Ray Archives

$3 million NIH grant to study APOL1 and HIV synergy

March 8, 2019

Zhe Han, Ph.D., (pictured) and Patricio E. Ray, M.D., have received a $3 million, five-year grant from the National Institutes of Health to study the mechanisms behind APOL1 and HIV nephropathies in children, using a combination of Drosophila models, cultured human podocytes and a preclinical model.

Two Children’s researchers have received a $3 million, five-year grant from the National Institutes of Health (NIH) to study the mechanisms of APOL1 and HIV nephropathies in children, using a combination of Drosophila models, cultured human podocytes and a preclinical model.

The APOL1 genetic variants G1 and G2, found almost exclusively in people of African ancestry, lead to a four-fold higher risk of end-stage kidney disease. HIV infection alone also increases the risk of kidney disease but not significantly. However, HIV-positive people who also carry the APOL1 risk alleles G1 or G2 are about 30 times more likely to develop HIV-nephropathy (HIVAN) and chronic kidney disease.

For more than 25 years, Children’s pediatric nephrology program has studied HIV/renal diseases and recently developed Drosophila APOL1-G0 and G1 transgenic lines. That pioneering research suggests that HIV-1 acts as a “second hit,” precipitating HIV-renal disease in children by infecting podocytes through a mechanism that increases expression of the APOL1-RA beyond toxic thresholds.

With this new infusion of NIH funding, labs led by Zhe Han, Ph.D., and Patricio E. Ray, M.D., will determine the phenotype of Drosophila Tg lines that express APOL1-G0/G1/G2 and four HIV genes in nephrocytes to assess how they affect structure and function. The teams also will determine whether APOL1-RA precipitates the death of nephrocytes expressing HIV genes by affecting autophagic flux.

“Our work will close a critical gap in understanding about how HIV-1 interacts with the APOL1 risk variants in renal cells to trigger chronic kidney disease, and we will develop the first APOL1/HIV transgenic fly model to explore these genetic interactions in order to screen new drugs to treat these renal diseases,” says Dr. Ray, a Children’s nephrologist.

While a large number of people from Africa have two copies of APOL1 risk alleles, they do not necessarily develop kidney disease. However, if a patient has two copies of APOL1 risk alleles and is HIV-positive, they almost certainly will develop kidney disease.

“Our work will close a critical gap in understanding about how HIV-1 interacts with the APOL1 risk variants in renal cells to trigger chronic kidney disease, and we will develop the first APOL1/HIV transgenic fly model to explore these genetic interactions in order to screen new drugs to treat these renal diseases,” says Dr. Ray, a Children’s nephrologist.

“Many teams want to solve the puzzle of how APOL1 and HIV synergize to cause kidney failure,” says Han, associate professor in Children’s Center for Genetic Medicine Research. “We are in the unique position of combining a powerful new kidney disease model system, Drosophila, with long-standing human podocyte and HIVAN studies.”

The team hypothesizes that even as an active HIV infection is held in check by powerful new medicines, preventing the virus from proliferating or infecting new cells, HIV can act as a Trojan horse by making the human cells it infects express HIV protein.

To investigate this hypothesis, the team will create a series of fly models, each expressing a major HIV protein, and will test the genetic interaction between these HIV genes with APOL1. Similar studies also will be performed using cultured human podocytes. Identified synergy will be studied further using biochemical and transcription profile analyses.

“Drosophila is a basic model system, but it has been used to make fundamental discoveries, including genetic control of how the body axes is determined and how the biological clock works – two studies that led to Nobel prizes,” Han adds. “I want to use the fly model to do something close to human disease. That is where my research passion lies.”

Toward a better definition for AKI in newborns

August 9, 2017

The National Institute of Diabetes and Digestive and Kidney Diseases convened a meeting of expert neonatologists and pediatric nephrologists, including Dr. Patricio Ray, to review state-of-the-art knowledge about acute kidney injury in neonates and to evaluate the best method to assess these patients’ kidney function.

Each year, thousands of infants in the United States end up in neonatal intensive care units (NICUs) with acute kidney injury (AKI), a condition in which the kidneys falter in performing the critical role of filtering waste products and excess fluid from the blood to produce urine. Being able to identify neonates during the early stages of AKI is critical to doctors and clinician-scientists who treat and study this condition, explains Patricio Ray, M.D., a nephrologist at Children’s National Health System.

Without an accurate definition and early identification of newborns with AKI, it is difficult for doctors to limit the use of antibiotics or other medications that can be harmful to the kidneys. Neonates who have AKI should not receive large volumes of fluids, a treatment that can cause severe complications when the kidneys do not properly function.

Until recently, there was no standard definition for AKI, leaving doctors and researchers to develop their own guidelines. Lacking set criteria led to confusion, Dr. Ray says. For example, different studies estimating the percentage of infants in NICUs with AKI ranged from 8 percent to 40 percent, depending on which definition was used. In 2012, a group known as the Kidney Disease Improved Global Outcome (KDIGO) issued practice guidelines for AKI that provide a standard for doctors and researchers to follow. They focus largely on measuring the relative levels of serum creatinine, a protein produced by muscles that is filtered by the kidneys, and the amount of urine output, which typically declines in adults and older children with failing kidneys.

The problem with these guidelines, Dr. Ray explains, is they are not sensitive enough to identify newborns experiencing the early stages of AKI during the first week of life. Newborns can have high serum creatinine levels during the first week of life due to residual levels transferred from mothers through the placenta. Also, because their kidneys are immature, failure often can mean higher – not diminished – urine production.

In 2013, the National Institute of Diabetes and Digestive and Kidney Diseases, part of the National Institutes of Health, convened a meeting of leading neonatologists and pediatric nephrologists – including Dr. Ray – to review state-of-the-art knowledge about AKI in neonates and to evaluate the best manner to assess kidney function in these patients. They published a summary of their discussion online June 12, 2017 in Pediatric Research.

Among other findings, the group concluded that the current definition of AKI lacks the sensitivity needed to identify the early stages of AKI in neonates’ first week of life. They also said that more research was needed to fill this gap.

That’s where Dr. Ray’s current research comes in. Working with fellow Children’s Nephrologist Charu Gupta, M.D., and Children’s Neonatologist An Massaro, M.D., the three clinician-scientists reviewed the medical records of 106 infants born at term with a condition known as hypoxic ischemic encephalopathy (HIE), in which the brain doesn’t receive enough oxygen. Not only does this often lead to brain injury, but it also greatly increases the risk of AKI.

Because these babies had been followed closely in the NICU to assess the possibility of AKI, their serum creatinine had been checked frequently. The researchers found that about 69 percent of the infants with HIE followed at Children’s National never developed signs of kidney failure during their first week of life. These babies’ serum creatinine concentrations dropped by 50 percent or more by the time they were 1 week old, about the same as reported previously in healthy neonates. Another 12 percent of the infants with HIE developed AKI according to the definition established by the KDIGO group in 2012. These infants:

Required more days of mechanical ventilation and medications to increase their blood pressure
Had higher levels of antibiotics in their bloodstreams
Retained more fluid
Had lower urinary levels of a molecule that their kidneys should have been cleared and
Had to stay in the hospital longer

A third group of the infants with HIE, about 19 percent, did not meet the standard criteria for AKI. However, these babies had a rate of decline of serum creatinine that was significantly slower than the normal newborns and the infants with HIE who had excellent outcomes. Rather, their outcomes matched those of infants with established AKI.

Dr. Ray notes that by following the rate of serum creatinine decline during the first week of life physicians could identify neonates with impaired kidney function. This approach provides a more sensitive method to identify the early stages of AKI in neonates. “By looking at how fast babies were clearing their serum creatinine compared with the day they were born, we could predict how well their kidneys were working,” he says. Dr. Ray and colleagues published these findings July 2016 in Pediatric Nephrology.

He adds that further studies will be necessary to confirm the utility of this new approach to assess the renal function of term newborns with other diseases and preterm neonates. Eventually, he hopes this new approach will become uniform clinical practice.

Supplement might help kidney disease

April 25, 2017

A research team was able to “rescue” phenotypes caused by silencing the fly CoQ2 gene by providing nephrocytes with a normal human CoQ2 gene, as well as by providing flies with Q10, a popular supplement.

A new study led by Children’s National research scientists shows that coenzyme Q10 (CoQ10), a popular over-the-counter supplement sold for pennies a dose, could alleviate genetic problems that affect kidney function. The work, done in genetically modified fruit flies — a common model for human genetic diseases since people and fruit flies share a majority of genes — could give hope to human patients with problems in the same genetic pathway.

The new study, published April 20 by Journal of the American Society of Nephrology, focuses on genes the fly uses to create CoQ10.

“Transgenic Drosophila that carry mutations in this critical pathway are a clinically relevant model to shed light on the genetic mutations that underlie severe kidney disease in humans, and they could be instrumental for testing novel therapies for rare diseases, such as focal segmental glomerulosclerosis (FSGS), that currently lack treatment options,” says Zhe Han, Ph.D., principal investigator and associate professor in the Center for Cancer & Immunology Research at Children’s National and senior study author.

Nephrotic syndrome (NS) is a cluster of symptoms that signal kidney damage, including excess protein in the urine, low protein levels in blood, swelling and elevated cholesterol. The version of NS that is resistant to steroids is a major cause of end stage renal disease. Of the more than 40 genes that cause genetic kidney disease, the research team concentrated on mutations in genes involved in the biosynthesis of CoQ10, an important antioxidant that protects the cell against damage from reactive oxygen.

Drosophila pericardial nephrocytes perform renal cell functions including filtering of hemolymph (the fly’s version of blood), recycling of low molecular weight proteins and sequestration of filtered toxins. Nephrocytes closely resemble, in structure and function, the podocytes of the human kidney. The research team tailor-made a Drosophila model to perform the first systematic in vivo study to assess the roles of CoQ10 pathway genes in renal cell health and kidney function.

One by one, they silenced the function of all CoQ genes in nephrocytes. If any individual gene’s function was silenced, fruit flies died prematurely. But silencing three specific genes in the pathway associated with NS in humans – Coq2, Coq6 and Coq8 – resulted in abnormal localization of slit diaphragm structures, the most important of the kidney’s three filtration layers; collapse of membrane channel networks surrounding the cell; and increased numbers of abnormal mitochondria with deformed inner membrane structure.

Journal of the American Society of Nephrology September 2017 cover

The flies also experienced a nearly three-fold increase in levels of reactive oxygen, which the study authors say is a sufficient degree of oxidative stress to cause cellular injury and to impair function – especially to the mitochondrial inner membrane. Cells rely on properly functioning mitochondria, the cell’s powerhouse, to convert energy from food into a useful form. Impaired mitochondrial structure is linked to pathogenic kidney disease.

The research team was able to “rescue” phenotypes caused by silencing the fly CoQ2 gene by providing nephrocytes with a normal human CoQ2 gene, as well as by providing flies with Q10, a readily available dietary supplement. Conversely, a mutant human CoQ2 gene from an patient with FSGS failed to rescue, providing evidence in support of that particular CoQ2 gene mutation causing the FSGS. The finding also indicated that the patient could benefit from Q10 supplementation.

“This represents a benchmark for precision medicine,” Han adds. “Our gene-replacement approach silenced the fly homolog in the tissue of interest – here, the kidney cells – and provided a human gene to supply the silenced function. When we use a human gene carrying a mutation from a patient for this assay, we can discover precisely how a specific mutation – in many cases only a single amino acid change – might lead to severe disease. We can then use this personalized fly model, carrying a patient-derived mutation, to perform drug testing and screening to find and test potential treatments. This is how I envision using the fruit fly to facilitate precision medicine.”

‘Trojan horse’ macrophage TNF-alpha opens door for HIV-1 to enter kidney epithelial cells, causing nephropathy

November 18, 2016

Like a Trojan horse, the macrophage sits atop the epithelial cell with HIV hidden inside, opening a doorway into the kidney cell for high levels of HIV-1 to enter.

When nephrologist Patricio Ray, M.D., began investigating human immunodeficiency virus (HIV) as a renal fellow, children infected with the virus had a life expectancy of no more than seven years, and kids of African descent curiously were developing a type of HIV-related kidney disease.

HIV-associated nephropathy (HIVAN) is a progressive kidney disease seen in people who are both HIV-positive and of African ancestry. Kids who carry a modified protein that protects them against sleeping sickness are 80 times more likely to develop this type of kidney disease. Due to the kidney damage, they can have abnormal amounts of protein in their urine, focal segmental glomerulosclerosis, and microcystic tubular dilation, which can lead to enlarged kidneys and chronic kidney failure.

“No one understood how HIV could affect kidney cells that lack the receptors expressed in T cells and white cells,” recalls Dr. Ray, Robert Parrott Professor of Pediatrics at Children’s National Health System. Virologists said kidney epithelial cells that lacked CD4, a major receptor where HIV attaches, could not be infected with the virus. Nephrologists, meanwhile, were seeing that HIV infection was damaging these cells.

It’s taken two decades to unravel the medical mystery, aided by urine samples he coaxed kids to donate by offering them the latest music from New Kids on the Block in exchange for each urine bottle. Many of the kids died years ago, but their immortalized cells were essential in determining, through a process of elimination, which renal cell types were capable of being infected by HIV-1.

The paper represents the capstone of Dr. Ray’s career.

“This is how difficult it is to get an important contribution in science,” he says. “It’s 20 years of work involving the excellent contributions of many people, but that’s why research is called research. In the end, it’s all a learning process. But, it’s amazing how the puzzle pieces begin to fit. When the puzzle fits, it’s good.”

Dr. Ray, in collaboration with lead author Jinliang Li, Ph.D., and four additional Children’s National co-authors, published a paper November 3 in the Journal of the American Society of Nephrology that establishes a new role for transmembrane TNF-alpha, that of a facilitator that makes it easier for the HIV virus to enter certain cell types and replicate there. Like a Trojan horse, the macrophage sits atop the epithelial cell with HIV hidden inside, opening a doorway into the kidney cell for high levels of HIV-1 to enter.

As a starting point, the research team cultured podocytes from the urine of kids with HIVAN. Through a number of steps, they isolated the unique contributions of the HIV envelope, heparan sulfate proteoglycans as attachment receptors – the glue that binds HIV to podocytes – and the essential role played by TNF-a, a 212-amino acid long type 2 transmembrane protein, in regulating at least two processes, including viral entry and fusion. They used a fluorescent marker to tag HIV-1 viruses, so it lit up bright green. Thus primed with transmembrane TNF-a, the podocytes were susceptible to HIV-1 infection when exposed to high viral loads.

Additional research is needed, such as in vitro work to help understand how HIV traffics within the cell, Dr. Ray says. Those insights could winnow the list of existing therapies that could block key steps, such as attachment to the viral envelope, which could help all people of African descent carrying the genetic mutation, including underserved kids in sub-Saharan Africa.

Another open research question is that certain cells located in the placenta and cervix express TNF-a, and may be more likely to be infected by HIV. Blocking that process could help prevent pregnant HIV-positive mothers from transmitting illness to their offspring.

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