FlowCT for the analysis of large immunophenotypic datasets and biomarker discovery in cancer immunology
Cirino Botta 1 , Catarina Da Silva Maia 2 , Juan-José Garcés 3 , Rosalinda Termini 4 , Cristina Perez 5 , Irene Manrique 6 , Leire Burgos 1 , Aintzane Zabaleta 7 , Diego Alignani 8 , Sarai Sarvide 9 , Juana Merino 10 , Noemi Puig 11 , Maria-Teresa Cedena 12 , Marco Rossi 13 , Pierfrancesco Tassone 13 , Massimo Gentile 14 , Pierpaolo Correale 15 , Ivan Borrello 16 , Evangelos Terpos 17 , Tomas Jelinek 18 , Artur Paiva 19 , Aldo M Roccaro 20 , Hartmut Goldschmidt 21 , Hervé Avet-Loiseau 22 , Laura Rosinol Dachs 23 , Maria-Victoria Mateos 24 , Joaquin Martinez-Lopez 25 , Juan-Jose Lahuerta 26 , Joan Bladé 27 , Jesus F San-Miguel 28 , Bruno Paiva 29
Large-scale immune monitoring is becoming routinely used in clinical trials to identify determinants of treatment responsiveness, particularly to immunotherapies.
Flow cytometry remains one of the most versatile and high throughput approaches for single-cell analysis; however, manual interpretation of multidimensional data poses a challenge to capture full cellular diversity and provide reproducible results.
We present FlowCT, a semi-automated workspace empowered to analyze large datasets that includes pre-processing, normalization, multiple dimensionality reduction techniques, automated clustering and predictive modeling tools.
As a proof of concept, we used FlowCT to compare the T cell compartment in bone marrow (BM) vs peripheral blood (PB) of patients with smoldering multiple myeloma (MM); identify minimally-invasive immune biomarkers of progression from smoldering to active MM; define prognostic T cell subsets in the BM of patients with active MM after treatment intensification; and assess the longitudinal effect of maintenance therapy in BM T cells. A total of 354 samples were analyzed and immune signatures predictive of malignant transformation in 150 smoldering MM patients (hazard ratio [HR]: 1.7; P <.001), and of progression-free (HR: 4.09; P <.0001) and overall survival (HR: 3.12; P =.047) in 100 active MM patients, were identified.
New data also emerged about stem cell memory T cells, the concordance between immune profiles in BM vs PB and the immunomodulatory effect of maintenance therapy. FlowCT is a new open-source computational approach that can be readily implemented by research laboratories to perform quality-control, analyze high-dimensional data, unveil cellular diversity and objectively identify biomarkers in large immune monitoring studies.
CITATION Blood Adv. 2022 Jan 25;6(2):690-703. doi: 10.1182/bloodadvances.2021005198.