Unpacking the Complexities of Companion Diagnostics for Cell and Gene Therapies

In a world of increasingly precise therapies, companion diagnostics (CDx) are gaining importance. Yet the need for a CDx is often unclear, particularly for emerging cell and gene therapies (CGT) where patient eligibility may not simply depend on the presence or absence of a targetable mutation.

A CDx is defined by the U.S. Food and Drug Administration (FDA) as a medical device that provides essential information for the safe and effective use of a corresponding drug or biological product. CDx are used to identify patients who are most likely to benefit from a particular therapeutic product or those likely to be at increased risk for serious side effects from that treatment. They can also be used to monitor treatment responses to achieve improved safety or effectiveness.

At present there are 188 CDx listed as “cleared” or “approved” by the FDA. All but two of these are for use alongside drugs, typically targeted immunotherapies, to treat cancer. In addition, there are currently 44 FDA-approved cell and gene therapy products. Of these, just three have a CDx.

The question is, why are there so few CDx for CGT when so much investment goes into creating these precision treatments? The answer, according to experts in the field, is nuanced and reflects unique scientific, regulatory, and business challenges.

“It’s important to emphasize that determination of whether a CDx is required for cell and gene therapy products is made by the FDA’s Center for Biologics Evaluation and Research,” said Monica Veldman, director of global regulatory policy at the Alliance for Regenerative Medicine.

She explained that the “FDA’s enforcement of this requirement in the cell and gene therapy space has evolved over time and, in the specific context of adeno-associated virus (AAV)-based gene therapies, has shifted from not requiring a CDx to generally requiring one for the safe and effective use of the CGT product.”

Veldman added that “many AAV gene therapies approved with a CDx requirement include the CDx approval as a post-market commitment to the Biologics License Application, meaning the CDx is approved after the gene therapy itself.”

She said that, overall, the limited number of CDx for CGT products largely reflects the fact that CGT is still an emerging field, unlike non-CGT oncology products which have a much longer regulatory history.

CDx for gene therapies

The rationale for gene therapy was first described in Science in 1972 by Theodore Friedmann, MD, and Richard Roblin, PhD. In simple terms, it is the use of genetic material to treat disease. Gene therapy can involve gene addition, where a functional gene is inserted into a cell to make more copies of a specific protein; gene silencing, in which the genetic material inhibits genes that may be overproducing proteins; and gene editing, which is used to correct pieces of DNA by changing or deleting the information within the affected individual’s gene.

Gene therapies are usually delivered to cells via a genetically engineered virus vector. The virus of choice is often AAV due to its minimal pathogenicity and ability to establish long-term gene expression in different tissues.

However, a potential limitation for recombinant (r)AAV vectors is pre-existing anti-AAV antibodies that may be present in a patient following natural AAV infection. It is estimated that approximately 30–60% of individuals have pre-existing anti-AAV antibodies, but this varies across different AAV serotypes, by geographic region, and with the age of the individual. Anti-AAV antibody levels can also change over time within an individual.

Anti-AAV antibodies are problematic for companies developing gene therapies using rAAV vectors because they have the potential to reduce the efficacy of the treatment or trigger an adverse immune response.

This is where a CDx can help. The test can be used to screen for patients with anti-AAV antibodies. Indeed, both CDx currently approved for use with gene therapies measure anti-AAV antibody levels.

The first, AAV5 DetectCDx^® is a bridging immunoassay, developed by ARUP Laboratories, that detects antibodies to AAV serotype 5 in plasma specimens. It is used to determine eligibility for treatment with ROCTAVIAN (valoctocogene roxaparvovec-rvox), Biomarin’s gene therapy for severe hemophilia A. Only patients who demonstrate no detectable anti-AAV5 antibodies can be treated.

The second, LabCorp’s nAbCyte™ Anti-AAVRh74var HB-FE Assay is a CDx to determine patient eligibility for treatment with BEQVEZ™ (fidanacogene elaparvovec-dzkt), Pfizer’s FDA-approved gene therapy for patients with moderate-to-severe hemophilia B. The cell-based assay detects pre-existing neutralizing antibodies to AAV serotype Rh74var. A negative test result indicates that an individual can be considered for BEQVEZ therapy.

Seven of the remaining 13 FDA-approved gene therapies also use AAV vectors, while the others use either a herpes simplex virus vector, a lentiviral vector, autologous stem cell transplantation, or encapsulated cell-based gene therapy. None have a CDx.

“It comes down to the risk profile of the therapy, the route of administration, and the expected age of the patients,” explained Deborah Phippard, PhD, chief scientific officer at Precision for Medicine. “You can’t just say every gene therapy must have a companion diagnostic, because that is not the case.”

She points out that treatments being delivered at immune-privileged sites such as the eyes, brain, and central nervous system are less likely to be exposed to anti-AAV antibodies than those being administered systemically. In addition, younger patients, who are often candidates for gene therapies to treat rare diseases, are less likely to have antibodies than an adolescent or adult with an evolved immune system. Pre-existing immunity may also depend on the type of AAV vector. The amount of virus being delivered is another consideration.

Overcoming hurdles and driving forward

Ultimately, it is up to the company developing the therapy to work with the FDA and other regulatory authorities to determine the requirement for a CDx.

Yet manufacturers would argue that there is a need for more guidance on when a CDx is compulsory.

“I’d like to know what the rules are, what boxes to check,” said Christos Petropoulos, PhD, vice president of LabCorp. “In other industries, you have guidelines for consideration from the FDA and I think we need to get there with CGT.”

LabCorp’s nAbCyte assay was the first CDx to use a cell-based format. “We didn’t have a playbook, we had to figure it out as we went along,” said Petropoulos. “Hopefully, in the future we’ll have that playbook.”

Irene Bacalocostantis, PhD, executive director of regulatory affairs, CDx, at LabCorp, added that it would be useful for the FDA to consider industry feedback on the challenges involved in developing CDx, particularly in the early stages.

“There have been instances where the FDA has required significant amounts of data to be submitted in an Investigational Device Exemption prior to clinical trial, but this can be difficult to obtain in the early stages,” she remarked.

Petropoulos agreed: “These are rare diseases, so there’s not a lot of study subjects and not a great opportunity to generate the data that you need to understand how the CDx should be regulated or how it should be used.”

The process is also expensive, which can be a sticking point with CGT manufacturers. “They have an early phase, non-registrational trial and don’t yet know if their drug is going to succeed, but they’ve been asked to pay a few million dollars for the development of a CDx,” said Bacalocostantis. “I think that’s a huge hurdle.”

Although the FDA is there to guide and regulate the use of CDx for CGT, they are not the only stakeholders when it comes to the development of new treatments. The payers may also have an impact.

“Payers may well be a driver in the future, because they don’t want to pay for an expensive treatment if somebody’s not going to respond due to significant levels of pre-existing immunity,” said Phippard. This may mean that they require a CDx before they will consider reimbursement.

Phippard noted that CDx development adds significant cost to early phase studies, but would encourage the gene therapy developers to work with a CDx partner early in the process.

Companies like Precision for Medicine and LabCorp have been supporting various gene therapy developers for many years. Both Phippard and Petropoulos said that they have often been approached for CDx support when the drug developer has already planned a clinical trial timeline that does not allow for the development of validated assays. If a regulatory agency then requires a validated assay, this can result in costly delays to a clinical study while the CDx is developed and manufactured.

“I would say companies get caught blindsided regularly, and then they’re shocked with how long it takes to make a CDx,” Phippard remarked. “I always say, ‘Engage with the regulatory system and ask for a significant or a nonsignificant risk determination,’ because if the FDA says there’s significant risk, that puts you on a very different pathway. If you need a CDx, it’s going to take you a year or more to find a company and make one.”

Planning for an increase in CDx for cell therapies

Gene therapies have been a focus for CDx because of the potential impact of anti-AAV antibodies on efficacy and safety, but CDx for cell therapies is also a growing area. Cell therapy involves the transfer of intact, live cells into a patient to treat or cure a disease. The cells may originate from the patient (autologous cells) or a donor (allogeneic cells) and may be unmodified or gene edited. Chimeric antigen receptor (CAR) T cell therapies are an example of gene-edited cell therapies that have been successfully used to treat some cancers.

Among the 19 CAR-T and other cell therapies that have FDA approval, only one has an approved CDx so far. TECLERA^® (afamitresgene autoleucel) is a genetically modified autologous T cell immunotherapy for synovial sarcoma that targets melanoma-associated antigen A4 (MAGE-A4), a cancer-testis antigen overexpressed in various cancers. In August 2024, the treatment, developed by Adaptimmune, became the first approved engineered cell therapy for a solid tumor indication in the United States.

Two CDx are associated with TECLERA. The first, SeCore™ CDx HLA A Sequencing System from One Lambda, uses a sequence-based typing method to screen for human leukocyte antigen (HLA)-A alleles in genomic DNA purified from whole blood samples to ensure that the modified cells are not rejected by the patient’s immune system. The second, Agilent’s MAGE-A4 IHC 1F9 pharmDx, is an immunohistochemistry assay used to detect MAGE-A4 expression in synovial sarcoma tissue.

There are currently no FDA-approved CDx for allogenic cell therapies (ACTs) but a recently published article by The College of American Pathologists (CAP) highlighted patient selection and compatibility as a potential challenge in the development and implementation of ACTs. They say that “HLA matching of the allogeneic cell product may be required to avoid GvHD [graft versus host disease] or to ensure efficacy.”

“The article was written to try and prepare the pathology community for what is to come with regards to diagnostic tools for CGT,” explained Fabienne Lucas, MD, PhD, assistant professor of hematopathology at the University of Washington, Seattle, and Matthew Anderson, MD, PhD, executive vice president and chief medical officer at Versiti. Together, they lead the ACT project within the CAP Personalized Health Care Committee.

“As a pathology community, we have seen the effects of not looking ahead to the therapies coming down the pipeline and essentially scrambling to keep up with all the changes that are happening, so we’re really intent on getting ahead of the curve,” said Anderson.

Lucas added: “One promise of this type of therapy is their ‘off-the-shelf’ availability, meaning that patients can be treated or monitored more widely. We therefore want to prepare the pathology community at large, including the labs and pathologists not necessarily involved with specialized diagnostic or monitoring tools, in how to handle patient samples and what they might show.”

This will be increasingly important as the CGT market grows, and thus by default the need for diagnostic testing and tools, including CDx, expands.

Sharing the development burden

“As CGT therapies become more common, there is likely to be a significant expansion in the field of CDx, driven by new scientific discoveries, evolution of technologies, and advancements in non-viral gene editing methods, allogeneic therapies, and applications beyond cancer,” said Gulzar Sandhu, PhD, chief business officer of the companion diagnostics division at Agilent.

Companies like Agilent, Precision for Medicine, and LabCorp are already seeing a growing demand for diagnostic support related to CGT trials and commercialization, with therapy areas expanding from oncology and rare diseases to more common conditions like congestive heart failure with a genetic component and neurological conditions such as Parkinson’s disease. Phippard believes these new additions could “change the paradigm for how you think about CDx for gene therapy and making that accessible globally.”

There is also interest in standardizing or streamlining the approach to developing CDx. “As more therapies utilize shared delivery systems, the ability to use one CDx across multiple products, such as AAV-GTs that share a common vector, could reduce duplicative development efforts and lower overall regulatory and financial burdens,” said Veldman.

However, Karina Kulangara, PhD, associate vice president of the companion diagnostics division at Agilent also cautions that “a more standardized CDx approach for the CGT pipeline necessitates a CDx technology that addresses the broad need of CGT and flexibility to incorporate specific biomarkers. It would require robust regulatory frameworks, continuous innovation in diagnostic technologies, and collaboration between biopharma companies and diagnostic developers.”

With this in mind, the CGT field will be closely monitoring how regulators handle early CDx implementations. “The Alliance for Regenerative Medicine is actively working with stakeholders to recommend regulatory approaches that support broader CDx applicability,” said Veldman. “These approaches will be critical to enabling a scalable, efficient CDx infrastructure that keeps pace with innovation in the CGT space.”