1
|
Ma J, Fu L, Lu Z, Sun Y. Evaluating the Causal Effects of Circulating Proteome on the Risk of Sepsis and Related Outcomes. ACS OMEGA 2024; 9:23864-23872. [PMID: 38854583 PMCID: PMC11154893 DOI: 10.1021/acsomega.4c01934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/09/2024] [Accepted: 05/17/2024] [Indexed: 06/11/2024]
Abstract
The current investigation deployed Mendelian randomization (MR) to elucidate the causal relationship between circulating proteins and sepsis. A rigorous two-sample MR analysis evaluated the effect of plasma proteins on the sepsis susceptibility. To affirm the integrity of MR findings, a suite of supplementary analyses, including Bayesian colocalization, Steiger filtering, the assessment of protein-altering polymorphisms, and the correlation between expression quantitative trait loci and protein quantitative trait loci (pQTLs), was employed. The study further integrated the examination of protein-protein interactions and pathway enrichment, along with the identification of pharmacologically actionable targets, to advance our comprehension and outline potential sepsis therapies. Subsequent analyses leveraging cis-pQTLs within MR studies unveiled noteworthy relationships: 94 specific proteins exhibited significant links with sepsis-related 28 day mortality, while 96 distinct proteins correlated with survival outcomes in sepsis. Furthermore, incorporating both cis- and trans-pQTLs in MR investigations revealed more comprehensive findings, associating 201 unique proteins with sepsis-related 28 day mortality and 199 distinct proteins with survival outcomes in sepsis. Markedly, colocalization analyses confirmed that eight of these proteins exhibited prominent evidence for colocalization, emphasizing their potential criticality in sepsis pathophysiology. Further in silico analyses were conducted to delineate putative regulatory networks and to highlight prospective drug targets among these proteins. Employing the MR methodology has shed light on plasma proteins implicated in the etiopathogenesis of sepsis. This novel approach unveiled numerous biomarkers and targets, providing a scientific rationale for the development of new therapeutic strategies and prophylactic measures against sepsis.
Collapse
Affiliation(s)
- Jiawei Ma
- The
First Department of Critical Care Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China
- Department
of Critical Care Medicine, Wuxi No. 2 People’s
Hospital, Wuxi 214002, China
- Department
of Critical Care Medicine, Aheqi County
People’s Hospital, Xinjiang 843599, China
| | - Lu Fu
- The
First Department of Critical Care Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China
| | - Zhonghua Lu
- The
First Department of Critical Care Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China
| | - Yun Sun
- The
First Department of Critical Care Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China
| |
Collapse
|
2
|
Hsiung CCS, Wilson CM, Sambold NA, Dai R, Chen Q, Teyssier N, Misiukiewicz S, Arab A, O'Loughlin T, Cofsky JC, Shi J, Gilbert LA. Engineered CRISPR-Cas12a for higher-order combinatorial chromatin perturbations. Nat Biotechnol 2024:10.1038/s41587-024-02224-0. [PMID: 38760567 DOI: 10.1038/s41587-024-02224-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/28/2024] [Indexed: 05/19/2024]
Abstract
Multiplexed genetic perturbations are critical for testing functional interactions among coding or non-coding genetic elements. Compared to double-stranded DNA cutting, repressive chromatin formation using CRISPR interference (CRISPRi) avoids genotoxicity and is more effective for perturbing non-coding regulatory elements in pooled assays. However, current CRISPRi pooled screening approaches are limited to targeting one to three genomic sites per cell. We engineer an Acidaminococcus Cas12a (AsCas12a) variant, multiplexed transcriptional interference AsCas12a (multiAsCas12a), that incorporates R1226A, a mutation that stabilizes the ribonucleoprotein-DNA complex via DNA nicking. The multiAsCas12a-KRAB fusion improves CRISPRi activity over DNase-dead AsCas12a-KRAB fusions, often rescuing the activities of lentivirally delivered CRISPR RNAs (crRNA) that are inactive when used with the latter. multiAsCas12a-KRAB supports CRISPRi using 6-plex crRNA arrays in high-throughput pooled screens. Using multiAsCas12a-KRAB, we discover enhancer elements and dissect the combinatorial function of cis-regulatory elements in human cells. These results instantiate a group testing framework for efficiently surveying numerous combinations of chromatin perturbations for biological discovery and engineering.
Collapse
Affiliation(s)
- C C-S Hsiung
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Arc Institute, Palo Alto, CA, USA
| | - C M Wilson
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Arc Institute, Palo Alto, CA, USA
- Tetrad Graduate Program, University of California, San Francisco, CA, USA
| | | | - R Dai
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Arc Institute, Palo Alto, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Q Chen
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - N Teyssier
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - S Misiukiewicz
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - A Arab
- Arc Institute, Palo Alto, CA, USA
| | - T O'Loughlin
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - J C Cofsky
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - J Shi
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - L A Gilbert
- Department of Urology, University of California, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Arc Institute, Palo Alto, CA, USA.
| |
Collapse
|
3
|
Brown PA. Genes Differentially Expressed Across Major Arteries Are Enriched in Endothelial Dysfunction-Related Gene Sets: Implications for Relative Inter-artery Atherosclerosis Risk. Bioinform Biol Insights 2024; 18:11779322241251563. [PMID: 38765020 PMCID: PMC11100403 DOI: 10.1177/11779322241251563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 04/13/2024] [Indexed: 05/21/2024] Open
Abstract
Atherosclerosis differs across major arteries. Although the biological basis is not fully understood, limited evidence of genetic differences has been documented. This study, therefore, was aimed to identify differentially expressed genes between clinically relevant major arteries and investigate their enrichment in endothelial dysfunction-related gene sets. A bioinformatic analysis of publicly available gene-level read counts for coronary, aortic, and tibial arteries was performed. Differential gene expression was conducted with DeSeq2 at a false discovery rate of 0.05. Differentially expressed genes were then subjected to over-representation analysis and active-subnetwork-oriented enrichment analysis, both at a false discovery rate of 0.005. Enriched terms common to both analyses were categorized for each contrast into immunity/inflammation-, membrane biology-, lipid metabolism-, and coagulation-related terms, and the top differentially expressed genes validated against Swiss Institute of Bioinformatics' Bgee database. There was mostly upregulation of differentially expressed genes for the coronary/tibial and aorta/tibial contrasts, but milder changes for the coronary/aorta contrast. Transcriptomic differences between coronary or aortic versus tibial samples largely involved immunity/inflammation-, membrane biology-, lipid metabolism-, and coagulation-related genes, suggesting potential to modulate endothelial dysfunction and atherosclerosis. These results imply atheroprone coronary and aortic environments compared with tibial artery tissue, which may explain observed relative inter-artery atherosclerosis risk.
Collapse
Affiliation(s)
- Paul A Brown
- Department of Basic Medical Sciences, Faculty of Medical Sciences Teaching and Research Complex, The University of the West Indies, Kingston, Jamaica
| |
Collapse
|
4
|
Taiwo M, Huang E, Pathak V, Bellar A, Welch N, Dasarathy J, Streem D, McClain CJ, Mitchell MC, Barton BA, Szabo G, Dasarathy S, Schaefer EA, Luther J, Day LZ, Ouyang X, Suyavaran A, Mehal WZ, Jacobs JM, Goodman RP, Rotroff DM, Nagy LE. Proteomics identifies complement protein signatures in patients with alcohol-associated hepatitis. JCI Insight 2024; 9:e174127. [PMID: 38573776 PMCID: PMC11141929 DOI: 10.1172/jci.insight.174127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 03/27/2024] [Indexed: 04/06/2024] Open
Abstract
Diagnostic challenges continue to impede development of effective therapies for successful management of alcohol-associated hepatitis (AH), creating an unmet need to identify noninvasive biomarkers for AH. In murine models, complement contributes to ethanol-induced liver injury. Therefore, we hypothesized that complement proteins could be rational diagnostic/prognostic biomarkers in AH. Here, we performed a comparative analysis of data derived from human hepatic and serum proteome to identify and characterize complement protein signatures in severe AH (sAH). The quantity of multiple complement proteins was perturbed in liver and serum proteome of patients with sAH. Multiple complement proteins differentiated patients with sAH from those with alcohol cirrhosis (AC) or alcohol use disorder (AUD) and healthy controls (HCs). Serum collectin 11 and C1q binding protein were strongly associated with sAH and exhibited good discriminatory performance among patients with sAH, AC, or AUD and HCs. Furthermore, complement component receptor 1-like protein was negatively associated with pro-inflammatory cytokines. Additionally, lower serum MBL associated serine protease 1 and coagulation factor II independently predicted 90-day mortality. In summary, meta-analysis of proteomic profiles from liver and circulation revealed complement protein signatures of sAH, highlighting a complex perturbation of complement and identifying potential diagnostic and prognostic biomarkers for patients with sAH.
Collapse
Affiliation(s)
| | | | - Vai Pathak
- Department of Quantitative Health Sciences, and
| | | | - Nicole Welch
- Department of Inflammation and Immunity
- Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, Ohio, USA
| | - Jaividhya Dasarathy
- Department of Family Medicine, Metro Health Medical Center, Cleveland, Ohio, USA
| | - David Streem
- Department of Psychiatry and Psychology, Cleveland Clinic Lutheran Hospital, Cleveland, Ohio, USA
| | - Craig J. McClain
- Department of Medicine, University of Louisville, Louisville, Kentucky, USA
| | - Mack C. Mitchell
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Bruce A. Barton
- Department of Population and Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Gyongyi Szabo
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Srinivasan Dasarathy
- Department of Inflammation and Immunity
- Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, Ohio, USA
- Department of Molecular Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | | | - Esperance A. Schaefer
- Alcohol Liver Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Jay Luther
- Alcohol Liver Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Le Z. Day
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Xinshou Ouyang
- Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Arumugam Suyavaran
- Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Wajahat Z. Mehal
- Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Jon M. Jacobs
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Russell P. Goodman
- Alcohol Liver Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Endocrine Unit, Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Daniel M. Rotroff
- Department of Quantitative Health Sciences, and
- Endocrine and Metabolism Institute and
- Center for Quantitative Metabolic Research, Cleveland Clinic, Cleveland, Ohio, USA
| | - Laura E. Nagy
- Department of Inflammation and Immunity
- Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, Ohio, USA
- See Supplemental Acknowledgments for information on the AlcHepNet Consortium
| |
Collapse
|
5
|
Lim RR, Shirali S, Rowlan J, Engel AL, Nazario, M, Gonzalez K, Tong A, Neitz J, Neitz M, Chao JR. CFH Haploinsufficiency and Complement Alterations in Early-Onset Macular Degeneration. Invest Ophthalmol Vis Sci 2024; 65:43. [PMID: 38683564 PMCID: PMC11059804 DOI: 10.1167/iovs.65.4.43] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 04/03/2024] [Indexed: 05/01/2024] Open
Abstract
Purpose Complement dysregulation is a key component in the pathogenesis of age-related macular degeneration (AMD) and related diseases such as early-onset macular drusen (EOMD). Although genetic variants of complement factor H (CFH) are associated with AMD risk, the impact of CFH and factor H-like protein 1 (FHL-1) expression on local complement activity in human retinal pigment epithelium (RPE) remains unclear. Methods We identified a novel CFH variant in a family with EOMD and generated patient induced pluripotent stem cell (iPSC)-derived RPE cells. We assessed CFH and FHL-1 co-factor activity through C3b breakdown assays and measured complement activation by immunostaining for membrane attack complex (MAC) formation. Expression of CFH, FHL-1, local alternative pathway (AP) components, and regulators of complement activation (RCA) in EOMD RPE cells was determined by quantitative PCR, western blot, and immunostaining. Isogenic EOMD (cEOMD) RPE was generated using CRISPR/Cas9 gene editing. Results The CFH variant (c.351-2A>G) resulted in loss of CFH and FHL-1 expression and significantly reduced CFH and FHL-1 protein expression (∼50%) in EOMD iPSC RPE cells. These cells exhibited increased MAC deposition upon exposure to normal human serum. Under inflammatory or oxidative stress conditions, CFH and FHL-1 expression in EOMD RPE cells paralleled that of controls, whereas RCA expression, including MAC formation inhibitors, was elevated. CRISPR/Cas9 correction restored CFH/FHL-1 expression and mitigated alternative pathway complement activity in cEOMD RPE cells. Conclusions Identification of a novel CFH variant in patients with EOMD resulting in reduced CFH and FHL-1 and increased local complement activity in EOMD iPSC RPE supports the involvement of CFH haploinsufficiency in EOMD pathogenesis.
Collapse
Affiliation(s)
- Rayne R. Lim
- Department of Ophthalmology, University of Washington, Seattle, Washington, United States
| | - Sharlene Shirali
- Department of Ophthalmology, University of Washington, Seattle, Washington, United States
| | - Jessica Rowlan
- Department of Ophthalmology, University of Washington, Seattle, Washington, United States
| | - Abbi L. Engel
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Institute, Seattle, Washington, United States
| | - Marcos Nazario,
- Department of Ophthalmology, University of Washington, Seattle, Washington, United States
| | - Kelie Gonzalez
- Department of Ophthalmology, University of Washington, Seattle, Washington, United States
| | - Aspen Tong
- Department of Ophthalmology, University of Washington, Seattle, Washington, United States
| | - Jay Neitz
- Department of Ophthalmology, University of Washington, Seattle, Washington, United States
| | - Maureen Neitz
- Department of Ophthalmology, University of Washington, Seattle, Washington, United States
| | - Jennifer R. Chao
- Department of Ophthalmology, University of Washington, Seattle, Washington, United States
- Roger and Angie Karalis Johnson Retina Center, University of Washington School of Medicine, Seattle, Washington, United States
| |
Collapse
|
6
|
Holers VM, Frank RM, Zuscik M, Keeter C, Scheinman RI, Striebich C, Simberg D, Clay MR, Moreland LW, Banda NK. Decay-Accelerating Factor Differentially Associates With Complement-Mediated Damage in Synovium After Meniscus Tear as Compared to Anterior Cruciate Ligament Injury. Immune Netw 2024; 24:e17. [PMID: 38725672 PMCID: PMC11076301 DOI: 10.4110/in.2024.24.e17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 04/01/2024] [Accepted: 04/08/2024] [Indexed: 05/12/2024] Open
Abstract
We have reported that anterior cruciate ligament (ACL) injury leads to the differential dysregulation of the complement system in the synovium as compared to meniscus tear (MT) and proposed this as a mechanism for a greater post-injury prevalence of post traumatic osteoarthritis (PTOA). To explore additional roles of complement proteins and regulators, we determined the presence of decay-accelerating factor (DAF), C5b, and membrane attack complexes (MACs, C5b-9) in discarded surgical synovial tissue (DSST) collected during arthroscopic ACL reconstructive surgery, MT-related meniscectomy, osteoarthritis (OA)-related knee replacement surgery and normal controls. Multiplexed immunohistochemistry was used to detect and quantify complement proteins. To explore the involvement of body mass index (BMI), after these 2 injuries, we examined correlations among DAF, C5b, MAC and BMI. Using these approaches, we found that synovial cells after ACL injury expressed a significantly lower level of DAF as compared to MT (p<0.049). In contrast, C5b staining synovial cells were significantly higher after ACL injury (p<0.0009) and in OA DSST (p<0.039) compared to MT. Interestingly, there were significantly positive correlations between DAF & C5b (r=0.75, p<0.018) and DAF & C5b (r=0.64 p<0.022) after ACL injury and MT, respectively. The data support that DAF, which should normally dampen C5b deposition due to its regulatory activities on C3/C5 convertases, does not appear to exhibit that function in inflamed synovia following either ACL injury or MT. Ineffective DAF regulation may be an additional mechanism by which relatively uncontrolled complement activation damages tissue in these injury states.
Collapse
Affiliation(s)
- V. Michael Holers
- Division of Rheumatology, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Rachel M. Frank
- Department of Orthopedics and the Colorado Program for Musculoskeletal Research, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michael Zuscik
- Department of Orthopedics and the Colorado Program for Musculoskeletal Research, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Carson Keeter
- Department of Orthopedics and the Colorado Program for Musculoskeletal Research, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Robert I. Scheinman
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Christopher Striebich
- Division of Rheumatology, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Dmitri Simberg
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michael R. Clay
- Department of Pathology, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Larry W. Moreland
- Division of Rheumatology, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Orthopedics and the Colorado Program for Musculoskeletal Research, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Nirmal K. Banda
- Division of Rheumatology, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| |
Collapse
|
7
|
Bos JW, Groen EJN, Otten HG, Budding K, van Eijk RPA, Curial C, Kardol-Hoefnagel T, Goedee HS, van den Berg LH, van der Pol WL. A 21-bp deletion in the complement regulator CD55 promotor region is associated with multifocal motor neuropathy and its disease course. J Peripher Nerv Syst 2024. [PMID: 38528725 DOI: 10.1111/jns.12620] [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: 11/21/2023] [Revised: 02/22/2024] [Accepted: 03/04/2024] [Indexed: 03/27/2024]
Abstract
BACKGROUND AND AIMS To further substantiate the role of antibody-mediated complement activation in multifocal motor neuropathy (MMN) immunopathology, we investigated the distribution of promotor polymorphisms of genes encoding the membrane-bound complement regulators CD46, CD55, and CD59 in patients with MMN and controls, and evaluated their association with disease course. METHODS We used Sanger sequencing to genotype five common polymorphisms in the promotor regions of CD46, CD55, and CD59 in 133 patients with MMN and 380 controls. We correlated each polymorphism to clinical parameters. RESULTS The genotype frequencies of rs28371582, a 21-bp deletion in the CD55 promotor region, were altered in patients with MMN as compared to controls (p .009; Del/Del genotype 16.8% vs. 7.7%, p .005, odds ratio: 2.43 [1.27-4.58]), and patients carrying this deletion had a more favorable disease course (mean difference 0.26 Medical Research Council [MRC] points/year; 95% confidence interval [CI]: 0.040-0.490, p .019). The presence of CD59 rs141385724 was associated with less severe pre-diagnostic disease course (mean difference 0.940 MRC point/year; 95% CI: 0.083-1.80, p .032). INTERPRETATION MMN susceptibility is associated with a 21-bp deletion in the CD55 promotor region (rs2871582), which is associated with lower CD55 expression. Patients carrying this deletion may have a more favorable long-term disease outcome. Taken together, these results point out the relevance of the pre-C5 level of the complement cascade in the inflammatory processes underlying MMN.
Collapse
Affiliation(s)
- Jeroen W Bos
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Ewout J N Groen
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Henny G Otten
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Kevin Budding
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Ruben P A van Eijk
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
- Biostatistics & Research Support, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Chantall Curial
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Tineke Kardol-Hoefnagel
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - H Stephan Goedee
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Leonard H van den Berg
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - W Ludo van der Pol
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| |
Collapse
|
8
|
Arredondo-Damián JG, Martínez-Soto JM, Molina-Pelayo FA, Soto-Guzmán JA, Castro-Sánchez L, López-Soto LF, Candia-Plata MDC. Systematic review and bioinformatics analysis of plasma and serum extracellular vesicles proteome in type 2 diabetes. Heliyon 2024; 10:e25537. [PMID: 38356516 PMCID: PMC10865249 DOI: 10.1016/j.heliyon.2024.e25537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/28/2024] [Accepted: 01/29/2024] [Indexed: 02/16/2024] Open
Abstract
Background Type 2 diabetes (T2D) is a complex metabolic ailment marked by a global high prevalence and significant attention in primary healthcare settings due to its elevated morbidity and mortality rates. The pathophysiological mechanisms underlying the onset and progression of this disease remain subjects of ongoing investigation. Recent evidence underscores the pivotal role of the intricate intercellular communication network, wherein cell-derived vesicles, commonly referred to as extracellular vesicles (EVs), emerge as dynamic regulators of diabetes-related complications. Given that the protein cargo carried by EVs is contingent upon the metabolic conditions of the originating cells, particular proteins may serve as informative indicators for the risk of activating or inhibiting signaling pathways crucial to the progression of T2D complications. Methods In this study, we conducted a systematic review to analyze the published evidence on the proteome of EVs from the plasma or serum of patients with T2D, both with and without complications (PROSPERO: CRD42023431464). Results Nine eligible articles were systematically identified from the databases, and the proteins featured in these articles underwent Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. We identified changes in the level of 426 proteins, with CST6, CD55, HBA1, S100A8, and S100A9 reported to have high levels, while FGL1 exhibited low levels. Conclusion These proteins are implicated in pathophysiological mechanisms such as inflammation, complement, and platelet activation, suggesting their potential as risk markers for T2D development and progression. Further studies are required to explore this topic in greater detail.
Collapse
Affiliation(s)
| | | | | | | | - Luis Castro-Sánchez
- University Center for Biomedical Research, University of Colima, Colima, Colima, Mexico
- CONAHCYT-University of Colima, Colima, Colima, Mexico
| | | | | |
Collapse
|
9
|
Hsiung CC, Wilson CM, Sambold NA, Dai R, Chen Q, Misiukiewicz S, Arab A, Teyssier N, O'Loughlin T, Cofsky JC, Shi J, Gilbert LA. Higher-order combinatorial chromatin perturbations by engineered CRISPR-Cas12a for functional genomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.18.558350. [PMID: 37781594 PMCID: PMC10541102 DOI: 10.1101/2023.09.18.558350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Multiplexed genetic perturbations are critical for testing functional interactions among coding or non-coding genetic elements. Compared to double-stranded DNA cutting, repressive chromatin formation using CRISPR interference (CRISPRi) avoids genotoxicity and is more effective for perturbing non-coding regulatory elements in pooled assays. However, current CRISPRi pooled screening approaches are limited to targeting 1-3 genomic sites per cell. To develop a tool for higher-order ( > 3) combinatorial targeting of genomic sites with CRISPRi in functional genomics screens, we engineered an Acidaminococcus Cas12a variant -- referred to as mul tiplexed transcriptional interference AsCas12a (multiAsCas12a). multiAsCas12a incorporates a key mutation, R1226A, motivated by the hypothesis of nicking-induced stabilization of the ribonucleoprotein:DNA complex for improving CRISPRi activity. multiAsCas12a significantly outperforms prior state-of-the-art Cas12a variants in combinatorial CRISPRi targeting using high-order multiplexed arrays of lentivirally transduced CRISPR RNAs (crRNA), including in high-throughput pooled screens using 6-plex crRNA array libraries. Using multiAsCas12a CRISPRi, we discover new enhancer elements and dissect the combinatorial function of cis-regulatory elements. These results instantiate a group testing framework for efficiently surveying potentially numerous combinations of chromatin perturbations for biological discovery and engineering.
Collapse
|
10
|
Liu D, Winer BY, Chou MY, Tam H, Xu Y, An J, Gardner JM, Cyster JG. Dynamic encounters with red blood cells trigger splenic marginal zone B cell retention and function. Nat Immunol 2024; 25:142-154. [PMID: 38049580 PMCID: PMC10761324 DOI: 10.1038/s41590-023-01690-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 10/24/2023] [Indexed: 12/06/2023]
Abstract
Spleen marginal zone (MZ) B cells are important for antibody responses against blood-borne antigens. The signals they use to detect exposure to blood are not well defined. Here, using intravital two-photon microscopy in mice, we observe transient contacts between MZ B cells and red blood cells that are in flow. We show that MZ B cells use adhesion G-protein-coupled receptor ADGRE5 (CD97) for retention in the spleen. CD97 function in MZ B cells depends on its ability to undergo autoproteolytic cleavage and signaling via Gα13 and ARHGEF1. Red blood cell expression of the CD97 ligand CD55 is required for MZ B cell homeostasis. Applying a pulling force on CD97-transfected cells using an optical C-trap and CD55+ beads leads to accumulation of active RhoA and membrane retraction. Finally, we show that CD97 deficiency leads to a reduced T cell-independent IgM response. Thus, our studies provide evidence that MZ B cells use mechanosensing to position in a manner that enhances antibody responses against blood-borne antigens.
Collapse
Affiliation(s)
- Dan Liu
- Howard Hughes Medical Institute and Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA.
- Westlake Laboratory of Life Sciences and Biomedicine, Westlake University School of Life Sciences, Institute of Basic Medical Sciences and Westlake Institute for Advanced Study, Hangzhou, China.
| | - Benjamin Y Winer
- Howard Hughes Medical Institute and Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marissa Y Chou
- Howard Hughes Medical Institute and Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Hanson Tam
- Howard Hughes Medical Institute and Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Ying Xu
- Howard Hughes Medical Institute and Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Jinping An
- Howard Hughes Medical Institute and Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - James M Gardner
- Diabetes Center and Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Jason G Cyster
- Howard Hughes Medical Institute and Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA.
| |
Collapse
|
11
|
Kashyap MP, Mishra B, Sinha R, Jin L, Kumar N, Goliwas KF, Deshane J, Elewski BE, Elmets CA, Athar M, Shahid Mukhtar M, Raman C. NK and NKT cells in the pathogenesis of Hidradenitis suppurativa: Novel therapeutic strategy through targeting of CD2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.31.565057. [PMID: 37961206 PMCID: PMC10634971 DOI: 10.1101/2023.10.31.565057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Hidradenitis suppurativa (HS) is a chronic debilitating inflammatory skin disease with poorly understood pathogenesis. Single-cell RNAseq analysis of HS lesional and healthy individual skins revealed that NKT and NK cell populations were greatly expanded in HS, and they expressed elevated CD2, an activation receptor. Immunohistochemistry analyses confirmed significantly expanded numbers of CD2+ cells distributed throughout HS lesional tissue, and many co-expressed the NK marker, CD56. While CD4+ T cells were expanded in HS, CD8 T cells were rare. CD20+ B cells in HS were localized within tertiary follicle like structures. Immunofluorescence microscopy showed that NK cells (CD2 + CD56 dim ) expressing perforin, granzymes A and B were enriched within the hyperplastic follicular epidermis and tunnels of HS and juxtaposed with apoptotic cells. In contrast, NKT cells (CD2 + CD3 + CD56 bright ) primarily expressed granzyme A and were associated with α-SMA expressing fibroblasts within the fibrotic regions of the hypodermis. Keratinocytes and fibroblasts expressed high levels of CD58 (CD2 ligand) and they interacted with CD2 expressing NKT and NK cells. The NKT/NK maturation and activating cytokines, IL-12, IL-15 and IL-18, were significantly elevated in HS. Inhibition of cognate CD2-CD58 interaction with blocking anti-CD2 mAb in HS skin organotypic cultures resulted in a profound reduction of the inflammatory gene signature and secretion of inflammatory cytokines and chemokines in the culture supernate. In summary, we show that a cellular network of heterogenous NKT and NK cell populations drives inflammation, tunnel formation and fibrosis in the pathogenesis of HS. Furthermore, CD2 blockade is a viable immunotherapeutic approach for the management of HS.
Collapse
|
12
|
Lee SM, Min SW, Kwon HS, Bae GD, Jung JH, Park HI, Lee SH, Lim CS, Ko BJ, Lee JC, Jung ST. Effective clearance of rituximab-resistant tumor cells by breaking the mirror-symmetry of immunoglobulin G and simultaneous binding to CD55 and CD20. Sci Rep 2023; 13:18275. [PMID: 37880350 PMCID: PMC10600224 DOI: 10.1038/s41598-023-45491-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 10/19/2023] [Indexed: 10/27/2023] Open
Abstract
Complement-dependent cytotoxicity (CDC), which eliminates aberrant target cells through the assembly and complex formation of serum complement molecules, is one of the major effector functions of anticancer therapeutic antibodies. In this study, we discovered that breaking the symmetry of natural immunoglobulin G (IgG) antibodies significantly increased the CDC activity of anti-CD20 antibodies. In addition, the expression of CD55 (a checkpoint inhibitor in the CDC cascade) was significantly increased in a rituximab-resistant cell line generated in-house, suggesting that CD55 overexpression might be a mechanism by which cancer cells acquire rituximab resistance. Based on these findings, we developed an asymmetric bispecific antibody (SBU-CD55 × CD20) that simultaneously targets both CD55 and CD20 to effectively eliminate rituximab-resistant cancer cells. In various cancer cell lines, including rituximab-resistant lymphoma cells, the SBU-CD55 × CD20 antibody showed significantly higher CDC activity than either anti-CD20 IgG antibody alone or a combination of anti-CD20 IgG antibody and anti-CD55 IgG antibody. Furthermore, the asymmetric bispecific antibody (SBU-CD55 × CD20) exhibited significantly higher CDC activity against rituximab-resistant cancer cells compared to other bispecific antibodies with symmetric features. These results demonstrate that enhancing CDC with an asymmetric CD55-binding bispecific antibody could be a new strategy for developing therapeutics to treat patients with relapsed or refractory cancers.
Collapse
Affiliation(s)
- Sang Min Lee
- Department of Biomedical Sciences, Graduate School of Medicine, Korea University, 73 Goryeodae-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
- Department of Applied Chemistry, Kookmin University, 77, Jeongneung-ro, Seongbuk-gu, Seoul, 02707, Republic of Korea
| | - Sung-Won Min
- SG Medical, 3-11, Ogeum-ro 13-gil, Songpa-gu, Seoul, 05548, Republic of Korea
| | - Hyeong Sun Kwon
- SG Medical, 3-11, Ogeum-ro 13-gil, Songpa-gu, Seoul, 05548, Republic of Korea
| | - Gong-Deuk Bae
- SG Medical, 3-11, Ogeum-ro 13-gil, Songpa-gu, Seoul, 05548, Republic of Korea
| | - Ji Hae Jung
- SG Medical, 3-11, Ogeum-ro 13-gil, Songpa-gu, Seoul, 05548, Republic of Korea
| | - Hye In Park
- SG Medical, 3-11, Ogeum-ro 13-gil, Songpa-gu, Seoul, 05548, Republic of Korea
| | - Seung Hyeon Lee
- Department of Biomedical Sciences, Graduate School of Medicine, Korea University, 73 Goryeodae-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Chung Su Lim
- New Drug Development Center, Osong Medical Innovation Foundation 123, Cheongju, Chungcheongbuk-do, 28160, Republic of Korea
| | - Byoung Joon Ko
- School of Biopharmaceutical and Medical Science, Sungshin Women's University, 55, Dobonng-Ro 76ga-gil, Gangbuk, Seoul, 01133, Republic of Korea
| | - Ji Chul Lee
- SG Medical, 3-11, Ogeum-ro 13-gil, Songpa-gu, Seoul, 05548, Republic of Korea.
| | - Sang Taek Jung
- Department of Biomedical Sciences, Graduate School of Medicine, Korea University, 73 Goryeodae-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea.
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea.
- Institute of Human Genetics, Korea University College of Medicine, Seoul, 02841, Republic of Korea.
- Biomedical Research Center, Korea University Anam Hospital, Seoul, 02841, Republic of Korea.
| |
Collapse
|
13
|
Frost I, Mendoza AM, Chiou TT, Kim P, Aizenberg J, Kohn DB, De Oliveira SN, Weiss PS, Jonas SJ. Fluorinated Silane-Modified Filtroporation Devices Enable Gene Knockout in Human Hematopoietic Stem and Progenitor Cells. ACS APPLIED MATERIALS & INTERFACES 2023; 15:41299-41309. [PMID: 37616579 PMCID: PMC10485797 DOI: 10.1021/acsami.3c07045] [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: 05/16/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023]
Abstract
Intracellular delivery technologies that are cost-effective, non-cytotoxic, efficient, and cargo-agnostic are needed to enable the manufacturing of cell-based therapies as well as gene manipulation for research applications. Current technologies capable of delivering large cargoes, such as plasmids and CRISPR-Cas9 ribonucleoproteins (RNPs), are plagued with high costs and/or cytotoxicity and often require substantial specialized equipment and reagents, which may not be available in resource-limited settings. Here, we report an intracellular delivery technology that can be assembled from materials available in most research laboratories, thus democratizing access to intracellular delivery for researchers and clinicians in low-resource areas of the world. These filtroporation devices permeabilize cells by pulling them through the pores of a cell culture insert by the application of vacuum available in biosafety cabinets. In a format that costs less than $10 in materials per experiment, we demonstrate the delivery of fluorescently labeled dextran, expression plasmids, and RNPs for gene knockout to Jurkat cells and human CD34+ hematopoietic stem and progenitor cell populations with delivery efficiencies of up to 40% for RNP knockout and viabilities of >80%. We show that functionalizing the surfaces of the filters with fluorinated silane moieties further enhances the delivery efficiency. These devices are capable of processing 500,000 to 4 million cells per experiment, and when combined with a 3D-printed vacuum application chamber, this throughput can be straightforwardly increased 6-12-fold in parallel experiments.
Collapse
Affiliation(s)
- Isaura
M. Frost
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
- UCLA
Medical Scientist Training Program, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department
of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Alexandra M. Mendoza
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los
Angeles, California 90095, United States
- California
NanoSystems Institute, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Tzu-Ting Chiou
- Department
of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Philseok Kim
- John A. Paulson
School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Joanna Aizenberg
- John A. Paulson
School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Donald B. Kohn
- Department
of Molecular and Medical Pharmacology, University
of California, Los Angeles, Los
Angeles, California 90095, United States
- Department
of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, California 90095, United States
- Eli
and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Satiro N. De Oliveira
- Department
of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Paul S. Weiss
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los
Angeles, California 90095, United States
- California
NanoSystems Institute, University of California,
Los Angeles, Los Angeles, California 90095, United States
- Department
of Materials Science and Engineering, University
of California, Los Angeles, Los
Angeles, California 90095, United States
| | - Steven J. Jonas
- Department
of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
- California
NanoSystems Institute, University of California,
Los Angeles, Los Angeles, California 90095, United States
- Eli
and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, California 90095, United States
- Children’s
Discovery and Innovation Institute, University
of California, Los Angeles, Los
Angeles, California 90095, United States
| |
Collapse
|
14
|
Chen C, Ren A, Yi Q, Cai J, Khan M, Lin Y, Huang Z, Lin J, Zhang J, Liu W, Xu A, Tian Y, Yuan Y, Zheng R. Therapeutic hyperthermia regulates complement C3 activation and suppresses tumor development through HSPA5/NFκB/CD55 pathway in nasopharyngeal carcinoma. Clin Exp Immunol 2023; 213:221-234. [PMID: 37249005 PMCID: PMC10361742 DOI: 10.1093/cei/uxad060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 04/09/2023] [Accepted: 05/29/2023] [Indexed: 05/31/2023] Open
Abstract
Nasopharyngeal carcinoma (NPC) is endemic in Southern China and Southeast Asia. Hyperthermia is widely used in combination with chemotherapy and radiotherapy to enhance therapeutic efficacy in NPC treatment, but the underlying anti-tumor mechanisms of hyperthermia remain unclear. Complement C3 has been reported to participate in the activation of immune system in the tumor microenvironment, leading to tumor growth inhibition. In this study, we aimed to explore the effect and mechanisms of hyperthermia and investigate the functional role of complement C3 in NPC hyperthermia therapy (HT). The serum levels of complement C3 before and after hyperthermia therapy in patients with NPC were analyzed. NPC cell lines SUNE1 and HONE1 were used for in vitro experiment to evaluate the function of complement C3 and HT on cell proliferation and apoptosis. SUNE1 xenograft mouse model was established and tumor-bearing mice were treated in water bath at a constant temperature of 43°C. Tumor samples were collected at different time points to verify the expression of complement C3 by immunohistochemical staining and western blot. The differential expressed genes after hyperthermia were analyzed by using RNA sequencing. We found that complement could enhance hyperthermia effect on suppressing proliferation and promoting apoptosis of tumor cells in NPC. Hyperthermia decreased the mRNA expression of complement C3 in tumor cells, but promoted the aggregation and activation circulating C3 in NPC tumor tissue. By using in vitro hyperthermia-treated NPC cell lines and SUNE1 xenograft tumor-bearing mice, we found that the expression of heat shock protein 5 (HSPA5) was significantly upregulated. Knockdown of HSPA5 abrogated the anti-tumor effect of hyperthermia. Moreover, we demonstrated that hyperthermia downregulated CD55 expression via HSPA5/NFκB (P65) signaling and activated complement cascade. Our findings suggest that therapeutic hyperthermia regulates complement C3 activation and suppresses tumor development via HSPA5/NFκB/CD55 pathway in NPC.
Collapse
Affiliation(s)
- Chengcong Chen
- Department of Radiation Oncology, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Anbang Ren
- Department of Radiation Oncology, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Qi Yi
- Department of Radiation Oncology, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Jiazuo Cai
- Department of Radiation Oncology, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Muhammad Khan
- Department of Radiation Oncology, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Yunen Lin
- Department of Pathology, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Zhong Huang
- Department of Radiation Oncology, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Jie Lin
- Department of Radiation Oncology, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Jian Zhang
- Department of Radiation Oncology, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Wei Liu
- Department of Radiation Oncology, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Anan Xu
- Department of Radiation Oncology, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Yunhong Tian
- Department of Radiation Oncology, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - YaWei Yuan
- Department of Radiation Oncology, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Ronghui Zheng
- Department of Radiation Oncology, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| |
Collapse
|
15
|
van Kuijk K, McCracken IR, Tillie RJHA, Asselberghs SEJ, Kheder DA, Muitjens S, Jin H, Taylor RS, Wichers Schreur R, Kuppe C, Dobie R, Ramachandran P, Gijbels MJ, Temmerman L, Kirkwoord PM, Luyten J, Li Y, Noels H, Goossens P, Wilson-Kanamori JR, Schurgers LJ, Shen YH, Mees BME, Biessen EAL, Henderson NC, Kramann R, Baker AH, Sluimer JC. Human and murine fibroblast single-cell transcriptomics reveals fibroblast clusters are differentially affected by ageing and serum cholesterol. Cardiovasc Res 2023; 119:1509-1523. [PMID: 36718802 PMCID: PMC10318398 DOI: 10.1093/cvr/cvad016] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 10/21/2022] [Accepted: 11/04/2022] [Indexed: 02/01/2023] Open
Abstract
AIMS Specific fibroblast markers and in-depth heterogeneity analysis are currently lacking, hindering functional studies in cardiovascular diseases (CVDs). Here, we established cell-type markers and heterogeneity in murine and human arteries and studied the adventitial fibroblast response to CVD and its risk factors hypercholesterolaemia and ageing. METHODS AND RESULTS Murine aorta single-cell RNA-sequencing analysis of adventitial mesenchymal cells identified fibroblast-specific markers. Immunohistochemistry and flow cytometry validated platelet-derived growth factor receptor alpha (PDGFRA) and dipeptidase 1 (DPEP1) across human and murine aorta, carotid, and femoral arteries, whereas traditional markers such as the cluster of differentiation (CD)90 and vimentin also marked transgelin+ vascular smooth muscle cells. Next, pseudotime analysis showed multiple fibroblast clusters differentiating along trajectories. Three trajectories, marked by CD55 (Cd55+), Cxcl chemokine 14 (Cxcl14+), and lysyl oxidase (Lox+), were reproduced in an independent RNA-seq dataset. Gene ontology (GO) analysis showed divergent functional profiles of the three trajectories, related to vascular development, antigen presentation, and/or collagen fibril organization, respectively. Trajectory-specific genes included significantly more genes with known genome-wide associations (GWAS) to CVD than expected by chance, implying a role in CVD. Indeed, differential regulation of fibroblast clusters by CVD risk factors was shown in the adventitia of aged C57BL/6J mice, and mildly hypercholesterolaemic LDLR KO mice on chow by flow cytometry. The expansion of collagen-related CXCL14+ and LOX+ fibroblasts in aged and hypercholesterolaemic aortic adventitia, respectively, coincided with increased adventitial collagen. Immunohistochemistry, bulk, and single-cell transcriptomics of human carotid and aorta specimens emphasized translational value as CD55+, CXCL14+ and LOX+ fibroblasts were observed in healthy and atherosclerotic specimens. Also, trajectory-specific gene sets are differentially correlated with human atherosclerotic plaque traits. CONCLUSION We provide two adventitial fibroblast-specific markers, PDGFRA and DPEP1, and demonstrate fibroblast heterogeneity in health and CVD in humans and mice. Biological relevance is evident from the regulation of fibroblast clusters by age and hypercholesterolaemia in vivo, associations with human atherosclerotic plaque traits, and enrichment of genes with a GWAS for CVD.
Collapse
Affiliation(s)
- Kim van Kuijk
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- Institute of Experimental Medicine and Systems Biology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Ian R McCracken
- BHF Centre for Cardiovascular Sciences (CVS), Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Renée J H A Tillie
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Sebastiaan E J Asselberghs
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- Department of Vascular Surgery, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Dlzar A Kheder
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Stan Muitjens
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Han Jin
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Richard S Taylor
- BHF Centre for Cardiovascular Sciences (CVS), Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Ruud Wichers Schreur
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Christoph Kuppe
- Institute of Experimental Medicine and Systems Biology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
- Division of Nephrology and Clinical Immunology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Ross Dobie
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | - Prakesh Ramachandran
- Department of Medical Biochemistry, Experimental Vascular Biology, Amsterdam UMC, Amsterdam, The Netherlands
| | - Marion J Gijbels
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- Department of Medical Biochemistry, Experimental Vascular Biology, Amsterdam UMC, Amsterdam, The Netherlands
- GROW, School for Oncology and Development Biology, Maastricht University, Maastricht, The Netherlands
| | - Lieve Temmerman
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Phoebe M Kirkwoord
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | - Joris Luyten
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- Department of Vascular Surgery, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Yanming Li
- Division of Cardiothoracic Surgery, Baylor College of Medicine, Houston, TX, USA
- Department of Cardiovascular Surgery, Texas Heart Institute, Houston, TX, USA
| | - Heidi Noels
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Pieter Goossens
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
| | - John R Wilson-Kanamori
- Division of Nephrology and Clinical Immunology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Leon J Schurgers
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- Institute of Experimental Medicine and Systems Biology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Ying H Shen
- Division of Cardiothoracic Surgery, Baylor College of Medicine, Houston, TX, USA
- Department of Cardiovascular Surgery, Texas Heart Institute, Houston, TX, USA
| | - Barend M E Mees
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- Department of Vascular Surgery, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Erik A L Biessen
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- Institute for Molecular Cardiovascular Research, RWTH Aachen University, Aachen, Germany
| | - Neil C Henderson
- Division of Nephrology and Clinical Immunology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Rafael Kramann
- Institute of Experimental Medicine and Systems Biology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
- Department of Vascular Surgery, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Andrew H Baker
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- BHF Centre for Cardiovascular Sciences (CVS), Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Judith C Sluimer
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- BHF Centre for Cardiovascular Sciences (CVS), Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| |
Collapse
|
16
|
Gaykema LH, van Nieuwland RY, Dekkers MC, van Essen MF, Heidt S, Zaldumbide A, van den Berg CW, Rabelink TJ, van Kooten C. Inhibition of complement activation by CD55 overexpression in human induced pluripotent stem cell derived kidney organoids. Front Immunol 2023; 13:1058763. [PMID: 36713440 PMCID: PMC9880527 DOI: 10.3389/fimmu.2022.1058763] [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: 09/30/2022] [Accepted: 12/12/2022] [Indexed: 01/15/2023] Open
Abstract
End stage renal disease is an increasing problem worldwide driven by aging of the population and increased prevalence of metabolic disorders and cardiovascular disease. Currently, kidney transplantation is the only curative option, but donor organ shortages greatly limit its application. Regenerative medicine has the potential to solve the shortage by using stem cells to grow the desired tissues, like kidney tissue. Immune rejection poses a great threat towards the implementation of stem cell derived tissues and various strategies have been explored to limit the immune response towards these tissues. However, these studies are limited by targeting mainly T cell mediated immune rejection while the rejection process also involves innate and humoral immunity. In this study we investigate whether inhibition of the complement system in human induced pluripotent stem cells (iPSC) could provide protection from such immune injury. To this end we created knock-in iPSC lines of the membrane bound complement inhibitor CD55 to create a transplant-specific protection towards complement activation. CD55 inhibits the central driver of the complement cascade, C3 convertase, and we show that overexpression is able to decrease complement activation on both iPSCs as well as differentiated kidney organoids upon stimulation with anti-HLA antibodies to mimic the mechanism of humoral rejection.
Collapse
Affiliation(s)
- Lonneke H. Gaykema
- Department of Internal Medicine-Nephrology, Leiden University Medical Center, Leiden, Netherlands,Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Rianne Y. van Nieuwland
- Department of Internal Medicine-Nephrology, Leiden University Medical Center, Leiden, Netherlands
| | - Mette C. Dekkers
- Department of Internal Medicine-Nephrology, Leiden University Medical Center, Leiden, Netherlands
| | - Mieke F. van Essen
- Department of Internal Medicine-Nephrology, Leiden University Medical Center, Leiden, Netherlands
| | - Sebastiaan Heidt
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands,Eurotransplant Reference Laboratory, Leiden University Medical Center, Leiden, Netherlands
| | - Arnaud Zaldumbide
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Cathelijne W. van den Berg
- Department of Internal Medicine-Nephrology, Leiden University Medical Center, Leiden, Netherlands,The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, Netherlands
| | - Ton J. Rabelink
- Department of Internal Medicine-Nephrology, Leiden University Medical Center, Leiden, Netherlands,The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, Netherlands,*Correspondence: Ton J. Rabelink,
| | - Cees van Kooten
- Department of Internal Medicine-Nephrology, Leiden University Medical Center, Leiden, Netherlands
| |
Collapse
|
17
|
Short MI, Fohner AE, Skjellegrind HK, Beiser A, Gonzales MM, Satizabal CL, Austin TR, Longstreth W, Bis JC, Lopez O, Hveem K, Selbæk G, Larson MG, Yang Q, Aparicio HJ, McGrath ER, Gerszten RE, DeCarli CS, Psaty BM, Vasan RS, Zare H, Seshadri S. Proteome Network Analysis Identifies Potential Biomarkers for Brain Aging. J Alzheimers Dis 2023; 96:1767-1780. [PMID: 38007645 PMCID: PMC10741337 DOI: 10.3233/jad-230145] [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] [Accepted: 10/04/2023] [Indexed: 11/27/2023]
Abstract
BACKGROUND Alzheimer's disease and related dementias (ADRD) involve biological processes that begin years to decades before onset of clinical symptoms. The plasma proteome can offer insight into brain aging and risk of incident dementia among cognitively healthy adults. OBJECTIVE To identify biomarkers and biological pathways associated with neuroimaging measures and incident dementia in two large community-based cohorts by applying a correlation-based network analysis to the plasma proteome. METHODS Weighted co-expression network analysis of 1,305 plasma proteins identified four modules of co-expressed proteins, which were related to MRI brain volumes and risk of incident dementia over a median 20-year follow-up in Framingham Heart Study (FHS) Offspring cohort participants (n = 1,861). Analyses were replicated in the Cardiovascular Health Study (CHS) (n = 2,117, mean 6-year follow-up). RESULTS Two proteomic modules, one related to protein clearance and synaptic maintenance (M2) and a second to inflammation (M4), were associated with total brain volume in FHS (M2: p = 0.014; M4: p = 4.2×10-5). These modules were not significantly associated with hippocampal volume, white matter hyperintensities, or incident all-cause or AD dementia. Associations with TCBV did not replicate in CHS, an older cohort with a greater burden of comorbidities. CONCLUSIONS Proteome networks implicate an early role for biological pathways involving inflammation and synaptic function in preclinical brain atrophy, with implications for clinical dementia.
Collapse
Affiliation(s)
- Meghan I. Short
- Glenn Biggs Institute for Alzheimer’s & Neurodegenerative Diseases, University of Texas Health Science Center, San Antonio, TX, USA
- Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, MA, USA
- Department of Medicine, Tufts University School of Medicine, Boston, MA, USA
| | - Alison E. Fohner
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
| | - Håvard K. Skjellegrind
- HUNT Research Centre, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, Levanger, Norway
- Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
| | - Alexa Beiser
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Mitzi M. Gonzales
- Glenn Biggs Institute for Alzheimer’s & Neurodegenerative Diseases, University of Texas Health Science Center, San Antonio, TX, USA
- Department of Neurology, University of Texas Health Science Center, San Antonio, TX, USA
| | - Claudia L. Satizabal
- Glenn Biggs Institute for Alzheimer’s & Neurodegenerative Diseases, University of Texas Health Science Center, San Antonio, TX, USA
- Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- Department of Population Health Sciences, University of Texas Health Science Center, San Antonio, TX, USA
| | - Thomas R. Austin
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
| | - W.T. Longstreth
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Neurology, University of Washington, Seattle, WA, USA
| | - Joshua C. Bis
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
| | - Oscar Lopez
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kristian Hveem
- HUNT Research Centre, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, Levanger, Norway
- K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Geir Selbæk
- Norwegian National Centre for Ageing and Health, Vestfold Hospital Trust, Tønsberg, Norway
- Department of Geriatric Medicine, Oslo University Hospital, Oslo, Norway
| | - Martin G. Larson
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Qiong Yang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Hugo J. Aparicio
- Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Emer R. McGrath
- Framingham Heart Study, Framingham, MA, USA
- School of Medicine, National University of Ireland Galway, Galway, Ireland
- HRB Clinical Research Facility, National University of Ireland Galway, Galway, Ireland
| | - Robert E. Gerszten
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Charles S. DeCarli
- Department of Neurology, School of Medicine and Imaging of Dementia and Aging Laboratory, Center for Neuroscience, University of California, Davis, Sacramento, CA, USA
| | - Bruce M. Psaty
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Ramachandran S. Vasan
- Framingham Heart Study, Framingham, MA, USA
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
- Boston University Center for Computing and Data Science, Boston, MA, USA
| | - Habil Zare
- Glenn Biggs Institute for Alzheimer’s & Neurodegenerative Diseases, University of Texas Health Science Center, San Antonio, TX, USA
- Department of Cell Systems and Anatomy, University of Texas Health Science Center, San Antonio, TX, USA
| | - Sudha Seshadri
- Glenn Biggs Institute for Alzheimer’s & Neurodegenerative Diseases, University of Texas Health Science Center, San Antonio, TX, USA
- Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| |
Collapse
|
18
|
Bharti R, Dey G, Lin F, Lathia J, Reizes O. CD55 in cancer: Complementing functions in a non-canonical manner. Cancer Lett 2022; 551:215935. [PMID: 36216147 PMCID: PMC11019835 DOI: 10.1016/j.canlet.2022.215935] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 11/02/2022]
Abstract
CD55, or decay accelerating factor, is a membrane lipid microdomain-associated, GPI-anchored protein implicated in the shielding of cells from complement-mediated attack via accelerating decay of C3 and C5. Loss of CD55 is associated with a number of pathologies due to hyperactivation of the complement system. CD55 is also implicated in cancer progression thought to be driven via its role in cell shielding mechanisms. We now appreciate that CD55 can signal intracellularly to promote malignant transformation, cancer progression, cell survival, angiogenesis, and inhibition of apoptosis. Outside-in signaling via CD55 is mediated by signaling pathways including JNK, JAK/STAT, MAPK/NF-κB, and LCK. Moreover, CD55 is enriched in the cancer stem cell (CSC) niche of multiple tumors including breast, ovarian, cervical, and can be induced by chemotherapeutics and hypoxic environments. CSCs are implicated in tumor recurrence and chemoresistance. Here, we review the unexpected roles of CD55 in cancer including the roles of canonical and noncanonical pathways that CD55 orchestrates. We will highlight opportunities for therapeutic targeting CD55 and gaps in the field that require more in-depth mechanistic insights.
Collapse
Affiliation(s)
- Rashmi Bharti
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Goutam Dey
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Feng Lin
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Justin Lathia
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Case Comprehensive Cancer Center, Cleveland, OH, USA
| | - Ofer Reizes
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Case Comprehensive Cancer Center, Cleveland, OH, USA.
| |
Collapse
|
19
|
Guan B, Chai Y, Amantai X, Chen X, Cao X, Yue X. A new sight to explore site-specific N-glycosylation in donkey colostrum milk fat globule membrane proteins with glycoproteomics analysis. Food Res Int 2022; 162:111938. [DOI: 10.1016/j.foodres.2022.111938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/10/2022] [Accepted: 09/12/2022] [Indexed: 11/04/2022]
|
20
|
3D analysis of CROMER (DAF) and a new antigen CRAG. BLOOD TRANSFUSION = TRASFUSIONE DEL SANGUE 2022; 20:483-488. [PMID: 35175190 PMCID: PMC9726615 DOI: 10.2450/2022.0285-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 01/17/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Cromer antigens are carried on decay accelerating factor (DAF, CD55), for which the crystal structure is available. We investigated two samples with an unidentified antibody to a high prevalence antigen and evaluate the location and characteristics of amino acids associated with antigens on the CD55 by 3D modelling. MATERIALS AND METHODS Antigen typing and antibody identification were by standard methods. CD55 was sequenced, and Cromer variants were generated using the protein's crystal structure (1OK3, chain A). Antigen-associated residues and intraprotein interactions were investigated in 3D (Naccess, Protein Interactions Calculator). RESULTS The antibody in the sample from a woman of Kashmiri descent was identified as anti-IFC (anti-CROM7). Her RBCs were negative for high-prevalence Cromer antigens including IFC. CD55 sequencing revealed a silent c.147G>A (p.Leu49=) and c.148G>T (p.Glu50Ter) changes, designated CROM*01N.05. The antibody in the sample from a woman of Greek ancestry was only compatible with IFC- RBCs but her RBCs were positive for known high-prevalence Cromer antigens. CD55 sequencing found she was homozygous for c.173A>G (p.Asp58Gly). The high prevalence antigen was named CRAG (ISBT CROM18 or 021018) and the allele designated CROM*01.-18. By 3D analysis, all known antigen-associated residues, including the new CRAG antigen, were exposed at the protein surface. Interactions between antigen-associated residues within the same CD55 domains were identified. DISCUSSION Identification of antibodies to high prevalence Cromer antigens can be challenging. The surface exposure of antigen-associated residues likely accounts for their immunogenicity. 3D analysis of CD55 provides insight into previous serologic observations regarding the influence of some Cromer antigens on the expression of others.
Collapse
|
21
|
Xu X, Zhang W, Gao H, Tan Y, Guo Y, He T. Polyadenylate-binding protein cytoplasmic 1 mediates alternative splicing events of immune-related genes in gastric cancer cells. Exp Biol Med (Maywood) 2022; 247:1907-1916. [PMID: 36112850 PMCID: PMC9742748 DOI: 10.1177/15353702221121631] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Polyadenylate-binding protein cytoplasmic 1 (PABPC1) is dysregulated in malignancies, which is considered as a potential therapeutic target for many cancer types. By alternative splicing (AS) for gastric cancer (GC), we described PABPC1-modulated AS events in this study. PABPC1 expression was analyzed in 408 GC tissues from The Cancer Genome Altas (TCGA) database. Human gastric adenocarcinoma (AGS) cells were transfected with PABPC1-specific small interfering RNA (siPABPC1) with siCtrl as a negative control. Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) was done for the determination of transcripts. To detect the differentially expressed genes (DEGs) and 10 different types of AS events, RNA sequencing (RNA-seq) was performed. DEGs were analyzed for functional categories including gene ontology, and the Kyoto encyclopedia of genes and genomes pathway were analyzed for DEGs. GC displayed an elevated expression of PABPC1. PABPC1 was efficiently knocked down in AGS cells. Here, we excavated 1234 PABPC1-regulated DEGs, among which 502 were down-regulated and 732 were up-regulated compared to the siCtrl group. A total of 94 DEGs were involved in inflammation and immune response. Results from qRT-PCR validated the up-regulation of 10 immune and inflammation-related DEGs in the siPABPC1 group. PABPC1 deficiency causes 1304 AS events differentially occurred in AGS cells. The most common type of AS events regulated by PABPC2 is alternative 5' splice sites. qRT-PCR confirmed the transcription level of five immune-related genes, in which AS events were detected in the siPABPC1 group. PABPC1 knockdown mediates AS events and thus the transcript level of immune and inflammation-related genes in AGS cells. PABPC1-regulated oncogenic AS events display potential as targets for therapeutic development.
Collapse
|
22
|
Kaneko K, Zaitoun AM, Letley DP, Rhead JL, Torres J, Spendlove I, Atherton JC, Robinson K. The active form of Helicobacter pylori vacuolating cytotoxin induces decay-accelerating factor CD55 in association with intestinal metaplasia in the human gastric mucosa. J Pathol 2022; 258:199-209. [PMID: 35851954 PMCID: PMC9543990 DOI: 10.1002/path.5990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 06/27/2022] [Accepted: 07/15/2022] [Indexed: 11/19/2022]
Abstract
High-level expression of decay-accelerating factor, CD55, has previously been found in human gastric cancer (GC) and intestinal metaplasia (IM) tissues. Therapeutic effects of CD55 inhibition in cancer have been reported. However, the role of Helicobacter pylori infection and virulence factors in the induction of CD55 and its association with histological changes of the human gastric mucosa remain incompletely understood. We hypothesised that CD55 would be increased during infection with more virulent strains of H. pylori, and with more marked gastric mucosal pathology. RT-qPCR and immunohistochemical analyses of gastric biopsy samples from 42 H. pylori-infected and 42 uninfected patients revealed that CD55 mRNA and protein were significantly higher in the gastric antrum of H. pylori-infected patients, and this was associated with the presence of IM, but not atrophy, or inflammation. Increased gastric CD55 and IM were both linked with colonisation by vacA i1-type strains independently of cagA status, and in vitro studies using isogenic mutants of vacA confirmed the ability of VacA to induce CD55 and sCD55 in gastric epithelial cell lines. siRNA experiments to investigate the function of H. pylori-induced CD55 showed that CD55 knockdown in gastric epithelial cells partially reduced IL-8 secretion in response to H. pylori, but this was not due to modulation of bacterial adhesion or cytotoxicity. Finally, plasma samples taken from the same patients were analysed for the soluble form of CD55 (sCD55) by ELISA. sCD55 levels were not influenced by IM and did not correlate with gastric CD55 mRNA levels. These results suggest a new link between active vacA i1-type H. pylori, IM, and CD55, and identify CD55 as a molecule of potential interest in the management of IM as well as GC treatment. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
Collapse
Affiliation(s)
- Kazuyo Kaneko
- Nottingham Digestive Diseases Biomedical Research CentreNottingham University Hospitals NHS Trust and University of NottinghamNottinghamUK
| | - Abed M Zaitoun
- Department of Cellular PathologyNottingham University Hospitals NHS Trust, Queen's Medical Centre CampusNottinghamUK
| | - Darren P Letley
- Nottingham Digestive Diseases Biomedical Research CentreNottingham University Hospitals NHS Trust and University of NottinghamNottinghamUK
| | - Joanne L Rhead
- Nottingham Digestive Diseases Biomedical Research CentreNottingham University Hospitals NHS Trust and University of NottinghamNottinghamUK
| | - Javier Torres
- Unidad de Investigación en Enfermedades InfecciosasHospital de Pediatría, Centro Médico Nacional Siglo XXI, IMSSMexico CityMexico
| | - Ian Spendlove
- Division of Cancer and Stem Cells, School of MedicineUniversity of Nottingham Biodiscovery InstituteNottinghamUK
| | - John C Atherton
- Nottingham Digestive Diseases Biomedical Research CentreNottingham University Hospitals NHS Trust and University of NottinghamNottinghamUK
| | - Karen Robinson
- Nottingham Digestive Diseases Biomedical Research CentreNottingham University Hospitals NHS Trust and University of NottinghamNottinghamUK
| |
Collapse
|
23
|
Tan SM, Snelson M, Østergaard JA, Coughlan MT. The Complement Pathway: New Insights into Immunometabolic Signaling in Diabetic Kidney Disease. Antioxid Redox Signal 2022; 37:781-801. [PMID: 34806406 PMCID: PMC9587781 DOI: 10.1089/ars.2021.0125] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Significance: The metabolic disorder, diabetes mellitus, results in microvascular complications, including diabetic kidney disease (DKD), which is partly believe to involve disrupted energy generation in the kidney, leading to injury that is characterized by inflammation and fibrosis. An increasing body of evidence indicates that the innate immune complement system is involved in the pathogenesis of DKD; however, the precise mechanisms remain unclear. Recent Advances: Complement, traditionally thought of as the prime line of defense against microbial intrusion, has recently been recognized to regulate immunometabolism. Studies have shown that the complement activation products, Complement C5a and C3a, which are potent pro-inflammatory mediators, can mediate an array of metabolic responses in the kidney in the diabetic setting, including altered fuel utilization, disrupted mitochondrial respiratory function, and reactive oxygen species generation. In diabetes, the lectin pathway is activated via autoreactivity toward altered self-surfaces known as danger-associated molecular patterns, or via sensing altered carbohydrate and acetylation signatures. In addition, endogenous complement inhibitors can be glycated, whereas diet-derived glycated proteins can themselves promote complement activation, worsening DKD, and lending support for environmental influences as an additional avenue for propagating complement-induced inflammation and kidney injury. Critical Issues: Recent evidence indicates that conventional renoprotective agents used in DKD do not target the complement, leaving this web of inflammatory stimuli intact. Future Directions: Future studies should focus on the development of novel pharmacological agents that target the complement pathway to alleviate inflammation, oxidative stress, and kidney fibrosis, thereby reducing the burden of microvascular diseases in diabetes. Antioxid. Redox Signal. 37, 781-801.
Collapse
Affiliation(s)
- Sih Min Tan
- Department of Diabetes, Central Clinical School, Alfred Medical Research and Education Precinct, Monash University, Melbourne, Australia
| | - Matthew Snelson
- Department of Diabetes, Central Clinical School, Alfred Medical Research and Education Precinct, Monash University, Melbourne, Australia
| | - Jakob A Østergaard
- Department of Diabetes, Central Clinical School, Alfred Medical Research and Education Precinct, Monash University, Melbourne, Australia.,Department of Endocrinology and Internal Medicine, Aarhus University Hospital, Aarhus, Denmark.,Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Melinda T Coughlan
- Department of Diabetes, Central Clinical School, Alfred Medical Research and Education Precinct, Monash University, Melbourne, Australia.,Baker Heart & Diabetes Institute, Melbourne, Australia
| |
Collapse
|
24
|
Complement Regulation in Immortalized Fibroblast-like Synoviocytes and Primary Human Endothelial Cells in Response to SARS-CoV-2 Nucleocapsid Protein and Pro-Inflammatory Cytokine TNFα. Life (Basel) 2022; 12:life12101527. [PMID: 36294967 PMCID: PMC9604721 DOI: 10.3390/life12101527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/16/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Case reports are available showing that patients develop symptoms of acute arthritis during or after recovery from SARS-CoV-2 infection. Since the interrelation is still unknown, our aim was to study the impact of the SARS-CoV-2 nucleocapsid protein (NP) on human fibroblast-like synoviocytes and human endothelial cells (hEC) in terms of complement and cytokine regulation. Methods: Non-arthritic (K4IM) synoviocyte, arthritic (HSE) synoviocyte cell lines and primary hEC were stimulated with recombinant NP and/or TNFα. Analyses of cell viability, proliferation, gene and protein expression of cytokines and complement factors were performed. Results: NP suppressed significantly the vitality of hEC and proliferation of HSE. NP alone did not induce any significant changes in the examined gene expressions. However, NP combined with TNFα induced significantly higher TNFα in HSE and K4IM as well as higher IL-6 and CD55 gene expression in HSE and suppressed C3aR1 gene expression in hEC. HSE proliferated twice as fast as K4IM, but showed significantly lesser gene expressions of CD46, CD55, CD59 and TNFα with significantly higher IL-6 gene expression. CD35 gene expression was undetectable in K4IM, HSE and hEC. Conclusions: NP might contribute in combination with other inflammatory factors to complement regulation in arthritis.
Collapse
|
25
|
Deng Y, Bartosovic M, Ma S, Zhang D, Kukanja P, Xiao Y, Su G, Liu Y, Qin X, Rosoklija GB, Dwork AJ, Mann JJ, Xu ML, Halene S, Craft JE, Leong KW, Boldrini M, Castelo-Branco G, Fan R. Spatial profiling of chromatin accessibility in mouse and human tissues. Nature 2022; 609:375-383. [PMID: 35978191 PMCID: PMC9452302 DOI: 10.1038/s41586-022-05094-1] [Citation(s) in RCA: 105] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 07/08/2022] [Indexed: 12/12/2022]
Abstract
Cellular function in tissue is dependent on the local environment, requiring new methods for spatial mapping of biomolecules and cells in the tissue context1. The emergence of spatial transcriptomics has enabled genome-scale gene expression mapping2-5, but the ability to capture spatial epigenetic information of tissue at the cellular level and genome scale is lacking. Here we describe a method for spatially resolved chromatin accessibility profiling of tissue sections using next-generation sequencing (spatial-ATAC-seq) by combining in situ Tn5 transposition chemistry6 and microfluidic deterministic barcoding5. Profiling mouse embryos using spatial-ATAC-seq delineated tissue-region-specific epigenetic landscapes and identified gene regulators involved in the development of the central nervous system. Mapping the accessible genome in the mouse and human brain revealed the intricate arealization of brain regions. Applying spatial-ATAC-seq to tonsil tissue resolved the spatially distinct organization of immune cell types and states in lymphoid follicles and extrafollicular zones. This technology progresses spatial biology by enabling spatially resolved chromatin accessibility profiling to improve our understanding of cell identity, cell state and cell fate decision in relation to epigenetic underpinnings in development and disease.
Collapse
Affiliation(s)
- Yanxiang Deng
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Marek Bartosovic
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Sai Ma
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Di Zhang
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Petra Kukanja
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Yang Xiao
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Graham Su
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Yang Liu
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Xiaoyu Qin
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Gorazd B Rosoklija
- Department of Psychiatry, Columbia University, New York, NY, USA
- Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, USA
- Macedonian Academy of Sciences & Arts, Skopje, Republic of Macedonia
| | - Andrew J Dwork
- Department of Psychiatry, Columbia University, New York, NY, USA
- Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, USA
- Macedonian Academy of Sciences & Arts, Skopje, Republic of Macedonia
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - J John Mann
- Department of Psychiatry, Columbia University, New York, NY, USA
- Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, USA
- Department of Radiology, Columbia University, New York, NY, USA
| | - Mina L Xu
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Stephanie Halene
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
- Section of Hematology, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
- Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Joseph E Craft
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Kam W Leong
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Maura Boldrini
- Department of Psychiatry, Columbia University, New York, NY, USA
- Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, USA
| | - Gonçalo Castelo-Branco
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden.
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA.
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA.
- Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT, USA.
| |
Collapse
|
26
|
Mahmoud DE, Kaabachi W, Sassi N, Tarhouni L, Rekik S, Jemmali S, Sehli H, Kallel-Sellami M, Cheour E, Laadhar L. The synovial fluid fibroblast-like synoviocyte: A long-neglected piece in the puzzle of rheumatoid arthritis pathogenesis. Front Immunol 2022; 13:942417. [PMID: 35990693 PMCID: PMC9388825 DOI: 10.3389/fimmu.2022.942417] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/13/2022] [Indexed: 12/14/2022] Open
Abstract
Rheumatoid arthritis (RA) is a systemic autoimmune disease during which fibroblast-like synoviocytes (FLS) contribute to both joint inflammation and destruction. FLS represent the core component of the synovial membrane. Following inflammation of this membrane, an effusion of cell-rich synovial fluid (SF) fills the joint cavity. Unlikely, SF has been shown to contain fibroblasts with some shared phenotypic traits with the synovial membrane FLS. These cells are called SF-FLS and their origin is still unclear. They are either brought into the synovium via migration through blood vessels, or they could originate within the synovium and exist in projections of the synovial membrane. SF-FLS function and phenotype are poorly documented compared to recently well-characterized synovial membrane FLS subsets. Furthermore, no study has yet reported a SF-FLS single-cell profiling analysis. This review will discuss the origin and cellular characteristics of SF-FLS in patients with RA. In addition, recent advances on the involvement of SF-FLS in the pathogenesis of RA will be summarized. Current knowledge on possible relationships between SF-FLS and other types of fibroblasts, including synovial membrane FLS, circulating fibrocytes, and pre- inflammatory mesenchymal (PRIME) cells will also be addressed. Finally, recent therapeutic strategies employed to specifically target SF-FLS in RA will be discussed.
Collapse
Affiliation(s)
- Dorra Elhaj Mahmoud
- Immuno-Rheumatology Research Laboratory, Rheumatology Department, La Rabta Hospital, University of Tunis-El Manar, Tunis, Tunisia
- Unité de Recherche Infections Respiratoires Fongiques (IRF), Structure Fédérative de Recherche “Interactions Cellulaires et Applications Thérapeutiques” (SFR ICAT), Université d’Angers, Angers, France
| | - Wajih Kaabachi
- Immuno-Rheumatology Research Laboratory, Rheumatology Department, La Rabta Hospital, University of Tunis-El Manar, Tunis, Tunisia
| | - Nadia Sassi
- Immuno-Rheumatology Research Laboratory, Rheumatology Department, La Rabta Hospital, University of Tunis-El Manar, Tunis, Tunisia
| | - Lamjed Tarhouni
- Department of Hand and Reconstructive Surgery, Kassab Institute of Traumatic and Orthopedic Surgery, Tunis, Tunisia
| | - Sonia Rekik
- Immuno-Rheumatology Research Laboratory, Rheumatology Department, La Rabta Hospital, University of Tunis-El Manar, Tunis, Tunisia
| | - Samia Jemmali
- Immuno-Rheumatology Research Laboratory, Rheumatology Department, La Rabta Hospital, University of Tunis-El Manar, Tunis, Tunisia
| | - Hela Sehli
- Immuno-Rheumatology Research Laboratory, Rheumatology Department, La Rabta Hospital, University of Tunis-El Manar, Tunis, Tunisia
| | - Maryam Kallel-Sellami
- Immuno-Rheumatology Research Laboratory, Rheumatology Department, La Rabta Hospital, University of Tunis-El Manar, Tunis, Tunisia
| | - Elhem Cheour
- Immuno-Rheumatology Research Laboratory, Rheumatology Department, La Rabta Hospital, University of Tunis-El Manar, Tunis, Tunisia
| | - Lilia Laadhar
- Immuno-Rheumatology Research Laboratory, Rheumatology Department, La Rabta Hospital, University of Tunis-El Manar, Tunis, Tunisia
- *Correspondence: Lilia Laadhar,
| |
Collapse
|
27
|
Cheng J, Clayton JS, Acemel RD, Zheng Y, Taylor RL, Keleş S, Franke M, Boackle SA, Harley JB, Quail E, Gómez-Skarmeta JL, Ulgiati D. Regulatory Architecture of the RCA Gene Cluster Captures an Intragenic TAD Boundary, CTCF-Mediated Chromatin Looping and a Long-Range Intergenic Enhancer. Front Immunol 2022; 13:901747. [PMID: 35769482 PMCID: PMC9235356 DOI: 10.3389/fimmu.2022.901747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/05/2022] [Indexed: 12/03/2022] Open
Abstract
The Regulators of Complement Activation (RCA) gene cluster comprises several tandemly arranged genes with shared functions within the immune system. RCA members, such as complement receptor 2 (CR2), are well-established susceptibility genes in complex autoimmune diseases. Altered expression of RCA genes has been demonstrated at both the functional and genetic level, but the mechanisms underlying their regulation are not fully characterised. We aimed to investigate the structural organisation of the RCA gene cluster to identify key regulatory elements that influence the expression of CR2 and other genes in this immunomodulatory region. Using 4C, we captured extensive CTCF-mediated chromatin looping across the RCA gene cluster in B cells and showed these were organised into two topologically associated domains (TADs). Interestingly, an inter-TAD boundary was located within the CR1 gene at a well-characterised segmental duplication. Additionally, we mapped numerous gene-gene and gene-enhancer interactions across the region, revealing extensive co-regulation. Importantly, we identified an intergenic enhancer and functionally demonstrated this element upregulates two RCA members (CR2 and CD55) in B cells. We have uncovered novel, long-range mechanisms whereby autoimmune disease susceptibility may be influenced by genetic variants, thus highlighting the important contribution of chromatin topology to gene regulation and complex genetic disease.
Collapse
Affiliation(s)
- Jessica Cheng
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Joshua S. Clayton
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia,Centre for Medical Research, The University of Western Australia, Crawley, WA, Australia
| | - Rafael D. Acemel
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Sevilla, Spain
| | - Ye Zheng
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States,Department of Statistics, University of Wisconsin-Madison, Madison, WI, United States
| | - Rhonda L. Taylor
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia,Centre for Medical Research, The University of Western Australia, Crawley, WA, Australia
| | - Sündüz Keleş
- Department of Statistics, University of Wisconsin-Madison, Madison, WI, United States,Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, United States
| | - Martin Franke
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Sevilla, Spain
| | - Susan A. Boackle
- Department of Medicine, Division of Rheumatology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States,Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, CO, United States
| | - John B. Harley
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States,US Department of Veterans Affairs Medical Centre, US Department of Veterans Affairs, Cincinnati, OH, United States
| | - Elizabeth Quail
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia,School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Sevilla, Spain
| | - Daniela Ulgiati
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia,*Correspondence: Daniela Ulgiati,
| |
Collapse
|
28
|
Suryawanshi H, Yang H, Lubetzky M, Morozov P, Lagman M, Thareja G, Alonso A, Li C, Snopkowski C, Belkadi A, Mueller FB, Lee JR, Dadhania DM, Salvatore SP, Seshan SV, Sharma VK, Suhre K, Suthanthiran M, Tuschl T, Muthukumar T. Detection of infiltrating fibroblasts by single-cell transcriptomics in human kidney allografts. PLoS One 2022; 17:e0267704. [PMID: 35657798 PMCID: PMC9165878 DOI: 10.1371/journal.pone.0267704] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 04/13/2022] [Indexed: 02/06/2023] Open
Abstract
We tested the hypothesis that single-cell RNA-sequencing (scRNA-seq) analysis of human kidney allograft biopsies will reveal distinct cell types and states and yield insights to decipher the complex heterogeneity of alloimmune injury. We selected 3 biopsies of kidney cortex from 3 individuals for scRNA-seq and processed them fresh using an identical protocol on the 10x Chromium platform; (i) HK: native kidney biopsy from a living donor, (ii) AK1: allograft kidney with transplant glomerulopathy, tubulointerstitial fibrosis, and worsening graft function, and (iii) AK2: allograft kidney after successful treatment of active antibody-mediated rejection. We did not study T-cell-mediated rejections. We generated 7217 high-quality single cell transcriptomes. Taking advantage of the recipient-donor sex mismatches revealed by X and Y chromosome autosomal gene expression, we determined that in AK1 with fibrosis, 42 months after transplantation, more than half of the kidney allograft fibroblasts were recipient-derived and therefore likely migratory and graft infiltrative, whereas in AK2 without fibrosis, 84 months after transplantation, most fibroblasts were donor-organ-derived. Furthermore, AK1 was enriched for tubular progenitor cells overexpressing profibrotic extracellular matrix genes. AK2, eight months after successful treatment of rejection, contained plasmablast cells with high expression of immunoglobulins, endothelial cell elaboration of T cell chemoattractant cytokines, and persistent presence of cytotoxic T cells. In addition to these key findings, our analysis revealed unique cell types and states in the kidney. Altogether, single-cell transcriptomics yielded novel mechanistic insights, which could pave the way for individualizing the care of transplant recipients.
Collapse
Affiliation(s)
- Hemant Suryawanshi
- Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY, United States of America
- * E-mail: (HS); (TT); (TM)
| | - Hua Yang
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, NY, United States of America
| | - Michelle Lubetzky
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, NY, United States of America
- Department of Transplantation Medicine, New York Presbyterian Hospital-Weill Cornell Medical College, New York, NY, United States of America
| | - Pavel Morozov
- Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY, United States of America
| | - Mila Lagman
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, NY, United States of America
| | - Gaurav Thareja
- Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Doha, Qatar
| | - Alicia Alonso
- Epigenomics Core Facility, Weill Cornell Medical College, New York, NY, United States of America
| | - Carol Li
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, NY, United States of America
| | - Catherine Snopkowski
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, NY, United States of America
| | - Aziz Belkadi
- Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Doha, Qatar
| | - Franco B. Mueller
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, NY, United States of America
| | - John R. Lee
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, NY, United States of America
- Department of Transplantation Medicine, New York Presbyterian Hospital-Weill Cornell Medical College, New York, NY, United States of America
| | - Darshana M. Dadhania
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, NY, United States of America
- Department of Transplantation Medicine, New York Presbyterian Hospital-Weill Cornell Medical College, New York, NY, United States of America
| | - Steven P. Salvatore
- Division of Renal Pathology, Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, United States of America
| | - Surya V. Seshan
- Division of Renal Pathology, Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, United States of America
| | - Vijay K. Sharma
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, NY, United States of America
| | - Karsten Suhre
- Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Doha, Qatar
| | - Manikkam Suthanthiran
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, NY, United States of America
- Department of Transplantation Medicine, New York Presbyterian Hospital-Weill Cornell Medical College, New York, NY, United States of America
| | - Thomas Tuschl
- Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY, United States of America
- * E-mail: (HS); (TT); (TM)
| | - Thangamani Muthukumar
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, NY, United States of America
- Department of Transplantation Medicine, New York Presbyterian Hospital-Weill Cornell Medical College, New York, NY, United States of America
- * E-mail: (HS); (TT); (TM)
| |
Collapse
|
29
|
Yoda H, Weiss WA. CD55, a potential immunotherapeutic target for MYCN-amplified neuroblastoma. Neuro Oncol 2022; 24:886-887. [PMID: 35090034 PMCID: PMC9159426 DOI: 10.1093/neuonc/noac020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Affiliation(s)
- Hiroyuki Yoda
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
- Department of Neurology, University of California, San Francisco, San Francisco, California, USA
| | - William A Weiss
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
- Department of Neurology, University of California, San Francisco, San Francisco, California, USA
- Departments of Neurology, Pediatrics, and Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| |
Collapse
|
30
|
Hamilton A, Rizzo R, Brod S, Ono M, Perretti M, Cooper D, D'Acquisto F. The immunomodulatory effects of social isolation in mice are linked to temperature control. Brain Behav Immun 2022; 102:179-194. [PMID: 35217174 DOI: 10.1016/j.bbi.2022.02.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 01/17/2022] [Accepted: 02/18/2022] [Indexed: 12/25/2022] Open
Abstract
Living in isolation is considered an emerging societal problem that negatively affects the physical wellbeing of its sufferers in ways that we are just starting to appreciate. This study investigates the immunomodulatory effects of social isolation in mice, utilising a two-week program of sole cage occupancy followed by the testing of immune-inflammatory resilience to bacterial sepsis. Our results revealed that mice housed in social isolation showed an increased ability to clear bacterial infection compared to control socially housed animals. These effects were associated with specific changes in whole blood gene expression profile and an increased production of classical pro-inflammatory cytokines. Interestingly, equipping socially isolated mice with artificial nests as a substitute for their natural huddling behaviour reversed the increased resistance to bacterial sepsis. Together these results suggest that the control of body temperature through social housing and huddling behaviour are important factors in the regulation of the host immune response to infection in mice and might provide another example of the many ways by which living conditions influence immunity.
Collapse
Affiliation(s)
- Alice Hamilton
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Raffaella Rizzo
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Samuel Brod
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Masahiro Ono
- University of London Imperial College Science Technology & Medicine, Department of Life Science, Faculty of Natural Science, London SW7 2AZ, England
| | - Mauro Perretti
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Dianne Cooper
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Fulvio D'Acquisto
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK; School of Life and Health Science, University of Roehampton, London SW15, 4JD, UK.
| |
Collapse
|
31
|
Tang Z, Wang L, Huang Z, Guan H, Leung W, Chen X, Xia H, Zhang W. CD55 is upregulated by cAMP/PKA/AKT and modulates human decidualization via Src and ERK pathway and decidualization-related genes. Mol Reprod Dev 2022; 89:256-268. [PMID: 35474595 DOI: 10.1002/mrd.23569] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/22/2022] [Accepted: 03/25/2022] [Indexed: 12/12/2022]
Abstract
Decidualization is an essential process for embryo implantation and maintenance of pregnancy, and abnormal decidualization contributed to several pregnancy disorders like a miscarriage. The objective of this study was to explore the regulation and function of CD55 in human decidualization. By immunohistochemical staining, it was found that CD55 expression was higher in first-trimester decidua than in the endometrium. In both primary endometrial stromal cells and immortalized cell line T-hESCs, CD55 was upregulated by induction of in vitro decidualization with medroxyprogesterone acetate (MPA) and 8-Br-cAMP. During decidualization in vitro, CD55 was stimulated by 8-Br-cAMP in a time- and concentration-dependent manner, which was reversed by a PKA inhibitor H89 and partially by an AKT activator SC79. Knocking down CD55 expression diminished the expression of decidualization markers prolactin (PRL) and insulin-like growth factor-binding protein 1 (IGFBP1), accompanied by inhibition of Src, aberrant activation of ERK and decreased expression of several decidualization-related genes, including FOXO1, EGFR, and STAT3. Furthermore, the decidua of unexplained miscarriage women and the endometrium of unexplained infertile women both exhibited decreased CD55 expression. Collectively, these findings revealed that 8-Br-cAMP promotes CD55 expression via PKA activation and AKT dephosphorylation, and decreased CD55 impairs decidualization by inactivation of Src, aberrant activation of ERK pathway, and compromised expression of decidualization-related genes, indicating that CD55 deficiency may contribute to the pathogenesis of spontaneous miscarriage and infertility.
Collapse
Affiliation(s)
- Zhijing Tang
- Department of Reproductive Endocrinology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| | - Lu Wang
- Department of Reproductive Endocrinology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Zengshu Huang
- Department of Reproductive Endocrinology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| | - Haiyun Guan
- Department of Reproductive Endocrinology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| | - Wingting Leung
- Department of Reproductive Endocrinology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| | - Xiuying Chen
- Department of Reproductive Endocrinology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Hexia Xia
- Department of Reproductive Endocrinology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Wei Zhang
- Department of Reproductive Endocrinology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| |
Collapse
|
32
|
Berghäll E, Hultström M, Frithiof R, Lipcsey M, Hahn-Strömberg V. The Evolution of Blood Cell Phenotypes, Intracellular and Plasma Cytokines and Morphological Changes in Critically Ill COVID-19 Patients. Biomedicines 2022; 10:934. [PMID: 35625671 PMCID: PMC9138896 DOI: 10.3390/biomedicines10050934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/12/2022] [Accepted: 04/15/2022] [Indexed: 11/24/2022] Open
Abstract
Background: Severe coronavirus disease 2019 (COVID-19) causes a strong inflammatory response. To obtain an overview of inflammatory mediators and effector cells, we studied 25 intensive-care-unit patients during the timeframe after off-label chloroquine treatment and before an introduction of immunomodulatory drugs. Material and methods: Blood samples were weekly examined with flow cytometry (FCM) for surface and intracytoplasmic markers, cytokine assays were analyzed for circulating interleukins (ILs), and blood smears were evaluated for morphological changes. Samples from healthy volunteers were used for comparison. Organ function data and 30-day mortality were obtained from medical records. Results: Compared to that of the healthy control group, the expression levels of leukocyte surface markers, i.e., the cluster of differentiation (CD) markers CD2, CD4, CD8, CD158d, CD25, CD127, and CD19, were lower (p < 0.001), while those of leukocytes expressing CD33 were increased (p < 0.05). An aberrant expression of CD158d on granulocytes was found on parts of the granulocyte population. The expression levels of intracellular tumor necrosis factor alpha (TNFα) and IL-1 receptor type 2 in leukocytes were lower (p < 0.001), and the plasma levels of TNFα, IL-2, IL-6, IL-8, IL-10 (p < 0.001), interferon gamma (IFNγ) (p < 0.01), and granulocyte-macrophage colony-stimulating factor (GM-CSF) (p < 0.05) were higher in patients with severe COVID-19 than in the control group. The expression levels of CD33+ leukocytes and circulating IL-6 were higher (p < 0.05) among patients with arterial oxygen partial pressure-to-fractional inspired oxygen (PaO2/FiO2) ratios below 13.3 kPa compared to in the remaining patients. The expression levels of TNFα, IL-2, IL-4, IL-6, IL-8, and IL-10 were higher in patients treated with continuous renal replacement therapy (CRRT) (p < 0.05), and the levels of the maximum plasma creatinine and TNFα Spearman’s rank-order correlation coefficient (rho = 0.51, p < 0.05) and IL-8 (rho = 0.44, p < 0.05) correlated. Blood smears revealed neutrophil dysplasia with pseudo-Pelger forms being most common. Conclusion: These findings suggest that patients with severe COVID-19, in addition to augmented ILs, lymphopenia, and increased granulocytes, also had effects on the bone marrow.
Collapse
Affiliation(s)
- Elisabeth Berghäll
- Department of Surgical Sciences, Anesthesiology and Intensive Care, Uppsala University, 75185 Uppsala, Sweden; (M.H.); (R.F.); (M.L.)
| | - Michael Hultström
- Department of Surgical Sciences, Anesthesiology and Intensive Care, Uppsala University, 75185 Uppsala, Sweden; (M.H.); (R.F.); (M.L.)
- Department of Medical Cell Biology, Uppsala University, 75123 Uppsala, Sweden;
| | - Robert Frithiof
- Department of Surgical Sciences, Anesthesiology and Intensive Care, Uppsala University, 75185 Uppsala, Sweden; (M.H.); (R.F.); (M.L.)
| | - Miklos Lipcsey
- Department of Surgical Sciences, Anesthesiology and Intensive Care, Uppsala University, 75185 Uppsala, Sweden; (M.H.); (R.F.); (M.L.)
- Hedenstierna Laboratory, CIRRUS, Anesthesiology and Intensive Care, Department of Surgical Sciences, Uppsala University, 75185 Uppsala, Sweden
| | | |
Collapse
|
33
|
Application of Proteogenomics to Urine Analysis towards the Identification of Novel Biomarkers of Prostate Cancer: An Exploratory Study. Cancers (Basel) 2022; 14:cancers14082001. [PMID: 35454907 PMCID: PMC9031064 DOI: 10.3390/cancers14082001] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 12/15/2022] Open
Abstract
Simple Summary Prostate cancer (PCa) is one of the most common cancers. Due to the limited and invasive approaches for PCa diagnosis, it is crucial to identify more accurate and non-invasive biomarkers for its detection. The aim of our study was to non-invasively uncover new protein targets for detecting PCa using a proteomics and proteogenomics approach. This work identified several dysregulated mutant protein isoforms in urine from PCa patients, some of them predicted to have a protective or an adverse role in these patients. These results are promising given urine’s non-invasive nature and offers an auspicious opportunity for research and development of PCa biomarkers. Abstract To identify new protein targets for PCa detection, first, a shotgun discovery experiment was performed to characterize the urinary proteome of PCa patients. This revealed 18 differentially abundant urinary proteins in PCa patients. Second, selected targets were clinically tested by immunoblot, and the soluble E-cadherin fragment was detected for the first time in the urine of PCa patients. Third, the proteogenome landscape of these PCa patients was characterized, revealing 1665 mutant protein isoforms. Statistical analysis revealed 6 differentially abundant mutant protein isoforms in PCa patients. Analysis of the likely effects of mutations on protein function and PPIs involving the dysregulated mutant protein isoforms suggests a protective role of mutations HSPG2*Q1062H and VASN*R161Q and an adverse role of AMBP*A286G and CD55*S162L in PCa patients. This work originally characterized the urinary proteome, focusing on the proteogenome profile of PCa patients, which is usually overlooked in the analysis of PCa and body fluids. Combined analysis of mass spectrometry data using two different software packages was performed for the first time in the context of PCa, which increased the robustness of the data analysis. The application of proteogenomics to urine proteomic analysis can be very enriching in mutation-related diseases such as cancer.
Collapse
|
34
|
Liu D, Duan L, Cyster JG. Chemo- and mechanosensing by dendritic cells facilitate antigen surveillance in the spleen. Immunol Rev 2022; 306:25-42. [PMID: 35147233 PMCID: PMC8852366 DOI: 10.1111/imr.13055] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 12/05/2021] [Indexed: 12/30/2022]
Abstract
Spleen dendritic cells (DC) are critical for initiation of adaptive immune responses against blood-borne invaders. Key to DC function is their positioning at sites of pathogen entry, and their abilities to selectively capture foreign antigens and promptly engage T cells. Focusing on conventional DC2 (cDC2), we discuss the contribution of chemoattractant receptors (EBI2 or GPR183, S1PR1, and CCR7) and integrins to cDC2 positioning and function. We give particular attention to a newly identified role in cDC2 for adhesion G-protein coupled receptor E5 (Adgre5 or CD97) and its ligand CD55, detailing how this mechanosensing system contributes to splenic cDC2 positioning and homeostasis. Additional roles of CD97 in the immune system are reviewed. The ability of cDC2 to be activated by circulating missing self-CD47 cells and to integrate multiple red blood cell (RBC)-derived inputs is discussed. Finally, we describe the process of activated cDC2 migration to engage and prime helper T cells. Throughout the review, we consider the insights into cDC function in the spleen that have emerged from imaging studies.
Collapse
Affiliation(s)
- Dan Liu
- Howard Hughes Medical Institute and Department of Microbiology and Immunology University of California San Francisco California USA
| | - Lihui Duan
- Howard Hughes Medical Institute and Department of Microbiology and Immunology University of California San Francisco California USA
| | - Jason G. Cyster
- Howard Hughes Medical Institute and Department of Microbiology and Immunology University of California San Francisco California USA
| |
Collapse
|
35
|
Luo S, Chen Y, Yang L, Gong X, Wu Z. The complement system in retinal detachment with choroidal detachment. Curr Eye Res 2022; 47:809-812. [PMID: 35176953 DOI: 10.1080/02713683.2022.2038634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
PURPOSE This study aims to explore the differences in the levels of complement components and complement regulatory factors in the vitreous humor of patients with retinal detachment with choroidal detachment (RRDCD), patients with rhegmatogenous retinal detachment (RRD). METHODS A prospective case-control study design was used to recruit 20 patients with RRDCD and 20 patients with RRD in consecutive cases who underwent pars plana vitrectomy from March 2019 to January 2020. The control group comprised 15 patients with epiretinal membrane and 5 eyes from cadavers. The concentrations of complement C2, complement C4b, complement C5/C5a, complement C9, complement factor D (CFD), lectin, and complement factor I (CFI) were measured using Multiplex Luminex Assay, and the concentration of soluble decay acceleration factor (sDAF) was measured using ELISA. RESULTS As compared with the RRD and control groups, complement C2, complement C4b, complement C5/C5a, complement C9, CFD, lectin, CFI, and sDAF were significantly increased in the RRDCD group. Additionally, as compared with the control group, the concentrations of complement component C2 and CFD were significantly increased in the vitreous humor of the RRD group. CONCLUSION Components of all three complement pathways were elevated in eyes with RRDCD. Interestingly, while there was evidence of early complement activation in RRD, the final common pathway components were not elevated. In contrast, RRDCD eyes showed significant elevations of the MAC complex components, underscoring a potential pathophysiologic impact of complement activation in this condition.
Collapse
Affiliation(s)
- Shasha Luo
- Department of Ophthalmology, Nanjing Medical University Affiliated Wuxi Second Hospital, Wuxi, Jiangsu Province, People's Republic of China.,Department of Ophthalmology, Affiliated Wuxi Clinical College of Nantong University, Wuxi, Jiangsu Province, People's Republic of China
| | - Yanghao Chen
- Department of Ophthalmology, Anqing No.2 People's Hospital, Anqing, Anhui Province, People's Republic of China
| | - Lufei Yang
- Department of Ophthalmology, Nanjing Medical University Affiliated Wuxi Second Hospital, Wuxi, Jiangsu Province, People's Republic of China
| | - Xuechun Gong
- Department of Ophthalmology, Nanjing Medical University Affiliated Wuxi Second Hospital, Wuxi, Jiangsu Province, People's Republic of China
| | - Zhifeng Wu
- Department of Ophthalmology, Nanjing Medical University Affiliated Wuxi Second Hospital, Wuxi, Jiangsu Province, People's Republic of China.,Department of Ophthalmology, Affiliated Wuxi Clinical College of Nantong University, Wuxi, Jiangsu Province, People's Republic of China
| |
Collapse
|
36
|
Liu D, Duan L, Rodda LB, Lu E, Xu Y, An J, Qiu L, Liu F, Looney MR, Yang Z, Allen CDC, Li Z, Marson A, Cyster JG. CD97 promotes spleen dendritic cell homeostasis through the mechanosensing of red blood cells. Science 2022; 375:eabi5965. [PMID: 35143305 PMCID: PMC9310086 DOI: 10.1126/science.abi5965] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Dendritic cells (DCs) are crucial for initiating adaptive immune responses. However, the factors that control DC positioning and homeostasis are incompletely understood. We found that type-2 conventional DCs (cDC2s) in the spleen depend on Gα13 and adhesion G protein-coupled receptor family member-E5 (Adgre5, or CD97) for positioning in blood-exposed locations. CD97 function required its autoproteolytic cleavage. CD55 is a CD97 ligand, and cDC2 interaction with CD55-expressing red blood cells (RBCs) under shear stress conditions caused extraction of the regulatory CD97 N-terminal fragment. Deficiency in CD55-CD97 signaling led to loss of splenic cDC2s into the circulation and defective lymphocyte responses to blood-borne antigens. Thus, CD97 mechanosensing of RBCs establishes a migration and gene expression program that optimizes the antigen capture and presentation functions of splenic cDC2s.
Collapse
Affiliation(s)
- Dan Liu
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Lihui Duan
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Lauren B Rodda
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Erick Lu
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ying Xu
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jinping An
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Longhui Qiu
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Fengchun Liu
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mark R Looney
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Zhiyong Yang
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94143, USA.,Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Christopher D C Allen
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94143, USA.,Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Zhongmei Li
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Alexander Marson
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Jason G Cyster
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| |
Collapse
|
37
|
Molecular basis of differential receptor usage for naturally occurring CD55-binding and -nonbinding coxsackievirus B3 strains. Proc Natl Acad Sci U S A 2022; 119:2118590119. [PMID: 35046043 PMCID: PMC8794823 DOI: 10.1073/pnas.2118590119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2021] [Indexed: 12/11/2022] Open
Abstract
Receptor usage defines cell tropism and contributes to cell entry and infection. Coxsackievirus B (CVB) engages coxsackievirus and adenovirus receptor (CAR), and selectively utilizes the decay-accelerating factor (DAF; CD55) to infect cells. However, the differential receptor usage mechanism for CVB remains elusive. This study identified VP3-234 residues (234Q/N/V/D/E) as critical population selection determinants during CVB3 virus evolution, contributing to diverse binding affinities to CD55. Cryoelectron microscopy (cryo-EM) structures of CD55-binding/nonbinding isolates and their complexes with CD55 or CAR were obtained under both neutral and acidic conditions, and the molecular mechanism of VP3-234 residues determining CD55 affinity/specificity for naturally occurring CVB3 strains was elucidated. Structural and biochemical studies in vitro revealed the dynamic entry process of CVB3 and the function of the uncoating receptor CAR with different pH preferences. This work provides detailed insight into the molecular mechanism of CVB infection and contributes to an in-depth understanding of enterovirus attachment receptor usage.
Collapse
|
38
|
Yudin NS, Yurchenko AA, Larkin DM. [Signatures of selection and candidate genes for adaptation to extreme environmental factors in the genomes of Turano-Mongolian cattle breeds]. Vavilovskii Zhurnal Genet Selektsii 2021; 25:190-201. [PMID: 34901717 PMCID: PMC8627871 DOI: 10.18699/vj21.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/18/2020] [Accepted: 10/20/2020] [Indexed: 11/19/2022] Open
Abstract
Changes in the environment force populations of organisms to adapt to new conditions, either through phenotypic plasticity or through genetic or epigenetic changes. Signatures of selection, such as specific changes in the frequency of alleles and haplotypes, as well as the reduction or increase in genetic diversity, help to identify changes in the cattle genome in response to natural and artificial selection, as well as loci and genetic variants directly affecting adaptive and economically important traits. Advances in genetics and biotechnology enable a rapid transfer of unique genetic variants that have originated in local cattle breeds in the process of adaptation to local environments into the genomes of cosmopolitan high-performance breeds, in order to preserve their outstanding performance in new environments. It is also possible to use genomic selection approach to increase the frequency of already present adaptive alleles in cosmopolitan breeds. The review examines recent work on the origin and evolution of Turano-Mongolian cattle breeds, adaptation of Turano-Mongolian cattle to extreme environments, and summarizes available information on potential candidate genes for climate adaptation of Turano-Mongolian breeds, including cold resistance genes, immune response genes, and high-altitude adaptation genes. The authors conclude that the current literature data do not provide preference to one of the two possible scenarios of Turano-Mongolian breed origins: as a result of the domestication of a wild aurochs at East Asia or as a result of the migration of taurine proto-population from the Middle East. Turano-Mongolian breeds show a high degree of adaptation to extreme climatic conditions (cold, heat, lack of oxygen in the highlands) and parasites (mosquitoes, ticks, bacterial and viral infections). As a result of high-density genotyping and sequencing of genomes and transcriptomes, prospective candidate genes and genetic variants involved in adaptation to environmental factors have recently been identified.
Collapse
Affiliation(s)
- N S Yudin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A A Yurchenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - D M Larkin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia The Royal Veterinary College, University of London, London, United Kingdom
| |
Collapse
|
39
|
Fu G, Chen T, Wu J, Jiang T, Tang D, Bonaroti J, Conroy J, Scott MJ, Deng M, Billiar TR. Single-Cell Transcriptomics Reveals Compartment-Specific Differences in Immune Responses and Contributions for Complement Factor 3 in Hemorrhagic Shock Plus Tissue Trauma. Shock 2021; 56:994-1008. [PMID: 33710107 PMCID: PMC8429528 DOI: 10.1097/shk.0000000000001765] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
ABSTRACT Hemorrhagic shock with tissue trauma (HS/T) leads to the activation of a system-wide immune-inflammatory response that involves all organs and body compartments. Recent advances in single-cell analysis permit the simultaneous assessment of transcriptomic patterns in a large number of cells making it feasible to survey the landscape of immune cell responses across numerous anatomic sites. Here, we used single-cell RNA sequencing of leukocytes from the blood, liver, and spleen to identify the major shifts in gene expression by cell type and compartment in a mouse HS/T model. At 6 h, dramatic changes in gene expression were observed across multiple-cell types and in all compartments in wild-type mice. Monocytes from circulation and liver exhibited a significant upregulation of genes associated with chemotaxis and migration and a simultaneous suppression of genes associated with interferon signaling and antigen presentation. In contrast, liver conventional DC exhibited a unique pattern compared with other myeloid cells that included a pronounced increase in major histocompatibility complex class II (MHCII) gene expression. The dominant pattern across all compartments for B and T cells was a suppression of genes associated with cell activation and signaling after HS/T. Using complement factor 3 (C3) knockout mice we unveiled a role for C3 in the suppression of monocyte Major Histocompatibility Complex class II expression and activation of gene expression associated with migration, phagocytosis and cytokine upregulation, and an unexpected role in promoting interferon-signaling in a subset of B and T cells across all three compartments after HS/T. This transcriptomic landscape study of immune cells provides new insights into the host immune response to trauma, as well as a rich resource for further investigation of trauma-induced immune responses and complement in driving interferon signaling.
Collapse
Affiliation(s)
- Guang Fu
- Department of General Surgery, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Surgery, University of Pittsburgh, PA, USA
| | - Tianmeng Chen
- Department of Surgery, University of Pittsburgh, PA, USA
- Cellular and Molecular Pathology Program, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Junru Wu
- Department of General Surgery, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Surgery, University of Pittsburgh, PA, USA
| | - Ting Jiang
- Department of Surgery, University of Pittsburgh, PA, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Da Tang
- Department of General Surgery, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Surgery, University of Pittsburgh, PA, USA
| | | | - Julia Conroy
- Department of Surgery, University of Pittsburgh, PA, USA
| | - Melanie J Scott
- Department of Surgery, University of Pittsburgh, PA, USA
- Trauma Research Center, University of Pittsburgh, PA, USA
| | - Meihong Deng
- Department of Surgery, University of Pittsburgh, PA, USA
- Department of Surgery, Ohio State University, Ohio, USA
| | - Timothy R Billiar
- Department of Surgery, University of Pittsburgh, PA, USA
- Trauma Research Center, University of Pittsburgh, PA, USA
| |
Collapse
|
40
|
Sandholt AKS, Wattrang E, Lilja T, Ahola H, Lundén A, Troell K, Svärd SG, Söderlund R. Dual RNA-seq transcriptome analysis of caecal tissue during primary Eimeria tenella infection in chickens. BMC Genomics 2021; 22:660. [PMID: 34521339 PMCID: PMC8438895 DOI: 10.1186/s12864-021-07959-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/29/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Coccidiosis is an infectious disease with large negative impact on the poultry industry worldwide. It is an enteric infection caused by unicellular Apicomplexan parasites of the genus Eimeria. The present study aimed to gain more knowledge about interactions between parasites and the host immune system during the early asexual replication phase of E. tenella in chicken caeca. For this purpose, chickens were experimentally infected with E. tenella oocysts, sacrificed on days 1-4 and 10 after infection and mRNA from caecal tissues was extracted and sequenced. RESULTS Dual RNA-seq analysis revealed time-dependent changes in both host and parasite gene expression during the course of the infection. Chicken immune activation was detected from day 3 and onwards with the highest number of differentially expressed immune genes recorded on day 10. Among early (days 3-4) responses up-regulation of genes for matrix metalloproteinases, several chemokines, interferon (IFN)-γ along with IFN-stimulated genes GBP, IRF1 and RSAD2 were noted. Increased expression of genes with immune suppressive/regulatory effects, e.g. IL10, SOCS1, SOCS3, was also observed among early responses. For E. tenella a general up-regulation of genes involved in protein expression and energy metabolism as well as a general down-regulation genes for DNA and RNA processing were observed during the infection. Specific E. tenella genes with altered expression during the experiment include those for proteins in rhoptry and microneme organelles. CONCLUSIONS The present study provides novel information on both the transcriptional activity of E. tenella during schizogony in ceacal tissue and of the local host responses to parasite invasion during this phase of infection. Results indicate a role for IFN-γ and IFN-stimulated genes in the innate defence against Eimeria replication.
Collapse
Affiliation(s)
- Arnar K S Sandholt
- Department of Microbiology, National Veterinary Institute, Uppsala, Sweden
| | - Eva Wattrang
- Department of Microbiology, National Veterinary Institute, Uppsala, Sweden.
| | - Tobias Lilja
- Department of Microbiology, National Veterinary Institute, Uppsala, Sweden
| | - Harri Ahola
- Department of Microbiology, National Veterinary Institute, Uppsala, Sweden
| | - Anna Lundén
- Department of Microbiology, National Veterinary Institute, Uppsala, Sweden
| | - Karin Troell
- Department of Microbiology, National Veterinary Institute, Uppsala, Sweden
| | - Staffan G Svärd
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Robert Söderlund
- Department of Microbiology, National Veterinary Institute, Uppsala, Sweden
| |
Collapse
|
41
|
Hughes CHK, Inskeep EK, Pate JL. Temporal changes in the corpus luteum during early pregnancy reveal regulation of pathways that enhance steroidogenesis and suppress luteolytic mechanisms†. Biol Reprod 2021; 103:70-84. [PMID: 32285125 DOI: 10.1093/biolre/ioaa047] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/01/2020] [Accepted: 04/09/2020] [Indexed: 11/14/2022] Open
Abstract
Although rescue of the corpus luteum (CL) is required for pregnancy, luteal function during maternal recognition of pregnancy remains largely unexplored. CL were collected from pregnant cattle on days 14, 17, 20, and 23, to encompass the maternal recognition of pregnancy period. Next-generation sequencing was used to profile mRNA abundance during this time, while tandem mass spectrometry and nanostring technology were used to profile proteins and miRNA, respectively. A total of 1157 mRNA were differentially abundant, while 27 miRNA changed, and 29 proteins tended to change. mRNA that increased were regulators of interferon signaling and DNA repair, while those that decreased were associated with luteolytic processes, such as calcium signaling and matrix metallopeptidase (MMP) signaling, indicating inhibition of these processes. One of these, MMP12, was regulated by prostaglandin F2A in vitro. mRNA that were maximally abundant on day 20 were primarily associated with immune processes. Two of these, C-C motif chemokine ligand 1 and NFKB inhibitor alpha, were regulated by interferon tau in vitro. MiRNA that increased were predicted to inhibit phosphatidylinositol signaling, while those that decreased may be negative regulators of steroidogenesis. One protein that was greater on day 20 than on day 14 was aldehyde dehydrogenase 1 family member A1 (ALDH1A1), which synthesizes retinoic acid. Pharmacological inhibition of this enzyme, or of retinoic acid receptor signaling, led to suppression of progesterone production in vitro. Overall, these data indicate that there are changes in the CL of pregnancy that are important for continued luteal function.
Collapse
Affiliation(s)
- C H K Hughes
- Center for Reproductive Biology & Health, Department of Animal Science, Pennsylvania State University, University Park, PA, USA
| | - E K Inskeep
- Division of Animal & Nutritional Sciences, West Virginia University, Morgantown, WV, USA
| | - J L Pate
- Center for Reproductive Biology & Health, Department of Animal Science, Pennsylvania State University, University Park, PA, USA
| |
Collapse
|
42
|
A structure-based approach for the development of a bicyclic peptide acting as a miniaturized anti-CD55 antibody. Int J Biol Macromol 2021; 182:1455-1462. [PMID: 34015405 DOI: 10.1016/j.ijbiomac.2021.05.092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 01/20/2023]
Abstract
CD55 is a major regulator of the complement system, a complex network of proteins that cooperate to clear tissue and blood pathogens from the organism. Indeed, overexpression of CD55 is associated with many diseases and is connected to the resistance mechanisms exhibited by several cancers towards immunotherapy approaches. High level of CD55 expression on tumour cells renders it a good target for both imaging and immunotherapy. Indeed, a conceivable approach to tackle disease is to interfere with CD55-mediated complement regulation with the use of CD55-targeting antibodies. However, the large size and poor tissue penetration together with to the high costs of antibodies often limits their widespread therapeutic use. Here, we employed bioinformatic and chemical approaches to design and synthesize molecules of small dimensions able to mimic a CD55 blocking antibody. As a result, a bicyclic peptide, named as miniAB55, proved to bind CD55 with nanomolar affinity. This molecule represents an attracting chemical scaffold for CD55-directed diagnostic tools in diseases associated with CD55 overproduction. To further support the applicative potential of miniAB55, we prove that the miniAB55 binds CD55 on the same region involved in inactivation of the complement C3 and C5 convertases, thus opening promising scenarios for the development of complement-modulating tools.
Collapse
|
43
|
|
44
|
Angeletti A, Cantarelli C, Petrosyan A, Andrighetto S, Budge K, D'Agati VD, Hartzell S, Malvi D, Donadei C, Thurman JM, Galešić-Ljubanović D, He JC, Xiao W, Campbell KN, Wong J, Fischman C, Manrique J, Zaza G, Fiaccadori E, La Manna G, Fribourg M, Leventhal J, Da Sacco S, Perin L, Heeger PS, Cravedi P. Loss of decay-accelerating factor triggers podocyte injury and glomerulosclerosis. J Exp Med 2021; 217:151976. [PMID: 32717081 PMCID: PMC7478737 DOI: 10.1084/jem.20191699] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 02/28/2020] [Accepted: 04/27/2020] [Indexed: 12/24/2022] Open
Abstract
Kidney glomerulosclerosis commonly progresses to end-stage kidney failure, but pathogenic mechanisms are still poorly understood. Here, we show that podocyte expression of decay-accelerating factor (DAF/CD55), a complement C3 convertase regulator, crucially controls disease in murine models of adriamycin (ADR)-induced focal and segmental glomerulosclerosis (FSGS) and streptozotocin (STZ)-induced diabetic glomerulosclerosis. ADR induces enzymatic cleavage of DAF from podocyte surfaces, leading to complement activation. C3 deficiency or prevention of C3a receptor (C3aR) signaling abrogates disease despite DAF deficiency, confirming complement dependence. Mechanistic studies show that C3a/C3aR ligations on podocytes initiate an autocrine IL-1β/IL-1R1 signaling loop that reduces nephrin expression, causing actin cytoskeleton rearrangement. Uncoupling IL-1β/IL-1R1 signaling prevents disease, providing a causal link. Glomeruli of patients with FSGS lack DAF and stain positive for C3d, and urinary C3a positively correlates with the degree of proteinuria. Together, our data indicate that the development and progression of glomerulosclerosis involve loss of podocyte DAF, triggering local, complement-dependent, IL-1β–induced podocyte injury, potentially identifying new therapeutic targets.
Collapse
Affiliation(s)
- Andrea Angeletti
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY.,Division of Nephrology, Dialysis, Transplantation, Giannina Gaslini Children's Hospital, Genoa, Italy
| | - Chiara Cantarelli
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY.,Dipartimento di Medicina e Chirurgia Università di Parma, UO Nefrologia, Azienda Ospedaliera-Universitaria Parma, Parma, Italy
| | - Astgik Petrosyan
- GOFARR Laboratory for Organ Regenerative Research and Cell Therapeutics in Urology, Children's Hospital Los Angeles, Los Angeles, CA.,Division of Urology, Saban Research Institute, University of Southern California, Los Angeles, CA
| | - Sofia Andrighetto
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY.,Renal Unit, Department of Medicine, University Hospital of Verona, Verona, Italy
| | - Kelly Budge
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Vivette D D'Agati
- Department of Pathology, College of Physicians and Surgeons, Columbia University, New York, NY
| | - Susan Hartzell
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Deborah Malvi
- "F. Addarii" Institute of Oncology and Transplantation Pathology, Bologna University, Bologna, Italy
| | - Chiara Donadei
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY.,Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Policlinico Sant'Orsola-Malpighi, Bologna, Italy
| | - Joshua M Thurman
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO
| | | | - John Cijiang He
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Wenzhen Xiao
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Kirk N Campbell
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jenny Wong
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Clara Fischman
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Joaquin Manrique
- Nephrology Service, Complejo Hospitalario de Navarra, Pamplona, Spain
| | - Gianluigi Zaza
- Renal Unit, Department of Medicine, University Hospital of Verona, Verona, Italy
| | - Enrico Fiaccadori
- Dipartimento di Medicina e Chirurgia Università di Parma, UO Nefrologia, Azienda Ospedaliera-Universitaria Parma, Parma, Italy
| | - Gaetano La Manna
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Policlinico Sant'Orsola-Malpighi, Bologna, Italy
| | - Miguel Fribourg
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jeremy Leventhal
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Stefano Da Sacco
- GOFARR Laboratory for Organ Regenerative Research and Cell Therapeutics in Urology, Children's Hospital Los Angeles, Los Angeles, CA.,Division of Urology, Saban Research Institute, University of Southern California, Los Angeles, CA
| | - Laura Perin
- GOFARR Laboratory for Organ Regenerative Research and Cell Therapeutics in Urology, Children's Hospital Los Angeles, Los Angeles, CA.,Division of Urology, Saban Research Institute, University of Southern California, Los Angeles, CA
| | - Peter S Heeger
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Paolo Cravedi
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| |
Collapse
|
45
|
Predicting pleural metastasis by detecting CD55 using an ultrasound-enhanced scintillation proximity assay. J Radioanal Nucl Chem 2021. [DOI: 10.1007/s10967-020-07559-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
46
|
The complement system in primary Sjögren's syndrome: the expression of certain cascade and regulatory proteins in labial salivary glands - observational study. Reumatologia 2020; 58:357-366. [PMID: 33456078 PMCID: PMC7792541 DOI: 10.5114/reum.2020.102000] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/24/2020] [Indexed: 11/17/2022] Open
Abstract
Introduction The complement cascade and regulatory proteins are involved in the pathogenesis of the Sjögren's syndrome and other autoimmune diseases. The complement activation via the alternative pathway was recognized as a major pathogenic mechanism in autoimmune conditions. The aim of this study was to assess expression of complement cascade components and regulatory proteins in minor salivary glands in patients with primary Sjögren's syndrome (pSS). Materials and methods The expression of C1q and C5b-9 - membrane attack complex and regulatory proteins such as: membrane cofactor protein (MCP), decay-accelerating factor (DAF) and protectin were examined using immunochemistry method in specimens from biopsy of minor salivary glands in pSS patients. The biopsy material was obtained from 20 pSS patients, 5 patients with non-specific sialadenitis and from 5 patients with suspicion of dryness syndrome without sialadenitis confirmation. Results None of the examined samples showed the expression of C1q or the effector C5b-9. Membrane cofactor protein expression was lower in pSS group than in both non-specific sialadenitis and noninflamed salivary glands. The inflammatory cells in pSS samples partially expressed MCP. There were differences in the sites and intensity of membrane protectin expression exclusively on the luminal surfaces in pSS; on the luminal and, partially, antiluminal surface in non-specific inflammation, and on the entire cell surface in unaffected salivary glands. There were no DAF expression in salivary gland tissue in biopsy specimens in all studied subjects. Conclusions The study demonstrated the absence of complement-cascade proteins (C1q, MAC) in the salivary glands of pSS patients, which may indicated a lack of local complement activation via the classical pathway and the observed gland tissue damage being due to a mechanism other than MAC-induced cytolysis. The differences in the expression of complement regulatory proteins between pSS, non-specific sialadenitis, and normal salivary glands may indicate that alternative functions of these regulatory proteins may be of greater significance in pSS. Low MCP expression in pSS in comparison with non-specific sialadenitis and normal salivary glands, may suggest altered modulation of cell-mediated immunity in pSS. The differences in the location and intensity of protectin (CD59) expression indicates a possibility of reducing the proinflammatory effect of protectin in pSS.
Collapse
|
47
|
Wymann S, Dai Y, Nair AG, Cao H, Powers GA, Schnell A, Martin-Roussety G, Leong D, Simmonds J, Lieu KG, de Souza MJ, Mischnik M, Taylor S, Ow SY, Spycher M, Butcher RE, Pearse M, Zuercher AW, Baz Morelli A, Panousis C, Wilson MJ, Rowe T, Hardy MP. A novel soluble complement receptor 1 fragment with enhanced therapeutic potential. J Biol Chem 2020; 296:100200. [PMID: 33334893 PMCID: PMC7948397 DOI: 10.1074/jbc.ra120.016127] [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: 09/22/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 12/13/2022] Open
Abstract
Human complement receptor 1 (HuCR1) is a pivotal regulator of complement activity, acting on all three complement pathways as a membrane-bound receptor of C3b/C4b, C3/C5 convertase decay accelerator, and cofactor for factor I-mediated cleavage of C3b and C4b. In this study, we sought to identify a minimal soluble fragment of HuCR1, which retains the complement regulatory activity of the wildtype protein. To this end, we generated recombinant, soluble, and truncated versions of HuCR1 and compared their ability to inhibit complement activation in vitro using multiple assays. A soluble form of HuCR1, truncated at amino acid 1392 and designated CSL040, was found to be a more potent inhibitor than all other truncation variants tested. CSL040 retained its affinity to both C3b and C4b as well as its cleavage and decay acceleration activity and was found to be stable under a range of buffer conditions. Pharmacokinetic studies in mice demonstrated that the level of sialylation is a major determinant of CSL040 clearance in vivo. CSL040 also showed an improved pharmacokinetic profile compared with the full extracellular domain of HuCR1. The in vivo effects of CSL040 on acute complement-mediated kidney damage were tested in an attenuated passive antiglomerular basement membrane antibody-induced glomerulonephritis model. In this model, CSL040 at 20 and 60 mg/kg significantly attenuated kidney damage at 24 h, with significant reductions in cellular infiltrates and urine albumin, consistent with protection from kidney damage. CSL040 thus represents a potential therapeutic candidate for the treatment of complement-mediated disorders.
Collapse
Affiliation(s)
- Sandra Wymann
- Research and Development, CSL Behring AG, Bern, Switzerland
| | - Yun Dai
- CSL Ltd, Bio21 Institute, Victoria, Australia
| | - Anup G Nair
- CSL Ltd, Bio21 Institute, Victoria, Australia
| | - Helen Cao
- CSL Ltd, Bio21 Institute, Victoria, Australia
| | | | - Anna Schnell
- Research and Development, CSL Behring AG, Bern, Switzerland
| | | | - David Leong
- CSL Ltd, Bio21 Institute, Victoria, Australia
| | | | - Kim G Lieu
- CSL Ltd, Bio21 Institute, Victoria, Australia
| | | | - Marcel Mischnik
- Research and Development, CSL Behring GmbH, Marburg, Germany
| | | | - Saw Yen Ow
- CSL Ltd, Bio21 Institute, Victoria, Australia
| | - Martin Spycher
- Research and Development, CSL Behring AG, Bern, Switzerland
| | | | | | | | | | | | | | - Tony Rowe
- CSL Ltd, Bio21 Institute, Victoria, Australia
| | | |
Collapse
|
48
|
Hernández Cordero AI, Li X, Yang CX, Milne S, Bossé Y, Joubert P, Timens W, van den Berge M, Nickle D, Hao K, Sin DD. Gene expression network analysis provides potential targets against SARS-CoV-2. Sci Rep 2020; 10:21863. [PMID: 33318519 PMCID: PMC7736291 DOI: 10.1038/s41598-020-78818-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 11/30/2020] [Indexed: 01/02/2023] Open
Abstract
Cell entry of SARS-CoV-2, the novel coronavirus causing COVID-19, is facilitated by host cell angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2). We aimed to identify and characterize genes that are co-expressed with ACE2 and TMPRSS2, and to further explore their biological functions and potential as druggable targets. Using the gene expression profiles of 1,038 lung tissue samples, we performed a weighted gene correlation network analysis (WGCNA) to identify modules of co-expressed genes. We explored the biology of co-expressed genes using bioinformatics databases, and identified known drug-gene interactions. ACE2 was in a module of 681 co-expressed genes; 10 genes with moderate-high correlation with ACE2 (r > 0.3, FDR < 0.05) had known interactions with existing drug compounds. TMPRSS2 was in a module of 1,086 co-expressed genes; 31 of these genes were enriched in the gene ontology biologic process 'receptor-mediated endocytosis', and 52 TMPRSS2-correlated genes had known interactions with drug compounds. Dozens of genes are co-expressed with ACE2 and TMPRSS2, many of which have plausible links to COVID-19 pathophysiology. Many of the co-expressed genes are potentially targetable with existing drugs, which may accelerate the development of COVID-19 therapeutics.
Collapse
Affiliation(s)
| | - Xuan Li
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, BC, Canada
| | - Chen Xi Yang
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, BC, Canada
| | - Stephen Milne
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, BC, Canada
- Division of Respiratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Yohan Bossé
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec City, QC, Canada
| | - Philippe Joubert
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec City, QC, Canada
| | - Wim Timens
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Maarten van den Berge
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - David Nickle
- Merck Research Laboratories, Genetics and Pharmacogenomics, Boston, MA, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine At Mount Sinai, New York, NY, USA
| | - Don D Sin
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, BC, Canada
- Division of Respiratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
49
|
Khan MA, Shamma T, Kazmi S, Altuhami A, Ahmed HA, Assiri AM, Broering DC. Hypoxia-induced complement dysregulation is associated with microvascular impairments in mouse tracheal transplants. J Transl Med 2020; 18:147. [PMID: 32234039 PMCID: PMC7110829 DOI: 10.1186/s12967-020-02305-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 03/16/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Complement Regulatory Proteins (CRPs), especially CD55 primarily negate complement factor 3-mediated injuries and maintain tissue homeostasis during complement cascade activation. Complement activation and regulation during alloimmune inflammation contribute to allograft injury and therefore we proposed to investigate a crucial pathological link between vascular expression of CD55, active-C3, T cell immunity and associated microvascular tissue injuries during allograft rejection. METHODS Balb/c→C57BL/6 allografts were examined for microvascular deposition of CD55, C3d, T cells, and associated tissue microvascular impairments during rejection in mouse orthotopic tracheal transplantation. RESULTS Our findings demonstrated that hypoxia-induced early activation of HIF-1α favors a cell-mediated inflammation (CD4+, CD8+, and associated proinflammatory cytokines, IL-2 and TNF-α), which proportionally triggers the downregulation of CRP-CD55, and thereby augments the uncontrolled release of active-C3, and Caspase-3 deposition on CD31+ graft vascular endothelial cells. These molecular changes are pathologically associated with microvascular deterioration (low tissue O2 and Blood flow) and subsequent airway epithelial injuries of rejecting allografts as compared to non-rejecting syngrafts. CONCLUSION Together, these findings establish a pathological correlation between complement dysregulation, T cell immunity, and microvascular associated injuries during alloimmune inflammation in transplantation.
Collapse
Affiliation(s)
- Mohammad Afzal Khan
- Organ Transplant Research Section, Comparative Medicine Department, King Faisal Specialist Hospital and Research Centre, Riyadh, Kingdom of Saudi Arabia.
| | - Talal Shamma
- Organ Transplant Research Section, Comparative Medicine Department, King Faisal Specialist Hospital and Research Centre, Riyadh, Kingdom of Saudi Arabia
| | - Shadab Kazmi
- Organ Transplant Research Section, Comparative Medicine Department, King Faisal Specialist Hospital and Research Centre, Riyadh, Kingdom of Saudi Arabia
| | - Abdullah Altuhami
- Organ Transplant Research Section, Comparative Medicine Department, King Faisal Specialist Hospital and Research Centre, Riyadh, Kingdom of Saudi Arabia
| | - Hala Abdalrahman Ahmed
- Comparative Medicine Department, King Faisal Specialist Hospital and Research Centre, Riyadh, Kingdom of Saudi Arabia
| | - Abdullah Mohammed Assiri
- Comparative Medicine Department, King Faisal Specialist Hospital and Research Centre, Riyadh, Kingdom of Saudi Arabia.,College of Medicine, Alfaisal University, Riyadh, Kingdom of Saudi Arabia.,Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Kingdom of Saudi Arabia
| | - Dieter Clemens Broering
- Organ Transplant Research Section, Comparative Medicine Department, King Faisal Specialist Hospital and Research Centre, Riyadh, Kingdom of Saudi Arabia
| |
Collapse
|
50
|
Helgadottir HT, Lundin P, Wallén Arzt E, Lindström AK, Graff C, Eriksson M. Somatic mutation that affects transcription factor binding upstream of CD55 in the temporal cortex of a late-onset Alzheimer disease patient. Hum Mol Genet 2020; 28:2675-2685. [PMID: 31216356 PMCID: PMC6688063 DOI: 10.1093/hmg/ddz085] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 03/20/2019] [Accepted: 04/18/2019] [Indexed: 01/09/2023] Open
Abstract
Alzheimer’s disease (AD) is the most common neurodegenerative disease worldwide. Familial cases suggest genetic components; however, monogenetic causes are few, and the vast majority of incidences have unknown cause. Sequencing efforts have focused on germline mutations, but improved technology has opened up for studies on somatic mutations in affected brain tissue samples. Here we use ultra-deep sequencing on brain and blood from early-onset AD (EOAD) and late-onset AD (LOAD) patients and non-AD individuals (n = 16). In total, 2.86 Mb of genomic regions, previously associated with AD, were targeted included 28 genes and upstream and downstream regulatory regions. Tailored downstream bioinformatics filtering identified 11 somatic single nucleotide variants in the temporal cortex in AD patients and none in the controls. One variant was validated to be present at 0.4% allele frequency in temporal cortex of a LOAD patient. This variant was predicted to affect transcription factor binding sites upstream of the CD55 gene, contributing to AD pathogenesis by affecting the complement system. Our results suggest that future studies targeting larger portions of the genome for somatic mutation analysis are important to obtain an increased understanding for the molecular basis of both EOAD and LOAD.
Collapse
Affiliation(s)
- Hafdis T Helgadottir
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Pär Lundin
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Emelie Wallén Arzt
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Anna-Karin Lindström
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division for Neurogeriatrics, Karolinska Institutet, Solna, Sweden.,Unit for Hereditary Dementias, Theme Aging, Karolinska University Hospital, Solna, Sweden
| | - Caroline Graff
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division for Neurogeriatrics, Karolinska Institutet, Solna, Sweden.,Unit for Hereditary Dementias, Theme Aging, Karolinska University Hospital, Solna, Sweden
| | - Maria Eriksson
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden
| |
Collapse
|