Single Cell Gene Expression Studies Reveal Kidney Clues by Bridget M

KidneyNewsJune 2018 | Vol. 10, Number 6 Single Cell Gene Expression Studies Reveal Kidney Clues By Bridget M. Kuehn distinct role in kidney health, making it a challenge for tial information at a basic science level that will ultimately scientists to study. Traditionally, scientists have tried to result in a better understanding of many renal diseases,” distinguish these various cell types by their location in the Knepper said. kidney and appearance under a microscope, according to Katalin Susztak, MD, PhD, a professor of medicine at the Emerging insights Perelman School of Medicine at the University of Penn- A groundbreaking study by Susztak and colleagues sylvania. But rapid advances in genetic techniques are giv- using single cell sequencing identified several new ing scientists new tools for studying these cells. types of cells in the kidney, and showed that some Whole genome sequencing studies have allowed scien- cells in the kidney can transition back and forth tists to document an individual’s entire genetic blueprint. between two cell types to help the kidney adapt to Now the technology has advanced to allow scientists to changing conditions. look at which genes are turned on or off in individual cells. In their study, published in Science, Susztak and her “Every cell in your body has a full complement of colleagues took one kidney from seven different male DNA coding for approximately 21,000 proteins,” said mice and used droplet-based single cell RNA sequencing Mark Knepper, MD, PhD, a senior investigator at the Na- to analyze the gene expression in the more than 43,745 tional Heart, Lung and Blood Institute. “However, each cells in each kidney. They used a special machine to con- cell expresses only around 6000 to 8000 of these genes.” nect each cell with a bead that is able to capture all the new genetic technique called single cell genetic Single cell RNA sequencing allows scientists to deter- genes that are active in that cell. Then, they sorted the sequencing is helping to reveal new insights about mine which 6000 to 8000 genes are turned on in each cells based on these genes. This method is far cheaper than the cells that make up the kidney—insights that cell, which “provides a road map” for studying specific cell previous RNA sequencing methods, costing just 10 to 20 Aare essential to understanding what goes wrong in kidney types, Knepper said. cents per sample, Susztak said, compared with older tech- disease and how it might be reversed. “The single cell RNA sequencing approach and other Many types of cells make up the kidney, each with a next generation sequencing methods will provide essen- Continued on page 3 > Has Momentum for Changes in MOC Shifted to Exam Boards? Inside By Eric Seaborg Findings s physicians and state medical societies continue to ed to the American Board of Medical Specialties (ABMS) Restricting fluids during abdominal revolt against high-stakes maintenance of certifica- and individual specialty boards, which are promising signifi- surgery results in higher AKI risk tion (MOC) tests and increased MOC require- cant change. A “The leadership of the American Board of Internal Medi- Patients at the Center ments, more state legislatures have considered legislation to limit the use of MOC in professional requirements. This cine has heard clearly that it must change,” according to Kidney patients take center stage year, Tennessee and South Carolina became the fourth and Jeffrey S. Berns, MD, chair of ABIM’s nephrology board. at Kidney Health Initiative meeting fifth states to pass legislation restricting the use of MOC in ABIM will begin offering nephrologists and internists the areas such as licensure, reimbursement, employment, mal- option of replacing the 10-year test with an open-book every- Hyperoxaluria practice insurance, and insurance panel participation. two-year test in 2018. A Kidney Health Initiative project And ABMS has announced a collaborative re-evaluation Legislation in more than a dozen other states died or lan- aims to find surrogate endpoints for clinical trials guished in committee as the nexus for change may have shift- Continued on page 3 > Detective Nephron A case of hyperkalemia stumps Detective Nephron’s acolytes Fellows Corner Simultaneous liver-kidney transplant CRRT BUILT FOR my ICU. The PRISMAFLEX System is one of the best tools we’ve used in our ICU. And with Baxter’s support, we can do so much for our patients now that we’ve implemented our Super User Program and CRRT Task Force.” Juan Carlos Aycinena, MD Dr. Aycinena dedicated himself to becoming a nephrologist because he wanted to be able to offer hope to the sickest patients. In the past 4 years that he has been using the PRISMAFLEX System, he feels like his team has been able to do so much more for those patients, especially since implementing a CRRT Task Force. Including Baxter on that Task Force was an important decision and just one example of how we are always striving to partner with our customers. Baxter is committed to supporting Dr. Aycinena and his team as they continue to optimize their CRRT program. Watch Dr. Aycinena’s story at renalacute.com/stories COMPLETE SUPPORT | PATIENT SAFETY | FLEXIBILITY The PRISMAFLEX Control Unit is intended for: Continuous Renal Replacement Therapy (CRRT) for patients weighing 20 kilograms or more with acute renal failure and/or fluid overload. Therapeutic Plasma Exchange (TPE) therapy for patients weighing 20 kilograms or more with diseases where fluid removal of plasma components is indicated. Rx Only. For safe and proper use of this device, refer to the Operator’s Manual. Baxter and Prismaflex are registered trademarks of Baxter International Inc. or its subsidiaries. USMP/MG120/18-0006 02/18 BXRN-17005 CRRT Ad-Juan-10.5x14.5-KN.indd 3/13/18 4 Color n/a 0 -.5" 10.5" x 14.5" 11" x 15” ASN KIDNEY NEWS June 2018 | ASN Kidney News | 3 Single Cell Gene generated in the study. Susztak and colleagues also showed Center, who was the co-principal investigator, along with that the genes for specific kidney diseases were expressed Jill P. Buyon, MD, director of the division of rheuma- by just one type of cell. For example, genes linked with tology at New York University School of Medicine, and Expression high and low blood pressure were traced to one type of Thomas Tuschl, PhD, head of the Laboratory for RNA Continued from page 1 cell. This insight may help scientists trying to pinpoint Molecular Biology at Rockefeller University in New York. the cause of certain diseases. Susztak suggested this likely Putterman said that if other larger studies confirm the niques that could cost $300 for a single sample. means that there is a very clear division of labor among potential prognostic value of single cell RNA sequencing, “Because the cost is much lower, we can actually se- kidney cells, and if one type of cell is not working prop- it might encourage physicians to intensify initial treat- quence a large number of cells,” she explained. erly, for example because of a gene mutation, the others do ments for patients exhibiting molecular predictors of a Another advantage of this approach is that it provides not pick up the slack. more aggressive disease. an “unbiased” way of grouping cells, she said. The ap- The next step for Susztak’s research will be to start cata- The researchers also did single cell sequencing on skin proach classifies cells only on the genetic information be- loguing single gene expression in kidneys affected by dis- ing used in each cell instead of more superficial physical ease to understand how gene expression changes. In the cells collected from patients with lupus to see if it might cell characteristics that might be shared by multiple types meantime, she hopes the data from her current study will provide useful information about the progression of the of cells. This allowed the researchers to discover that 1 of help fuel other researchers’ work. disease. Putterman explained that kidney biopsies are the 3 types of cells previously identified in the collecting “We generated the periodic table for the kidney, so critical to assessing patients with lupus nephritis, but its duct of the kidney are actually just cells in transition from now we know where all the elements in the kidney are,” invasive nature together with the potential risks associated one type to another. These results reinforce findings from she said. “All the researchers who study kidney physiology with the procedure limit how many times it can be re- a previous study by Knepper and colleagues that had sug- or kidney homeostasis will be able to put the elements to- peated. Skin cells could be more easily and safely collected gested a transitional cell type in the collecting duct. gether and understand disease development, and how the over time. The study showed that some of the same lupus- “Both of us found hybrid cells that express markers of kidney works under [healthy] conditions.” linked genetic changes occurring in kidney cells may also both principal cells and intercalated cells,” Knepper said. be seen in skin cells. “This finding adds to additional evidence from ‘fate map- Clinical implications “If we can use the skin to reflect what’s happening ping’ studies that principal cells may convert into interca- in the kidney, that would be a major advance forward,” Already some groups have begun to apply single cell lated cells. This is currently a hot area of research.” Putterman said. sequencing techniques to samples taken from pa- Scientists know that the collecting duct and its cells While single cell sequencing is an enormously promis- tients with kidney disease.

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