Registered report: androgen receptor splice variants determine taxane sensitivity in prostate cancer

Sampling

• The experiment will use at least 11 mice per group for a final power of at least 84.95%.

  • See Power Calculations section for details

• Each experiment has two cohorts, each of which is split into two groups (4 groups total):

  • Cohort 1, Group 1: Mice bearing LuCaP 86.2 prostate cancer xenografts, uninjected

    • N = 11 mice

  • Cohort 1, Group 2: Mice bearing LuCaP 86.2 prostate cancer xenografts, treated with docetaxel

    • N = 11 mice

  • Cohort 2, Group 1: Mice bearing LuCaP 23.1 prostate cancer xenografts, uninjected

    • N = 11 mice

  • Cohort 2, Group 2: Mice bearing LuCaP 23.1 prostate cancer xenografts, treated with docetaxel

    • N = 11 mice

  • In total, 24 mice with LuCaP 86.2 tumors and 24 mice with LuCaP 23.1 tumors are generated.

Materials and reagents

Procedure

Notes:

• Fresh tumor tissue, shipped overnight from the original authors, will be used; tissue will not be frozen.

• Tumor tissue will be screened with a Rodent Pathogen Panel to confirm no pathogens are present.

• Information in this protocol is derived from Mostaghel et al. (2011), Wu et al. (2006) and Zhang et al. (2011).

• Docetaxel is prepared fresh on the day it will be used in 13% ethanol/0.9% NaCl.

• ^* Experimenters should be blinded to the treatment of the mice.

1. Mince fresh LuCaP 86.2 and LuCaP 23.1 tumor tissue into small fragments 20 mm³ in size.

   1. If multiple tumors are provided, optimally only a single tumor will be used for implantation. If multiple tumors are needed to generate enough fragments for implantation, all tumors will be minced to appropriate sizes and half the mice will receive tissue from one tumor, while the other half receive tissue from the other tumor. The donating tumor will be recorded for each mouse.

2. Subcutaneously implant non-castrated 6–8 week old male SCID mice on the right flank-shoulder area with tumor fragments 20 mm³ in size.

   1. Generate 24 mice bearing LuCaP 86.2 tumors.

   2. Generate 24 mice bearing LuCaP 23.1 tumors.

3. Let tumors grow to 100 mm³ prior to the start of treatment.

   1. Measure tumor volume twice weekly.

      1. Volume = length × width × height × 0.5236

   2. Growth characteristics can be variable; time to enrollment may be between one to two months.

   3. Note: treatment initiation will not be synchronized across tumors.

4. Randomly assign mice to the treatment group and the control group. Once tumors reach 100 mm³, non-control mice are treated by intraperitoneal injections every other week for eight weeks.

   1. ^# Animals are randomized according to a stratified randomization procedure balanced for final tumor volume and spread of tumor volume.

   2. Control mice receive no injections.

      1. Note: This information is based on communication from the original authors.

   3. Treated mice receive 10 mg/kg docetaxel in 400 µL 13% ethanol/0.9% NaCl per injection.

      1. Note: This information is based on communication from the original authors.

5. Measure tumor volume twice weekly for duration of experiment.

6. Continue treatment for 8 weeks.

   1. ^* Inject mice in weeks 1, 3, 5, and 7.

   2. Euthanize animals when they display one or more of the following conditions:

      1. Tumor volume exceeds 1,000 mm³

      2. >20% body weight loss

      3. Animals become compromised (hunched posture, piloerected, rapid respiration, lethargic)

7. In Week 8, sacrifice mice.

   1. For each untreated group, randomly select three mice and harvest tumor tissue (6 tumors total; 3 uninjected LuCaP 86.2, 3 uninjected LuCaP 23.1).

      1. ^# Snap freeze tumor tissue in liquid nitrogen and stored at −80 °C until ready for use.

Deliverables

• Data to be collected:

  • All mouse health records (age, gender, date of implantation, size of injected tissue fragment, treatment regimen, date and cause of euthanasia)

  • Raw measurements of tumor size and calculated tumor volume for each mouse for all weeks measured

  • Graph of average tumor size per group each week, as seen in Fig. 6A.

    • To generate weekly mean measurements, first average the two measurements for that week for each tumor. Then average the averaged tumor measurements within each group to generate a group mean tumor volume.

  • ^* Graph of median tumor size per group each week.

    • Unlike the average measurements, do not combine weekly tumor size measurements when calculating the media tumor size per group each week.

• Sample delivered for further analysis:

  • Snap frozen control-group tumor tissues ready for use in Protocol 2.

Confirmatory analysis plan

• Statistical Analysis of the Replication Data:

  • Note: At the time of analysis we will perform the Shapiro–Wilk test and generate a quantile–quantile plot to assess the normality of the data. We will also perform Levene’s test to assess homoscedasticity. If the data appears skewed we will perform the appropriate transformation in order to proceed with the proposed statistical analysis. If this is not possible we will perform the planned comparison using the appropriate nonparametric test.

  • One-way ANOVA on Week 8 time points followed by Bonferroni corrected t-tests comparing:

    • LuCaP86.2 untreated vs. LuCaP 86.2 treated with docetaxel

      • As performed by the original authors

• Meta-analysis of original and replication attempt effect sizes:

  • This replication attempt will perform the statistical analysis listed above, compute the effects sizes, compare them against the reported effect size in the original paper and use a meta-analytic approach to combine the original and replication effects, which will be presented as a forest plot.

• Additional Analysis of the Replication Data:

  • Two-way ANOVA (2 × 2) assessing area under the curve followed by Bonferroni corrected t-test comparisons:

    • LuCaP86.2 untreated vs. LuCaP 86.2 treated with docetaxel

    • LuCaP 86.2 treated with docetaxel vs. LuCaP 23.1 treated with docetaxel

Known differences from the original study

All known differences in reagents and supplies are listed in the materials and reagents section above, with the originally used item listed in the comments section. All differences have the same capabilities as the original and are not predicted to alter experimental outcome.

Provisions for quality control

All data obtained from the experiment—raw data, data analysis, control data and quality control data—will be made publicly available, either in the published manuscript or as an open access dataset available on the Open Science Framework (https://osf.io/gkd2u/).

• Results of the Rodent Pathogen Panel screening

Sampling

• The experiment has two cohorts, derived from Protocol 1;

  • Cohort 1: 3 random tumors derived from uninjected LuCaP 86.2 prostate cancer xenografts

  • Cohort 2: 3 random tumors derived from uninjected LuCaP 23.1 prostate cancer xenografts

• Each sample will be probed with antibodies for the following targets:

  • ARN20

    • Detects the full length AR as well as the AR567 splice variant, which runs slightly faster than the full length AR

  • Arv567es

    • Detects the Arv567 splice variant

  • Arv7

    • Detects the ARv7 splice variant

  • Beta-Actin

    • Housekeeping control

• The experiment will be performed on 3 samples per cohort.

  • This experiment is exploratory in nature, and thus no power calculations are necessary.

Materials and reagents

Procedure

Notes:

1. Information in this protocol obtained from Darshan and colleagues (2011) and from the replicating lab.

2. This protocol will use snap frozen tumor tissue generated in Protocol 1.

3. Preparation of samples: Lyse cells in TNES buffer.

   1. TNES buffer: 50 mM Tris pH 6.0, 100 mM NaCl, 2 mM EDTA, 1% Nonidet P-40, 1X Protease Inhibitor

   2. ^# Frozen tissue will be homogenized/sonicated on ice, then spun down at 13,000 rpm at 4 °C.

   3. ^# Supernatant is diluted 1:1 to perform a Bradford Protein Assay according to manufacturer’s protocol.

4. Separate ^#50 µg per well of protein on a 10% SDS-PAGE gel.

5. Transfer protein to ^# nitrocellulose membrane.

6. ^# Block with 1% non-fat dry milk in PBS/0.05% Tween-20 for 60 min at room temperature (RT).

   1. Wash 3 × 5 min in PBS/0.05% Tween-20.

7. ^# Incubate primary antibodies (at denoted concentration/dilution) in PBS/0.05% Tween-20 overnight at 4 °C.

   1. α ARN20: 1:200

   2. α Arv567es; 1:3,000

   3. α ARv7: 2 µg/µL

   4. α Beta-actin: 1:25,000

8. ^# Wash 3 × 5 min in PBS/0.05% Tween-20.

9. ^# Incubate with secondary antibodies for 60 min at RT.

   1. Goat-anti-mouse IgG-HRP; 1:10,000

   2. Goat anti-rabbit IgG-HRP; 1:2,000

10. ^# For detection:

    1. Incubate membrane with 5 mL of TMB detection reagent. Stop with distilled water upon achieving desired color development

11. ^# Image using an 8.0 megapixel digital camera.

Deliverables:

• Data to be collected:

  • All raw gel images including ladder marker indication

Confirmatory analysis plan

• None necessary

Known differences from the original study

All known differences in reagents and supplies are listed in the materials and reagents section above, with the originally used item listed in the comments section. All differences have the same capabilities as the original and are not predicted to alter experimental outcome.

• The replication will exclude the LuCaP35 cell line from this experiment.

• The replicating lab will use their in-house Western blot protocol with colorimetric detection. This replaces the LiCOR Odyssey detection used by the original lab.

• At the recommendation of the original authors, we will use an Arv567es specific antibody (Abcam 200827) to detect the V567es variant protein instead of relying upon the ARN20 antibody to detect both full length ant v567es proteins.

Provisions for quality control

All data obtained from the experiment—raw data, data analysis, control data and quality control data—will be made publicly available, either in the published manuscript or as an open access dataset available on the Open Science Framework (https://osf.io/gkd2u/).

Summary of original data

• Stdev was calculated using formula SD = SEM*(SQRT n).

Test family

• One-way ANOVA on Week 8 time points followed by Bonferroni corrected t-tests comparing:

  • LuCaP86.2 untreated vs. LuCaP 86.2 treated with docetaxel

    • As performed by the original authors

• Additional analyses:

  • Two-way ANOVA (2 × 2) assessing Area Under the Curve followed by Bonferroni corrected t-test comparisons:

    • LuCaP86.2 untreated vs. LuCaP 86.2 treated with docetaxel

    • LuCaP 86.2 treated with docetaxel vs. LuCaP 23.1 treated with docetaxel

Power calculations

• Power calculations were performed using R (R Core Team, 2014), GraphPad PRISM v6 for Mac and G*Power (version 3.1.7) (Faul et al., 2007)

• One way ANOVA as originally performed.

  • Note: This excludes the LuCaP 23.1 cohort that is missing an 8 week time point.

• Two-way ANOVA on area under the curve followed by Bonferroni corrected t-test comparisons

  • Calculated with R (R Core Team, 2014).