A Chinese research team composed of Shenzhen Second People’s Hospital, BGI and other institutes reports their latest study on bladder cancer genomics. The discoveries were made using whole-genome and exome sequencing technologies and provide evidence that genetic alterations affecting the sister chromatid cohesion and segregation (SCCS) process may be involved in bladder tumorigenesis and open a new way for the treatment of bladder cancer.

Transitional cell carcinoma (TCC) is the most common type of bladder cancer diagnosed, accounting for 90% of all bladder malignancies in North America, South America, Europe, and Asia. It’s reported that there were an estimated 386,300 new bladder cancer cases and 150,200 deaths in 2008 alone. And the number was up to 170,000 deaths in 2010. Until now, there has been no complete genomic data available for developing new therapeutic approaches to combat bladder cancer.

To have a deeper understanding of the genetic basis underlying TCC, Chinese scientists conducted exome sequencing on the tumour and matched peripheral blood samples from 99 TCC patients, and identified 1,023 somatic substitutions and 67 indels respectively. They performed whole genome sequencing (WGS) to detect copy number alterations (CNAs) and obtained 4-fold mean haploid coverage for each sample.
After evaluating the genetic alterations or variants, researchers found frequent alterations in two genes, STAG2 and ESPL1, which are associated with the sister chromatid cohesion and segregation (SCCS) process. Among them, STAG2 was particularly notable as to harbour a greater number of non-synonymous mutations and a higher ratio of non-synonymous to synonymous mutations. Their study indicated that chromosomal instability and aneuploidy had an influence on bladder cancer, and provided evidence that bladder cancer became the first type of cancer with major genetic lesions in SCCS genes.

Furthermore, researchers detected a recurrent fusion involving two other SCCS-associated genes, FGFR3 and TACC3, by transcriptome sequencing of 42 DNA-sequenced tumors. They suggested that FGFR3/TACC3 is related with bladder tumorigenesis, and the high expression of TACC3 was mediated by transcriptional regulatory elements in the promoter of the fusion partner, FGFR3, not the amplification of TACC3. BGI

Johns Hopkins researchers say that by measuring levels of certain proteins in cerebrospinal fluid (CSF), they can predict when people will develop the cognitive impairment associated with Alzheimer’s disease years before the first symptoms of memory loss appear.
Identifying such biomarkers could provide a long-sought tool to guide earlier use of potential drug treatments to prevent or halt the progression of Alzheimer’s while people are still cognitively normal.
To date, medications designed to stop the brain damage have failed in clinical trials, possibly, many researchers say, because they are given to those who already have symptoms and too much damage to overcome.
‘When we see patients with high blood pressure and high cholesterol, we don’t say we will wait to treat you until you get congestive heart failure. Early treatments keep heart disease patients from getting worse, and it’s possible the same may be true for those with pre-symptomatic Alzheimer’s,’ says Marilyn Albert, Ph.D., a professor of neurology at the Johns Hopkins University School of Medicine. ‘But it has been hard to see Alzheimer’s disease coming, even though we believe it begins developing in the brain a decade or more before the onset of symptoms,’ she adds.
For the new study, the Hopkins team used CSF collected for the Biomarkers for Older Controls at Risk for Dementia (BIOCARD) project between 1995 and 2005, from 265 middle-aged healthy volunteers. Some three-quarters of the group had a close family member with Alzheimer’s disease, a factor putting them at higher than normal risk of developing the disorder. Annually during those years and again beginning in 2009, researchers gave the subjects a battery of neuropsychological tests and a physical exam.
They found that particular baseline ratios of two proteins — phosphorylated tau and beta amyloid found in CSF — were a harbinger of mild cognitive impairment (often a precursor to Alzheimer’s) more than five years before symptom onset. They also found that the rate of change over time in the ratio was also predictive. The more tau and the less beta amyloid found in the spinal fluid, the more likely the development of symptoms. And, Albert says, the more rapidly the ratio of tau to beta amyloid goes up, the more likely the eventual development of symptoms.
Researchers have known that these proteins were in the spinal fluid of patients with advanced disease. ‘But we wondered if we could measure something in the cerebral spinal fluid when people are cognitively normal to give us some idea of when they will develop difficulty,’ Albert says. ‘The answer is yes.’ John Hopkins Medicine

A collaborative team of researchers has used next generation sequencing to identify clinically relevant genetic variants associated with a rare pediatric speech disorder.
Childhood apraxia of speech (CAS) is a rare, severe speech disorder that in some patients also affects cognitive, language, and learning processes.

In this study, Elizabeth Worthey, PhD, assistant professor of paediatrics (genomic paediatrics and bioinformatics) at the Medical College of Wisconsin, working with Dr. Lawrence Shriberg at the Waisman Center, University of Wisconsin – Madison and their colleagues used whole exome sequencing to search for variants associated with CAS.

Prior studies have identified a few genes associated with CAS. In this study, ten pediatric patients were sequenced, and in eight of the cases, clinically significant variants associated with CAS were identified. In some cases patients were found to have apparently deleterious variants in more than one gene. The findings both confirmed previous reports of candidate causal genes and identified novel candidate associations.

‘This study exemplifies the potential productivity of whole exome sequencing for complex neurodevelopmental disorders such as CAS. The current list price to test individual genes is far in excess of the cost of whole exome, and it is also more time effective to perform these tests concurrently rather than looking at one gene at a time,’ said Dr. Worthey. ‘It is likely that a significant proportion of patients with complex phenotypes will be found to have deleterious variants in multiple genes; single gene testing would be unlikely to identify such cases.’ Medical College of Wisconsin

Researchers at Boston University School of Medicine (BUSM) have discovered a molecule that could help lead to the non-invasive detection of lung cancer as well as its treatment. Using RNA sequencing, the team looked at airway epithelial cells and identified a regulatory molecule that was less abundant in people with lung cancer and inhibits lung cancer cell growth. The findings suggest that this molecule may aid in diagnosing lung cancer in earlier stages and could potentially, when at healthy levels, aid in treating the disease.
According to the National Cancer Institute (NCI), lung cancer is the leading cause of cancer death among both men and women in the United States, and 90 percent of lung cancer deaths among men and approximately 80 percent of lung cancer deaths among women are due to smoking. The NCI also estimates that approximately 373,489 Americans are living with lung cancer and its treatment costs approximately $10.3 billion in the United States each year.
MicroRNA’s are a new class of molecules classified as important regulators of the activity of other genes. In this study, the research team used a next-generation RNA sequencing technology and identified that a microRNA named miR-4423 in epithelial airway cells plays a major role in how these cells develop. In epithelial cells from the airway of smokers with lung cancer, levels of miR-4423 were decreased.
‘These results suggest measuring the levels of microRNAs like miR-4423 in cells that line the airway could aid in lung cancer detection through a relatively non-invasive procedure,’ said Avrum Spira, MD, MSc, the Alexander Graham Bell professor of medicine and chief of the division of computational biomedicine at BUSM, one of the study’s senior authors.
Using experimental models in vitro and in vivo, the research team demonstrated that miR-4423 can both promote the development of the normal airway cells and suppress lung cancer cell growth. This suggests that miR-4423 plays a major regulatory role in cell fate decisions made by airway epithelial cells during maturation and low levels of miR-4423 contributes to lung cancer development. Interestingly, throughout the body, miR-4423 seems only to be present in high levels in the airway epithelium, suggesting this could be a very specific process occurring only in the lungs.
‘Our findings open up the option to study whether returning miR-4423 levels to normal in the airway could help stop cancer growth and potentially be a way to treat lung cancer,’ said Catalina Perdomo, PhD, a researcher in the division of computational biomedicine at BUSM who is the paper’s lead author.
‘Interestingly, when we examined the genomes of other species for microRNAs that might function like miR-4423, we did not find anything in non-primates,’ said Marc Lenburg, PhD, an associate professor in computational medicine and bioinformatics at BUSM who is one the study’s senior authors. ‘It makes us wonder what it is different about lung development in primates and excited that this could be a very specific process to target for lung cancer treatment.’ EurekAlert

A 30-year-old woman with a history of upper respiratory infections had no idea she carried an immunodeficiency disorder – until her 6-year-old son was diagnosed with the same illness.
After learning she has common variable immunodeficiency (CVID), a disorder characterised by recurrent infections, such as pneumonia, and decreased antibodies, the woman, her husband, their three children and parents joined a multidisciplinary University of Utah study and researchers identified a novel gene mutation that caused the disease in the mom and two of her children. The researchers discovered that a mutation in the NFKB2 gene impairs a protein from functioning properly, which interferes with the body’s ability to make antibodies and fight infection. The children’s father did not have the mutation, nor did a third sibling or the woman’s parents.
Another 35 people with CVID were tested for the gene mutation, and one other unrelated person was found to have it. His father wasn’t tested, but no one else in his family immediate family had the mutation, so the researchers don’t know whether he could have inherited the disorder from his father or developed the gene mutation sporadically.
CVID typically doesn’t present with symptoms until adulthood and it’s not uncommon for someone to reach their 20s, 30s or beyond before being diagnosed, according to Karin Chen, M.D., co-first author of the study published Thursday, Oct. 17, 2013, in the American Journal of Human Genetics online. Identifying the NFKB2 mutation will make it easier to recognise and treat the disorder, particularly after a test developed in conjunction with the study by ARUP Laboratories becomes available as early as next May.
‘If we can screen patients for genetic mutations, we can identify disease complications associated with that gene, start looking for them and treating them sooner,’ says Chen, instructor of pediatric immunology at the University’s School of Medicine.
There’s no cure for CVID, but it can be treated with monthly infusions of antibodies at a cost of $5,000 to $10,000 per treatment.
Identifying the gene mutation and developing the test for it took approximately two years, a fast turnaround made possible because of the multidisciplinary research that the University of Utah Health Sciences encourages and is known for doing. The study involved researchers from the U School of Medicine’s Departments of Pediatrics, Pathology, Human Genetics and Program in Molecular Medicine and ARUP, which is a University-owned, nationwide testing laboratory.
Emily M. Coonrod, Ph.D., a research scientist with the ARUP Institute for Clinical and Experimental Pathology, is co-first author with Chen. Karl V. Voelkerding, M.D., also of the Institute for Clinical and Experimental Pathology and a U professor of pathology, is the senior author.
CVID probably is underdiagnosed, making it hard to know how common it is. But the disorder is estimated to occur in one in 10,000 people to one in 50,000 people, meaning it is one of more common types of immunodeficiency disorders, according to Chen. University physicians currently treat about 150 CVID patients in the Intermountain Region. Historically, CVID has been diagnosed clinically by doctors who are aware of the symptoms and then have individuals tested for low levels of antibodies.
No mutation had been identified in NFKB2 before this study. But Attila Kumánovics, M.D., assistant professor of pathology and co-author on the study, had perused the medical literature and found that a mouse model had been developed that carried a similar mutation in the NFKB2 gene and also had immunodeficiency. That was a key development, according to Voelkerding. ‘This meant that the finding in our patients could be correlated to literature.’ University of Utah Health Care