Halbrook, C. J., Lyssiotis, C. A., Pasca di Magliano, M. & Maitra, A. Pancreatic most cancers: advances and challenges. Cell 186, 1729–1754 (2023).
Hidalgo, M. et al. Addressing the challenges of pancreatic most cancers: future instructions for enhancing outcomes. Pancreatology 15, 8–18 (2015).
Park, W., Chawla, A. & O’Reilly, E. M. Pancreatic most cancers: a assessment. JAMA 326, 851–862 (2021).
Groot, V. P. et al. Implications of the sample of illness recurrence on survival following pancreatectomy for pancreatic ductal adenocarcinoma. Ann. Surg. Oncol. 25, 2475–2483 (2018).
Liu, Okay. H. et al. Lung metastases in sufferers with stage IV pancreatic most cancers: prevalence, threat components, and survival affect. J. Clin. Med. 8, 1402 (2019).
Sahin, I. H., Elias, H., Chou, J. F., Capanu, M. & O’Reilly, E. M. Pancreatic adenocarcinoma: insights into patterns of recurrence and illness habits. BMC Most cancers 18, 769 (2018).
Yachida, S. et al. Distant metastasis happens late in the course of the genetic evolution of pancreatic most cancers. Nature 467, 1114–1117 (2010).
Yachida, S. et al. Medical significance of the genetic panorama of pancreatic most cancers and implications for identification of potential long-term survivors. Clin. Most cancers Res. 18, 6339–6347 (2012).
Makohon-Moore, A. P. et al. Restricted heterogeneity of recognized driver gene mutations among the many metastases of particular person sufferers with pancreatic most cancers. Nat. Genet. 49, 358–366 (2017).
Reiter, J. G. et al. Minimal useful driver gene heterogeneity amongst untreated metastases. Science 361, 1033–1037 (2018).
Notta, F. et al. A renewed mannequin of pancreatic most cancers evolution primarily based on genomic rearrangement patterns. Nature 538, 378–382 (2016).
McDonald, O. G. et al. Epigenomic reprogramming throughout pancreatic most cancers development hyperlinks anabolic glucose metabolism to distant metastasis. Nat. Genet. 49, 367–376 (2017).
Kim, M. S. et al. Heterogeneity of pancreatic most cancers metastases in a single affected person revealed by quantitative proteomics. Mol. Cell. Proteomics 13, 2803–2811 (2014).
Erickson, A. et al. Spatially resolved clonal copy quantity alterations in benign and malignant tissue. Nature 608, 360–367 (2022).
O’Kane, G. M. et al. GATA6 expression distinguishes classical and basal-like subtypes in superior pancreatic most cancers. Clin. Most cancers Res. 26, 4901–4910 (2020).
Raghavan, S. et al. Microenvironment drives cell state, plasticity, and drug response in pancreatic most cancers. Cell 184, 6119–6137 (2021).
Wormann, S. M. et al. APOBEC3A drives deaminase domain-independent chromosomal instability to advertise pancreatic most cancers metastasis. Nat. Most cancers 2, 1338–1356 (2021).
Collisson, E. A. et al. Subtypes of pancreatic ductal adenocarcinoma and their differing responses to remedy. Nat. Med. 17, 500–503 (2011).
Bailey, P. et al. Genomic analyses determine molecular subtypes of pancreatic most cancers. Nature 531, 47–52 (2016).
Gavish, A. et al. Hallmarks of transcriptional intratumour heterogeneity throughout a thousand tumours. Nature 618, 598–606 (2023).
Gabitova-Cornell, L. et al. Ldl cholesterol pathway inhibition induces TGF-β signaling to advertise basal differentiation in pancreatic most cancers. Most cancers Cell 38, 567–583 (2020).
Zhang, D. et al. Inferring super-resolution tissue structure by integrating spatial transcriptomics with histology. Nat. Biotechnol. 42, 1372–1377 (2024).
Elyada, E. et al. Cross-species single-cell evaluation of pancreatic ductal adenocarcinoma reveals antigen-presenting cancer-associated fibroblasts. Most cancers Discov. 9, 1102–1123 (2019).
Sahai, E. et al. A framework for advancing our understanding of cancer-associated fibroblasts. Nat. Rev. Most cancers 20, 174–186 (2020).
Dilly, J. et al. Mechanisms of resistance to oncogenic KRAS inhibition in pancreatic most cancers. Most cancers Discov. 14, 2135–2161 (2024).
Zhang, Y. et al. Macropinocytosis in cancer-associated fibroblasts depends on CaMKK2/ARHGEF2 signaling and capabilities to assist tumor and stromal cell health. Most cancers Discov. 11, 1808–1825 (2021).
Ma, R. Y., Black, A. & Qian, B. Z. Macrophage range in most cancers revisited within the period of single-cell omics. Developments Immunol. 43, 546–563 (2022).
Blando, J. et al. Comparability of immune infiltrates in melanoma and pancreatic most cancers highlights VISTA as a possible goal in pancreatic most cancers. Proc. Natl Acad. Sci. USA 116, 1692–1697 (2019).
Carstens, J. L. et al. Spatial computation of intratumoral T cells correlates with survival of sufferers with pancreatic most cancers. Nat. Commun. 8, 15095 (2017).
Falcomata, C. et al. Context-specific determinants of the immunosuppressive tumor microenvironment in pancreatic most cancers. Most cancers Discov. 13, 278–297 (2023).
Biffi, G. et al. IL1-induced JAK/STAT signaling is antagonized by TGFβ to form CAF heterogeneity in pancreatic ductal adenocarcinoma. Most cancers Discov. 9, 282–301 (2019).
Feig, C. et al. Concentrating on CXCL12 from FAP-expressing carcinoma-associated fibroblasts synergizes with anti-PD-L1 immunotherapy in pancreatic most cancers. Proc. Natl Acad. Sci. USA 110, 20212–20217 (2013).
Jiang, H. et al. Concentrating on focal adhesion kinase renders pancreatic cancers conscious of checkpoint immunotherapy. Nat. Med. 22, 851–860 (2016).
He, S. et al. Excessive-plex imaging of RNA and proteins at subcellular decision in fastened tissue by spatial molecular imaging. Nat. Biotechnol. 40, 1794–1806 (2022).
Connor, A. A. et al. Integration of genomic and transcriptional options in pancreatic most cancers reveals elevated cell cycle development in metastases. Most cancers Cell 35, 267–282 (2019).
Chan-Seng-Yue, M. et al. Transcription phenotypes of pancreatic most cancers are pushed by genomic occasions throughout tumor evolution. Nat. Genet. 52, 231–240 (2020).
Moffitt, R. A. et al. Digital microdissection identifies distinct tumor- and stroma-specific subtypes of pancreatic ductal adenocarcinoma. Nat. Genet. 47, 1168–1178 (2015).
Puleo, F. et al. Stratification of pancreatic ductal adenocarcinomas primarily based on tumor and microenvironment options. Gastroenterology 155, 1999–2013 (2018).
Lee, J. J. et al. Elucidation of tumor-stromal heterogeneity and the ligand-receptor interactome by single-cell transcriptomics in real-world pancreatic most cancers biopsies. Clin. Most cancers Res. 27, 5912–5921 (2021).
Topham, J. T. et al. Subtype-discordant pancreatic ductal adenocarcinoma tumors present intermediate medical and molecular traits. Clin. Most cancers Res. 27, 150–157 (2021).
Williams, H. L. et al. Spatially resolved single-cell evaluation of pancreatic most cancers expression subtypes reveals co-expressor phenotypes and in depth intratumoral heterogeneity. Most cancers Res. 83, 441–455 (2023).
Wang, Z. et al. Carcinomas assemble a filamentous CXCL12-keratin-19 coating that suppresses T cell-mediated immune assault. Proc. Natl Acad. Sci. USA 119, e2119463119 (2022).
Yan, R., Moresco, P., Gegenhuber, B. & Fearon, D. T. T cell-mediated improvement of stromal fibroblasts with an immune-enhancing chemokine profile. Most cancers Immunol. Res. 11, 1044–1054 (2023).
Meylan, M. et al. Tertiary lymphoid buildings generate and propagate anti-tumor antibody-producing plasma cells in renal cell most cancers. Immunity 55, 527–541 (2022).
Regulation, H. C. et al. The proteomic panorama of pancreatic ductal adenocarcinoma liver metastases identifies molecular subtypes and associations with medical response. Clin. Most cancers Res. 26, 1065–1076 (2020).
Stuart, T. et al. Complete integration of single-cell knowledge. Cell 177, 1888–1902 (2019).
McInnes, L., Healy, J., Saul, N. & Grossberger, L. UMAP: uniform manifold approximation and projection. J. Open Supply Softw. 3, 861 (2018).
Chu, Y. et al. Pan-cancer T cell atlas hyperlinks a mobile stress response state to immunotherapy resistance. Nat. Med. 29, 1550–1562 (2023).
Wang, R. et al. Evolution of immune and stromal cell states and ecotypes throughout gastric adenocarcinoma development. Most cancers Cell 41, 1407–1426 (2023).
Wang, R. et al. Single-cell dissection of intratumoral heterogeneity and lineage range in metastatic gastric adenocarcinoma. Nat. Med. 27, 141–151 (2021).
Sans, M. et al. Spatial transcriptomics of intraductal papillary mucinous neoplasms of the pancreas identifies NKX6-2 as a driver of gastric differentiation and indolent organic potential. Most cancers Discov. 13, 1844–1861 (2023).
Yu, G., Smith, D. Okay., Zhu, H., Guan, Y. & Lam, T. T. Y. ggtree: an R package deal for visualization and annotation of phylogenetic bushes with their covariates and different related knowledge. Strategies Ecol. Evol. 8, 28–36 (2017).
Gao, R. et al. Delineating copy quantity and clonal substructure in human tumors from single-cell transcriptomes. Nat. Biotechnol. 39, 599–608 (2021).
De Falco, A., Caruso, F., Su, X.-D., Iavarone, A. & Ceccarelli, M. A variational algorithm to detect the clonal copy quantity substructure of tumors from scRNA-seq knowledge. Nat. Commun. 14, 1074 (2023).
Schliep, Okay. phangorn: phylogenetic evaluation in R. Bioinformatics 27, 592–593 (2011).
Liberzon, A. et al. The Molecular Signatures Database (MSigDB) hallmark gene set assortment. Cell Syst. 1, 417–425 (2015).
Hao, D. et al. The one-cell immunogenomic panorama of B and plasma cells in early-stage lung adenocarcinoma. Most cancers Discov. 12, 2626–2645 (2022).
Liao, Y., Wang, J., Jaehnig, E. J., Shi, Z. & Zhang, B. WebGestalt 2019: gene set evaluation toolkit with revamped UIs and APIs. Nucleic Acids Res. 47, W199–W205 (2019).
Benjamini, Y. & Hochberg, Y. Controlling the false discovery price: a sensible and highly effective method to a number of testing. J. R. Stat. Soc. B 57, 289–300 (1995).
Ohlund, D. et al. Distinct populations of inflammatory fibroblasts and myofibroblasts in pancreatic most cancers. J. Exp. Med. 214, 579–596 (2017).
Cable, D. M. et al. Sturdy decomposition of cell sort mixtures in spatial transcriptomics. Nat. Biotechnol. 40, 517–526 (2022).
Wei, R. et al. Spatial charting of single-cell transcriptomes in tissues. Nat. Biotechnol. 40, 1190–1199 (2022).
Vahid, M. R. et al. Excessive-resolution alignment of single-cell and spatial transcriptomes with CytoSPACE. Nat. Biotechnol. 41, 1543–1548 (2023).
Pei, G. et al. deCS: a instrument for systematic cell sort annotations of single-cell RNA sequencing knowledge amongst human tissues. Genomics Proteomics Bioinformatics 21, 370–384 (2023).
Belle, J. I. & DeNardo, D. G. A single-cell window into pancreas most cancers fibroblast heterogeneity. Most cancers Discov. 9, 1001–1002 (2019).
Boyd, L. N. C., Andini, Okay. D., Peters, G. J., Kazemier, G. & Giovannetti, E. Heterogeneity and plasticity of cancer-associated fibroblasts within the pancreatic tumor microenvironment. Semin. Most cancers Biol. 82, 184–196 (2022).
Hanzelmann, S., Castelo, R. & Guinney, J. GSVA: gene set variation evaluation for microarray and RNA-seq knowledge. BMC Bioinformatics 14, 7 (2013).