Spatiotemporal Transcriptomic Dissection of Tumor-Associated Macrophage Heterogeneity and Dual-Function Molecular Nodes in Pancreatic Ductal Adenocarcinoma

Research Article
Open access

Spatiotemporal Transcriptomic Dissection of Tumor-Associated Macrophage Heterogeneity and Dual-Function Molecular Nodes in Pancreatic Ductal Adenocarcinoma

Mengfei Li 1*
  • 1 Department of biology science, Shandong university, Shandong, Qingdao    
  • *corresponding author 202223142018@mail.sdu.edu.cn
TNS Vol.113
ISSN (Print): 2753-8826
ISSN (Online): 2753-8818
ISBN (Print): 978-1-80590-161-7
ISBN (Online): 978-1-80590-162-4

Abstract

Many studies have shown that pancreatic cancer is one of the cancers with extremely high mortality. The poor prognosis and lack of early diagnostic methods remain major challenges in the treatment of this cancer. In this article, in order to better detect the occurrence of pancreatic cancer, tools such as monocle3, singleR, harmony in R, and scanpy in Python were used to analyze the cells and genes of pancreatic cancer tissues in mice. By analyzing the data, the following results were obtained: T-cells in healthy PBMCs exhibited broader spatial dispersion than in PDAC tissues, suggesting tumor-driven immune surveillance impairment, while PDAC-associated macrophages displayed expanded distribution linked to pro-tumorigenic functions such as COL1A1-mediated ECM remodeling; Pseudotemporal trajectory analysis revealed myeloid progenitor bifurcation into monocytes/macrophages, with PDAC macrophages showing epigenetically silenced cytotoxic pathways such as suppressed GZMA/NKG7 and enhanced ribosomal biogenesis; Tissue-specific markers such as LCN2 in healthy and CTRB1/AMY2A in PDAC) and spatial co-localization of macrophages/tumor cells highlighted NOP53 as a dual-function hub—inhibiting PI3K-AKT while activating p53—and SPP1 as a paradoxical regulator of metastasis and antitumor immunity; Differential expression and GO enrichment analyses identified ribosomal biogenesis and cytoplasmic translation as PDAC-enriched pathways, contrasting with suppressed stress responses. Our spatial transcriptomic profiling further resolved elevated NOP53, CFB, and SPP1 expression gradients in PDAC tissues, proposing these as diagnostic biomarkers.

Keywords:

Pancreatic ductal adenocarcinoma (PDAC), Tumor-associated macrophages (TAMs), Spatial transcriptomics, Single-cell RNA sequencing, Immune suppression, Ribosomal biogenesis

Li,M. (2025). Spatiotemporal Transcriptomic Dissection of Tumor-Associated Macrophage Heterogeneity and Dual-Function Molecular Nodes in Pancreatic Ductal Adenocarcinoma. Theoretical and Natural Science,113,61-83.
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References

[1]. Chouari, T. et al. Advances in Immunotherapeutics in Pancreatic Ductal Adenocarcinoma. Cancers 15, 4265 (2023).

[2]. Ilic, M. & Ilic, I. Epidemiology of pancreatic cancer. World J. Gastroenterol. 22, 9694 (2016).

[3]. Klein, A. P. Pancreatic cancer epidemiology: understanding the role of lifestyle and inherited risk factors. Nat. Rev. Gastroenterol. Hepatol. 18, 493–502 (2021).

[4]. Ho, T. T. B. et al. Combination of gemcitabine and anti-PD-1 antibody enhances the anticancer effect of M1 macrophages and the Th1 response in a murine model of pancreatic cancer liver metastasis. J. Immunother. Cancer 8, e001367 (2020).

[5]. Zhu, Y. et al. CSF1/CSF1R Blockade Reprograms Tumor-Infiltrating Macrophages and Improves Response to T-cell Checkpoint Immunotherapy in Pancreatic Cancer Models. Cancer Res. 74, 5057–5069 (2014).

[6]. Locati, M., Curtale, G. & Mantovani, A. Diversity, Mechanisms, and Significance of Macrophage Plasticity. Annu. Rev. Pathol. Mech. Dis. 15, 123–147 (2020).

[7]. Wynn, T. A., Chawla, A. & Pollard, J. W. Macrophage biology in development, homeostasis and disease. Nature 496, 445–455 (2013).

[8]. Mantovani, A., Marchesi, F., Malesci, A., Laghi, L. & Allavena, P. Tumour-associated macrophages as treatment targets in oncology. Nat. Rev. Clin. Oncol. 14, 399–416 (2017).

[9]. Wu, Y. et al. Macrophage cell membrane-based nanoparticles: a new promising biomimetic platform for targeted delivery and treatment. J. Nanobiotechnology 20, 542 (2022).

[10]. Cai, H., Zhang, Y., Wang, J. & Gu, J. Defects in Macrophage Reprogramming in Cancer Therapy: The Negative Impact of PD-L1/PD-1. Front. Immunol. 12, 690869 (2021).

[11]. Ruffell, B. & Coussens, L. M. Macrophages and Therapeutic Resistance in Cancer. Cancer Cell 27, 462–472 (2015).

[12]. DeNardo, D. G. & Ruffell, B. Macrophages as regulators of tumour immunity and immunotherapy. Nat. Rev. Immunol. 19, 369–382 (2019).

[13]. Ngambenjawong, C., Gustafson, H. H. & Pun, S. H. Progress in tumor-associated macrophage (TAM)-targeted therapeutics. Adv. Drug Deliv. Rev. 114, 206–221 (2017).

[14]. Dai, E. et al. Autophagy-dependent ferroptosis drives tumor-associated macrophage polarization via release and uptake of oncogenic KRAS protein. Autophagy 16, 2069–2083 (2020).

[15]. Mehla, K. & Singh, P. K. Metabolic Regulation of Macrophage Polarization in Cancer. Trends Cancer 5, 822–834 (2019).

[16]. Fendl, B., Berghoff, A. S., Preusser, M. & Maier, B. Macrophage and monocyte subsets as new therapeutic targets in cancer immunotherapy. ESMO Open 8, 100776 (2023).

[17]. Wei, C. et al. Crosstalk between cancer cells and tumor associated macrophages is required for mesenchymal circulating tumor cell-mediated colorectal cancer metastasis. Mol. Cancer 18, 64 (2019).

[18]. Wu, K. et al. Redefining Tumor-Associated Macrophage Subpopulations and Functions in the Tumor Microenvironment. Front. Immunol. 11, 1731 (2020).

[19]. Seyfried, T. N. & Huysentruyt, L. C. On the Origin of Cancer Metastasis. Crit. Rev. Oncog. 18, 43–73 (2013).

[20]. Cao, L., Meng, X., Zhang, Z., Liu, Z. & He, Y. Macrophage heterogeneity and its interactions with stromal cells in tumour microenvironment. Cell Biosci. 14, 16 (2024).

[21]. Zhang, X., Ji, L. & Li, M. O. Control of tumor-associated macrophage responses by nutrient acquisition and metabolism. Immunity 56, 14–31 (2023).

[22]. Zhang, X., Ji, L. & Li, M. O. Control of tumor-associated macrophage responses by nutrient acquisition and metabolism. Immunity 56, 14–31 (2023).

[23]. Gao, J., Liang, Y. & Wang, L. Shaping Polarization Of Tumor-Associated Macrophages In Cancer Immunotherapy. Front. Immunol. 13, 888713 (2022).

[24]. Mills, C. D., Lenz, L. L. & Harris, R. A. A Breakthrough: Macrophage-Directed Cancer Immunotherapy. Cancer Res. 76, 513–516 (2016).

[25]. Wang, H., Yung, M. M. H., Ngan, H. Y. S., Chan, K. K. L. & Chan, D. W. The Impact of the Tumor Microenvironment on Macrophage Polarization in Cancer Metastatic Progression. Int. J. Mol. Sci. 22, 6560 (2021).

[26]. Li, M. et al. Metabolism, metabolites, and macrophages in cancer. J. Hematol. Oncol.J Hematol Oncol 16, 80 (2023).

[27]. Halbrook, C. J. et al. Macrophage-Released Pyrimidines Inhibit Gemcitabine Therapy in Pancreatic Cancer. Cell Metab. 29, 1390-1399.e6 (2019).

[28]. Menjivar, R. E. et al. Arginase 1 is a key driver of immune suppression in pancreatic cancer. eLife 12, e80721 (2023).

[29]. Kuen, J., Darowski, D., Kluge, T. & Majety, M. Pancreatic cancer cell/fibroblast co-culture induces M2 like macrophages that influence therapeutic response in a 3D model. PLOS ONE 12, e0182039 (2017).

[30]. LaRue, M. M. et al. Metabolic reprogramming of tumor-associated macrophages by collagen turnover promotes fibrosis in pancreatic cancer. Proc. Natl. Acad. Sci. 119, e2119168119 (2022).

[31]. Kemp, S. B. et al. Apolipoprotein E Promotes Immune Suppression in Pancreatic Cancer through NF-κB–Mediated Production of CXCL1. Cancer Res. 81, 4305–4318 (2021).

[32]. Kemp, S. B. et al. Pancreatic cancer is marked by complement-high blood monocytes and tumor-associated macrophages. Life Sci. Alliance 4, e202000935 (2021).

[33]. Padoan, A., Plebani, M. & Basso, D. Inflammation and Pancreatic Cancer: Focus on Metabolism, Cytokines, and Immunity. Int. J. Mol. Sci. 20, 676 (2019).

[34]. Lee, B. Y. et al. Heterocellular OSM-OSMR signalling reprograms fibroblasts to promote pancreatic cancer growth and metastasis. Nat. Commun. 12, 7336 (2021).

[35]. Lankadasari, M. B., Mukhopadhyay, P., Mohammed, S. & Harikumar, K. B. TAMing pancreatic cancer: combat with a double edged sword. Mol. Cancer 18, 48 (2019).

[36]. Yang, Y. et al. M2 Macrophage-Derived Exosomes Promote Angiogenesis and Growth of Pancreatic Ductal Adenocarcinoma by Targeting E2F2. Mol. Ther. 29, 1226–1238 (2021).

[37]. Gross, A. et al. Technologies for Single-Cell Isolation. Int. J. Mol. Sci. 16, 16897–16919 (2015).

[38]. Nasir, I. et al. Tumor macrophage functional heterogeneity can inform the development of novel cancer therapies. Trends Immunol. 44, 971–985 (2023).

[39]. Yang, K., Yang, T., Yu, J., Li, F. & Zhao, X. Integrated transcriptional analysis reveals macrophage heterogeneity and macrophage-tumor cell interactions in the progression of pancreatic ductal adenocarcinoma. BMC Cancer 23, 199 (2023).

[40]. Marx, V. Method of the Year: spatially resolved transcriptomics. Nat. Methods 18, 9–14 (2021).

[41]. Gerlinger, M. et al. Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing. N. Engl. J. Med. 366, 883–892 (2012).

[42]. Multimodal Mapping of the Tumor and Peripheral Blood Immune Landscape in Human Pancreatic Cancer (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE155698)

[43]. Pancreatic Cancer with Xenium Human Multi-Tissue and Cancer Panel (https://www.10xgenomics.com/datasets/pancreatic-cancer-with-xenium-human-multi-tissue-and-cancer-panel-1-standard)


Cite this article

Li,M. (2025). Spatiotemporal Transcriptomic Dissection of Tumor-Associated Macrophage Heterogeneity and Dual-Function Molecular Nodes in Pancreatic Ductal Adenocarcinoma. Theoretical and Natural Science,113,61-83.

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The datasets used and/or analyzed during the current study will be available from the authors upon reasonable request.

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Volume title: Proceedings of ICBioMed 2025 Symposium: AI for Healthcare: Advanced Medical Data Analytics and Smart Rehabilitation

ISBN:978-1-80590-161-7(Print) / 978-1-80590-162-4(Online)
Editor:Alan Wang
Conference date: 17 October 2025
Series: Theoretical and Natural Science
Volume number: Vol.113
ISSN:2753-8818(Print) / 2753-8826(Online)

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References

[1]. Chouari, T. et al. Advances in Immunotherapeutics in Pancreatic Ductal Adenocarcinoma. Cancers 15, 4265 (2023).

[2]. Ilic, M. & Ilic, I. Epidemiology of pancreatic cancer. World J. Gastroenterol. 22, 9694 (2016).

[3]. Klein, A. P. Pancreatic cancer epidemiology: understanding the role of lifestyle and inherited risk factors. Nat. Rev. Gastroenterol. Hepatol. 18, 493–502 (2021).

[4]. Ho, T. T. B. et al. Combination of gemcitabine and anti-PD-1 antibody enhances the anticancer effect of M1 macrophages and the Th1 response in a murine model of pancreatic cancer liver metastasis. J. Immunother. Cancer 8, e001367 (2020).

[5]. Zhu, Y. et al. CSF1/CSF1R Blockade Reprograms Tumor-Infiltrating Macrophages and Improves Response to T-cell Checkpoint Immunotherapy in Pancreatic Cancer Models. Cancer Res. 74, 5057–5069 (2014).

[6]. Locati, M., Curtale, G. & Mantovani, A. Diversity, Mechanisms, and Significance of Macrophage Plasticity. Annu. Rev. Pathol. Mech. Dis. 15, 123–147 (2020).

[7]. Wynn, T. A., Chawla, A. & Pollard, J. W. Macrophage biology in development, homeostasis and disease. Nature 496, 445–455 (2013).

[8]. Mantovani, A., Marchesi, F., Malesci, A., Laghi, L. & Allavena, P. Tumour-associated macrophages as treatment targets in oncology. Nat. Rev. Clin. Oncol. 14, 399–416 (2017).

[9]. Wu, Y. et al. Macrophage cell membrane-based nanoparticles: a new promising biomimetic platform for targeted delivery and treatment. J. Nanobiotechnology 20, 542 (2022).

[10]. Cai, H., Zhang, Y., Wang, J. & Gu, J. Defects in Macrophage Reprogramming in Cancer Therapy: The Negative Impact of PD-L1/PD-1. Front. Immunol. 12, 690869 (2021).

[11]. Ruffell, B. & Coussens, L. M. Macrophages and Therapeutic Resistance in Cancer. Cancer Cell 27, 462–472 (2015).

[12]. DeNardo, D. G. & Ruffell, B. Macrophages as regulators of tumour immunity and immunotherapy. Nat. Rev. Immunol. 19, 369–382 (2019).

[13]. Ngambenjawong, C., Gustafson, H. H. & Pun, S. H. Progress in tumor-associated macrophage (TAM)-targeted therapeutics. Adv. Drug Deliv. Rev. 114, 206–221 (2017).

[14]. Dai, E. et al. Autophagy-dependent ferroptosis drives tumor-associated macrophage polarization via release and uptake of oncogenic KRAS protein. Autophagy 16, 2069–2083 (2020).

[15]. Mehla, K. & Singh, P. K. Metabolic Regulation of Macrophage Polarization in Cancer. Trends Cancer 5, 822–834 (2019).

[16]. Fendl, B., Berghoff, A. S., Preusser, M. & Maier, B. Macrophage and monocyte subsets as new therapeutic targets in cancer immunotherapy. ESMO Open 8, 100776 (2023).

[17]. Wei, C. et al. Crosstalk between cancer cells and tumor associated macrophages is required for mesenchymal circulating tumor cell-mediated colorectal cancer metastasis. Mol. Cancer 18, 64 (2019).

[18]. Wu, K. et al. Redefining Tumor-Associated Macrophage Subpopulations and Functions in the Tumor Microenvironment. Front. Immunol. 11, 1731 (2020).

[19]. Seyfried, T. N. & Huysentruyt, L. C. On the Origin of Cancer Metastasis. Crit. Rev. Oncog. 18, 43–73 (2013).

[20]. Cao, L., Meng, X., Zhang, Z., Liu, Z. & He, Y. Macrophage heterogeneity and its interactions with stromal cells in tumour microenvironment. Cell Biosci. 14, 16 (2024).

[21]. Zhang, X., Ji, L. & Li, M. O. Control of tumor-associated macrophage responses by nutrient acquisition and metabolism. Immunity 56, 14–31 (2023).

[22]. Zhang, X., Ji, L. & Li, M. O. Control of tumor-associated macrophage responses by nutrient acquisition and metabolism. Immunity 56, 14–31 (2023).

[23]. Gao, J., Liang, Y. & Wang, L. Shaping Polarization Of Tumor-Associated Macrophages In Cancer Immunotherapy. Front. Immunol. 13, 888713 (2022).

[24]. Mills, C. D., Lenz, L. L. & Harris, R. A. A Breakthrough: Macrophage-Directed Cancer Immunotherapy. Cancer Res. 76, 513–516 (2016).

[25]. Wang, H., Yung, M. M. H., Ngan, H. Y. S., Chan, K. K. L. & Chan, D. W. The Impact of the Tumor Microenvironment on Macrophage Polarization in Cancer Metastatic Progression. Int. J. Mol. Sci. 22, 6560 (2021).

[26]. Li, M. et al. Metabolism, metabolites, and macrophages in cancer. J. Hematol. Oncol.J Hematol Oncol 16, 80 (2023).

[27]. Halbrook, C. J. et al. Macrophage-Released Pyrimidines Inhibit Gemcitabine Therapy in Pancreatic Cancer. Cell Metab. 29, 1390-1399.e6 (2019).

[28]. Menjivar, R. E. et al. Arginase 1 is a key driver of immune suppression in pancreatic cancer. eLife 12, e80721 (2023).

[29]. Kuen, J., Darowski, D., Kluge, T. & Majety, M. Pancreatic cancer cell/fibroblast co-culture induces M2 like macrophages that influence therapeutic response in a 3D model. PLOS ONE 12, e0182039 (2017).

[30]. LaRue, M. M. et al. Metabolic reprogramming of tumor-associated macrophages by collagen turnover promotes fibrosis in pancreatic cancer. Proc. Natl. Acad. Sci. 119, e2119168119 (2022).

[31]. Kemp, S. B. et al. Apolipoprotein E Promotes Immune Suppression in Pancreatic Cancer through NF-κB–Mediated Production of CXCL1. Cancer Res. 81, 4305–4318 (2021).

[32]. Kemp, S. B. et al. Pancreatic cancer is marked by complement-high blood monocytes and tumor-associated macrophages. Life Sci. Alliance 4, e202000935 (2021).

[33]. Padoan, A., Plebani, M. & Basso, D. Inflammation and Pancreatic Cancer: Focus on Metabolism, Cytokines, and Immunity. Int. J. Mol. Sci. 20, 676 (2019).

[34]. Lee, B. Y. et al. Heterocellular OSM-OSMR signalling reprograms fibroblasts to promote pancreatic cancer growth and metastasis. Nat. Commun. 12, 7336 (2021).

[35]. Lankadasari, M. B., Mukhopadhyay, P., Mohammed, S. & Harikumar, K. B. TAMing pancreatic cancer: combat with a double edged sword. Mol. Cancer 18, 48 (2019).

[36]. Yang, Y. et al. M2 Macrophage-Derived Exosomes Promote Angiogenesis and Growth of Pancreatic Ductal Adenocarcinoma by Targeting E2F2. Mol. Ther. 29, 1226–1238 (2021).

[37]. Gross, A. et al. Technologies for Single-Cell Isolation. Int. J. Mol. Sci. 16, 16897–16919 (2015).

[38]. Nasir, I. et al. Tumor macrophage functional heterogeneity can inform the development of novel cancer therapies. Trends Immunol. 44, 971–985 (2023).

[39]. Yang, K., Yang, T., Yu, J., Li, F. & Zhao, X. Integrated transcriptional analysis reveals macrophage heterogeneity and macrophage-tumor cell interactions in the progression of pancreatic ductal adenocarcinoma. BMC Cancer 23, 199 (2023).

[40]. Marx, V. Method of the Year: spatially resolved transcriptomics. Nat. Methods 18, 9–14 (2021).

[41]. Gerlinger, M. et al. Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing. N. Engl. J. Med. 366, 883–892 (2012).

[42]. Multimodal Mapping of the Tumor and Peripheral Blood Immune Landscape in Human Pancreatic Cancer (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE155698)

[43]. Pancreatic Cancer with Xenium Human Multi-Tissue and Cancer Panel (https://www.10xgenomics.com/datasets/pancreatic-cancer-with-xenium-human-multi-tissue-and-cancer-panel-1-standard)