Shipment of Your Compounds
Oncolines B.V.
Attn. Mr. J. de Roos
Building OP
Kloosterstraat 9
5349 AB Oss
The Netherlands
Tel.: +31 412 700 501
Mail: services@oncolines.com
Your shipper should be able to advise. Description of the materials should be on the Airway Bill.
Description of the materials: “Novel research compound for NON-human research”.
Please add MSDS (Safety Sheet).
You can ship your compound at any time. The turnaround time starts at arrival of the compounds at Oncolines.
Deliverables
The study results are owned by the Client. Oncolines destroys study related material after a pre-defined period.
Quality
The maximum concentration of DMSO in the wells is 0.4%. All wells contain the same DMSO concentration, including the control.
We have selected cell lines for the panel that show sufficient window in a 3 day proliferation assay. We have also validated the assays for five day incubation time.
Our assay stocks have undergone 10 passages at maximum.
The doubling time of each cell line is monitored in each study. When the doubling time is beyond the quality criteria, the cell stock will be replaced.
Yes, we have optimized the cell number for each cell line. This is to ensure that they are in exponential growth phase when we expose them to compounds.
3 versus 5 days incubation time can indeed make a difference for the effect of compounds. In particular, this was shown for the efficacy (% effect), which is related to number of cell cycles. See for instance Maia et al. (2015).
We have done real time image analysis to look at chromosome mis-segregation induced by TTK inhibitors. This is illustrated by Libouban et al. (2017).
The level of DMSO (0.4% in the wells) does not interfere with the readout and interpretation of the results.
We always include untreated wells in the studies, as well as the reference compound doxorubicin.
We can solve the compound at the day of the experiment. For frozen solutions, the total time between thawing and aliquoting on cells can be decreased to approximately 1 hour.
Yes, we have worked with antibodies, antibody-drug conjugates, peptides, … etc.
Water soluble compounds are dissolved in PBS, as water is not isotonic.
Proliferation Assays
The selection of cell lines was based on a good representation of:
- Cancer gene mutations – according to occurrence in patients
- Tissue types – currently 25
Other selection criteria are the growth characteristics of the cell lines and the absence of restrictions for use. We have a commercial licence from the ATCC for all cell lines in the Oncolines® panel.
You are free to choose your preferred dilution steps. By default we use √10 dilution steps. With 9 dilution points, the √10 dilution steps cover 4 log decades. With a maximum test concentration of 31.6 µM, the mimimum test concentration is 3.16 nM.
Based on your request we can add cell lines to a panel study. We have validated proliferation assays for more than 200 cell lines.
Bioinformatics Analysis – Gene Mutation Analysis
These are mutations which are very frequently found on specific gene positions in cancer patients; so called ‘hotspot’ mutations (e.g. BRAF[V600E]). For completeness, copy number variations in the genes with hotspot mutations are included. The gene alterations included in this analysis are all well-known to be relevant in cancer.
The ‘proprietary selection’ of cancer genes refers to the list of 98 genes, after filtering of the genes from the public domain. The aim of the filtering was to generate a list of genes with reported relevance in the cancer field, so to exclude genes that may not be relevant for cancer after all. Non-coding mutations have been filtered out (e.g. silent mutations) and only mutations that have been reported in cancer patients were kept. In addition, relevant copy number variations are included in the analysis.
The subset of 38 ‘commonly occurring and well known genes’ are a subset of the 98 genes. It contains the 35 most frequently mutated, amplified or deleted genes (TP53, CDKN2A, KRAS etc.) + 3 well known genes that everybody would miss if they are not included (BRCA2, SMAD4, and the BCR-ABL translocation). The ANOVA analysis is restricted to 38 genes for statistical reasons (due to the number of cell lines).
Yes – based on your specific needs we can adapt the analysis.
The criteria for selection of oncogenes are a.o.:
- Single nucleotide polymorphisms removed
- Only mutations in protein coding sequences retained
- Mutations filtered for occurrence in cancer patients
The mutant status of relevant oncogenes and tumor suppressors in the cell lines, e.g. B-RAF, CDKN2A, CTNNB1, EGFR, H-RAS, K-RAS, N-RAS, PIK3CA, TP53 etc. was confirmed by in-house DNA sequencing.
Bioinformatics Analysis – Tissue Sensitivity Analysis
Annotation of disease indication conforms to the Cellosaurus database. The associated tissue types are hierarchically organized according to the Oncotree classification.
Indeed we observe that cell lines from hematological origins, which are all grown in suspension, are more sensitive to some cytotoxic therapies. Some of this is also discussed in our earlier work (Uitdehaag et al. (2014)). We do not know if this originates from the way of growing, from the hematological lineage, or from the historic focus on leukemias for drug development.
Bioinformatics Analysis – Comparative Analysis
The Anti-Cancer Drugs Database can be requested via services@oncolines.com, or you can call us at +31 412 700 501.
The colors are indicative for clusters of compounds.
The distance between compounds is not related to similarity. The relative similarity ranking of your compound with other compounds, is shown in a separate correlation table.
Bioinformatics Analysis – Gene Expression Analysis
It is log2-transformed ‘RMA-normalized data’ based on microarray. Since it is log2, a difference of 1 unit between genes and/or cell lines is similar to a 2-fold difference. For instance, Gene X has an expression value of 3 in Cell line A and an expression value of 4 in Cell line B. The difference is 1 unit (= factor 2), so the expression of Gene X is 2x higher in Cell line B than in Cell line A. A difference of 2 units means a 22 = 4-fold difference in expression; a difference of 3 means a 23 = 8-fold difference in expression.
As you see, the values are relative values, meaning that the values can be used to compare genes and cell lines. The values cannot be used in an absolute manner, for instance ‘1 ug of my sample contains 10,000 mRNA transcripts of Gene X’.
RNAseq data. Both methods are reproducible and have a high correlation between gene expression profiles generated by the two.
SynergyFinder™
We test 3 ratios to confirm that a synergy in a specific mixture is observed in different settings. Generally, you would expect that a synergy is ratio independent. NB. when a synergy is observed, we always re-test it in an independent replicate experiment.
In general there are two synergy ‘Schools of Thought’: Bliss additivity and Loewe additivity. The first uses %-effects and the other focuses on dosage. This is explained well by Foucquier and Guedj (2015). ‘HAS’, highest-single-agent, is also a Bliss-based model, using %-effect, but very simply taking the most potent compound as a reference. We do not use this. We base our calculations on Loewe additivity and use the isobologram and the Chou-Talalay CI Index as ways to visualize and quantify synergistic effects.
SynergyFinder™ is generally used for small-scale combination studies. The advantage is the determination of synergy according to curve shift analysis, CI Index and isobolograms; it is based on full dose response curves of both single agents and 3 mixtures per combination (ratios 1:4; 1:1; 4:1). Literature references are: Uitdehaag et al. (2014); Straetemans et al. (2005) and Chou (2010).
SynergyScreen™ is generally used for broad combination screening. Advantage: less laborious and therefore quicker and lower price. It concerns determination of synergy according to curve shift analysis; based on full dose response curve of 1 single compound and mixture curve of that compound with a fixed concentration of the 2nd compound.
Let’s say we need 50 µL of the mixture, IC50 of compound A is 1 nM and IC50 of compound B is 10 nM. In that case we take 25 µL of compound A and 25 µL of compound B. The total of 50 µL is subsequently diluted to generate the dose response curve. Since the compounds are equally effective, 25 µL of compound A can be added to 25 µL of compound B without a ‘dilution effect’.
The combination is synergistic when the CI is lower than 1. In those cases, the experiment will be replicated before submission of the final report. Just to confirm that the observed synergistic effect is reproducible.
We have several cases of CI of around 0.7 in our cell-based studies, which are confirmed synergies in vivo and have been approved for clinical use.
For instance, the combination of dabrafenib and trametinib for patients with BRAF mutation and the combination of olaparib and cisplatin for ovarian cancer patients.
Mechanistic Cell Biology
Based on initial discussions about your interests in proof of concept studies, we prepare a workplan and a quotation. Using your input we’ll provide a proposal that is focused on your specific goals. After agreement, we will start the work. Study results and scientific insights are discussed during regular update meetings. It is work in progress, meaning that the workplan can be adapted based on new results if desired.
The study results are owned by the Client. Of course we can support in the preparation of new scientific papers if desired.
ResidenceTimer™
If you are uncertain about the concentration range, we recommend to start with a relatively high concentration range.
It is recommended to choose a range that includes the biochemical potency (IC50) of the compound at the lower part of the test concentration range. For example, for a compound with an IC50 of 3 nM, we would advise to use a range of 1 -100 nM.
The affinity is the most precise determination of the interaction between a drug and its target. It is the ratio between the dissociation and association rate constants. In contrast to an SPR-based affinity constant, a biochemical activity-based IC50 may be an underestimation of the real binding affinity. This is due to a lower limit of detection in biochemical activity assays which is dependent on the enzyme concentration.
It is recommended to choose a range that includes the biochemical potency (IC50) of the compound at the lower part of the test concentration range. For example, for a compound with an IC50 of 3 nM, we would advise to use a range of 1 -100 nM.
We can work with, for instance, up to 5% DMSO. The standard concentration is 1% DMSO.
In principle the quote is prepared for reversible compounds. In the case of irreversible compounds, additional material costs (protein and chip) apply.
Target residence time and half-life are calculated from the dissociation rate.
The compound response will be subtracted with both the reference channel response and the blank injection (double referencing).
We can be flexible and can increase the time of the dissociation phase if desired.
We can work with a variety of chips, for instance Ni-NTA chips for his-tagged proteins, protein A chips for antibodies, and CM5 chips for untagged proteins.
Yes, we can also perform assays that are different from the experiments described on our website.
QuickScout™
Results are provided in Excel format. Interim data is uploaded to a secured website within 1 week of initiating your study and the Final report is emailed to you upon completion of the study. A PDF report describing the study is sent via email and in printed form upon completion of the project.
The 1 mM ATP profiling assay is useful in determining the potential selectivity of your inhibitor using conditions approaching physiological ATP concentrations. The 1 mM ATP assay can also help identify possible allosteric inhibitors when IC50 data generated at ATP Km is also available.
Submission in 96 well plates with columns 1 & 2 empty are preferred but acceptable with tubes and 384 well plates. Compound preparation conditions : 100% DMSO solution of 100 x the top concentration.
We use semi-log dilution series to generate 10 point curves, all compound concentrations are assayed in duplicate.
Yes, you can contact Carna Biosciences directly via carnabio.com. However, European clients will be kindly redirected to Oncolines, since we represent Carna for Europe. So, if you are from Europe, please contact us via the Contact Form, send a mail to services@oncolines.com or call us at: +31 412 700 501.
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It can be done either way, whatever you prefer. The shipment address of Oncolines is:
Oncolines B.V.
Attn. Mrs. N. Willemsen-Seegers
Building OP
Kloosterstraat 9
5349 AB Oss
The Netherlands
Tel.: +31 412 700 501
Mail: services@oncolines.com
The shipment address of Carna is:
Carna Bioscience, Inc.
Attn. Dr. Yusuke Kawase
Sales and Marketing
BMA 3F 1-5-5 Minatojima-Minamimachi
Chuo-ku, Kobe 650-0047
Japan
Tel.: +81 78 302 7091
Mail: yusuke.kawase@carnabio.com
You can cherry-pick the kinases of your interest, – you can even select just one kinase for profiling.
ELISA assay request is acceptable if your target is listed on Carna’s QSS Assist™ ELISA Assay Kit. Detailed information targets can be requested via the Contact Form (below) or services@oncolines.com.
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The service incorporates a 30 minute pre-incubation at room temperature with the test compound(s) prior to measuring the activity in our standard Mobility Shift Assay.
Indeed, high-throughput screening of more than 100,000 compounds is offered via the Mobility Shift Assay.
The serine/threonine (STK) panel represents a variety of groups, with the exception of tyrosine kinases.