From genotype to phenotype: decoding mutations in blasts by holo-tomographic flow cytometry

Daniele Pirone; Concetta Di Natale; Maria Di Summa; Nicola Mosca; Giusy Giugliano; Michela Schiavo; Daniele Florio; Daniela Marasco; Pier Luca Maffettone; Lisa Miccio; Pasquale Memmolo; Pietro Ferraro

doi:10.1038/s41377-025-01913-y

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From genotype to phenotype: decoding mutations in blasts by holo-tomographic flow cytometry

Original Articles

- From genotype to phenotype: decoding mutations in blasts by holo-tomographic flow cytometry
- Light: Science & Applications Vol. 14, Issue 9, Pages: 2445-2462(2025)
- Affiliations：
  
  1.CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Pozzuoli, Italy
  2.Dipartimento di Ingegneria Chimica, dei Materiali e della Produzione Industriale. Università di Napoli "Federico II", Napoli, Italy
  3.CNRSTIIMA, Institute of Intelligent Industrial Technologies and Systems for Advanced Manufacturing, National Research Council of Italy, Bari, Italy
  4.Department of Mathematics and Physics, University of Campania "Luigi Vanvitelli", Caserta, Italy
  5.TIGEM, Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
  6.Department of Advanced Biomedical Science, University of Naples "Federico II", Napoli, Italy
  7.Department of Pharmacy, University of Naples "Federico II", Napoli, Italy
- Author bio：
  
  Concetta Di Natale (concetta.dinatale@unina.it)
  Lisa Miccio (lisa.miccio@isasi.cnr.it)
  Pasquale Memmolo (pasquale.memmolo@isasi.cnr.it)
- Funds：
- DOI：10.1038/s41377-025-01913-y
  CLC：
- Received：28 October 2024，
  
  Revised：2025-05-16，
  
  Accepted：30 May 2025，
  
  Published Online：02 July 2025，
  
  Published：30 September 2025
- Accepted：
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Pirone, D. et al. From genotype to phenotype: decoding mutations in blasts by holo-tomographic flow cytometry. Light: Science & Applications, 14, 2445-2462 (2025).
DOI：

Pirone, D. et al. From genotype to phenotype: decoding mutations in blasts by holo-tomographic flow cytometry. Light: Science & Applications, 14, 2445-2462 (2025). DOI： 10.1038/s41377-025-01913-y.

摘要

Abstract

Cup-like nuclear morphological alterations in acute myeloid leukemia (AML) blasts have been widely correlated with Nucleophosmin 1 (NPM1) mutations. NPM1-mutated AML has earned recognition as a distinct entity among myeloid tumors

but the absence of a thoroughly established tool for its morphological analysis remains a notable gap. Holographic tomography (HT) can offer a label-free solution for quantitatively assessing the 3D shape of the nucleus based on the volumetric variations of its refractive indices (RIs). However

traditional HT methods analyze adherent cells in a 2D layer

leading to non-isotropic reconstructions due to missing cone artifacts. Here we show for the first time that holo-tomographic flow cytometry (HTFC) achieves quantitative specificity and precise capture of the nucleus volumetric shape in AML cells in suspension. To retrieve nucleus specificity in label-free RI tomograms of flowing AML cells

we conceive and demonstrate in a real-world clinical case a novel strategy for segmenting 3D concave nuclei. This method implies that the correlation between the "phenotype" and "genotype" of nuclei is demonstrated through HTFC by creating a challenging link not yet explored between the aberrant morphological features of AML nuclei and NPM1 mutations. We conduct an ensemble-level statistical characterization of NPM1-wild type and NPM1-mutated blasts to discern their complex morphological and biophysical variances. Our findings suggest that characterizing cup-like nuclei in NPM1-related AML cells by HTFC may enhance the diagnostic approach for these tumors. Furthermore

we integrate virtual reality to provide an immersive fruition of morphological changes in AML cells within a true 3D environment.

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references

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