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Erschienen in: Archivum Immunologiae et Therapiae Experimentalis 1/2022

01.12.2022 | Review

Special Issue: Novel Diagnostic and Therapeutic Approach Options in Lupus Nephritis

Transcriptome Studies in Lupus Nephritis

verfasst von: Marta E. Alarcón-Riquelme

Erschienen in: Archivum Immunologiae et Therapiae Experimentalis | Ausgabe 1/2022

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Abstract

The present review is aimed at describing the main works that have used gene expression to analyze tissue kidney samples of lupus nephritis patients. Most studies used the gene expression arrays, which enormously advanced our knowledge on the possible mechanisms behind lupus nephritis. However, using bulk gene expression platforms, either as arrays, or as sequencing of RNA is not enough to go into detail of the cells and their molecular patterns and single cell mechanisms of disease. More recently, the first single cell RNA Sequencing study was published and this will also be discussed in the context of lupus nephritis. Single cell RNA sequencing allows to retrieve the genes expressed in each cell in the tissue of interest or in blood. In this context, the results of such studies give us a first glimpse of how a lupus nephritis kidney looks like, but much is still to be done to understand the changes that occur with treatment or with the different pathological subtypes of lupus nephritis and their cellular content.
Literatur
Zurück zum Zitat Abdelati AA, Eshak NY, Donia HM et al (2021) Urinary cellular profile as a biomarker for lupus nephritis. J Clin Rheumatol 27:e469–e476CrossRefPubMed Abdelati AA, Eshak NY, Donia HM et al (2021) Urinary cellular profile as a biomarker for lupus nephritis. J Clin Rheumatol 27:e469–e476CrossRefPubMed
Zurück zum Zitat Banchereau R, Hong S, Cantarel B et al (2016) Personalized immunomonitoring uncovers molecular networks that stratify lupus patients. Cell 165:1548–1550CrossRefPubMed Banchereau R, Hong S, Cantarel B et al (2016) Personalized immunomonitoring uncovers molecular networks that stratify lupus patients. Cell 165:1548–1550CrossRefPubMed
Zurück zum Zitat Blazer A, Dey ID, Nwaukoni J et al (2021) Apolipoprotein L1 risk genotypes in Ghanaian patients with systemic lupus erythematosus: a prospective cohort study. Lupus Sci Med 8:e000460CrossRefPubMedPubMedCentral Blazer A, Dey ID, Nwaukoni J et al (2021) Apolipoprotein L1 risk genotypes in Ghanaian patients with systemic lupus erythematosus: a prospective cohort study. Lupus Sci Med 8:e000460CrossRefPubMedPubMedCentral
Zurück zum Zitat Bolin K, Sandling JK, Zickert A et al (2013) Association of STAT4 polymorphism with severe renal insufficiency in lupus nephritis. PLoS ONE 8:e84450CrossRefPubMedPubMedCentral Bolin K, Sandling JK, Zickert A et al (2013) Association of STAT4 polymorphism with severe renal insufficiency in lupus nephritis. PLoS ONE 8:e84450CrossRefPubMedPubMedCentral
Zurück zum Zitat Chaussabel D, Quinn C, Shen J et al (2008) A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus. Immunity 29:150–164CrossRefPubMedPubMedCentral Chaussabel D, Quinn C, Shen J et al (2008) A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus. Immunity 29:150–164CrossRefPubMedPubMedCentral
Zurück zum Zitat Der E, Suryawanshi H, Morozov P et al (2019) Tubular cell and keratinocyte single-cell transcriptomics applied to lupus nephritis reveal type I IFN and fibrosis relevant pathways. Nat Immunol 20:915–927CrossRefPubMedPubMedCentral Der E, Suryawanshi H, Morozov P et al (2019) Tubular cell and keratinocyte single-cell transcriptomics applied to lupus nephritis reveal type I IFN and fibrosis relevant pathways. Nat Immunol 20:915–927CrossRefPubMedPubMedCentral
Zurück zum Zitat Dey-Rao R, Smith JR, Chow S et al (2014) Differential gene expression analysis in CCLE lesions provides new insights regarding the genetics basis of skin vs. systemic disease. Genomics 104:144–155CrossRefPubMed Dey-Rao R, Smith JR, Chow S et al (2014) Differential gene expression analysis in CCLE lesions provides new insights regarding the genetics basis of skin vs. systemic disease. Genomics 104:144–155CrossRefPubMed
Zurück zum Zitat Freedman BI, Langefeld CD, Andringa KK et al (2014) End-stage renal disease in African Americans with lupus nephritis is associated with APOL1. Arthritis Rheum 66:390–396CrossRef Freedman BI, Langefeld CD, Andringa KK et al (2014) End-stage renal disease in African Americans with lupus nephritis is associated with APOL1. Arthritis Rheum 66:390–396CrossRef
Zurück zum Zitat Hagberg N, Ronnblom L (2019) Interferon-alpha enhances the IL-12-induced STAT4 activation selectively in carriers of the STAT4 SLE risk allele rs7574865[T]. Ann Rheum Dis 78:429–431CrossRefPubMed Hagberg N, Ronnblom L (2019) Interferon-alpha enhances the IL-12-induced STAT4 activation selectively in carriers of the STAT4 SLE risk allele rs7574865[T]. Ann Rheum Dis 78:429–431CrossRefPubMed
Zurück zum Zitat Jourde-Chiche N, Whalen E, Gondouin B et al (2017) Modular transcriptional repertoire analyses identify a blood neutrophil signature as a candidate biomarker for lupus nephritis. Rheumatology 56:477–487PubMed Jourde-Chiche N, Whalen E, Gondouin B et al (2017) Modular transcriptional repertoire analyses identify a blood neutrophil signature as a candidate biomarker for lupus nephritis. Rheumatology 56:477–487PubMed
Zurück zum Zitat Ju W, Nair V, Smith S et al (2015) Tissue transcriptome-driven identification of epidermal growth factor as a chronic kidney disease biomarker. Sci Transl Med 7:316ra193CrossRefPubMedPubMedCentral Ju W, Nair V, Smith S et al (2015) Tissue transcriptome-driven identification of epidermal growth factor as a chronic kidney disease biomarker. Sci Transl Med 7:316ra193CrossRefPubMedPubMedCentral
Zurück zum Zitat Khan SQ, Khan I, Gupta V (2018) CD11b activity modulates pathogenesis of lupus nephritis. Front Med 5:52CrossRef Khan SQ, Khan I, Gupta V (2018) CD11b activity modulates pathogenesis of lupus nephritis. Front Med 5:52CrossRef
Zurück zum Zitat Kim-Howard X, Maiti AK, Anaya JM et al (2010) ITGAM coding variant (rs1143679) influences the risk of renal disease, discoid rash and immunological manifestations in patients with systemic lupus erythematosus with European ancestry. Ann Rheum Dis 69:1329–1332CrossRefPubMed Kim-Howard X, Maiti AK, Anaya JM et al (2010) ITGAM coding variant (rs1143679) influences the risk of renal disease, discoid rash and immunological manifestations in patients with systemic lupus erythematosus with European ancestry. Ann Rheum Dis 69:1329–1332CrossRefPubMed
Zurück zum Zitat Kitagawa A, Tsuboi N, Yokoe Y et al (2019) Urinary levels of the leukocyte surface molecule CD11b associate with glomerular inflammation in lupus nephritis. Kidney Int 95:680–692CrossRefPubMed Kitagawa A, Tsuboi N, Yokoe Y et al (2019) Urinary levels of the leukocyte surface molecule CD11b associate with glomerular inflammation in lupus nephritis. Kidney Int 95:680–692CrossRefPubMed
Zurück zum Zitat Lewis MJ, Barnes MR, Blighe K et al (2019) Molecular portraits of early rheumatoid arthritis identify clinical and treatment response phenotypes. Cell Rep 28:2455-2470.e2455CrossRefPubMedPubMedCentral Lewis MJ, Barnes MR, Blighe K et al (2019) Molecular portraits of early rheumatoid arthritis identify clinical and treatment response phenotypes. Cell Rep 28:2455-2470.e2455CrossRefPubMedPubMedCentral
Zurück zum Zitat Lin CP, Adrianto I, Lessard CJ et al (2012) Role of MYH9 and APOL1 in African and non-African populations with lupus nephritis. Genes Immun 13:232–238CrossRefPubMed Lin CP, Adrianto I, Lessard CJ et al (2012) Role of MYH9 and APOL1 in African and non-African populations with lupus nephritis. Genes Immun 13:232–238CrossRefPubMed
Zurück zum Zitat Liu K, Li QZ, Delgado-Vega AM et al (2009) Kallikrein genes are associated with lupus and glomerular basement membrane-specific antibody-induced nephritis in mice and humans. J Clin Invest 119:911–923CrossRefPubMedPubMedCentral Liu K, Li QZ, Delgado-Vega AM et al (2009) Kallikrein genes are associated with lupus and glomerular basement membrane-specific antibody-induced nephritis in mice and humans. J Clin Invest 119:911–923CrossRefPubMedPubMedCentral
Zurück zum Zitat Mejia-Vilet JM, Parikh SV, Song H et al (2019) Immune gene expression in kidney biopsies of lupus nephritis patients at diagnosis and at renal flare. Nephrol Dial Transplant 34:1197–1206CrossRefPubMed Mejia-Vilet JM, Parikh SV, Song H et al (2019) Immune gene expression in kidney biopsies of lupus nephritis patients at diagnosis and at renal flare. Nephrol Dial Transplant 34:1197–1206CrossRefPubMed
Zurück zum Zitat Nakou M, Knowlton N, Frank MB et al (2008) Gene expression in systemic lupus erythematosus: bone marrow analysis differentiates active from inactive disease and reveals apoptosis and granulopoiesis signatures. Arthritis Rheum 58:3541–3549CrossRefPubMedPubMedCentral Nakou M, Knowlton N, Frank MB et al (2008) Gene expression in systemic lupus erythematosus: bone marrow analysis differentiates active from inactive disease and reveals apoptosis and granulopoiesis signatures. Arthritis Rheum 58:3541–3549CrossRefPubMedPubMedCentral
Zurück zum Zitat Nath SK, Han S, Kim-Howard X et al (2008) A nonsynonymous functional variant in integrin-alpha(M) (encoded by ITGAM) is associated with systemic lupus erythematosus. Nat Genet 40:152–154CrossRefPubMed Nath SK, Han S, Kim-Howard X et al (2008) A nonsynonymous functional variant in integrin-alpha(M) (encoded by ITGAM) is associated with systemic lupus erythematosus. Nat Genet 40:152–154CrossRefPubMed
Zurück zum Zitat Nzeusseu Toukap A, Galant C, Theate I et al (2007) Identification of distinct gene expression profiles in the synovium of patients with systemic lupus erythematosus. Arthritis Rheum 56:1579–1588CrossRefPubMed Nzeusseu Toukap A, Galant C, Theate I et al (2007) Identification of distinct gene expression profiles in the synovium of patients with systemic lupus erythematosus. Arthritis Rheum 56:1579–1588CrossRefPubMed
Zurück zum Zitat Pamfil C, Makowska Z, Groof De et al (2018) Intrarenal activation of adaptive immune effectors is associated with tubular damage and impaired renal function in lupus nephritis. Ann Rheum Dis 77:1782–1789CrossRefPubMed Pamfil C, Makowska Z, Groof De et al (2018) Intrarenal activation of adaptive immune effectors is associated with tubular damage and impaired renal function in lupus nephritis. Ann Rheum Dis 77:1782–1789CrossRefPubMed
Zurück zum Zitat Peterson KS, Huang JF, Zhu J et al (2004) Characterization of heterogeneity in the molecular pathogenesis of lupus nephritis from transcriptional profiles of laser-captured glomeruli. J Clin Invest 113:1722–1733CrossRefPubMedPubMedCentral Peterson KS, Huang JF, Zhu J et al (2004) Characterization of heterogeneity in the molecular pathogenesis of lupus nephritis from transcriptional profiles of laser-captured glomeruli. J Clin Invest 113:1722–1733CrossRefPubMedPubMedCentral
Zurück zum Zitat Reid S, Hagberg N, Sandling JK et al (2021) Interaction between the STAT4 rs11889341 (T) risk allele and smoking confers increased risk of myocardial infarction and nephritis in patients with systemic lupus erythematosus. Ann Rheum Dis 80:1183–1189CrossRefPubMed Reid S, Hagberg N, Sandling JK et al (2021) Interaction between the STAT4 rs11889341 (T) risk allele and smoking confers increased risk of myocardial infarction and nephritis in patients with systemic lupus erythematosus. Ann Rheum Dis 80:1183–1189CrossRefPubMed
Zurück zum Zitat Richman IB, Taylor KE, Chung SA et al (2012) European genetic ancestry is associated with a decreased risk of lupus nephritis. Arthritis Rheum 64:3374–3382CrossRefPubMed Richman IB, Taylor KE, Chung SA et al (2012) European genetic ancestry is associated with a decreased risk of lupus nephritis. Arthritis Rheum 64:3374–3382CrossRefPubMed
Zurück zum Zitat Rubtsova K, Rubtsov AV, Cancro MP et al (2015) Age-associated B cells: a T-bet-dependent effector with roles in protective and pathogenic immunity. J Immunol 195:1933–1937CrossRefPubMed Rubtsova K, Rubtsov AV, Cancro MP et al (2015) Age-associated B cells: a T-bet-dependent effector with roles in protective and pathogenic immunity. J Immunol 195:1933–1937CrossRefPubMed
Zurück zum Zitat Sanchez E, Nadig A, Richardson BC et al (2011) Phenotypic associations of genetic susceptibility loci in systemic lupus erythematosus. Ann Rheum Dis 70:1752–1757CrossRefPubMed Sanchez E, Nadig A, Richardson BC et al (2011) Phenotypic associations of genetic susceptibility loci in systemic lupus erythematosus. Ann Rheum Dis 70:1752–1757CrossRefPubMed
Zurück zum Zitat Sanchez E, Rasmussen A, Riba L et al (2012) Impact of genetic ancestry and sociodemographic status on the clinical expression of systemic lupus erythematosus in American Indian-European populations. Arthritis Rheum 64:3687–3694CrossRefPubMedPubMedCentral Sanchez E, Rasmussen A, Riba L et al (2012) Impact of genetic ancestry and sociodemographic status on the clinical expression of systemic lupus erythematosus in American Indian-European populations. Arthritis Rheum 64:3687–3694CrossRefPubMedPubMedCentral
Zurück zum Zitat Taylor KE, Remmers EF, Lee AT et al (2008) Specificity of the STAT4 genetic association for severe disease manifestations of systemic lupus erythematosus. PLoS Genet 4:e1000084CrossRefPubMedPubMedCentral Taylor KE, Remmers EF, Lee AT et al (2008) Specificity of the STAT4 genetic association for severe disease manifestations of systemic lupus erythematosus. PLoS Genet 4:e1000084CrossRefPubMedPubMedCentral
Zurück zum Zitat Toro-Dominguez D, Martorell-Marugan J, Goldman D et al (2018) Stratification of systemic lupus erythematosus patients into three groups of disease activity progression according to longitudinal gene expression. Arthritis Rheumatol 70:2025–2035CrossRefPubMedPubMedCentral Toro-Dominguez D, Martorell-Marugan J, Goldman D et al (2018) Stratification of systemic lupus erythematosus patients into three groups of disease activity progression according to longitudinal gene expression. Arthritis Rheumatol 70:2025–2035CrossRefPubMedPubMedCentral
Zurück zum Zitat Weening JJ, D’Agati VD, Schwartz MM et al (2004) The classification of glomerulonephritis in systemic lupus erythematosus revisited. Kidney Int 65:521–530CrossRefPubMed Weening JJ, D’Agati VD, Schwartz MM et al (2004) The classification of glomerulonephritis in systemic lupus erythematosus revisited. Kidney Int 65:521–530CrossRefPubMed
Zurück zum Zitat Wither JE, Prokopec SD, Noamani B et al (2018) Identification of a neutrophil-related gene expression signature that is enriched in adult systemic lupus erythematosus patients with active nephritis: Clinical/pathologic associations and etiologic mechanisms. PLoS ONE 13:e0196117CrossRefPubMedPubMedCentral Wither JE, Prokopec SD, Noamani B et al (2018) Identification of a neutrophil-related gene expression signature that is enriched in adult systemic lupus erythematosus patients with active nephritis: Clinical/pathologic associations and etiologic mechanisms. PLoS ONE 13:e0196117CrossRefPubMedPubMedCentral
Zurück zum Zitat Yang W, Zhao M, Hirankarn N et al (2009) ITGAM is associated with disease susceptibility and renal nephritis of systemic lupus erythematosus in Hong Kong Chinese and Thai. Hum Mol Genet 18:2063–2070CrossRefPubMedPubMedCentral Yang W, Zhao M, Hirankarn N et al (2009) ITGAM is associated with disease susceptibility and renal nephritis of systemic lupus erythematosus in Hong Kong Chinese and Thai. Hum Mol Genet 18:2063–2070CrossRefPubMedPubMedCentral
Zurück zum Zitat Zumaquero E, Stone SL, Scharer CD et al (2019) IFNgamma induces epigenetic programming of human T-bet(hi) B cells and promotes TLR7/8 and IL-21 induced differentiation. Elife 8:e41641CrossRefPubMedPubMedCentral Zumaquero E, Stone SL, Scharer CD et al (2019) IFNgamma induces epigenetic programming of human T-bet(hi) B cells and promotes TLR7/8 and IL-21 induced differentiation. Elife 8:e41641CrossRefPubMedPubMedCentral
Metadaten
Titel
Special Issue: Novel Diagnostic and Therapeutic Approach Options in Lupus Nephritis
Transcriptome Studies in Lupus Nephritis
verfasst von
Marta E. Alarcón-Riquelme
Publikationsdatum
01.12.2022
Verlag
Springer International Publishing
Erschienen in
Archivum Immunologiae et Therapiae Experimentalis / Ausgabe 1/2022
Print ISSN: 0004-069X
Elektronische ISSN: 1661-4917
DOI
https://doi.org/10.1007/s00005-022-00651-y

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