Automated identification of cell populations in flow cytometry data with transformers

Wödlinger, Matthias; Reiter, Michael J.; Weijler, Lisa; Maurer‐Granofszky, Margarita; Schumich, Angela; Sajaroff, E.O.; Groeneveld-Krentz, Stefanie; Rossi, Jorge; Karawajew, Leonid; Ratei, Richard; Dworzak, Michael

doi:10.1016/j.compbiomed.2022.105314

Cited by 16 publications

(15 citation statements)

References 15 publications

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“…Flow cytometry (FC) is a reliable technique for evaluation of cancer cell progression 72 – 74 . Illumination of the cells by lasers can identify the stained propidium iodide (PI) DNA cell content in stoichiometric population value.…”

Section: Resultsmentioning

confidence: 99%

Development of spiro-3-indolin-2-one containing compounds of antiproliferative and anti-SARS-CoV-2 properties

Fawazy

Panda

Mostafa

et al. 2022

Sci Rep

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A series of 1″-(alkylsulfonyl)-dispiro[indoline-3,2′-pyrrolidine-3′,3″-piperidine]-2,4″-diones 6a‒o has been synthesized through regioselective multi-component azomethine dipolar cycloaddition reaction of 1-(alkylsulfonyl)-3,5-bis(ylidene)-piperidin-4-ones 3a‒h. X-ray diffraction studies (6b‒d,h) confirmed the structures. The majority of the synthesized analogs reveal promising antiproliferation properties against a variety of human cancer cell lines (MCF7, HCT116, A431 and PaCa2) with good selectivity index towards normal cell (RPE1). Some of the synthesized agents exhibit potent inhibitory properties against the tested cell lines with higher efficacies than the standard references (sunitinib and 5-fluorouracil). Compound 6m is the most potent. Multi-targeted inhibitory properties against EGFR and VEGFR-2 have been observed for the synthesized agents. Flow cytometry supports the antiproliferation properties and shows the tested agents as apoptosis and necrosis forming. Vero cell viral infection model demonstrates the anti-SARS-CoV-2 properties of the synthesized agents. Compound 6f is the most promising (about 3.3 and 4.8 times the potency of the standard references, chloroquine and hydroxychloroquine). QSAR models explain and support the observed biological properties.

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Section: Resultsmentioning

confidence: 99%

Development of spiro-3-indolin-2-one containing compounds of antiproliferative and anti-SARS-CoV-2 properties

Fawazy

Panda

Mostafa

et al. 2022

Sci Rep

View full text Add to dashboard Cite

show abstract

“…Examples include Gaussian models, 32 neural networks 33,34,43 and linear discriminant analysis 44 . The European Autoflow Consortium and collaborators have used Gaussian mixture models and transformer networks to determine computational MRD in B‐ALL, demonstrating high F1‐scores 32,33 . Recently, Salama et al used deep neural networks to detect CLL MRD, demonstrating excellent correlation (Pearson's r > 0.99) and concordance (97.1%) with expert analysis in 34 validation cases 34 .…”

Section: Discussionmentioning

confidence: 99%

“…32,34 In supervised algorithms, the training set consists of annotated FCS files in which cells have been manually labelled by an expert. Examples include Gaussian models, 32 neural networks 33,34,43 and linear discriminant analysis. 44 The European Autoflow Consortium and collaborators have used Gaussian mixture models and transformer networks to determine computational MRD in B-ALL, demonstrating high F1-scores.…”

Section: Discussionmentioning

confidence: 99%

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Computational flow cytometry provides accurate assessment of measurable residual disease in chronic lymphocytic leukaemia

Nguyen

Baldwin

et al. 2023

Br J Haematol

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SummaryUndetectable measurable residual disease (MRD) is associated with favourable clinical outcomes in chronic lymphocytic leukaemia (CLL). While assessment is commonly performed using multiparameter flow cytometry (MFC), this approach is associated with limitations including user bias and expertise that may not be widely available. Implementation of unsupervised clustering algorithms in the laboratory can address these limitations and have not been previously reported in a systematic quantitative manner. We developed a computational pipeline to assess CLL MRD using FlowSOM. In the training step, a self‐organising map was generated with nodes representing the full breadth of normal immature and mature B cells along with disease immunophenotypes. This map was used to detect MRD in multiple validation cohorts containing a total of 456 samples. This included an evaluation of atypical CLL cases and samples collected from two different laboratories. Computational MRD showed high correlation with expert analysis (Pearson's r > 0.99 for typical CLL). Binary classification of typical CLL samples as either MRD positive or negative demonstrated high concordance (>98%). Interestingly, computational MRD detected disease in a small number of atypical CLL cases in which MRD was not detected by expert analysis. These results demonstrate the feasibility and value of automated MFC analysis in a diagnostic laboratory.

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“…Flow cytometry (FC) is a reliable technique for evaluation of cancer cell progression. [72][73][74] Illumination of the cells by lasers can identify the stained propidium iodide (PI) DNA cell content in stoichiometric population value. This is a commonly accessible methodology for studying cancer cell antiproliferation and cell cycle phase suppression.…”

Section: Cell Cycle Studiesmentioning

confidence: 99%

Spiro-3-indolin-2-ones: Synthesis, biological properties and computational studies

Fawazy

Panda

Mostafa

et al. 2022

Preprint

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A series of 1''-(alkylsulfonyl)-dispiro[indoline-3,2'-pyrrolidine-3',3''-piperidine]-2,4''-diones 6a‒o has been synthesized through regioselective multi-component azomethine dipolar cycloaddition reaction of 1-(alkylsulfonyl)-3,5-bis(ylidene)-piperidin-4-ones 3a‒h. X-ray diffraction studies (6b‒d,h) confirmed the structures. The majority of the synthesized analogs reveal promising antiproliferation properties against a variety of human cancer cell lines (MCF7, HCT116, A431 and PaCa2) with good selectivity index towards normal cell (RPE1). Some of the synthesized agents exhibit potent inhibitory properties against the tested cell lines with higher efficacies than the standard references (sunitinib and 5-fluorouracil). Compound 6m is the most potent. Multi-targeted inhibitory properties against EGFR and VEGFR-2 have been observed for the synthesized agents. Flow cytometry supports the antiproliferation properties and shows the tested agents as apoptosis and necrosis forming. Vero cell viral infection model demonstrates the anti-SARS-CoV-2 properties of the synthesized agents. Compound 6f is the most promising (about 3.3 and 4.8 times the potency of the standard references, chloroquine and hydroxychloroquine). QSAR models explain and support the observed biological properties.

show abstract

Automated identification of cell populations in flow cytometry data with transformers

Cited by 16 publications

References 15 publications

Development of spiro-3-indolin-2-one containing compounds of antiproliferative and anti-SARS-CoV-2 properties

Development of spiro-3-indolin-2-one containing compounds of antiproliferative and anti-SARS-CoV-2 properties

Computational flow cytometry provides accurate assessment of measurable residual disease in chronic lymphocytic leukaemia

Spiro-3-indolin-2-ones: Synthesis, biological properties and computational studies

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