Monday, December 12, 2022

FDA’s Approval of IND Application Allows Kyverna Therapeutics to Explore Role of CARs in Lupus, and Possibly Other Immune-Moderated Diseases

 By John Otrompke

                Immunology company Kyverna Therapeutics, Inc., will be exploring a new role for CAR T-cells in treating lupus nephritis, after the company received approval on Nov. 11 from the FDA for its investigational new drug application to begin trying its agent, KYV-101, in humans.

“CAR Ts are very effective depleters of B-cells, which in lupus nephritis are abnormally located in nephrotic tissues,” explained chief medical officer James Chung, MD PhD. The Emeryville, California, company plans to begin a phase 1 / 2 trial next year, and should have clinical data within 6 months, he added.

“This is sort of a ‘Goldilocks’ moment, because the agent has efficacy on B-cells, and on the other hand, it also has a great safety profile. These lupus nephritis patients can live 20 or 30 years, so we can’t give them the level of side effects you see in oncology patients,” noted CEO Peter Maag, PhD, who was hired by the company in October. (Maag had previously served as the CEO of Brisbane, California-based CareDx, Inc., a personalized medicine company in the transplant medicine space).

The announcement comes on the heels of an article published in October in Nature Medicine, which described the success of the therapy in treating five patients. (“Anti-CD19 CAR T cell therapy for refractory systemic lupus erythematosus,” Mackensen A, Müller F, Mougiakakos D, et al. Nat Med. 2022 Oct;28(10):2124-2132. doi: 10.1038/s41591-022-02017-5. Epub 2022 Sep 15. Erratum in: Nat Med. 2022 Nov 3;: PMID: 36109639).

“Seventeen months out, they still have no need for additional immune suppression. If that’s true in five patients, the discovery might amount to a paradigm shift, achieved by pushing the immune system’s reset button through the deep depletion of B-cells,” added Maag.

Lupus occurs mostly in young women with about 65% of cases occurring in those between the ages of 16 and 55. Approximately 40% of adults will develop lupus nephritis, 60% of whom will fail standard of care and approved treatments, said Chung, and up to 40% of those with diffuse disease will ultimately develop kidney failure, requiring dialysis or a kidney transplant to stay alive.

The treatment, an anti-CD19 chimeric antigen receptor T-cell (CAR T) construct for which Kyverna has obtained exclusive, global licensing from the NIH to use in both autologous and allogeneic CAR T-cell therapies, will be tested first in open label clinical trials, Maag said.

“The FDA and other health agencies have accepted objective endpoints for lupus nephritis, such as serum creatinine, which is a measure of renal function,” Chung noted.

While multiple gene signatures have been identified in lupus patients, KYV-101 does not target them; instead, the company hopes to target a broader population of lupus patients through depletion of B cells.

“There are a number of diseases in which B-cell depletion might be relevant; there is some evidence in multiple sclerosis, for example,” said Maag, adding that the company is in talks with the FDA regarding such an application.

Friday, November 4, 2022

The Clinical Imperative of Personalized Medicine Makes Broader Reimbursement for Genetic Diagnostics Assured

 A Discussion of Several Panels at the 16th Annual Meeting of the Personalized Medicine Coalition

by John Otrompke

                Although reimbursement coverage is now available for select use cases for molecular diagnostics, these use cases have been demonstrated to be too narrow. Almost 10% of colorectal cancer patients treated at Mayo Clinic Cancer Centers for the two years before the pandemic had actionable germline genetic variants that would not have been identified by contemporaneous guidelines from medical societies such as the National Comprehensive Cancer Network (NCCN), or the 20-gene sequencing panel based on those guidelines, according to a recent article. (Uson P, Riegert-Johnson D, Boardman L, et al. Germline Cancer Susceptibility Gene Testing in Unselected Patients With Colorectal Adenocarcinoma: A Multicenter Prospective Study, Clinical Gastroenterology and Hepatology 2022;20:e508–e528).

                Next generation sequencing was performed on the 361 patients using the 84-gene Multi-Cancer Panel from Invitae Corp. (NVTA, San Francisco). Researchers found incrementally actionable variants in 9.4% patients that would not have been identified by the 20-gfene panel from the same company.

“We collaborated with the Mayo Clinic, and the study showed that family history and age are imperfect predictors of whether you have Lynch syndrome, so we ought to test every patient,” explained Robert Nussbaum, MD, CMO at Invitae, a co-author on the article.

The company also recently launched its personal care monitoring service, which measures minimal residual disease in the form of cell-free DNA. “Does the patient need adjuvant treatment? Will they relapse, and if so, when?” added Nussbaum, who also spoke on a panel about diagnostics at this year’s annual Personalized Medicine Conference at Dana Point, California, in May. Some payors are reimbursing for the diagnostic test, Nussbaum said.

Reimbursement for genetic diagnostics is likely to grow in the future as researchers develop more evidence about the clinical and economic benefits that such testing can provide. If genetic diagnostics are not reimbursed consistently, drugmakers may have a harder time marketing genetically guided therapeutics.

“Even in the primary care setting, virtually every patient should be assessed for hereditary risk factors,” noted Lisa Alderson, CEO and founder of Genome Medical, Inc., in South San Francisco, CA. “While 7% of the population has a single-gene variant that impacts their health, a much larger percentage, approximately 17%, have moderate risk variants that may influence treatment or preventive options.” Fully 85% of people have genetic factors that impact their response to prescribed drugs and could change dosing or therapeutic selection, particularly in the areas of pain management, oncology, and mental and behavioral health, added Alderson, who also spoke at a session at the PMC conference on precision medicine in differently-structured health systems.

“We have a full-time team of leading molecular geneticists, genetics counsellors and a pharmacist, as well as a contract network of specialists and primary care doctors whom we bring into specific patient’s cases as needed. We see patients directly and also support providers in appropriately utilizing genomics. We are simplifying the process of finding patients with need through our patient assessment and clinical support tools. Physicians just point patients to our platform, which identifies those who meet NCCN guidelines for oncology testing and hereditary cancer risk assessment,” she added.

“Genome Medical is a covered benefit for approximately 170 million people, including all beneficiaries of United Healthcare, CIGNA, and most of the Blues,” said Alderson. “Many payors are bringing Genome Medical in network to better support this complex area of medicine. Today, we have both underutilization and overutilization of genetic testing in the market. The majority of patients meeting guidelines are not identified and when testing is ordered, up to 25 percent of the time, it is the wrong test. We also support clinical decision making to ensure action is taken on the results.

“Take colon cancer as an example. If somebody is at an elevated risk for cancer because of their genetic make-up, that changes the standard of care for cancer screening. The standard of care is for the average patient to have their first colonoscopy at age 45, but if they are at higher risk, the first colonoscopy may take place when they are in their 30s. If they have a colonoscopy earlier, the cost is quite low compared to that of treatment, because removing polyps means you can prevent colon cancer from forming,” she explained.

“There is a pretty steep lag between when you demonstrate clinical utility and when you have broad-based adoption, but we’re trying to build a future model in which providers order genomics earlier and particularly for complex cases. There is a gap in knowledge which is creating a gap in clinical care, but by reducing underutilization and overutilization, we show a very immediate return-on-investment, a 5-times ROI,” Alderson said.

Speeding the Time to Clinical Acceptance

Colon cancer is far from the only example of a disease state in which genetic science is changing medicine and saving lives. “Sepsis accounts for half of all hospital deaths in the US. As it is a time-critical disease, earlier detection or prediction can help save lives. Currently, there is no single biomarker that can accurately predict sepsis. However, research has shown that the combination of a few in vitro diagnostic tests can significantly improve the prediction of sepsis,” said Okan Ekinci, MD, global head of marketing and innovation for Roche Diagnostics Information Solution in Basel, Switzerland. A recent study suggested that a combination of five biomarkers improved sepsis prediction in children compared with C-reactive protein alone, added Ekinci, who also spoke at the PMC conference panel on diagnostic tools.  (Rautiainen L, Cirko A, Pavare J, et al. Biomarker combinations in predicting sepsis in hospitalized children with fever. BMC Pediatrics [2022] 22:272).

Success stories such as those of Genome Medical and Invitae come as some payors express frustration with the lack of transparency regarding some diagnostic tools, such as smaller, locally-designed tests.

“It can take 14 to 17 years for a new test to get to widespread adoption, but hopefully we can get it under 10 years, and maybe as low as 7,” agreed Jill Hagenkord, MD, CMO at Optum Genomics in Eden Prairie, Minnesota. (Optum Genomics is currently part of United Healthcare).

To help reduce the time lag, Hagenkord is leading the roll-out of the Optum Evidence Engine, a service which connects developers of diagnostic tests with market access experts who can help design studies and communicate with investors.

“There is a lack of consistent regulatory oversight due the FDA’s exercise of its enforcement discretion, so that anything can go on the market, and does, without any clear criteria. It’s impossible to determine whether the tests do or don’t work at all. Nobody even knows how many tests are on the market, because we don’t have unique identifiers for them, which could make it easier for payors to distinguish between those that do and those that don’t work. So some payors decide that they’re either just going to pay for all laboratory-designed tests, or pay for none of them.” Those at the Optum Evidence Engine have finally begun to assign unique identifiers to the locally-designed tests within the past year, added Hagenkord, who spoke on a panel about reimbursement at this year’s annual PMC conference.

While there may be a significant time lag in personalized medicine between the demonstration of clinical utility and widespread adoption, it is undeniable that broader reimbursement for genetic testing is a fait accompli. Breast cancer is one important example of a clinical area where the clinical importance of personalized medicine has perhaps been longest-established.

“Anybody who has hormone receptor-positive breast cancer, and that’s 80% of breast cancers, is getting targeted therapy,” said Kevin Hughes, MD, director of cancer genetics at the University of South Carolina in Charleston.

Genetic testing for the approximately 13 gene signatures associated with breast cancer is almost always reimbursed, added Hughes, who is also a board member for the American Society of Breast Surgeons. “We’re trying to get the NCCN to change to guidelines to match ours, because they have a very complex set of criteria that ends up with about 50% of breast cancer patients testable,” he noted.

The author is a member of the Personalized Medicine Coalition

© 2022 John J. Otrompke, JD

Wednesday, January 19, 2022

All contents (c) 2022 John J. Otrompke

Time for an Epilepsy Moonshot Initiative? -Precision Medicine at AES

                         AES Poster Demonstrates the Increasing Relevance of a Genetic Diagnosis 

                                to the Treatment of Epileptic Children at a Center of Excellence


by John Otrompke

Genetic analysis led to a change in treatment for almost half of the children with epilepsy who received a consultation at Boston Children’s Hospital for whom a firm etiology was lacking, according to a poster presented on Dec. 5 at the 2021 annual meeting of the American Epilepsy Society in Chicago. Treatment was impacted in 45% of individuals, including 36% with an impact on anti-seizure medication choice.

In light of developing knowledge of the disease and emerging therapies, providers should routinely use genetic testing to evaluate children with epilepsy, according to abstract number 2.319, “Genetic Diagnosis in Pediatric Epilepsy Impacts Medical Management,” which was said to be the first study to report on the impact of a genetic diagnosis on the medical management of pediatric epilepsy in a clinical setting.

Pediatric epilepsy is unexplained in about two-thirds of cases, so a genetic diagnosis is especially important for children. Geneticists have determined that epilepsy is a highly variegated disease, with some studies reporting that up to 78% of patients with epilepsy of unknown cause having significant genetic variants.  

“There are over 500 genetic variants implicated in epilepsy, and they’re all very rare,” said Heather Olson, MD, attending physician at Boston Children’s Hospital, and assistant professor of neurology at Harvard Medical School, senior author on the poster. The poster found that in 10% of the patients, genetic testing had an influence on the discussion of participation in ongoing gene-specific clinical trials. 

In some forms, epilepsy is not only a severe, limiting condition, but can even be fatal. For example, some children with the BRAT-1 variant, which is thought to be related to mitochondrial homeostasis, die a few months after birth due to cardiopulmonary arrest.

Nevertheless, genetic testing remains controversial among insurers, with an ICER of around $15,000 per diagnosis.


                                                            About the Study

In the study, researchers examined course-of-treatment and other outcomes for 602 children with epilepsy who received next-generation genetic sequencing at Boston Children’s Hospital between 2012 and 2019. About one-quarter of the children who were tested received a genetic diagnosis. 

“Patients with childhood epilepsy usually receive genetic testing at our hospital when no other cause has been identified,” explained Isabel Haviland, MD, lead author and postdoctoral research fellow at Boston Children’s.

Of the children who received an epilepsy gene assay with or without exome, 152 received a clinical diagnosis of genetic epilepsy, which had an impact on medical management in 110 or 72% of those patients. Of those 110 patients, the choice of anti-seizure medication was impacted in 36% of patients, while 10% were eligible for gene-specific clinical trials or investigational new drug use. Another 3% of the 110 patients were treated off-label.

Of the 152 patients who received a genetic diagnosis, care coordination was impacted in 48%, and vitamin treatment and/or metabolic treatment such as the ketogenic diet was ordered in 7%.

Additionally, genetic testing led to a change in diagnosis in some children. “For two children who initially had a diagnosis of primary mitochondrial disorder, it was found that their epilepsy was in fact due to a genetic cause,” explained Haviland.

One child was found to have a variant in gene PRRT2 and was switched to a different anti-seizure medication, eventually becoming seizure-free.

                               A Diagnosis of Genetic Epilepsy Frequently Determines Treatment

Due to the variegated nature of genetic epilepsy, genetic diagnoses in the children resulted in differential treatment in the form of vitamin supplements, dietary regimens, off-label treatment with already approved drugs, new or experimental treatment with small molecule drugs, or enrollment in gene therapy clinical trials. 

While outright cures are very rare, even something as simple as supplementing the child’s diet with vitamins may partially correct the problem and treat the epilepsy. “For example, vitamin B6 is important for brain development, but some genetic disorders affect its pathway in the brain,” said Haviland.

Another nutritional intervention sometimes used is the ketogenic diet. “This results in changes in not only ketones, but insulin, glucose, and free fatty acids; all of these metabolic changes may have a role in reducing seizure frequency,” she added, noting that initiating the ketogenic diet in a child requires hospitalization.

Some drugs are already approved for the treatment of genetic epilepsy, such as fenfluramine, which was approved in June of 2020 to treat Dravet syndrome, one of the first established epilepsies.

“We recently published a case report  about an individual who had been having monthly seizures, who had to go into the intensive care unit each time. Having now received an accurate genetic diagnosis of Dravet syndrome, the patient is now three years seizure free,” said Olson.

Then there are the genetic epilepsies for which off-label treatments can be used, such as epilepsy with a variant in GRIN2A, a gene involved in brain cell communication, which has been treated with memantine, a drug approved only for Alzheimer’s disease. There are also small molecule drugs under development for some genetic epilepsies. 

“But generally, the only way to cure genetic epilepsy is with a gene therapy that modifies and corrects the variant in the patient’s gene, such as an antisense oligonucleotide (ASO). An ASO is designed just for one child, but these are very few and far between,” explained Olson.