC with aggressive characteristics, accounting for the majority of advanced cases. In cases where patients with advanced HGSOC potentially face high risk of unfavorable prognosis or disease advancement within a 12-month period, intensive medical monitoring is necessary. In the era of precision cancer medicine, accurate prediction of prognosis or 12-month RFS rate is critical for distinguishing patient groups requiring heightened surveillance. Patients could significantly benefit from timely modifications to treatment regimens based on the outcomes of clinical monitoring. Urine is an ideal resource for disease surveillance purposes due to its easy accessibility. Furthermore, molecules excreted in urine are less complex and more stable than those in other liquid samples. In the current study, we identified candidate prognostic biomarkers in urine specimens from patients with HGSOC and constructed prediction models for the 12-month RFS rate.
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Affiliation(s)
- Maowei Ni
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China; Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Danying Wan
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China; Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Junzhou Wu
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China; Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Wangang Gong
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China; Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Junjian Wang
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China; Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Zhiguo Zheng
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China; Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.
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Li YD, Ma MW, Hassan MM, Hunkeler M, Teng M, Puvar K, Rutter JC, Lumpkin RJ, Sandoval B, Jin CY, Schmoker AM, Ficarro SB, Cheong H, Metivier RJ, Wang MY, Xu S, Byun WS, Groendyke BJ, You I, Sigua LH, Tavares I, Zou C, Tsai JM, Park PMC, Yoon H, Majewski FC, Sperling HT, Marto JA, Qi J, Nowak RP, Donovan KA, Słabicki M, Gray NS, Fischer ES, Ebert BL. Template-assisted covalent modification underlies activity of covalent molecular glues. Nat Chem Biol 2024:10.1038/s41589-024-01668-4. [PMID: 39075252 DOI: 10.1038/s41589-024-01668-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 06/05/2024] [Indexed: 07/31/2024]
Abstract
Molecular glues are proximity-inducing small molecules that have emerged as an attractive therapeutic approach. However, developing molecular glues remains challenging, requiring innovative mechanistic strategies to stabilize neoprotein interfaces and expedite discovery. Here we unveil a trans-labeling covalent molecular glue mechanism, termed 'template-assisted covalent modification'. We identified a new series of BRD4 molecular glue degraders that recruit CUL4DCAF16 ligase to the second bromodomain of BRD4 (BRD4BD2). Through comprehensive biochemical, structural and mutagenesis analyses, we elucidated how pre-existing structural complementarity between DCAF16 and BRD4BD2 serves as a template to optimally orient the degrader for covalent modification of DCAF16Cys58. This process stabilizes the formation of BRD4-degrader-DCAF16 ternary complex and facilitates BRD4 degradation. Supporting generalizability, we found that a subset of degraders also induces GAK-BRD4BD2 interaction through trans-labeling of GAK. Together, our work establishes 'template-assisted covalent modification' as a mechanism for covalent molecular glues, which opens a new path to proximity-driven pharmacology.
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Affiliation(s)
- Yen-Der Li
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michelle W Ma
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Muhammad Murtaza Hassan
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Moritz Hunkeler
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Mingxing Teng
- Center for Drug Discovery, Department of Pathology & Immunology, and Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Kedar Puvar
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Justine C Rutter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ryan J Lumpkin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Brittany Sandoval
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Cyrus Y Jin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Anna M Schmoker
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Scott B Ficarro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Blais Proteomics Center and Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Hakyung Cheong
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rebecca J Metivier
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michelle Y Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shawn Xu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Woong Sub Byun
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Brian J Groendyke
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Inchul You
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Logan H Sigua
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Isidoro Tavares
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Blais Proteomics Center and Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Charles Zou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jonathan M Tsai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Paul M C Park
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hojong Yoon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Felix C Majewski
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Haniya T Sperling
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jarrod A Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Blais Proteomics Center and Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Radosław P Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Mikołaj Słabicki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, USA.
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Boston, MA, USA.
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Winegar PH, Hudson GA, Dell LB, Astolfi MCT, Reed J, Payet RD, Ombredane HCJ, Iavarone AT, Chen Y, Gin JW, Petzold CJ, Osbourn AE, Keasling JD. Verazine biosynthesis from simple sugars in engineered Saccharomyces cerevisiae. Metab Eng 2024; 85:145-158. [PMID: 39074544 DOI: 10.1016/j.ymben.2024.07.011] [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: 05/08/2024] [Revised: 07/08/2024] [Accepted: 07/23/2024] [Indexed: 07/31/2024]
Abstract
Steroidal alkaloids are FDA-approved drugs (e.g., Zytiga) and promising drug candidates/leads (e.g., cyclopamine); yet many of the ≥697 known steroidal alkaloid natural products remain underutilized as drugs because it can be challenging to scale their biosynthesis in their producing organisms. Cyclopamine is a steroidal alkaloid produced by corn lily (Veratrum spp.) plants, and it is an inhibitor of the Hedgehog (Hh) signaling pathway. Therefore, cyclopamine is an important drug candidate/lead to treat human diseases that are associated with dysregulated Hh signaling, such as basal cell carcinoma and acute myeloid leukemia. Cyclopamine and its semi-synthetic derivatives have been studied in (pre)clinical trials as Hh inhibitor-based drugs. However, challenges in scaling the production of cyclopamine have slowed efforts to improve its efficacy and safety profile through (bio)synthetic derivatization, often limiting drug development to synthetic analogs of cyclopamine such as the FDA-approved drugs Odomzo, Daurismo, and Erivedge. If a platform for the scalable and sustainable production of cyclopamine were established, then its (bio)synthetic derivatization, clinical development, and, ultimately, widespread distribution could be accelerated. Ongoing efforts to achieve this goal include the biosynthesis of cyclopamine in Veratrum plant cell culture and the semi-/total chemical synthesis of cyclopamine. Herein, this work advances efforts towards a promising future approach: the biosynthesis of cyclopamine in engineered microorganisms. We completed the heterologous microbial production of verazine (biosynthetic precursor to cyclopamine) from simple sugars (i.e., glucose and galactose) in engineered Saccharomyces cerevisiae (S. cerevisiae) through the inducible upregulation of the native yeast mevalonate and lanosterol biosynthetic pathways, diversion of biosynthetic flux from ergosterol (i.e., native sterol in S. cerevisiae) to cholesterol (i.e., biosynthetic precursor to verazine), and expression of a refactored five-step verazine biosynthetic pathway. The engineered S. cerevisiae strain that produced verazine contains eight heterologous enzymes sourced from seven different species. Importantly, S. cerevisiae-produced verazine was indistinguishable via liquid chromatography-mass spectrometry from both a commercial standard (Veratrum spp. plant-produced) and Nicotiana benthamiana-produced verazine. To the best of our knowledge, this is the first report describing the heterologous production of a steroidal alkaloid in an engineered yeast. Verazine production was ultimately increased through design-build-test-learn cycles to a final titer of 83 ± 3 μg/L (4.1 ± 0.1 μg/g DCW). Together, this research lays the groundwork for future microbial biosynthesis of cyclopamine, (bio)synthetic derivatives of cyclopamine, and other steroidal alkaloid natural products.
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Affiliation(s)
- Peter H Winegar
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; California Institute for Quantitative Biosciences (QB3 Institute), University of California, Berkeley, CA, 94720, USA
| | - Graham A Hudson
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; California Institute for Quantitative Biosciences (QB3 Institute), University of California, Berkeley, CA, 94720, USA
| | - Luisa B Dell
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
| | - Maria C T Astolfi
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
| | - James Reed
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Rocky D Payet
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | - Anthony T Iavarone
- California Institute for Quantitative Biosciences (QB3 Institute), University of California, Berkeley, CA, 94720, USA
| | - Yan Chen
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jennifer W Gin
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Anne E Osbourn
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Jay D Keasling
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; California Institute for Quantitative Biosciences (QB3 Institute), University of California, Berkeley, CA, 94720, USA; Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, CA, 94720, USA; The Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, Kemitorvet, Building 220, Kongens, Lyngby, 2800, Denmark.
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Ahn HS, Lee SY, Kang MJ, Hong SB, Song JW, Do KH, Yeom J, Yu J, Oh Y, Hong JY, Chung EH, Kim K, Hong SJ. Polyhexamethylene guanidine aerosol causes irreversible changes in blood proteins that associated with the severity of lung injury. JOURNAL OF HAZARDOUS MATERIALS 2024; 478:135359. [PMID: 39126856 DOI: 10.1016/j.jhazmat.2024.135359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 07/04/2024] [Accepted: 07/26/2024] [Indexed: 08/12/2024]
Abstract
Polyhexamethylene guanidine (PHMG) is a positively charged polymer used as a disinfectant that kills microbes but can cause pulmonary fibrosis if inhaled. After the long-term risks were confirmed in South Korea, it became crucial to measure toxicity through diverse surrogate biomarkers, not only proteins, especially after these hazardous chemicals had cleared from the body. These biomarkers, identified by their biological functions rather than simple numerical calculations, effectively explained the imbalance of pulmonary surfactant caused by fibrosis from PHMG exposure. These long-term studies on children exposed to PHMG has shown that blood protein indicators, primarily related to apolipoproteins and extracellular matrix, can distinguish the degree of exposure to humidifier disinfectants (HDs). We defined the extreme gradient boosting models and computed reflection scores based on just ten selected proteins, which were also verified in adult women exposed to HD. The reflection scores successfully discriminated between the HD-exposed and unexposed groups in both children and adult females (AUROC: 0.957 and 0.974, respectively) and had a strong negative correlation with lung function indicators. Even after an average of more than 10 years, blood is still considered a meaningful specimen for assessing the impact of environmental exposure to toxic substances, with proteins providing in identifying the pathological severity of such conditions.
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Affiliation(s)
- Hee-Sung Ahn
- Convergence Medicine Research Center, Asan Institute for Life Sciences, Seoul, South Korea.
| | - So-Yeon Lee
- Department of Pediatrics, Childhood Asthma Atopy Center, Humidifier Disinfectant Health Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea.
| | - Mi-Jin Kang
- Humidifier Disinfectant Health Center, Asan Medical Center, Seoul, South Korea.
| | - Sang Bum Hong
- Department of Pulmonary and Critical Care Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea.
| | - Jin Woo Song
- Department of Pulmonary and Critical Care Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea
| | - Kyung Hyun Do
- Department of Radiology and Research Institute of Radiology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea.
| | - Jeounghun Yeom
- Prometabio Research Institute, prometabio co., ltd., Gyeonggi-do, South Korea.
| | - Jiyoung Yu
- Convergence Medicine Research Center, Asan Institute for Life Sciences, Seoul, South Korea.
| | - Yumi Oh
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea.
| | - Jeong Yeon Hong
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea.
| | - Eun Hee Chung
- Department of Pediatrics, Chungnam National University Hospital, Chungnam National University School of Medicine, Daejeon, South Korea.
| | - Kyunggon Kim
- Convergence Medicine Research Center, Asan Institute for Life Sciences, Seoul, South Korea; Department of Biomedical Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea.
| | - Soo-Jong Hong
- Department of Pediatrics, Childhood Asthma Atopy Center, Humidifier Disinfectant Health Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea.
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39
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Chapman A, McAfee A, Tarpy DR, Fine J, Rempel Z, Peters K, Currie R, Foster LJ. Common viral infections inhibit egg laying in honey bee queens and are linked to premature supersedure. Sci Rep 2024; 14:17285. [PMID: 39068210 PMCID: PMC11283550 DOI: 10.1038/s41598-024-66286-5] [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: 04/29/2024] [Accepted: 07/01/2024] [Indexed: 07/30/2024] Open
Abstract
With their long lives and extreme reproductive output, social insect queens have escaped the classic trade-off between fecundity and lifespan, but evidence for a trade-off between fecundity and immunity has been inconclusive. This is in part because pathogenic effects are seldom decoupled from effects of immune induction. We conducted parallel, blind virus infection experiments in the laboratory and in the field to interrogate the idea of a reproductive immunity trade-off in honey bee (Apis mellifera) queens and to better understand how these ubiquitous stressors affect honey bee queen health. We found that queens injected with infectious virus had smaller ovaries and were less likely to recommence egg-laying than controls, while queens injected with UV-inactivated virus displayed an intermediate phenotype. In the field, heavily infected queens had smaller ovaries and infection was a meaningful predictor of whether supersedure cells were observed in the colony. Immune responses in queens receiving live virus were similar to queens receiving inactivated virus, and several of the same immune proteins were negatively associated with ovary mass in the field. This work supports the hypothesized relationship between virus infection and symptoms associated with queen failure and suggests that a reproductive-immunity trade-off is partially, but not wholly responsible for these effects.
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Affiliation(s)
- Abigail Chapman
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, Canada.
| | - Alison McAfee
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - David R Tarpy
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Julia Fine
- Invasive Species and Pollinator Health Research Unit, USDA-ARS, Davis, CA, USA
| | - Zoe Rempel
- Department of Entomology, University of Manitoba, Winnipeg, MB, Canada
| | - Kira Peters
- Department of Entomology, University of Manitoba, Winnipeg, MB, Canada
| | - Rob Currie
- Department of Entomology, University of Manitoba, Winnipeg, MB, Canada
| | - Leonard J Foster
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
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40
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Tsukidate T, Stiving AQ, Rivera S, Sahoo A, Madabhushi S, Li X. diaPASEF Enables High-Throughput Proteomic Analysis of Host Cell Proteins for Biopharmaceutical Process Development. Anal Chem 2024. [PMID: 39060242 DOI: 10.1021/acs.analchem.4c00977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
Monitoring and quantifying host cell proteins (HCPs) in biotherapeutic production processes is crucial to ensure product quality, stability, and safety. Liquid chromatography-mass spectrometry (LC-MS) analysis has emerged as an important tool for identifying and quantifying individual HCPs. However, LC-MS-based approaches face challenges due to the wide dynamic range between HCPs and the therapeutic protein as well as laborious sample preparation and long instrument time. To address these limitations, we evaluated the application of parallel accumulation-serial fragmentation combined with data-independent acquisition (diaPASEF) to HCP analysis for biopharmaceutical process development applications. We evaluated different library generation strategies and LC methods, demonstrating the suitability of these workflows for various HCP analysis needs, such as in-depth characterization and high-throughput analysis of process intermediates. Remarkably, the diaPASEF approach enabled the quantification of hundreds of HCPs that were undetectable by a standard data-dependent acquisition mode while considerably improving sample requirement, throughput, coverage, quantitative precision, and data completeness.
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Affiliation(s)
- Taku Tsukidate
- Analytical Research & Development Mass Spectrometry, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Alyssa Q Stiving
- Analytical Research & Development Mass Spectrometry, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Shannon Rivera
- Analytical Research & Development Mass Spectrometry, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Ansuman Sahoo
- Biologics Process Research & Development, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Sri Madabhushi
- Biologics Process Research & Development, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Xuanwen Li
- Analytical Research & Development Mass Spectrometry, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
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41
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Godbole S, Voß H, Gocke A, Schlumbohm S, Schumann Y, Peng B, Mynarek M, Rutkowski S, Dottermusch M, Dorostkar MM, Korshunov A, Mair T, Pfister SM, Kwiatkowski M, Hotze M, Neumann P, Hartmann C, Weis J, Liesche-Starnecker F, Guan Y, Moritz M, Siebels B, Struve N, Schlüter H, Schüller U, Krisp C, Neumann JE. Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level. Nat Commun 2024; 15:6237. [PMID: 39043693 PMCID: PMC11266559 DOI: 10.1038/s41467-024-50554-z] [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: 02/09/2023] [Accepted: 07/11/2024] [Indexed: 07/25/2024] Open
Abstract
Medulloblastomas (MBs) are malignant pediatric brain tumors that are molecularly and clinically heterogenous. The application of omics technologies-mainly studying nucleic acids-has significantly improved MB classification and stratification, but treatment options are still unsatisfactory. The proteome and their N-glycans hold the potential to discover clinically relevant phenotypes and targetable pathways. We compile a harmonized proteome dataset of 167 MBs and integrate findings with DNA methylome, transcriptome and N-glycome data. We show six proteome MB subtypes, that can be assigned to two main molecular programs: transcription/translation (pSHHt, pWNT and pG3myc), and synapses/immunological processes (pSHHs, pG3 and pG4). Multiomic analysis reveals different conservation levels of proteome features across MB subtypes at the DNA methylome level. Aggressive pGroup3myc MBs and favorable pWNT MBs are most similar in cluster hierarchies concerning overall proteome patterns but show different protein abundances of the vincristine resistance-associated multiprotein complex TriC/CCT and of N-glycan turnover-associated factors. The N-glycome reflects proteome subtypes and complex-bisecting N-glycans characterize pGroup3myc tumors. Our results shed light on targetable alterations in MB and set a foundation for potential immunotherapies targeting glycan structures.
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Affiliation(s)
- Shweta Godbole
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hannah Voß
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Antonia Gocke
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Simon Schlumbohm
- Chair for High Performance Computing, Helmut Schmidt University, Hamburg, Germany
| | - Yannis Schumann
- Chair for High Performance Computing, Helmut Schmidt University, Hamburg, Germany
| | - Bojia Peng
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Mynarek
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Rutkowski
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Matthias Dottermusch
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mario M Dorostkar
- Center for Neuropathology, Ludwig-Maximilians-University, Munich, Germany
- German Center for Neurodegenerative Diseases, Munich, Germany
| | - Andrey Korshunov
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Mair
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Madlen Hotze
- Institute of Biochemistry, University of Innsbruck, Innsbruck, Austria
| | - Philipp Neumann
- Chair for High Performance Computing, Helmut Schmidt University, Hamburg, Germany
| | - Christian Hartmann
- Department of Neuropathology, Hannover Medical School (MHH), Hannover, Germany
| | - Joachim Weis
- Institute of Neuropathology, RWTH Aachen University Hospital, Aachen, Germany
| | | | - Yudong Guan
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Manuela Moritz
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Bente Siebels
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nina Struve
- Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Radiotherapy & Radiation Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hartmut Schlüter
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ulrich Schüller
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Christoph Krisp
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julia E Neumann
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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42
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Schmidt L, Saynisch M, Hoegsbjerg C, Schmidt A, Mackey A, Lackmann JW, Müller S, Koch M, Brachvogel B, Kjaer M, Antczak P, Krüger M. Spatial proteomics of skeletal muscle using thin cryosections reveals metabolic adaptation at the muscle-tendon transition zone. Cell Rep 2024; 43:114374. [PMID: 38900641 DOI: 10.1016/j.celrep.2024.114374] [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: 12/07/2023] [Revised: 04/05/2024] [Accepted: 05/31/2024] [Indexed: 06/22/2024] Open
Abstract
Morphological studies of skeletal muscle tissue provide insights into the architecture of muscle fibers, the surrounding cells, and the extracellular matrix (ECM). However, a spatial proteomics analysis of the skeletal muscle including the muscle-tendon transition zone is lacking. Here, we prepare cryotome muscle sections of the mouse soleus muscle and measure each slice using short liquid chromatography-mass spectrometry (LC-MS) gradients. We generate 3,000 high-resolution protein profiles that serve as the basis for a network analysis to reveal the complex architecture of the muscle-tendon junction. Among the protein profiles that increase from muscle to tendon, we find proteins related to neuronal activity, fatty acid biosynthesis, and the renin-angiotensin system (RAS). Blocking the RAS in cultured mouse tenocytes using losartan reduces the ECM synthesis. Overall, our analysis of thin cryotome sections provides a spatial proteome of skeletal muscle and reveals that the RAS acts as an additional regulator of the matrix within muscle-tendon junctions.
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Affiliation(s)
- Luisa Schmidt
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Michael Saynisch
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Christian Hoegsbjerg
- Institute of Sports Medicine Copenhagen, Department of Orthopaedic Surgery, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark; Part of IOC Research Center Copenhagen and Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Abigail Mackey
- Institute of Sports Medicine Copenhagen, Department of Orthopaedic Surgery, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark; Part of IOC Research Center Copenhagen and Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jan-Wilm Lackmann
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Stefan Müller
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Manuel Koch
- Institute for Dental Research and Oral Musculoskeletal Biology, Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany
| | - Bent Brachvogel
- Department of Pediatrics and Adolescent Medicine, Experimental Neonatology, Medical Faculty, University of Cologne, Cologne, Germany; Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany
| | - Michael Kjaer
- Institute of Sports Medicine Copenhagen, Department of Orthopaedic Surgery, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark; Part of IOC Research Center Copenhagen and Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Philipp Antczak
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany; Center for Molecular Medicine (CMMC), University of Cologne, 50931 Cologne, Germany.
| | - Marcus Krüger
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany; Center for Molecular Medicine (CMMC), University of Cologne, 50931 Cologne, Germany.
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43
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ElGrawani W, Sun G, Kliem FP, Sennhauser S, Pierre-Ferrer S, Rosi-Andersen A, Boccalaro I, Bethge P, Heo WD, Helmchen F, Adamantidis AR, Forger DB, Robles MS, Brown SA. BDNF-TrkB signaling orchestrates the buildup process of local sleep. Cell Rep 2024; 43:114500. [PMID: 39046880 DOI: 10.1016/j.celrep.2024.114500] [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: 05/15/2024] [Accepted: 06/27/2024] [Indexed: 07/27/2024] Open
Abstract
Sleep debt accumulates during wakefulness, leading to increased slow wave activity (SWA) during sleep, an encephalographic marker for sleep need. The use-dependent demands of prior wakefulness increase sleep SWA locally. However, the circuitry and molecular identity of this "local sleep" remain unclear. Using pharmacology and optogenetic perturbations together with transcriptomics, we find that cortical brain-derived neurotrophic factor (BDNF) regulates SWA via the activation of tyrosine kinase B (TrkB) receptor and cAMP-response element-binding protein (CREB). We map BDNF/TrkB-induced sleep SWA to layer 5 (L5) pyramidal neurons of the cortex, independent of neuronal firing per se. Using mathematical modeling, we here propose a model of how BDNF's effects on synaptic strength can increase SWA in ways not achieved through increased firing alone. Proteomic analysis further reveals that TrkB activation enriches ubiquitin and proteasome subunits. Together, our study reveals that local SWA control is mediated by BDNF-TrkB-CREB signaling in L5 excitatory cortical neurons.
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Affiliation(s)
- Waleed ElGrawani
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland; Neuroscience Center Zurich (ZNZ), University of Zurich, Zurich, Switzerland.
| | - Guanhua Sun
- Department of Mathematics, University of Michigan, Ann Arbor, MI, USA
| | - Fabian P Kliem
- Institute of Medical Psychology and Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Germany
| | - Simon Sennhauser
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Sara Pierre-Ferrer
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland; Neuroscience Center Zurich (ZNZ), University of Zurich, Zurich, Switzerland
| | - Alex Rosi-Andersen
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland; Neuroscience Center Zurich (ZNZ), University of Zurich, Zurich, Switzerland
| | - Ida Boccalaro
- Zentrum für Experimentelle Neurologie, Department of Neurology, Inselspital University Hospital Bern, Bern, Switzerland
| | - Philipp Bethge
- Neuroscience Center Zurich (ZNZ), University of Zurich, Zurich, Switzerland; Brain Research Institute, University of Zurich, Zurich, Switzerland
| | - Won Do Heo
- Department of Biological Science, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Fritjof Helmchen
- Neuroscience Center Zurich (ZNZ), University of Zurich, Zurich, Switzerland; Brain Research Institute, University of Zurich, Zurich, Switzerland; University Research Priority Program (URPP), Adaptive Brain Circuits in Development and Learning, University of Zurich, Zurich, Switzerland
| | - Antoine R Adamantidis
- Zentrum für Experimentelle Neurologie, Department of Neurology, Inselspital University Hospital Bern, Bern, Switzerland.
| | - Daniel B Forger
- Department of Mathematics, University of Michigan, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
| | - Maria S Robles
- Institute of Medical Psychology and Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Germany.
| | - Steven A Brown
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
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Chang MEK, Lange J, Cartier JM, Moore TW, Soriano SM, Albracht B, Krawitzky M, Guturu H, Alavi A, Stukalov A, Zhou X, Elgierari EM, Chu J, Benz R, Cuevas JC, Ferdosi S, Hornburg D, Farokhzad O, Siddiqui A, Batzoglou S, Leach RJ, Liss MA, Kopp RP, Flory MR. A Scaled Proteomic Discovery Study for Prostate Cancer Diagnostic Markers Using Proteograph TM and Trapped Ion Mobility Mass Spectrometry. Int J Mol Sci 2024; 25:8010. [PMID: 39125581 PMCID: PMC11311733 DOI: 10.3390/ijms25158010] [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: 06/12/2024] [Revised: 07/03/2024] [Accepted: 07/09/2024] [Indexed: 08/12/2024] Open
Abstract
There is a significant unmet need for clinical reflex tests that increase the specificity of prostate-specific antigen blood testing, the longstanding but imperfect tool for prostate cancer diagnosis. Towards this endpoint, we present the results from a discovery study that identifies new prostate-specific antigen reflex markers in a large-scale patient serum cohort using differentiating technologies for deep proteomic interrogation. We detect known prostate cancer blood markers as well as novel candidates. Through bioinformatic pathway enrichment and network analysis, we reveal associations of differentially abundant proteins with cytoskeletal, metabolic, and ribosomal activities, all of which have been previously associated with prostate cancer progression. Additionally, optimized machine learning classifier analysis reveals proteomic signatures capable of detecting the disease prior to biopsy, performing on par with an accepted clinical risk calculator benchmark.
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Affiliation(s)
- Matthew E. K. Chang
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201, USA; (M.E.K.C.); (S.M.S.)
| | - Jane Lange
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201, USA; (M.E.K.C.); (S.M.S.)
| | - Jessie May Cartier
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201, USA; (M.E.K.C.); (S.M.S.)
| | - Travis W. Moore
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201, USA; (M.E.K.C.); (S.M.S.)
| | - Sophia M. Soriano
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201, USA; (M.E.K.C.); (S.M.S.)
| | - Brenna Albracht
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | | | | | | | | | | | | | | | - Ryan Benz
- Seer Inc., Redwood City, CA 94065, USA
| | | | | | | | | | | | | | - Robin J. Leach
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Michael A. Liss
- Roger L. & Laura D. Zeller Charitable Foundation in Urologic Oncology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Ryan P. Kopp
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201, USA; (M.E.K.C.); (S.M.S.)
| | - Mark R. Flory
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201, USA; (M.E.K.C.); (S.M.S.)
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45
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Lapcik P, Synkova K, Janacova L, Bouchalova P, Potesil D, Nenutil R, Bouchal P. A hybrid DDA/DIA-PASEF based assay library for a deep proteotyping of triple-negative breast cancer. Sci Data 2024; 11:794. [PMID: 39025866 PMCID: PMC11258311 DOI: 10.1038/s41597-024-03632-2] [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: 02/14/2024] [Accepted: 07/10/2024] [Indexed: 07/20/2024] Open
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer, and deeper proteome coverage is needed for its molecular characterization. We present comprehensive library of targeted mass spectrometry assays specific for TNBC and demonstrate its applicability. Proteins were extracted from 105 TNBC tissues and digested. Aliquots were pooled, fractionated using hydrophilic chromatography and analyzed by LC-MS/MS in data-dependent acquisition (DDA) parallel accumulation-serial fragmentation (PASEF) mode on timsTOF Pro LC-MS system. 16 individual lysates were analyzed in data-independent acquisition (DIA)-PASEF mode. Hybrid library was generated in Spectronaut software and covers 244,464 precursors, 168,006 peptides and 11,564 protein groups (FDR = 1%). Application of our library for pilot quantitative analysis of 16 tissues increased identification numbers in Spectronaut 18.5 and DIA-NN 1.8.1 software compared to library-free setting, with Spectronaut achieving the best results represented by 190,310 precursors, 140,566 peptides, and 10,463 protein groups. In conclusion, we introduce assay library that offers the deepest coverage of TNBC proteome to date. The TNBC library is available via PRIDE repository (PXD047793).
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Grants
- NU22-08-00230 Ministerstvo Zdravotnictví Ceské Republiky (Ministry of Health of the Czech Republic)
- NU22-08-00230 Ministerstvo Zdravotnictví Ceské Republiky (Ministry of Health of the Czech Republic)
- NU22-08-00230 Ministerstvo Zdravotnictví Ceské Republiky (Ministry of Health of the Czech Republic)
- NU22-08-00230 Ministerstvo Zdravotnictví Ceské Republiky (Ministry of Health of the Czech Republic)
- LX22NPO5102 Ministerstvo Školství, Mládeže a Tělovýchovy (Ministry of Education, Youth and Sports)
- LX22NPO5102 Ministerstvo Školství, Mládeže a Tělovýchovy (Ministry of Education, Youth and Sports)
- LX22NPO5102 Ministerstvo Školství, Mládeže a Tělovýchovy (Ministry of Education, Youth and Sports)
- LX22NPO5102 Ministerstvo Školství, Mládeže a Tělovýchovy (Ministry of Education, Youth and Sports)
- CZ.02.1.01/0.0/0.0/18_046/0015974 Ministerstvo Školství, Mládeže a Tělovýchovy (Ministry of Education, Youth and Sports)
- LM2023033 Ministerstvo Školství, Mládeže a Tělovýchovy (Ministry of Education, Youth and Sports)
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Affiliation(s)
- Petr Lapcik
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Klara Synkova
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Lucia Janacova
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Pavla Bouchalova
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - David Potesil
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Rudolf Nenutil
- Department of Oncological Pathology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Pavel Bouchal
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic.
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46
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Honrath S, Scherer D, Burger M, Leroux JC. Interaction proteomics analysis to provide insight into TFAMoplex-mediated transfection. J Control Release 2024; 373:252-264. [PMID: 39009084 DOI: 10.1016/j.jconrel.2024.07.025] [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: 03/05/2024] [Revised: 06/06/2024] [Accepted: 07/09/2024] [Indexed: 07/17/2024]
Abstract
In an earlier investigation, our group introduced the TFAMoplex, a transfection agent based on the mitochondrial transcription factor A (TFAM) protein, which complexes DNA into nanoparticles. The original TFAMoplex further contained a bacterial phospholipase to achieve endosomal escape, and the vaccinia-related kinase 1 (VRK1), which significantly boosted the transfection efficiency of the system by an unknown mechanism. This study aims at replacing VRK1 within the TFAMoplex with dynein light chain proteins, specifically RP3, to directly tether the complexes to the dynein motor complex for enhanced cytosolic transport. To confirm the interaction between the dynein complex and the resulting fusion protein, we examined the binding kinetics of TFAM-RP3 to the dynein intermediate chains 1 and 2. Furthermore, we established a proteomics-based assay to compare cytosolic protein interactions of different TFAMoplex variants, including the RP3-modified version and the original VRK1-containing system. In the group of the VRK1-containing TFAMoplex, significant shifts of protein interactors were observed, especially for nucleolar proteins. Leveraging this knowledge, we incorporated one of these nuclear proteins, leucine-rich repeat-containing protein 59 (LRRC59), into the TFAMoplex, resulting in a significant improvement of transfection properties compared to the RP3-modified system and comparable levels versus the original, VRK1-containing version. This study not only advances our comprehension of the TFAMoplex system but also offers broader insights into the potential of protein engineering for designing effective gene delivery systems.
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Affiliation(s)
- Steffen Honrath
- ETH Zurich, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - David Scherer
- ETH Zurich, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Michael Burger
- ETH Zurich, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland..
| | - Jean-Christophe Leroux
- ETH Zurich, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland..
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47
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Tu T, Gao Z, Li L, Chen J, Ye K, Xu T, Mai S, Han Q, Chen C, Wu S, Dong Y, Chen J, Huang L, Guan Y, Xie F, Chen X. Soybean symbiotic-nodule zonation and cell differentiation are defined by NIN2 signaling and GH3-dependent auxin homeostasis. Dev Cell 2024:S1534-5807(24)00424-6. [PMID: 39053471 DOI: 10.1016/j.devcel.2024.07.001] [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: 12/07/2023] [Revised: 04/18/2024] [Accepted: 07/02/2024] [Indexed: 07/27/2024]
Abstract
Symbiotic nodules comprise two classes, indeterminate and determinate, defined by the presence/absence of apical meristem and developmental zonation. Why meristem and zonation are absent from determinate nodules remains unclear. Here, we define cell types in developing soybean nodules, highlighting the undifferentiated infection zones and differentiated nitrogen-fixation zones. Auxin governs infection zone maintenance. GRETCHEN HAGEN 3 (GH3) enzymes deactivate auxin by conjugation and promote cell differentiation. gh3 mutants increased undifferentiated cells and enlarged infection zones. The central symbiosis-transcription factor NIN2a activates GH3.1 to reduce auxin levels and facilitates cell differentiation. High auxin promotes NIN2a protein accumulation and enhances signaling, further deactivating auxin and depleting infection zones. Our findings shed light on the NIN2a-GH3-auxin module that drives soybean nodule cell differentiation. This study challenges our understanding of determinate nodule development and proposes that the regulation of nodule zonation offers valuable insights into broader mechanisms of cell differentiation across plant species.
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Affiliation(s)
- Tianli Tu
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhen Gao
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Linfang Li
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, China; College of Agriculture and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Jiansheng Chen
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, China; College of Agriculture and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Kangzhuo Ye
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, China; College of Agriculture and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Tao Xu
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, China; College of Agriculture and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Siyuan Mai
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, China; College of Agriculture and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Qingqing Han
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chaofan Chen
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shengwei Wu
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, China; College of Agriculture and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yankun Dong
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiaomei Chen
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Laimei Huang
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuefeng Guan
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Fang Xie
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xu Chen
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, China.
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48
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Pérez-Burgos M, Herfurth M, Kaczmarczyk A, Harms A, Huber K, Jenal U, Glatter T, Søgaard-Andersen L. A deterministic, c-di-GMP-dependent program ensures the generation of phenotypically similar, symmetric daughter cells during cytokinesis. Nat Commun 2024; 15:6014. [PMID: 39019889 PMCID: PMC11255338 DOI: 10.1038/s41467-024-50444-4] [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: 02/18/2024] [Accepted: 07/10/2024] [Indexed: 07/19/2024] Open
Abstract
Phenotypic heterogeneity in bacteria can result from stochastic processes or deterministic programs. The deterministic programs often involve the versatile second messenger c-di-GMP, and give rise to daughter cells with different c-di-GMP levels by deploying c-di-GMP metabolizing enzymes asymmetrically during cell division. By contrast, less is known about how phenotypic heterogeneity is kept to a minimum. Here, we identify a deterministic c-di-GMP-dependent program that is hardwired into the cell cycle of Myxococcus xanthus to minimize phenotypic heterogeneity and guarantee the formation of phenotypically similar daughter cells during division. Cells lacking the diguanylate cyclase DmxA have an aberrant motility behaviour. DmxA is recruited to the cell division site and its activity is switched on during cytokinesis, resulting in a transient increase in the c-di-GMP concentration. During cytokinesis, this c-di-GMP burst ensures the symmetric incorporation and allocation of structural motility proteins and motility regulators at the new cell poles of the two daughters, thereby generating phenotypically similar daughters with correct motility behaviours. Thus, our findings suggest a general c-di-GMP-dependent mechanism for minimizing phenotypic heterogeneity, and demonstrate that bacteria can ensure the formation of dissimilar or similar daughter cells by deploying c-di-GMP metabolizing enzymes to distinct subcellular locations.
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Affiliation(s)
- María Pérez-Burgos
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Marco Herfurth
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | | | - Andrea Harms
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Katrin Huber
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Urs Jenal
- Biozentrum, University of Basel, Basel, Switzerland
| | - Timo Glatter
- Core Facility for Mass Spectrometry & Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Lotte Søgaard-Andersen
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
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49
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Shitara Y, Konno R, Yoshihara M, Kashima K, Ito A, Mukai T, Kimoto G, Kakiuchi S, Ishikawa M, Kakihara T, Nagamatsu T, Takahashi N, Fujishiro J, Kawakami E, Ohara O, Kawashima Y, Watanabe E. Host-derived protein profiles of human neonatal meconium across gestational ages. Nat Commun 2024; 15:5543. [PMID: 39019879 PMCID: PMC11255260 DOI: 10.1038/s41467-024-49805-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: 12/06/2023] [Accepted: 06/19/2024] [Indexed: 07/19/2024] Open
Abstract
Meconium, a non-invasive biomaterial reflecting prenatal substance accumulation, could provide valuable insights into neonatal health. However, the comprehensive protein profile of meconium across gestational ages remains unclear. Here, we conducted an extensive proteomic analysis of first meconium from 259 newborns across varied gestational ages to delineate protein composition and elucidate its relevance to neonatal diseases. The first meconium samples were collected, with the majority obtained before feeding, and the mean time for the first meconium passage from the anus was 11.9 ± 9.47 h. Our analysis revealed 5370 host-derived meconium proteins, which varied depending on sex and gestational age. Specifically, meconium from preterm infants exhibited elevated concentrations of proteins associated with the extracellular matrix. Additionally, the protein profiles of meconium also exhibited unique variations depending on both specific diseases, including gastrointestinal diseases, congenital heart diseases, and maternal conditions. Furthermore, we developed a machine learning model to predict gestational ages using meconium proteins. Our model suggests that newborns with gastrointestinal diseases and congenital heart diseases may have immature gastrointestinal systems. These findings highlight the intricate relationship between clinical parameters and meconium protein composition, offering potential for a novel approach to assess neonatal gastrointestinal health.
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Affiliation(s)
- Yoshihiko Shitara
- Department of Pediatrics, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ryo Konno
- Department of Applied Genomics, Kazusa DNA Research Institute, Chiba, Japan
| | - Masahito Yoshihara
- Institute for Advanced Academic Research (IAAR), Chiba University, Chiba, Japan
- Department of Artificial Intelligence Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
- Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Suita, Osaka, Japan
| | - Kohei Kashima
- Department of Pediatrics, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Atsushi Ito
- Department of Pediatrics, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takeo Mukai
- Department of Pediatrics, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Goh Kimoto
- Department of Pediatrics, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Satsuki Kakiuchi
- Department of Pediatrics, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masaki Ishikawa
- Department of Applied Genomics, Kazusa DNA Research Institute, Chiba, Japan
| | - Tomo Kakihara
- Department of Pediatric Surgery, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takeshi Nagamatsu
- Department of Obstetrics and Gynecology, Faculty of Medicine, International University of Health and Welfare, Chiba, Japan
| | - Naoto Takahashi
- Department of Pediatrics, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jun Fujishiro
- Department of Pediatric Surgery, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Eiryo Kawakami
- Institute for Advanced Academic Research (IAAR), Chiba University, Chiba, Japan
- Department of Artificial Intelligence Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
- Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, RIKEN, Kanagawa, Japan
| | - Osamu Ohara
- Department of Applied Genomics, Kazusa DNA Research Institute, Chiba, Japan
| | - Yusuke Kawashima
- Department of Applied Genomics, Kazusa DNA Research Institute, Chiba, Japan.
| | - Eiichiro Watanabe
- Department of Pediatric Surgery, Faculty of Medicine, The University of Tokyo, Tokyo, Japan.
- Department of Surgery, Gunma Children's Medical Center, Gunma, Japan.
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50
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Kitano E, Nisbet G, Demyanenko Y, Kowalczyk KM, Iselin L, Cross S, Castello A, Mohammed S. Repurposed 3D Printer Allows Economical and Programmable Fraction Collection for Proteomics of Nanogram Scale Samples. Anal Chem 2024; 96:11439-11447. [PMID: 38968027 PMCID: PMC11256012 DOI: 10.1021/acs.analchem.4c01731] [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: 04/02/2024] [Revised: 06/21/2024] [Accepted: 06/21/2024] [Indexed: 07/07/2024]
Abstract
In this work, we describe the construction and application of a repurposed 3D-printer as a fraction collector. We utilize a nano-LC to ensure minimal volumes and surfaces although any LC can be coupled. The setup operates as a high-pH fractionation system capable of effectively working with nanogram scales of lysate digests. The 2D RP-RP system demonstrated superior proteome coverage over single-shot data-dependent acquisition (DDA) analysis using only 5 ng of human cell lysate digest with performance increasing with increasing amounts of material. We found that the fractionation system allowed over 60% signal recovery at the peptide level and, more importantly, we observed improved protein level intensity coverage, which indicates the complexity reduction afforded by the system outweighs the sample losses endured. The application of data-independent acquisition (DIA) and wide window acquisition (WWA) to fractionated samples allowed nearly 8000 proteins to be identified from 50 ng of the material. The utility of the 2D system was further investigated for phosphoproteomics (>21 000 phosphosites from 50 μg starting material) and pull-down type experiments and showed substantial improvements over single-shot experiments. We show that the 2D RP-RP system is a highly versatile and powerful tool for many proteomics workflows.
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Affiliation(s)
- Eduardo
S. Kitano
- Rosalind
Franklin Institute, Harwell
Campus, Didcot OX11 0QX, United Kingdom
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, United Kingdom
| | - Gareth Nisbet
- Diamond
Light Source, Harwell
Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Yana Demyanenko
- Rosalind
Franklin Institute, Harwell
Campus, Didcot OX11 0QX, United Kingdom
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, United Kingdom
| | - Katarzyna M Kowalczyk
- Rosalind
Franklin Institute, Harwell
Campus, Didcot OX11 0QX, United Kingdom
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, United Kingdom
| | - Louisa Iselin
- MRC-University
of Glasgow Centre for Virus Research, Glasgow G61 1QH, United Kingdom
- Nuffield
Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, United
Kingdom
| | - Stephen Cross
- Rosalind
Franklin Institute, Harwell
Campus, Didcot OX11 0QX, United Kingdom
| | - Alfredo Castello
- MRC-University
of Glasgow Centre for Virus Research, Glasgow G61 1QH, United Kingdom
| | - Shabaz Mohammed
- Rosalind
Franklin Institute, Harwell
Campus, Didcot OX11 0QX, United Kingdom
- Department
of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
- Department
of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
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