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A Protocol for Low-Input RNA-Sequencing of Patients with Febrile Neutropenia Captures Relevant Immunological
Victoria Probst1, Lotte Møller Smedegaard2, Arman Simonyan1
1Department of Genomic Medicine, Rigshospitalet, 2100 Copenhagen, Denmark.
Insights
Diagnosing infections in children with cancer is difficult. A new low-input RNA sequencing method successfully analyzed blood samples from children with leukemia, potentially improving infection diagnosis.
Area of Science:
- Pediatric Oncology
- Infectious Disease Diagnostics
- Molecular Biology
Background:
- Accurate diagnosis of infectious diseases in pediatric cancer patients is crucial to avoid unnecessary antibiotic use and hospitalizations.
- Fever in these patients often stems from non-bacterial causes, complicating treatment decisions.
- Host whole blood RNA transcriptomic signatures show promise in differentiating bacterial infections from other fever causes.
Purpose of the Study:
- To evaluate a low-input RNA sequencing protocol for transcriptome profiling in pediatric cancer patients with suspected infections.
- To address the challenge of low white blood cell (WBC) counts hindering RNA extraction in this population.
Main Methods:
- A prospective cohort study was conducted.
- A novel low-input RNA extraction protocol was employed for whole blood samples.
- RNA sequencing was performed on samples from children with leukemia and suspected infections.
Main Results:
- The low-input protocol enabled successful RNA sequencing in 95% of the analyzed samples.
- This method overcomes the limitation of low white blood cell (WBC) counts in pediatric cancer patients.
- Immune gene signatures were captured for potential diagnostic use.
Conclusions:
- The developed low-input RNA sequencing protocol is a viable solution for transcriptome profiling in children with cancer and low WBC counts.
- Further research is needed to validate the clinical utility of captured immune gene signatures as a diagnostic tool for suspected infections in this vulnerable group.
Abstract:
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.
