Abstract 1891: Breaking barriers to access intracellular targets with T-cell engagers: Discovery of diverse, developable, and ultra-specific antibodies against a MAGE-A4 pMHC

In this study, we describe the discovery of antibodies against a MAGE-A4 peptide-major histocompatibility complex (pMHC). These antibodies will form the basis for the tumor-binding arm of T-cell engagers (TCEs) against this target.

Bispecific CD3 TCEs have the potential to transform cancer treatment by redirecting T cells to tumor targets, but technological barriers have limited their development for solid tumors. Targets for TCEs have generally been limited to surface-expressed proteins, however, access to intracellular proteins that are mutated and/or differentially expressed in cancer cells would expand the target pool. Peptides of these intracellular proteins presented on MHC class I (MHC-I) provide opportunities for TCE development. Technologies powering discovery of rare antibodies that are ultra-specific, high-affinity pMHC binders are needed to expand this promising class of tumor targets.

We have developed a technology platform for the discovery of optimal TCEs, including a diverse panel of CD3-binding antibodies and an antibody discovery and development engine that includes multispecific engineering capabilities, powered by OrthoMabTM. We are applying this platform to develop TCEs against MAGE-A4, an intracellular tumor target expressed by many solid tumors, but not by healthy tissues.

Using proprietary immunization technologies, we triggered robust, diverse antibody responses against a complex of a human MAGE-A4 peptide presented on MHC-I. We used high-throughput microfluidic technology to screen single B cells using a multiplexed bead-binding assay to identify antibodies specific to the target, but not closely-related pMHCs. We then expressed and purified antibodies for downstream validation and characterization. Antibody specificity was initially validated using a panel of related pMHC complexes, and developability properties were assessed, including hydrophobicity, self-association, polyspecificity, stability, and aggregation.

With complex data integration and analysis, we identified a panel of diverse and developable antibodies that bind with high affinity to a human MAGE-A4 peptide sequence of 10 amino acids presented on MHC-I (HLA:02*01). Strategic selection and pairing of these target-binding antibodies with our large and diverse panel of fully human CD3-binders will power the discovery of ultra-specific MAGE-A4 TCEs with optimal potency and cytokine release.

Citation Format: Davide Tortora, Peter Bergqvist, Grace P. Leung, Elena Vigano, Antonios Samiotakis, Harveer Dhupar, Wei Wei, Shirley R. Zhi, Yukiko Sato, Allison Goodman, Cindy-Lee Crichlow, Melissa Cid, Jessica Fernandes Scortecci, Ping Xiang, Ahn Lee, Vivian Li, Stephanie Masterman, Sherie Duncan, Aaron Yamniuk, Kush Dalal, Tim Jacobs, Raffi Tonikian, Bryan C. Barnhart. Breaking barriers to access intracellular targets with T-cell engagers: Discovery of diverse, developable, and ultra-specific antibodies against a MAGE-A4 pMHC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1891.

Abstract 3480: TMEM30A loss-of-function mutations drive lymphomagenesis and confer therapeutically exploitable vulnerability in B-cell lymphoma

Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoma subtype worldwide, accounting for 40% of all non-Hodgkin lymphomas. DLBCL presents as an aggressive disease requiring immediate treatment. Although significant improvement in outcome has been achieved, ~40% of patients still experience treatment failure. Here, we characterized the recurrent genetic alterations and transcriptomic signatures in diagnostic biopsies from a population registry-based cohort of 347 patients with de novo DLBCL uniformly treated with R-CHOP. This analysis revealed bi-allelic loss of function mutations of TMEM30A that were associated with favorable treatment outcome. TMEM30A is a chaperone protein, involved in maintaining the asymmetric distribution of phosphatidylethanolamine and phosphatidylserine, an integral component of the plasma membrane and “eat-me” signal recognized by macrophages. Using TMEM30A knockout systems by CRISPR genome editing techniques, we have functionally characterized this loss-of-function mutation in representative human and mouse DLBCL cell line models. We have discovered that TMEM30A loss is associated with increased B-cell signaling following antigen stimulation, including a two-fold increase in the diffusion rate of B-cell receptor (BCR) clustering, using high resolution Single Particle Tracking (SPT) technology. In addition, we have measured three-fold increase in chemotherapeutic drug accumulation in both knockout cell lines and randomly selected patient biopsies with TMEM30A biallelic loss. This observation was validated in a xenograft mouse model, which presented improved survival and limited tumor growth following vincristine treatment in mice injected with TMEM30A null DLBCL cell lines compared with native cell lines. This phenotype explains the improved prognosis observed in DLBCL patients following R-CHOP treatment. Furthermore, we have observed over two fold higher numbers of tumor-associated macrophages in B-cell lymphoma syngeneic mouse models with Tmem30a loss-of-function, prior to any form of treatment, suggesting the existence of “hot” and primed tumors. Our data highlight a multi-faceted role for TMEM30A and plasma membrane physiology in B-cell lymphomagenesis, and characterize intrinsic and extrinsic vulnerabilities of cancer cells that can be therapeutically exploited. Characterization of these mechanisms will address a missing link in the cancer field as related insights in lymphoma will outline therapeutic approaches that can be extended to cancer therapy in general.

Citation Format: Shannon Healy, Daisuke Ennishi, Ali Bashashati, Saeed Saberi, Christoffer Hother, Anja Mottok, Fong Chun Chan, Lauren Chong, Robert Kridel, Merrill Boyle, Barbara Meissner, Tomohiro Aoki, Katsuyoshi Takata, Bruce W. Woolcock, Elena Vigano, Libin Abraham, Michael Gold, Adele Telenius, Pedro Farinha, Graham Slack, Susana Ben-Neriah, Daniel Lai, Allen W. Zhang, Sohrab Salehi, Hennady P. Shulha, Derek S. Chiu, Sara Mostafavi, Alina S. Gerrie, Diego Villa, Laurie H. Sehn, Kerry J. J. Savage, Andrew J. J. Mungall, Andrew P. Weng, Marcel Bally, Ryan D. Morin, Gabriela V. Cohen Freue, Joseph M. Connors, Marco A. Marra, Sohrab P. Shah, Randy D. Gascoyne1, David W. Scott, Christian Steidl, Ulrich Steidl. TMEM30A loss-of-function mutations drive lymphomagenesis and confer therapeutically exploitable vulnerability in B-cell lymphoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3480.

Abstract 3765: Somatic JAK-STAT mutations in subtypes of aggressive B-cell lymphomas with DLBCL morphology

Aberrant activation of the JAK-STAT pathway is a hallmark of a variety of lymphomas and can alter the lymphoma cells secretome and the composition of the tumor microenvironment (TME). The up-regulation of the immune regulatory chemokine CCL17 has been shown to be mediated by STATs-dependent mechanism in primary mediastinal B cell lymphoma (PMBCL). Here, we assembled a cohort of 340 R-CHOP-treated aggressive lymphomas with diffuse large B cell lymphoma (DLBCL) morphology to investigate JAK-STAT mutations (targeted gene sequencing), copy number (CN) alterations (SNP arrays), gene expression (RNAseq) and TME composition (IHC). The cohort was evaluated using FISH for BCL2, BCL6 and MYC rearrangements and the molecular classification assay, Lymph2Cx, to distinguish ABC vs GBC vs double-hit lymphomas with DLBCL morphology (DH-DLBCL). Among the 317 evaluable cases, 26 were DH-DLBCLs, 101 ABC, 155 GCB and 35 unclassified. In addition, we used the recently published Lymph3Cx assay (Mottok A. et al., Blood 2018) to identify cases with a molecular PMBCL (mPMBCL) expression signature within the GCB-DLBCL group (6.5%, 10/155 cases). Twenty-five of 155 GCB cases (16.1%) were classified as ‘uncertain PMBCL/DLBCL’. Mutational analysis of all cases (n=340) revealed the presence of JAK-STAT pathway mutations at the following frequencies: SOCS1 21.6%, STAT6 4.8%, IL4R 5.3% and 9p24 amplification 11.3%. These mutations were significantly enriched in the mPMBCL (n=10) group compared to the bona fide GCB (n=118) and intermediate phenotype group (uncertain PMBCL/DLBCL) (n=25) (p<0.05). The relative frequency of any JAK-STAT mutations was 100% (10/10) in mPMBCL, 29.2% (35/118) in bona fide GCB and 56% (14/25) in uncertain PMBCL/DLBCL. Among the GCB samples with follow-up data (n=107, incl. bona fide GCB and mPMBCL), cases carrying mutations in IL4R (n=11, 10.3%) had an inferior disease-specific survival (p=0.011) and time to progression (p=0.0048) after R-CHOP therapy. Interestingly, IL4R mutations were also detected in the DH-DLBCL group with an incidence of 11.5% (3/26 cases). Mutations in the extracellular and transmembrane domains of IL4R resulted in gain-of-function mutations leading to constitutive activation of the JAK-STAT pathway in vitro. IL4R gain-of-function increased CCL17 expression through a STAT6-dependent mechanism in vitro. Similarly, gene expression analysis of primary patient samples carrying activating IL4R mutations displayed increased CCL17expression (p<0.05), which positively correlated with the level of the T-regulatory marker FOXP3 (p<0.05) by IHC. In summary, aberrant JAK-STAT activation driven by alterations, such as activating IL4R mutations, plays a significant role in altering chemokine expression profiles and TME changes. Our data strongly suggest the biological and clinical relevance of Lymph3Cx to define a subgroup of aggressive lymphoma harboring a molecular PMBCL signature.

Citation Format: Elena Vigano, Gerben Duns, Daisuke Ennishi, Clementine Sarkozy, Bruce Woolcock, Faith Cheung, Elizabeth Chavez, Stacy S. Hung, Katsuyoshi Takata, Anja Mottok, Randy Gascoyne, Kerry J. Savage, Ryan Morin, David W. Scott, Christian Steidl. Somatic JAK-STAT mutations in subtypes of aggressive B-cell lymphomas with DLBCL morphology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3765.

Genome-wide analysis of the genetic regulation of gene expression in human neutrophils

Neutrophils are an abundant immune cell type involved in both antimicrobial defence and autoimmunity. The regulation of their gene expression, however, is still largely unknown. Here we report an eQTL study on isolated neutrophils from 114 healthy individuals of Chinese ethnicity, identifying 21,210 eQTLs on 832 unique genes. Unsupervised clustering analysis of these eQTLs confirms their role in inflammatory responses and immunological diseases but also indicates strong involvement in dermatological pathologies. One of the strongest eQTL identified (rs2058660) is also the tagSNP of a linkage block reported to affect leprosy and Crohn's disease in opposite directions. In a functional study, we can link the C allele with low expression of the β-chain of IL18-receptor (IL18RAP). In neutrophils, this results in a reduced responsiveness to IL-18, detected both on the RNA and protein level. Thus, the polymorphic regulation of human neutrophils can impact beneficial as well as pathological inflammatory responses.

Neutrophils are abundant immune cells important for antimicrobial defence and in autoimmunity. Here, by mapping expression quantitative trait loci (eQTL) in neutrophils of Chinese ethnicity from Singapore, Andiappan et al. provide a resource for understanding immune-related trait associated genetic variants.

The Glu632-Leu633 deletion in cysteine rich domain of Ret induces constitutive dimerization and alters the processing of the receptor protein

Mutations of the RET gene, encoding a receptor tyrosine kinase, have been associated with the inherited cancer syndromes MEN 2A and MEN 2B. They have also further been associated with both familial and sporadic medullary thyroid carcinomas. Missense mutations affecting cysteine residues within the extracellular domain of the receptor causes constitutive tyrosine kinase activation through the formation of disulfide-bonded homodimers. We have recently reported that a somatic 6 bp in-frame deletion, originally coding for Glu632-Leu633, potently activates the RET gene. This activation is increased with respect to the frequent MEN 2A-associated missense mutation Cys634Arg. This finding specifically correlated to the clinic behavior of the corresponding tumor, which was characterized by an unusually aggressive progression with both multiple and recurrent metastases. By examining the possibility that this deletion acts in a manner similar to cysteine substitution, we have analysed the molecular mechanism by which this oncogenic activation occurs. Phosphorylated dimers of the deleted Ret receptor were detected in immunoprecipitates separated under non-reducing conditions. Like other Cys point mutations, this 6 bp deletion affecting two amino acid residues between two adjacent Cys, is capable of activating the transforming ability of Ret by promoting receptor dimerization. These results suggest that alteration to cysteine residue position or pairing is capable of inducing ligand independent dimerization. Furthermore, we present data demonstrating that the processing and sorting of the Ret membrane receptor to the cell surface is affected by mutation type.

Full activation of MEN2B mutant RET by an additional MEN2A mutation or by ligand GDNF stimulation

Germline mutations of RET gene, encoding a receptor tyrosine kinase, have been associated with the MEN2A and MEN2B inherited cancer syndromes. In MEN2A mutations affecting cysteine residues in the extracellular domain of the receptor cause constitutive activation of the tyrosine kinase by the formation of disulfide-bonded homodimers. In MEN2B a single mutation in the tyrosine kinase domain (Met918Thr) has been identified. This mutation does not lead to dimer formation, but has been shown (both biologically and biochemically) to cause ligand-independent activation of the Ret protein, but to a lesser extent than MEN2A mutations. Intramolecular activation by cis-autophosphorylation of RetMEN2B monomers has been proposed as a model for activation, although alternative mechanisms can be envisaged. Here we show that the activity of RetMEN2B can be increased by stable dimerization of the receptor. Dimerization was achieved experimentally by constructing a double mutant receptor with a MEN2A mutation (Cys634Arg) in addition to the MEN2B mutation, and by chronic exposure of RetMEN2B-expressing cells to the Ret ligand GDNF. In both cases full activation of RetMEN2B, measured by 'in vitro' transfection assays and biochemical parameters, was seen. These results indicate that the MEN2B phenotype could be influenced by the tissue distribution or concentration of Ret ligand(s).

Molecular and biochemical analysis of RET/PTC4, a novel oncogenic rearrangement between RET and ELE1 genes, in a post-Chernobyl papillary thyroid cancer

A post-Chernobyl papillary thyroid cancer, displaying a novel ELE1/RET oncogenic rearrangement with an anomalous fusion transcript, was molecularly characterized. In spite of the presence of a normal breakpoint in exon 5 of the activating ELE1 gene, the sequence of the rearranged genomic DNA showed a previously unreported intra-exonic breakpoint in the RET protooncogene. As a consequence, a cDNA sequence 93 nucleotides larger than the regular one, and with the exon 5 of ELE1 joined to exon 11 instead of exon 12 of RET, is formed. To characterize the product of this new oncogenic ELE1/RET rearrangement, here designated as RET/PTC4, we performed an immunoprecipitation and Western blot analysis on cell extracts from NIH3T3 transfectants. The results showed the presence of two isoforms of the chimeric protein, displaying a constitutive tyrosine phosphorylation. As expected, the molecular weight of this protein was higher than that of RET/ PTC3 protein (p80 and p85, instead of p76 and p81). Previous reports, from our and other laboratories, showed that post-Chernobyl papillary thyroid carcinomas are characterized by a high frequency (about 60%) of RET oncogenic rearrangements (Fugazzola et al., 1995; Klugbauer et al., 1995; Ito et al., 1994). These events predominantly involve ELE1 activating sequence, thus producing RET/PTC3 oncogene (Fugazzola et al., 1995; Klugbauer et al., 1995). Hence, this elevated frequency of RET rearrangements could increase the probability of selecting unusual events as that here described. Alternatively, targeted radiation effects could be responsible for the atypical RET rearrangement producing RET/PTC4 oncogene.

Cardiologic abnormalities in patients with long-term lupus nephritis

To assess the cardiological status of patients with long-term lupus nephritis we evaluated 30 patients (mean age 43 +/- 11 years) with lupus nephritis lasting from at least 10 years (mean 15 +/- 5 years). At the time of cardiological evaluation the mean plasma creatinine was 132.6 +/- 11.1 mumol/l and in 28 patients lupus had been quiescent for at least 3 years. Fourteen patients (46.6%) showed one or more cardiac abnormalities: 10 had valvular lesions (1 verrucous endocarditis, 9 thickening and stiffness of one or more valves)--4 patients had regional myocardial akinesis as a consequence of a previous cardiac infarct (one had valvular abnormalities too). One patient had pulmonary hypertension probably secondary to pulmonary vasculitis. No patient had pericarditis. These cardiac abnormalities proved to be statistically correlated with the number of ARA criteria (p = 0.045), the number of lupus flares (p = 0.004), the serum levels of cholesterol (p = 0.04) and of triglycerides (p = 0.025) as well as the duration of hypercholesterolemia (p = 0.005) and of hypertriglyceridemia (p = 0.007). In conclusion, in patients with long-term lupus nephritis cardiac lesions are frequent. The main lesions are non-verrucous valvulopathy (probably a consequence of healing verrucous endocarditis) and cardiac infarct (caused by an accelerated atherosclerosis). On the contrary cardiac lesions caused by active lupus as pericarditis, myocarditis and verrucous endocarditis are rare.