9 A pan-cancer multi-omic immune single-cell atlas for cancer immunotherapy: focus on CD4+ T cells

9 Figure 1 Composition of the CITA A. Pipeline for the Cancer Immunotherapy T-cell Atlas (CITA) integration including the use of consensus annotated CD4+ T-cell states based on FACS-sorted CD4 single-cell datasets. UMAP of 1.3M T cells from 23 single cell datasets from individuals with cancer, for 30 different cancer types and 9 tissue types (center). B,C. CITA harmonized metadata overview, with sampled tissue type per cancer type and treatment type by cancer type. LUAD: lung adenocarcinoma; SKCM, skin cancer melanoma; GBM, glioblastoma; LUSC, lung squamous cell carcinoma; CC/CRC, colorectal carcinoma; LIHC, liver hepatocellular carcinoma; BC/ BCC, basal cell carcinoma; THCA, thyroid carcinoma; NPC, nasopharyngeal cancer; CHOL, cholangiocarcinoma; UCEC, uterine corpus endometrial carcinoma; DLBCL, diffuse large B cell lymphoma; ESCA, esophageal cancer; RC, renal cancer; PACA, pancreatic adenocarcinoma; O, oligodendroglioma; HCC, hepatocellular carcinoma; AA, anaplastic astrocytoma; MM, multiple myeloma; SCC, squamous cell carcinoma; BRCA, breast cancer; LUAS, lung adeno/squamous carcinoma; BC, basal cell carcinoma; BCL, B cell lymphoma; OV, ovarian serous cystadenocarcinoma; IV, glioma stage 4; FTC, fallopian tube carcinoma; ASC, ascite; JTNAT, joint tumor normal tissue; LN, lymph node; MET, metastasis; N, normal; NAT, normal adjacent tissue; PB, peripheral blood; PE, pleural effusion; T, tumor; CARBO, carboplatin; PEME, Pemetrexed; PACL, paclitaxel; Adv, adenovirus; RESECT, resection Abstract 9 Figure 2 Pan-cancer CD4+ T-cell consensus annotation A. UMAP of consensus annotation of CD4+ sorted cells from peripheral blood (PB), tumor (T) and normal adjacent tissue (NAT) from individuals with lung, colorectal or liver cancer. CD4 RPL: high ribosomal protein, T prolif: proliferating, Tmp: memory precursors; Tcm: central memory, Tact: activated, Tem: effector memory, Tfh: follicular helper, Th1 CTL: T helper 1 cytolytic lymphocytes, Trm: tissue resident memory, cTregs: circulating regulatory T cells, eTregs: effector regulatory T cells, trTregs: tissue resident regulatory T cells. B. Barplot of cancer type and tissue type fractions for each cell annotation. C. UMAP of gene signature scores for cell cycle and a curated T-cell activation/terminal differentiation gene signature (n=26 genes) consisting of terminal differentiation transcription factors (e.g. ID2, RUNX3, PRDM1, TOX), cytolytic markers (e.g. GZMA, GZMB, GZMH, PRF1), co-stimulatory receptors (e.g. ICOS, TNFRSF18, TNFRSF4), and chemokines/chemokine receptors (e.g. CXCR3, CX3CR1, CXCL13) for dataset described in (A). D. Dotplot of the five most significant differentially expressed genes for each cell annotation contrasted against each other cell annotation http://dx.doi.org/10.1136/jitc-2022-SITC2022.0009 Abstracts J Immunother Cancer 2022;10(Suppl 2):A1–A1603 A11 on Jauary 8, 2023 by gest. P rocted by coright. http/jitc.bm jcom / J Im m unther C acer: frst pulished as 10.11jitc-2022-S IT C 20.0009 on 7 N ovem er 222. D ow nladed fom

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