Kherbek, Haidara

Abstract Purpose: Germ cell tumors (GCTs) pose significant diagnostic challenges due to the limited sensitivity and specificity of current tumor markers. Hereby we utilize phage immunoprecipitation sequencing (PhIP-Seq) technique to develop a unique immunosignature panel (iSIGN) with high sensitivity and specificity to improve the diagnosis and differentiation of GCTs. Patients and Methods: Serum samples from patients with confirmed gonadal or extragonadal GCTs and controls were collected from Mayo Clinic repositories. Controls included benign testicular lesions, autoimmune diseases, neurodegenerative disorders, and other cancers. Samples were randomized into development and validation cohorts. PhIP-Seq identified antigen-autoantibody interactions, and enrichment scores were calculated to develop a biomarker panel distinguishing GCT from non-GCT cases. A second biomarker panel was developed to predict seminoma from nonseminoma cases. Results: A total of 427 serum samples were analyzed, including 150 from GCT patients and 277 controls. For our primary model to distinguish GCT cases (GCT-iSIGN), 24 peptides from 16 antigens were identified based on significant differential autoantibody binding enrichment in GCT patients (p < 0.05), ≥2 peptides per antigen, and enrichment scores ≥ 2.5-fold. GCT-iSIGN was highly sensitive (93%) and specific (99%) for identifying GCT cases from controls with an area under curve (AUC) of 0.93 and 9% Unknown Case Rate (UCR). The secondary panel (Sem-iSIGN) included 17 peptides corresponding to 5 unique proteins with high specificity (93%), moderate sensitivity (65%) and AUC of 0.77 to distinguish seminoma from nonseminoma GCT cases. Conclusion: This study demonstrates the potential use of PhIP-Seq to identify unique immunosignature panels that can serve as reliable biomarkers for GCT. These panels address the limitations of traditional markers and other proteomic techniques. This immunosignature model represents a cost-effective, stable, and scalable approach to enhancing GCT diagnosis and management. Citation Format: M Bakri Hammami, Andrew Knight, Haidara Kherbek, Brian Costello, Silvana De Lorenzo, Bradley C. Leibovich, John C. Cheville, Yong Guo, Jessica Sagen, Janet E. Olson, Alicia Algeciras-Schimnich, Sean J. Pittock, John R. Mills, Surendra Dasari, Divyanshu Dubey. iSIGN panel identifies germ cell tumors via whole-proteome phage immunoprecipitation sequencing [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Mechanisms of Cancer Immunity and Cancer-related Autoimmunity; 2025 Sep 24-27; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Immunol Res 2025;13(9 Suppl):Abstract nr B027.

ABSTRACTCavin‐4 was identified as a potential autoantigen for immune‐mediated rippling muscle disease (iRMD). To validate this, we developed and tested various immunoassays, including a cell‐based assay (CBA), cavin‐4 recombinant protein ELISA, and multi‐peptide ELISA. Among 19 iRMD patients, all exhibited muscle rippling, and 13 had percussion‐induced mounding. All immunoassays demonstrated clinical and analytical specificities greater than 95%. The protein ELISA had the highest sensitivity (94.7%) and specificity (99.9%), outperforming CBA (sensitivity 89.5%, specificity 99.6%) and the multi‐peptide ELISA (sensitivity 79.0%, specificity 97.2%). Our results suggest that the cavin‐4 protein ELISA is a promising tool for high‐throughput clinical testing in iRMD.

AbstractObjectiveTo describe the phenotypes, oncological associations, biomarker profiles, and outcomes across different age groups in patients with ANNA1 (anti‐Hu) autoimmunity.MethodsA retrospective review of patients with ANNA1‐IgG in serum/CSF between January 1, 2001, and December 31,2019 was performed. Patients were classified into three groups based on the age of symptom onset. Phage immunoprecipitation sequencing (PhIP‐Seq) and neurofilament light chain (NfL) measurements were done in patient sera/CSF with archived samples.ResultsOf 122 patients, 81 (66%), 20 (16%), and 21 (17%) patients belonged to older adults, young adults, and pediatric groups, respectively. Lung cancer and neuromuscular presentations were more common in older adults (p < 0.001), while limbic encephalitis and neuroblastoma were more common in pediatric patients (p < 0.005). Most young adults (75%) did not have cancer identified. Proportions of patients with a favorable response to immunotherapy were 20%, 30%, and 52% among older adults, young adults, and pediatric groups, respectively. PhIP‐Seq demonstrated significant enrichment for ELAVL4 peptides especially for amino acids 240–289, in the majority of samples evaluated (36/67, 54%). ZIC and SOX2 peptides were significantly enriched in those with central nervous system presentations. Serum NfL levels were elevated in patients with cancer and those with poor long‐term outcomes.InterpretationYoung adults with ANNA1 autoimmunity phenotypically resembled older adults but rarely had an underlying cancer. Pediatric patients frequently presented with limbic encephalitis and neuroblastoma and often responded favorably to immunotherapy. Distinct antigenic signatures may underlie differences in clinical presentations. Serum NfL levels may be a biomarker of poor long‐term outcomes in ANNA1 autoimmunity.