A new study provides insight on the potential role played by RNA (ribonucleic acid) editing in cancer.

The findings may further our understanding of an emerging mechanism implicated in tumour initiation and progression, and may thus lead to the development of better treatment options in the future.

In every healthy human cell, the genetic information hard-wired into the DNA is transcribed into messenger RNA, which is in turn translated into proteins, the workhorses of all body tissues and organs. The prevailing view is that most malignancies are caused by DNA mutations, which can lead to the aberrant activation or inactivation of the corresponding protein products and to the consequent out-of-control growth and proliferation of malignant cells. RNA editing, the process by which ‘mutations’ of the RNA sequence are introduced post-transcriptionally, has the potential to impact a variety of cellular processes yet the precise mechanism of how has been poorly understood until now.

Previous studies have shown that more than one million sites in the genome are edited to various degrees. Despite the fact that a majority of these editing sites fall within regions that are not translated to protein, it has been shown that the differences in RNA editing levels between tumour and normal tissues are associated with different clinical outcomes. Currently, only a few coding RNA editing sites have been functionally characterized. However, it is still a puzzle whether and how the majority of the RNA editing events in the un-translated regions affect tumour growth.

Researchers from Boston University School of Medicine (BUSM) analysed 14 tumour types, and identified more than 2,000 genes showing significant changes in RNA editing level between tumour and normal tissues.

“This study suggests that RNA editing may serve as an important epigenetic mechanism of cellular regulation beyond the genetic/DNA level,” explained corresponding author Stefano Monti, PhD, associate professor of medicine at BUSM. “We show that the effect of one epigenetic component can be offset by changes in another epigenetic component. Thus, it is important to have a comprehensive picture of changes in the cancer genome, which may point to vulnerabilities amenable to targeted treatment,” added lead author Liye Zhang, PhD, postdoctoral fellow at BUSM. Boston University School of Medicine

Rheonix Inc., a developer of fully automated molecular diagnostics solutions, has been granted patent 9,132,398, “Integrated Microfluidic Device and Methods,” for the Rheonix CARD^® cartridge, which enables assays to be performed on the company’s EncompassMDx^® and Encompass Optimum™ instruments. The CARD, which stands for Chemistry and Reagent Device, will make molecular diagnostics simpler and easier to perform through an innovative and functional design that delivers a fully automated molecular assay at a fraction of the cost of other options. All assay steps are performed within the fully enclosed cartridge, thus eliminating the potential for contamination, reducing user error, and streamlining workflow.
The CARD’s design enables adoption of advanced molecular technology by laboratories of all types, from small community hospital labs to highly complex, centralized laboratories. The design also facilitates implementation across a wide range of market opportunities, including next-generation sequencing (NGS) sample prep, research-use-only testing, food and beverage industry applications, and in vitro diagnostics.  
The ’398 patent allows researchers and clinicians to quickly, easily, and cost-effectively run several samples through a fully integrated and automated nucleic acid amplification test, from raw sample input through detection, with no user intervention. Each CARD allows for simultaneous testing of four different samples and can handle a broad range of sample types, such as fresh tissue, urine, whole blood, serum, saliva, swabs, and formalin-fixed, paraffin-embedded (FFPE) tissue. The Rheonix CARD performs multiple molecular techniques, including sample preparation, such as chemical and enzymatic lysis and DNA purification; amplification, such as endpoint polymerase chain reaction (PCR), reverse transcriptase PCR, and quantitative PCR; and detection on a low-density microarray or lateral flow strip.
“The ’398 patent recognizes the groundbreaking achievement we have reached with the Rheonix CARD. From the device’s hardware to its process, it will help make molecular diagnostics a reality in laboratories worldwide,” said Tony Eisenhut, president of Rheonix. “With the lowest cost of ownership of any molecular platform, the patent confirms the novelty of the Rheonix approach to molecular diagnostics. Where other systems have traditionally emphasized either multiplex or throughput, Rheonix has designed single-use cartridges that do both and can perform sophisticated functions with a simple design. This lowers laboratory costs by eliminating waste in time, equipment and consumables, and reduces the amount of highly skilled labour. Rheonix is helping bring powerful molecular tools to laboratories that could not previously afford to purchase or run them.”
The dual-layer design of the Rheonix CARD automatically manipulates reagents internally with its active fluidic network of pumps, valves and channels. The upper surface of the CARD contains reservoirs that hold reagents used in the extraction, purification, amplification and detection process and any resulting liquid waste. The channels and pumps located on the lower surface of the CARD are used to transport and mix reagents and move wastes into the reservoirs on the top. By actively pumping fluids from reservoir to reservoir within the CARD, molecular diagnostic tests can be performed automatically.

www.rheonix.com

Researchers at the University of California, San Diego School of Medicine developed a method to expand the types of chromosomal abnormalities that non-invasive prenatal testing (NIPT) can detect. The study uses a semiconductor sequencing platform to identify small chromosomal deletions or duplications, such as occur in Cri du Chat Syndrome and DiGeorge Syndrome, with a simple blood test from the expectant mother.
Detecting these types of small chromosomal abnormalities with conventional techniques usually requires an invasive procedure to obtain foetal DNA, such as amniocentesis or chorionic villus sampling. These procedures carry a small but concerning risk for miscarriage and infection. Since the recent discovery that foetal DNA can be found in the blood of pregnant women, NIPT has been increasingly used to detect certain chromosomal abnormalities through a maternal blood test. So far, though, NIPT is typically used only to detect abnormalities that result from larger chromosomal abnormalities — too many or too few of a particular chromosome, for example, such as occurs in Down syndrome.

“We have found that NIPT can be extended in a way that allows us to zoom in and examine a small segment of a chromosome,” said Kang Zhang, MD, PhD, professor of ophthalmology and chief of Ophthalmic Genetics at UC San Diego School of Medicine, who led the study with collaborators in China. “And while this study focused on cell-free DNA sequencing in pregnant women, this method could be applied more broadly to other genetic diagnoses, such as analysing circulating tumour DNA for detection of cancer.”
Zhang and his team analysed blood plasma from 1,476 pregnant women with foetal structural abnormalities detected by ultrasound. These women also underwent an invasive diagnostic procedure and conventional foetal DNA analysis. The researchers compared that information to semiconductor sequencing results on circulating foetal DNA obtained from a blood test on the pregnant women at an average gestational age of 24 weeks. The new semiconductor sequencing method detected 69 of 73 (94.5 percent) of abnormalities of a certain size (greater than one million base pairs) detected by the conventional method.

According to the researchers, the cost of NIPT with semiconductor sequencing has the potential to be less expensive than the conventional, invasive prenatal testing method, especially as genetic sequencing technologies continue to decrease in cost.

While promising, there is still need for improvement before this NIPT application can be used clinically. In the study, semiconductor sequencing detected 55 false positives, of which 35 (63.6 percent) were due to maternal, rather than foetal, chromosomal abnormalities. That means the new method will require a validation test to screen out maternal abnormalities.

NIPT with semiconductor sequencing also needs to be tested at early time points in the pregnancy — at 12 to 16 weeks — and the researchers hope to further improve the technique to be able to detect even smaller genetic abnormalities.
The problem is that the more variations they are able to detect, the more they are likely to pick up chromosomal deletions or duplications of unknown clinical significance or with mild clinical consequences. Many of the abnormalities detected could be normal inherited variations. UC San Diego Health

In the first study to run a genome-wide analysis of Short Tandem Repeats (STRs) in gene expression, a large team of computational geneticists led by investigators from Columbia Engineering and the New York Genome Center have shown that STRs, thought to be just neutral, or ‘junk,’ actually play an important role in regulating gene expression.

“Our work expands the repertoire of functional genetic elements,” says the study’s leader Yaniv Erlich, who is an assistant professor of computer science at Columbia Engineering, a member of Columbia’s Data Science Institute, and a core member of the New York Genome Center. “We expect our findings will lead to a better understanding of disease mechanisms and perhaps eventually help to identify new drug targets.”

Genomic variants are what makes our DNA different from each other, and come,
Erlich explains, “like spelling errors in different flavours.” The most common
variants are SNPs (single nucleotide polymorphisms). Computational geneticists
have been focused mostly on SNPs that look like a single letter typo—mother vs.
muther—and their effect on complex human traits.

Erlich’s study looked at Short Tandem Repeats (STRs), variants that create what
look like typos: stutter vs. stututututututter. Most researchers, assuming that
STRs were neutral, dismissed them as not important. In addition, these variants
are extremely hard to study. “They look so different to analysis algorithms,” Erlich notes, “that they just usually classify them as noise and skip these positions.”

Erlich used a multitude of statistical genetic and integrative genomics analyses to
reveal that STRs have a function: they act like springs or knobs that can expand
and contract, and fine-tune the nearby gene expression. Different lengths
correspond to different tensions of the spring and can control gene expression and disease traits. He is calling these variants eSTRs, or expression STRs, to note that they regulate gene expression. He and his team also discovered that these eSTRs can be associated with a range of conditions including Crohn’s diseases, high blood pressure, and a range of metabolites. These eSTRs explain on average 10 to 15% the genetic differences of gene expression between individuals.
“We’ve known that STRs are known to play a role in these diseases, but no one has ever conducted a genome-wide scan to find their effect on complex traits,” Erlich adds. “If we want to do personalized medicine, we really need to understand every part of the genome, including repeat elements—there’s a lot of exciting biologyahead.” New York Genome Centre