For the first time, large-scale information on the biochemical makeup of small interfering RNA (siRNA) molecules is available publicly. These molecules are used in research to help scientists better understand how genes function in disease. Making these data accessible to researchers worldwide increases the potential of finding new treatments for patients.
NIH’s National Center for Advancing Translational Sciences (NCATS) collaborated with Life Technologies Corporation of Carlsbad, Calif., which owns the siRNA information, to make it available to all researchers.
RNA interference(RNAi), a cellular process that can stop specific proteins from being coded by silencing the genes that produce them.
The siRNA molecules, which can selectively inhibit the activity of genes, are used in RNA interference (RNAi) research. RNAi is a natural process that cells use to control the activity of specific genes. Its discovery led to the 2006 Nobel Prize in Physiology or Medicine.
Last month, a team of NIH scientists, led by Richard Youle, Ph.D., at the National Institute of Neurological Disorders and Stroke (NINDS), and Scott Martin, Ph.D., at NCATS, used RNAi to find genes that linked to Parkinson’s disease, a devastating movement disorder. The new genes may represent new starting points for developing treatments.
Scientists have harnessed the power of RNAi to study the function of many individual genes by reducing their activity levels, or silencing them. This process enables researchers to identify genes and molecules that are linked to particular diseases. To do this, researchers use siRNAs, which are RNA molecules that have a complementary chemical makeup, or sequence, to that of a targeted gene. While the gene is silenced, researchers look for changes in cell functions to gain insights about what it normally does. By silencing genes in the cell one at a time, scientists can explore and understand their complex relation to other genes in the context of disease.
Until now, a major limitation in the scientific community’s use of RNAi data has been the lack of a publicly available dataset, along with siRNA sequences directed against every human gene. Historically, providers have not allowed publishing of proprietary siRNA sequence information. To address this problem, NCATS and Life Technologies are providing all researchers with access to siRNA data from Life Technologies’ Silencer Select siRNA library, which includes 65,000 siRNA sequences targeting more than 20,000 human genes. Simultaneously, NCATS is releasing complementary data on the effects of each siRNA molecule on biological functions. All of this information is available to the public free-of-charge through NIH’s public database PubChem.
‘Producing and releasing these data demonstrate NCATS’ commitment to speeding the translational process for all diseases,’ said NCATS Director Christopher P. Austin, M.D. ‘The Human Genome Project showed that public data release is critical to scientific progress. Similarly, I believe that making RNAi data publicly available will revolutionise the study of biology and medicine.’
Experts from the NIH RNAi initiative, administered by NCATS’ Division of Pre-Clinical Innovation, conduct screens for NIH investigators. They will add new RNAi data into PubChem on an ongoing basis, making the database a growing resource for gene function studies.
‘By releasing all our siRNA sequences, we are enabling novel strategies to advance fundamental understanding of biology and discovery of new potential drug targets,’ said Mark Stevenson, president and chief operating officer of Life Technologies.
NIH invites other companies that sell siRNA libraries and researchers who conduct genome-wide RNAi screens with the Life Technologies library to deposit sequence data and biological activity information into PubChem. For assistance with submitting data to PubChem, researchers may contact info@ncbi.nlm.nih.gov.
‘Translation of siRNA library screening results into impactful downstream experiments is the ultimate goal of scientists using our library,’ said Alan Sachs, M.D., Ph.D., head of global research and development for Life Technologies. ‘The availability of these sequence data should greatly facilitate this effort because scientists no longer will be blinded to the actual sequence they are targeting.’ National Institutes of Health

A study done by researchers at Fox Chase Cancer Center shows that many relatives of patients who undergo testing for a gene linked to breast and ovarian cancers misinterpret the results, and less than half of those who could benefit from genetic testing say they plan to get tested themselves—despite the fact that knowing your genetic status may help catch the disease in its earliest stages.
‘People don’t always understand genetic information, so there’s confusion,’ says study author Mary B. Daly, MD, PhD, chair of the Department of Clinical Genetics at Fox Chase. ‘Family members are either not understanding what they’re hearing, not realising it has implications for them, or they’re not hearing it at all.’
For a long time, Daly says she ‘naively’ assumed that, once one family member knew whether or not they carried genes linked to breast and ovarian cancers—known as BRCA1/2—their entire family would understand the result, and what it meant for their own genetic risk. ‘Over time, we realised that wasn’t happening, or it wasn’t happening very well.’
Some genetic information is straightforward, says Daly. For example, when a woman learns she carries BRCA1/2 that means her parents, siblings and children may also carry the gene. But there are more ‘indeterminate’ results, which are harder to interpret, she adds. If a woman with a strong family history of breast and ovarian cancers tests negative for the BRCA1/2 genes, that does not mean her relatives are not at risk, says Daly—her siblings could still carry the gene, or there could be additional genes present that predispose them to cancer that clinicians don’t yet know how to test for.
‘When you look at some of these families who are so full of breast and ovarian cancer, and the person tests negative, you think there’s got to be something going on here. We just can’t find it. That’s a difficult thing for someone to explain to a relative,’ says Daly.
To understand better what was (and was not) being communicated after people underwent genetic testing, Daly and her team called 438 relatives of 253 people who had undergone genetic testing and said they’d shared their results. More than one-quarter of family members reported the test result incorrectly. They were most likely to understand positive results—like their family member carries the BRCA1/2 gene. But only 60% understood the so-called ‘indeterminate’ results, where their relative tested negative for the gene but they and other family members could still be at risk. Nearly one-third said they had trouble understanding the result.
Concerningly, only half (52%) of family members whose relative tested positive for the BRCA1/2 gene said they planned to get tested themselves. Among those whose relative tested negative for the BRCA1/2 gene, but knew the gene was present in their families (meaning they could still carry the gene), only 36% said they were going to find out their own genetic risk. ‘These findings imply the family members did not fully understand the significance of these results for their own risk,’ says Daly.
People were more likely to share their results with adult children than parents or siblings, and particularly with female relatives. ‘Over and over you hear people say ‘I’m doing this for my children’s sake,” says Daly.
As part of the study, Daly and her colleagues had asked half of the people getting tested to participate in two coaching sessions to help them communicate their results to relatives, such as through role playing. However, these people were no more likely to communicate the result of their tests than people who had simply sat through educational sessions about overall health. ‘It didn’t matter which group they were in, unfortunately,’ says Daly. ‘That disappointed me.’
But it also inspired her to develop the next project—exploring the effect of directly reaching out to the relatives of someone who underwent genetic testing (with that person’s permission), to see if hearing the results from an expert who’s not personally involved in the situation helps family members understand what they mean. Fox Chase Cancer Center

St. Jude Children’s Research Hospital scientists led a study showing that mutations in a gene responsible for amyotrophic lateral sclerosis (ALS) disrupt the RNA transport system in nerve cells.
The findings offer a new avenue for researchers to pursue in the quest for desperately needed treatments for ALS, a disorder that kills most patients within five years of diagnosis. ALS, also known as Lou Gehrig’s disease, is diagnosed in about 5,600 individuals nationwide each year and is associated with muscle weakness and paralysis.
The gene, TDP-43, carries instructions for making a protein of the same name. While mutations in TDP-43 were known to cause ALS and a related neurodegenerative disorder, until now the mechanism involved was a mystery. This study showed for the first time that the mutations disrupt efficient movement within nerve cells of RNA molecules. These RNA molecules direct protein assembly based on instructions carried in DNA. Correct transport of these RNAs permits proteins to be made in the right place at the right time.
Working in motor neurons derived from patients with ALS, researchers demonstrated that each of three different TDP-43 mutations impaired delivery of RNA molecules to their final destination near the junction where a nerve and its target muscle meet. Without the RNA molecules, nerves cannot make proteins necessary to function normally and respond quickly when stimulated. Motor neurons govern movement, including breathing. Their death and deterioration is a hallmark of ALS.
The results also provide insight into how problems in RNA metabolism, including disturbances in RNA regulation and functioning, lead to ALS and other neurodegenerative diseases.
‘Five years of tremendous progress in ALS genetics has revealed that RNA metabolism is a critical pathway that is impaired in this disease,’ said the study’s corresponding author J. Paul Taylor, M.D., Ph.D., a member of the St. Jude Department of Developmental Neurobiology. ‘But RNA metabolism is a complex process that involves multiple steps that are carried out in different parts of the cell. This study provides a more refined understanding of how ALS-causing mutations impair RNA metabolism so we know what needs fixing therapeutically.’
TDP-43 belongs to a family of proteins that bind to RNA and regulate its function. Normally TDP-43 is stored in the cell’s command center, the nucleus. There the protein prepares DNA for translation into the proteins that do the work of cells and shuttles the resulting RNA, called mRNA, from the nucleus to the cytoplasm, the cell’s liquid center. While clumps of TDP-43 were known to accumulate in the cytoplasm of the motor neurons of patients with ALS and other neurodegenerative diseases, the protein’s function there was unknown.
This study provides an answer. The work was done in motor neurons from the fruit fly Drosophila melanogaster, mouse brain cells and human motor neurons produced by reprogramming cells from ALS patients with three different TDP-43 mutations. Co-first author Nael Alami, Ph.D., a postdoctoral fellow in Taylor’s laboratory, developed a florescent RNA beacon that let investigators track movement of RNA molecules in living cells.
Researchers demonstrated that TDP-43 is part of a molecule called an RNA transport granule. These granules are responsible for moving mRNA efficiently to the end of the axon where the molecule is translated into a protein. For this study, scientists used Neurofilament-L (NEFL) mRNA, which is known to bind TDP-43.
In human motor neurons growing in the laboratory, investigators found that transport granules with mutant TDP-43 were more likely than granules with unaltered TDP-43 to stall en route to the nerve ending and sometimes reverse direction. The defect in the human ALS motor neurons was apparent after the first week.
Evidence from mice suggests TDP-43 mutations selectively rather than globally disrupt movement in nerve cells. The mutations did not affect movement of another cell structure, the mitochondria, along the axon where mRNA movement was impaired.
‘We know neurodegenerative disorders, including Parkinson’s and Alzheimer’s diseases, seem to share a common mechanism,’ Alami said. ‘We plan to use our finding from this study to look for similar defects in those diseases.’ St. Jude Children’s Research Hospital

The once sketchy landscape of the molecular defects behind bladder cancer now resembles a road map to new, targeted treatments thanks to the unified efforts of scientists and physicians at 40 institutions.
Deep molecular analysis of 131 muscle-invasive bladder cancer tumours found recurring defects in 32 genes for the cancer that currently has no targeted therapies.
‘By dramatically increasing our knowledge of the molecular basis of bladder cancers, this project casts a spotlight on particular molecules and biological pathways that may serve as targets for a more individualised approach to therapy,’ said project co-chair, lead and senior author John Weinstein, M.D., Ph.D., professor and chair of the Department of Bioinformatics and Computational Biology at The University of Texas M.D. Anderson Cancer Center in Houston.
‘While many of these genomic alterations have been tied to other cancers, nine of these genes have never been reported as significantly mutated in any other type of malignancy,’ Weinstein said. ‘These findings mark additional progress away from defining cancer by organ site and toward molecular classification that spans tumour types.’
Basis for investigating novel therapies and new uses of existing drugs
The most common bladder cancer, urothelial carcinoma, will kill an estimated 15,000 Americans in 2014, with 10 times as many deaths worldwide. Muscle-invasive disease is the most lethal form. Current treatment includes surgery, cisplatin-based multi-agent chemotherapy and radiation.
‘These TCGA data provide a perfect storm for advancing treatment for muscle invasive and hard-to-treat cancer,’ said project co-leader and co-senior author Seth P. Lerner, M.D., professor and chair of Urologic Oncology and Bladder Cancer program leader at Baylor College of Medicine in Houston.
‘We found potential therapeutic targets in 69 percent of tumours and identified bladder cancer subtypes based on gene mutation and expression data,’ Lerner said. ‘One subtype looks similar to squamous cell cancer of the head, neck and lung and basal-like breast cancer. Another subtype looks similar to luminal A breast cancer. These genomic similarities create a logical path to test targeted therapies from these other subtypes of cancer rather than treating bladder cancers as one disease.’
Lerner said long-term planning for clinical trials based on the TCGA data has begun in earnest and will continue this week during the 2014 Genitourinary Cancers Symposium in San Francisco.
Researchers analysed tumours for genetic mutations, gene copy number (deletions and amplifications), gene expression of messenger RNA, microRNA and protein expression, among other factors.
Two biological pathways provided the most common therapeutic targets, including molecules addressed by drugs in clinical trials or approved for other types of cancer.
45 percent of tumours had targets in the growth-factor-signalling receptor tyrosine kinase/MAPK pathway, including HER2 – best known as a drug target in about one third of breast cancers – in 15 percent of tumours, EGFR in 9 percent and FGFR3 in 17 percent.
42 percent had targets in the PI3K/AKT/mTOR pathway, including PIK3CA, which occurred in 17 percent of tumours, TSC1 or TSC2 in 9 percent and AKT3 in 10 percent of tumours. PI3K inhibitors are under development and mTOR inhibitors have been approved for select cancers.
A striking new finding, Weinstein said, was of frequent alterations in genes involved with the regulation of chromatin, the combination of DNA and histone proteins that makes up chromosomes.
Chromatin remodelling greatly influences gene expression and the team found alterations in this pathway in 89 percent of tumours, more than in any other type of cancer analysed to date. This makes bladder cancer a prime candidate for a new class of drugs under development, the authors noted.
Viral DNA was found in 6 percent of tumours, suggesting that viral infection might play a role in the development of a small percentage of bladder cancers. M D Anderson Cancer Center

New research from Queen Mary University of London has identified a novel genetic defect among patients with bone marrow failure, which could reveal its underlying cause.
The study detected and identified a new disease gene (ERCC6L2). In its normal form, the gene plays a key role in protecting DNA from damaging agents, but when the gene is mutated the cell is not able to protect itself in the normal way.
The research findings suggest that the gene defect and the subsequent DNA damage was the underlying cause of bone marrow failure among the study participants.
Bone marrow failure is a term used for a group of life threatening disorders associated with an inability of the bone marrow to make an adequate number of mature blood cells.
Patients were recruited from all over the world to join an international bone marrow failure registry and researchers used new DNA sequencing technologies to study cases of bone marrow failure with similar clinical features. These included bone marrow failure associated with neurological abnormalities (learning defects and developmental delay), and patients whose parents were first cousins.
The findings mean it is now possible to carry out a reliable genetic test (including antenatal testing) in these families and get an accurate diagnosis. In the long term, with further research, the findings could lead to the development of new treatment for this specific gene defect.
Professor Inderjeet Dokal, Chair of Paediatrics and Child Health at Queen Mary University of London, comments: ‘New DNA sequencing technology has enabled us to identify and define a new gene defect which causes a particular type of bone marrow failure. This is a promising finding which we hope one day could lead to finding an effective treatment for this type of gene defect. Clinicians treating patients with bone marrow failure should now include analysis for this gene in their investigation.
‘Now we know this research technique works, we plan to carry out further studies to shed more light on the genetic basis of many other cases of bone marrow failure.’ Queen Mary University