One of the central questions in human biology is to understand how our genes determine which diseases we get and how severe they might be. Knowing just the DNA sequence, or the blueprint, is not enough. We must figure out how proteins, the genes’ products, work too.

Now an international team of researchers, jointly led by Dr. Fritz Roth (at Mount Sinai Hospital’s Lunenfeld-Tanenbaum Research Institute and the Donnelly Centre of the University of Toronto), and Dr. Marc Vidal (with the Dana-Farber Cancer Institute and Harvard Medical School in Boston), have produced the largest ever map of human protein interactions. This publicly available resource will be invaluable to anyone trying to understand complex genetic traits and develop new disease therapies.

“It is realistic to think that many of the people reading this will have their genomes sequenced within their lifetimes. The next challenge is to figure out what their genomes mean,” says Dr. Roth. “You cannot figure out how the car works based on the parts list. You have to know how they fit together.”

This is because genes do not do the work in a cell. Rather, the work is usually done by the proteins that genes provide the plans for. Some pairs of proteins stick together, or ‘interact’ when they are in close contact with each other. These interactions underlie all of cell’s biology and mediate processes such as gene expression, cell metabolism, and transporting other molecules within a cell.

Having a detailed map of protein interactions bring us one step closer to understanding the relationship between our genes (genotype) and our physiology in health and disease (phenotype).

Drs. Roth and Vidal, and their colleagues, analysed direct interactions in pairwise combinations between 13,000 proteins. Out of 85 million possible interactions they found 14,000 directly-interacting protein pairs. This more than doubles the previous set of known interactions, making it the largest ever experimentally determined human protein interaction map.

“We’ve managed to peer into the car and connect a fraction of the parts,” says Dr. Roth.

The study reveals several important findings. The new map can be used to identify novel genes involved in diseases. If a novel protein, which we know nothing about, interacts with a known protein that has a role in a disease, then the novel protein is highly likely to be involved in that same disease. Dr. Roth and colleagues illustrate this point by identifying a novel cancer gene STAT3 based on its interactions with known cancer genes. Their finding was confirmed when STAT3 subsequently became included into the cancer gene database based on independent evidence.
 Further unbiased analyses identified 100 strong cancer candidate genes, 60 of which were connected to known cancer molecular pathways. Some of these genes are completely novel. This shows the potential of the human interaction map in revealing new disease genes and promising therapeutic targets.

Mapping all human protein interactions is a colossal task and will require several different approaches. This is because not every method can find every protein interaction. Dr. Roth estimates that they found, using a yeast two hybrid method, 5-10% of all protein interactions, a substantial increase from their previous paper that reported 1% of interactions.

“Although much sweat and some tears were put into analysing this new map, it is clear that we have only scratched the surface of what these interactions can tell us about human disease. It is personally very exciting to anticipate the discoveries to come, as it passes from our hands into the research community,” says Dr. Roth. Lunenfeld-Tanenbaum Research Institute

HORIBA Medical and NoemaLife announced in January a non-exclusive agreement, for the worldwide distribution of Halia, the web-based Laboratory Automation System by NoemaLife which allows central management of all pre-analytical, analytical and post-analytical instruments, making it possible to connect multiple sites, multiple Laboratory Information Systems and multiple instruments of various disciplines of the laboratory. “The addition of Halia to HORIBA Medical ’s Hematology product line makes it possible for a wide range of clinical laboratories to realize efficiencies resulting from a powerful yet very user friendly data management. NoemaLife is pleased to serve as HORIBA Medical‘s middleware provider in this effort” said Piero Tassoni, Diagnostic Marketing & Alliance Director NoemaLife, “HORIBA Medical equips more than 30,000 laboratories throughout the world, distributed in 110 countries in 5 continents. Not only we are proud to work with a partner who holds world records in its industry, but we are confident that this agreement has huge potential.” The specific version of the Halia middleware distributed by HORIBA Medical will soon integrate all the Hematology Expert validation station features that HORIBA Medical so far proposed exclusively in its “ABX Pentra ML” Work Station, the all-in-one validation system entirely dedicated to whole blood. “Halia is an important evolution to our hematology solution’s offer” said Olivier Pou, Corporate Marketing Director, HORIBA Medical. “The addition of a specific version of the Halia middleware to our product offer makes it possible for HORIBA Medical to provide a complete solution to our worldwide base of customers around the hematology expertise but also to facilitate the integrated management of hematology within the global IVD laboratory”.

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The scientific community has made significant strides in recent years in identifying important genetic contributors to malignancy and developing therapeutic agents that target altered genes and proteins.  A recent approach to treat cancer called synthetic lethality takes advantage of genetic alterations in cancer cells that make them more susceptible to certain drugs. Alan F. List, MD, president and CEO of Moffitt Cancer Center, co-authored an article on synthetic lethality.

“Genetic alterations in cancer in humans may involve gene inactivation, amplification or inactivation,” said List.  These changes are not present in non-malignant cells. Common chemotherapeutic agents aggressively kill tumour cells irrespective of genetic alterations.  They also have a negative impact on normal cells and can cause significant side effects. Synthetic lethality harnesses the genetic differences between tumour cells and normal cells to minimize the effects on normal cells, and maximize a drug’s effects on cancer cells.

Synthetic lethality can target a variety of cellular defects, including alterations in DNA repair, cell-cycle control and metabolism.  This approach can also be used to target interactions between tumour cells and surrounding normal cells that promote tumour survival and oncogenes that drive tumorigenesis that are difficult to target directly.  Many of the synthetic lethal drugs and targets have been identified in large-scale drug screens of the entire human genome.

An example of synthetic lethality is the recent approach being investigated to treat breast cancer patients with BRCA1 and BRCA2 mutations. BRCA1 plays an important role is repairing damaged DNA.  Women who have mutations in BRCA1 or BRCA2 have an increased risk of developing breast and ovarian cancer because their cells cannot properly repair DNA. This suggests that BRCA mutated breast cancer cells may be more susceptible to drugs that target DNA.  Laboratory studies have confirmed this hypothesis by showing that agents that target another DNA repair protein called PARP significantly kill BRCA mutated cells. Several PARP inhibitors are now being investigated in clinical trials in breast cancer patients, and early results are promising.

“The goal of current anticancer approaches is to offer individualized and highly selective therapy. The treatment model for many anticancer approaches has been expanded, with movement away from dose-intensive, non-targeted cytotoxic agents to combination chemoimmunotherapy, new therapeutic combinations and targeted agents,” said List. Synthetic lethality approaches may provide an additional avenue for individualized patient treatment. Moffitt Cancer Center

Using a basic genetic difference between men and women, the Translational Genomics Research Institute (TGen) has uncovered a way to track down the source of a neurological disorder in a young girl.

TGen’s discovery relies on a simple genetic fact: Men have one X and one Y chromosome, while women have two X chromosomes. This women-only factor was leveraged by TGen investigators to develop a highly accurate method of tracking down a previously unrecognized disorder of the X-chromosome. 

The study was of a pre-teen girl, who went years with an undiagnosed neurobehavioral condition.

TGen’s findings were made within its Dorrance Center for Rare Childhood Disorders, where investigators and clinicians apply the latest tools of genomic medicine to provide answers for parents seeking to identify the disease or disorder affecting their child.

The scientists sequenced, or spelled out in order, the complete genetic codes of DNA and RNA of the girl. Because girls inherit an X chromosome from each of their parents (boys inherit a Y chromosome from their father), they also sequenced her mother and father. On average, about half of all X chromosomes active in a female come from the mother and the other half from the father.

‘We now have the tools to significantly accelerate the diagnostic process, reducing the need for children to undergo multiple tests that can be emotionally and physically taxing for the entire family,’ said Dr. David Craig, TGen’s Deputy Director of Bioinformatics, Co-Director of the Dorrance Center and the paper’s senior author.

Sequencing would reveal the proportion of X chromosomes, and if disproportionate, whether the more abundant of the two were damaged in some way, which often leads to X-linked genetic conditions.

‘At the time of enrollment, we suspected the girl had a complex neurobehavioral condition, based on her attention deficit, and delays in development and learning,’ said Dr. Vinodh Narayanan, Medical Director of the Dorrance Center. ‘Her brain MRI scans were normal. We needed to find out more – at the genetic level – about what might be causing her disorder.’

By sequencing the DNA and RNA, TGen investigators were able to precisely identify which cells contained active X chromosomes from the girl’s mother, which contained active X chromosomes from the father, in what proportions, and whether they were associated with any known disorders.

They discovered that the X chromosome from the father contained a segment shown to be associated with neurobehavioral conditions. Interestingly, however, the proportion of X chromosomes active in the girl’s cells skewed toward the normal X inherited from her mother. This skewing may have led to a milder, harder to diagnose condition undetected by conventional methods.

‘This study shows the power sequencing holds when scanning for potential disease causing and disease-modifying genetic variations,’ said Dr. Matt Huentelman, the other Co-Director of the Dorrance Center and an author of the paper. TGen

Copy number variations (deletions or duplications of large chunks of the genome) are a major cause of birth defects, intellectual disability, autism spectrum disorder and other developmental disorders. Still, geneticists can definitively say how a CNV, once discovered in someone’s DNA, leads to one of these conditions in just a fraction of cases.

To aid in the interpretation of CNVs, researchers at Emory University School of Medicine have completed detailed maps of 184 duplications found in the genomes of individuals referred for genetic testing.

‘Ours is the first study to investigate a large cohort of clinically relevant duplications throughout the genome,’ says senior author Katie Rudd, PhD, assistant professor of human genetics at Emory University School of Medicine. ‘These new data could help geneticists explain CNV test results to referring doctors and parents, and also reveal mechanisms of how duplications form in the first place.’

Despite advances in ‘next generation’ DNA sequencing, the first step for patients who are referred to a clinical geneticist is currently a microarray. This is a scan using many probes across the genome, testing if someone’s DNA has one, two, three or more copies of the DNA corresponding to the probe. (Two is the baseline.) From this scan, geneticists will have a ballpark estimate of where a deletion or duplication starts and ends, but won’t know the breakpoints exactly.

‘In a few years, advances in sequencing will make it possible to routinely capture data on copy number variation and breakpoints at the same time,’ Rudd says. ‘But for now, we have to do this extra step.’

In addition, in comparison with deletions, duplications are more complicated. The extra DNA has to land somewhere, sometimes resulting in the disruption or warped regulation of nearby genes, which make it more difficult to pinpoint particular genes responsible for the individual’s medical condition.

Most healthy people have a deletion or duplication of at least 100 kilobases in size. The individuals in the study were referred for clinical microarray testing with indications including intellectual disability, developmental delay, autism spectrum disorders, congenital anomalies, and dysmorphic features. Their CNVs were larger, with an average size of more than 500 kilobases.

Rudd’s team examined 184 duplications, and found that most are in tandem (head-to-tail) orientation and adjacent to the duplicated area. Most of the CNVs in the study were inherited from a parent. The researchers also found examples where a duplicated gene inserted into and disrupted another gene on a different chromosome.

In a few cases, a duplicated gene was fused together with another gene. This is a phenomenon often seen in cancer cells, where a DNA rearrangement leads to an abnormal activation of a growth- or survival-promoting gene. In these cases, the fusions were present in all cells in the body and not related to cancer, but could be responsible for the patient’s condition.

‘These fusion genes are intriguing but we don’t know, just from looking at the DNA, if the gene is expressed,’ Rudd says. ‘These findings could be the starting point for follow-up investigation.’ Emory University School of Medicine