Toronto researchers led by U of T Professor Jason Moffat switched off almost 90 per cent of the entire human genome, to find the genes essential for cell survival
Scientists have mapped out the genes that keep our cells alive, creating a long-awaited foothold for understanding how our genome works and which genes are crucial in disease like cancer.

A team of Toronto researchers, led by Professor Jason Moffat from the University of Toronto’s Donnelly Centre, with a contribution from Stephane Angers from the Faculty of Pharmacy, have switched off, one by one, almost 18,000 genes, 90 per cent of the entire human genome, to find the genes that are essential for cell survival.

By turning genes off in five different cancer cell lines, including brain, retinal, ovarian, and two kinds of colorectal cancer cells, the team uncovered that each tumour relies on a unique set of genes that can be targeted by specific drugs. The finding raises hope of devising new treatments that would target only cancer cells, leaving the surrounding healthy tissue unharmed.

“It’s when you get outside the core set of essential genes, that it starts to get interesting in terms of how to target particular genes in different cancers and other disease states,” says Moffat, who is also a professor in the department of molecular genetics and a Senior Fellow at the Canadian Institute For Advanced Research (CIFAR).

Sequencing of the human genome 12 years ago allowed scientists to compile a list of parts – our 20,000 genes – that make up our cells and bodies. Despite this major achievement, we still didn’t understand the function of each gene, or how some genes make us sick when they go wrong. To do this, scientists realized they would have to switch genes off, one by one across the entire genome to determine what processes go wrong in the cells. But the available tools were either inaccurate or too slow.

The recent arrival of the gene editing technology CRISPR has finally made it possible to turn genes off, swiftly and with pinpoint accuracy, kicking off a global race among multiple competing research teams. The Toronto study, along with the paper from Harvard and MIT , found that roughly 10 per cent of our genes are essential for cell survival.

These findings show the majority of human genes play more subtle roles in the cell because switching them off doesn’t kill the cell. But if two or more of such genes are mutated at the same time, or the cells are under environmental stress, their loss begins to count.

Because different cancers have different mutations, they tend to rely on different sets of genes to survive. Moffatt’s team have identified distinct sets of “smoking gun” genes for each of the tested cancers – each set susceptible to different drugs.

“We can now interrogate our genome at unprecedented resolution in human cells that we grow in the lab with incredible speed and accuracy. In short order, this will lead to a functional map of cancer that will link drug targets to DNA sequence variation,” says Moffat.

His team has already shown how this can work. In his study, metformin, a widely prescribed diabetes drugs successfully killed brain cancer cells and those of one form of colorectal cancer – but was useless against the other cancers he studied. However, the antibiotics chloramphenicol and linezolid were effective against another form of colorectal cancer, and not against brain or other cancers studied. These data illustrate the clinical potential of the data in pointing to more precise treatments for the different cancers – and show the value of personalized medicine. University of Toronto

ELISA and indirect immunofluorescence tests (IIFT) have been developed for sensitive and specific detection of antibodies against Zika virus in patient serum samples. The assays are suitable for diagnosing acute infections as well as for disease surveillance. In particular, serological analyses can aid the differentiation of infections with Zika virus, dengue virus and chikungunya virus, which manifest with similar symptoms and are endemic in much the same geographic regions. Anti-Zika Virus ELISA (IgM or IgG) are based on highly specific recombinant Zika NS1 protein which avoids cross reactivity with other flaviviruses. Data from panels of well characterized sera have confirmed that there is no cross reactivity with flaviviruses including dengue, West Nile, yellow fever and Japanese encephalitis viruses. In studies on clinically and serologically characterized samples the IgM and IgG ELISA showed 100% sensitivity and 100% specificity. Anti-Zika Virus IIFT (IgM or IgG) utilize Zika virus-infected cells as the antigenic substrate. Positive and negative results are evaluated by fluorescence microscopy. With the Arboviral Fever Mosaic 2 the Zika virus substrate is incubated in parallel with substrates for chikungunya virus and dengue virus serotypes 1 to 4. This BIOCHIP combination can help in the differential diagnosis of Zika, dengue and chikungunya virus infections. Due to the use of whole virus particles, cross reactivities between flavivirus antibodies can occur. Serological tests provide a longer window for diagnosis than direct detection methods, which are only effective during the viremic phase within the first week after onset of symptoms. Detection of specific IgM or a significant rise in specific IgG in a pair of samples taken seven to ten days apart is evidence of an acute infection. Serological analyses are also important for prenatal monitoring, screening of donated blood and epidemiological studies. Zika virus is the pathogenic agent of Zika fever, an infectious topical disease which manifests with fever, exanthema and arthritis. Zika virus infection has been linked to congenital malformations, in particular microcephaly, and neurological complications such as Guillain-Barré syndrome. The virus is transmitted by mosquitoes of the Aedes family. Zika virus is currently spreading explosively in the Americas.

Euroimmunwww.euroimmun.de

Unravelling the genetic sequences of cancer that has spread to the brain could offer unexpected targets for effective treatment, according to new research.

Researchers say that they found that the original, or primary, cancer in a patient’s body may have important differences at a genetic level from cancer that has spread to the patient’s brain (brain metastases). This insight could suggest new lines of treatment.

Dr Priscilla Brastianos, MD, a neuro-oncologist and Director of the Brain Metastasis Program at Massachusetts General Hospital, Boston, USA, said: “Brain metastases are a devastating complication of cancer. Approximately eight to ten percent of cancer patients will develop brain metastases, and treatment options are limited. Even where treatment is successfully controlling cancer elsewhere in the body, brain metastases often grow rapidly.”

Dr Brastianos and her colleagues studied tissue samples from 104 adults with cancer. In collaboration with Dr Scott Carter and Dr Gad Getz at the Broad Institute, Cambridge, USA, they analysed the genetics of biopsies taken from the primary tumour, brain metastases and normal tissues in each adult. For 20 patients, they also had access to metastases elsewhere in the body.

Brain metastases often manifest years after the primary tumour. Before this study was carried out, the extent to which the genetic profiles of brain metastases differ from that of the primary was unknown.

The researchers found that, in every patient, the brain metastasis and primary tumour shared some of their genetics, but there were also key differences. In 56% of patients, genetic alterations that potentially could be targeted with drugs were found in the brain metastasis but not in the primary tumour.

“We found genetic alterations in brain metastases that could affect treatment decisions in more than half of the patients in our study,” Dr Brastianos will say. “We could not detect these genetic alterations in the biopsy of the primary tumour. This means that when we rely on analysis of a primary tumour we may miss mutations in the brain metastases that we could potentially target and treat effectively with drugs.”

This study also found that if a patient had more than one brain metastasis, each was genetically similar.

To date, scientists have had limited understanding of how cancers change genetically, or evolve, as they spread from the primary tumour. The researchers used their findings to map the evolution of a cancer through a patient’s body, and draw up a so-called phylogenetic tree for each patient to demonstrate how the cancer had spread and where each metastasis had come from.

They concluded that brain metastases and the primary tumour share a common genetic ancestor. Once a cancer cell, or clone, has moved from the primary site to the brain, it continues to develop and amass genetic mutations. The genetic similarity of the brain metastases in individual patients suggests that each brain metastasis has developed from a single clone entering the brain.

The genetic changes in brain metastases are independent of any occurring at the same time in the primary tumour, and in metastases elsewhere in the body, the researchers said.

Characterisation of the genetics of a patient’s primary cancer can be used to optimise treatment decisions, so that drugs that target specific mutations in the cancer can be chosen. However, brain metastases are not routinely biopsied and analysed. ECC 2015

Fragments of cancer DNA circulating in a patient’s bloodstream could help doctors deliver more personalized treatment for liver cancer, Japanese researchers report.

The new research may help address a particular challenge posed by liver cancers, which can be difficult to analyse safely. One serious risk of existing biopsy methods is that doctors who want to obtain a tumour sample for analysis might cause the cancer to spread into the space around organs.

‘Doctors need non-invasive methods that will allow them to safely study cancer progression and characterize the genomic features of a patient’s tumour,’ said Professor Kazuaki Chayama, a principal investigator in this study. ‘Testing for these circulating DNA fragments may be a much easier and safer way of doing this than conventional liver biopsy.’

The researchers showed that detecting DNA released by damaged cancer cells, called circulating tumour DNA (ctDNA), in serum before surgery could predict the recurrence of cancer and its spread through the body (metastasis) in patients with an advanced form of the most common type of liver cancer. They also demonstrated that the level of serum ctDNA reflected the treatment effect and the progression of hepatocellular carcinoma (HCC).

Recent studies have suggested that ctDNA might be a useful biomarker in various cancers. The new study brings this technique closer to clinical reality in patients with advanced HCC by showing that ctDNA provided valuable clinical information about the patient’s disease progression.

Professor Chayama and colleagues in Hiroshima University including Dr. Atsushi Ono, together with researchers at RIKEN and the University of Tokyo, investigated whether they could detect ctDNA in serum of 46 HCC patients. They found ctDNA in seven patients. These patients were more likely than the others to experience recurrence and metastasis of their cancer. ‘Furthermore, we found that the level of ctDNA correlated with progression of HCC and the treatment,’ said Professor Chayama.

The Japanese team also says that ctDNA has the potential to be a non-invasive way of studying the genetic rearrangements that a cancer has undergone. This information could help doctors provide targeted therapy specific to a patient’s cancer, they note.

Recently, detection of cancer-specific mutations by genome sequencing has attracted attention as a way to help select appropriate therapy selection, Professor Chayama said. The researchers were able to identify 25 common mutations in samples of cell-free DNA, which includes DNA from both normal cells and cancer cells, and DNA from tumours themselves. Furthermore, 83% of mutations identified in the tumour tissues could be detected in the cell-free DNA.

Although further study is necessary to develop more effective methods, the new study adds to growing evidence about the usefulness of ctDNA in cancer treatment, and shows that it is a promising biomarker that provides a new way to treat liver cancer. EurekAlert