BMC Cancer
RESPONSE TO REVIEWERS COMMENTS:
Reviewer's report
Title: Isolation and Genomic Analysis of Circulating Tumor Cells from Castration
Resistant Metastatic Prostate Cancer
Version: 1 Date: 14 September 2011
Reviewer: Minetta Liu
Reviewer's report:
OVERVIEW
The authors provide a well written summary of a pilot study with a limited number
of metastatic prostate cancer patients. They describe an internally developed
method of circulating tumor cell (CTC) isolation for genome-wide copy number
analysis. Blood from nine subjects was analyzed, two of which had available
archived primary tumor specimens for comparison of aCGH findings.
- We thank the reviewer for all of these very constructive suggestions.
MAJOR COMPULSORY REVISIONS
1. The manuscript is proposed an article on technical advances. The research
group is well known for related work in the setting of metastatic breast cancer,
where CTC analysis using the IE/FACS method and aCGH has been
incorporated into multi-institutional clinical trials. Acknowledging that the work
herein is in the setting of prostate cancer, is there a reason not to incorporate the
findings in both disease states to strengthen support for this novel approach?
- We agree that this method of CTC isolation and aCGH analysis is being pursued on
a large scale via multi-institutional clinical trials, and we appreciate the question from
the reviewer about this. The reason for this prostate cancer report is: 1) it is truly a
separate study involving a pilot evaluation to assess feasibility in prostate cancer
patients; and 2) we wish to emphasize the novel finding regarding the detection via
aCGH of focal amplification in the X chromosome (AR) in CTCs, which is a prostate
cancer specific observation.
2. Please provide the time frame for the accrual of 20 patients. Please describe
the barriers (if any) to recruiting more than 20 subjects to a protocol that involves
a one-time blood draw.
- We have added the following text to the Methods and Discussion sections:
Clinical samples were obtained from 20 castration-resistant prostate cancer patients
who were recruited from November 2008 to August 2009 at the University of
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California San Francisco (UCSF) to participate in our study (Table 1). Twenty
patients were selected based on statistical considerations for a pilot study.
A major limitation of this study is that it was designed as a pilot feasibility study with a
small sample size.
3. Please provide some background in the development of this technological
advance. For example: (1) please describe how your group determined that
blood collection in a CellSave tube [versus an EDTA or other tube] would yield
optimal results; and (2) please describe why BAC arrays were used [i.e., as
opposed to the available oligonucleotide arrays].
- (1) We have added the following text to the Methods section:
Blood was collected in three CellSave™ tubes (Veridex). This allowed us to use one
tube for an initial CTC enumeration using the published CellSearch™ method, and
the two remaining tubes to be combined for IE/FACS isolation.
- (2) We have added the following text to the Methods section:
In initial studies we performed aCGH analysis using oligonucleotide microarrays
(Affymetrix 50K SNP array), but observed significant experimental variability and
background noise with our WGA4 amplified DNA samples. Similarly, studies by
Fuhrmann et al [1] and Nowak et al [2] showed that bacterial artificial chromosome
(BAC) arrays outperformed oligonucleotide microarrays in detecting small gains or
losses [1] and showed far fewer outliers and less technical noise [2].
4. Please provide the rationale for limiting the decision to proceed with IE/FACS
to those subjects with >5 CTCs per 7.5 mL blood by the CellSearch method.
Technically, a “positive” CTC result by CellSearch is defined by the detection of
CTCs, and use of the <5 versus > or = 5 CTCs cut-off is for purposes of
prognostication and prediction.
- We have added the following text to the Methods section:
To increase the likelihood of isolating CTCs for molecular analysis, we first performed
CTC enumeration using the automated CellSearch™ assay to identify patients with
>5 CTCs per 7.5mL. We then isolated CTCs by IE/FACS from the remaining blood
sample in these patients.
5. Please clarify what is meant by “pools of CTCs.” How are these “pools”
derived and defined? Table 1 should include a column providing information on
the number of “pools of ~20 cells” derived from the blood samples of each
patient, the number of “input cells” used for aCGH analysis, and the number of
replicate analyses performed for each subject. The only place that actual
numbers of CTCs isolated by IE/FACS are provided is in the figures. Also, if the
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“pools” were derived to include “~20 cells” each, how is it that Patient #3 had 50
cells in the copy number analysis (Supplementary Figure 2a)?
- To avoid confusion, we have eliminated the term “pools of cells” and added the
following text to the Methods section:
During FACS analysis, we sorted a range of 18-50 CTCs. Table 1 shows the number
of isolated CTCs used for WGA, and the number of replicate analyses performed for
each subject.
6. aCGH protocols typically require more genomic material than can be provided
with the limited number of CTCs obtained. Please describe the rationale for
selecting the GenomePlex Single Cell WGA4 Kit as the best method for whole
genome amplification. Also, how was quality of the whole genome amplification
product assessed?
- We have added the following text to the Methods section:
Optimization of whole genome amplification (WGA). ACGH protocols typically
use between 100ng and 1µg of specimen DNA in the labeling reaction, equivalent to
~20,000-200,000 cells, which does not permit reliable analysis of important samples
containing small numbers of tumor cells such as CTCs in blood. Analyzing these
samples for copy number aberration requires a high-fidelity whole genome
amplification (WGA) step. To select the best strategy for WGA of limiting amounts of
input DNA, we tested four WGA protocols: multiple displacement amplification [3],
random prime amplification [4], ligation-mediated-PCR [5], and the GenomePlex®
WGA4 [6-7]. We compared aCGH results generated from diluted BT474 breast
cancer cell line genomic DNA (equivalent to ~10,000 to 10 cells) to non-limiting
unamplifed BT474 DNA (600ng). We found GenomePlex® WGA4 to be most reliable
and reproducible (data not shown). We also did not observe artifacts or bias via BAC
aCGH analysis. Other groups have also demonstrated the reproducibility and
reliability of the GenomePlex® WGA4 protocol [2, 6].
The average yield after WGA of ~20 CTCs is ~10µg. Early tests via aCGH analysis of
samples with WGA product yield less than <5µg revealed non-specific amplification.
Therefore samples with low yield (<5µg) were excluded from further downstream
assays.
MINOR ESSENTIAL REVISIONS
1. Please explain why subject eligibility was restricted to patients who had
received three or more cycles of docetaxel based chemotherapy.
- At the time when this study was approved by the Urology Tissue Utilization
Committee at UCSF, several ongoing protocols were already collecting blood
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samples from CRPC patients in the pre-chemotherapy space. Additional blood
collection from this patient cohort was problematic, and so the protocol was restricted
to chemotherapy patients.
2. According to the package insert, CTCs collected in CellSave preservation
tubes remain intact for up to 96 hours. Please explain why CTC enumeration by
CellSearch was done within 24 hours, and CTC isolation by IE/FACS was done
within 48 hours after blood draw.
- We have added the following text to the Methods:
In initial studies, we observed that whole genome amplification of DNA from CTCs
was less efficient when CTCs were isolated after 48 hours post-phlebotomy.
Therefore, enumeration was performed within 24 hours and isolation of CTCs via
IE/FACS within 48 hours after blood draw.
3. Please describe how the blood samples were handled for IE/FACS. For
example, if two additional CellSave tubes were available after CellSearch
enumeration, were the two volumes combined or processed separately?
- We have added the following text to the Methods:
Blood was collected in three CellSaveTM tubes (Veridex). This allowed us to use one
tube for an initial CTC enumeration using the published CellSearch™ method, and
the two remaining tubes to be combined for IE/FACS isolation.
4. Please specify which version of the BAC array was used to analyze the human
samples and the preclinical samples.
- We have added the following text to the Methods:
We performed our aCGH analysis using a bacterial artificial chromosome (BAC)
array (Version 3.2) containing 2,464 clones printed in triplicate [8].
5. Please define the “UCSF Spot Program” and “UCSF Sproc” as referred to in
the Methods Section under “Array CGH Analysis.”
- We have added the following text to the Methods:
The arrays were imaged using a custom built CCD array imaging system [9] and
analyzed using the UCSF Spot Program to calculate Cy3/Cy5 ratios. The UCSF Spot
Program is a fully automated system for microarray imaging that locates both
subarray grids and individual spots [10]. Ratios are then computed based on explicit
segmentation of each spot. The resultant log2 ratios were analyzed by UCSF Sproc
to yield the mean and standard deviation of the log2 ratios over replicate spots. The
UCSF Sproc is a companion program to UCSF Spot that maps each spot on the
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array to a specific clone and chromosome position, and averages over replicate spots
in order to output a final ratio value for each clone on the array. Clones with a
standard deviation of the log2 ratios of the triplicate spots greater than 0.2 for were
excluded from analysis.
6. Readers would benefit from possible explanations for the greater yield of
CTCs with IE/FACS versus CellSearch. (Presumably this is because two
anti-EpCAM antibodies are used instead of one?)
- We have added the following text to the Methods:
To increase the likelihood of isolating CTCs for molecular analysis, we first performed
CTC enumeration using the automated CellSearch™ assay to identify patients with
>5 CTCs per 7.5mL. We then isolated CTCs by IE/FACS from the remaining blood
sample in these patients. Cell counts via CellSearch correlated closely with cell
counts via IE/FACS (Park, unpublished data).
7. Twelve subjects were determined to meet the established parameters to move
forward with IE/FACS for CTC isolation. Only 9/12 subjects had blood samples
that were successfully analyzed for copy number aberrations. Granted that the
sample size is extremely small, but the 25% failure rate should be addressed.
What measures could be implemented to increase the likelihood of success?
- We have added the following text to the Results:
Three of the 12 samples that met the established parameters to move forward with
IE/FACS did not yield informative aCGH results (25% failure rate) due to FACS
instrument error, inadequate WGA yield, or failed microarray hybridization. Two of the
samples (patients #15 and #19) were processed 2 days after blood draw (Table 1).
Based on this observation, we suggest implementing IE/FACS within 24 hours after
blood draw.
8. The Results Section describes that the “replicates were moderately correlated
(r=0.78).” Shouldn’t greater correlation be required if this technology is to be used
in making important treatment decisions for individual patients?
- We have added the following text to the Discussion:
Although this approach for whole genome amplification and aCGH of isolated CTCs
is not designed to be a clinical test, it is possible that the observations here, such as
focal amplification in the X chromosome (AR) in CTCs, could serve as the basis for
new CTC-based clinical applications.
9. Please consistently refer to the subjects in the tables and figures. For
example, Table 1, Figures 2 and 5, and Supplementary Figure 3 refer to subjects
5
as “Patient No. X,” but Figure 4 and Supplementary Figure 2 refer to subjects as
“PCa #X.”
- We have revised the text to improve consistency as suggested by the Reviewer.
DISCRETIONARY REVISIONS
None.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: Yes, but I do not feel adequately qualified to assess the
statistics.
Declaration of competing interests:
I have no competing interests to declare.
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Reviewer's report
Title: Isolation and Genomic Analysis of Circulating Tumor Cells from Castration
Resistant Metastatic Prostate Cancer
Version: 1 Date: 31 August 2011
Reviewer: Thomas Höfner
Reviewer's report:
- Major Compulsory Revisions
1. The authors of Magbanua et al. want to address the significance of detected
gene copy number variants (CNV) in metastastic prostate cancer, specifically in
detected circulating tumor cells. In general the paper argues quite uncritical with
the subject CTC detection in prostate cancer in general. So the biological
question behind studying CNV in CTCs is in my opinion not well defined.
It was never shown up to now that EpCAM positive selected CTCs in prostate
cancer could show a definite biological function in vivo (xenograft studies).
- We have added the following text to the Introduction:
The biological relevance of CTCs in prostate cancer is unknown, including their
putative role in metastasis and progression. Therefore, it is of interest to develop
approaches to further characterize these cells.
The only thing known today is that if CTCs are detected by CellSearch, there is a
correlation with overall survival in CRPC patients. Studies so far with CellSearch
often did not include multivariate analysis and especially did not correlate
significance of CTC detection with the other published nomograms to predict
prognosis in advanced prostate cancer. We do not know, if detection of CTCs is in
any way better than what we have already in the clinic.
- We have added the following text to the Introduction:
The utility of CTC detection in the clinical management of prostate cancer, including
its role in relation to standard diagnostic tools, remains unclear.
The way to advance in this field is not to go into detailed genetic analysis at the first
place, but to begin to define the biological phenotype first before genetic screens
start, and by the way address also the question if not the EpCAM negative circulating
tumor cells are the really important cells for the patients (referring to the so called
EMT program). If one decides to do genetic screens first before biological meanings
or phenotypes are known, one has to reason why and the whole conclusions should
be very critical and carefully addressed. This is not the case in this article.
- We have added the following text in the Discussion section:
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Another potential limitation of this approach is that it was only focused on EpCAMpositive CTCs. EpCAM-based selection methods, such as IE/FACS and
CellSearch™, may miss CTCs expressing low levels of EpCAM. The clinical
significance of EpCAM-negative CTCs has yet to be determined, but it has been
hypothesized that this may include cells undergoing epithelial-mesenchymal
transition [11].
2. Are the methods appropriate and well described?
This is for me the most critical aspect of the paper. The authors state, that they
use a novel method for CTC isolation. This is not true, as magnetic and FACS
sorting of CTCs has been done numerous times before. They do not
demonstrate one single FACS analysis, which is not acceptable. Our own
experiences with CTC analyses clearly demonstrate the difficulties that arise
when circulating tumor cells are to be analyzed. Separation of significant CTC
numbers from whole blood is very difficult, and it is not sufficient to demonstrate
only numbers from spiked in experiments, it is crucial to demonstrate the FACS
plots before and after magnetic separation, and before and after FACS sorting.
In my opinion including for example 7-AAD or PI as dead cell exclusion dye.
Otherwise one cannot believe reliable analysis of only 20 cells.
- We are not aware of any publication that has demonstrated the isolation of highly
pure EpCAM-positive CTCs via a combination of IE and FACS.
- We have added a complete FACS analysis from a representative patient
(Supplementary Figure 1).
How was ensured, that microdissected tumor areas included at least 80% tumor.
How was the microdissection done?
- We have added the following text to the Methods:
Using H&E stained slides, the pathologist (J.S.) demarcated tissue containing at least
80% tumor. The H&E stained slide was then used as a guide to microdissect the
tumor area using a surgical blade (Feather #15) on non-stained deparaffinized
sections (10 sections x 5µM thickness).
The included patients (table 1) have to be described in more detail: What was the
PSA level in these patients? Did the patients had hormonal treatment?
- All patients received hormonal treatment. We did not capture PSA data because the
study was not designed to find clinical correlates.
3. Are the data sound?
Compared to what is known so far about CNV in prostate cancer (see DNA copy
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number alterations in prostate cancers: a combined analysis of published
CGH-studies, Prostate, 2007, Sun et al.) the results are not new to the field:
Gains and losses in chromosomes 8q and 8p are not surprising. What is
surprising instead, the authors claim the CGH analysis of patient 9 to be
indicative of malignant origin with focal amplification in 11q13. Interestingly
however, this region was not widely described before as being a major spot for
CNVs in prostate cancer.
- We have modified the text in the Discussion as follows:
Molecular profiling of CTCs revealed genomic aberrations that have been previously
described in prostate cancer including gains in 8q, 11q13 and losses in 8p [12-13].
4. Does the manuscript adhere to the relevant standards for reporting and data
deposition?
No, in my opinion it is essential to describe the exact chromosome spot of CNVs
including the mega-bases interval. Furthermore it would be essential to mention
examples of tumor related genes, that are encoded in these regions, as I
mentioned in the first part: We do not know the biologic phenotype of “EpCAM+
CTCs” yet and we do not know e.g. the biologic phenotype of a focal
amplification in 11q13, but if we would know the related genes other researchers
could go into biological studies, e.g. knock-down/overexpression studies.
- We have added Supplementary Table 1 to show the exact chromosome region
(peaks) with aberrations (gain or loss) present in >50% of the samples. We also list
the genes and microRNA in the regions involved.
5. Are the discussion and conclusions well balanced and adequately supported
by the data?
No
- We have made multiple revisions to the Discussion as described above.
6. Are limitations of the work clearly stated?
No, this would be necessary
- We have made multiple revisions to the Discussion as described above.
In summary the paper should be rejected because of the following main reasons:
1. Important FACS plots to understand that the method used by the authors is
working, are missing.
- We have added a complete FACS analysis from a representative patient.
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2. Uncritical reporting about the importance of CTC in prostate cancer in general
and about the own results in particular.
- We have made multiple revisions to the Introduction and Discussion as described
above.
3. Only one result (gain in AR locus) is new to the field, the CTC detection
method is already known.
- This CTC method, which involves novel IE/FACS isolation as well as aCGH
profiling, is novel and has not been previously reported.
Level of interest: An article of limited interest
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests
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