i-Cellulo: a SaaS platform for the automatic statistical analysis of cell impedance signals

HAL Id: hal-01670076

https://hal.archives-ouvertes.fr/hal-01670076

Submitted on 21 Dec 2017

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i-Cellulo: a SaaS platform for the automatic statistical analysis of cell impedance signals

Levy Batista, Yaël Kolasa, Thierry Bastogne

To cite this version:

Levy Batista, Yaël Kolasa, Thierry Bastogne. i-Cellulo: a SaaS platform for the automatic statistical analysis of cell impedance signals. 8th International Meeting on Statistical Methods in Biopharmacy, SMB 2017, Sep 2017, Paris, France. �hal-01670076�

i-Cellulo: a SaaS platform for the automatic statistical analysis of cell impedance signals

L. BATISTA ^1,2,3 , Y. KOLASA ³ , T. BASTOGNE ^1,2,3

1 CRAN, ² INRIA BIGS, ³ CYBERnano

Objectives. Label-free methods such as cell impedance assays are in vitro tests increasingly used in drug development. An indirect difficulty with those technologies is the large amount of kinetic responses to be processed. Our objective is to automate the processing and analysis of those data with a web computational server available to all biologists and able to perform multivariate tests, response profile clustering and dynamic AC50 estimation.

The proposed solution relies on a SaaS platform in which R-language algorithms have been implemented for the on-line processing of cell impedance signals. Three generic statistical problems are addressed: clustering of response profiles to screen compounds, multivariate testing to compare their activity and AC50 estimation to determine their concentration effects. ANOVA, Kruskall-Wallis and Tuckey’s range tests have been implemented for the multivariate testing. Hierarchical clustering based on Singular Spectrum Analysis were used for the non-supervised response profile classification. A Hill’s model structure and a maximum likelihood estimator were adopted for the AC50 calculation.

Fig.4: Estimation of the AC50 profiles. Left: AC50 values estimation based on the Hill’s model. Right: time profil of the AC50 estimates

Results

Hundreds of tests were carried out on real in vitro signals to assess the practical relevance of i-Cellulo for the fast analysis and characterization of anti-cancer activities in early steps of drug development. Results clearly show the ability of this web-based solution to correctly discriminate, classify, compare and rank the anti-cancer responses of tested compounds compared to gold standards.

Conclusion

With the advent of real-time cell measurement technologies in preclinical tests, new services for the analysis of high-content data are needed. i–Cellulo is a solution to that challenge and allows biologists to speed up their data analysis and facilitate interpretation of their results.

8-th International Meeting on Statistical Methods in Biopharmacy, Paris, Sep. 2017

Fig.3: Clustering Cell Index P r o f i l e s f o r S c r e e n i n g A p p l i c a t i o n s . L e f t : dendrogram of culture wells. Right: 3 clusters of response.

Fig.2: Multiple test of CI responses. Left: groups of CI responses to be compared.

Right: ANOVA results

Fig.1: Comparing 2 groups of cell impedance profiles.

Left: original CI responses to be compared. Right: t-Test results

Methods

Our SaaS pla(orm saas.cybernano.eu

Our Algos Data

i-Report

Data Results Biologist

Clinician

Biosta;s;cian Supervisor

Labs & Hospitals

0 10 20 30 40 50 60 70

02468

Black: Group 1 − Red: Group 2 Time samples

Mean CI values

0 10 20 30 40 50 60 70

02468

Results of the t−Test

Black: Group 1 − Red: Group 2 (x: significant difference)

Time samples

Mean CI values

10 20 30 40 50 60 70

0.00.51.01.5

Double−Normalized Impedance Profiles

Black: reference, Gray: reference (edge), Colors: treatment wells Time (h)

Normalized CI values (A.U.)

1 2 3 4 5 6 7 8 9 10

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0.00.51.01.52.0

ANOVA Test

(dot: NS variation, circle: significant variation, solid circle: validated variation)

Time (h)

Mean & Normalized CI values (A.U.)

Black: Control − Colors: tested groups − p=0.05)

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0.00.51.01.5

Clusters of Similar CI Profiles

Time (h)

Cell Index (A.U)

P1B4 P1F3 P1A4 P1G3 P1C4 P1C3 P1A3 P1G4 P1E4 P1E3 P1D3 P1D4 P1B3 P1F4 P1H3 P1H4

Cluster Dendrogram

Wells Distance 051015

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0.10.20.51.02.05.010.020.0

Time variation of the IC50 values

(Red): Absolute IC50, (Black): Relative IC50, Solid circles: confident IC50 values Time (h)

IC50 (uM)

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0.1 0.2 0.5 1.0 2.0 5.0 10.0

0.00.51.01.5

AC50a = 4.68 uM − AC50r = 4.2 uM

Measured values (red), Predicted values (black), Relative AC50 (blue), Absolute AC50 (green)

Concentration (uM)

Normalized CI