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Rubicon Genomics' John Langmore |
Rubicon Sets Its Sights on Methylation Markers
Laurie Sullivan
Rubicon Genomics has
successfully developed, validated, and sold its GenomePlex and TransPlex
technologies for whole genome amplification and total RNA amplification,
respectively. Now that it has licensed both these technologies to
Sigma-Aldrich, Rubicon is poised to employ its newest technology, called
MethylPlex, to develop diagnostic products based on methylated DNA
biomarkers.
In an interview with Pharma
DD, John Langmore, Rubicon's Vice President of Commercial Development,
talks about the unique advantages of the TransPlex and MethylPlex
technologies, and the significance of this latest deal with Sigma-Aldrich to
Rubicon's future.
PDD:
Briefly describe Rubicon’s business model.
Dr.
Langmore:
Rubicon develops and commercializes research products used for drug
development as well as diagnostic products, which are co-developed with
pharmaceutical and diagnostic partners. The two types of products undergo
different commercial cycles, but the underlying DNA and RNA amplification
technologies are the same.
For
research products, the first step is developing a technology to meet an
industry need. The technology is refined and validated via fee-for-service
contracts with pharmaceutical companies and universities. Once the
technology has proven itself in that context, Rubicon packages and sells it
as a research kit for approximately one year to demonstrate market
acceptance before out-licensing the technology.
The
rationale behind out-licensing our research products is that our licensees
can reach a much broader market, enabling pharmaceutical and diagnostic
companies to adopt the technology in their product development processes.
These research applications benefit both Rubicon and its licensees in the
form of royalties and sales revenue. In addition, end users are encouraged
to further develop the technology for pharmacogenomic applications to
generate human testing products, which we also benefit from in terms of
royalties from the drug or diagnostic company.
Rubicon
uses the same underlying technologies to internally develop diagnostic
products. While we hope to commercialize these diagnostics independently in
the future, we currently have a number of partnerships within the
pharmaceutical and diagnostics industry to co-develop products for patient
testing. For example, one such partnership is with Abbott Laboratories using
our MethylPlex technology.
PDD:
Describe Rubicon’s history with Sigma-Aldrich, culminating in last
week’s deal for the TransPlex technology.
Dr.
Langmore:
GenomePlex whole genome amplification is an earlier research product, which
underwent the same type of commercial cycle as described above. Rubicon
internally developed GenomePlex in 2002, and subsequently validated its
performance in the course of a human genotyping project completed by
GlaxoSmithKline and Illumina. Rubicon began selling GenomePlex as a kit in
2003 while continuing to offer the technology as a fee-for-service to major
pharma companies. In 2004, Rubicon entered its first licensing agreement
with Sigma-Aldrich for GenomePlex, which has developed multiple new kits
based on the technology.
The
GenomePlex technology amplifies DNA for genotyping or CGH applications,
starting from a miniscule sample size, and it also works on degraded DNA
(e.g. from a biopsy sample). TransPlex is the same type of technology, only
it is used to amplify total RNA and therefore used for gene expression
profiling. Rubicon validated TransPlex by offering it as a service in 2004,
selling our own kits in 2005, and has now licensed the TransPlex technology
to Sigma, who will be responsible for all future sales, marketing,
distribution, and further development for R&D applications. Sigma is
free to develop versions of the kit to better meet the needs of niche
segments of the research market. For example, Sigma may opt to optimize the
technology for application to expression profiling of single cells,
single-molecule sequencing, or for virus detection.
PDD:
How will Rubicon benefit from the TransPlex licensing agreement with
Sigma-Aldrich?
Dr.
Langmore:
Licensing TransPlex to Sigma-Aldrich frees Rubicon to hone its focus on
developing diagnostic products. Sigma-Aldrich has proven to be a very
competent partner through its successful marketing and support of the
GenomePlex kits.
Importantly,
the deal provides Rubicon with revenue to support our diagnostic products.
As described below, going forward, Rubicon will focus on DNA methylation
markers of disease. Licensing the TransPlex technology to Sigma-Aldrich also
increases the chances that other parties will develop diagnostic products
based on the technology, which Rubicon will benefit from in the form of
royalties on patient tests.
PDD:
What are TransPlex’s unique advantages over other RNA-amplification
products?
Dr.
Langmore: The
Eberwine in vitro transcription process is almost universally used to
amplify RNA for microarray-based expression profiling. While the technique
works pretty well, it has two disadvantages. One, it is both labor- and
time-intensive, requiring many steps and a lot of hands-on technician time.
For example, it would take two days to amplify the RNA one million-fold with
the in vitro transcription process compared with less than four hours using
TransPlex, which is a simple single-tube, two-step process. The simplicity
of TransPlex is responsible for its robustness, reproducibility, and low
background—all necessary to do microarray expression profiling starting
from as little as 1 ng of total RNA.
Two,
the in vitro transcription process usually amplifies the RNA from the poly-A
tail (or, from one end of the transcript). If the transcript is degraded,
then the amplification process stops prematurely—it starts at one end of
the molecule and can only go to the other end if the entire molecule is
intact. Let’s say the molecule has been reduced to 500 bases—in that
case the Eberwine terminal amplification would amplify only those first 500
bases and then it would lose everything else beyond that.
It’s
important to understand what goes on over the whole transcript because in
many diseases, including cancer, there are exon splicing events, which can
take place differently at various stages of the disease. All the information
about splice events is revealed further down the transcript, far from the
poly-A tail. Obtaining information about splice variants therefore requires
amplification of all the RNA in the message, which is robustly achieved by
TransPlex regardless of whether the RNA is degraded or intact.
RNA
degradation becomes a critically important issue when doing retrospective
studies from formalin-fixed material. There are millions of patient biopsies
and surgical samples archived in the
US
and
Europe
, which are temporal snapshots of disease annotated with important
information about long-term clinical outcomes. It is possible to do very
effective drug target discovery or pharmacogenomic studies using such
retrospectively-enrolled patient samples, but only if the information can be
retrieved from the highly-degraded RNA within the formalin-fixed tissue
samples.
The
in vitro transcription methodology has been incorporated into many kits
(e.g. from Affymetrix, Ambion) and used across the board. There are some
newer companies with technologies that do not depend on in vitro
transcription, which have been tried by users doing profiling from
formalin-fixed materials. To my knowledge, those technologies haven’t
given reproducible results. Time isn’t a factor for that type of sample
but the quality of the results is. What people like about Rubicon’s
technology is that it is very reproducible and yields good gene expression
information, even from very old formalin-fixed paraffin-embedded samples.
PDD:
Please describe Rubicon’s focus moving forward.
Dr.
Langmore:
Rubicon’s newest technology, MethylPlex whole methylome amplification,
substantially simplifies discovery and validation of methylated DNA
biomarkers and increases the sensitivity and specificity of the resulting
patient tests. Methylation markers are very promising for several reasons.
They’re very stable in common clinical samples such as blood and biopsies,
and can be detected with high sensitivity (for example, one cancer cell in a
background of 10,000 normal cells). Third, DNA methylation is directly
linked to the biology of the disease. The levels of gene methylation are
qualitatively and quantitatively related to progression of many diseases,
including cancer. The traditional methods of detecting DNA methylation are
cumbersome, however, because they are based on organic chemistry and are not
very sensitive. To improve test sensitivity, Rubicon developed its
proprietary MethylPlex method to enzymatically amplify methylated DNA
sequences such that a single 1–5 nanogram sample of patient DNA becomes
sufficient to test for tens, hundreds, or thousands of methylated genes in
the course of a biomarker discovery/validation project.
We’ve
shown that the use of just a few methylated DNA markers is tremendously
powerful for distinguishing among different types of cancer. While gene
expression has been used to stratify patients according to cancer type and
treatment outcome, a large number of expression markers have been required
in order to have an effective test. For example, the Genomic Health Oncotype
DX breast cancer assay uses 21 genes, and Agendia’s MammaPrint gene
expression profiling service for breast cancer uses 70 genes. We think we
have the same or better power to test breast cancer samples using only a
handful of methylated DNA markers.
Rubicon
has a number of partnerships in place to develop methylation diagnostic
products, including some with drug companies interested in using methylation
analysis as part of their drug target discovery process. Eventually we hope
to market companion diagnostic tests. We’re very excited about MethylPlex
because of the high performance of this second-generation technology, and we
anticipate it will have great benefit for early detection and management of
disease in the future.
Copyright
2006, Cambridge Healthtech Institute. All Rights Reserved.
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