Monthly Archives: March 2015

A study using super-resolution microscopy reveals that our genome is not regularly packaged and links these packaging differences to stem cell state

VIDEO:A study using super-resolution microscopy reveals that our genome is not regularly packaged and links these packaging differences to stem cell state. A multidisciplinary approach allowed scientists to view and... view more

In 1953 Watson and Crick first published the discovery of the double helix structure of the DNA. They were able to visualize the DNA structure by means of X-Ray diffraction. Techniques, such as electron microscopy, allowed scientists to identify nucleosomes, the first and most basic level of chromosome organisation. Until now it was known that our DNA is packaged by regular repeating units of those nucleosomes throughout the genome giving rise to chromatin. However, due to the lack of suitable techniques and instruments, the chromatin organisation inside a cell nucleus could not be observed in a non-invasive way with the sufficient resolution. Now, for the first time, a group of scientists at the CRG and ICFO in Barcelona, have been able to visualise and even count the smallest units which, packaged together, form our genome. This study was possible thanks to the use of super-resolution microscopy, a new cutting-edge optical technique that received the Nobel Prize in Chemistry in 2014. In combination with innovative quantitative approaches and numerical simulations, they were also able to define the genome architecture at the nano-scale. Most importantly, they found that the nucleosomes are assembled in irregular groups across the chromatin and nucleosome-free-DNA regions separate these groups.

Biologists and physicists have been working together to take a step forward in chromatin fibre observations and studies. "By using the STORM technique, a new super-resolution microscopy method, we have been able to view and even count nucleosomes across the chromatin fibers and determine their organisation. STORM overcomes the diffraction limit that normally restricts the spatial resolution of conventional microscopes and enables us to precisely define the chromatin fibre structure", states Prof. Melike Lakadamyali, group leader at ICFO.

This enabling technique allowed the researchers to go deeper and, by comparing stem cells to differentiated cells (specialised cells that have already acquired their role), they observed key differences in the chromatin fibre architectures of both cells. Pia Cosma, group leader and ICREA research professor at the CRG explains, "We found that stem cells have a different chromatin structure than somatic (specialised) cells. At the same time, this difference correlates with the level of pluripotency. The more pluripotent a cell is, the less dense is its packaging. It gives us new clues to understand the stem cells functioning and their genomic structure, which will be helpful for example, in studying cell reprogramming".

What scientists have found is that DNA is not regularly packaged with nucleosomes, instead nucleosomes are assembled in groups of varying sizes, called "nucleosome clutches" -because of their similarity to egg clutches-. They found that pluripotent stem cells have, on average, clutches with less density of nucleosomes. In addition, clutch size is related to the pluripotency potential of stem cells, meaning that the more pluripotent a cell is, the less nucleosomes are included in its clutches.

Even though all the cells in our body have the same genetic information, they are not expressing all the genes at the same time. So, when a cell specialises, some of the DNA regions are silenced or less accessible to the molecule that reads the genome: the RNA polymerase. Depending on the specialisation of the cells, different levels of DNA packaging will occur. This new work published in the prestigious journal Cell, establishes a new understanding of how the chromatin fibre is assembled and packaged forming a specific DNA structure in every cell.

This research definitively contributes to the understanding of a novel feature of stem cells and their DNA structure, which is important for maintaining an induced pluripotent state. A joint patent has been filed by ICFO and CRG, who are now exploring business opportunities for marketing the classification of "stemness" state of cells, ie, their degree of pluripotency. This technique could determine with single cell sensitivity the pluripotency potential of stem cells, thus having the capacity of becoming a standard method of quality control of stem or pluripotent cells before their use in cell therapy or research in biomedicine.

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This work has been carried out by scientists from the Centre for Genomic Regulation Maria Aurelia Ricci and ICREA Research Prof. Pia Cosma together with Dr. Carlo Manzo, ICREA Research Prof. Mara Garca-Parajo, and Prof. Melike Lakadamyali from the Institute of Photonic Sciences. The outcome of this study has shown the successful collaboration between biologists and physicists from two of the leading research institutes of their respective fields in Europe, both located in Barcelona. It reinforces the importance of having multidisciplinary collaborations in search for the advancement of science.

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Super-resolution microscopes reveal the link between genome packaging and cell pluripotency

BALTIMORE, March 12, 2015 /PRNewswire/ --Personal Genome Diagnostics Inc. (PGDx), a provider of advanced cancer genome analysis and testing services, today announced that it has been selected by the US Department of Veterans Affairs (VA) New England Veteran's Integrated Service Network (VISN 1) to provide targeted genomic testing services for a new Precision Oncology Program (POP). PGDx's CancerSelectTM targeted gene panel will be run for patients in the program with newly-diagnosed lung cancer. CancerSelect detects alterations in 88 well-characterized genes that include nearly all targets of currently available or investigational cancer treatments.

The Precision Oncology Program is being established by the Department of Veterans Affairs VISN 1 to support the collection and enhanced analysis of data on all patients seen in VISN 1 network hospitals who have a lung cancer diagnosis. It aims to provide state-of-the-art clinical care to veterans as well as opportunities for the discovery and validation of new cancer biomarkers. Evaluation measures in the program will enable assessments of how the POP is impacting VA cancer patient outcomes.

Jeffrey Boschwitz, PhD, Chief Operating Officer at PGDx, commented, "We are honored that the VA's VISN 1 has selected PGDx to provide targeted DNA profiling for the Precision Oncology Program, and applaud its leadership in this field that is rapidly transforming the treatment of cancer. We specifically designed our CancerSelect panel to have unsurpassed sensitivity and specificity while maintaining its cost-effectiveness, so that it can be available to patients in a range of healthcare settings, including programs such as POP. We welcome the opportunity to support this innovative program and the veterans it serves."

The Precision Oncology Program is initially focusing on newly-diagnosed non-small cell lung cancer patients served by the New England Veterans Integrated Service Network. However, program organizers hope to offer testing to all VA hospitals nationwide, and view the initial effort as the forerunner to a larger initiative intended to increase access to cancer genomic testing, targeted therapies and clinical trials across the VA system.

CancerSelect uses next-generation sequencing technology to identify somatic mutations, focal amplifications, and translocations in the genes that have the greatest potential to impact treatment decisions. Many cancer gene tests only identify point mutations; yet all three types of genetic alterations can play a role in disease progression and response to treatment. PGDx's proprietary bioinformatics pipeline enables CancerSelect to maintain high sensitivity and specificity at mutant allele frequencies as low as 2%, which is lower than any other test currently available.

PGDx was awarded this contract with the Department of Veterans Affairs based on a competitive process. Further details were not disclosed.

About Personal Genome DiagnosticsPersonal Genome Diagnostics (PGDx) provides advanced cancer genome analyses to oncologyresearchers, drug developers, clinicians and patients. The company uses advanced genomic methods and its deep expertise in cancer biology to identify and characterize the unique genomic alterations in tumors. PGDx's proprietary methods for genome sequencing and analysis are complemented by its extensive experience in cancer genomics and clinical oncology. Co-founders Luis Diaz, MD, and Victor Velculescu, MD, PhD, are internationally recognized leaders in cancer genomics who have extensive experience in the practical application of advanced genomic technologies to research, drug development and clinical practice. PGDx's CLIA-certified facility provides personalized cancer genome analyses to patients and their physicians. For more information, visit http://www.personalgenome.com.

Contacts PGDx Corporate: Jeffrey Boschwitz, PhD 443-330-7585 jboschwitz@personalgenome.com

PGDx Media: BLL Partners, LLC Barbara Lindheim212-584-2276 blindheim@bllbiopartners.com

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Personal Genome Diagnostics Selected By Department of Veterans Affairs VISN 1 To Provide Targeted DNA Testing For Its ...