Differentiating Mutagenesis From Genotoxic Risk in Secondary Malignancies

In an interview with CancerNetwork® at the 2026 Society of Hematologic Oncology (SOHO) Annual Meeting, Jasmine Zain, MD, attending physician in the Lymphoma Division of Memorial Sloan Kettering Cancer Center, outlined the diagnostic approach to characterizing secondary T-cell malignancies arising after CAR T-cell therapy. The FDA’s class-wide boxed warning on T-cell malignancies, first issued in November 2023 and mandated across all 6 approved CAR T-cell products in April 2024, has made mechanistic attribution a clinically meaningful question for treating teams.^1-3

Zain described a stepwise molecular investigation that begins with confirming the secondary malignancy as a T-cell lymphoma through standard hematopathologic methods, then detecting the presence of the CAR transgene within tumor cells using polymerase chain reaction (PCR)–based sequencing. She explained that insertional mutagenesis is most plausible when the viral integration site falls within 300 base pairs of a proto-oncogene or tumor suppressor gene promoter region. She also discussed an additional, non-insertional oncogenic pathway driven by mutational burden accumulating through rapid CAR T-cell expansion, underscoring that causation in these cases is rarely straightforward.

Transcript:

CancerNetwork: Given the FDA’s class-wide boxed warnings regarding second primary malignancies after CAR T-cell therapy, how do you clinically differentiate between malignancies directly driven by retroviral or lentiviral insertional mutagenesis vs those resulting from cumulative genotoxic stress?

Zain: That is the key to determining the causation of these secondary lymphomas. First, I want to clarify that it is very rare to develop T-cell malignancies [resulting from] what we think may be CAR T-cell–related mutagenesis. There are secondary malignancies that can arise in the setting of CAR T-cell therapy or other anti-cancer and anti-lymphoma therapies that are not directly related to the CAR T cell.

In terms of how we determine [causation], you have to dig very deep into the malignant tissue, into the malignant T cell. You must first establish that it is a T-cell malignancy through clonality, flow cytometry, and the usual methods of diagnosing T-cell lymphoma. After that, you have to look for the presence of the CAR vector in the tumor genome, and for that, you need molecular biology techniques such as PCR. You need to know the sequence of the CAR T product so you can search for it in the tumor and then perform further molecular studies to determine where the insertion site is in relation to oncogenes or tumor suppressor genes to assess whether it is directly causing mutagenesis and malignancy.

The prevailing theory is that the insertion site should be within 300 base pairs of the initiation or promoter region of the proto-oncogene or tumor suppressor gene, or involve a direct insertion into the promoter site, which can either activate or deactivate the relevant gene leading to mutagenesis. However, there is thought that this may not be the only event. Secondary events may occur [because of] the rapid cell division stimulated by these CAR T cells, and something called mutational burden may develop. You may have secondary events that lead to mutagenesis and that lymphoma.

References

1. Zain JM. Understanding the risk of second malignancies after CAR T therapies. Presented at: 2026 Society of Hematologic Oncology (SOHO) Annual Meeting; September 9-12, 2026; Houston, TX.
2. FDA investigating serious risk of T-cell malignancy following BCMA-directed or CD19-directed autologous chimeric antigen receptor (CAR) T cell immunotherapies. News release. FDA. November 28, 2023. Accessed September 16, 2026. https://tinyurl.com/9ch9rkpn
3. FDA requires boxed warning for T cell malignancies following treatment with BCMA-directed or CD19-directed autologous chimeric antigen receptor (CAR) T cell immunotherapies. News release. FDA. April 18, 2024. Accessed September 16, 2026. https://tinyurl.com/4pncpfjv