Effective discovery of synergistic combinations by in silico prioritization

Oss, 20 March 2019 – Successful cancer therapies are often based on drug combinations to halt cancer growth and prevent resistance mechanisms. A good way to find novel, unexpected synergistic drug combinations is unbiased high throughput screening on cancer cell lines, such as the NTRC SynergyScreen™ platform. The effort involved in handling large numbers of possible combinations may constrain broad screening. NTRC therefore launches two additions to its SynergyScreen™ platform: diversity-based library screening and in silico prioritization.
In diversity-based screening, the drug of interest is screened in combination with a set of 43-exemplars that were selected from a library of 162 therapeutics [1]. The library represents the known variety of anti-cancer mechanisms under investigation and approved for clinical use (Figure 1). Only if synergistic hits are found for an exemplar, the other compounds from the exemplar’s cluster are screened in a second step. In an example for the PARP inhibitor niraparib, screening of 50% less compounds identified more than 70% of the validated synergistic hits from the broad screen.
In the in silico prioritization workflow, the Oncolines™ drug responses of the compound of interest are combined with known clinically validated synthetic lethal interactions [2], to generate a list of likely synergistic partners for the single agent. This list is then prioritized for actual combination screening. The in silico prioritization workflow was highly succesful in predicting synergistic pairs that are reported in the combination screening literature, and in NTRC internal screens.
The new technologies will be presented at the American Association of Cancer Research meeting in Atlanta, April 1st, abstract no. 2158.


Figure 1: Anti-cancer mechanisms and their exemplars (red dots).

Literature references
1. Uitdehaag et al. (2016) Mol Cancer Ther 15, 3097-3109.
2. Lee et al. (2018) Nature Communications, 9, 2546..

About NTRC

NTRC is a precision medicine company dedicated to the development of new anti-cancer drugs. NTRC facilitates the development of novel therapies by providing custom-based assays with primary patient material and high-throughput cancer cell line profiling services (Oncolines™, GeneNominator™, SynergyFinder™ and SynergyScreen™), as well as target residence time measurements for protein kinases (ResidenceTimer™) on a fee-for-service basis. Arginase Gold™ and NFK GreenScreen™ are assay read-outs for the cancer immunotherapy drug targets Arginase-1, and IDO1 and TDO respectively. Assay kits are supplied to clients globally. For more information please visit www.ntrc.nl or contact info@ntrc.nl

 

Tissue-type analysis included in Oncolines™ cancer cell line profiling

Oss, 12 February 2019 – The approval label of many drugs specifically states use in cancer of a certain tissue type, for instance, breast or lung. In any approach to precision medicine, cancer lineage should therefore be taken into account. NTRC’s Oncolines™ cancer cell line profiling service1,2 now includes such tissue-type analysis, indicating whether drugs or drug candidates show preferential activity in a certain cancer tissue type. Annotation of disease indication conforms to the Cellosaurus database.3 The associated tissue types are hierarchically organized according to the Oncotree classification.4 Figure 1 shows an example in which Oncolines™ tissue-type analysis reveals that the CDK4/6 inhibitor ribociclib (Kisqali®) potently inhibits proliferation of cell lines of neuroblastoma origin. This finding supports ongoing clinical studies.5


Figure 1: Tissue-based boxplot of the CDK4/6 inhibitor ribociclib. Ribociclib is in under investigation in clinical trials for neuroblastoma.

About Oncolines™
NTRC Oncolines™ is a screening service on a panel of 102 cancer cell lines, which enables drug sensitivity analyses, biomarker discovery and the mapping of drug candidates within the competitive field. The panel yields highly reproducible data and captures drug response through various metrics.1,2 Gene mutations, copy number variations and gene expression variations can be associated with drug response by bioinformatics. Validation of markers is part of our follow-up workflow. The tissue type boxplot is part of the standard analysis included in Oncolines™ profiling.

Literature references
1. Uitdehaag et al. (2016) Mol Cancer Ther 15, 3097-3109.
2. Uitdehaag et al. (2019) Mol Cancer Ther, 18, 470-481.
3. Bairoch A. (2018) The Cellosaurus, a cell line knowledge resource. J Biomol Tech 29, 25-38.
4. Memorial Sloan Kettering Cancer Center http://oncotree.mskcc.org/#/home
5. Geoerger et al. (2017) Clin Cancer Res 23, 2433-2441

About NTRC

NTRC is a precision medicine company dedicated to the development of new anti-cancer drugs. NTRC facilitates the development of novel therapies by providing custom-based assays with primary patient material and high-throughput cancer cell line profiling services (Oncolines™, GeneNominator™, SynergyFinder™ and SynergyScreen™), as well as target residence time measurements for protein kinases (ResidenceTimer™) on a fee-for-service basis. Arginase Gold™ and NFK GreenScreen™ are assay read-outs for the cancer immunotherapy drug targets Arginase-1, and IDO1 and TDO respectively. Assay kits are supplied to clients globally. For more information please visit www.ntrc.nl or contact info@ntrc.nl

 

NTRC expands ResidenceTimer™ kinase panel with CDKs, MERTK, TYRO3 and GSKβ

Oss, 20 November 2018 – Analysis of drug binding kinetics is important in predicting the physiological activity and selectivity of drugs. To make such experiments readily accessible on a single platform, NTRC has developed its ResidenceTimer™ service. It comprises over 72 kinase drug targets, all validated by reproducible binding of reference drugs [1].
As of today, NTRC has added six new important kinase drug targets to its ResidenceTimer™ service: CDK9/CycK, CDK9/CycT1, CDK7/CycH/MAT1, MERTK, TYRO3, and GSK3β. The cyclin dependent kinases CDK7 and CDK9 play a role in transcription and are important targets for the treatment of cancer and immune-related diseases. For instance, CDK7 is overexpressed in some types of breast cancer, and CDK9 is overexpressed in pancreatic cancer. MERTK, TYRO3 and GSK3β are important drug targets for cancer and immune-related diseases. After immobilizing the kinases, NTRC scientists were able to show that for instance dinaciclib, a CDK inhibitor currently in Phase III clinical trials, slowly dissociates from two different CDK9 complexes and fast from CDK7 (Figure 1). On the other hand, the more experimental CDK inhibitor PHA-793887 binds more strongly to CDK7 compared to CDK9, indicating that it is possible to develop selective inhibitors for either CDK7 or CDK9.

Figure 1 Binding and dissociation of dinaciclib on different CDK9 and CDK7 complexes

The ResidenceTimer™ platform is based on surface plasmon resonance in combination with specific immobilization of biotin-labelled kinases. The kinases were expressed and purified by NTRC’s partner Carna Biosciences Inc. from Kobe, Japan.

Literature references

[1] Willemsen-Seegers et al. (2017) Compound Selectivity and Target Residence Time of Kinase Inhibitors Studied with Surface Plasmon Resonance. J. Mol. Biol., 429: 574-586.

About NTRC

NTRC is a precision medicine company dedicated to the development of new anti-cancer drugs. NTRC facilitates the development of novel therapies by providing custom-based assays with primary patient material and high-throughput cancer cell line profiling services (Oncolines™, GeneNominator™, SynergyFinder™ and SynergyScreen™), as well as target residence time measurements for protein kinases (ResidenceTimer™) on a fee-for-service basis. Arginase Gold™ and NFK GreenScreen™ are assay read-outs for the cancer immunotherapy drug targets Arginase-1, and IDO1 and TDO respectively.  Assay kits are supplied to clients globally. For more information please visit www.ntrc.nl or contact info@ntrc.nl

 

NTRC launches the first High-throughput Screening Assay for Arginase-1 inhibitors at ENA2018

Arginase-1 (Arg-1) is an important drug target for cancer immunotherapy. Expression of Arg-1 by tumour-infiltrating myeloid derived suppressor cells induces local L-arginine depletion, which results in reduced T-cell and natural killer cell proliferation. Despite increased insight in the role of Arg-1 in tumour immune suppression, there is still a limited number of Arg-1 inhibiting chemotypes available. To identify novel inhibitors, a new high-throughput screening (HTS) assay was developed by NTRC. The assay will be launched as Arginase Gold™ at the EORTC-AACR-NCI symposium, November 13-18, in Dublin.

Arginase Gold™ is a homogenous mix-and-measure assay based on a novel and proprietary chemical probe. In contrast to previously reported arginase assays, this assay requires only two addition steps, short incubation times and mild reaction conditions. Moreover, it is a gain-of-signal fluorescence assay and allows for kinetic measurements. The Arginase Gold™ assay was validated for 384-well automated HTS. Profiling of known Arg-1 inhibitors revealed new insights into their binding kinetics.

NTRC will be happy to provide more information at booth A5 during the exhibition of the ENA2018 conference – Suzanne van Gerwen, Sales & Marketing Manager, will be your hosts at the booth.

Furthermore, NTRC will present 2 scientific posters during the conference. The first is on biomarker identification for patient stratification by cancer cell panel profiling and related clinical relevance, the second is on the assay technology for screening Arginase-1 inhibitors. Details are provided below.

The posters are:

Title: Cell panel profiling yields additional drug response biomarkers for kinase inhibitors approved for clinical use, presented during the Poster Session on Molecular Targeted Agents – PART I, on November 13th 2018, 12h – 19h. Presented by Joost Uitdehaag, Senior Investigator.

Title: Identification and characterization of Arginase-1 inhibitors for cancer immunotherapy using a novel high-throughput screening assay, presented during the Poster Session on Immune Checkpoints,  on November 14th 2018, 10h-17.30h. Presented by Yvonne Grobben, Research Scientist.

 

New predictive drug response biomarkers for approved kinase inhibitors

Oss, November, 02, 2018 –  Kinase inhibitors illustrate the successful translation of basic scientific knowledge of cancer into new targeted therapies. Selecting the right patient population based on the occurrence of specific cancer driver events is key.

In a new study, which appeared online today in the journal Molecular Cancer Therapeutics from the American Association of Cancer Research (AACR), Uitdehaag et al. describe the discovery of new predictive drug response biomarkers for seventeen approved kinase inhibitors [1]. The biomarkers are either mutations in cancer driver genes (oncogenes or tumor suppressors), or are based on the expression of cancer genes. The article studies all small molecule kinase inhibitor drugs that were approved between end 2013 and mid 2018, including inhibitors of ALK, CDK4/6, BTK, HER2 and PI3-kinase. The compounds were profiled in a panel of more than hundred cancer cell line proliferation assays, the Oncolines™ panel. The cell lines in the panel originate from different human cancers and have been characterized with regard to the presence of mutations and expression of more than 300 known cancer genes.

The study of Uitdehaag et al. is based on cancer cell lines, yet there is also direct clinical relevance of the results. Importantly, the authors demonstrate that the relative sensitivity of cancer cell lines represents the selectivity of targeted inhibitors for patient stratification markers as validated in the clinic. Interestingly, clinically approved biomarkers showed at least tenfold selectivity for the cancer gene corresponding to the drug label. By also including failed biomarker-based clinical trials in their analyses, the authors provide guidance for improved clinical trial design based on cancer cell panel profiling data. In total, the article contains the profiles of the seventeen kinase inhibitors on 280 biochemical kinase assays. For most of these inhibitors, this is the first, parallel and kinome-wide biochemical profiling study in the public domain. The article provides a rich resource for scientists that are active in the design and development of new kinase inhibitor drugs.

Figure 1. Clustering of seventeen new kinase inhibitors discussed in article [1] according to cancer cell line inhibition profile (IC50 profile) in proliferation assays in the Oncolines™ panel. Kinase inhibitors profiled in a previous study [2] and anticancer agents with other mechanisms of action, but that show similarity in their Oncolines™ IC50 profile [3], are also included in the network tree.

Literature references

[1] Uitdehaag JCM,1  Kooijman JJ,1 de Roos JADM,1 Prinsen MBW,1 Dylus J,1 Willemsen-Seegers,1 Kawase Y,2 Sawa M,2 de Man J,1 van Gerwen SJC,1 Buijsman RC,1 & Zaman GJR.1 Combined cellular and biochemical profiling to identify predictive drug response biomarkers for kinase inhibitors approved for clinical use between 2013 and 2017. Molecular Cancer Therapeutics, advanced publication online

Affiliations: 1 Netherlands Translational Research Center B.V., Oss, The Netherlands; 2 Carna Biosciences, Inc., Kobe, Japan.

[2] PLoS ONE 9: e92146; 2014.
[3] Molecular Cancer Therapeutics 15:3097-109; 2016.

About NTRC

NTRC is a precision medicine company dedicated to the development of new anti-cancer drugs. NTRC facilitates the development of novel therapies by providing cancer cell line profiling services (Oncolines™, OncolinesProfiler™, GeneNominator™, SynergyFinder™ and SynergyScreen™) and target residence time measurements for protein kinases (ResidenceTimer™) on a fee-for-service basis. NFK GreenScreen™, an assay read-out for the cancer immunotherapy drug targets IDO1 and TDO, is supplied to clients globally. For more information please visit www.ntrc.nl or contact info@ntrc.nl

NTRC presents at Rare Diseases and Orphan Drugs conference

Oss, October, 28th, 2018 – At the Rare Diseases and Orphan Drugs Global Forum, held in Belgrade (Serbia) 1st and 2nd November, Dr. Guido Zaman will present on NTRC’s precision medicine platforms for drug discovery for oncology and neurodegenerative disease. The Rare Diseases and Orphan Drugs Forum will bring together around fifty individuals from charities, patient organizations, investors, companies and academia with the aim to stimulate collaboration and to improve treatment options for rare disease patients. NTRC supports the development of new precision medicines by linking cellular drug response to cancer gene mutations and gene expression. In a recent study, that will be presented at the conference, all protein forty protein kinase inhibitor drugs that have been approved for clinical use in cancer to date were profiled on a panel of 280 biochemical kinase assays at Carna (www.carnabio.com) and on a panel of more than hundred genetically characterized cancer cell lines from diverse tumour tissue origins (NTRC’s Oncolines™ panel). Biochemical cross-reactivities were linked to cellular response biomarkers and signal transduction pathways. New predictive drug response biomarkers were identified for several kinase inhibitors, suggesting potential new indications for approved anti-cancer drugs. At the conference, Dr. Guido Zaman will also present on NTRC’s internal drug discovery project on the tryptophan metabolizing enzyme TDO. Tryptophan and its metabolites formed in the kynurenine pathway play a role in the body’s immune response against cancer cells and in the development of neurodegenerative disorders, such as Parkinson’s disease. In an ongoing study at NTRC, the expression and activity of tryptophan metabolizing enzymes and the levels of tryptophan and metabolites in liquid biopsies from patients are related to disease status and drug response. In this way, patients with an overactive kynurenine pathway can be selected for treatment with IDO1 or TDO inhibitors. NTRC is one of the corporate sponsors of the Rare Diseases and Orphan Drugs Global Forum.

For more information on the conference and registration, follow: https://www.rarebase.co.uk/rare-diseases-and-orphan-drugs-global-forum-2018

About NTRC

NTRC is a precision medicine company dedicated to the development of new anti-cancer drugs. NTRC facilitates the development of novel therapies by providing cancer cell line profiling services (Oncolines™, OncolinesProfiler™, GeneNominator™, SynergyFinder™ and SynergyScreen™) and target residence time measurements for protein kinases (ResidenceTimer™) on a fee-for-service basis. NTRC has internal drug discovery programs on IDO1 for cancer immunotherapy and TDO for Parkinson’s disease. For more information please visit www.ntrc.nl or contact info@ntrc.nl

Oncolines™ at Discovery on Target conference in Boston

Oss, September 25th, 2018 – In the Kinase Inhibitor symposium of the Discovery on Target conference, held in Boston this week, Dr. Guido Zaman will present the Oncolines™ profiling of all kinase inhibitors that have been approved for clinical use. New drug response biomarkers were identified by the genomic biomarker analysis that is an integral part of Oncolines™. The cancer cell line profiling data is complemented with biochemical assay data on 280 kinases performed at Carna Biosciences, Inc.

Symposium: Kinase Inhibitor Discovery

Title: Full kinome and cancer cell panel profiling of all kinase inhibitor drugs approved for clinical use

Presenter: Dr. Guido Zaman

Date: Thursday, September, 27th, 2018

Time: 5.30 p.m.

Heat map showing the Oncolines™ profiles of recently approved kinase inhibitor drugs for oncology

About NTRC

NTRC is a precision medicine company dedicated to the development of new anti-cancer drugs. NTRC facilitates the development of novel therapies by providing cancer cell line profiling services (Oncolines™, OncolinesProfiler™, GeneNominator™, SynergyFinder™ and SynergyScreen™) and target residence time measurements for protein kinases (ResidenceTimer™) on a fee-for-service basis. NFK GreenScreen™, an assay read-out for the cancer immunotherapy drug targets IDO1 and TDO, is supplied to clients globally. For more information please visit www.ntrc.nl or contact info@ntrc.nl

NTRC presents at European Association of Cancer Research conference in Amsterdam

The 25th biannual conference of the European Association of Cancer Research (EACR) with the theme From Fundamental Insight to Rational Cancer Treatment will take place from June 30th to July 2nd in Amsterdam.

NTRC will present 2 posters in the session Experimental/Molecular Therapeutics, Pharmacogenomics:

1. Two-step screening and confirmation approach for synergistic drug combinations

Combination studies with the PARP inhibitor niraparib are presented.

2. Cancer cell line profiling of clinically approved kinase inhibitors for cancer treatment

Case studies show pharmacogenomic analyses for, a.o., the ALK inhibitor brigatinib and the EGFR inhibitor osimertinib.

In addition, a poster on collaborative work between the Radboud University Medical Center (Nijmegen) and NTRC will be presented in the session Translational Research:

3. Prediction of chemotherapy sensitivity on ascites of ovarian cancer patients

The poster describes the work to correlate in vitro characteristics of tumor cells from ascites and clinical results.

The poster presenters are: 1. Martine Prinsen (NTRC), 2. Jeffrey Kooijman (NTRC) and 3. Judith den Ouden (Radboud UMC).

NTRC expands OncolinesProfiler™ reference compound database to 162 anti-cancer agents

Oss, June, 11th, 2018 – NTRC’s OncolinesProfiler™ service compares inhibitory IC50 signatures of anticancer drugs across 102 cell lines. The signatures belong to a proprietary database generated from the cell line profiling service Oncolines™, which is used for drug sensitivity analyses and biomarker discovery. NTRC has now expanded its reference compound database to 162 different anti-cancer agents. New compounds include Herceptin® (trastuzumab), the antibody drug conjugate Kadcyla®, the SUMOylation inhibitor ML-792, and the selective BTK inhibitor acalabrutinib. The database also includes many classic chemotherapeutic agents and targeted agents with diverse mechanisms of action, such as epigenetic modulators and PARP inhibitors. All recently added compounds were profiled on 102 genetically well-characterized human cancer cell lines from diverse tumor origins (the Oncolines™ panel). For the new release of the OncolinesProfiler™ database twenty-three agents that were previously profiled on 66 cell lines [1] were re-profiled on the 102 cell line panel.

OncolinesProfiler™ compares the IC50 fingerprint of a compound tested on the full Oncolines™ panel with the IC50 fingerprint of 162 different anti-cancer agents. NTRC proprietary  implementations of state-of-the-art clustering and network analyses are used to determine the similarity of one compound with all agents in the library. The result provides insight into how unique a compound is compared to other anti-cancer agents. OncolinesProfiler™ may also provide insight into the mechanism of action of a compound in proliferation assays, as was shown for ibrutinib in reference [1]. In reference [2], OncolinesProfiler™ was used to establish the primary molecular target of reversine, a compound that was originally discovered in a phenotypic screen. OncolinesProfiler™ is included in Oncolines™. For further inquiries or quotations, please contact services@ntrc.nl

Figure 1: Comparative analysis of ibrutinib in OncolinesProfiler™. (A) Hierarchical tree clustering. (B) Correlation matrix. (C) Network tree.

Literature reference

[1] Uitdehaag et al. (2016) Molecular Cancer Therapeutics 16, 2609-2617
[2] Libouban et al. (2017) Oncotarget 8, 38309-38325

About NTRC

NTRC is a precision medicine company dedicated to the development of new anti-cancer drugs. NTRC facilitates the development of novel therapies by providing cancer cell line profiling services, target residence time measurements, and immune oncology assays on a fee-for-service basis. For more information please visit www.ntrc.nl/services or contact services@ntrc.nl

NTRC presents novel high-throughput screening assay for Arginase I inhibitors for cancer immunotherapy at AACR Annual Meeting in Chicago

NTRC will present two scientific posters at the AACR Annual Meeting 2018, to be held from April 14th to 18th in Chicago. The first poster relates to Arginase, a promising target in the field of cancer immunotherapy. The poster describes a novel high-throughput assay technology that was used to screen for small molecule inhibitors of Arginase I. The screen was performed in collaboration with the Pivot Park Screening Centre.

The second poster relates to targeted therapies and drug response biomarkers. The poster presents the biochemical kinase assay and cell panel profiling data of all kinase inhibitors approved for clinical use. GeneNominator™ gene expression analysis revealed novel drug response biomarkers for BTK and CDK4/6 inhibitors, which will be presented in case studies.

Furthermore, representatives of NTRC will gladly welcome you at booth #1055 in the Exhibition Hall.

Details on the poster presentations are given below:

Title: High-throughput fluorescence-based assay for screening of Arginase I inhibitors for cancer immunotherapy
Presented by: Yvonne Grobben
Session Date and Time: Monday Apr 16, 2018 8:00 am – 12:00 pm
Poster Board Number: 19
Permanent Abstract Number: 1944

Title: Profiling of all clinically approved kinase inhibitors reveals novel drug response biomarkers for BTK and CDK4/6 inhibitors
Presented by: Joost Uitdehaag
Session Date and Time: Tuesday Apr 17, 2018 1:00 pm – 5:00 pm
Poster Board Number: 3
Permanent Abstract Number: 4907

About NTRC

NTRC is a precision medicine company dedicated to the development of new anti-cancer drugs. NTRC facilitates the development of novel therapies by providing cancer cell line profiling services, target residence time measurements, and immune oncology assays on a fee-for-service basis. For more information please visit www.ntrc.nl/services or contact services@ntrc.nl