Periodic Reporting for period 4 - LUPUSCARE (PRECISION CARE IN SYSTEMIC AUTOIMMUNITY: AN INTEGRATED MULTI-TISSUE/LEVEL APPROACH FOR SYSTEMIC LUPUS ERYTHEMATOSUS (SLE))
Reporting period: 2022-03-01 to 2023-08-31
Systemic lupus erythematosus (SLE) is an autoimmune, potential life-threatening disease that affects predominantly women of the reproductive age. In this project we (a) defined the genomic architecture of human SLE and provided clues to the understanding of the systemic multi-organ nature and its marked clinical and molecular heterogeneity; (b) discovered novel therapeutic targets and biomarkers for diagnosis/monitoring; (c) defined the cellular response to DNA damage; (d) delineated the transcriptomic basis of the female predominance defining specific genes involved in this process; and (e) w traced the SLE immune abnormalities back to the early progenitor cells in the bone marrow defining novel targets to inhibit the flow of cells from the bone marrow to the peripheral organs.
SLE genomic architecture and its implications.
Using murine kidney-specific genes as disease predictors and machine learning pipeline, we developed a peripheral blood-based algorithm that discriminates LN patients from normal individuals and non-LN SLE patients. The kidney-specific gene predictors will facilitate prevention and early intervention trials. We also reported four disease-activity-associated long non-coding RNAs (lncRNAs) that represent hub genes associated with LN. These could be explored as blood-based biomarkers and potential liquid biopsy on LN avoiding the invasive kidney biopsy.
DNA damage response (DDR) in SLE and its pathologic correlates
Increased DNA damage and defective DNA repair are key features of SLE linking genetic with environmental factors. We defined the DDR in the B cells of SLE and provided evidence that has a key role in autoreactivity. In non-classical monocytes (NCM), we found enhanced inflammatory features such as deregulated DNA repair, cell cycle, and heightened IFN signaling. Enhanced DNA damage, elevated p53 expression, G0 arrest and increased autophagy, stress the NCM differentiation potential. This immunogenic profile is associated with an activated macrophage phenotype with M1 characteristics in the circulation that fuels the inflammatory response.
SLE a disease that epitomizes sex dimorphism
Sex dimorphism of various diseases regarding susceptibility and severity of the disease and response to treatment is receiving increased attention. Of note, two genes stand out in between healthy female vs SLE female individuals including the Cohesin Complex as well as the MLL4 complex.
The emerging role of bone marrow in SLE
We have introduced for the first time the concept that immune abnormalities in SLE can be traced back to the progenitor cells in the BM and have produced data -by the use of novel methods and technologies such as single-cell RNA-seq and bone-marrow-on-a-chip supporting this. In SLE, we found evidence of deregulation of hematopoiesis with skewing towards the myeloid lineage at the expense of lymphopoiesis; we also found priming of HSPCs that exhibit a ‘trained immunity’ signature which contributes to inflammation and increases the risk of flare.
Using murine kidney-specific genes as disease predictors and machine learning pipeline, we developed a peripheral blood-based algorithm that discriminates LN patients from normal individuals and non-LN SLE patients. The kidney-specific gene predictors will facilitate prevention and early intervention trials. We also reported four disease-activity-associated long non-coding RNAs (lncRNAs) that represent hub genes associated with LN. These could be explored as blood-based biomarkers and potential liquid biopsy on LN avoiding the invasive kidney biopsy.
DNA damage response (DDR) in SLE and its pathologic correlates
Increased DNA damage and defective DNA repair are key features of SLE linking genetic with environmental factors. We defined the DDR in the B cells of SLE and provided evidence that has a key role in autoreactivity. In non-classical monocytes (NCM), we found enhanced inflammatory features such as deregulated DNA repair, cell cycle, and heightened IFN signaling. Enhanced DNA damage, elevated p53 expression, G0 arrest and increased autophagy, stress the NCM differentiation potential. This immunogenic profile is associated with an activated macrophage phenotype with M1 characteristics in the circulation that fuels the inflammatory response.
SLE a disease that epitomizes sex dimorphism
Sex dimorphism of various diseases regarding susceptibility and severity of the disease and response to treatment is receiving increased attention. Of note, two genes stand out in between healthy female vs SLE female individuals including the Cohesin Complex as well as the MLL4 complex.
The emerging role of bone marrow in SLE
We have introduced for the first time the concept that immune abnormalities in SLE can be traced back to the progenitor cells in the BM and have produced data -by the use of novel methods and technologies such as single-cell RNA-seq and bone-marrow-on-a-chip supporting this. In SLE, we found evidence of deregulation of hematopoiesis with skewing towards the myeloid lineage at the expense of lymphopoiesis; we also found priming of HSPCs that exhibit a ‘trained immunity’ signature which contributes to inflammation and increases the risk of flare.
SLE genomic architecture and its implications
Our discovery of three distinct gene expression signatures namely susceptibility, activity and severity is novel and could be used a) for testing people at risk for SLE to facilitate early diagnosis and b) inform treatment decisions based on the likelihood to develop severe disease with involvement of major organs such as the kidneys which may tailor the intensity of therapy for each patient. An additional novel finding is the involvement of the liver and brain as causal tissues in SLE. LncRNAs found to be associated with LN and could be further explored as blood-based biomarkers and potential liquid biopsy on LN. Kidney-specific genes predict LN as they discriminate LN patients from healthy individuals and non-LN SLE patients which may facilitate prevention and early intervention trials for enal disease in SLE.
DNA damage response (DDR) in SLE and its pathologic correlates
We have demonstrated IFNα-mediated deregulation of mitochondrial metabolism and impairment of autophagic degradation, leading to accumulation of mtDNA that is sensed via stimulator of IFN genes to promote induction of autoinflammatory antigen presenting DCs. Our findings also identify disturbed DNA damage and response in Tregs. Importantly, scavenging of mtROS reverses their DNA damage response and ameliorates the autoimmune phenotype through contraction of Th1 and Th17 responses. In addition, we demonstrated enhanced activation of the ATR/Chk1 DDR pathway in B cells of SLE patients with active disease; pharmacologic inhibition of ATR attenuated their immunogenic profile. Thus, the IRF1-ATR axis is essential for B cell activity in SLE.
SLE a disease that epitomizes sex dimorphism
Analysis of RNA-seq data led to identification of 39 genes differentially expressed between male and female patients, 6 of which did not demonstrate differential expression within the control cohorts. Molecular pathways altered specifically on SLE female transcriptomes include the Cohesin Complex as well as the MLL4 complex. SMC1A binding was increased on enhancers and promoters of inflammation-associated genes. Integration of transcriptome and epigenome revealed that genomic regions with enriched SMC1A binding significantly overlapped with the regions with increased chromatin accessibility.
The emerging role of bone marrow in SLE
During systemic inflammation there is activation of HSPCs in the BM, resulting in their proliferation and differentiation towards the myeloid lineage. These cells also promote extramedullary hematopoiesis in SLE providing the inflammatory license to the myeloid cell produced to cause tissue injury and damage. Re-establishment of the appropriate myeloid vs lymphoid balance and alleviation of cell exhaustion improve transplantability of HSPCs and could restore immune function. We have also created a device which represents a pure in vitro and scaffold-free bone-marrow-on-a-chip device, intended to generate and sustain the perivascular hematopoietic niche for studies of the pathogenesis and treatment of SLE.
Our discovery of three distinct gene expression signatures namely susceptibility, activity and severity is novel and could be used a) for testing people at risk for SLE to facilitate early diagnosis and b) inform treatment decisions based on the likelihood to develop severe disease with involvement of major organs such as the kidneys which may tailor the intensity of therapy for each patient. An additional novel finding is the involvement of the liver and brain as causal tissues in SLE. LncRNAs found to be associated with LN and could be further explored as blood-based biomarkers and potential liquid biopsy on LN. Kidney-specific genes predict LN as they discriminate LN patients from healthy individuals and non-LN SLE patients which may facilitate prevention and early intervention trials for enal disease in SLE.
DNA damage response (DDR) in SLE and its pathologic correlates
We have demonstrated IFNα-mediated deregulation of mitochondrial metabolism and impairment of autophagic degradation, leading to accumulation of mtDNA that is sensed via stimulator of IFN genes to promote induction of autoinflammatory antigen presenting DCs. Our findings also identify disturbed DNA damage and response in Tregs. Importantly, scavenging of mtROS reverses their DNA damage response and ameliorates the autoimmune phenotype through contraction of Th1 and Th17 responses. In addition, we demonstrated enhanced activation of the ATR/Chk1 DDR pathway in B cells of SLE patients with active disease; pharmacologic inhibition of ATR attenuated their immunogenic profile. Thus, the IRF1-ATR axis is essential for B cell activity in SLE.
SLE a disease that epitomizes sex dimorphism
Analysis of RNA-seq data led to identification of 39 genes differentially expressed between male and female patients, 6 of which did not demonstrate differential expression within the control cohorts. Molecular pathways altered specifically on SLE female transcriptomes include the Cohesin Complex as well as the MLL4 complex. SMC1A binding was increased on enhancers and promoters of inflammation-associated genes. Integration of transcriptome and epigenome revealed that genomic regions with enriched SMC1A binding significantly overlapped with the regions with increased chromatin accessibility.
The emerging role of bone marrow in SLE
During systemic inflammation there is activation of HSPCs in the BM, resulting in their proliferation and differentiation towards the myeloid lineage. These cells also promote extramedullary hematopoiesis in SLE providing the inflammatory license to the myeloid cell produced to cause tissue injury and damage. Re-establishment of the appropriate myeloid vs lymphoid balance and alleviation of cell exhaustion improve transplantability of HSPCs and could restore immune function. We have also created a device which represents a pure in vitro and scaffold-free bone-marrow-on-a-chip device, intended to generate and sustain the perivascular hematopoietic niche for studies of the pathogenesis and treatment of SLE.