November 19, 2020
The LRA is proud to share the extraordinary work presented at ACR Convergence 2020 by research members of the Accelerating Medicines Partnership Rheumatoid Arthritis (RA) and Systemic Lupus Erythematosus (SLE) program (AMP RA/SLE). AMP is a public-private partnership between the National Institutes of Health (NIH), eight biopharmaceutical companies, the LRA and several other nonprofit groups and managed by the Foundation for the NIH (FNIH).
The AMP SLE program is designed to provide a deep molecular characterization of kidney biopsy samples from patients with Lupus Nephritis, or kidney inflammation. Over 350 lupus patients have contributed to this program, many of whom have contributed kidney biopsy samples, which require a surgical procedure, and samples of urine and blood. Additionally, physicians are following these patients to see how their lupus nephritis responds to therapy. A return to good kidney function is viewed as a complete response, whereas an improvement but not a return to normal function is viewed as a partial response to therapy. These studies are also designed to measure how well patients with Lupus Nephritis respond to their current medications, and if there are molecular pathways that can be linked with disease progression and response to therapy. This information may allow physicians to better treat their patients with current medications and enable discovery of new medicines.
Following are summaries of the studies presented at ACR Convergence 2020 focusing on better ways to diagnose, monitor and treat lupus nephritis:
Patient safety was important for participation in the AMP SLE program.
Safety of Obtaining Research Tissue During Clinically Indicated Kidney Biopsies: Data from the Lupus Accelerating Medicines Partnership: Kristina Deonaraine.
The goal of this study was to define the safety of obtaining additional tissue for research studies during clinically indicated renal biopsies in SLE patients. In this study, tissues from kidney biopsies were obtained from 16 US clinical sites as part of the SLE AMP partnership. After obtaining the tissue by biopsy that was needed for clinical evaluation, a second tissue sample for research purposes was also taken during this same procedure. Patients were monitored for 30 days after the procedure and any adverse events or safety findings were noted. Results suggested that obtaining an additional sample for research purposes during a kidney biopsy procedure did not result in an increase in adverse events for SLE patients. This was a very important and reassuring result.
The AMP SLE program was featured in an oral session on Sunday November 8th, with four speakers:
Getting Single Cell RNA Sequencing Data From Human Kidney Biopsies: David Hildeman, PhD
Dr. Hildeman described the development of techniques to standardize and prepare samples from patients participating in the AMP SLE program. These samples from lupus patients include kidney biopsies, urine samples and blood samples. They are obtained at different medical sites by different physicians and need to be shipped to a shared research site for experimental analysis and comparisons. This makes it important to be sure that these valuable samples are all prepared the same way, that the samples are suitable for the technical analysis and that they can be stored until needed at the research site.
Dr Hildeman’s work nicely highlighted the success that the AMP SLE team had in developing and using protocols for preparing samples, shipping them and analyzing them at the research sites. He was also able to show that the cell types obtained in the urine samples were the same as those seen in the kidney biopsy sample, suggesting that urine samples will be a valuable resource for understanding kidney disease.
Single Cell Transcriptomic Analyses of Lupus Nephritis Kidney: Arnon Arazi, PhD
Dr Arazi presented data from the Phase I studies from the AMP SLE program, and some early work from ongoing Phase 2 studies. The Phase 1 studies compared molecular patterns from kidney biopsy samples and urine samples from a small number of patients with lupus nephritis using a technique called single cell RNA sequencing. This study showed that molecular information could be obtained from both the kidney biopsies and the urine samples, and that there was similarity between the two sample types. This means that important changes in molecular pathways seen in the kidneys that contribute to disease may also be detected in urine samples. Scientists could then work to develop tests from urine samples to monitor inflammation in the kidney, allowing more frequent and less invasive tests.
In the Phase 2 study, kidney biopsy samples from 160 lupus patients and 30 patients without lupus are being examined by single cell RNA sequencing to examine how different or similar the molecular patterns are among lupus patients. The goal will be to see if patients can be grouped based on these molecular patterns, and to find out if these molecular patterns are related to patients’ symptoms and their response to different medications. The Phase 2 study is ongoing, and the first samples have been successfully evaluated. Once this study is completed, these results will be shared with the entire lupus community as a basis for understanding lupus nephritis.
Urine Proteomics in Lupus Nephritis: Implications for a Liquid Biopsy: Andrea Fava, MD
Up to 50-70% of patients with SLE can develop lupus nephritis or kidney inflammatory disease. There is no FDA-approved treatment for lupus nephritis at this time. Current evaluation of patients with nephritis includes measuring total protein amounts in their urine and examining tissues from a kidney biopsy under a microscope. Information about the severity of disease can be obtained by microscopic analysis of these samples, and physicians use this to define two major stages of nephritis called proliferative or membranous nephritis.
Dr. Fava asked whether there are molecular patterns that associate with either stage of lupus nephritis. He examined individual proteins in the urine of 30 patients with lupus nephritis, and found different proteins in each of the two stages of nephritis. A class of proteins that recruit inflammatory cells into the kidney was found to be associated with the more inflammatory proliferative type of nephritis. One protein, called IL-16, was higher in urine samples from patients with more inflammatory nephritis and matched up with a measure of their disease activity. IL-16 was made by the immune cells that migrate into the kidney in SLE patients. Further studies with more patients are ongoing to confirm these findings. This study raises the possibility that urine samples may provide new information about a patient’s kidney disease and provide better ways for physicians to monitor each patient’s disease and perhaps help guide future treatment.
What Have We Learned About SLE from AMP, and Where Are We Going? Jill Buyon, MD.
Dr. Buyon reported on clinical findings from the group of AMP SLE patient volunteers. To date, 369 patients with lupus nephritis have contributed to the AMP SLE program by providing their clinical data and biological samples, including blood, urine and kidney biopsy samples. Note that kidney biopsies were carried out only when medically necessary.
Clinical information was considered for all 369 patients to see how clinical measurements may help physicians understand disease in lupus patients. Samples from 254 of these 369 patients were further selected for molecular analysis. The AMP SLE patient group was ethnically diverse with 28% identifying as Hispanic, 44% as Black, 17% as Asian and 13% as Non-Hispanic White.
Comparison of results from a clinical test called a UPCR, which measures total proteins in the urine, with the classification of kidney disease based on the kidney biopsy sample showed that lower UPCR scores did not reliably predict results from the kidney biopsy. This study indicated that about half of the patients with a low UPCR result had kidney disease that should be treated based on their kidney biopsy. Patients with UPCR scores greater than 1 usually had disease that required treatment.
Patients were treated and followed for at least one year after their first biopsy and their diagnosis of lupus nephritis. After one year, 51% of these patients achieved a complete or good response to therapy. However, patients having repeat biopsies, likely due to lupus flare, did not respond as well to therapy, with only 19% achieving a complete response to therapy. Patients who responded to therapy were more likely to have lower results for their UPCR test at diagnosis.
Additional clinical studies are ongoing. These clinical results will then be compared with the molecular characterization of the kidney, blood and urine samples. By combining the information obtained from these patients, the AMP SLE program aims to provide insights into lupus nephritis, including identifying better ways to monitor the activity of lupus nephritis, to see how race or ethnicity may influence disease, to identify disease drivers associated with the kidney or other tissues, and to provide physicians with insights into how to treat each patient.
Additional studies from the AMP SLE program were presented in other sessions:
Dr. Fava presented several talks and a poster, providing more information about his findings about understanding differences between types of lupus nephritis and their link to new molecular pathways and patterns. He also provided more information from the AMP SLE program on ethnic diversity in the study, as summarized below.
Trajectory Analysis of Repeat Renal Biopsies Identified Previous Endocapillary Proliferation as Predictor of Damage and End Stage Renal Disease in Pure Membranous Lupus Nephritis: Andrea Fava, MD
Levels of protein in the urine are measured regularly at physician visits, and if the level is high, physicians will likely order a kidney biopsy. If examination of the kidney sample shows evidence of lupus nephritis, patients are treated with immunosuppressants. Patients can be treated more aggressively if there is evidence of a type of nephritis associated with immune cell infiltration called proliferative disease, in comparison with patients with a type of nephritis called membranous.
The AMP SLE team evaluated 220 patients who had undergone two kidney biopsy procedures, typically around four years apart to see if the type of their nephritis changed over time. They found that patients often had a switch between types of lupus nephritis when comparing their two biopsies. This switch could occur at any time, and suggests that a single biopsy may not be enough to predict the course of the disease.
Urine Proteomics and Single Cell Transcriptomics Identify IL-16 as a Biomarker for Lupus Nephritis: Andrea Fava, MD
Lupus nephritis is diagnosed by measuring high protein levels in the urine (proteinuria) and examining kidney biopsies to detect the presence and severity of kidney disease. Better non-invasive methods of monitoring kidney disease in SLE patients are needed.
In this study, Dr. Fava and colleagues measured levels of 1,000 different proteins in the urine provided by 30 patients with lupus nephritis. They identified three proteins that were associated with different stages of lupus nephritis activity. One of these proteins called IL-16 was more highly evident in the urine from patients whose biopsies reflected more active kidney disease. The IL-16 was made by activated immune cells in the kidneys of some patients with lupus nephritis.
Patients were studied over the course of one year after being diagnosed with lupus nephritis to measure their response to therapy and to measure levels of urine IL-16. After one year, lower levels of IL-16 were seen in the urine of patients who responded to treatment for their lupus nephritis. No change was observed in this small study among patients who did not respond to therapy.
This study suggests that detection of specific proteins in the urine of patients with lupus nephritis may provide physicians with information about their kidney disease without requiring a kidney biopsy. This may allow better monitoring of treatment and response to therapy. Additional studies needed to confirm and extend these findings are ongoing in the AMP SLE program.
Lupus Nephritis and Renal Outcomes in African-Americans: The Accelerating Medicines Partnership Cohort Experience: Andrea Fava, MD.
The Accelerating Medicines Partnership (AMP) SLE program is focused on understanding Lupus Nephritis at the molecular level. African American patients can develop more lupus nephritis that other patients and have more serious disease. Research samples donated by 118 SLE patients from their clinically necessary kidney biopsies were used in this study. Clinical data from all participants was obtained at the time of the biopsy and at 12, 26 and 52 weeks after their biopsy. All patients were on medicines prescribed by their physicians.
Analysis of clinical data from these patients showed that African American patients had more serious kidney disease at the time of their first kidney biopsy, as compared with Asian, Caucasian and Hispanic patients. African American patients also were less likely to respond to treatment following their first episode of lupus nephritis.
This study highlights the need for better therapies for patients with lupus nephritis, in particular for African Americans. This study also suggests that personalized treatments are needed to improve outcomes in high-risk patients, such as African Americans.
Additional studies addressed disease treatment and progression in SLE patients:
Renal Responder Status and Associated Clinical Variables in the Lupus Accelerating Medicines Partnership Cohort: Philip Carlucci, BS
The goal of this study was to evaluate how lupus nephritis patients responded to standard of care therapy chosen by their provider. Overall, about half of the patients did not reach a partial or complete response in this study. This study revealed that only some patients can achieve a complete response on current medications, and that better treatments are needed for patients with lupus nephritis.
Of the patients who underwent their first biopsy for diagnosis of lupus nephritis, 36% had a complete response and 31% had a partial response to therapy at 26 weeks. At 52 weeks, complete remission was seen in 40% of patients and 20% had a partial remission. Patients who were having a repeat biopsy, suggesting a possible disease flare, had lower rates of complete remission (21%) and partial remission (21%) at 26 weeks, and at 52 weeks 19% of these patients had a complete remission, and 23% had a partial remission.
The Value of Renal Biopsy at Lower Levels of Proteinuria in Patients Enrolled in the Lupus Accelerating Medicines Partnership: Philip Carlucci BS
Physicians use a series of guidelines to decide whether to obtain a kidney sample by biopsy from patients with lupus nephritis. Elevated measurements of proteins in the urine, called a UPCR test, can suggest that a kidney biopsy is needed. In this study, the investigators examined the kidney biopsies from patients in the AMP SLE cohort to see how well their UPCR test results predicted whether they had lupus nephritis that needed treatment. Additional clinical measures were also examined. They found that patients with a high UPCR measurement of greater than 3 mg/gm were more likely to have relapsed lupus nephritis, meaning that it was under control but despite treatment, came back, and those with scores between 1 and 3 usually needed treatment. They also found that about half the patients with UPCR levels less than 1 mg/gm had lupus nephritis that needed treatment. These data suggest that kidney biopsies can provide important information to physicians even in patients with lower UPCR measurements.
Urine Proteomic Classifiers Predict Renal Histological Activity and Chronicity Indices and May Predict Treatment Response in Lupus Nephritis: Emma Weeding, MD:
Diagnosis and treatment of patients with Lupus Nephritis currently includes analysis of kidney biopsies and measurements of total protein in the urine of patients. Kidney biopsies, which require surgically removing a small sample of tissue, are more invasive than taking a urine specimen.
In this poster presentation, scientists from the SLE AMP program looked more closely at the proteins in urine to see if identifying specific proteins, rather than just measuring the total amount of proteins, could give clinicians another way to monitor kidney disease in patients with lupus nephritis, and to provide information about whether patients responded to treatment.
Researchers put two urine samples, taken at the time of diagnosis and a year after treatment through a process called proteomics that analyzes the proteins in detail; two scores were derived from these called CDK273 and LN120.
In a small study, both of these scores correlated with what was seen by examination of kidney biopsies at the time of diagnosis, although there was variation among patients. Interestingly, the urine LN120 score was lower when measured at one year for the four patients in the study who responded completely to their treatment. This was not observed for the total protein measurement or for the CDK273 measurement.
This result raises the possibility that a more detailed profile of the proteins in urine may give clinicians additional information about a patient’s kidney disease, and allow better patient monitoring. A larger study will be needed to determine how useful these proteomics scores are in more patients, and whether these scores could be improved to better reflect disease activity.
Mass Cytometry Reveals Activation Heterogeneity of Circulating Neutrophils in Systemic Lupus Erythematosus: Ricardo Grieshaber Bouyer, MD
An inflammatory cell type called neutrophils has been thought to contribute to disease in lupus. This study used a novel technology called CyToF to detect many proteins found on the surface of neutrophils. They compared these proteins released by neutrophils to determine if all neutrophils were the same in SLE patients and healthy volunteers.
Circulating neutrophils were isolated from the blood of 24 SLE patients and 10 healthy volunteers. The investigators found that there were differences among the neutrophils in terms of cell surface proteins in each patient’s blood. Additionally, some SLE patients had differences in their neutrophils as compared with healthy controls.
Further studies are needed to learn whether neutrophils play distinct roles in disease among SLE patients. Experiments to further understand how neutrophils may contribute to SLE are ongoing as a part of the AMP SLE consortium.