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Liu X, Yang M, Li J, Liu H, Dong Y, Zheng J, Huang Y. Identification of CFH and FHL2 as biomarkers for idiopathic pulmonary fibrosis. Front Med (Lausanne) 2024; 11:1363643. [PMID: 38784225 PMCID: PMC11111937 DOI: 10.3389/fmed.2024.1363643] [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: 01/03/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Background Idiopathic pulmonary fibrosis (IPF) is a fatal disease of unknown etiology with a poor prognosis, characterized by a lack of effective diagnostic and therapeutic interventions. The role of immunity in the pathogenesis of IPF is significant, yet remains inadequately understood. This study aimed to identify potential key genes in IPF and their relationship with immune cells by integrated bioinformatics analysis and verify by in vivo and in vitro experiments. Methods Gene microarray data were obtained from the Gene Expression Omnibus (GEO) for differential expression analysis. The differentially expressed genes (DEGs) were identified and subjected to functional enrichment analysis. By utilizing a combination of three machine learning algorithms, specific genes associated with idiopathic pulmonary fibrosis (IPF) were pinpointed. Then their diagnostic significance and potential co-regulators were elucidated. We further analyzed the correlation between key genes and immune infiltrating cells via single-sample gene set enrichment analysis (ssGSEA). Subsequently, a single-cell RNA sequencing data (scRNA-seq) was used to explore which cell types expressed key genes in IPF samples. Finally, a series of in vivo and in vitro experiments were conducted to validate the expression of candidate genes by western blot (WB), quantitative real-time PCR (qRT-PCR), and immunohistochemistry (IHC) analysis. Results A total of 647 DEGs of IPF were identified based on two datasets, including 225 downregulated genes and 422 upregulated genes. They are closely related to biological functions such as cell migration, structural organization, immune cell chemotaxis, and extracellular matrix. CFH and FHL2 were identified as key genes with diagnostic accuracy for IPF by three machine learning algorithms. Analysis using ssGSEA revealed a significant association of both CFH and FHL2 with diverse immune cells, such as B cells and NK cells. Further scRNA-seq analysis indicated CFH and FHL2 were specifically upregulated in human IPF tissues, which was confirmed by in vitro and in vivo experiments. Conclusion In this study, CFH and FHL2 have been identified as novel potential biomarkers for IPF, with potential diagnostic utility in future clinical applications. Subsequent investigations into the functions of these genes in IPF and their interactions with immune cells may enhance comprehension of the disease's pathogenesis and facilitate the identification of therapeutic targets.
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Affiliation(s)
- Xingchen Liu
- Department of Pathology, The First Affiliated Hospital of Naval Medical University, Navy Medical University, Shanghai, China
| | - Meng Yang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Naval Medical University, Navy Medical University, Shanghai, China
| | - Jiayu Li
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Naval Medical University, Navy Medical University, Shanghai, China
| | - Hangxu Liu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Naval Medical University, Navy Medical University, Shanghai, China
| | - Yuchao Dong
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Naval Medical University, Navy Medical University, Shanghai, China
| | - Jianming Zheng
- Department of Pathology, The First Affiliated Hospital of Naval Medical University, Navy Medical University, Shanghai, China
| | - Yi Huang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Naval Medical University, Navy Medical University, Shanghai, China
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Obata S, Vaz de Castro PAS, Riella LV, Cravedi P. Recurrent C3 glomerulopathy after kidney transplantation. Transplant Rev (Orlando) 2024; 38:100839. [PMID: 38412598 DOI: 10.1016/j.trre.2024.100839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 02/17/2024] [Accepted: 02/19/2024] [Indexed: 02/29/2024]
Abstract
The complement system is part of innate immunity and is pivotal in protecting the body against pathogens and maintaining host homeostasis. Activation of the complement system is triggered through multiple pathways, including antibody deposition, a mannan-binding lectin, or activated complement deposition. C3 glomerulopathy (C3G) is a rare glomerular disease driven by complement dysregulation with high post-transplantation recurrence rates. Its treatment is mainly based on immunosuppressive therapies, specifically mycophenolate mofetil and glucocorticoids. Recent years have seen significant progress in understanding complement biology and its role in C3G pathophysiology. New complement-tergeting treatments have been developed and initial trials have shown promising results. However, challenges persist in C3G, with recurrent post-transplantation cases leading to suboptimal outcomes. This review discusses the pathophysiology and management of C3G, with a focus on its recurrence after kidney transplantation.
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Affiliation(s)
- Shota Obata
- Precision Immunology Institute, Translational Transplant Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Pedro A S Vaz de Castro
- Interdisciplinary Laboratory of Medical Investigation, Unit of Pediatric Nephrology, Faculty of Medicine, Federal University of Minas Gerais (UFMG), Brazil
| | - Leonardo V Riella
- Division of Nephrology and Center for Transplantation Sciences, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Paolo Cravedi
- Precision Immunology Institute, Translational Transplant Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America.
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Liu YH, Luo C, Golding SG, Ioffe JB, Zhou XM. Tradeoffs in alignment and assembly-based methods for structural variant detection with long-read sequencing data. Nat Commun 2024; 15:2447. [PMID: 38503752 PMCID: PMC10951360 DOI: 10.1038/s41467-024-46614-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 03/04/2024] [Indexed: 03/21/2024] Open
Abstract
Long-read sequencing offers long contiguous DNA fragments, facilitating diploid genome assembly and structural variant (SV) detection. Efficient and robust algorithms for SV identification are crucial with increasing data availability. Alignment-based methods, favored for their computational efficiency and lower coverage requirements, are prominent. Alternative approaches, relying solely on available reads for de novo genome assembly and employing assembly-based tools for SV detection via comparison to a reference genome, demand significantly more computational resources. However, the lack of comprehensive benchmarking constrains our comprehension and hampers further algorithm development. Here we systematically compare 14 read alignment-based SV calling methods (including 4 deep learning-based methods and 1 hybrid method), and 4 assembly-based SV calling methods, alongside 4 upstream aligners and 7 assemblers. Assembly-based tools excel in detecting large SVs, especially insertions, and exhibit robustness to evaluation parameter changes and coverage fluctuations. Conversely, alignment-based tools demonstrate superior genotyping accuracy at low sequencing coverage (5-10×) and excel in detecting complex SVs, like translocations, inversions, and duplications. Our evaluation provides performance insights, highlighting the absence of a universally superior tool. We furnish guidelines across 31 criteria combinations, aiding users in selecting the most suitable tools for diverse scenarios and offering directions for further method development.
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Affiliation(s)
- Yichen Henry Liu
- Department of Computer Science, Vanderbilt University, 37235, Nashville, TN, USA
| | - Can Luo
- Department of Biomedical Engineering, Vanderbilt University, 37235, Nashville, TN, USA
| | - Staunton G Golding
- Department of Biomedical Engineering, Vanderbilt University, 37235, Nashville, TN, USA
| | - Jacob B Ioffe
- Department of Computer Science, Vanderbilt University, 37235, Nashville, TN, USA
| | - Xin Maizie Zhou
- Department of Computer Science, Vanderbilt University, 37235, Nashville, TN, USA.
- Department of Biomedical Engineering, Vanderbilt University, 37235, Nashville, TN, USA.
- Data Science Institute, Vanderbilt University, 37235, Nashville, TN, USA.
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Spasiano A, Palazzetti D, Dimartino L, Bruno F, Baccaro R, Pesce F, Grandaliano G. Underlying Genetics of aHUS: Which Connection with Outcome and Treatment Discontinuation? Int J Mol Sci 2023; 24:14496. [PMID: 37833944 PMCID: PMC10572301 DOI: 10.3390/ijms241914496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/15/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
Atypical hemolytic uremic syndrome (aHUS) is a rare disease caused by a genetic dysregulation of the alternative complement pathway, characterized by thrombocytopenia, hemolytic anemia, and acute kidney injury, and included in the group of thrombotic microangiopathies. With the introduction of humanized monoclonal antibodies that inhibit C5 activation, the natural history of aHUS completely changed, with a better prognosis, a quick recovery of renal function, and a significant reduction of end-stage renal disease incidence. Nowadays, there is an increasing interest in the molecular and genetic bases of this severe disease. The aim of this narrative review is to provide readers with a practical guide about different possible involved genes, elucidating the specific role of each transcribed protein in the pathogenesis of aHUS. Moreover, we analyzed the main current evidence about the relationship among genetic mutations, outcomes, and the risk of recurrence of this manifold disease.
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Affiliation(s)
- Andrea Spasiano
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (A.S.); (G.G.)
- Nephrology Unit, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario A. Gemelli, 00168 Rome, Italy
| | - Daniela Palazzetti
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (A.S.); (G.G.)
- Nephrology Unit, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario A. Gemelli, 00168 Rome, Italy
| | - Lucrezia Dimartino
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (A.S.); (G.G.)
- Nephrology Unit, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario A. Gemelli, 00168 Rome, Italy
| | - Francesca Bruno
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (A.S.); (G.G.)
- Nephrology Unit, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario A. Gemelli, 00168 Rome, Italy
| | - Rocco Baccaro
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (A.S.); (G.G.)
- Nephrology Unit, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario A. Gemelli, 00168 Rome, Italy
| | - Francesco Pesce
- Division of Renal Medicine, Fatebenefratelli Isola Tiberina—Gemelli Isola, 00186 Rome, Italy
| | - Giuseppe Grandaliano
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (A.S.); (G.G.)
- Nephrology Unit, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario A. Gemelli, 00168 Rome, Italy
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Dubowsky JG, Estevez JJ, Craig JE, Appukuttan B, Carr JM. Disease profiles in the Indigenous Australian population are suggestive of a common complement control haplotype. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023:105453. [PMID: 37245779 DOI: 10.1016/j.meegid.2023.105453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/05/2023] [Accepted: 05/23/2023] [Indexed: 05/30/2023]
Abstract
Aboriginal and Torres Strait Islander People (respectfully referred to as Indigenous Australians herein) are disparately burdened by many infectious and chronic diseases relative to Australians with European genetic ancestry. Some of these diseases are described in other populations to be influenced by the inherited profile of complement genes. These include complement factor B, H, I and complement factor H-related (CFHR) genes that can contribute to a polygenic complotype. Here the focus is on the combined deletion of CFHR1 and 3 to form a common haplotype (CFHR3-1Δ). The prevalence of CFHR3-1Δ is high in people with Nigerian and African American genetic ancestry and correlates to a higher frequency and severity of systemic lupus erythematosus (SLE) but a lower prevalence of age-related macular degeneration (AMD) and IgA-nephropathy (IgAN). This pattern of disease is similarly observed among Indigenous Australian communities. Additionally, the CFHR3-1Δ complotype is also associated with increased susceptibility to infection with pathogens, such as Neisseria meningitidis and Streptococcus pyogenes, which also have high incidences in Indigenous Australian communities. The prevalence of these diseases, while likely influenced by social, political, environmental and biological factors, including variants in other components of the complement system, may also be suggestive of the CFHR3-1Δ haplotype in Indigenous Australians. These data highlight a need to define the Indigenous Australian complotypes, which may lead to the discovery of new risk factors for common diseases and progress towards precision medicines for treating complement-associated diseases in Indigenous and non-Indigenous populations. Herein, the disease profiles suggestive of a common complement CFHR3-1Δ control haplotype are examined.
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Affiliation(s)
- Joshua G Dubowsky
- Microbiology and Infectious Diseases, College of Medicine and Public Health, and Flinders Health and Medical Research Institute, Flinders University, Bedford Park, South Australia, Australia
| | - Jose J Estevez
- Wardliparingga Aboriginal Health Equity Theme, South Australia Health and Medical Research Institute, Adelaide, South Australia, Australia; Flinders Centre for Ophthalmology, Eye and Vision Research, Department of Ophthalmology, Flinders University, Bedford Park, South Australia, Australia; Caring Futures Institute, College of Nursing and Health Sciences, Optometry and Vision Science, Flinders University, Adelaide, Australia
| | - Jamie E Craig
- Flinders Centre for Ophthalmology, Eye and Vision Research, Department of Ophthalmology, Flinders University, Bedford Park, South Australia, Australia
| | - Binoy Appukuttan
- Molecular Medical Science, College of Medicine and Public Health, Flinders University, Bedford Park, South Australia, Australia
| | - Jillian M Carr
- Microbiology and Infectious Diseases, College of Medicine and Public Health, and Flinders Health and Medical Research Institute, Flinders University, Bedford Park, South Australia, Australia.
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Gastoldi S, Aiello S, Galbusera M, Breno M, Alberti M, Bresin E, Mele C, Piras R, Liguori L, Santarsiero D, Benigni A, Remuzzi G, Noris M. An ex vivo test to investigate genetic factors conferring susceptibility to atypical haemolytic uremic syndrome. Front Immunol 2023; 14:1112257. [PMID: 36845135 PMCID: PMC9949374 DOI: 10.3389/fimmu.2023.1112257] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/20/2023] [Indexed: 02/11/2023] Open
Abstract
Introduction Comprehensive genetic analysis is essential to clinical care of patients with atypical haemolytic uremic syndrome (aHUS) to reinforce diagnosis, and to guide treatment. However, the characterization of complement gene variants remains challenging owing to the complexity of functional studies with mutant proteins. This study was designed: 1) To identify a tool for rapid functional determination of complement gene variants; 2) To uncover inherited complement dysregulation in aHUS patients who do not carry identified gene variants. Methods To address the above goals, we employed an ex-vivo assay of serum-induced C5b-9 formation on ADP-activated endothelial cells in 223 subjects from 60 aHUS pedigrees (66 patients and 157 unaffected relatives). Results Sera taken from all aHUS patients in remission induced more C5b-9 deposition than control sera, independently from the presence of complement gene abnormalities. To avoid the possible confounding effects of chronic complement dysregulation related to aHUS status, and considering the incomplete penetrance for all aHUS-associated genes, we used serum from unaffected relatives. In control studies, 92.7% of unaffected relatives with known pathogenic variants exhibited positive serum-induced C5b-9 formation test, documenting a high sensitivity of the assay to identify functional variants. The test was also specific, indeed it was negative in all non-carrier relatives and in relatives with variants non-segregating with aHUS. All but one variants in aHUS-associated genes predicted in-silico as likely pathogenic or of uncertain significance (VUS) or likely benign resulted as pathogenic in the C5b-9 assay. At variance, variants in putative candidate genes did not exhibit a functional effect, with the exception of a CFHR5 variant. The C5b-9 assay in relatives was helpful in defining the relative functional effect of rare variants in 6 pedigrees in which the proband carried more than one genetic abnormality. Finally, for 12 patients without identified rare variants, the C5b-9 test in parents unmasked a genetic liability inherited from an unaffected parent. Discussion In conclusion, the serum-induced C5b-9 formation test in unaffected relatives of aHUS patients may be a tool for rapid functional evaluation of rare complement gene variants. When combined with exome sequencing the assay might be of help in variant selection, to identify new aHUS-associated genetic factors.
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Affiliation(s)
- Sara Gastoldi
- Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | - Sistiana Aiello
- Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | - Miriam Galbusera
- Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | - Matteo Breno
- Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | - Marta Alberti
- Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | - Elena Bresin
- Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | - Caterina Mele
- Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | - Rossella Piras
- Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | - Lucia Liguori
- Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | - Donata Santarsiero
- Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | - Ariela Benigni
- Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | - Giuseppe Remuzzi
- Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
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Piras R, Valoti E, Alberti M, Bresin E, Mele C, Breno M, Liguori L, Donadelli R, Rigoldi M, Benigni A, Remuzzi G, Noris M. CFH and CFHR structural variants in atypical Hemolytic Uremic Syndrome: Prevalence, genomic characterization and impact on outcome. Front Immunol 2023; 13:1011580. [PMID: 36793547 PMCID: PMC9923232 DOI: 10.3389/fimmu.2022.1011580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 12/28/2022] [Indexed: 01/31/2023] Open
Abstract
Introduction Atypical hemolytic uremic syndrome (aHUS) is a rare disease that manifests with microangiopathic hemolytic anemia, thrombocytopenia, and acute renal failure, and is associated with dysregulation of the alternative complement pathway. The chromosomal region including CFH and CFHR1-5 is rich in repeated sequences, favoring genomic rearrangements that have been reported in several patients with aHUS. However, there are limited data on the prevalence of uncommon CFH-CFHR genomic rearrangements in aHUS and their impact on disease onset and outcomes. Methods In this study, we report the results of CFH-CFHR Copy Number Variation (CNV) analysis and the characterization of resulting structural variants (SVs) in a large cohort of patients, including 258 patients with primary aHUS and 92 with secondary forms. Results We found uncommon SVs in 8% of patients with primary aHUS: 70% carried rearrangements involving CFH alone or CFH and CFHR (group A; n=14), while 30% exhibited rearrangements including only CFHRs (group B; n=6). In group A, 6 patients presented CFH::CFHR1 hybrid genes, 7 patients carried duplications in the CFH-CFHR region that resulted either in the substitution of the last CFHR1 exon(s) with those of CFH (CFHR1::CFH reverse hybrid gene) or in an internal CFH duplication. In group A, the large majority of aHUS acute episodes not treated with eculizumab (12/13) resulted in chronic ESRD; in contrast, anti-complement therapy induced remission in 4/4 acute episodes. aHUS relapse occurred in 6/7 grafts without eculizumab prophylaxis and in 0/3 grafts with eculizumab prophylaxis. In group B, 5 subjects had the CFHR31-5::CFHR410 hybrid gene and one had 4 copies of CFHR1 and CFHR4. Compared with group A, patients in group B exhibited a higher prevalence of additional complement abnormalities and earlier disease onset. However, 4/6 patients in this group underwent complete remission without eculizumab treatment. In secondary forms we identified uncommon SVs in 2 out of 92 patients: the CFHR31-5::CFHR410 hybrid and a new internal duplication of CFH. Discussion In conclusion, these data highlight that uncommon CFH-CFHR SVs are frequent in primary aHUS and quite rare in secondary forms. Notably, genomic rearrangements involving the CFH are associated with a poor prognosis but carriers respond to anti-complement therapy.
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Abstract
Dysregulation and accelerated activation of the alternative pathway (AP) of complement is known to cause or accentuate several pathologic conditions in which kidney injury leads to the appearance of hematuria and proteinuria and ultimately to the development of chronic renal failure. Multiple genetic and acquired defects involving plasma- and membrane-associated proteins are probably necessary to impair the protection of host tissues and to confer a significant predisposition to AP-mediated kidney diseases. This review aims to explore how our current understanding will make it possible to identify the mechanisms that underlie AP-mediated kidney diseases and to discuss the available clinical evidence that supports complement-directed therapies. Although the value of limiting uncontrolled complement activation has long been recognized, incorporating complement-targeted treatments into clinical use has proved challenging. Availability of anti-complement therapy has dramatically transformed the outcome of atypical hemolytic uremic syndrome, one of the most severe kidney diseases. Innovative drugs that directly counteract AP dysregulation have also opened new perspectives for the management of other kidney diseases in which complement activation is involved. However, gained experience indicates that the choice of drug should be tailored to each patient's characteristics, including clinical, histologic, genetic, and biochemical parameters. Successfully treating patients requires further research in the field and close collaboration between clinicians and researchers who have special expertise in the complement system.
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Affiliation(s)
- Erica Daina
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | - Monica Cortinovis
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | - Giuseppe Remuzzi
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
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Heiderscheit AK, Hauer JJ, Smith RJH. C3 glomerulopathy: Understanding an ultra-rare complement-mediated renal disease. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2022; 190:344-357. [PMID: 35734939 PMCID: PMC9613507 DOI: 10.1002/ajmg.c.31986] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/27/2022] [Accepted: 06/10/2022] [Indexed: 01/29/2023]
Abstract
C3 glomerulopathy (C3G) describes a pathologic pattern of injury diagnosed by renal biopsy. It is characterized by the dominant deposition of the third component of complement (C3) in the renal glomerulus as resolved by immunofluorescence microscopy. The underlying pathophysiology is driven by dysregulation of the alternative pathway of complement in the fluid-phase and in the glomerular microenvironment. Characterization of clinical features and a targeted evaluation for indices and drivers of complement dysregulation are necessary for optimal patient care. Autoantibodies to the C3 and C5 convertases of complement are the most commonly detected drivers of complement dysregulation, although genetic mutations in complement genes can also be found. Approximately half of patients progress to end-stage renal disease within 10 years of diagnosis, and, while transplantation is a viable option, there is high risk for disease recurrence and allograft failure. This poor outcome reflects the lack of disease-specific therapy for C3G, relegating patients to symptomatic treatment to minimize proteinuria and suppress renal inflammation. Fortunately, the future is bright as several anti-complement drugs are currently in clinical trials.
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Affiliation(s)
- Amanda K. Heiderscheit
- Molecular Otolaryngology and Renal Research Laboratories, Carver College of MedicineUniversity of IowaIowa CityIowaUSA,Graduate PhD Program in Immunology, Carver College of MedicineUniversity of IowaIowa CityIowaUSA
| | - Jill J. Hauer
- Molecular Otolaryngology and Renal Research Laboratories, Carver College of MedicineUniversity of IowaIowa CityIowaUSA
| | - Richard J. H. Smith
- Molecular Otolaryngology and Renal Research Laboratories, Carver College of MedicineUniversity of IowaIowa CityIowaUSA,Graduate PhD Program in Immunology, Carver College of MedicineUniversity of IowaIowa CityIowaUSA
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Unraveling Structural Rearrangements of the CFH Gene Cluster in Atypical Hemolytic Uremic Syndrome Patients Using Molecular Combing and Long-Fragment Targeted Sequencing. J Mol Diagn 2022; 24:619-631. [PMID: 35398599 DOI: 10.1016/j.jmoldx.2022.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 02/01/2022] [Accepted: 02/25/2022] [Indexed: 11/22/2022] Open
Abstract
Complement factor H (CFH) and its related proteins have an essential role in regulating the alternative pathway of the complement system. Mutations and structural variants (SVs) of the CFH gene cluster, consisting of CFH and its five related genes (CFHR1-5), have been reported in renal pathologies as well as in complex immune diseases like age-related macular degeneration and systemic lupus erythematosus. SV analysis of this cluster is challenging because of its high degree of sequence homology. Following first-line next-generation sequencing gene panel sequencing, we applied Genomic Vision's Molecular Combing Technology to detect and visualize SVs within the CFH gene cluster and resolve its structural haplotypes completely. This approach was tested in three patients with atypical hemolytic uremic syndrome and known SVs and 18 patients with atypical hemolytic uremic syndrome or complement factor 3 glomerulopathy with unknown CFH gene cluster haplotypes. Three SVs, a CFH/CFHR1 hybrid gene in two patients and a rare heterozygous CFHR4/CFHR1 deletion in trans with the common CFHR3/CFHR1 deletion in a third patient, were newly identified. For the latter, the breakpoints were determined using a targeted enrichment approach for long DNA fragments (Samplix Xdrop) in combination with Oxford Nanopore sequencing. Molecular combing in addition to next-generation sequencing was able to improve the molecular genetic yield in this pilot study. This (cost-)effective approach warrants validation in larger cohorts with CFH/CFHR-associated disease.
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11
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Márquez-Tirado B, Gutiérrez-Tenorio J, Tortajada A, Lucientes Continente L, Caravaca-Fontán F, Malik TH, Roldán Montero R, Elías S, Saiz Gonzalez A, Fernández-Juarez G, Sánchez-Corral P, Pickering MC, Praga M, Rodríguez de Córdoba S, Goicoechea de Jorge E. Factor H-Related Protein 1 Drives Disease Susceptibility and Prognosis in C3 Glomerulopathy. J Am Soc Nephrol 2022; 33:1137-1153. [PMID: 35545301 PMCID: PMC9161805 DOI: 10.1681/asn.2021101318] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/01/2022] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND C3 glomerulopathy (C3G) is a heterogeneous group of chronic renal diseases characterized predominantly by glomerular C3 deposition and complement dysregulation. Mutations in factor H-related (FHR) proteins resulting in duplicated dimerization domains are prototypical of C3G, although the underlying pathogenic mechanism is unclear. METHODS Using in vitro and in vivo assays, we performed extensive characterization of an FHR-1 mutant with a duplicated dimerization domain. To assess the FHR-1 mutant's association with disease susceptibility and renal prognosis, we also analyzed CFHR1 copy number variations and FHR-1 plasma levels in two Spanish C3G cohorts and in a control population. RESULTS Duplication of the dimerization domain conferred FHR-1 with an increased capacity to interact with C3-opsonized surfaces, which resulted in an excessive activation of the alternative pathway. This activation does not involve C3b binding competition with factor H. These findings support a scenario in which mutant FHR-1 binds to C3-activated fragments and recruits native C3 and C3b; this leads to formation of alternative pathway C3 convertases, which increases deposition of C3b molecules, overcoming FH regulation. This suggests that a balanced FHR-1/FH ratio is crucial to control complement amplification on opsonized surfaces. Consistent with this conceptual framework, we show that the genetic deficiency of FHR-1 or decreased FHR-1 in plasma confers protection against developing C3G and associates with better renal outcome. CONCLUSIONS Our findings explain how FHR-1 mutants with duplicated dimerization domains result in predisposition to C3G. They also provide a pathogenic mechanism that may be shared by other diseases, such as IgA nephropathy or age-related macular degeneration, and identify FHR-1 as a potential novel therapeutic target in C3G.
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Affiliation(s)
- Bárbara Márquez-Tirado
- Department of Immunology, Complutense University and Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain
| | - Josué Gutiérrez-Tenorio
- Department of Immunology, Complutense University and Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain
| | - Agustín Tortajada
- Department of Immunology, Complutense University and Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain
| | - Laura Lucientes Continente
- Department of Immunology, Complutense University and Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain
| | | | - Talat H. Malik
- Centre for Inflammatory Disease, Imperial College London, London, United Kingdom
| | | | - Sandra Elías
- Nephrology Department, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Ana Saiz Gonzalez
- Pathological Anatomy, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | | | - Pilar Sánchez-Corral
- Hospital La Paz Institute for Health Research (IdiPAZ), La Paz University Hospital, Center for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain
| | - Matthew C. Pickering
- Centre for Inflammatory Disease, Imperial College London, London, United Kingdom
| | - Manuel Praga
- Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain
- Department of Medicine, Complutense University of Madrid, Madrid, Spain
| | | | - Elena Goicoechea de Jorge
- Department of Immunology, Complutense University and Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain
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Freiwald T, Afzali B. Renal diseases and the role of complement: Linking complement to immune effector pathways and therapeutics. Adv Immunol 2021; 152:1-81. [PMID: 34844708 PMCID: PMC8905641 DOI: 10.1016/bs.ai.2021.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The complement system is an ancient and phylogenetically conserved key danger sensing system that is critical for host defense against pathogens. Activation of the complement system is a vital component of innate immunity required for the detection and removal of pathogens. It is also a central orchestrator of adaptive immune responses and a constituent of normal tissue homeostasis. Once complement activation occurs, this system deposits indiscriminately on any cell surface in the vicinity and has the potential to cause unwanted and excessive tissue injury. Deposition of complement components is recognized as a hallmark of a variety of kidney diseases, where it is indeed associated with damage to the self. The provenance and the pathophysiological role(s) played by complement in each kidney disease is not fully understood. However, in recent years there has been a renaissance in the study of complement, with greater appreciation of its intracellular roles as a cell-intrinsic system and its interplay with immune effector pathways. This has been paired with a profusion of novel therapeutic agents antagonizing complement components, including approved inhibitors against complement components (C)1, C3, C5 and C5aR1. A number of clinical trials have investigated the use of these more targeted approaches for the management of kidney diseases. In this review we present and summarize the evidence for the roles of complement in kidney diseases and discuss the available clinical evidence for complement inhibition.
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Affiliation(s)
- Tilo Freiwald
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), Bethesda, MD, United States; Department of Nephrology, University Hospital Frankfurt, Goethe-University, Frankfurt am Main, Germany
| | - Behdad Afzali
- Department of Nephrology, University Hospital Frankfurt, Goethe-University, Frankfurt am Main, Germany.
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