With Phase 2 of the Accelerating Medicines Partnership (AMP) study of systemic lupus erythematosus (SLE) underway, an ACR Convergence 2020 session featured a panel that reviewed the methods being used to generate data and discussed some of the findings and insight gained from ongoing analyses of kidney and urine.
Registered attendees have on-demand access to watch a replay of the session, Molecular Insights from the Accelerating Medicines Partnership (AMP): Systemic Lupus Erythematosus, through Wednesday, March 11, 2021.
David Hildeman, PhD, professor and director of the Division of Immunobiology at Cincinnati Children’s Hospital, opened the session by discussing the methods used for generating single-cell RNA sequencing data from kidney biopsies.
“One of the things we needed early on was a source of biopsies to really establish dissociation conditions,” Dr. Hildeman said. “We used two sources of biopsies. One was from kidney nephrectomy patients undergoing chronic allograft rejection, and these are hematopoietic-cell rich because hematopoietic cells are the ones actually driving rejection of tissue. On the other hand, we also used some discarded kidneys that were not suitable for transplantation.”
He said that the ability to freeze the intact biopsies is important because it allows peripheral sites to ship the biopsies to central sites where the biopsies can be processed and digested, thereby making multicenter studies feasible.
“And recent AMP data shows that biopsies that have been cryopreserved for over six years have the same quality. So that’s really exciting because it means that these studies can go on for a long time collecting samples,” Dr. Hildeman said.
Arnon Arazi, PhD, assistant professor at the Feinstein Institutes for Medical Research, spoke about single-cell RNA sequencing analyses of kidney biopsies from AMP Phase 1 and offered some early insights from recently generated AMP Phase 2 data.
He cited some of the proof-of-concept data published last year by one of the groups working in Phase 1. The report included data from 24 kidney samples from lupus nephritis patients, 10 kidney samples from healthy controls, and also included urine cells from 8 lupus nephritis patients.
“And what we’ve done with these samples is isolate individual cells and measure gene expression in them using plate-based single cell RNA sequencing,” Dr. Arazi said. “In Phase 2, we are looking at a much larger cohort than Phase 1. So, we get many more cells per sample, and while we do have less genes per cell, it doesn’t seem to be affecting sensitivity much, at least at this point, in our ability to identify rare populations of cells.”
Andrea Fava, MD, fellow in training at Johns Hopkins University, discussed urine proteomics in lupus nephritis and potential implications for liquid biopsy.
“In the initial phases of AMP, preliminary data were generated in order to test and optimize the protocols and advise the best strategies for Phase 2, which is ongoing at full force,” Dr. Fava said. “Urine proteomics may greatly enhance renal biopsies by providing insights on the active renal biological pathways. It can be used as a biomarker to noninvasively monitor treatment responses, but also can serve as a discovery tool. I’m confident that with more data from Phase 2, we will be able to develop a liquid biopsy based on urine.”
Phase 2, he said, will include data on 199 unique patients, 600 longitudinal urine samples, and important negative controls.
Jill Buyon, MD, director of the Division of Rheumatology at NYU School of Medicine, talked about the progress of the AMP SLE Network and its potential relevance in patient stratification and targeted therapy.
“Phenotypic data and collected specimens across a nationwide network will be applied to various technologies to provide insights into pathogenesis by identifying correlates with histology class, activity, and chronicity, and dominant pathways by race, ethnicity, intra-renal, and extra-renal contributions, all of which will help us formulate precision treatments,” Dr. Buyon said. “We hope AMP will provide insights into clinical management. For example, when to biopsy, predictors of response, flare, and progression, as well as implications for trial design.”