[GRG] NewAbs: 3-D Genomics and Disease

To Members and Friends of the Los Angeles Gerontology
Research Group:3-D
Genomics/Chromatin and disease… — Steve Coles

“Solving 3-D Genomics Puzzles Holds
Key to Understanding Human

April 30, 2014; (Genetic Engineering and Biotechnology News)
— Scientists
at McGill
University say they have discovered that the 3-D shape of
a leukemia
cell’s genome holds a key to solving the puzzle of human diseases. The
researchers report their findings (“Classifying leukemia types
with chromatin
conformation data”) in Genome Biology.
Dostie, Ph.D., a researcher in the Faculty of Medicine in the Department
of Biochemistry, focused on the shape made by the region spanning the
Homeobox A (HOXA) genes in human cells, a set of 11 genes encoding
proteins that are highly relevant to numerous types of cancers. Dr.
Dostie and colleagues discovered that the shape of this region of the
genome provided an excellent indicator for determining the subtype of
leukemia it comes from.“We
explore whether chromatin conformation can be used to classify human
leukemia. We map the conformation of the HOXA gene cluster in a panel of
cell lines with 5C chromosome conformation capture technology, and use
the data to train and test a support vector machine classifier named
3D-SP,” wrote the investigators. “We show that 3D-SP is able to
accurately distinguish leukemias expressing MLL-fusion proteins from
those expressing only wild-type MLL, and that it can also classify
leukemia subtypes according to MLL fusion partner, based solely on 5C
data. Our study provides the first proof-of-principle demonstration that
chromatin conformation contains the information value necessary for
classification of leukemia subtypes.”It is not
clear at the moment whether the genome shape plays a role in causing
the cancer, or
whether the cancer causes the genome to change shape. Further studies are
needed to determine whether genome shape is as good at indicating other
types of cancer.“Our study
validates a new research avenue: the application of
3-D genomics
for developing medical diagnostics or treatments that could be explored
for diseases where current technologies, including gene expression data,
have failed to improve patient care,” says Dr. Dostie, “While the use of
3-D genomics in the clinic is still remote when considering the technical
challenges required for translating the information to the bedside, we
discovered a new approach for classifying human disease that must be
explored further, if only for what it can reveal about how the human
genome works.”

L. Stephen Coles, M.D., Ph.D., Co-Founder
Los Angeles Gerontology Research GroupURL:
E-mail: scoles@grg.orgE-mail:


About Johnny Adams

My full-time commitment is to slow and ultimately reverse age related functional decline to increase healthy years of life. I’ve been active in this area since the 1970s, steadily building skills and accomplishments. I have a good basic understanding of the science of aging, and have many skills that complement those of scientists so they can focus on science to advance our shared mission. Broad experience Top skills: administration, management, information technology (data and programming), communications, writing, marketing, market research and analysis, public speaking, forging ethical win-win outcomes among stakeholders (i.e. high level "selling"). Knowledge in grant writing, fundraising, finance. Like most skilled professionals, I’m best described as a guy who defines an end point, then figures out how to get there. I enjoy the conception, design, execution and successful completion of a grand plan. Executive Director Gerontology Research Group (GRG). Manages Email discussion forum, web site, meetings and oversees supercentenarian (oldest humans, 110+ years) research. CEO / Executive Director Carl I. Bourhenne Medical Research Foundation (Aging Intervention Foundation), an IRS approved 501(c)(3) nonprofit. http://www.AgingIntervention.org Early contributor to Supercentenarian Research Foundation. Co-Founder Geroscience Healthspan Forum. Active contributor to numerous initiatives to increase healthy years of life. Co-authored book on conventional, practical methods available today to slow the processes of aging – nutrition, exercise, behavior modification and motivation, stress reduction, proper supplementation, damage caused by improper programs, risk reduction and others. Fundamental understanding of, and experience in the genomics of longevity (internship analyzing and curating longevity gene papers). Biological and technical includes information technology, software development and computer programming, bioinformatics and protein informatics, online education, training programs, regulatory, clinical trials software, medical devices (CAT scanners and related), hospital electrical equipment testing program. Interpersonal skills – good communication, honest, well liked, works well in teams or alone. Real world experience collaborating in interdisciplinary teams in fast paced organizations. Uses technology to advance our shared mission. Education: MBA 1985 University of Southern California -- Deans List, Albert Quon Community Service Award (for volunteering with the American Longevity Association and helping an elderly lady every other week), George S. May Scholarship, CA State Fellowship. BA psychology, psychobiology emphasis 1983 California State University Fullerton Physiological courses as well as core courses (developmental, abnormal etc). UCLA Psychobiology 1978, one brief but fast moving and fulfilling quarter. Main interest was the electrochemical basis of consciousness. Also seminars at the NeuroPsychiatric Institute. Other: Ongoing conferences, meetings and continuing education. Aging, computer software and information technology. Some molecular biology, biotech, bio and protein informatics, computer aided drug design, clinical medical devices, electronics, HIPAA, fundraising through the Assoc. of Fundraising Professionals. Previous careers include: Marketing Increasing skill set and successes in virtually all phases, with valuable experience in locating people and companies with the greatest need and interest in a product or service, and sitting across the table with decision makers and working out agreements favorable to all. Information Technology: Management, data analysis and programming in commercial and clinical trials systems, and bioinformatics and protein informatics. As IT Director at Newport Beach, CA based technology organization Success Family of Continuing Education Companies, provided online software solutions for insurance and financial professionals in small to Fortune 500 size companies. We were successful with lean team organization (the slower moving competition was unable to create similar software systems). Medical devices: At Omnimedical in Paramount CA developed and managed quality assurance dept. and training depts. for engineers, physicians and technicians. Designed hospital equipment testing program for hospital services division. In my early 20’s I was a musician, and studied psychology and music. Interned with the intention of becoming a music therapist. These experiences helped develop valuable skills used today to advance our shared mission of creating aging solutions.
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