Brain Cancer, Alzheimer’s Share Cellular Process

By Tiffany Trader

April 22, 2014

Using the advanced computational resources at the Texas Advanced Computing Center (TACC) at The University of Texas at Austin, researchers uncovered a link between Alzheimer’s disease and cancer that may pave the way for better treatment options and new medicines. The two afflictions share a pathway in gene transcription, a process essential for cell reproduction and growth. The team, led by Houston Methodist Research Institute (HMRI), published its findings in December 2013 in the open access journal Scientific Reports by the Nature Publishing Group.

The scientists used TACC’s Lonestar and Stampede supercomputers to analyze and compare data from thousands of genes, looking for common cell signaling pathways shared by the two diseases. The Lonestar and Stampede systems are part of the Extreme Science and Engineering Discovery Environment (XSEDE), a virtual science environment that supports the interactive sharing of compute resources, data and expertise. Funding for the research comes from the T.T. and W.F. Chao Foundation, and by grants from the National Institutes of Health (NIH).

 

gliobalstoma-alzheimers-diagram

When comparing with normal brain tissues, the microarray profiles for brain tissues from Alzheimer’s disease and GBM patients show significantly reversed signaling activities, highlighted by Gene Ontology terms (nodes) enriched with genes down-regulated in AD (shown as blue in the node face, with darker color indicate larger fold changes) and up-regulated in GBM (red in the node boundary). Credit: Image and caption used with permission by Stephen Wong.

According to lead investigator Stephen Wong, a medical researcher and bioengineer with HMRI, the study is the first to establish a link at the molecular level between Alzheimer’s disease, the most prevalent type of neurodegenerative disease, and glioblastoma multiform (GBM), the most aggressive type of brain cancer.

Earlier studies in 2012 and 2013 found an inverse association between Alzheimer’s disease, which is characterized by nerve cell death and tissue loss in the brain, and with cancer, which occurs when abnormal cells grow and spread very fast. The data pointed to a common genetic pathway, but the details weren’t there.

“No one understands why this link is there, in a biological sense,” Wong said. “And that’s the reason we did this study. I think we are among the first to study it this way.”

The first step in finding the common genes expressed in each disease is to use DNA microarray to reveal the active and inactive genes shared between the two diseases.

The active genes are then mapped to known pathways through a process called pathway analysis. The group began with a working list of potential common pathways and narrowed this down through validation tests performed with cell cultures and live mice.

Knowing this pathway will be a huge step forward in the search for new therapies for this debilitating and deadly diseases.

The results of this study show that the ERK/MAPK cell signal pathway is up-regulated in brain cancer, while the Angiopoietin Signaling pathway is up-regulated in Alzheimer’s disease. In Alzheimer’s cells from mice, tumor suppression is mediated by the ERK-AKT-p21-cell cycle pathway and anti-angiogenesis pathway.

“Although GBM and Alzheimer’s both affect nearly 50% for aged population between 65 and 85 years of age, the body itself has very fine regulation at a very detailed level within the individual signaling pathways to make these two diseases exclude each other,” said study co-author Hong Zhao with the HMRI. “Different kinds of cells, like Alzheimer’s disease cells or cancer cells, have very fine and elaborated regulations on the general molecular signaling pathways, which depend on the cells’ response to the microenvironments.”

The study relied on microarray data covering 524 AD and 1,091 GBM subjects. The analysis included gene annotation, pathway expansion, enrichment analysis, and other details, which was enabled by TACC’s powerful supercomputers.

From this data set, the scientists identified more than 2,000 significant genes with 15 gene ontology terms marked as significantly changed.

“TACC helped us in accomplishing data analysis. We’re using TACC’s Lonestar and Stampede supercomputing clusters to do all this number crunching,” Wong said.

While this study mainly looked at “fairly manageable” data sets of microarray data, the next stage will require that the team analyze much more fine-grained and computationally costly gene sequencing data.

“The gene sequencing data size would easily be 1000-fold larger than the microarray data in the reported study,” Wong said, “which means the need to use TACC’s Lonestar and Stampede supercomputing clusters for number crunching is even more eminent.”

Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industy updates delivered to you every week!

Inspur Establishes Artificial Intelligence (AI) Department

Google Showcases 2017 AI Research Highlights

January 23, 2018

Looking for a good snapshot of the state of AI research? Cloud giant Google recently reviewed its 2017 AI research and application highlights in a two-part blog. While hardly comprehensive, it’s a worthwhile, fast read Read more…

By John Russell

UCSD, AIST Forge Tighter Alliance with AI-Focused MOU

January 18, 2018

The rich history of collaboration between UC San Diego and AIST in Japan is getting richer. The organizations entered into a five-year memorandum of understanding on January 10. The MOU represents the continuation of a 1 Read more…

By Tiffany Trader

New Blueprint for Converging HPC, Big Data

January 18, 2018

After five annual workshops on Big Data and Extreme-Scale Computing (BDEC), a group of international HPC heavyweights including Jack Dongarra (University of Tennessee), Satoshi Matsuoka (Tokyo Institute of Technology), Read more…

By John Russell

HPE Extreme Performance Solutions

HPE and NREL Take Steps to Create a Sustainable, Energy-Efficient Data Center with an H2 Fuel Cell

As enterprises attempt to manage rising volumes of data, unplanned data center outages are becoming more common and more expensive. As the cost of downtime rises, enterprises lose out on productivity and valuable competitive advantage without access to their critical data. Read more…

Researchers Measure Impact of ‘Meltdown’ and ‘Spectre’ Patches on HPC Workloads

January 17, 2018

Computer scientists from the Center for Computational Research, State University of New York (SUNY), University at Buffalo have examined the effect of Meltdown and Spectre security updates on the performance of popular H Read more…

By Tiffany Trader

UCSD, AIST Forge Tighter Alliance with AI-Focused MOU

January 18, 2018

The rich history of collaboration between UC San Diego and AIST in Japan is getting richer. The organizations entered into a five-year memorandum of understandi Read more…

By Tiffany Trader

New Blueprint for Converging HPC, Big Data

January 18, 2018

After five annual workshops on Big Data and Extreme-Scale Computing (BDEC), a group of international HPC heavyweights including Jack Dongarra (University of Te Read more…

By John Russell

Researchers Measure Impact of ‘Meltdown’ and ‘Spectre’ Patches on HPC Workloads

January 17, 2018

Computer scientists from the Center for Computational Research, State University of New York (SUNY), University at Buffalo have examined the effect of Meltdown Read more…

By Tiffany Trader

Fostering Lustre Advancement Through Development and Contributions

January 17, 2018

Six months after organizational changes at Intel's High Performance Data (HPDD) division, most in the Lustre community have shed any initial apprehension aroun Read more…

By Carlos Aoki Thomaz

When the Chips Are Down

January 11, 2018

In the last article, "The High Stakes Semiconductor Game that Drives HPC Diversity," I alluded to the challenges facing the semiconductor industry and how that may impact the evolution of HPC systems over the next few years. I thought I’d lift the covers a little and look at some of the commercial challenges that impact the component technology we use in HPC. Read more…

By Dairsie Latimer

How Meltdown and Spectre Patches Will Affect HPC Workloads

January 10, 2018

There have been claims that the fixes for the Meltdown and Spectre security vulnerabilities, named the KPTI (aka KAISER) patches, are going to affect applicatio Read more…

By Rosemary Francis

Momentum Builds for US Exascale

January 9, 2018

2018 looks to be a great year for the U.S. exascale program. The last several months of 2017 revealed a number of important developments that help put the U.S. Read more…

By Alex R. Larzelere

ANL’s Rick Stevens on CANDLE, ARM, Quantum, and More

January 8, 2018

Late last year HPCwire caught up with Rick Stevens, associate laboratory director for computing, environment and life Sciences at Argonne National Laboratory, f Read more…

By John Russell

Inventor Claims to Have Solved Floating Point Error Problem

January 17, 2018

"The decades-old floating point error problem has been solved," proclaims a press release from inventor Alan Jorgensen. The computer scientist has filed for and Read more…

By Tiffany Trader

US Coalesces Plans for First Exascale Supercomputer: Aurora in 2021

September 27, 2017

At the Advanced Scientific Computing Advisory Committee (ASCAC) meeting, in Arlington, Va., yesterday (Sept. 26), it was revealed that the "Aurora" supercompute Read more…

By Tiffany Trader

Japan Unveils Quantum Neural Network

November 22, 2017

The U.S. and China are leading the race toward productive quantum computing, but it's early enough that ultimate leadership is still something of an open questi Read more…

By Tiffany Trader

AMD Showcases Growing Portfolio of EPYC and Radeon-based Systems at SC17

November 13, 2017

AMD’s charge back into HPC and the datacenter is on full display at SC17. Having launched the EPYC processor line in June along with its MI25 GPU the focus he Read more…

By John Russell

Nvidia Responds to Google TPU Benchmarking

April 10, 2017

Nvidia highlights strengths of its newest GPU silicon in response to Google's report on the performance and energy advantages of its custom tensor processor. Read more…

By Tiffany Trader

IBM Begins Power9 Rollout with Backing from DOE, Google

December 6, 2017

After over a year of buildup, IBM is unveiling its first Power9 system based on the same architecture as the Department of Energy CORAL supercomputers, Summit a Read more…

By Tiffany Trader

Fast Forward: Five HPC Predictions for 2018

December 21, 2017

What’s on your list of high (and low) lights for 2017? Volta 100’s arrival on the heels of the P100? Appearance, albeit late in the year, of IBM’s Power9? Read more…

By John Russell

Chip Flaws ‘Meltdown’ and ‘Spectre’ Loom Large

January 4, 2018

The HPC and wider tech community have been abuzz this week over the discovery of critical design flaws that impact virtually all contemporary microprocessors. T Read more…

By Tiffany Trader

Leading Solution Providers

Perspective: What Really Happened at SC17?

November 22, 2017

SC is over. Now comes the myriad of follow-ups. Inboxes are filled with templated emails from vendors and other exhibitors hoping to win a place in the post-SC thinking of booth visitors. Attendees of tutorials, workshops and other technical sessions will be inundated with requests for feedback. Read more…

By Andrew Jones

Researchers Measure Impact of ‘Meltdown’ and ‘Spectre’ Patches on HPC Workloads

January 17, 2018

Computer scientists from the Center for Computational Research, State University of New York (SUNY), University at Buffalo have examined the effect of Meltdown Read more…

By Tiffany Trader

Tensors Come of Age: Why the AI Revolution Will Help HPC

November 13, 2017

Thirty years ago, parallel computing was coming of age. A bitter battle began between stalwart vector computing supporters and advocates of various approaches to parallel computing. IBM skeptic Alan Karp, reacting to announcements of nCUBE’s 1024-microprocessor system and Thinking Machines’ 65,536-element array, made a public $100 wager that no one could get a parallel speedup of over 200 on real HPC workloads. Read more…

By John Gustafson & Lenore Mullin

How Meltdown and Spectre Patches Will Affect HPC Workloads

January 10, 2018

There have been claims that the fixes for the Meltdown and Spectre security vulnerabilities, named the KPTI (aka KAISER) patches, are going to affect applicatio Read more…

By Rosemary Francis

Delays, Smoke, Records & Markets – A Candid Conversation with Cray CEO Peter Ungaro

October 5, 2017

Earlier this month, Tom Tabor, publisher of HPCwire and I had a very personal conversation with Cray CEO Peter Ungaro. Cray has been on something of a Cinderell Read more…

By Tiffany Trader & Tom Tabor

Flipping the Flops and Reading the Top500 Tea Leaves

November 13, 2017

The 50th edition of the Top500 list, the biannual publication of the world’s fastest supercomputers based on public Linpack benchmarking results, was released Read more…

By Tiffany Trader

GlobalFoundries, Ayar Labs Team Up to Commercialize Optical I/O

December 4, 2017

GlobalFoundries (GF) and Ayar Labs, a startup focused on using light, instead of electricity, to transfer data between chips, today announced they've entered in Read more…

By Tiffany Trader

HPC Chips – A Veritable Smorgasbord?

October 10, 2017

For the first time since AMD's ill-fated launch of Bulldozer the answer to the question, 'Which CPU will be in my next HPC system?' doesn't have to be 'Whichever variety of Intel Xeon E5 they are selling when we procure'. Read more…

By Dairsie Latimer

  • arrow
  • Click Here for More Headlines
  • arrow
Share This