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Integrated prediction of lung cancer histology and molecular profiles from small bronchoscopic tumor specimens

Karadzovska-Kotevska, Marija LU orcid ; Karlsson, Anna LU ; Brunnström, Hans LU orcid ; Jönsson, Mats LU ; Kosieradzki, Jaroslaw LU ; Barath, Stefan LU ; Näslund, Anders LU ; Estberg, Christel LU ; Arbajian, Elsa LU and Rosengren, Frida LU , et al. (2026) In NPJ precision oncology 10.
Abstract

Treatment decisions in lung cancer rely on comprehensive molecular and histological characterization, but the limited amount of tumor tissue available from diagnostic procedures remains a major challenge. In this proof-of-concept study, we investigated whether preserving small bronchoscopic tumor specimens in RNAlater enables integrated molecular and histological profiling. Bronchial forceps biopsies and endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) specimens were collected during the diagnostic work-up of patients with suspected lung cancer, preserved in RNAlater, and used for DNA, RNA, and protein extraction. RNA was analyzed using NanoString gene expression profiling and RNA-sequencing to assess... (More)

Treatment decisions in lung cancer rely on comprehensive molecular and histological characterization, but the limited amount of tumor tissue available from diagnostic procedures remains a major challenge. In this proof-of-concept study, we investigated whether preserving small bronchoscopic tumor specimens in RNAlater enables integrated molecular and histological profiling. Bronchial forceps biopsies and endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) specimens were collected during the diagnostic work-up of patients with suspected lung cancer, preserved in RNAlater, and used for DNA, RNA, and protein extraction. RNA was analyzed using NanoString gene expression profiling and RNA-sequencing to assess treatment-relevant gene fusions, MET exon 14 skipping events, and histological subtypes. Somatic mutations were identified by massively parallel sequencing, and proteomics-based non-small cell lung cancer (NSCLC) subtypes were characterized by mass spectrometry. High-quality DNA, RNA, and proteins were successfully recovered from all tumors. Gene fusion analysis was successful in 44 of 45 cases. Gene expression-based histological classification showed good concordance with the clinical pathology diagnosis, although some discrepancies were observed. Mutation profiling was fully concordant with routine clinical testing, and comprehensive proteomic data were successfully generated. Collectively, these findings demonstrate that RNAlater-preserved bronchoscopic specimens provide material of sufficient quality for integrated multi-omics analyses, enabling comprehensive molecular profiling from a single, small tumor biopsy.

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Contribution to journal
publication status
published
subject
in
NPJ precision oncology
volume
10
article number
292
publisher
Springer Nature
external identifiers
  • pmid:42509268
ISSN
2397-768X
DOI
10.1038/s41698-026-01623-7
language
English
LU publication?
yes
additional info
© 2026. The Author(s).
id
af28e2b5-0302-4075-86ac-e070fe573c7e
date added to LUP
2026-07-29 10:26:18
date last changed
2026-07-29 13:43:33
@article{af28e2b5-0302-4075-86ac-e070fe573c7e,
  abstract     = {{<p>Treatment decisions in lung cancer rely on comprehensive molecular and histological characterization, but the limited amount of tumor tissue available from diagnostic procedures remains a major challenge. In this proof-of-concept study, we investigated whether preserving small bronchoscopic tumor specimens in RNAlater enables integrated molecular and histological profiling. Bronchial forceps biopsies and endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) specimens were collected during the diagnostic work-up of patients with suspected lung cancer, preserved in RNAlater, and used for DNA, RNA, and protein extraction. RNA was analyzed using NanoString gene expression profiling and RNA-sequencing to assess treatment-relevant gene fusions, MET exon 14 skipping events, and histological subtypes. Somatic mutations were identified by massively parallel sequencing, and proteomics-based non-small cell lung cancer (NSCLC) subtypes were characterized by mass spectrometry. High-quality DNA, RNA, and proteins were successfully recovered from all tumors. Gene fusion analysis was successful in 44 of 45 cases. Gene expression-based histological classification showed good concordance with the clinical pathology diagnosis, although some discrepancies were observed. Mutation profiling was fully concordant with routine clinical testing, and comprehensive proteomic data were successfully generated. Collectively, these findings demonstrate that RNAlater-preserved bronchoscopic specimens provide material of sufficient quality for integrated multi-omics analyses, enabling comprehensive molecular profiling from a single, small tumor biopsy.</p>}},
  author       = {{Karadzovska-Kotevska, Marija and Karlsson, Anna and Brunnström, Hans and Jönsson, Mats and Kosieradzki, Jaroslaw and Barath, Stefan and Näslund, Anders and Estberg, Christel and Arbajian, Elsa and Rosengren, Frida and Veerla, Srinivas and Lehtiö, Janne and Orre, Lukas M and Staaf, Johan and Planck, Maria}},
  issn         = {{2397-768X}},
  language     = {{eng}},
  month        = {{07}},
  publisher    = {{Springer Nature}},
  series       = {{NPJ precision oncology}},
  title        = {{Integrated prediction of lung cancer histology and molecular profiles from small bronchoscopic tumor specimens}},
  url          = {{http://dx.doi.org/10.1038/s41698-026-01623-7}},
  doi          = {{10.1038/s41698-026-01623-7}},
  volume       = {{10}},
  year         = {{2026}},
}