May 20, 2019—(BRONX, NY)— In research that could make biopsies more useful for many diseases, scientists have used a powerful new tool to zero in on individual cells in a patient’s diseased organ and reveal the cells’ underlying glitches in gene expression—information that may allow for more precise and effective treatment. The findings, by scientists at Albert Einstein College of Medicine, Montefiore Health System, and other medical institutions, are published online today in Nature Immunology.
The researchers looked at nephritis (kidney inflammation), which affects half of all people who have systemic lupus erythematosus (SLE), a chronic autoimmune disease that inflames and damages tissues and organs throughout the body.
“Lupus inflammation can destroy kidney tissue and is a leading cause of death among patients with SLE,” said Chaim Putterman, M.D., the paper’s co-corresponding author, professor of medicine and of microbiology & immunology, and chief of rheumatology at Einstein and Montefiore.
The kidney biopsy has been the gold standard for diagnosing the condition, assessing its severity, and monitoring patients’ response to therapy. But it requires interpretation of stained tissue sections, which is not always sufficiently accurate for assessing disease severity or guiding treatment decisions.
Harnessing Advanced Technology
By contrast, said Dr. Putterman, “We used a much more sensitive tool called single-cell RNA sequencing, or scRNA-seq, which requires only a tiny amount of clinically obtained tissue to reveal the gene expression of individual cells. With scRNA-seq, we can see the inner workings of different types of kidney cells and identify disease-associated genetic ‘signatures’ within those cell types.”
Dr. Putterman and colleagues also found that scRNA-seq testing of skin cells mirrored the results obtained on kidney cells—opening up the possibility that patients with lupus nephritis may one day be able to avoid kidney biopsies altogether.
The Nature Immunology paper involved 21 patients in the New York area, primarily women between the ages of 16 and 53 who have lupus nephritis. Researchers used scRNA-seq to analyze the gene expression in several types of biopsied cells, including skin cells and cells from tubules, the tiny kidney structures that reabsorb essential filtered substances and transport wastes that end up in the urine. Damage to tubules determines the ultimate severity of kidney damage in lupus nephritis patients.
Seeking Genetic Signatures
The researchers first focused on genes involved in the interferon-response pathway. Interferons are proteins that regulate the immune response. Previous studies showed that interferons play a role in SLE and appear to cause flare-ups in patients with lupus nephritis patients. In both tubule cells and skin cells from these patients, interferon-pathway genes were expressed at a significantly higher level than in comparable cells obtained from a control group (three healthy women who did not have lupus). Moreover, those with lupus nephritis who had not responded to treatment six months after their biopsies had significantly higher interferon scores in their tubular cells at baseline as compared with patients who responded partly or completely to treatment.
While our study focused on the kidney, we're optimistic that scRNA-seq can potentially be similarly employed to improve on results obtained from many other types of clinical biopsies, such as those done on the prostate, breast, and skin.
Chaim Putterman, M.D.
“This finding suggests that those with lupus nephritis whose scRNA-seq test showed high interferon scores could potentially be good candidates for drugs now in clinical trials that inhibit interferon signaling,” said Dr. Putterman. “It also makes sense that interferon-associated genes activated in kidney tubules would be activated in their skin cells as well, since skin cells of these patients are exposed to the same interferons in the bloodstream.”
Next, the researchers analyzed the patients’ tubule and skin cells for genes involved in scarring—a serious consequence of lupus nephritis. Once again, those with lupus nephritis who proved unresponsive to therapy six months after biopsy had higher expression of scarring-associated genes in both skin and tubule cells than patients who responded well to treatment. Notably, standard kidney biopsy testing done on several treatment-unresponsive patients did not detect scarring; this suggests that scRNA-seq testing can detect kidney scarring at an early stage, when aggressive treatment might prevent scar formation from leading to kidney failure.
“While our study focused on the kidney,” said Dr. Putterman, “we're optimistic that scRNA-seq can potentially be similarly employed to improve on results obtained from many other types of clinical biopsies, such as those done on the prostate, breast, and skin."
In addition to Dr. Putterman, other Einstein and Montefiore researchers involved in the paper, “Tubular Cell and Keratinocyte Single-cell Transcriptomics Applied to Lupus Nephritis Reveal Type 1 IFN and Fibrosis Relevant Pathways,” are: Evan Der, Ph.D., Beatrice Goilav, M.D., Mordecai Koenigsberg, M.D., Michele Mokrzycki, M.D., Helen Rominieki, N.P., Jay A. Graham, M.D., Juan P. Rocca, M.D., Nicole Jordan, Emma Schulte, and James Pullman, M.D., Ph.D. Other researchers involved in the study are co-corresponding authors Jill Buyon, M.D., of NYU School of Medicine and Thomas Tuschl, Ph.D., of Rockefeller University; Hemant Suryawanshi, Ph.D., Pavel Morozov and Manjunath Kustagi of Rockefeller University; Peter Izmirly, M.D., Robert Clancy, Ph.D., H. Michael Belmont, M.D., Nicole Bornkamp, and Ming Wu, M .D., of NYU School of Medicine; Kamil Slowikowski , Ph.D., and Soumya Raychaudhuri, M.D., Ph.D., of the Broad Institute of MIT and Harvard; Saritha Ranabathou, M.D., of Arkansas Children’s Hospital; Joel Guthridge, M.D., and Judith James, M.D., Ph.D., of the Oklahoma Medical Research Foundation, and the Accelerating Medicine Partnership Rheumatoid Arthritis and Systemic Lupus Erythematosus Consortium.
Funding support for the study was provided by grants from the National Institutes of Health, with additional funding support from the Accelerating Medicines Partnership Rheumatoid Arthritis/Lupus Network.