A Protocol for Low-Input RNA-Sequencing of Patients with Febrile Neutropenia Captures Relevant Immunological Information
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A Protocol for Low-Input RNA-Sequencing of Patients with Febrile Neutropenia Captures Relevant Immunological Information. / Probst, Victoria; Smedegaard, Lotte Møller; Simonyan, Arman; Guo, Yuliu; Østrup, Olga; Dungu, Kia Hee Schultz; Vissing, Nadja Hawwa; Nygaard, Ulrikka; Bagger, Frederik Otzen.
In: International Journal of Molecular Sciences, Vol. 24, No. 12, 10251, 2023.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - A Protocol for Low-Input RNA-Sequencing of Patients with Febrile Neutropenia Captures Relevant Immunological Information
AU - Probst, Victoria
AU - Smedegaard, Lotte Møller
AU - Simonyan, Arman
AU - Guo, Yuliu
AU - Østrup, Olga
AU - Dungu, Kia Hee Schultz
AU - Vissing, Nadja Hawwa
AU - Nygaard, Ulrikka
AU - Bagger, Frederik Otzen
N1 - Publisher Copyright: © 2023 by the authors.
PY - 2023
Y1 - 2023
N2 - Improved methods are needed for diagnosing infectious diseases in children with cancer. Most children have fever for other reasons than bacterial infection and are exposed to unnecessary antibiotics and hospital admission. Recent research has shown that host whole blood RNA transcriptomic signatures can distinguish bacterial infection from other causes of fever. Implementation of this method in clinics could change the diagnostic approach for children with cancer and suspected infection. However, extracting sufficient mRNA to perform transcriptome profiling by standard methods is challenging due to the patient’s low white blood cell (WBC) counts. In this prospective cohort study, we succeeded in sequencing 95% of samples from children with leukaemia and suspected infection by using a low-input protocol. This could be a solution to the issue of obtaining sufficient RNA for sequencing from patients with low white blood cell counts. Further studies are required to determine whether the captured immune gene signatures are clinically valid and thus useful to clinicians as a diagnostic tool for patients with cancer and suspected infection.
AB - Improved methods are needed for diagnosing infectious diseases in children with cancer. Most children have fever for other reasons than bacterial infection and are exposed to unnecessary antibiotics and hospital admission. Recent research has shown that host whole blood RNA transcriptomic signatures can distinguish bacterial infection from other causes of fever. Implementation of this method in clinics could change the diagnostic approach for children with cancer and suspected infection. However, extracting sufficient mRNA to perform transcriptome profiling by standard methods is challenging due to the patient’s low white blood cell (WBC) counts. In this prospective cohort study, we succeeded in sequencing 95% of samples from children with leukaemia and suspected infection by using a low-input protocol. This could be a solution to the issue of obtaining sufficient RNA for sequencing from patients with low white blood cell counts. Further studies are required to determine whether the captured immune gene signatures are clinically valid and thus useful to clinicians as a diagnostic tool for patients with cancer and suspected infection.
KW - febrile neutropenia
KW - low-input RNA-sequencing
KW - neutropenia
KW - paediatrics
KW - transcriptomics
KW - white blood cells
UR - http://www.scopus.com/inward/record.url?scp=85164020950&partnerID=8YFLogxK
U2 - 10.3390/ijms241210251
DO - 10.3390/ijms241210251
M3 - Journal article
C2 - 37373397
AN - SCOPUS:85164020950
VL - 24
JO - International Journal of Molecular Sciences (Online)
JF - International Journal of Molecular Sciences (Online)
SN - 1661-6596
IS - 12
M1 - 10251
ER -
ID: 369354883