Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Correspondence
  • Published:

Reply to ‘Enhancing spatial transcriptomics in clear-cell renal cell carcinoma’

Nature Reviews Urology volume 22, page 790 (2025)Cite this article

Subjects

We appreciate the thoughtful feedback from Chengming Li, Junxiu Sheng and Guangzhen Wu and the constructive effort to expand upon the translational potential of spatial transcriptomics in clear-cell renal cell carcinoma (ccRCC) detailed in our recent Review1 (Lessons learned from spatial transcriptomic analyses in clear-cell renal cell carcinoma. Nat. Rev. Urol. https://doi.org/10.1038/s41585-024-00980-x; 2025)1, which are valuable (Enhancing spatial transcriptomics in clear-cell renal cell carcinoma. Nat. Rev. Urol. https://doi.org/10.1038/s41585-025-01085-9; 2025)2. We have taken the opportunity to respond to the points raised.

We agree that transcript and protein levels often diverge and that proteomic and metabolomic validation can strengthen the functional interpretation of transcriptomic data. However, we do want to highlight that, in the context of biomarker development, transcriptional patterns alone have shown predictive value3,4,5,6 and in certain circumstances might be sufficient to delineate clinically relevant phenotypes without protein-level confirmation.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on SpringerLink
  • Instant access to the full article PDF.

USD 39.95

Prices may be subject to local taxes which are calculated during checkout

References

  1. Jespersen, J., Lindgaard, C., Iisager, L., Ahrenfeldt, J. & Lyskjær, I. Lessons learned from spatial transcriptomic analyses in clear-cell renal cell carcinoma. Nat. Rev. Urol. https://doi.org/10.1038/s41585-024-00980-x (2025).

    Article  PubMed  Google Scholar 

  2. Li, C., Sheng, J. & Wu, G. Enhancing spatial transcriptomics in clear-cell renal cell carcinoma. Nat. Rev. Urol. https://doi.org/10.1038/s41585-025-01085-9 (2025).

    Article  PubMed  Google Scholar 

  3. Zheng, Y., Carrillo-Perez, F., Pizurica, M., Heiland, D. H. & Gevaert, O. Spatial cellular architecture predicts prognosis in glioblastoma. Nat. Commun. 14, 4122 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Smelik, M. et al. Combining spatial transcriptomics, pseudotime, and machine learning enables discovery of biomarkers for prostate cancer. Cancer Res. 85, 2514–2526 (2025).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Arora, R. et al. Spatial transcriptomics reveals distinct and conserved tumor core and edge architectures that predict survival and targeted therapy response. Nat. Commun. 14, 5029 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Li, R. et al. Mapping single-cell transcriptomes in the intra-tumoral and associated territories of kidney cancer. Cancer Cell 40, 1583–1599.e10 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Blise, K. E., Sivagnanam, S., Banik, G. L., Coussens, L. M. & Goecks, J. Single-cell spatial architectures associated with clinical outcome in head and neck squamous cell carcinoma. npj Precis. Oncol. 6, 10 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Sorin, M. et al. Single-cell spatial landscapes of the lung tumour immune microenvironment. Nature 614, 548–554 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark

    Jesper Jespersen & Iben Lyskjær

Authors
  1. Jesper Jespersen
    View author publications

    Search author on:PubMed Google Scholar

  2. Iben Lyskjær
    View author publications

    Search author on:PubMed Google Scholar

Corresponding author

Correspondence to Iben Lyskjær.

Ethics declarations

Competing interests

The authors declare no competing interests.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Jespersen, J., Lyskjær, I. Reply to ‘Enhancing spatial transcriptomics in clear-cell renal cell carcinoma’. Nat Rev Urol 22, 790 (2025). https://doi.org/10.1038/s41585-025-01086-8

Download citation

  • Published:

  • Version of record:

  • Issue date:

  • DOI: https://doi.org/10.1038/s41585-025-01086-8

Search

Advanced search

Quick links

Nature Briefing: Translational Research

Sign up for the Nature Briefing: Translational Research newsletter — top stories in biotechnology, drug discovery and pharma.

Get what matters in translational research, free to your inbox weekly. Sign up for Nature Briefing: Translational Research