The largest genome-wide association study to date of the malaria parasite Plasmodium falciparum unveils a complex genetic architecture that enables the parasite to develop resistance to our most effective antimalarial drug, artemisinin. The results could help to improve early detection of emerging artemisinin resistance.

The global research collaboration analysed 1612 samples from 15 locations in Southeast Asia and Africa finding 20 mutations in the kelch13 gene, a known artemisinin resistance marker, that appear to work in concert with a set of background mutations in four other genes to support artemisinin resistance.

‘Our findings suggest that these background mutations emerged with limited impact on artemisinin resistance – until mutations occurred in the kelch13 gene,’ explains Dr Roberto Amato, a first author and Research Associate in Statistical Genomics at the Wellcome Trust Sanger Institute and Oxford University’s Wellcome Trust Centre for Human Genetics. ‘It’s similar to what we see with pre-cancerous cells which accumulate genetic changes but only become malignant when they acquire critical driver mutations that kick-off growth.’

The variety of kelch13 mutations associated with artemisinin resistance, with new variants continually emerging, makes it difficult to use this gene alone as a marker for genetic surveillance.

Monitoring parasite populations for a specific genetic background – in this case, a fixed set of four well-defined mutations in the fd, arps10, mdr2, and crt genes – could allow researchers to assess the likelihood of new resistance-causing mutations emerging in different locations, helping to target high-risk regions even before resistant parasites take hold.

‘We are at a pivotal point for malaria control. While malaria deaths have been halved, this progress is at risk if artemisinin ceases to be effective,’ says Nick Day, Director of the Mahidol-Oxford Tropical Medicine Research Unit (MORU) in Bangkok, Thailand. ‘We need to use every tool at our disposal to protect this drug. Monitoring parasites for background mutations could provide an early warning system to identify areas at risk for artemisinin resistance.’

Researchers also uncovered new clues about how artemisinin resistance has evolved in Southeast Asia. By comparing parasites from Cambodia, Vietnam, Laos, Thailand, Myanmar and Bangladesh, scientists found that the distribution of different kelch13 mutations are localised within relatively well-defined geographical areas.

Whilst artemisinin resistant parasites do appear to have migrated across national borders, this only happened on a limited scale and, in fact, the most widespread kelch13 mutation, C580Y, appeared to have emerged independently on several occasions. Notably parasites along the Thailand-Myanmar border appear to have acquired this mutation separately from those in Cambodia and Vietnam. Crucially, parasite populations in both regions possess the genetic background mutations, even though they are clearly genetically distinct.

There remain many unanswered questions. ‘We don’t yet know the role of these background mutations,’ says Dr Olivo Miotto, a first author and Senior Informatics Fellow at MORU and the Centre for Genomics and Global Health. ‘Some may not affect drug resistance directly, but rather provide an environment where drug resistance mutations are tolerated. Since kelch13 has hardly changed in 50 million years of Plasmodium evolution, we can assume that this gene is essential to parasite survival. Therefore, kelch13 mutations may severely handicap mutant parasites, compromising their survival unless some other change can counteract this negative effect.’

Mutations in the kelch13 gene were present, yet rare, in Africa but weren’t associated with artemisinin resistance and lacked the genetic background present in artemisinin-resistant parasites in Southeast Asia. This provides some reassurance for public health authorities working to prevent the spread of artemisinin resistance to Africa where most malaria deaths occur. Wellcome Trust Sanger Institute  

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

Moffitt Cancer Center researchers have found that breast and lung cancer patients who have low levels of a protein called tristetraprolin (TTP) have more aggressive tumours and a poorer prognosis than those with high levels of the protein. 

Cancer arises through the increased activity of oncogenes, proteins that drive cancer growth, and the decreased activity of tumour suppressors, proteins that block malignant growth and progression. TTP is a recently discovered tumour suppressor protein, and scientists at Moffitt have found that this protein can prevent lymphoma growth in mice.

Researchers wanted to further investigate the importance of TTP in cancer patients and what other genes it is associated with in cancer. Using a detailed catalogue of genetic changes in cancer developed by the National Institutes of Health, called The Cancer Genome Atlas, Moffitt scientists compared patients who had low levels of TTP to those with high levels of the protein.

These researchers found a network of 50 different genes associated with low levels of TTP in breast, lung and colon tumours. This genetic network was also present in other tumour types, including prostate, pancreatic and bladder cancer.  This demonstrates that TTP is involved in a variety of mechanisms important for tumour development and growth, and suggests that developing agents that target this network may be an effective therapeutic strategy across a wide spectrum of tumours.

They also reported that low levels of TTP were associated with poor prognosis in certain cancers, including a higher rate of relapse in breast cancer patients and lower rates of survival in lung adenocarcinoma patients.  Additionally, breast and lung cancer patients with low levels of TTP tended to have more aggressive types of tumors.

“Identifying this network allows us to set up future research projects focused on understanding how TTP functions as a tumor suppressor with the ultimate goal of developing treatments specific for patients that have low levels of TTP,” explained Robert Rounbehler, Ph.D., research scientist at Moffitt. Moffitt Cancer Center

Finding out whether you have been infected with dengue may soon be as easy as spitting into a rapid test kit. The Institute of Bioengineering and Nanotechnology (IBN) of A*STAR has developed a paper-based disposable device that will allow dengue-specific antibodies to be detected easily from saliva within 20 minutes. This device is currently undergoing further development for commercialization.

IBN Executive Director Professor Jackie Y. Ying shared, “Our rapid diagnostic kit can detect a key dengue antibody from saliva that is present in early-stage secondary infection. The ability to differentiate between primary and secondary dengue infections makes it a valuable early diagnosis tool that would help to ensure timely treatment and proper care of patients.”

Patients with secondary infection, who have previously been infected with other serotypes of dengue virus, stand a higher risk of developing dengue haemorrhagic fever or dengue shock syndrome.

According to Singapore’s National Environment Agency, dengue fever and its more severe form, dengue haemorrhagic fever, are the most common mosquito-borne viral diseases in the world. This disease poses a serious health threat, and is a leading cause of illness and death in tropical and subtropical climates. There are four known serotypes of the dengue virus, but no vaccine or medicine has been developed to treat the illness. The incubation period before symptoms develop generally ranges from 4 to 10 days after infection. Therefore, early diagnosis would enable the patient to receive prompt medical attention and avoid further complications.

Currently, dengue infection is diagnosed in the laboratory by testing the patient’s blood sample for the presence of dengue antigens or antibodies. IBN’s device, on the other hand, is capable of detecting IgG, a dengue-specific antibody found at the onset of secondary infections, directly from saliva in one step.

Unlike blood samples, saliva can be collected easily and painlessly for rapid point-of-care diagnostics. However, unlike other body fluids, it cannot be applied directly to commercially available test kits as it would cause the sensor nanoparticles to stick haphazardly to the test strip. In addition, conventional paper-based tests are not designed to handle the larger sample volume of saliva required.

As described in the journal Lab on a Chip, the IBN researchers used an innovative stacking flow design to overcome key challenges faced by existing lateral flow designs, such as those used in pregnancy test kits.

In IBN’s device, different flow paths are created for samples and reagents through a multiple stacked system. This allows the saliva sample to flow separately through a fibre glass matrix, which removes the substances that would interfere with the nanoparticle-based sensing system before it mixes with the sensor nanoparticles. IBN’s device configuration also helps to regulate the flow in the test strip, generating uniform test lines for more accurate results.

By simplifying the diagnostic procedure, the researchers hope to make the device as easy to use as over-the-counter pregnancy or fertility test kits. IBN’s oral test kit may be adapted to detect other infectious diseases. The IBN researchers are also investigating the use of other common fluid samples, such as blood, urine and serum for rapid, high-sensitivity test kits.

The Institute is currently collaborating with ARKRAY Inc., a pioneer in the field of automated analysis systems, to commercialize its paper-based diagnostic technology. In 2013, ARKRAY opened its first Asian research center outside Japan in IBN with an investment of S$9.1 million over five years. The research center is focused on developing novel detection kits for infectious diseases based on IBN’s innovative diagnostic platforms. Agency for Science, Technology and Research (A*STAR)

Scientists have proposed a new idea for detecting brain conditions including Alzheimer’s – a skin test. Their work, which is at an early stage, found the same abnormal proteins that accumulate in the brain in such disorders can also be found in skin.

Early diagnosis is key to preventing the loss of brain tissue in dementia, which can go undetected for years. But experts said even more advanced tests, including ones of spinal fluid, were still not ready for use. If they were, then doctors could treat them at the earliest stages, before irreversible brain damage or mental decline has taken place.

Investigators have been hunting for suitable biomarkers in the body – molecules in blood or exhaled breath, for example, that can be measured to accurately and reliably signal if a disease or disorder is present.

Dr Ildefonso Rodriguez-Leyva and colleagues from the University of San Luis Potosi, Mexico, believe skin is a good candidate for uncovering hidden brain disorders.

Skin has the same origin as brain tissue in the developing embryo and might, therefore, be a good window to what’s going on in the mind in later life – at least at a molecular level – they reasoned.

Post-mortem studies of people with Parkinson’s also reveal that the same protein deposits which occur in the brain with this condition also accumulate in the skin.

To test if the same was true in life as after death, the researchers recruited 65 volunteers – 12 who were healthy controls and the remaining 53 who had either Parkinson’s disease, Alzheimer’s or another type of dementia.

They took a small skin biopsy from behind the ear of each volunteer to test in their laboratory for any telltale signs of disease. Specifically, they looked for the presence of two proteins – tau and alpha-synuclein.

The 20 people with Alzheimer’s and the 16 with Parkinson’s had raised levels of both these proteins in their skin compared to the healthy controls and the patients with other types of dementia.

The people with Parkinson’s also had higher levels of alpha-synuclein protein.

Dr Rodriguez-Leyva, who will soon present his findings to the annual meeting of the American Academy of Neurology, said: ‘More research is needed to confirm these results, but the findings are exciting because we could potentially begin to use skin biopsies from living patients to study and learn more about these diseases.

‘This new test offers a potential biomarker that may allow doctors to identify and diagnose these diseases earlier on.’ It could also guide research into new treatments, he said. BBC