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The evolution of pancreatic ductal adenocarcinoma (PDAC) from tumor initiation to metastases requires years to decades, providing a window of opportunity for the prevention of premalignant progression. One of the first genetic mutations to occur early in development is in KRAS, an oncogene that is expressed by over 90% of PDACs. KRAS mutations (mKRAS) are attractive targets as they are recurrent hot–spot drivers that are expressed by, and drive the growth of all PDAC cells. Preclinical data provide compelling evidence that targeting mKRAS proteins using a Listeria-based vaccination approach in KPC mouse model results in prevention of progression from precursor lesions to PDAC. Based on these data, we hypothesize that targeting mKRAS in combination with bypassing early immune–suppressive signals will slow or even halt the progression of precursor lesions to PDA in subjects who are at high–risk. We have thus developed a clinical–grade long peptide vaccine targeting the six most common mKRAS proteins (G12V, G12R, G12A, G12C, G12D, and G13D) in PDAC patients. To establish initial safety and immunogenicity, our KRAS vaccine has been tested in 11 patients thus far in a Phase 1 clinical trial (NCT04117087) in combination with checkpoint blockade in patients who have undergone surgery and peri–operative chemotherapy and remained disease–free on imaging. Longitudinal immune data demonstrates an induction of activated and poly-functional mKRAS-specific CD4+ and CD8+ T cells, as well as effector and central memory T cells post–vaccination. In parallel, we performed paired single-cell RNA and TCR sequencing in PBMCs from a patient to obtain greater resolution of the vaccine–induced cytotoxic anti–tumor T cells. We captured 66,869 immune cells across three timepoints for analysis. Notably, we similarly observed an expansion of central memory CD4+ and CD8+ T cells post–vaccination. Using a novel computational algorithm (developed in collaboration with Dr. Elana Fertig’s lab) that takes into account physiochemical similarity of known mKRAS TCRs, we used our single–cell dataset to identify mKRAS-reactive TCRs` in the periphery that were functionally validated in vitro using CRISPR-Cas12a-based genome editing of human T cells. Overall, these studies suggest the induction of de novo, high quality mutant KRAS–specific T cells in the peripheral blood post–vaccination. Based on these immune data, we are enrolling onto a second clinical trial testing our mKRAS peptide vaccine in patients who are at high risk for developing PDAC (NCT05013216). These high-risk groups include those with strong family histories of PDAC or known pathogenic germline variants with a lifetime risk of up to 10% of developing PDA. Our preliminary data in our first three vaccinated patients shows an induction of mKRAS–specific T cell responses in the peripheral blood. Further studies characterizing the T cell response will lay the foundation for peripheral T cell–based biomarkers that could be used to predict response in a prevention setting. Citation Format: Neeha Zaidi, Amanda Huff, Emily Marcisak-Davis, Daniel Haldar, Thatcher Heumann, Max Konig, Brian Mog, Janelle Montagne, Gabriella Longway, Lalitya Andaloori, Melissa Lyman, Ludmila Danilova, Julie Nauroth, Luciane Kagohara, Elana Fertig, Nilo Azad, Elizabeth Jaffee. Intercepting pancreatic cancer development with mutant KRAS-targeted immunotherapy [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr IA013.

Sporadic inclusion body myositis (IBM) is the most common acquired muscle disease in adults over age 50, yet it remains unclear whether the disease is primarily driven by T cell-mediated autoimmunity. IBM muscle biopsies exhibit nuclear clearance and cytoplasmic aggregation of TDP-43 in muscle cells, a pathologic finding observed initially in neurodegenerative disease, and nuclear loss of TDP-43 in neurons causes aberrant RNA splicing. Here, we show that loss of TDP-43 splicing repression, as determined by inclusion of cryptic exons, occurs in skeletal muscle of IBM patients. Out of 119 muscle biopsies tested, RT-PCR-mediated detection of cryptic exon expression is 84% sensitive and 99% specific for diagnosing IBM, indicating utility as a functional and diagnostic biomarker. To determine the role of T cells in pathogenesis, we generated a novel xenograft model by transplanting human IBM muscle into the hindlimb of immunodeficient mice. Xenografts from IBM patients display robust regeneration of human myofibers and recapitulate both inflammatory and degenerative features of the disease. Myofibers in IBM xenografts are invaded by human, oligoclonal CD8+ T cells and exhibit MHC-I upregulation, rimmed vacuoles, mitochondrial pathology, p62-positive inclusions, and nuclear clearance and cytoplasmic aggregation of TDP-43, resulting in expression of cryptic exons. Depletion of human T cells within IBM xenografts by treating mice intraperitoneally with anti-CD3 (OKT3) suppresses MHC-I upregulation, but rimmed vacuoles and loss of TDP-43 function persist. These data suggest that myofiber degeneration occurs independent of T cells, and muscle cell-intrinsic mechanisms, such as loss of TDP-43 splicing repression, drive IBM pathogenesis.One Sentence SummaryDepletion of T cells in a xenograft model of sporadic inclusion body myositis suppresses inflammation but not TDP-43 pathology or muscle degeneration.

Background Myositis, or idiopathic inflammatory myopathy (IIM), is a group disorders of unknown etiology characterized by the inflammation of skeletal muscle. The role of T cells and their antigenic targets in IIM initiation and progression is poorly understood. T cell receptor (TCR) repertoire sequencing is a powerful approach for characterizing complex T cell responses. However, current TCR sequencing methodologies are complex, expensive, or both, greatly limiting the scale of feasible studies. Methods Here we present Framework Region 3 AmplifiKation sequencing (“FR3AK-seq”), a simplified multiplex PCR-based approach for the ultra-efficient and quantitative analysis of TCR complementarity determining region 3 (CDR3) repertoires. By using minimal primer sets targeting a conserved region immediately upstream of CDR3, undistorted amplicons are analyzed via short read, single-end sequencing. We also introduce the novel algorithm Inferring Sequences via Efficiency Projection and Primer Incorporation (“ISEPPI”) for linking CDR3s to their associated variable genes. Findings We find that FR3AK-seq is sensitive and quantitative, performing comparably to two different industry standards. FR3AK-seq and ISEPPI were used to efficiently and inexpensively characterize the T cell infiltrates of surgical muscle biopsies obtained from 145 patients with IIM and controls. A cluster of closely related TCRs was identified in samples from patients with sporadic inclusion body myositis (IBM). Interpretation The ease and minimal cost of FR3AK-seq removes critical barriers to routine, large-scale TCR CDR3 repertoire analyses, thereby democratizing the quantitative assessment of human TCR repertoires in disease-relevant target tissues. Importantly, discovery of closely related TCRs in muscle from patients with IBM provides evidence for a shared antigen-driven T cell response in this disease of unknown pathogenesis. Funding This work was supported by NIH grant U24AI118633 and a Prostate Cancer Foundation Young Investigator Award.

Objective: Sjogren's syndrome (SS) patients may be affected by the neuromyelitis optica spectrum disorder (NMOSD), a severe demyelinating syndrome associated with anti-aquaporin 4 antibodies (anti-AQP4 antibodies). The relationship between SS and NMOSD has been a sustained focus of investigation. Among SS patients, anti-AQP4 antibodies have been detected exclusively in those with NMOSD. It has therefore been speculated that NMOSD is not a neurological complication of SS. However, such studies evaluated small numbers of SS patients, often admixed with other inflammatory disorders. Methods: We compared frequencies of anti-AQP4 and SS-associated antibodies in 109 SS patients, including 11 with NMOSD, 8 with non-NMOSD demyelinating syndromes, and 90 without demyelinating syndromes. Results: When assessed using a fluorescence-activated cell sorting (FACS) assay, anti-AQP4 antibodies were seen exclusively in those SS patients with NMOSD (72.7%), but not in SS patients without NMOSD (p

A key mediator in cold-sensation is the protein transient receptor potential melastatin 8 (TRPM8), which is expressed on sensory nerves and cutaneous blood vessels. These receptors are activated by cold temperatures and play a key role in body thermoregulation. Cold sensitivity and Raynaud's phenomenon are frequent clinical features in scleroderma, and are thought to be secondary to a local defect in cutaneous thermoregulation. We investigated whether autoantibodies targeting TRPM8 were present in the sera of patients with scleroderma as evidence for a possible mechanism for an acquired immune mediated defect in thermoregulation.Sera from 50 well-characterised scleroderma patients with Raynaud's phenomenon were studied. TRPM8 autoantibodies were assayed as follows: 1. immunoprecipitation with 35S-methionine-labelled TRPM8 generated by in vitro transcription and translation, 2. immunoblotting lysates made from cells transiently transfected with TRPM8 cDNA, 3. Immunoprecipitation of TRPM8 transfected lysates with detection by blotting and 4. flow cytometry.Fifty scleroderma patients with Raynaud's phenomenon (41 female, 39 Caucasian, 23 with limited scleroderma, and 20 with history of cancer) were studied. Four different methods to assay for TRPM8 antibodies were set up, optimised and validated using commercial antibodies. All 50 scleroderma patients' sera were assayed using each of the above methods, and all were negative for TRPM8 autoantibodies.Antibodies against TRPM8 are not found in scleroderma patient sera, suggesting that the abnormal cold sensitivity and associated abnormal vascular reactivity in scleroderma patients is not the result of an immune process targeting TRPM8.