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Gianazza E, Brioschi M, Eligini S, Banfi C. Mass spectrometry for the study of adipocyte cell secretome in cardiovascular diseases. MASS SPECTROMETRY REVIEWS 2024; 43:752-781. [PMID: 36161723 DOI: 10.1002/mas.21812] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 08/04/2022] [Accepted: 09/03/2022] [Indexed: 06/16/2023]
Abstract
Adipose tissue is classically considered the primary site of lipid storage, but in recent years has garnered appreciation for its broad role as an endocrine organ, capable of remotely signaling to other tissues to alter their metabolic program. The adipose tissue is now recognized as a crucial regulator of cardiovascular health, mediated by the secretion of several bioactive products, with a wide range of endocrine and paracrine effects on the cardiovascular system. Thanks to the development and improvement of high-throughput mass spectrometry, the size and components of the human secretome have been characterized. In this review, we summarized the recent advances in mass spectrometry-based studies of the cell and tissue secretome for the understanding of adipose tissue biology, which may help to decipher the complex molecular mechanisms controlling the crosstalk between the adipose tissue and the cardiovascular system, and their possible clinical translation.
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Affiliation(s)
- Erica Gianazza
- Centro Cardiologico Monzino IRCCS, Unit of Functional Proteomics, Metabolomics and Network Analysis, Milan, Italy
| | - Maura Brioschi
- Centro Cardiologico Monzino IRCCS, Unit of Functional Proteomics, Metabolomics and Network Analysis, Milan, Italy
| | - Sonia Eligini
- Centro Cardiologico Monzino IRCCS, Unit of Functional Proteomics, Metabolomics and Network Analysis, Milan, Italy
| | - Cristina Banfi
- Centro Cardiologico Monzino IRCCS, Unit of Functional Proteomics, Metabolomics and Network Analysis, Milan, Italy
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2
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Udani S, Langerman J, Koo D, Baghdasarian S, Cheng B, Kang S, Soemardy C, de Rutte J, Plath K, Di Carlo D. Associating growth factor secretions and transcriptomes of single cells in nanovials using SEC-seq. NATURE NANOTECHNOLOGY 2024; 19:354-363. [PMID: 38082117 DOI: 10.1038/s41565-023-01560-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 10/31/2023] [Indexed: 01/23/2024]
Abstract
Cells secrete numerous bioactive molecules that are essential for the function of healthy organisms. However, scalable methods are needed to link individual cell secretions to their transcriptional state over time. Here, by developing and using secretion-encoded single-cell sequencing (SEC-seq), which exploits hydrogel particles with subnanolitre cavities (nanovials) to capture individual cells and their secretions, we simultaneously measured the secretion of vascular endothelial growth factor A (VEGF-A) and the transcriptome for thousands of individual mesenchymal stromal cells. Our data indicate that VEGF-A secretion is heterogeneous across the cell population and is poorly correlated with the VEGFA transcript level. The highest VEGF-A secretion occurs in a subpopulation of mesenchymal stromal cells characterized by a unique gene expression signature comprising a surface marker, interleukin-13 receptor subunit alpha 2 (IL13RA2), which allowed the enrichment of this subpopulation. SEC-seq enables the identification of gene signatures linked to specific secretory states, facilitating mechanistic studies, the isolation of secretory subpopulations and the development of means to modulate cellular secretion.
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Affiliation(s)
- Shreya Udani
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA
| | - Justin Langerman
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Doyeon Koo
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA
| | - Sevana Baghdasarian
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, CA, USA
| | - Brian Cheng
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA
| | - Simran Kang
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA
| | - Citradewi Soemardy
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Kathrin Plath
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA, USA.
- Eli and Edythe Broad Stem Cell Research Center, University of California Los Angeles, Los Angeles, CA, USA.
| | - Dino Di Carlo
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA.
- Partillion Bioscience, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA, USA.
- Department of Mechanical and Aerospace Engineering, University of California Los Angeles, Los Angeles, CA, USA.
- California NanoSystems Institute (CNSI), University of California Los Angeles, Los Angeles, CA, USA.
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3
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Jafari A, Farahani M, Abdollahpour-Alitappeh M, Manzari-Tavakoli A, Yazdani M, Rezaei-Tavirani M. Unveiling diagnostic and therapeutic strategies for cervical cancer: biomarker discovery through proteomics approaches and exploring the role of cervical cancer stem cells. Front Oncol 2024; 13:1277772. [PMID: 38328436 PMCID: PMC10847843 DOI: 10.3389/fonc.2023.1277772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 12/27/2023] [Indexed: 02/09/2024] Open
Abstract
Cervical cancer (CC) is a major global health problem and leading cause of cancer deaths among women worldwide. Early detection through screening programs has reduced mortality; however, screening compliance remains low. Identifying non-invasive biomarkers through proteomics for diagnosis and monitoring response to treatment could improve patient outcomes. Here we review recent proteomics studies which have uncovered biomarkers and potential drug targets for CC. Additionally, we explore into the role of cervical cancer stem cells and their potential implications in driving CC progression and therapy resistance. Although challenges remain, proteomics has the potential to revolutionize the field of cervical cancer research and improve patient outcomes.
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Affiliation(s)
- Ameneh Jafari
- Student Research Committee, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoumeh Farahani
- Skin Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Asma Manzari-Tavakoli
- Department of Biology, Faculty of Science, Rayan Center for Neuroscience and Behavior, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohsen Yazdani
- Laboratory of Bioinformatics and Drug Design, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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4
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Manivannan HP, Veeraraghavan VP, Francis AP. Identification of molecular targets of Trigonelline for treating breast cancer through network pharmacology and bioinformatics-based prediction. Mol Divers 2023:10.1007/s11030-023-10780-x. [PMID: 38145425 DOI: 10.1007/s11030-023-10780-x] [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: 08/01/2023] [Accepted: 11/21/2023] [Indexed: 12/26/2023]
Abstract
Breast cancer, a highly prevalent and fatal cancer that affects the female population worldwide, stands as a significant health challenge. Despite the abundance of chemotherapy drugs, the adverse side effects associated with them have initiated an investigation into natural plant-based compounds. Trigonelline, an alkaloid found in Trigonella foenum-graecum, was previously reported for its anticancer properties by the researchers. In this present study, we have identified the molecular targets of Trigonelline in breast cancer and predicted its drug-like properties and toxicity. By analyzing breast cancer targets from databases including TTD, TCGA, Gene cards, and Trigonelline targets obtained from CTD, we identified 14 specific targets of Trigonelline in the context of breast cancer. The protein-protein interaction (PPI) network of the 14 Trigonelline targets provided insights into the complex relationships between different genes and targets. Heatmap analysis demonstrated the expression patterns of these 14 genes at the protein and RNA levels in breast cancer cells and breast tissues. Notably, four genes, namely EGF, BAX, EGFR, and MTOR, were enriched in the breast cancer pathway. At the same time, PARP1, DDIT3, BAX, and TNF were associated with the apoptosis pathway according to KEGG pathway enrichment analyses. Molecular docking studies between Trigonelline and target proteins from the Protein Data Bank (PDB) revealed favorable binding affinity. Furthermore, mutation analysis of target genes within a dataset of 1918 samples from cBioPortal revealed the absence of mutations. Remarkably, Trigonelline also exhibited binding affinity towards two mutant proteins, and based on these findings, we predicted that Trigonelline could be utilized to target breast cancer genes and their mutants through network pharmacology. Additionally, this was supported by molecular dynamic simulation studies. As our study is preliminary, further validation through in vitro and in vivo studies is essential to confirm the efficacy of Trigonelline in breast cancer treatment.
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Affiliation(s)
- Hema Priya Manivannan
- Centre of Molecular Medicine and Diagnostics (COMManD), Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, 600077, India
| | - Vishnu Priya Veeraraghavan
- Centre of Molecular Medicine and Diagnostics (COMManD), Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, 600077, India
| | - Arul Prakash Francis
- Centre of Molecular Medicine and Diagnostics (COMManD), Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, 600077, India.
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5
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Emfinger CH, Clark LE, Yandell B, Schueler KL, Simonett SP, Stapleton DS, Mitok KA, Merrins MJ, Keller MP, Attie AD. Novel regulators of islet function identified from genetic variation in mouse islet Ca 2+ oscillations. eLife 2023; 12:RP88189. [PMID: 37787501 PMCID: PMC10547476 DOI: 10.7554/elife.88189] [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: 10/04/2023] Open
Abstract
Insufficient insulin secretion to meet metabolic demand results in diabetes. The intracellular flux of Ca2+ into β-cells triggers insulin release. Since genetics strongly influences variation in islet secretory responses, we surveyed islet Ca2+ dynamics in eight genetically diverse mouse strains. We found high strain variation in response to four conditions: (1) 8 mM glucose; (2) 8 mM glucose plus amino acids; (3) 8 mM glucose, amino acids, plus 10 nM glucose-dependent insulinotropic polypeptide (GIP); and (4) 2 mM glucose. These stimuli interrogate β-cell function, α- to β-cell signaling, and incretin responses. We then correlated components of the Ca2+ waveforms to islet protein abundances in the same strains used for the Ca2+ measurements. To focus on proteins relevant to human islet function, we identified human orthologues of correlated mouse proteins that are proximal to glycemic-associated single-nucleotide polymorphisms in human genome-wide association studies. Several orthologues have previously been shown to regulate insulin secretion (e.g. ABCC8, PCSK1, and GCK), supporting our mouse-to-human integration as a discovery platform. By integrating these data, we nominate novel regulators of islet Ca2+ oscillations and insulin secretion with potential relevance for human islet function. We also provide a resource for identifying appropriate mouse strains in which to study these regulators.
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Affiliation(s)
| | - Lauren E Clark
- Department of Biochemistry, University of Wisconsin-MadisonMadisonUnited States
| | - Brian Yandell
- Department of Statistics, University of Wisconsin-MadisonMadisonUnited States
| | - Kathryn L Schueler
- Department of Biochemistry, University of Wisconsin-MadisonMadisonUnited States
| | - Shane P Simonett
- Department of Biochemistry, University of Wisconsin-MadisonMadisonUnited States
| | - Donnie S Stapleton
- Department of Biochemistry, University of Wisconsin-MadisonMadisonUnited States
| | - Kelly A Mitok
- Department of Biochemistry, University of Wisconsin-MadisonMadisonUnited States
| | - Matthew J Merrins
- Department of Medicine, Division of Endocrinology, University of Wisconsin-MadisonMadisonUnited States
- William S. Middleton Memorial Veterans HospitalMadisonUnited States
| | - Mark P Keller
- Department of Biochemistry, University of Wisconsin-MadisonMadisonUnited States
| | - Alan D Attie
- Department of Biochemistry, University of Wisconsin-MadisonMadisonUnited States
- Department of Medicine, Division of Endocrinology, University of Wisconsin-MadisonMadisonUnited States
- Department of Chemistry, University of Wisconsin-MadisonMadisonUnited States
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6
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Priester J, Meier-Soelch J, Weiser H, Heylmann D, Weber A, Linne U, Kracht M. Metabolic labeling and LC-MS/MS-based identification of interleukin-1α-induced secreted proteomes from epithelial cells in the presence or absence of serum. STAR Protoc 2023; 4:102195. [PMID: 37004159 PMCID: PMC10090805 DOI: 10.1016/j.xpro.2023.102195] [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: 11/29/2022] [Revised: 02/11/2023] [Accepted: 03/03/2023] [Indexed: 04/03/2023] Open
Abstract
The unbiased identification of cytokine-induced, secreted proteins from cells cultured in serum-containing medium is challenging. Here, we describe an experimental and bioinformatics workflow to label interleukin-1α-regulated proteins in living cells with the methionine analogue L-homopropargylglycine. We detail their purification and identification by means of CLICK-chemistry-based biotinylation followed by nanoHPLC-MS/MS. A side-by-side comparison of enriched proteins and their ontologies to serum-free conditions demonstrates the sensitivity and specificity of this approach to study the inducible secreted proteomes of epithelial cells.
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Affiliation(s)
- Jasmin Priester
- Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, 35392 Giessen, Germany
| | - Johanna Meier-Soelch
- Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, 35392 Giessen, Germany
| | - Hendrik Weiser
- Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, 35392 Giessen, Germany
| | - Daniel Heylmann
- Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, 35392 Giessen, Germany
| | - Axel Weber
- Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, 35392 Giessen, Germany
| | - Uwe Linne
- Mass Spectrometry Facility of the Department of Chemistry, Philipps University, 35032 Marburg, Germany.
| | - Michael Kracht
- Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, 35392 Giessen, Germany; Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany; Cardio-Pulmonary Institute (CPI), Giessen, Germany.
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7
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Rosenkranz AA, Slastnikova TA. Prospects of Using Protein Engineering for Selective Drug Delivery into a Specific Compartment of Target Cells. Pharmaceutics 2023; 15:pharmaceutics15030987. [PMID: 36986848 PMCID: PMC10055131 DOI: 10.3390/pharmaceutics15030987] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/13/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
A large number of proteins are successfully used to treat various diseases. These include natural polypeptide hormones, their synthetic analogues, antibodies, antibody mimetics, enzymes, and other drugs based on them. Many of them are demanded in clinical settings and commercially successful, mainly for cancer treatment. The targets for most of the aforementioned drugs are located at the cell surface. Meanwhile, the vast majority of therapeutic targets, which are usually regulatory macromolecules, are located inside the cell. Traditional low molecular weight drugs freely penetrate all cells, causing side effects in non-target cells. In addition, it is often difficult to elaborate a small molecule that can specifically affect protein interactions. Modern technologies make it possible to obtain proteins capable of interacting with almost any target. However, proteins, like other macromolecules, cannot, as a rule, freely penetrate into the desired cellular compartment. Recent studies allow us to design multifunctional proteins that solve these problems. This review considers the scope of application of such artificial constructs for the targeted delivery of both protein-based and traditional low molecular weight drugs, the obstacles met on the way of their transport to the specified intracellular compartment of the target cells after their systemic bloodstream administration, and the means to overcome those difficulties.
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Affiliation(s)
- Andrey A Rosenkranz
- Laboratory of Molecular Genetics of Intracellular Transport, Institute of Gene Biology of Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory St., 119234 Moscow, Russia
| | - Tatiana A Slastnikova
- Laboratory of Molecular Genetics of Intracellular Transport, Institute of Gene Biology of Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
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8
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From the Catastrophic Objective Irreproducibility of Cancer Research and Unavoidable Failures of Molecular Targeted Therapies to the Sparkling Hope of Supramolecular Targeted Strategies. Int J Mol Sci 2023; 24:ijms24032796. [PMID: 36769134 PMCID: PMC9917659 DOI: 10.3390/ijms24032796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/22/2023] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
The unprecedented non-reproducibility of the results published in the field of cancer research has recently come under the spotlight. In this short review, we try to highlight some general principles in the organization and evolution of cancerous tumors, which objectively lead to their enormous variability and, consequently, the irreproducibility of the results of their investigation. This heterogeneity is also extremely unfavorable for the effective use of molecularly targeted medicine. Against the seemingly comprehensive background of this heterogeneity, we single out two supramolecular characteristics common to all tumors: the clustered nature of tumor interactions with their microenvironment and the formation of biomolecular condensates with tumor-specific distinctive features. We suggest that these features can form the basis of strategies for tumor-specific supramolecular targeted therapies.
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9
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Berrone E, Chiorino G, Guana F, Benedetti V, Palmitessa C, Gallo M, Calvo A, Casale F, Manera U, Favole A, Crociara P, Testori C, Carta V, Tessarolo C, D’Angelo A, De Marco G, Caramelli M, Chiò A, Casalone C, Corona C. SOMAscan Proteomics Identifies Novel Plasma Proteins in Amyotrophic Lateral Sclerosis Patients. Int J Mol Sci 2023; 24:ijms24031899. [PMID: 36768220 PMCID: PMC9916400 DOI: 10.3390/ijms24031899] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/09/2023] [Accepted: 01/14/2023] [Indexed: 01/21/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a complex disease characterized by the interplay of genetic and environmental factors for which, despite decades of intense research, diagnosis remains rather delayed, and most therapeutic options fail. Therefore, unravelling other potential pathogenetic mechanisms and searching for reliable markers are high priorities. In the present study, we employ the SOMAscan assay, an aptamer-based proteomic technology, to determine the circulating proteomic profile of ALS patients. The expression levels of ~1300 proteins were assessed in plasma, and 42 proteins with statistically significant differential expression between ALS patients and healthy controls were identified. Among these, four were upregulated proteins, Thymus- and activation-regulated chemokine, metalloproteinase inhibitor 3 and nidogen 1 and 2 were selected and validated by enzyme-linked immunosorbent assays in an overlapping cohort of patients. Following statistical analyses, different expression patterns of these proteins were observed in the familial and sporadic ALS patients. The proteins identified in this study might provide insight into ALS pathogenesis and represent potential candidates to develop novel targeted therapies.
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Affiliation(s)
- Elena Berrone
- S.C. Neuroscienze, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Turin, Italy
| | - Giovanna Chiorino
- Cancer Genomics Laboratory, Fondazione Edo ed Elvo Tempia, 13900 Biella, Italy
| | - Francesca Guana
- Cancer Genomics Laboratory, Fondazione Edo ed Elvo Tempia, 13900 Biella, Italy
| | - Valerio Benedetti
- S.C. Neuroscienze, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Turin, Italy
| | - Claudia Palmitessa
- S.C. Neuroscienze, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Turin, Italy
| | - Marina Gallo
- S.C. Neuroscienze, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Turin, Italy
| | - Andrea Calvo
- Rita Levi Montalcini Department of Neuroscience, University of Turin, 10126 Turin, Italy
- Neurology, Hospital Department of Neuroscience and Mental Health, Città della Salute e della Scienza Hospital of Turin, 10126 Turin, Italy
| | - Federico Casale
- Rita Levi Montalcini Department of Neuroscience, University of Turin, 10126 Turin, Italy
| | - Umberto Manera
- Rita Levi Montalcini Department of Neuroscience, University of Turin, 10126 Turin, Italy
- Neurology, Hospital Department of Neuroscience and Mental Health, Città della Salute e della Scienza Hospital of Turin, 10126 Turin, Italy
| | - Alessandra Favole
- S.C. Neuroscienze, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Turin, Italy
- Correspondence: (A.F.); (A.C.)
| | - Paola Crociara
- S.C. Neuroscienze, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Turin, Italy
- ASL TO4, 10034 Chivasso, Italy
| | - Camilla Testori
- S.C. Neuroscienze, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Turin, Italy
| | - Valerio Carta
- S.C. Neuroscienze, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Turin, Italy
| | - Carlotta Tessarolo
- S.C. Neuroscienze, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Turin, Italy
| | - Antonio D’Angelo
- Department of Veterinary Science, University of Turin, 10095 Grugliasco, Italy
| | - Giovanni De Marco
- Rita Levi Montalcini Department of Neuroscience, University of Turin, 10126 Turin, Italy
- Neurology, Hospital Department of Neuroscience and Mental Health, Città della Salute e della Scienza Hospital of Turin, 10126 Turin, Italy
| | - Maria Caramelli
- S.C. Neuroscienze, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Turin, Italy
| | - Adriano Chiò
- Rita Levi Montalcini Department of Neuroscience, University of Turin, 10126 Turin, Italy
- Neurology, Hospital Department of Neuroscience and Mental Health, Città della Salute e della Scienza Hospital of Turin, 10126 Turin, Italy
- Correspondence: (A.F.); (A.C.)
| | - Cristina Casalone
- S.C. Neuroscienze, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Turin, Italy
| | - Cristiano Corona
- S.C. Neuroscienze, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Turin, Italy
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10
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Udani S, Langerman J, Koo D, Baghdasarian S, Cheng B, Kang S, Soemardy C, de Rutte J, Plath K, Carlo DD. Secretion encoded single-cell sequencing (SEC-seq) uncovers gene expression signatures associated with high VEGF-A secretion in mesenchymal stromal cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.07.523110. [PMID: 36711480 PMCID: PMC9881958 DOI: 10.1101/2023.01.07.523110] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Cells secrete numerous bioactive molecules essential for the function of healthy organisms. However, there are no scalable methods to link individual cell secretions to their transcriptional state. By developing and using secretion encoded single-cell sequencing (SEC-seq), which exploits hydrogel nanovials to capture individual cells and their secretions, we simultaneously measured the secretion of vascular endothelial growth factor A (VEGF-A) and the transcriptome for thousands of individual mesenchymal stromal cells (MSCs). We found that VEGF-A secretion is heterogeneous across the cell population and lowly correlated with the VEGFA transcript level. While there is a modest population-wide increase in VEGF-A secretion by hypoxic induction, highest VEGF-A secretion across normoxic and hypoxic culture conditions occurs in a subpopulation of MSCs characterized by a unique gene expression signature. Taken together, SEC-seq enables the identification of specific genes involved in the control of secretory states, which may be exploited for developing means to modulate cellular secretion for disease treatment.
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Affiliation(s)
- Shreya Udani
- Department of Bioengineering, University of California - Los Angeles, Los Angeles, CA 90095, USA
| | - Justin Langerman
- Department of Biological Chemistry, David Geffen School of Medicine, University of California - Los Angeles, Los Angeles, CA 90095, USA
| | - Doyeon Koo
- Department of Bioengineering, University of California - Los Angeles, Los Angeles, CA 90095, USA
| | - Sevana Baghdasarian
- Department of Chemical and Biomolecular Engineering, University of California - Los Angeles, Los Angeles, CA 90095, USA
| | - Brian Cheng
- Department of Bioengineering, University of California - Los Angeles, Los Angeles, CA 90095, USA
| | - Simran Kang
- Department of Bioengineering, University of California - Los Angeles, Los Angeles, CA 90095, USA
| | - Citradewi Soemardy
- Department of Bioengineering, University of California - Los Angeles, Los Angeles, CA 90095, USA
| | | | - Kathrin Plath
- Department of Biological Chemistry, David Geffen School of Medicine, University of California - Los Angeles, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, University of California - Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Stem Cell Research Center, University of California - Los Angeles, Los Angeles, CA 90095, USA
| | - Dino Di Carlo
- Department of Bioengineering, University of California - Los Angeles, Los Angeles, CA 90095, USA
- Partillion Bioscience, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, University of California - Los Angeles, Los Angeles, CA 90095, USA
- Department of Mechanical and Aerospace Engineering, University of California - Los Angeles, Los Angeles, CA 90095, USA
- California NanoSystems Institute (CNSI), University of California - Los Angeles, Los Angeles, CA 90095, USA
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11
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Kim H, Leng K, Park J, Sorets AG, Kim S, Shostak A, Embalabala RJ, Mlouk K, Katdare KA, Rose IVL, Sturgeon SM, Neal EH, Ao Y, Wang S, Sofroniew MV, Brunger JM, McMahon DG, Schrag MS, Kampmann M, Lippmann ES. Reactive astrocytes transduce inflammation in a blood-brain barrier model through a TNF-STAT3 signaling axis and secretion of alpha 1-antichymotrypsin. Nat Commun 2022; 13:6581. [PMID: 36323693 PMCID: PMC9630454 DOI: 10.1038/s41467-022-34412-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022] Open
Abstract
Astrocytes are critical components of the neurovascular unit that support blood-brain barrier (BBB) function. Pathological transformation of astrocytes to reactive states can be protective or harmful to BBB function. Here, using a human induced pluripotent stem cell (iPSC)-derived BBB co-culture model, we show that tumor necrosis factor (TNF) transitions astrocytes to an inflammatory reactive state that causes BBB dysfunction through activation of STAT3 and increased expression of SERPINA3, which encodes alpha 1-antichymotrypsin (α1ACT). To contextualize these findings, we correlated astrocytic STAT3 activation to vascular inflammation in postmortem human tissue. Further, in murine brain organotypic cultures, astrocyte-specific silencing of Serpina3n reduced vascular inflammation after TNF challenge. Last, treatment with recombinant Serpina3n in both ex vivo explant cultures and in vivo was sufficient to induce BBB dysfunction-related molecular changes. Overall, our results define the TNF-STAT3-α1ACT signaling axis as a driver of an inflammatory reactive astrocyte signature that contributes to BBB dysfunction.
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Affiliation(s)
- Hyosung Kim
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Kun Leng
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
| | - Jinhee Park
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Alexander G Sorets
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Suil Kim
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
| | - Alena Shostak
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Kate Mlouk
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
| | - Ketaki A Katdare
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
| | - Indigo V L Rose
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Sarah M Sturgeon
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Emma H Neal
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Yan Ao
- Department of Neurobiology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Shinong Wang
- Department of Neurobiology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Michael V Sofroniew
- Department of Neurobiology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jonathan M Brunger
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Douglas G McMahon
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Matthew S Schrag
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Ethan S Lippmann
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA.
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA.
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA.
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA.
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA.
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12
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Negroni E, Kondili M, Muraine L, Bensalah M, Butler-Browne GS, Mouly V, Bigot A, Trollet C. Muscle fibro-adipogenic progenitors from a single-cell perspective: Focus on their “virtual” secretome. Front Cell Dev Biol 2022; 10:952041. [PMID: 36200044 PMCID: PMC9527288 DOI: 10.3389/fcell.2022.952041] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
Skeletal muscle is a highly plastic tissue composed of a number of heterogeneous cell populations that, by interacting and communicating with each other, participate to the muscle homeostasis, and orchestrate regeneration and repair in healthy and diseased conditions. Although muscle regeneration relies on the activity of muscle stem cells (MuSCs), many other cellular players such as inflammatory, vascular and tissue-resident mesenchymal cells participate and communicate with MuSCs to sustain the regenerative process. Among them, Fibro-Adipogenic Progenitors (FAPs), a muscle interstitial stromal population, are crucial actors during muscle homeostasis and regeneration, interacting with MuSCs and other cellular players and dynamically producing and remodelling the extra-cellular matrix. Recent emerging single-cell omics technologies have resulted in the dissection of the heterogeneity of each cell populations within skeletal muscle. In this perspective we have reviewed the recent single-cell omics studies with a specific focus on FAPs in mouse and human muscle. More precisely, using the OutCyte prediction tool, we analysed the “virtual” secretome of FAPs, in resting and regenerating conditions, to highlight the potential of RNAseq data for the study of cellular communication.
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13
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Szeitz B, Megyesfalvi Z, Woldmar N, Valkó Z, Schwendenwein A, Bárány N, Paku S, László V, Kiss H, Bugyik E, Lang C, Szász AM, Pizzatti L, Bogos K, Hoda MA, Hoetzenecker K, Marko-Varga G, Horvatovich P, Döme B, Schelch K, Rezeli M. In-depth proteomic analysis reveals unique subtype-specific signatures in human small-cell lung cancer. Clin Transl Med 2022; 12:e1060. [PMID: 36149789 PMCID: PMC9506422 DOI: 10.1002/ctm2.1060] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/31/2022] [Accepted: 09/06/2022] [Indexed: 11/12/2022] Open
Abstract
Background Small‐cell lung cancer (SCLC) molecular subtypes have been primarily characterized based on the expression pattern of the following key transcription regulators: ASCL1 (SCLC‐A), NEUROD1 (SCLC‐N), POU2F3 (SCLC‐P) and YAP1 (SCLC‐Y). Here, we investigated the proteomic landscape of these molecular subsets with the aim to identify novel subtype‐specific proteins of diagnostic and therapeutic relevance. Methods Pellets and cell media of 26 human SCLC cell lines were subjected to label‐free shotgun proteomics for large‐scale protein identification and quantitation, followed by in‐depth bioinformatic analyses. Proteomic data were correlated with the cell lines’ phenotypic characteristics and with public transcriptomic data of SCLC cell lines and tissues. Results Our quantitative proteomic data highlighted that four molecular subtypes are clearly distinguishable at the protein level. The cell lines exhibited diverse neuroendocrine and epithelial–mesenchymal characteristics that varied by subtype. A total of 367 proteins were identified in the cell pellet and 34 in the culture media that showed significant up‐ or downregulation in one subtype, including known druggable proteins and potential blood‐based markers. Pathway enrichment analysis and parallel investigation of transcriptomics from SCLC cell lines outlined unique signatures for each subtype, such as upregulated oxidative phosphorylation in SCLC‐A, DNA replication in SCLC‐N, neurotrophin signalling in SCLC‐P and epithelial–mesenchymal transition in SCLC‐Y. Importantly, we identified the YAP1‐driven subtype as the most distinct SCLC subgroup. Using sparse partial least squares discriminant analysis, we identified proteins that clearly distinguish four SCLC subtypes based on their expression pattern, including potential diagnostic markers for SCLC‐Y (e.g. GPX8, PKD2 and UFO). Conclusions We report for the first time, the protein expression differences among SCLC subtypes. By shedding light on potential subtype‐specific therapeutic vulnerabilities and diagnostic biomarkers, our results may contribute to a better understanding of SCLC biology and the development of novel therapies.
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Affiliation(s)
- Beáta Szeitz
- Division of Oncology, Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
| | - Zsolt Megyesfalvi
- National Korányi Institute of Pulmonology, Budapest, Hungary.,Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria.,Department of Thoracic Surgery, National Institute of Oncology, Semmelweis University, Budapest, Hungary
| | - Nicole Woldmar
- Division of Clinical Protein Science, & Imaging, Department of Clinical Sciences (Lund) and Department of Biomedical Engineering, Lund University, Lund, Sweden.,Laboratory of Molecular Biology and Proteomics of Blood/LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Zsuzsanna Valkó
- National Korányi Institute of Pulmonology, Budapest, Hungary.,Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - Anna Schwendenwein
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - Nándor Bárány
- National Korányi Institute of Pulmonology, Budapest, Hungary.,Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria.,First Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Sándor Paku
- First Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Viktória László
- National Korányi Institute of Pulmonology, Budapest, Hungary.,Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - Helga Kiss
- Department of Thoracic Surgery, National Institute of Oncology, Semmelweis University, Budapest, Hungary.,University of Pécs, Pécs, Hungary
| | - Edina Bugyik
- National Korányi Institute of Pulmonology, Budapest, Hungary.,First Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Christian Lang
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - Attila Marcell Szász
- National Korányi Institute of Pulmonology, Budapest, Hungary.,Department of Bioinformatics, Semmelweis University, Budapest, Hungary
| | - Luciana Pizzatti
- Laboratory of Molecular Biology and Proteomics of Blood/LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Krisztina Bogos
- National Korányi Institute of Pulmonology, Budapest, Hungary
| | - Mir Alireza Hoda
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - Konrad Hoetzenecker
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - György Marko-Varga
- Division of Clinical Protein Science, & Imaging, Department of Clinical Sciences (Lund) and Department of Biomedical Engineering, Lund University, Lund, Sweden
| | - Peter Horvatovich
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Balázs Döme
- National Korányi Institute of Pulmonology, Budapest, Hungary.,Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria.,Department of Thoracic Surgery, National Institute of Oncology, Semmelweis University, Budapest, Hungary.,Department of Translational Medicine, Lund University, Lund, Sweden
| | - Karin Schelch
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Melinda Rezeli
- Division of Clinical Protein Science, & Imaging, Department of Clinical Sciences (Lund) and Department of Biomedical Engineering, Lund University, Lund, Sweden
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14
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Hur HJ, Lee JY, Kim DH, Cho MS, Lee S, Kim HS, Kim DW. Conditioned Medium of Human Pluripotent Stem Cell-Derived Neural Precursor Cells Exerts Neurorestorative Effects against Ischemic Stroke Model. Int J Mol Sci 2022; 23:7787. [PMID: 35887140 PMCID: PMC9319001 DOI: 10.3390/ijms23147787] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/09/2022] [Accepted: 07/12/2022] [Indexed: 02/01/2023] Open
Abstract
Previous studies have shown that early therapeutic events of neural precursor cells (NPCs) transplantation to animals with acute ischemic stroke readily protected neuronal cell damage and improved behavioral recovery through paracrine mechanisms. In this study, we tested the hypothesis that administration of conditioned medium from NPCs (NPC-CMs) could recapitulate the beneficial effects of cell transplantation. Rats with permanent middle cerebral artery occlusion (pMCAO) were randomly assigned to one of the following groups: PBS control, Vehicle (medium) controls, single (NPC-CM(S)) or multiple injections of NPC-CM(NPC-CM(M)) groups. A single intravenous injection of NPC-CM exhibited strong neuroregenerative potential to induce behavioral recovery, and multiple injections enhanced this activity further by suppressing inflammatory damage and inducing endogenous neurogenesis leading to histopathological and functional recovery. Proteome analysis of NPC-CM identified a number of proteins that are known to be associated with nervous system development, neurogenesis, and angiogenesis. In addition, transcriptome analysis revealed the importance of the inflammatory response during stroke recovery and some of the key hub genes in the interaction network were validated. Thus, our findings demonstrated that NPC-CM promoted functional recovery and reduced cerebral infarct and inflammation with enhanced endogenous neurogenesis, and the results highlighted the potency of NPC-CM in stroke therapy.
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Affiliation(s)
- Hye-Jin Hur
- Department of Physiology, Yonsei University College of Medicine, Seoul 03722, Korea; (H.-J.H.); (D.-H.K.)
- Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Ji Yong Lee
- Research Institute of Hyperbaric Medicine and Science, Yonsei University Wonju College of Medicine, Wonju-si 26426, Korea;
| | - Do-Hun Kim
- Department of Physiology, Yonsei University College of Medicine, Seoul 03722, Korea; (H.-J.H.); (D.-H.K.)
- S. Biomedics Co., Ltd., Seoul 04979, Korea;
| | | | - Sangsik Lee
- Department of Biomedical Engineering, College of Medical Convergence, Catholic Kwandong University, Gangneung-si 25601, Korea;
| | - Han-Soo Kim
- Department of Biomedical Sciences, College of Medical Convergence, Catholic Kwandong University, Gangneung-si 25601, Korea
| | - Dong-Wook Kim
- Department of Physiology, Yonsei University College of Medicine, Seoul 03722, Korea; (H.-J.H.); (D.-H.K.)
- Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
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15
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Abstract
PURPOSE OF REVIEW Liquid biopsies have emerged as a noninvasive alternative to tissue biopsy with potential applications during all stages of pediatric oncology care. The purpose of this review is to provide a survey of pediatric cell-free DNA (cfDNA) studies, illustrate their potential applications in pediatric oncology, and to discuss technological challenges and approaches to overcome these hurdles. RECENT FINDINGS Recent literature has demonstrated liquid biopsies' ability to inform treatment selection at diagnosis, monitor clonal evolution during treatment, sensitively detect minimum residual disease following local control, and provide sensitive posttherapy surveillance. Advantages include reduced procedural anesthesia, molecular profiling unbiased by tissue heterogeneity, and ability to track clonal evolution. Challenges to wider implementation in pediatric oncology, however, include blood volume restrictions and relatively low mutational burden in childhood cancers. Multiomic approaches address challenges presented by low-mutational burden, and novel bioinformatic analyses allow a single assay to yield increasing amounts of information, reducing blood volume requirements. SUMMARY Liquid biopsies hold tremendous promise in pediatric oncology, enabling noninvasive serial surveillance with adaptive care. Already integrated into adult care, recent advances in technologies and bioinformatics have improved applicability to the pediatric cancer landscape.
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Affiliation(s)
- R Taylor Sundby
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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16
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Martínez-Rodríguez F, Limones-González JE, Mendoza-Almanza B, Esparza-Ibarra EL, Gallegos-Flores PI, Ayala-Luján JL, Godina-González S, Salinas E, Mendoza-Almanza G. Understanding Cervical Cancer through Proteomics. Cells 2021; 10:1854. [PMID: 34440623 PMCID: PMC8391734 DOI: 10.3390/cells10081854] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/05/2021] [Accepted: 07/20/2021] [Indexed: 12/17/2022] Open
Abstract
Cancer is one of the leading public health issues worldwide, and the number of cancer patients increases every day. Particularly, cervical cancer (CC) is still the second leading cause of cancer death in women from developing countries. Thus, it is essential to deepen our knowledge about the molecular pathogenesis of CC and propose new therapeutic targets and new methods to diagnose this disease in its early stages. Differential expression analysis using high-throughput techniques applied to biological samples allows determining the physiological state of normal cells and the changes produced by cancer development. The cluster of differential molecular profiles in the genome, the transcriptome, or the proteome is analyzed in the disease, and it is called the molecular signature of cancer. Proteomic analysis of biological samples of patients with different grades of cervical intraepithelial neoplasia (CIN) and CC has served to elucidate the pathways involved in the development and progression of cancer and identify cervical proteins associated with CC. However, several cervical carcinogenesis mechanisms are still unclear. Detecting pathologies in their earliest stages can significantly improve a patient's survival rate, prognosis, and recurrence. The present review is an update on the proteomic study of CC.
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Affiliation(s)
- Fátima Martínez-Rodríguez
- Microbiology Department, Basic Science Center, Autonomous University of Aguascalientes, Aguascalientes 20100, Mexico;
| | | | - Brenda Mendoza-Almanza
- Academic Unit of Biological Sciences, Autonomous University of Zacatecas, Zacatecas 98068, Mexico; (B.M.-A.); (E.L.E.-I.); (P.I.G.-F.)
| | - Edgar L. Esparza-Ibarra
- Academic Unit of Biological Sciences, Autonomous University of Zacatecas, Zacatecas 98068, Mexico; (B.M.-A.); (E.L.E.-I.); (P.I.G.-F.)
| | - Perla I. Gallegos-Flores
- Academic Unit of Biological Sciences, Autonomous University of Zacatecas, Zacatecas 98068, Mexico; (B.M.-A.); (E.L.E.-I.); (P.I.G.-F.)
| | - Jorge L. Ayala-Luján
- Academic Unit of Chemical Sciences, Autonomous University of Zacatecas, Zacatecas 98160, Mexico; (J.L.A.-L.); (S.G.-G.)
| | - Susana Godina-González
- Academic Unit of Chemical Sciences, Autonomous University of Zacatecas, Zacatecas 98160, Mexico; (J.L.A.-L.); (S.G.-G.)
| | - Eva Salinas
- Microbiology Department, Basic Science Center, Autonomous University of Aguascalientes, Aguascalientes 20100, Mexico;
| | - Gretel Mendoza-Almanza
- Master in Biomedical Sciences, Autonomous University of Zacatecas, Zacatecas 98160, Mexico;
- National Council of Science and Technology, Autonomous University of Zacatecas, Zacatecas 98000, Mexico
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17
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Yu Y, Wang JL, Meng LL, Hu CT, Yan ZW, He ZP, Shi XQ, Fu GH, Zu LD. DDX54 Plays a Cancerous Role Through Activating P65 and AKT Signaling Pathway in Colorectal Cancer. Front Oncol 2021; 11:650360. [PMID: 33968751 PMCID: PMC8097168 DOI: 10.3389/fonc.2021.650360] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 03/17/2021] [Indexed: 12/15/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most malignant cancers, and its incidence is still steadily increasing. The DDX RNA helicase family members have been found to play a role in various cancers; however, the role of DDX54 in colorectal cancer is still unclear and needed to be defined. Here, we found DDX54 was overexpressed in CRC tissues by the label-free mass spectrum, which was also verified in tissue microarray of colon cancer, as well as the CRC cell lines and TCGA database. High DDX54 level was correlated with tumor stage and distant metastasis, which always indicated a poor prognosis to the CRC patients. DDX54 could promote the proliferation and mobility of CRC cells through increasing the phosphorylation level p65 and AKT leading to the tumorigenesis. Here, we have preliminarily studied the function of DDX54 in CRC, which would improve our understanding of the underlying biology of CRC and provide the new insight that could be translated into novel therapeutic approaches.
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Affiliation(s)
- Yi Yu
- Pathology Center, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jing-Long Wang
- Department of Pathology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li-Li Meng
- Department of Pathology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chun-Ting Hu
- Department of Pathology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhao-Wen Yan
- Department of Pathology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhi-Ping He
- Department of Pathology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiao-Qin Shi
- Pathology Center, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Guo-Hui Fu
- Pathology Center, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
- Department of Pathology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li-Dong Zu
- Department of Pathology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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18
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Saghaleyni R, Sheikh Muhammad A, Bangalore P, Nielsen J, Robinson JL. Machine learning-based investigation of the cancer protein secretory pathway. PLoS Comput Biol 2021; 17:e1008898. [PMID: 33819271 PMCID: PMC8049480 DOI: 10.1371/journal.pcbi.1008898] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 04/15/2021] [Accepted: 03/22/2021] [Indexed: 12/13/2022] Open
Abstract
Deregulation of the protein secretory pathway (PSP) is linked to many hallmarks of cancer, such as promoting tissue invasion and modulating cell-cell signaling. The collection of secreted proteins processed by the PSP, known as the secretome, is often studied due to its potential as a reservoir of tumor biomarkers. However, there has been less focus on the protein components of the secretory machinery itself. We therefore investigated the expression changes in secretory pathway components across many different cancer types. Specifically, we implemented a dual approach involving differential expression analysis and machine learning to identify PSP genes whose expression was associated with key tumor characteristics: mutation of p53, cancer status, and tumor stage. Eight different machine learning algorithms were included in the analysis to enable comparison between methods and to focus on signals that were robust to algorithm type. The machine learning approach was validated by identifying PSP genes known to be regulated by p53, and even outperformed the differential expression analysis approach. Among the different analysis methods and cancer types, the kinesin family members KIF20A and KIF23 were consistently among the top genes associated with malignant transformation or tumor stage. However, unlike most cancer types which exhibited elevated KIF20A expression that remained relatively constant across tumor stages, renal carcinomas displayed a more gradual increase that continued with increasing disease severity. Collectively, our study demonstrates the complementary nature of a combined differential expression and machine learning approach for analyzing gene expression data, and highlights key PSP components relevant to features of tumor pathophysiology that may constitute potential therapeutic targets. The secretory pathway is a series of intracellular compartments and enzymes that process and export proteins from the cell to its surrounding environment. Dysfunction of the secretory pathway is associated with many diseases, including cancer, and therefore constitutes a potential target for novel therapeutic strategies. The large number of interacting components that comprise the secretory pathway pose a challenge when attempting to identify where the dysfunction originates or how to restore healthy function. To improve our understanding of how the secretory pathway is changed within tumors, we used gene expression data from normal tissue and tumor samples from thousands of individuals which included many different types of cancers. The data was analyzed using different machine learning algorithms which we trained to predict sample characteristics, such as disease severity. This training quantified the relative degree to which each gene was associated with the tumor characteristic, allowing us to predict which secretory pathway components were important for processes such as tumor progression—both within specific cancer types and across many different cancer types. The machine learning-based approach demonstrated excellent performance compared to traditional gene expression analysis methods and identified several secretory pathway components with strong evidence of involvement in tumor development.
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Affiliation(s)
- Rasool Saghaleyni
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Azam Sheikh Muhammad
- Department of Computer Science and Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | | | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Wallenberg Center for Protein Research, Chalmers University of Technology, Gothenburg, Sweden
- BioInnovation Institute, Copenhagen, Denmark
| | - Jonathan L. Robinson
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Wallenberg Center for Protein Research, Chalmers University of Technology, Gothenburg, Sweden
- Department of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, Gothenburg, Sweden
- * E-mail:
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