Abstract B032: Spatial proteomics and transcriptomics reveal early immune cell organization in human pancreatic intraepithelial neoplasia
Authors: Lyman Melissa R. , Mitchell Jacob T. , Kagohara Luciane T. , Huff Amanda L. , Haldar Daniel , Shin Sarah , Guinn Samantha , Barrett Benjamin , Longway Gabriella , Hernandez Alexei , Coyne Erin , Yuan Xuan , Andaloori Lalitya , Lai Jiaying , Liu YunZhou , Karchin Rachel , Gupta Anuj , Kiemen Ashley , Forjaz André , Wirtz Denis , Wu Pei-Hsun , Deshpande Atul , Armstrong Todd , Azad Nilofer S. , Thompson Elizabeth , Anders Robert , Ho Won Jin , Jaffee Elizabeth , Fertig Elana , Zaidi Neeha 
Published: January 2024

Abstract
A common precursor of pancreatic adenocarcinoma (PDAC) are microscopic lesions, termed pancreatic intraepithelial neoplasia (or PanIN). These lesions are initiated at least a decade before overt PDAC forms, thus providing a large window of opportunity to modulate the immune microenvironment before significant pro-carcinogenic signals prevail. To best inform strategies for interception of these precursor lesions, it is critical to understand the quantity and spatial localization of the lymphoid compartment recruited to PanINs compared to PDAC. Here, we report the use of spatial–omics (proteomic and transcriptomics) to evaluate the recruitment of lymphoid cells to PanIN lesions compared to immune–enriched regions of PDAC in a unique cohort of 5 treatment–naïve PDAC patients who underwent resection of their primary pancreas tumor. Using imaging mass cytometry, we found lymphoid populations recruited preferentially to low–grade PanINs compared with normal tissue. This population of predominantly CD4+ T cells in low–grade PanINs was markedly different from the increased Treg and exhausted CD4+ T cell populations found infiltrating in the tumor. Interestingly, our approach to evaluate the spatial localization of these recruited lymphoid populations uncovered their capacity to organize into tertiary lymphoid structures (TLSs). Structurally and functionally immature TLSs were associated with PanIN lesions, while mature TLSs were found adjacent to the invasive tumor border of PDAC. Mature TLSs restricted to the outside of the tumor had markers of proliferation indicating functional capabilities; however, these aggregates also contained immunosuppressive lymphoid subtypes. Signatures of immature PanIN associated TLSs and mature PDAC associated TLSs were recapitulated by the spatial transcriptomics analysis performed on this same cohort. Additionally, the proteomic analysis identified that the immune population restricted to the periphery of the tumor was substantially denser and enriched with greater numbers of naïve CD4+ T cells and central memory T cells than the intra–tumoral population. Together, these data demonstrate that PanINs are capable of recruiting a substantial lymphoid population that can organize into immature TLSs. The quality and quantity of lymphoid cells recruited to PanINs compared to regions inside and surrounding PDAC provides evidence of the dynamic immune microenvironment in response to PanIN–to–PDAC progression. These data provide insight into the immunological landscape of PDAC development and will inform the next generation of strategies to prevent PanIN lesions from progressing to overt PDAC.
Citation Format: Melissa R. Lyman, Jacob T. Mitchell, Luciane T. Kagohara, Amanda L. Huff, Daniel Haldar, Sarah Shin, Samantha Guinn, Benjamin Barrett, Gabriella Longway, Alexei Hernandez, Erin Coyne, Xuan Yuan, Lalitya Andaloori, Jiaying Lai, YunZhou Liu, Rachel Karchin, Anuj Gupta, Ashley Kiemen, André Forjaz, Denis Wirtz, Pei-Hsun Wu, Atul Deshpande, Todd Armstrong, Nilofer S. Azad, Elizabeth Thompson, Robert Anders, Won Jin Ho, Elizabeth Jaffee, Elana Fertig, Neeha Zaidi. Spatial proteomics and transcriptomics reveal early immune cell organization in human pancreatic intraepithelial neoplasia [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr B032.