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Article ; Online: Recent Advancements in Subcellular Proteomics: Growing Impact of Organellar Protein Niches on the Understanding of Cell Biology.

Bhushan, Vanya / Nita-Lazar, Aleksandra

2024

Abstract: The mammalian cell is a complex entity, with membrane-bound and membrane-less organelles playing vital roles in regulating cellular homeostasis. Organellar protein niches drive discrete biological processes and cell functions, thus maintaining cell ... ...

Abstract	The mammalian cell is a complex entity, with membrane-bound and membrane-less organelles playing vital roles in regulating cellular homeostasis. Organellar protein niches drive discrete biological processes and cell functions, thus maintaining cell equilibrium. Cellular processes such as signaling, growth, proliferation, motility, and programmed cell death require dynamic protein movements between cell compartments. Aberrant protein localization is associated with a wide range of diseases. Therefore, analyzing the subcellular proteome of the cell can provide a comprehensive overview of cellular biology. With recent advancements in mass spectrometry, imaging technology, computational tools, and deep machine learning algorithms, studies pertaining to subcellular protein localization and their dynamic distributions are gaining momentum. These studies reveal changing interaction networks because of "moonlighting proteins" and serve as a discovery tool for disease network mechanisms. Consequently, this review aims to provide a comprehensive repository for recent advancements in subcellular proteomics subcontexting methods, challenges, and future perspectives for method developers. In summary, subcellular proteomics is crucial to the understanding of the fundamental cellular mechanisms and the associated diseases.
Language	English
Publishing date	2024-03-07
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.3c00839
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Article ; Online: Omics and systems view of innate immune pathways.

Rathore, Deepali / Marino, Matthew J / Nita-Lazar, Aleksandra

Proteomics

2023 Volume 23, Issue 13-14, Page(s) e2200407

Abstract: Multiomics approaches to studying systems biology are very powerful techniques that can elucidate changes in the genomic, transcriptomic, proteomic, and metabolomic levels within a cell type in response to an infection. These approaches are valuable for ... ...

Abstract	Multiomics approaches to studying systems biology are very powerful techniques that can elucidate changes in the genomic, transcriptomic, proteomic, and metabolomic levels within a cell type in response to an infection. These approaches are valuable for understanding the mechanisms behind disease pathogenesis and how the immune system responds to being challenged. With the emergence of the COVID-19 pandemic, the importance and utility of these tools have become evident in garnering a better understanding of the systems biology within the innate and adaptive immune response and for developing treatments and preventative measures for new and emerging pathogens that pose a threat to human health. In this review, we focus on state-of-the-art omics technologies within the scope of innate immunity.
MeSH term(s)	Humans ; Proteomics ; Pandemics ; COVID-19 ; Systems Biology/methods ; Immunity, Innate
Language	English
Publishing date	2023-06-03
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	2032093-0
ISSN	1615-9861 ; 1615-9853
ISSN (online)	1615-9861
ISSN	1615-9853
DOI	10.1002/pmic.202200407
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Zs.A 5386: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.A 1868: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)

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Article ; Online: EnsMOD: A Software Program for Omics Sample Outlier Detection.

Manes, Nathan P / Song, Jian / Nita-Lazar, Aleksandra

Journal of computational biology : a journal of computational molecular cell biology

2023 Volume 30, Issue 6, Page(s) 726–735

Abstract: Detection of omics sample outliers is important for preventing erroneous biological conclusions, developing robust experimental protocols, and discovering rare biological states. Two recent publications describe robust algorithms for detecting ... ...

Abstract	Detection of omics sample outliers is important for preventing erroneous biological conclusions, developing robust experimental protocols, and discovering rare biological states. Two recent publications describe robust algorithms for detecting transcriptomic sample outliers, but neither algorithm had been incorporated into a software tool for scientists. Here we describe Ensemble Methods for Outlier Detection (EnsMOD) which incorporates both algorithms. EnsMOD calculates how closely the quantitation variation follows a normal distribution, plots the density curves of each sample to visualize anomalies, performs hierarchical cluster analyses to calculate how closely the samples cluster with each other, and performs robust principal component analyses to statistically test if any sample is an outlier. The probabilistic threshold parameters can be easily adjusted to tighten or loosen the outlier detection stringency. EnsMOD can be used to analyze any omics dataset with normally distributed variance. Here it was used to analyze a simulated proteomics dataset, a multiomic (proteome and transcriptome) dataset, a single-cell proteomics dataset, and a phosphoproteomics dataset. EnsMOD successfully identified all of the simulated outliers, and subsequent removal of a detected outlier improved data quality for downstream statistical analyses.
MeSH term(s)	Software ; Algorithms ; Gene Expression Profiling ; Proteomics ; Multiomics
Language	English
Publishing date	2023-04-12
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	2030900-4
ISSN	1557-8666 ; 1066-5277
ISSN (online)	1557-8666
ISSN	1066-5277
DOI	10.1089/cmb.2022.0243
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Article ; Online: Phosphoproteome Analysis in Immune Cell Signaling.

Rathore, Deepali / Nita-Lazar, Aleksandra

Current protocols in immunology

2020 Volume 130, Issue 1, Page(s) e105

Abstract: Immune cell signaling is largely regulated by protein phosphorylation. Stimulation of toll-like receptors (TLRs) by pathogen-associated ligands drives the cascade of immune response, which can be influenced by differences in phosphoprotein abundance. ... ...

Abstract	Immune cell signaling is largely regulated by protein phosphorylation. Stimulation of toll-like receptors (TLRs) by pathogen-associated ligands drives the cascade of immune response, which can be influenced by differences in phosphoprotein abundance. Therefore, the analysis of phosphorylation signatures at a global level is central to understanding the complex and integrated signaling in macrophages upon pathogen attack. Here, we describe a mass spectrometry-based approach to identify and quantify phosphoproteome changes in response to the stimulation of TLR2, TLR4, and TLR7 with immune-response inducing ligands in cultured immune cells. This review will focus on the TLR stimulation of mouse macrophages as an example; however, the technique is applicable to any immortalized immune cell and any soluble stimuli. The methodology includes protocols for metabolic labeling of immune cells (stable isotope labeling of amino acids in cell culture, i.e., SILAC); ligand-initiated stimulation of immune receptors followed by cell lysis; in-solution trypsin digestion of proteins and enrichment of the resulting peptide mix for collecting phosphopeptides, which are then analyzed by high-resolution LC-MS/MS (liquid-chromatography tandem mass spectrometry). © 2020 Wiley Periodicals LLC. Basic Protocol 1: SILAC labeling of mouse macrophages Basic Protocol 2: Stimulation, cell lysis and Western Blotting Basic Protocol 3: Trypsin digestion, fractionation and phosphopeptide enrichment Basic Protocol 4: Quantitative mass spectrometry Alternate Protocol: Culturing SILAC-labeled cells from frozen mouse macrophages cells.
MeSH term(s)	Animals ; Blotting, Western ; Cell Culture Techniques ; Cells, Cultured ; Chemical Fractionation/methods ; Chromatography, Liquid/methods ; Immune System/cytology ; Immune System/immunology ; Immune System/metabolism ; Macrophages/immunology ; Macrophages/metabolism ; Mice ; Phosphopeptides ; Phosphoproteins/metabolism ; Phosphorylation ; Proteome ; Proteomics/methods ; Signal Transduction ; Staining and Labeling ; Tandem Mass Spectrometry/methods
Chemical Substances	Phosphopeptides ; Phosphoproteins ; Proteome
Language	English
Publishing date	2020-09-22
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	2179059-0
ISSN	1934-368X ; 1934-3671
ISSN (online)	1934-368X
ISSN	1934-3671
DOI	10.1002/cpim.105
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Article ; Online: Lipopolysaccharide Regulates the Macrophage RNA-Binding Proteome.

Rathore, Deepali / Marino, Matthew J / Issara-Amphorn, Jiraphorn / Hwan Yoon, Sung / Manes, Nathan P / Nita-Lazar, Aleksandra

Journal of proteome research

2024

Abstract: RNA-protein interactions within cellular signaling pathways have significant modulatory effects on RNA binding proteins' (RBPs') effector functions. During the innate immune response, specific RNA-protein interactions have been reported as a regulatory ... ...

Abstract	RNA-protein interactions within cellular signaling pathways have significant modulatory effects on RNA binding proteins' (RBPs') effector functions. During the innate immune response, specific RNA-protein interactions have been reported as a regulatory layer of post-transcriptional control. We investigated changes in the RNA-bound proteome of immortalized mouse macrophages (IMM) following treatment with lipopolysaccharide (LPS). Stable isotope labeling by amino acids in cell culture (SILAC) of cells followed by unbiased purification of RNP complexes at two time points after LPS stimulation and bottom-up proteomic analysis by LC-MS/MS resulted in a set of significantly affected RBPs. Global RNA sequencing and LFQ proteomics were used to characterize the correlation of transcript and protein abundance changes in response to LPS at different time points with changes in protein-RNA binding. Il1α, MARCKS, and ACOD1 were noted as RBP candidates involved in innate immune signaling. The binding sites of the RBP and RNA conjugates at amino acid resolution were investigated by digesting the cross-linked oligonucleotide from peptides remaining after elution using Nuclease P1. The combined data sets provide directions for further studies of innate immune signaling regulation by RBP interactions with different classes of RNA.
Language	English
Publishing date	2024-03-25
Publishing country	United States
Document type	Journal Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.3c00838
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Article: Molecular Mechanisms of the Toll-Like Receptor, STING, MAVS, Inflammasome, and Interferon Pathways.

Manes, Nathan P / Nita-Lazar, Aleksandra

mSystems

2021 , Page(s) e0033621

Abstract: Pattern recognition receptors (PRRs) form the front line of defense against pathogens. Many of the molecular mechanisms that facilitate PRR signaling have been characterized in detail, which is critical for the development of accurate PRR pathway models ... ...

Abstract	Pattern recognition receptors (PRRs) form the front line of defense against pathogens. Many of the molecular mechanisms that facilitate PRR signaling have been characterized in detail, which is critical for the development of accurate PRR pathway models at the molecular interaction level. These models could support the development of therapeutics for numerous diseases, including sepsis and COVID-19. This review describes the molecular mechanisms of the principal signaling interactions of the Toll-like receptor, STING, MAVS, and inflammasome pathways. A detailed molecular mechanism network is included as Data Set S1 in the supplemental material.
Language	English
Publishing date	2021-06-29
Publishing country	United States
Document type	Journal Article
ISSN	2379-5077
ISSN	2379-5077
DOI	10.1128/mSystems.00336-21
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Article: Experimental Analysis of Viral-Host Interactions.

Gillen, Joseph / Nita-Lazar, Aleksandra

Frontiers in physiology

2019 Volume 10, Page(s) 425

Abstract: Viral and pathogen protein complexity is often limited by their relatively small genomes, thus critical functions are often accomplished by complexes of host and pathogen proteins. This requirement makes the study of host-pathogen interactions critical ... ...

Abstract	Viral and pathogen protein complexity is often limited by their relatively small genomes, thus critical functions are often accomplished by complexes of host and pathogen proteins. This requirement makes the study of host-pathogen interactions critical for the understanding of pathogenicity and virology. This review article discusses proteomic methods that offer an opportunity to experimentally identify and analyze the binding partners of a target protein and presents the representative studies performed with these methods. These methods divide into two classes:
Language	English
Publishing date	2019-04-11
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2564217-0
ISSN	1664-042X
ISSN	1664-042X
DOI	10.3389/fphys.2019.00425
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Article ; Online: Approaching complexity: systems biology and ms-based techniques to address immune signaling.

Gillen, Joseph / Bridgwater, Caleb / Nita-Lazar, Aleksandra

Expert review of proteomics

2020 Volume 17, Issue 5, Page(s) 341–354

Abstract: Introduction: Studying immune signaling has been critical for our understanding of immunology, pathogenesis, cancer, and homeostasis. To enhance the breadth of the analysis, high throughput methods have been developed to survey multiple areas ... ...

Abstract	Introduction: Studying immune signaling has been critical for our understanding of immunology, pathogenesis, cancer, and homeostasis. To enhance the breadth of the analysis, high throughput methods have been developed to survey multiple areas simultaneously, including transcriptomics, reporter assays, and ELISAs. While these techniques have been extremely informative, mass-spectrometry-based technologies have been gaining momentum and starting to be widely used in the studies of immune signaling and systems immunology. Areas covered: We present established proteomic methods that have been used to address immune signaling and discuss the new mass-spectrometry- based techniques of interest to the expanding field of systems immunology. Established and new proteomic methods and their applications discussed here include post-translational modification analysis, protein quantification, secretome analysis, and interactomics. In addition, we present developments in small molecule and metabolite analysis, mass spectrometry imaging, and single cell analysis. Finally, we discuss the role of multi-omic integration in aiding leading edge investigation. Expert opinion: In science, available techniques enhance the breadth and depth of the studies. By incorporating proteomic techniques and their innovative use, it will be possible to expand the current studies and to address novel questions at the forefront of scientific discovery.
MeSH term(s)	Computational Biology ; Humans ; Immune System ; Mass Spectrometry ; Metabolomics ; Proteins/genetics ; Proteins/immunology ; Proteomics ; Signal Transduction/genetics ; Single-Cell Analysis ; Systems Biology
Chemical Substances	Proteins
Language	English
Publishing date	2020-06-21
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Review
ZDB-ID	2299100-1
ISSN	1744-8387 ; 1478-9450
ISSN (online)	1744-8387
ISSN	1478-9450
DOI	10.1080/14789450.2020.1780920
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Article ; Online: Myristoylated, alanine-rich C-kinase substrate (MARCKS) regulates toll-like receptor 4 signaling in macrophages.

Issara-Amphorn, Jiraphorn / Sjoelund, Virginie H / Smelkinson, Margery / Montalvo, Sebastian / Yoon, Sung Hwan / Manes, Nathan P / Nita-Lazar, Aleksandra

Scientific reports

2023 Volume 13, Issue 1, Page(s) 19562

Abstract: MARCKS (myristoylated alanine-rich C-kinase substrate) is a membrane-associated protein expressed in many cell types, including macrophages. MARCKS is functionally implicated in cell adhesion, phagocytosis, and inflammation. LPS (lipopolysaccharide) ... ...

Abstract	MARCKS (myristoylated alanine-rich C-kinase substrate) is a membrane-associated protein expressed in many cell types, including macrophages. MARCKS is functionally implicated in cell adhesion, phagocytosis, and inflammation. LPS (lipopolysaccharide) triggers inflammation via TLR4 (toll-like receptor 4).The presence of MARCKS and the formation of phospho-MARCKS in various cell types have been described, but the role(s) of MARCKS in regulating macrophage functions remain unclear. We investigated the role of MARCKS in inflammation. Confocal microscopy revealed that MARCKS and phospho-MARCKS increased localization to endosomes and the Golgi apparatus upon LPS stimulation.CRISPR-CAS9 mediated knockout of MARCKS in macrophages downregulated the production of TNF and IL6, suggesting a role for MARCKS in inflammatory responses. Our comprehensive proteomics analysis together with real-time metabolic assays comparing LPS-stimulation of WT and MARCKS knock-out macrophages provided insights into the involvement of MARCKS in specific biological processes including innate immune response, inflammatory response, cytokine production, and molecular functions such as extracellularly ATP-gated cation channel activity, electron transfer activity and oxidoreductase activity, uncovering specific proteins involved in regulating MARCKS activity upon LPS stimulation. MARCKS appears to be a key regulator of inflammation whose inhibition might be beneficial for therapeutic intervention in inflammatory diseases.
MeSH term(s)	Humans ; Toll-Like Receptor 4 ; Intracellular Signaling Peptides and Proteins ; Lipopolysaccharides/pharmacology ; Myristoylated Alanine-Rich C Kinase Substrate ; Macrophages ; Inflammation ; Phosphorylation
Chemical Substances	Toll-Like Receptor 4 ; Intracellular Signaling Peptides and Proteins ; Lipopolysaccharides ; Myristoylated Alanine-Rich C Kinase Substrate (125267-21-2) ; MARCKS protein, human
Language	English
Publishing date	2023-11-10
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Research Support, N.I.H., Extramural
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-46266-x
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Article: Myristoylated, Alanine-rich C-kinase Substrate (MARCKS) regulates Toll-like receptor 4 signaling in macrophages.

Issara-Amphorn, Jiraphorn / Sjoelund, Virginie / Smelkinson, Margery / Yoon, Sung Hwan / Manes, Nathan P / Nita-Lazar, Aleksandra

Research square

2023

Abstract: MARCKS (Myristoylated Alanine-rich C-kinase Substrate) is a membrane protein expressed in many cell types, including macrophages. MARCKS is functionally implicated in cell adhesion, phagocytosis, and inflammation. LPS (lipopolysaccharide) triggers ... ...

Abstract	MARCKS (Myristoylated Alanine-rich C-kinase Substrate) is a membrane protein expressed in many cell types, including macrophages. MARCKS is functionally implicated in cell adhesion, phagocytosis, and inflammation. LPS (lipopolysaccharide) triggers inflammation via TLR4 (Toll-like receptor 4). The presence of MARCKS and the formation of phospho-MARCKS in macrophages have been described, but the role(s) of MARCKS in regulating macrophage functions remain unclear. To investigate the role of MARCKS during inflammation, we activated macrophages using LPS with or without the addition of a PKC inhibitor. We found that PKC inhibition substantially decreased macrophage IL6 and TNF cytokine production. In addition, confocal microscopy revealed that MARCKS and phospho-MARCKS increased localization to endosomes and the Golgi apparatus upon LPS stimulation. CRISPR-CAS9 mediated knockout of MARCKS in macrophages downregulated TNF and IL6 production, suggesting a role for MARCKS in inflammatory responses. Our comprehensive proteomics analysis together with real-time metabolic assays comparing LPS-stimulation of WT and MARCKS knock-out macrophages provided insights into the involvement of MARCKS in specific biological processes and signaling pathways, uncovering specific proteins involved in regulating MARCKS activity upon LPS stimulation. MARCKS appears to be a key regulator of inflammation whose inhibition might be beneficial for therapeutic intervention in inflammatory related diseases.
Language	English
Publishing date	2023-07-10
Publishing country	United States
Document type	Preprint
DOI	10.21203/rs.3.rs-3094036/v1
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