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Spatial proteomics and transcriptomics reveal early immune cell organization in pancreatic intraepithelial neoplasia
Melissa R. Lyman, Jacob T. Mitchell, Sidharth Raghavan, Luciane T. Kagohara, Amanda L. Huff, Saurav D. Haldar, Sarah M. Shin, Samantha Guinn, Benjamin Barrett, Gabriella Longway, Alexei Hernandez, Erin M. Coyne, Xuan Yuan, Lalitya Andaloori, Jiaying Lai, Yun Zhou Liu, Rachel Karchin, Anuj Gupta, Ashley L. Kiemen, André Forjaz, Denis Wirtz, Pei-Hsun Wu, Atul Deshpande, Jae W. Lee, Todd D. Armstrong, Nilofer S. Azad, Jacquelyn W. Zimmerman, Laura D. Wood, Robert A. Anders, Elizabeth D. Thompson, Elizabeth M. Jaffee, Elana J. Fertig, Won Jin Ho, Neeha Zaidi
Melissa R. Lyman, Jacob T. Mitchell, Sidharth Raghavan, Luciane T. Kagohara, Amanda L. Huff, Saurav D. Haldar, Sarah M. Shin, Samantha Guinn, Benjamin Barrett, Gabriella Longway, Alexei Hernandez, Erin M. Coyne, Xuan Yuan, Lalitya Andaloori, Jiaying Lai, Yun Zhou Liu, Rachel Karchin, Anuj Gupta, Ashley L. Kiemen, André Forjaz, Denis Wirtz, Pei-Hsun Wu, Atul Deshpande, Jae W. Lee, Todd D. Armstrong, Nilofer S. Azad, Jacquelyn W. Zimmerman, Laura D. Wood, Robert A. Anders, Elizabeth D. Thompson, Elizabeth M. Jaffee, Elana J. Fertig, Won Jin Ho, Neeha Zaidi
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Research Article Immunology Inflammation Oncology

Spatial proteomics and transcriptomics reveal early immune cell organization in pancreatic intraepithelial neoplasia

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Abstract

Pancreatic ductal adenocarcinoma (PDAC) has a poor survival rate due to late detection. PDAC arises from precursor microscopic lesions, termed pancreatic intraepithelial neoplasia (PanIN), that develop at least a decade before overt disease; this provides an opportunity to intercept PanIN-to-PDAC progression. However, immune interception strategies require full understanding of PanIN and PDAC cellular architecture. Surgical specimens containing PanIN and PDAC lesions from a unique cohort of 5 treatment-naive patients with PDAC were surveyed using spatial omics (proteomic and transcriptomic). Findings were corroborated by spatial proteomics of PanIN and PDAC from tamoxifen-inducible KPC mice. We uncovered the organization of lymphoid cells into tertiary lymphoid structures (TLSs) adjacent to PanIN lesions. These TLSs lacked CD21+CD23+ B cells compared with more mature TLSs near the PDAC border. PanINs harbored mostly CD4+ T cells, with fewer Tregs and exhausted T cells than PDAC. Peritumoral space was enriched with naive CD4+ and central memory T cells. These observations highlight the opportunity to modulate the immune microenvironment in PanINs before immune exclusion and immunosuppression emerge during progression into PDAC.

Authors

Melissa R. Lyman, Jacob T. Mitchell, Sidharth Raghavan, Luciane T. Kagohara, Amanda L. Huff, Saurav D. Haldar, Sarah M. Shin, Samantha Guinn, Benjamin Barrett, Gabriella Longway, Alexei Hernandez, Erin M. Coyne, Xuan Yuan, Lalitya Andaloori, Jiaying Lai, Yun Zhou Liu, Rachel Karchin, Anuj Gupta, Ashley L. Kiemen, André Forjaz, Denis Wirtz, Pei-Hsun Wu, Atul Deshpande, Jae W. Lee, Todd D. Armstrong, Nilofer S. Azad, Jacquelyn W. Zimmerman, Laura D. Wood, Robert A. Anders, Elizabeth D. Thompson, Elizabeth M. Jaffee, Elana J. Fertig, Won Jin Ho, Neeha Zaidi

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Figure 3

Tertiary lymphoid structures (TLSs) associated with PanINs maintain an immature phenotype compared with a mature phenotype in peritumoral TLSs.

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Tertiary lymphoid structures (TLSs) associated with PanINs maintain an i...
(A) H&E staining of PDAC region annotated in blue marker by an expert pathologist, with the outline of the tumor region overlaid on an IHC stain for CD3+ (brown) of a serial section of the same tissue, demonstrating the localization of the lymphoid aggregates in the peritumoral region. (B) Representative H&E staining of a TLS found within 250 μm of the invasive edge of the tumor and one within 250 μm of the edge of a PanIN and corresponding IMC staining of CD20+, CD21+, CD23+, CD4+, and CD8+ cells, indicating a mature TLS adjacent to PDAC and an immature TLS adjacent to PanIN. In PanIN-adjacent TLS images, the entire TLS is circled with a dashed white line, while in the PDAC-adjacent TLS images, the germinal center is circled with a dashed white line. Scale bars: 50 μm (top 2 rows) and 100 μm (bottom 2 rows). (C) Percentage distribution of lymphoid cell types according to the region of each TLS included in the analysis. (D) Box plot of the density of CD20+CD45RA+ B cells in PanIN-, PDAC-, and CP-adjacent TLSs. (E) Box plot of the density of germinal center–associated B cells (CD20+CD21+CD23+). (F) Box plots of the density of dendritic cells (DCSIGN+) and high endothelial venules (PDPN+) in each region-specific TLS. Densities were calculated using the number of cells per mm2 of each ROI. Significance was determined using Wilcoxon’s rank-sum test. *P ≤ 0.05; **P ≤ 0.01. NS, P > 0.05.

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