Agrawal Laboratory

“If you cannot find a cause for an illness, it’s difficult to treat it,” says Pankaj Agrawal, M.D., MMSc, chief of Neonatology in the University of Miami Miller School of Medicine Department of Pediatrics and Jackson Health System.

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Dr. Agrawal is head of a team of researchers set to change what they call a “diagnostic odyssey” –– not only for patients connected to academic medicine hospitals but also those in community hospitals with fewer resources.

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As principal investigator for the Virtual Genome Center in Infant Health (VIGOR) Project, funded by a $5.4 million R01 grant from the National Institutes of Health (NIH), he and a team of researchers are partnering with 11 community hospital NICUs to provide rapid genome sequencing. They’re also educating clinicians at the partnering hospitals about how to recognize candidates for rapid genome testing and how to explain the results to families.

An international research group, led by scientists at the University of Miami Miller School of Medicine, has identified a novel gene associated with a neurodevelopmental condition. The mutated gene, WSB2, is part of a critical cellular system that recycles unneeded proteins. Without this process, bad proteins accumulate, hampering neural development and function. The study was published in the European Journal of Human Genetics.

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“We’ve worked on this gene and the associated phenotype for several years,” said Pankaj Agrawal, M.D., chief of the Division of Neonatology at the Miller School’s Department of Pediatrics and Jackson Health System. “We started with one patient carrying this recessive, loss-of-function WSB2 mutation and were unsure what it meant. Thanks to collaborations from around the world, we can now say this is the disease-causing mechanism, which opens many possibilities, including helping diagnose other patients and even finding treatments.”

Advancements in medicine can benefit patients are young as newborns. At Holtz Children’s Hospital, part of the Jackson Health System, genetic testing is being offered to babies as soon as they are born, even if they are premature or have an underlying condition.  

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Rather than having a baby spend up to six months in the NICU, genetic sequencing can decrease that time to as few as three days. Genetic sequencing uses DNA and RNA to get an accurate reading of inherited diseases and predict how premature babies will respond to treatments and scan for rare conditions that don’t show up in routing testing.  

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“We are implementing a roadmap for continuous optimization for the best possible health,” said Pankaj Agrawal, M.D., chief of the division of neonatology at Jackson Health System and professor of clinical pediatrics and genetics at the Miller School. “This testing saves money, time and pain for the families as they deal with the child’s unknown condition. We are harnessing technology like never before to advance health care.” 

In a study published in the journal Genetics in Medicine, researchers at the University of Miami Miller School of Medicine have developed powerful new insights into unique, highly constrained genes, including their biological pathways and potential impacts on health and disease. The study showed, based on large-scale data from healthy people, that these genes do not tolerate mutations, suggesting the critical roles they play in many cellular functions.

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“This is the first time these constrained genes have been studied so comprehensively,” said Pankaj Agrawal, M.D., chief of the Division of Neonatology at the Miller School’s Department of Pediatrics and Jackson Health System. “We used large datasets to really understand them and we found these genes translate into proteins that are critical to cellular function. Some have not yet been linked to human disease, but they need more study.”

Unfortunately, her blood pressure increased, and her kidneys and liver started shutting down as a result of her failing placenta. The team recognized that it was time to deliver the baby, despite being shy of 28 weeks.

In a review published in the journal Pediatric Research, scientists at the University of Miami Miller School of Medicine explored how several technologies can help diagnose rare diseases. In addition to genomics, which can identify the faulty genes that underlie many conditions, transcriptomics, proteomics, epigenomics and metabolomics could provide important diagnostic information to help solve profound medical mysteries.

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“We are improving the diagnostic capabilities of genomics, but sometimes genomics is not enough,” said Pankaj Agrawal, M.D., chief of the Division of Neonatology at the Miller School and Jackson Health System and senior author on the paper. “By bringing these other technologies into the mix, we can improve our ability to diagnose rare diseases and get answers for these families.”

A large, international study published in the journal Neurology has shown that genomic sequencing (exome or genome sequencing) can rapidly identify the underlying causes for neonatal hypotonia. These findings could help medical teams quickly diagnose infants and provide the most effective therapies.

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“Babies with hypotonia need to be diagnosed quickly,” said Pankaj Agrawal, M.D., chief of the Division of Neonatology at the University of Miami Miller School of Medicine and Jackson Health System and senior author on the paper. “Hypotonia can be caused by many different conditions and that can lead to a long, diagnostic odyssey, where babies receive test after test and nobody is certain about the cause. Meanwhile, these infants continue to stay in the NICU while families wait for answers so that appropriate therapies can be initiated. With genomic sequencing, we can cut to the chase.”

Researchers at the University of Miami Miller School of Medicine, Boston Children’s Hospital and the Manton Center for Orphan Disease Research have shown that mutations in the HBS1L gene disrupt eye function and cause retinal dystrophy.

The study was published in the journal Disease Models and Mechanisms.

“As far as we know, the mutations in this specific gene affect only one person in the world,” said Pankaj Agrawal, M.D., chief of the Division of Neonatology at the Miller School Department of Pediatrics and Jackson Health System. 

CF is caused by mutations in CFTR, leading to no or a faulty CFTR protein, which regulates the balance of salt and water in cells by moving chloride ions into and out of them. A lack of it causes thick and sticky mucus to accumulate in the lungs and other organs, driving the symptoms of CF.

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Even among people with the same CF-causing mutation, symptoms and clinical outcomes can vary widely. “Some CF patients live into their 50s, while others with the same mutation die before they turn 18,” Pankaj Agrawal, MD, of the University of Miami Miller School of Medicine and the study’s senior author, said in a university news release.

A large, international research collaboration has shown that whole genome sequencing (WGS) can better determine the genetic causes of rare diseases than whole exome sequencing (WES).

WES only reads protein-producing genes, around 2% of the genome, according to a study published in the New England Journal of Medicine.

“For many years, people have been asking whether genome or exome is the better approach,” said Pankaj Agrawal, M.D., chief of the Division of Neonatology at the University of Miami Miller School of Medicine Department of Pediatrics and Jackson Health System and co-author on the paper. 

Caused by mutations in the CFTR gene, cystic fibrosis (CF) affects multiple organs, particularly the lungs. While the condition has been heavily studied, a number of mysteries remain, including why patients with the most common DeltaF508 mutation in the CFTR gene can have radically different outcomes.

Researchers at the University of Miami Miller School of Medicine and other schools have shown that variants in a related gene, SLC26A9, can worsen CF. 

Riley Kogen never got the chance to realize her legacy of becoming a University of Miami Hurricane and follow in the footsteps of her mother, Ali Nathan, B.Sc. ’03, and grandfather, Bob Denholtz, B.B.A. ’71. Riley passed away a decade ago, at only five years of age, from panhypopituitarism, a rare condition that affects the production of hormones in the pituitary gland.

Hoping to prevent other families from experiencing similar heartbreak, her family created Riley’s Dance Fund, named in honor of the blue-eyed little girl who loved to twirl.

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Their philanthropy supports the groundbreaking work of Pankaj Agrawal, M.D., chief of the Division of Neonatology. 

In a study published in the Journal of Cachexia, Sarcopenia and Muscle (JCSM), researchers at the University of Miami Miller School of Medicine, Boston Children’s Hospital, Brigham & Women’s Hospital and Harvard Medical School have shown how mutations in the SPEG protein can derail muscle function and cause disease.

Using a complex, multi-omic approach, the team showed how SPEG interacts with multiple skeletal and heart muscle proteins and regulates them.

“We have been studying SPEG for more than 10 years,” said Pankaj Agrawal, M.D., chief of the Division of Neonatology at the University of Miami Miller School of Medicine.

Genome sequencing has proven its value many times over, particularly in the neonatal intensive care unit (NICU). Rapid sequencing can identify underlying genetic conditions, leading to precise diagnoses and effective treatments for newborns with very serious medical conditions.

But genomics is not yet a plug-and-play solution. Hospitals need infrastructure and expertise to make it work. Major academic teaching hospitals have the resources to get it done. Small community hospitals generally do not.

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In an effort to level the playing field, Pankaj Agrawal, M.D., chief of the Division of Neonatology in the University of Miami Miller School’s Department of Pediatrics, and colleagues at Boston Children’s Hospital and elsewhere created the Virtual Genome Center for Infant Health (VIGOR).

Genome sequencing can identify genetic variants that may cause disease, but the answers aren’t always clear. Variants of uncertain significance (VUS) can cloud the picture, leaving patients and families in a diagnostic no-man’s land.

Now, in a study published in the American Journal of Medical Genetics, researchers at the University of Miami Miller School of Medicine have shown that carefully reevaluating VUS can generate concrete diagnoses. These approaches could help physicians and researchers solve numerous medical mysteries, potentially matching patients with effective treatments and clinical trials.​

Genomic sequencing has the potential to diagnose rare genetic diseases in newborns. But these technologies have yet to be widely adopted, limiting access to care.

In a review published in the European Journal of Human Genetics, a Nature journal, neonatologists at the University of Miami Miller School of Medicine, Holtz Children’s Hospital of Jackson Health System, Harvard Medical School and Boston Children’s Hospital examined the current neonatal sequencing landscape to see how it can be improved.​

Ryan and Rachel Belanger have a bittersweet relationship with Pankaj Agrawal, M.D., chief of the Division of Neonatology in the Miller School’s Department of Pediatrics and Jackson Health System. In 2017, the renowned neonatologist identified the rare metabolic disorder that claimed the life of their newborn daughter, Bella. Years later, that same knowledge ensured that their two sons wouldn’t suffer the same fate.

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“When we met Dr. Agrawal, we knew we were in the best hands,” Rachel said. “The way he made us feel and the way he treated us, we knew that he wouldn’t stop searching for answers.”

About a year and a half ago, Robert Rothstein, MD, FAAP encountered a baby with a pattern of facial features and clinical findings that suggested a genetic syndrome. The available tests couldn’t pinpoint a diagnosis, and the family wanted a more definitive answer. So Rothstein and his colleagues transferred the newborn from Baystate Medical Center (Springfield, Mass.) to Boston Children’s Hospital — 90 miles away — for a more in-depth genetic workup.

By the time the parents met with the Boston Children’s team to discuss their baby’s genetic diagnosis, they were anxious and mistrustful. The neonatal intensive care unit (NICU) team in Boston suggested patching Rothstein into the family conferences and decision-making.

Suheil Day was born early, at 37 weeks. Aside from a slight head lag and mild muscle weakness, nothing seemed terribly amiss. But as the months progressed, he began having seizures.
 

“At the age of 4 to 5 months, he started waking up screaming and crying excessively, his eyes rolling up into his head,” says his mother, Nadeen.
 

Suheil’s physicians in Israel diagnosed him with West syndrome, an infantile spasm disorder, and treated him with adrenocorticotropic hormone. His seizures abated, but only for six months. After 15 other medications were tried without success, the Israeli hospital arranged for whole-exome sequencing to look for a genetic cause. The results showed variants in four genes. Two genes were ruled out after more testing; the other two were unknown.

A growing number of children with suspected genetic disorders are having their complete exomes sequenced, since it’s now often faster and cheaper to sequence all the protein-coding genes at once rather than test limited groups of genes. But even after whole-exome sequencing, 70 to 75 percent of children come away without a genetic explanation for their illness.

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More and more clinicians are sending these families to Pankaj Agrawal MD, MMSc, a neonatologist at Boston Children’s Hospital and medical director of the Gene Discovery Core at Boston Children’s Manton Center for Orphan Disease Research. The Core can then do a deeper dive. Its services are available to any patient or family looking for a second opinion, including families whose child is deceased.

Two rare groups of CF patients may reveal new approaches to treatment. They are outliers: patients whose disease progresses much more rapidly or slowly than is typical despite the same mutation.

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A Boston Children's team scoured the genomes of five outliers in search of genes that might modify the effects of the CF mutation and this explain these differences. They found several and are creating patient-specific stem cell models to further study the interactions of the modifier of CF genes. The team --physician scientist Ruobing Wang, stem cell scientists Carla Kim and George Q. Daley, and geneticist Pankaj Agrawal -- hopes that insights from outliers will lead to new treatments for CF patients who do not benefit from today's drugs.  

When the 1-year-old boy arrived from overseas, he was relying on total parenteral nutrition — a way of bypassing the digestive system to provide nutrients and calories completely intravenously — to survive. From the time of his birth, he had experienced unexplainable diarrhea. Answers were desperately needed.

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Sequencing his genes in search of clues, neonatologists and collaborators at the Manton Center for Orphan Disease Research at Boston Children’s Hospital identified a new gene mutation responsible for chronic congenital diarrhea — even finding a similar mutation in two other children as well.

The answer may be hidden in their genes.

Cystic fibrosis is an inherited disorder caused by genetic mutations that disrupt the normal movement of chloride in and out of cells. Among other health problems, cystic fibrosis compromises the lungs’ ability to fight infection and breathe efficiently, making it the most lethal genetic disease in the Caucasian population. Patients have an average lifespan of just 30 to 40 years.

Despite this narrow average lifespan, there is a big range in how severely cystic fibrosis (CF) affects the lungs and other organs depending on an individual’s specific genetic variation, and even in how long patients sharing the same, most common genetic mutation are able to survive with CF.

The first complete autopsy findings for a patient with AIFM1-associated disease are described in a paper from Morton et al. A novel variant in AIFM1 was identified in an infant who presented with severe metabolic acidosis, myopathy, and neuropathy. Shown here is a Gomori trichrome image of quadriceps muscle biopsy, 100×, showing features of mitochondrial myopathy including coarse stippling and scattered fibers with subsarcolemmal aggregates corresponding to mitochondria. (For details, see Morton et al., this issue; doi: 10.1101/mcs.a001560.)

Examining the tragedies of several families who each lost multiple children, two teams of researchers reveal a previously unappreciated role for a mitochondrial enzyme.

Head magnetic resonance imaging (MRI) findings in a female patient with severe mitochondrial disease presenting with developmental delay, hypotonia, lactic academia, and brain atrophy. Whole-exome sequencing identified two variants in the PMPCA gene, which encodes for α-mitochondrial processing peptidase (α-ΜPP), a protein likely involved in the processing of mitochondrial proteins. Shown here is the head MRI image of the patient at 6 months of age, which reveals cerebellar atrophy with enlarged interfolial spaces, whereas marked cerebral and cerebellar atrophy with enlarged ventricles were noted at 3 and 6 years. (For details, please see Joshi et al., this issue; doi: 10.1101/mcs.a000786.)

The coming year will see increased focus on genome sequencing of sick babies as an aid to their medical diagnosis and management. In 2013, the NIH funded four grantees across the U.S. to explore the use of genome sequencing in newborn health care for a period of five years, including a joint project from Boston Children’s and Brigham and Women’s Hospital. In the future, genomic sequencing may expand to all newborns as sequencing technologies get more affordable and sequence data get more interpretable. This may not only help improve care for those babies but also guide their families in making future decisions. —Pankaj Agrawal, MD, MMSC, Newborn Medicine Research Center, Boston Children’s Hospital

Sequencing a patient’s genome to figure out the exact source of his or her disease isn’t standard operating procedure — yet. But falling sequencing costs and a growing number of successes are starting to bring this approach into the mainstream, helping patients and families while advancing a broader understanding of their diseases.