Researchers have discovered the first inherited gene mutation linked exclusively to acute lymphoblastic leukemia (ALL) occurring in multiple relatives in individual families. The discovery of the PAX5 gene mutation was led by St. Jude Children’s Research Hospital and others.
The mutation was identified in two unrelated families in which pediatric ALL has been diagnosed in multiple generations. The mutation involved a single change in the DNA sequence of PAX5, a gene that is known to be deleted, mutated or rearranged in some B cell tumours, including ALL. This is the first time changes in PAX5 have been linked to an inherited cancer risk.
‘Pioneering work from St. Jude and others has identified inherited variations in other genes that modestly increase the risk of developing ALL, but few had been identified in familial leukaemia,’ said co-corresponding author Charles Mullighan, MBBS(Hons), MSc, M.D., an associate member of the St. Jude Department of Pathology. ‘Prior studies had identified inherited mutations in families with multiple types of cancer including leukaemia, but not in families with ALL alone.’
While inherited mutations have been linked to an increased risk of breast, colon and other cancers, particularly adult cancers, very few have been tied to childhood tumours. ALL affects about 3,000 children nationwide annually, making it the most common childhood tumour.
‘For families with several generations of cancer patients, it means a lot to know that scientists and clinicians are working together to better understand the genetic factors that explain their family’s increased risk,’ said co-author John T. Sandlund, a member of the St. Jude Department of Oncology. ‘They are hopeful that other families, as well as their own, might benefit from this research.’
The mutation was found in the normal cells and leukaemia cells of eight ALL patients from several generations of two unrelated families. The work was led by researchers at St. Jude, Memorial Sloan-Kettering Cancer Center in New York and the University of Washington, Seattle.
The newly identified mutation is a single letter change in the DNA sequence of PAX5. The change results in the amino acid glycine being substituted for serine at amino acid 183 in the PAX5 protein. While PAX5 sequence mutations are common in sporadic cases of ALL, this mutation is the first identified at this location in the protein.
The mutation was discovered by sequencing the exome of normal cells from seven ALL patients in the two families and the exomes of the leukemic cells of four of these patients. The exomes from three relatives unaffected by leukaemia were also sequenced.
Researchers reported that the leukaemia cells all carried a single copy of PAX5 that included the mutation. The patients had all lost the normal version of the gene due to the partial deletion of chromosome 9, where PAX5 is located. The loss resulted in a marked reduction of normal PAX5 activity in the leukaemia cells. In contrast, family members who carried the mutant gene, but who had not developed leukaemia, retained the normal copy of the gene.
Researchers studied 39 other families with a history of multiple tumors, including leukemia, without finding additional inherited PAX5 mutations. The researchers also examined more than 500 additional cases of non-inherited B cell ALL and found mutations at the same position of the PAX5 gene in two more patients. These two individuals had also lost the other copy of PAX5 through partial deletion of chromosome 9 in their leukemic cells. The findings suggested that the PAX5 mutation and deletion of the second, non-mutated copy of PAX5 contribute to the development of leukaemia.
The PAX5 gene encodes a transcription factor, which is a protein that regulates the activity of other genes. Working in cells growing in the laboratory, investigators found evidence that the newly identified PAX5 mutant resulted in reduced expression of genes normally regulated by PAX5 in developing and mature B cells. St. Jude Children’s Research Hospital

Kashin-Beck disease (KBD) and Keshan disease (KD) are major endemic diseases in China. Postgraduate Xi Wang et al., under the guidance of Professor Xiong Guo from the Institute of Endemic Diseases of the Faculty of Public Health, Medicine College of Xi’an Jiaotong University, Key Laboratory of Environment and Gene Related Diseases in Ministry of Education, Key Laboratory of Trace Elements and Endemic Diseases of Health Ministry, set out to tackle these two endemic diseases. After several years of innovative research, they have made significant progress in determining the etiology and pathogenesis of these diseases at a molecular level; in particular, the identification of some common differentially expressed genes.

KBD and KD are distributed from the northeast to the southwest of China, where the selenium content is low in the soil. In China, there are 660000 KBD and 40000 KD patients, and approximately 30 million people are at risk. KBD is an endemic osteoarthropathy, the pathologic changes of KBD included significant alterations in chondrocyte phenotype, necrosis, and apoptosis, and abnormal terminal chondrocyte differentiation. The mainly pathologic changes of KD are multifocal myocardial necrosis and fibrosis that can result in cardiogenic shock and congestive heart failure. KD is an endemic myocardosis that happened in women and pre-schoolers. Since osteoarthritis and myocardium deformities, the most of KBD and KD patients will partially or completely lose their abilities to work even self-care, which seriously reduces their quality of life, and also bring heavy medical burden to society; the etiology and pathogenesis of KBD and KD remain unclear. However, both diseases happened in the same area of China. Moreover, the living conditions of KBD and KD patients are similar, for example, most patients live in remote rural areas and the areas of awful transportation, have a meager income, and a simply diet. There is little research conducted to compare KBD and KD gene expression profiles. Therefore, the two diseases may have a further relationship at the molecular biology level.

In this study, the Agilent Human 1A Oligo microarray was used to compare gene expression profiles of peripheral blood mononuclear cells (PBMCs) between KBD or KD patients and healthy controls, and identified the common genes differentially expressed in both diseases groups. One hundred and thirty-six differentially expressed genes (53 up-regulated and 83 down-regulated) were identified between KBD and normal controls. Moreover, comparing KD and normal controls, 3310 differentially expressed genes (3154 up-regulated and 156 down-regulated) were identified. Comparing all identified differentially expressed genes, 16 genes showed differential expression in both diseases, including nine with synchronous and seven with asynchronous expression. These 16 genes were subdivided into 11 categories, namely metabolism, cytochrome enzymes, transcription-related, G-protein-related, receptor, cytokine factor, ion channel transport protein, signal transduction, hematopoietic related, interleukin, and immune-related.

The distribution of KBD and KD is in the similar geographical regions, although the clinical presentations and target pathological focus are not same. The common differentially expressed genes identified in both KBD and KD could be helpful to identify the potential mechanisms of the different organ lesions, caused by similar environmental risk factors, selenium deficiency. These findings make a great contribution towards clarifying the etiology and pathogenesis of KBD and KD. EurekAlert

Scientists at the European Molecular Biology Laboratory (EMBL) in Heidelberg and Regensburg University, both in Germany, and the University of Lisboa, in Portugal, have discovered a promising potential drug target for cystic fibrosis. Their work also uncovers a large set of genes not previously linked to the disease, demonstrating how a new screening technique can help identify new drug targets.

Cystic fibrosis is a hereditary disease caused by mutations in a single gene called CFTR. These mutations cause problems in various organs, most notably making the lining of the lungs secrete unusually thick mucus. This leads to recurrent life-threatening lung infections, which make it increasingly hard for patients to breathe. The disease is estimated to affect 1 in every 2500-6000 new-borns in Europe.

In patients with cystic fibrosis, the mutations to CFTR render it unable to carry out its normal tasks. Among other things, this means CFTR loses the ability to control a protein called the epithelial sodium channel (ENaC). Released from CFTR’s control, ENaC becomes hyperactive, cells in the lungs absorb too much sodium and – as water follows the sodium – the mucus in patients’ airways becomes thicker and the lining of the lungs becomes dehydrated. The only drug currently available that directly counteracts a cystic fibrosis-related mutation only works on the three percent of patients that carry one specific mutation out of the almost 2000 CFTR mutations scientists have found so far.

Thus, if you were looking for a more efficient way to fight cystic fibrosis, finding a therapy that would act upon ENaC instead of trying to correct that multitude of CFTR mutations would seem like a good option. But unfortunately, the drugs that inhibit ENaC, mostly developed to treat hypertension, don’t transfer well to cystic fibrosis, where their effects don’t last very long. So scientists at EMBL, Regensburg University and University of Lisboa set out to find alternatives.

‘In our screen, we attempted to mimic a drug treatment,’ says Rainer Pepperkok, whose team at EMBL developed the technique, ‘we’d knock down a gene and see if ENaC became inhibited.’

Starting with a list of around 7000 genes, the scientists systematically silenced each one, using a combination of genetics and automated microscopy, and analysed how this affected ENaC. They found over 700 genes which, when inhibited, brought down ENaC activity, including a number of genes no-one knew were involved in the process. Among their findings was a gene called DGKi. When they tested chemicals that inhibit DGKi in lung cells from cystic fibrosis patients, the scientists discovered that it appears to be a very promising drug target.

‘Inhibiting DGKi seems to reverse the effects of cystic fibrosis, but not block ENaC completely,’ says Margarida Amaral from the University of Lisboa, ‘indeed, inhibiting DGKi reduces ENaC activity enough for cells to go back to normal, but not so much that they cause other problems, like pulmonary oedema.’

These promising results have already raised the interest of the pharmaceutical industry and led the researchers to patent DGKi as a drug target, as they are keen to explore the issue further, searching for molecules that strongly inhibit DGKi without causing side-effects.

‘Our results are encouraging, but these are still early days,’ says Karl Kunzelmann from Regensburg University. ‘We have DGKi in our cells because it is needed, so we need to be sure that these drugs are not going to cause problems in the rest of the body.’ EMBL

Genes have an influence on whether we are left handed or right handed.

A genetic study has identified a biological process that influences whether we are right handed or left handed.
Scientists at the Universities of Oxford, St Andrews, Bristol and the Max Plank Institute in Nijmegen, the Netherlands, found correlations between handedness and a network of genes involved in establishing left-right asymmetry in developing embryos.
‘The genes are involved in the biological process through which an early embryo moves on from being a round ball of cells and becomes a growing organism with an established left and right side,’ explained first author William Brandler, a PhD student in the MRC Functional Genomics Unit at Oxford University.
The researchers suggest that the genes may also help establish left-right differences in the brain, which in turn influences handedness.
Humans are the only species to show such a strong bias in handedness, with around 90% of people being right-handed. The cause of this bias remains largely a mystery.
The researchers, led by Dr Silvia Paracchini at the University of St Andrews, were interested in understanding which genes might have an influence on handedness, in order to gain an insight into the causes and evolution of handedness.
The team carried out a genome-wide association study to identify any common gene variants that might correlate with which hand people prefer using.
The most strongly associated, statistically significant variant with handedness is located in the gene PCSK6, which is involved in the early establishment of left and right in the growing embryo.
The researchers then made full use of knowledge from previous studies of what PCSK6 and similar genes do in mice to reveal more about the biological processes involved.
Disrupting PCSK6 in mice causes ‘left-right asymmetry’ defects, such as abnormal positioning of organs in the body. They might have a heart and stomach on the right and their liver on the left, for example.
The researchers found that variants in other genes known to cause left-right defects when disrupted in mice were more likely to be associated with relative hand skill than you would expect by chance.
While the team has identified a role for genes involved in establishing left from right in embryo development, William Brandler cautioned that these results do not completely explain the variation in handedness seen among humans. He said: ‘As with all aspects of human behaviour, nature and nurture go hand-in-hand. The development of handedness derives from a mixture of genes, environment, and cultural pressure to conform to right-handedness.’
This work was supported by the University of St Andrews, the UK Medical Research Council, the Wellcome Trust, the Max Plank Society, and the EU 6th Framework Programme. University of Oxford

Autism spectrum disorders (ASD) are an increasingly diagnosed group of neurodevelopmental disorders. Although heritability suggests a strong genetic component, efforts to identify genes involved have had disappointing results, and the difference in disease state between identical (monozygotic) twins points to a potential role for epigenetic factors. Two new studies have found a significant correlation between DNA methylation (DNAm) patterns and ASD traits. Wong et al. performed a genome-wide analysis of DNAm in a sample of 50 monozygotic twin pairs sampled from a representative population cohort that included twins discordant and concordant for ASD, ASD-associated traits and no autistic phenotype [1]. Numerous differentially methylated regions associated with ASD were identified and significant correlations between DNAm and quantitatively measured autistic trait scores were reported. Ladd-Acosta et al. examined DNAm in post-mortem brain tissue from 19 autism cases and 21 unrelated controls. Over 485 000 CpG loci were measured across a diverse set of functionally relevant genomic regions and four genome-wide significant differentially methylated regions were identified [2].

<sub>1. Wong et al. Mol Psychiatry 2013; doi: 10.1038/mp.2013.114 (www.nature.com/mp/journal/vaop/ncurrent/full/mp201341a.html).
2. Ladd-Acosta et al. Mol Psychiatry 2013; doi: 10.1038/mp.2013.114 (www.nature.com/mp/journal/vaop/ncurrent/full/mp2013114a.htm).</sub>