Genomic Landscape of Lymphatic Malformations: A Case Series and Response to the PI3Kα Inhibitor Alpelisib in an N-of-One Clinical Trial

Background Lymphatic malformations (LMs) often pose treatment challenges due to a large size or a critical location that could lead to disfigurement, and there are no standardized treatment approaches for either refractory or unresectable cases. Methods We examined the genomic landscape of a patient cohort of LMs (n=30 cases) that underwent comprehensive genomic profiling (CGP) using a large-panel next generation sequencing (NGS) assay. Immunohistochemical analyses were completed in parallel. Results These LMs had low mutational burden with hotspot PIK3CA mutations and NRAS mutations being most frequent, and mutually exclusive. All LM cases with Kaposi sarcoma-like (kaposiform) histology had NRAS mutations. One index patient presented with subacute abdominal pain and was diagnosed with a large retroperitoneal lymphatic malformation harboring a somatic PIK3CA gain-of-function mutation (H1047R). The patient achieved a rapid and durable complete response to the PI3Kα inhibitor alpelisib within the context of a personalized N-of-1 clinical trial ([NCT03941782][1]). In translational correlative studies, canonical PI3Kα pathway activation was confirmed by immunohistochemistry and human LM-derived lymphatic endothelial cells carrying an allele with an activating mutation at the same locus were sensitive in vitro to alpelisib in a concentration-dependent manner. Conclusions Our findings establish that LM patients with conventional or kaposiform histology have distinct, yet targetable, driver mutations. Funding R.P. and W.A. are supported by awards from the Levy-Longenbaugh Fund. S.G. is supported by awards from the Hugs for Brady Foundation. This work has been funded in part by the NCI Cancer Center Support Grants (CCSG; P30) to the University of Arizona Cancer Center (CA023074), the University of New Mexico Comprehensive Cancer Center (CA118100), and the Rutgers Cancer Institute of New Jersey (CA072720). B.K.M. was supported by National Science Foundation via Graduate Research Fellowship DGE-1143953. Clinical trial number NCT03941782 ### Competing Interest Statement Conflict of interest statement: M.F.S. reports personal fees from Illumina, BMS, and Qiagen (outside of the submitted work). J.Y.T., E.S.S., and B.K.M. are employees of Foundation Medicine, Inc., a wholly owned subsidiary of Roche, and they own equity in Roche. S.G. has consulting agreements with Merck, Roche, Novartis, Foundation Medicine, EQRX, Foghorn Therapeutics, Silagene, and KayoThera and owns equity in Silagene; his spouse is an employee of Merck and owns equity in Merck (all outside of the submitted work). R.G. reports research funding/grant support for clinical trials (to his institution) from Regeneron, BMS, Merck/EMD Serano, Amgen, Roche/Genentech, Philogen; consulting/advisory board fees from Regeneron; and speaker fees for Deciphera (all outside of the submitted work). R.P. and W.A. are founders and equity stockholders of PhageNova Bio and of MBrace Therapeutics; R.P. is a paid consultant for PhageNova Bio and MBrace Therapeutics and also serves as the Chief Scientific Officer of PhageNova Bio and a member of the board for MBrace Therapeutics (all outside of the submitted work). For R.G., R.P., S.G., and W.A., these arrangements are managed in accordance with the established institutional conflict of interest policies of Rutgers, The State University of New Jersey. The remaining authors have declared no potential competing interests. ### Clinical Trial NCT03941782 ### Funding Statement R.P. and W.A. are supported by awards from the Levy-Longenbaugh Fund. S.G. is supported by awards from the Hugs for Brady Foundation. This work has been funded in part by the NCI Cancer Center Support Grants (CCSG; P30) to the University of Arizona Cancer Center (CA023074), the University of New Mexico Comprehensive Cancer Center (CA118100), and the Rutgers Cancer Institute of New Jersey (CA072720). B.K.M. was supported by National Science Foundation via Graduate Research Fellowship DGE-1143953. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Approval for this study, including a waiver of informed consent and Health Insurance Portability and Accountability Act waiver of authorization, was obtained from the Western Institutional Review Board (IRB; protocol #20152817). A single-institution personalized clinical protocol to treat the patient with the experimental PI3Ka inhibitor alpelisib was scientifically reviewed by the Protocol Review and Monitoring Committee (PRMC) and approved by the local Institutional Review Board (IRB) of the University of New Mexico Comprehensive Cancer Center. The study ([NCT03941782][1]) was conducted in accordance with the protocol, Good Clinical Practice guidelines, and the provisions of the Declaration of Helsinki. The index patient signed an informed written consent form. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes NGS data for this study were generated at Foundation Medicine, Inc on U.S. patients profiled during routine clinical care. Approval for this study, including a waiver of informed consent and Health Insurance Portability and Accountability Act waiver of authorization, was obtained from the Western Institutional Review Board (protocol #20152817). Due to potential for identifiability, patient level alteration data is not available. However, extensive data supporting the findings of this study are available in Table 1 and Figure 1A. [1]: /lookup/external-ref?link_type=CLINTRIALGOV&access_num=NCT03941782&atom=%2Fmedrxiv%2Fearly%2F2022%2F01%2F05%2F2022.01.03.21267856.atom