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Niu Y, Chen SJ, Klauda JB. Simulations of naïve and KLA-activated macrophage plasma membrane models. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184242. [PMID: 37866689 DOI: 10.1016/j.bbamem.2023.184242] [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: 03/27/2023] [Revised: 08/25/2023] [Accepted: 10/17/2023] [Indexed: 10/24/2023]
Abstract
Macrophages (MAs), which play vital roles in human immune responses and lipid metabolisms, are implicated in the development and progression of atherosclerosis, a major contributor to cardiovascular diseases. Specifically, the abnormal lipid metabolism of oxidized low-density lipids (oxLDLs) in MAs is believed to be a crucial factor. However, the precise mechanism by which the MA membrane contributes to this altered lipid metabolism remains unclear. Lipidomic studies have revealed significant differences in membrane composition between various MA phenotypes. This study serves to provide and characterize complex realistic computational models for naïve (M0) and Kdo2-lipid A-activated (M1) state MA. Analyses of surface area per lipid (SA/lip), area compressibility modulus (KA), carbon‑hydrogen order parameter (SCH), electron density profile (EDP), tilt angles, two-dimension radial distribution functions (2D RDFs), mean squared displacement (MSD), hydrogen bonds (H-bonds), lipid clustering, and lipid wobble were conducted for both models. Results indicate that the M1 state MA membrane is more tightly packed, with increased chain order across lipid species, and forms PSM-DOPG-CHOL and PSM-SLPC-CHOL clusters. Importantly, the bilayer thicknesses reported for the models are in good agreement with experimental data for the thicknesses of transmembrane regions for MA integral proteins. These findings validate the described models as physiologically accurate for future computational studies of MA membranes and their residing proteins.
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Affiliation(s)
- Yueqi Niu
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA
| | - Si Jia Chen
- Medical Scientist Training Program, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA; Institute for Physical Science and Technology, Biophysics Program, University of Maryland, College Park, MD 20742, USA.
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Triantaphyllopoulos KA. Long Non-Coding RNAs and Their "Discrete" Contribution to IBD and Johne's Disease-What Stands out in the Current Picture? A Comprehensive Review. Int J Mol Sci 2023; 24:13566. [PMID: 37686376 PMCID: PMC10487966 DOI: 10.3390/ijms241713566] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/23/2023] [Accepted: 08/27/2023] [Indexed: 09/10/2023] Open
Abstract
Non-coding RNAs (ncRNA) have paved the way to new perspectives on the regulation of gene expression, not only in biology and medicine, but also in associated fields and technologies, ensuring advances in diagnostic means and therapeutic modalities. Critical in this multistep approach are the associations of long non-coding RNA (lncRNA) with diseases and their causal genes in their networks of interactions, gene enrichment and expression analysis, associated pathways, the monitoring of the involved genes and their functional roles during disease progression from one stage to another. Studies have shown that Johne's Disease (JD), caused by Mycobacterium avium subspecies partuberculosis (MAP), shares common lncRNAs, clinical findings, and other molecular entities with Crohn's Disease (CD). This has been a subject of vigorous investigation owing to the zoonotic nature of this condition, although results are still inconclusive. In this review, on one hand, the current knowledge of lncRNAs in cells is presented, focusing on the pathogenesis of gastrointestinal-related pathologies and MAP-related infections and, on the other hand, we attempt to dissect the associated genes and pathways involved. Furthermore, the recently characterized and novel lncRNAs share common pathologies with IBD and JD, including the expression, molecular networks, and dataset analysis results. These are also presented in an attempt to identify potential biomarkers pertinent to cattle and human disease phenotypes.
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Affiliation(s)
- Kostas A Triantaphyllopoulos
- Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos St., 11855 Athens, Greece
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Khan A, Singh A, Singh P, Kumar R, Ojha KK, Singh VK, Srivastava A. LCN2-Fungal siderophore-iron binding and uptake leads to oxidative stress and cell death in hepatocellular carcinoma cell line HepG2. J Biomol Struct Dyn 2023; 41:12714-12733. [PMID: 36762696 DOI: 10.1080/07391102.2023.2175380] [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: 10/27/2022] [Accepted: 01/05/2023] [Indexed: 02/11/2023]
Abstract
Microorganisms produce non-ribosomal peptides called siderophores for the purpose of iron acquisition. Mammalian immune system is well-known for producing small secretory proteins called lipocalins upon bacterial infection. These proteins sequester siderophores produced by invading bacterial pathogens rendering them unable to acquire iron from the host. However, this is not their sole function. In addition to transferrin and lactoferrin, lipocalins are also known to transport siderophore-bound iron to the host cells. While binding of bacterial siderophores with human lipocalin is well studied, binding of the fungal counterpart is still not confirmed and fully understood. Apart from pathogen-affected cells, developing cancerous cells also show varying expression level of different proteins including those involved in iron transport. The possibility of exogenous fungal siderophore-mediated iron transport via lipocalin and its receptor in mammalian cells has not yet been explored much. In present investigation we have checked differential expression of human lipocalin, LCN2 in hepatocellular carcinoma cell lines HepG2 as well as its normal counterpart WRL-68 and computationally determined the feasibility of LCN2 binding with fungal siderophore. Further in case of a stable complex being formed, whether this complex has the ability to transport iron through its specific receptor was assessed. Also, we have tried to explore possible mechanism of fungal-siderophore mediated oxidative stress leading to significant cell death in cancerous cells. This study will thus be useful towards finding a new way of treating hepatocellular carcinoma via inducing siderophore-mediated cell death in cancerous cells.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Azmi Khan
- Department of Life Science, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar
| | - Ashutosh Singh
- Department of Life Science, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar
| | - Pratika Singh
- Department of Life Science, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar
| | - Rakesh Kumar
- Department of Bioinformatics, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar
| | - Krishna Kumar Ojha
- Department of Bioinformatics, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar
| | - Vijay Kumar Singh
- Department of Bioinformatics, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar
| | - Amrita Srivastava
- Department of Life Science, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar
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Holder A, Garty R, Elder C, Mesnard P, Laquerbe C, Bartens MC, Salavati M, Shabbir MZ, Tzelos T, Connelly T, Villarreal-Ramos B, Werling D. Analysis of Genetic Variation in the Bovine SLC11A1 Gene, Its Influence on the Expression of NRAMP1 and Potential Association With Resistance to Bovine Tuberculosis. Front Microbiol 2020; 11:1420. [PMID: 32714308 PMCID: PMC7341946 DOI: 10.3389/fmicb.2020.01420] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/02/2020] [Indexed: 11/13/2022] Open
Abstract
Bovine tuberculosis (bTB), caused by Mycobacterium bovis, is a chronic zoonotic disease where host genetics is thought to contribute to susceptibility or resistance. One of the genes implicated is the SLC11A1 gene, that encodes for the natural resistance-associated macrophage protein 1 (NRAMP1). The aim of this study was to identify SLC11A1 polymorphisms and to investigate any resulting functional differences in NRAMP1 expression that might be correlated with resistance/susceptibility to M. bovis infection. Sequencing of the SLC11A1 gene in cDNA isolated from Brown Swiss, Holstein Friesian, and Sahiwal cattle identified five single nucleotide polymorphisms (SNPs) in the coding region, but only one of these (SNP4, c.1066C>G, rs109453173) was present in all three cattle breeds and therefore warranted further investigation. Additionally, variations of 10, 11, and 12 GT repeats were identified in a microsatellite (MS1) in the SLC11A1 3′UTR. Measurement of NRAMP1 expression in bovine macrophages by ELISA showed no differences between cells generated from the different breeds. Furthermore, variations in the length of the MS1 microsatellite did not impact on NRAMP1 protein expression as analyzed by luciferase reporter assay. However, further analysis of the ELISA data identified that the presence of the alternative G allele at SNP4 was associated with increased expression of NRAMP1 in bovine macrophages. Since NRAMP1 has been shown to influence the survival of intracellular pathogens such as M. bovis through the sequestering of iron, it is possible that cattle expressing the alternative G allele might have an increased resistance to bTB through increased NRAMP1 expression in their macrophages.
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Affiliation(s)
- Angela Holder
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hertfordshire, United Kingdom
| | - Rachel Garty
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hertfordshire, United Kingdom
| | - Charlotte Elder
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hertfordshire, United Kingdom
| | - Paula Mesnard
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hertfordshire, United Kingdom.,EPLEFPA Agricampus La Roque, Rodez, France
| | - Celine Laquerbe
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hertfordshire, United Kingdom.,EPLEFPA Agricampus La Roque, Rodez, France
| | - Marie-Christine Bartens
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hertfordshire, United Kingdom
| | - Mazdak Salavati
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hertfordshire, United Kingdom.,The Roslin Institute, The University of Edinburgh, Midlothian, United Kingdom
| | | | - Thomas Tzelos
- The Roslin Institute, The University of Edinburgh, Midlothian, United Kingdom
| | - Timothy Connelly
- The Roslin Institute, The University of Edinburgh, Midlothian, United Kingdom
| | - Bernardo Villarreal-Ramos
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom.,APHA, Webybridge, United Kingdom
| | - Dirk Werling
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hertfordshire, United Kingdom
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