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Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity

Author

Listed:
  • Emelie Berglund

    (School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), Science for Life Laboratory)

  • Jonas Maaskola

    (School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), Science for Life Laboratory)

  • Niklas Schultz

    (Karolinska Institutet (KI), Science for Life Laboratory)

  • Stefanie Friedrich

    (Stockholm University, Science for Life Laboratory)

  • Maja Marklund

    (School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), Science for Life Laboratory)

  • Joseph Bergenstråhle

    (School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), Science for Life Laboratory)

  • Firas Tarish

    (Karolinska Institutet (KI), Science for Life Laboratory)

  • Anna Tanoglidi

    (University Uppsala Hospital)

  • Sanja Vickovic

    (School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), Science for Life Laboratory)

  • Ludvig Larsson

    (School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), Science for Life Laboratory)

  • Fredrik Salmén

    (School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), Science for Life Laboratory)

  • Christoph Ogris

    (Stockholm University, Science for Life Laboratory)

  • Karolina Wallenborg

    (Karolinska Institutet (KI), Science for Life Laboratory)

  • Jens Lagergren

    (School of Computer Science and Communication, Royal Institute of Technology (KTH), Science for Life Laboratory)

  • Patrik Ståhl

    (School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), Science for Life Laboratory)

  • Erik Sonnhammer

    (Stockholm University, Science for Life Laboratory)

  • Thomas Helleday

    (Karolinska Institutet (KI), Science for Life Laboratory)

  • Joakim Lundeberg

    (School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), Science for Life Laboratory)

Abstract

Intra-tumor heterogeneity is one of the biggest challenges in cancer treatment today. Here we investigate tissue-wide gene expression heterogeneity throughout a multifocal prostate cancer using the spatial transcriptomics (ST) technology. Utilizing a novel approach for deconvolution, we analyze the transcriptomes of nearly 6750 tissue regions and extract distinct expression profiles for the different tissue components, such as stroma, normal and PIN glands, immune cells and cancer. We distinguish healthy and diseased areas and thereby provide insight into gene expression changes during the progression of prostate cancer. Compared to pathologist annotations, we delineate the extent of cancer foci more accurately, interestingly without link to histological changes. We identify gene expression gradients in stroma adjacent to tumor regions that allow for re-stratification of the tumor microenvironment. The establishment of these profiles is the first step towards an unbiased view of prostate cancer and can serve as a dictionary for future studies.

Suggested Citation

  • Emelie Berglund & Jonas Maaskola & Niklas Schultz & Stefanie Friedrich & Maja Marklund & Joseph Bergenstråhle & Firas Tarish & Anna Tanoglidi & Sanja Vickovic & Ludvig Larsson & Fredrik Salmén & Chri, 2018. "Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity," Nature Communications, Nature, vol. 9(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-04724-5
    DOI: 10.1038/s41467-018-04724-5
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    Cited by:

    1. Shadi Shafighi & Agnieszka Geras & Barbara Jurzysta & Alireza Sahaf Naeini & Igor Filipiuk & Alicja Ra̧czkowska & Hosein Toosi & Łukasz Koperski & Kim Thrane & Camilla Engblom & Jeff E. Mold & Xinsong, 2024. "Integrative spatial and genomic analysis of tumor heterogeneity with Tumoroscope," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    2. S. Vickovic & B. Lötstedt & J. Klughammer & S. Mages & Å Segerstolpe & O. Rozenblatt-Rosen & A. Regev, 2022. "SM-Omics is an automated platform for high-throughput spatial multi-omics," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    3. Guidantonio Malagoli Tagliazucchi & Anna J. Wiecek & Eloise Withnell & Maria Secrier, 2023. "Genomic and microenvironmental heterogeneity shaping epithelial-to-mesenchymal trajectories in cancer," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
    4. Jie Liao & Jingyang Qian & Yin Fang & Zhuo Chen & Xiang Zhuang & Ningyu Zhang & Xin Shao & Yining Hu & Penghui Yang & Junyun Cheng & Yang Hu & Lingqi Yu & Haihong Yang & Jinlu Zhang & Xiaoyan Lu & Li , 2022. "De novo analysis of bulk RNA-seq data at spatially resolved single-cell resolution," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    5. Zhixing Zhong & Junchen Hou & Zhixian Yao & Lei Dong & Feng Liu & Junqiu Yue & Tiantian Wu & Junhua Zheng & Gaoliang Ouyang & Chaoyong Yang & Jia Song, 2024. "Domain generalization enables general cancer cell annotation in single-cell and spatial transcriptomics," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    6. Ziyang Tang & Zuotian Li & Tieying Hou & Tonglin Zhang & Baijian Yang & Jing Su & Qianqian Song, 2023. "SiGra: single-cell spatial elucidation through an image-augmented graph transformer," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    7. Simon Davis & Connor Scott & Janina Oetjen & Philip D. Charles & Benedikt M. Kessler & Olaf Ansorge & Roman Fischer, 2023. "Deep topographic proteomics of a human brain tumour," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    8. Bohan Li & Feng Bao & Yimin Hou & Fengji Li & Hongjue Li & Yue Deng & Qionghai Dai, 2024. "Tissue characterization at an enhanced resolution across spatial omics platforms with deep generative model," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    9. Linhua Wang & Mirjana Maletic-Savatic & Zhandong Liu, 2022. "Region-specific denoising identifies spatial co-expression patterns and intra-tissue heterogeneity in spatially resolved transcriptomics data," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    10. Yang Yang & Chenyu Chu & Li Liu & Chenbing Wang & Chen Hu & Shengan Rung & Yi Man & Yili Qu, 2023. "Tracing immune cells around biomaterials with spatial anchors during large-scale wound regeneration," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    11. Haoyang Li & Juexiao Zhou & Zhongxiao Li & Siyuan Chen & Xingyu Liao & Bin Zhang & Ruochi Zhang & Yu Wang & Shiwei Sun & Xin Gao, 2023. "A comprehensive benchmarking with practical guidelines for cellular deconvolution of spatial transcriptomics," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    12. Caravagna Giulio, 2020. "Measuring evolutionary cancer dynamics from genome sequencing, one patient at a time," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 19(4-6), pages 1-12, December.
    13. Maja Marklund & Niklas Schultz & Stefanie Friedrich & Emelie Berglund & Firas Tarish & Anna Tanoglidi & Yao Liu & Ludvig Bergenstråhle & Andrew Erickson & Thomas Helleday & Alastair D. Lamb & Erik Son, 2022. "Spatio-temporal analysis of prostate tumors in situ suggests pre-existence of treatment-resistant clones," Nature Communications, Nature, vol. 13(1), pages 1-18, December.

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