Deep Phenotyping of Urinary Leukocytes by Mass Cytometry Reveals a Leukocyte Signature for Early and Non-Invasive Prediction of Response to Treatment in Active Lupus Nephritis

Increased Urine Excretion of Neutrophil Granule Cargo in Active Proliferative Lupus Nephritis

Key Points

Neutrophil degranulation participates in glomerular injury in proliferative lupus nephritis. Urine excretion of neutrophil granule proteins is a potential diagnostic for proliferative lupus nephritis.

Background

Lupus nephritis (LN) occurs in more than half of patients with systemic lupus erythematosus, but the cellular and molecular events that contribute to LN are not clearly defined. We reported previously that neutrophil degranulation participates in glomerular injury in mouse models of acute LN. This study tests the hypothesis that glomerular recruitment and subsequent activation of neutrophils result in urine excretion of neutrophil granule constituents that are predictive of glomerular inflammation in proliferative LN.

Methods

Urine and serum levels of 11 neutrophil granule proteins were measured by antibody-based array in patients with proliferative LN and healthy donors (HDs), and the results were confirmed by ELISA. Glomerular neutrophil accumulation was assessed in biopsies of patients with LN who contributed urine for granule cargo quantitation and normal kidney tissue by microscopy. Degranulation was measured by flow cytometry in neutrophils isolated from patients with LN and HD controls by cell surface granule markers CD63 (azurophilic), CC66b (specific), and CD35 (secretory). Nonparametric statistical analyses were performed and corrected for multiple comparisons.

Results

Eight granule proteins (myeloperoxidase, neutrophil elastase, azurocidin, olfactomedin-4, lactoferrin, alpha-1-acid glycoprotein 1, matrix metalloproteinase 9, and cathelicidin) were significantly elevated in urine from patients with active proliferative LN by array and/or ELISA, whereas only neutrophil elastase was increased in LN serum. Urine excretion of alpha-1-acid glycoprotein 1 declined in patients who achieved remission. The majority of LN glomeruli contained ≥3 neutrophils. Basal levels of specific granule markers were increased in neutrophils from patients with LN compared with HD controls. Serum from patients with active LN stimulated specific and secretory, but not azurophilic granule, release by HD neutrophils.

Conclusions

Circulating neutrophils in patients with LN are primed for enhanced degranulation. Glomerular recruitment of those primed neutrophils leads to release and urine excretion of neutrophil granule cargo that serves as a urine marker of active glomerular inflammation in proliferative LN.

Monocyte-derived dendritic cells can be detected in urine of kidney transplant recipients with pathogenic asymptomatic bacteriuria

Urinary tract infections (UTI) are an important clinical problem in kidney transplant recipients (KTR). Asymptomatic bacteriuria (ASB) is frequent in these patients and often resolved by the immune system, but a significant proportion may progress to complicated UTI, which may compromise allograft function and survival. It is essential to determine the involvement of the immune system in the infectious process. Dendritic cells (DCs) are recognised as playing a pivotal role in initiating inflammatory responses capable of priming antigen-specific T cells, a crucial step in determining the fate of local inflammation. Little is known about their role in the control of UTI. In this brief communication, we report an incidental finding in a group of 16 stable KTR in which monocyte-derived dendritic cells (ModDCs), analysed by flow cytometry, were found in urine of patients with ASB and high bacterial counts >107 cfu/ml. Within this group, one patient developed pyelonephritis in the following days. These findings suggest that the immune system, in particular DCs, may be recruited during the course of a UTI and, to our knowledge, present for the first time evidence that inflammatory ModDCs can be detected in urine. Their frequency may reflect the degree of infection. This finding suggests the potential for exploring whether these cells may be useful in distinguishing between pathogenic ASB and those that can be resolved by the immune system.

Purification and analysis of kidney-infiltrating leukocytes in a mouse model of lupus nephritis

Renal injury often occurs as a complication in autoimmune diseases such as systemic lupus erythematosus (SLE). It is estimated that a minimum of 20% SLE patients develop lupus nephritis, a condition that can be fatal when the pathology progresses to end-stage renal disease. Studies in animal models showed that incidence of immune cell infiltrates in the kidney was linked to pathological injury and correlated with severe lupus nephritis. Thus, preventing immune cell infiltration into the kidney is a potential approach to impede the progression to an end-stage disease. A requirement to investigate the role of kidney-infiltrating leukocytes is the development of reproducible and efficient protocols for purification and characterization of immune cells in kidney samples. This chapter describes a detailed methodology that discriminates tissue-resident leukocytes from blood-circulating cells that are found in kidney. Our protocol was designed to maximize cell viability and to reduce variability among samples, with a combination of intravascular staining and magnetic bead separation for leukocyte enrichment. Experiments included as example were performed with FcγRIIb[KO] mice, a well-characterized murine model of SLE. We identified T cells and macrophages as the primary leukocyte subsets infiltrating into the kidney during severe nephritis, and we extensively characterized them phenotypically by flow cytometry.

Trends and perspectives for improving quality of chronic kidney disease care: conclusions from a Kidney Disease: Improving Global Outcomes (KDIGO) Controversies Conference

Chronic kidney disease (CKD) affects over 850 million people globally, and the need to prevent its development and progression is urgent. During the past decade, new perspectives have arisen related to the quality and precision of care for CKD, owing to the development of new tools and interventions for CKD diagnosis and management. New biomarkers, imaging methods, artificial intelligence techniques, and approaches to organizing and delivering healthcare may help clinicians recognize CKD, determine its etiology, assess the dominant mechanisms at given time points, and identify patients at high risk for progression or related events. As opportunities to apply the concepts of precision medicine for CKD identification and management continue to be developed, an ongoing discussion of the potential implications for care delivery is required. The 2022 KDIGO Controversies Conference on Improving CKD Quality of Care: Trends and Perspectives examined and discussed best practices for improving the precision of CKD diagnosis and prognosis, managing the complications of CKD, enhancing the safety of care, and maximizing patient quality of life. Existing tools and interventions currently available for the diagnosis and treatment of CKD were identified, with discussion of current barriers to their implementation and strategies for improving the quality of care delivered for CKD. Key knowledge gaps and areas for research were also identified.

Advanced methods and novel biomarkers in autoimmune diseases ‑ a review of the recent years progress in systemic lupus erythematosus

There are several autoimmune and rheumatic diseases affecting different organs of the human body. Multiple sclerosis (MS) mainly affects brain, rheumatoid arthritis (RA) mainly affects joints, Type 1 diabetes (T1D) mainly affects pancreas, Sjogren's syndrome (SS) mainly affects salivary glands, while systemic lupus erythematosus (SLE) affects almost every organ of the body. Autoimmune diseases are characterized by production of autoantibodies, activation of immune cells, increased expression of pro-inflammatory cytokines, and activation of type I interferons. Despite improvements in treatments and diagnostic tools, the time it takes for the patients to be diagnosed is too long, and the main treatment for these diseases is still non-specific anti-inflammatory drugs. Thus, there is an urgent need for better biomarkers, as well as tailored, personalized treatment. This review focus on SLE and the organs affected in this disease. We have used the results from various rheumatic and autoimmune diseases and the organs involved with an aim to identify advanced methods and possible biomarkers to be utilized in the diagnosis of SLE, disease monitoring, and response to treatment.

Decipher the Immunopathological Mechanisms and Set Up Potential Therapeutic Strategies for Patients with Lupus Nephritis

Lupus nephritis (LN) is one of the most severe complications in patients with systemic lupus erythematosus (SLE). Traditionally, LN is regarded as an immune complex (IC) deposition disease led by dsDNA-anti-dsDNA-complement interactions in the subendothelial and/or subepithelial basement membrane of glomeruli to cause inflammation. The activated complements in the IC act as chemoattractants to chemically attract both innate and adaptive immune cells to the kidney tissues, causing inflammatory reactions. However, recent investigations have unveiled that not only the infiltrating immune-related cells, but resident kidney cells, including glomerular mesangial cells, podocytes, macrophage-like cells, tubular epithelial cells and endothelial cells, may also actively participate in the inflammatory and immunological reactions in the kidney. Furthermore, the adaptive immune cells that are infiltrated are genetically restricted to autoimmune predilection. The autoantibodies commonly found in SLE, including anti-dsDNA, are cross-reacting with not only a broad spectrum of chromatin substances, but also extracellular matrix components, including α-actinin, annexin II, laminin, collagen III and IV, and heparan sulfate proteoglycan. Besides, the glycosylation on the Fab portion of IgG anti-dsDNA antibodies can also affect the pathogenic properties of the autoantibodies in that α-2,6-sialylation alleviates, whereas fucosylation aggravates their nephritogenic activity. Some of the coexisting autoantibodies, including anti-cardiolipin, anti-C1q, anti-ribosomal P autoantibodies, may also enhance the pathogenic role of anti-dsDNA antibodies. In clinical practice, the identification of useful biomarkers for diagnosing, monitoring, and following up on LN is quite important for its treatments. The development of a more specific therapeutic strategy to target the pathogenic factors of LN is also critical. We will discuss these issues in detail in the present article.

Pathogenic cellular and molecular mediators in lupus nephritis

Kidney involvement in patients with systemic lupus erythematosus - lupus nephritis (LN) - is one of the most important and common clinical manifestations of this disease and occurs in 40-60% of patients. Current treatment regimens achieve a complete kidney response in only a minority of affected individuals, and 10-15% of patients with LN develop kidney failure, with its attendant morbidity and considerable prognostic implications. Moreover, the medications most often used to treat LN - corticosteroids in combination with immunosuppressive or cytotoxic drugs - are associated with substantial side effects. Advances in proteomics, flow cytometry and RNA sequencing have led to important new insights into immune cells, molecules and mechanistic pathways that are instrumental in the pathogenesis of LN. These insights, together with a renewed focus on the study of human LN kidney tissue, suggest new therapeutic targets that are already being tested in lupus animal models and early-phase clinical trials and, as such, are hoped to eventually lead to meaningful improvements in the care of patients with systemic lupus erythematosus-associated kidney disease.

Artificial intelligence and high-dimensional technologies in the theragnosis of systemic lupus erythematosus

Systemic lupus erythematosus is a complex, systemic autoimmune disease characterised by immune dysregulation. Pathogenesis is multifactorial, contributing to clinical heterogeneity and posing challenges for diagnosis and treatment. Although strides in treatment options have been made in the past 15 years, with the US Food and Drug Administration approval of belimumab in 2011, there are still many patients who have inadequate responses to therapy. A better understanding of underlying disease mechanisms with a holistic and multiparametric approach is required to improve clinical assessment and treatment. This Review discusses the evolution of genomics, epigenomics, transcriptomics, and proteomics in the study of systemic lupus erythematosus and ways to amalgamate these silos of data with a systems-based approach while also discussing ways to strengthen the overall process. These mechanistic insights will facilitate the discovery of functionally relevant biomarkers to guide rational therapeutic selection to improve patient outcomes.

Tissue-resident memory T cells in renal autoimmune diseases

The discovery of tissue-resident memory T cells (T_RM cells) reinterpreted the potential of human tissue-specific immunity. Following T cell receptor (TCR) activation and clonal expansion, effector T cells migrate to peripheral tissues where they remain long-term and differentiate to T_RM cells after antigen clearance. This allows for prompt immunological responses upon antigen re-encounter. In addition to their protective properties in acute infections, recent studies have revealed that T_RM cells might lead to aggravation of autoimmune diseases, such as lupus nephritis (LN) and anti-neutrophil cytoplasmic antibody (ANCA)-associated glomerulonephritis (GN). These diseases present as proliferative and crescentic glomerulonephritis (cGN), which is a life-threatening condition leading to end-stage renal disease (ESRD) if left untreated. A better understanding of renal T_RM cells might lead to identifying new therapeutic targets for relapsing autoimmune diseases of the kidney. In this review, we summarize the current knowledge of renal T_RM cells and discuss their potential pathophysiological roles in renal autoimmune diseases.

Urinary single-cell sequencing captures kidney injury and repair processes in human acute kidney injury

Acute kidney injury (AKI) is a major health issue, the outcome of which depends primarily on damage and reparative processes of tubular epithelial cells. Mechanisms underlying AKI remain incompletely understood, specific therapies are lacking and monitoring the course of AKI in clinical routine is confined to measuring urine output and plasma levels of filtration markers. Here we demonstrate feasibility and potential of a novel approach to assess the cellular and molecular dynamics of AKI by establishing a robust urine-to-single cell RNA sequencing (scRNAseq) pipeline for excreted kidney cells via flow cytometry sorting. We analyzed 42,608 single cell transcriptomes of 40 urine samples from 32 patients with AKI and compared our data with reference material from human AKI post-mortem biopsies and published mouse data. We demonstrate that tubular epithelial cells transcriptomes mirror kidney pathology and reflect distinct injury and repair processes, including oxidative stress, inflammation, and tissue rearrangement. We also describe an AKI-specific abundant urinary excretion of adaptive progenitor-like cells. Thus, single cell transcriptomics of kidney cells excreted in urine provides noninvasive, unprecedented insight into cellular processes underlying AKI, thereby opening novel opportunities for target identification, AKI sub-categorization, and monitoring of natural disease course and interventions.

Urinary CD8+HLA-DR+ T Cell Abundance Non-invasively Predicts Kidney Transplant Rejection

Early detection of kidney transplant (KT) rejection remains a challenge in patient care. Non-invasive biomarkers hold high potential to detect rejection, adjust immunosuppression, and monitor KT patients. So far, no approach has fully satisfied requirements to innovate routine monitoring of KT patients. In this two-center study we analyzed a total of 380 urine samples. T cells and tubular epithelial cells were quantified in KT patients with graft deterioration using flow cytometry. Epigenetic urine cell quantification was used to confirm flow cytometric results. Moreover, a cohort of KT patients was followed up during the first year after transplantation, tracking cell subsets over time. Abundance of urinary cell counts differed in patients with and without rejection. Most strikingly, various T cell subsets were enriched in patients with T cell-mediated rejection (TCMR) compared to patients without TCMR. Among T cell subsets, CD8+HLA-DR+ T cells were most distinctive (AUC = 0.91, Spec.: 95.9%, Sens.: 76.5%). Epigenetic analysis confirmed T cell and tubular epithelial cell quantities as determined by flow cytometry. Urinary T cell abundance in new KT patients decreased during their first year after transplantation. In conclusion urinary T cells reflect intrarenal inflammation in TCMR. T cell subsets yield high potential to monitor KT patients and detect rejection. Hereby we present a promising biomarker to non-invasively diagnose TCMR.

Tissue-resident memory T cells in the urogenital tract

Our understanding of T cell memory responses changed drastically with the discovery that specialized T cell memory populations reside within peripheral tissues at key pathogen entry sites. These tissue-resident memory T (T_RM) cells can respond promptly to an infection without the need for migration, proliferation or differentiation. This rapid and local deployment of effector functions maximizes the ability of T_RM cells to eliminate pathogens. T_RM cells do not circulate through peripheral tissues but instead form isolated populations in the skin, gut, liver, kidneys, the reproductive tract and other organs. This long-term retention in the periphery might allow T_RM cells to fully adapt to the local conditions of their environment and mount customized responses to counter infection and tumour growth in a tissue-specific manner. In the urogenital tract, T_RM cells must adapt to a unique microenvironment to confer protection against potential threats, including cancer and infection, while preventing the onset of auto-inflammatory disease. In this Review, we discuss insights into the diversification of T_RM cells from other memory T cell lineages, the adaptations of T_RM cells to their local environment, and their enhanced capacity to counter infection and tumour growth compared with other memory T cell populations, especially in the urogenital tract.

Tissue-resident memory T cells in the kidney

The identification of tissue-resident memory T cells (T_RM cells) has significantly improved our understanding of immunity. In the last decade, studies have demonstrated that T_RM cells are induced after an acute T-cell response, remain in peripheral organs for several years, and contribute to both an efficient host defense and autoimmune disease. T_RM cells are found in the kidneys of healthy individuals and patients with various kidney diseases. A better understanding of these cells and their therapeutic targeting might provide new treatment options for infections, autoimmune diseases, graft rejection, and cancer. In this review, we address the definition, phenotype, and developmental mechanisms of T_RM cells. Then, we further discuss the current understanding of T_RM cells in kidney diseases, such as infection, autoimmune disease, cancer, and graft rejection after transplantation.

The Power of Systems Biology: Insights on Lupus Nephritis from the Accelerating Medicines Partnership

The Accelerating Medicines Partnership (AMP) SLE Network united resources from academic centers, government, nonprofit, and industry to accelerate discovery in lupus nephritis (LN). The AMP SLE Network developed a set of protocols for high-throughput analyses to systematically study kidney tissue, urine, and blood in LN. This article summarizes approaches and results from phase 1 of AMP SLE Network effort, including single cell RNA-seq analysis of LN kidney biopsies, cellular and proteomic studies of LN urine, and mass cytometry immunophenotyping of blood cells. This work provides a framework to guide studies of the clinical implications of active cellular/molecular pathways in LN.

Immune-Related Urine Biomarkers for the Diagnosis of Lupus Nephritis

The kidney is one of the main organs affected by the autoimmune disease systemic lupus erythematosus. Lupus nephritis (LN) concerns 30-60% of adult SLE patients and it is significantly associated with an increase in the morbidity and mortality. The definitive diagnosis of LN can only be achieved by histological analysis of renal biopsies, but the invasiveness of this technique is an obstacle for early diagnosis of renal involvement and a proper follow-up of LN patients under treatment. The use of urine for the discovery of non-invasive biomarkers for renal disease in SLE patients is an attractive alternative to repeated renal biopsies, as several studies have described surrogate urinary cells or analytes reflecting the inflammatory state of the kidney, and/or the severity of the disease. Herein, we review the main findings in the field of urine immune-related biomarkers for LN patients, and discuss their prognostic and diagnostic value. This manuscript is focused on the complement system, antibodies and autoantibodies, chemokines, cytokines, and leukocytes, as they are the main effectors of LN pathogenesis.

Clinical and Immunological Biomarkers for Systemic Lupus Erythematosus

Systemic lupus erythematosus (SLE) is characterized by immune system dysfunction and is clinically heterogeneous, exhibiting renal, dermatological, neuropsychiatric, and cardiovascular symptoms. Clinical and physiological assessment is usually inadequate for diagnosing and assessing pathophysiological processes in SLE. Clinical and immunological biomarkers could play a critical role in improving diagnosis, assessment, and ultimately, control of SLE. This article reviews clinical and immunological biomarkers that could diagnose and monitor disease activity in SLE, with and without organ-specific injury. In addition, novel SLE biomarkers that have been discovered through “omics” research are also reviewed.

ImmunoCluster provides a computational framework for the nonspecialist to profile high-dimensional cytometry data

High-dimensional cytometry is an innovative tool for immune monitoring in health and disease, and it has provided novel insight into the underlying biology as well as biomarkers for a variety of diseases. However, the analysis of large multiparametric datasets usually requires specialist computational knowledge. Here, we describe ImmunoCluster (https://github.com/kordastilab/ImmunoCluster), an R package for immune profiling cellular heterogeneity in high-dimensional liquid and imaging mass cytometry, and flow cytometry data, designed to facilitate computational analysis by a nonspecialist. The analysis framework implemented within ImmunoCluster is readily scalable to millions of cells and provides a variety of visualization and analytical approaches, as well as a rich array of plotting tools that can be tailored to users' needs. The protocol consists of three core computational stages: (1) data import and quality control; (2) dimensionality reduction and unsupervised clustering; and (3) annotation and differential testing, all contained within an R-based open-source framework.

Basophils as a potential marker of lupus nephritis by flow cytometry

Objective:

To establish a convenient and simple flow cytometry immunophenotyping panel to explore immune cellular alterations and potential cellular biomarkers in systemic lupus erythematosus.

Materials and methods:

This is a cross-sectional, case–control study including 60 patients with systemic lupus erythematosus and 20 sex- and age-matched healthy controls. A 14-color immunophenotyping panel was applied to detect proportions of circulating immune mononuclear cells, and comparisons between patients and healthy controls, and subgroups of patients, were performed. Correlations between cellular proportions and other parameters were investigated.

Results:

After multivariate analysis, significantly decreased proportions of CD4⁻CD8⁻ T cells, natural killer cells and innate lymphoid cells were observed in patients compared with healthy controls. The proportions of basophils were decreased significantly in patients with lupus nephritis (LN) compared with those in patients without LN.

Conclusion:

In the present study, we found that basophil proportions may be a biomarker of LN.

Systemic lupus erythematosus is a chronic, multisystem, autoimmune disorder that involves various abnormalities of immune cells and thus presents in a striking variety of ways. This study aimed to establish a biomarker panel that would enable the exploration of changes in immune cells and the relationships between immune cell subsets and clinical manifestations in patients with systemic lupus erythematosus. Our results showed that basophil cell proportions may be a biomarker of use in lupus nephritis.

Urinary sediments could differentiate endocapillary proliferative lupus nephritis and endocapillary proliferative IgA nephropathy

OBJECTIVE

This study investigated the differences in urinary sediment findings between patients with endocapillary proliferative lupus nephritis (LN) and patients with endocapillary proliferative IgA nephropathy (IgAN) and further evaluated the associations of leukocyturia with disease activity, pathological features and prognosis.

METHODS

The urinary sediments of 126 patients, including 92 with LN and 34 with IgAN, with renal-biopsy-proven endocapillary proliferative glomerulonephritis (EPGN) were examined by a standardized method. The urinary elements investigated included various cells, casts and crystals. The associations of leukocyturia with disease activity, pathological features and prognosis were further analyzed.

RESULTS

In the patients with EPGN, normal to mild leukocyturia (≤12/HPF) and moderate to severe leukocyturia (>12/HPF) were found in 52 (41.27%) and 74 (58.73%) patients, respectively. The proportion of moderate to severe leukocyturia and the frequencies of urinary white blood cell casts and waxy casts were significantly higher in endocapillary proliferative LN than those in endocapillary proliferative IgAN (P < 0.001, P = 0.020, P = 0.010, respectively). In the endocapillary proliferative LN group, the levels of leukocyturia were significantly correlated with serum creatinine (r = 0.288, P = 0.005), eGFR (r = -0.284, P = 0.006), serum C3 (r = -0.275, P = 0.009), SLEDAI scores (r = 0.383, P ≤ 0.001) and glomerular leukocyte infiltration (r = 0.285, P = 0.002). A multivariate analysis showed that leukocyturia was an independent risk factor for renal outcomes in endocapillary proliferative LN (HR: 1.456, 95% CI: 1.083-1.957, P = 0.013) but not in IgAN.

CONCLUSIONS

Urinary sediments of LN with EPGN and IgAN with EPGN differed in many aspects. Leukocyturia could reflect the disease activity and prognosis of EPGN, especially in endocapillary proliferative LN.