On the cutting edge

A roundup of instrumentation, software and other tools and technology news

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As we look at some of the interesting hardware and software technologies available to improve the work of life-sciences researchers and lab staff, we will see some “walkers” (no, not the kind from “The Walking Dead,” thankfully), computational chemistry software, biologics de-risking, sequencing analysis and new assays/panels.

Microscopic “walkers” find their way across cell surfaces
CAMBRIDGE, Mass.—In a case of technology that could provide a way to deliver probes or drugs to cell structures without outside guidance, a team of researchers at the Massachusetts Institute of Technology (MIT) led by Alfredo Alexander-Katz, the Walter Henry Gale Associate Professor of Materials Science and Engineering, has demonstrated a new target-finding mechanism. The new system allows microscopic devices to autonomously find their way to areas of a cell surface, for example, just by detecting an increase in surface friction in places where more cell receptors are concentrated.
“The idea was to find out if we could create a synthetic, active system that could sense gradients in biological receptors,” Alexander-Katz explains. “Currently, we don’t know of anything that can do that.”
Cells have a way of locating areas that bear a specific kind of chemical signature—a process called chemotaxis. That’s the method used by white blood cells, for example, to locate regions where pathogens are attacking body cells.
The new system uses a pair of linked particles with magnetic properties. In the presence of a magnetic field, the paired particles begin to tumble across a surface, with first one particle and then the other making contact—in effect, “walking” across the surface.
So far, the work has been carried out on a model cell surface, on a functionalized microscope slide, but the effect should work similarly with living cells, Alexander-Katz says. The team’s goal now is to demonstrate the ability of the microscopic walkers to find their way toward concentrations of receptors in actual living tissue.
The method could potentially have a variety of applications, Alexander-Katz says. For example, it could be developed as a method of locating tumor cells within the body by identifying their surface texture, perhaps in combination with other characteristics.

Nagoya University institute licenses Cresset’s computational chemistry software
CAMBRIDGE, U.K.—Cresset, innovative provider of computational chemistry software and services, announced in late fall 2014 that Nagoya University’s Institute of Transformative Bio-Molecules (ITbM), located in Nagoya, Japan, has licensed Cresset’s Forge, a computational chemistry suite for understanding SAR and molecular design.
“The focal point of ITbM is to develop transformative bio-molecules that will be key to solving urgent problems at the interface of chemistry and biology,” says Associate Prof. Ayato Sato, head of the Research Promotion Division and the chief coordinator of the ITbM Chemical Library Center. “We are confident that licensing Cresset’s software will accelerate our research to find candidates of transformative bio-molecules.”
“We are delighted that Cresset software is assisting Japanese biomolecular research,” says Dr David Bardsley, commercial director at Cresset. “Forge uses the shape and electrostatic character of molecules to create qualitative and quantitative 3D models of activity. It is the ideal tool to assist ITbM in their research.”

Chugai licenses EpiVax platform to de-risk biologics
PROVIDENCE, R.I.—Chugai Pharmaceutical Co. Ltd. recently signed an agreement with Rhode Island-based biotechnology company EpiVax Inc. to incorporate EpiVax's ISPRI (Interactive Protein Screening and Reengineering Interface) immunogenicity screening and deimmunization technology into Chugai's drug development toolbox. Researchers at Chugai will be utilizing the cloud-based in-silico ISPRI in conjunction with OptiMatrix, a tool for deimmunizing biologics, to screen and re-engineer therapeutic proteins for potential immunogenicity and deimmunize immune-dominant epitopes, known as clusters.
Dr. Tomoyuki Igawa, group manager of the Discovery Research Department at Chugai, said that “Integration of ISPRI into the Chugai's antibody engineering and optimization platform will reduce the immunogenicity risk and increase the likelihood of successful clinical development for important, human life-saving biologics.”
EpiVax says that ISPRI is the only screening system that takes into consideration Tregitopes (T regulatory epitopes), a unique EpiVax discovery that is associated with regulatory T cell induction.
“Our unique approach to developing safe and effective protein therapeutics by screening for T effector and T regulatory epitopes (Tregitopes) is at the core of the ISPRI Toolkit,” said Dr. Anne De Groot, president and CEO of EpiVax. “We have a demonstrated ability to use our immunoinformatics tools to screen and re-engineer protein therapeutics, in federally funded, peer-reviewed programs. We're impressed with the team at Chugai, and their plans to integrate the ISPRI Toolkit with the OptiMatrix Tool into their antibody engineering and optimization development process. We anticipate that Chugai scientists will be able to create a whole range of highly effective ‘new generation’ biologics at a highly accelerated pace.”

Software selected to automate and standardize NGS data analysis
TOKYO—Genedata, a provider of advanced software solutions for drug discovery and life-sciences research, recently announced that Takara Bio Inc., a global biotechnology company, has chosen Genedata Expressionist for Genomic Profiling as its key software platform for next-generation sequencing (NGS) data. The platform will be integrated with in-house and third-party data analysis tools and databases, providing a single integrated environment for fully automated multi-omics data processing and comprehensive data management.
“We are committed to deliver innovative services and highest-quality data to our customers. Genedata helps us to continue to deliver on our promise by providing a software platform which automates and manages NGS data analysis workflows for all relevant applications,” noted Masanari Kitagawa, executive officer of Takara Bio. “In addition, the platform enables us to utilize the latest technology developments for our own internal research projects.”
One of the reasons why Takara Bio chose the Genedata platform is its ability to integrate multi-omics data from internal and external data sources. The open and comprehensive software solution reportedly allows interdisciplinary teams to work together and to extract the most value from highly complex experimental datasets.

GO Clinical Workbench goes forth in two arenas
CLEVELAND—CompanionDx Reference La, LLC, a high-complexity CLIA-certified laboratory specializing in pharmacogenomics, cancer companion diagnostics and targeted next-generation sequencing (NGS), is offering a series of NGS-based assays related to cancer. To enable efficient and compliant clinical reporting from NGS, CompanionDx chose to partner with GenomOncology, an Ohio-based genomics technology and services provider, and put its GO Clinical Workbench to work.
“The ability to deliver therapy-driven clinical reports—rapidly and in a high-assurance manner—was an important requirement in our evaluation process,” David Lasecki, president of CompanionDx, states. “In addition, the GO Clinical Workbench enables our laboratory to manage increased volume and quickly add new assays to meet the needs of our oncologists.”
“Creating high-quality, reproducible data from NGS has become easier,” states Steve Gustafson, chief operating officer of GenomOncology. “However, the reporting process in the clinical laboratory poses several challenges. Our primary focus is optimizing this process from QC to clinical interpretation, sign out and delivery.”
In other GO Clinical Workbench news, GenomOncology announced that the Ohio State University College of Medicine’s Department Of Pathology will use GO Clinical Workbench to enable clinical reporting of mutations detected from NGS.
“Cancer is a complex disease, with tremendous diversity in pathology and genetics,” commented Dr. Weiqiang John Zhao, an assistant professor in the Clinical Pathology Branch of the university. “The determination of genomic information from an individual’s tumor by NGS can be used to devise treatment approaches that are specific to that patient.”
“NGS generates a significant amount of data and the process of developing clinically useful reports from this data is time consuming. The GO Clinical Workbench has helped us reduce the time to develop a clinically actionable report from half a day to less than an hour,” added Pamela Groen, laboratory manager.
GenomOncology’s GO Clinical Workbench streamlines the use of NGS data and allows molecular pathology laboratories to produce an actionable clinical report using the molecular profile of an individual patient’s tumor. The platform is installed within the institution’s firewall and is configured to each laboratory’s specific needs including integration with laboratory systems (LIMS, EMR, etc.), setting of quality control and annotation parameters and custom design of the clinical report.
“Today’s Molecular Pathology lab faces many challenges. Our goal is to enable the lab to produce a comprehensive clinical report that integrates therapy rules, supporting levels of evidence, active clinical trials and complimentary testing modalities to best serve their oncologists,” noteed Manuel Glynias, president and CEO of GenomOncology. “Generating this report in a highly efficient, scalable and compliant manner is our primary focus.”

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