A new Pathology Atlas has been launched with an analysis of all human genes in all major cancers showing the consequence of their corresponding protein levels for overall patient survival. The difference in expression patterns of individual cancers observed in the study strongly reinforces the need for personalized cancer treatment based on precision medicine. In addition, the systems level approach used to construct the Pathology Atlas demonstrates the power of “big data” to change how medical research is performed.
The dream of personalized treatment for cancer patients takes a major step forward with the launch by Swedish researchers of the Human Pathology Atlas. The Atlas is based on the analysis of 17 main cancer types using data from 8,000 patients. In addition, a new concept for showing patient survival data is introduced, called Interactive Survival Scatter plots, and the atlas includes more than 400,000 such plots. A national supercomputer centre was used to analyse more than 2.5 petabytes of underlying publicly available data from the Cancer Genome Atlas (TCGA) to generate more than 900,000 survival plots describing the consequence of RNA and protein levels on clinical survival. The Pathology Atlas also contains 5 million pathology-based images generated by the Human Protein Atlas consortium.
Professor Mathias Uhlen, Director of the Human Protein Atlas consortium and leader of the Pathology Atlas effort says: “This study differs from earlier cancer investigations, since it is not focused on the mutations in cancers, but the downstream effects of such mutations across all protein-coding genes. We show, for the first time, the influence of the gene expression levels demonstrating the power of “big data” to change how medical research is performed. It also shows the advantage of open access policies in science in which researchers share data with each other to allow integration of huge amounts of data from different sources.”
The article reports several important findings related to cancer biology and treatment. Firstly, a large fraction of genes is differentially expressed in cancers – and in many cases – have an impact on overall patient survival. The research also showed that gene expression patterns of individual tumours varied considerably, and could exceed the variation observed between different cancer types. Shorter patient survival was generally associated with up-regulation of genes involved in mitosis and cell growth, and down-regulation of genes involved in cellular differentiation. The data allowed the researchers to generate personalized genome-scale metabolic models for cancer patients to identify key genes involved in tumour growth.
The work depends heavily on the supercomputing power available to the Human Protein Atlas consortium through the Science for Life Laboratory (SciLifeLab). According to Dr. Adil Mardinoglu, SciLifeLab Fellow and leader of the systems biology effort in the project: “We are now in possession of incredibly powerful systems biology tools for medical research, allowing, for the first time, genome-wide analysis of individual patients with regards to the consequence of their expression profiles for clinical survival.”
The Pathology Atlas is available via an interactive open-access database.

EurekAlerthttp://tinyurl.com/y6ubo3qb

Cancer cells obtained from a blood test may be able to predict how early-stage lung cancer patients will fare, a team from the University of Michigan has shown.
This information could be used to determine which patients are most likely to benefit from additional therapies to head off the spread of the cancer to other areas of the body.
With a new single cell analysis service in U-M’s Comprehensive Cancer Center, the researchers are making the necessary technology more widely available in the university system. They hope these "liquid biopsies" will be offered to patients within the next five years.
Circulating tumour cells, representing only about one in a billion cells in the bloodstream, are largely untapped sources of information about tumours, but new methods are bringing their diagnostic value ever closer to patient care.
Sunitha Nagrath, U-M professor of chemical engineering who designs devices that can capture these rare cells, led a team including oncologists and surgeons to explore how cancer cells escape tumours and travel through the body in the bloodstream. This is how metastases, or satellite tumours elsewhere in the body, are thought to form.
"The tumours were constantly shedding cells even when they were small — that’s one thing we learned," Nagrath said. "Although we define the tumours as early stage, already they are disseminating cells in the body."
Early-stage lung cancer patients, whose tumours may only measure a few millimetres in diameter, are typically treated with surgical removal of the tumour, but the study results suggest that this may not be enough. A handful of patients had tumours that were shedding hundreds or thousands of tumour cells into the lung.
"Even though you removed the tumour, you left behind these hundreds and hundreds of cells," Nagrath said. "If you know this patient walking out of the clinic is going to relapse after less than a year because of these cells, why don’t we treat them now?"
With a relatively small sample of 36 patients, the team can’t definitively say that an actively shedding tumour will lead to metastasis within a year, but Nagrath is exploring the predictive power of cancer cells drawn from the blood. In particular, the study showed that clusters of two or more tumour cells indicated shorter survival times. Six of the nine patients whose cancer returned during the two to 26 months of follow-up had circulating tumour cells appearing in clusters.
"Ultimately, this method will help us look for and find potential markers for either metastatic spread or cancer detection," said Rishindra Reddy, U-M associate professor of surgery who coordinated the blood samples and designed the study with Nagrath and Nithya Ramnath, an associate professor of medical oncology at the U-M Medical School.

University of Michigan
www.mcancer.org/news/archive/blood-test-can-predict-early-lung-cancer-prognosis
 

Extending non-invasive prenatal screening to all 24 human chromosomes can detect genetic disorders that may explain miscarriage and abnormalities during pregnancy, according to a study by researchers at the National Institutes of Health and other institutions. Because of the way data have been analysed, typical genomic tests performed during pregnancy have targeted extra copies of chromosomes 21, 18 and 13, but rarely evaluated all 24 chromosomes. The study findings may ultimately improve the accuracy of these tests, including by explaining why some give false-positive results.
Women often request non-invasive screening tests to detect genetic conditions. These tests, however, typically focus only on Down syndrome and other common trisomies. A trisomy is a condition in which there are three instances of a certain chromosome instead of the standard two.
"Extending our analysis to all chromosomes allowed us to identify risk for serious complications and potentially reduce false-positive results for Down syndrome and other genetic conditions," said Diana W. Bianchi, M.D., senior author of the study and chief of the Prenatal Genomics and Therapy Section at NIH’s National Human Genome Research Institute (NHGRI). Dr. Bianchi is also the director of NIH’s Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD).
The investigators analysed DNA sequence data from nearly 90,000 samples of maternal plasma, the liquid portion of blood after all cells have been removed. Of these samples, 72,972 came from a U.S. cohort and 16,885 came from an Australian cohort. For each, researchers calculated a normalized chromosome denominator quality (NCDQ), which measures the likelihood that a sample has the standard two copies of each chromosome. Those with an NCDQ of 50 or below were flagged for further evaluation.
In the U.S. cohort, 328 (0.45 percent) samples were flagged and ultimately classified as abnormal. In the Australian cohort, 71 (0.42 percent) samples were deemed abnormal, 60 of which contained a rare trisomy. Trisomy 7 was observed most frequently in both study cohorts, followed by trisomies 15, 16 and 22.
Pregnancy and other outcome data were available for 52 of the 60 cases of rare trisomies found in the Australian cohort. Notably, researchers linked 22 samples with early miscarriage (occurring before 11 or 12 weeks gestation), including 13 of 14 samples with trisomy 15 and 3 of 5 samples with trisomy 22.
"We found that pregnancies at greatest risk of serious complications were those with very high levels of abnormal cells in the placenta," said Mark D. Pertile, Ph.D., co-first author of the study and head of the division of reproductive genetics at Victorian Clinical Genetics Services, part of Murdoch Childrens Research Institute in Melbourne, Australia. "Our results suggest that patients be given the option of receiving test results from all 24 chromosomes."

The National Human Genome Research Institute (NHGRI)
www.genome.gov/27569418/2017-news-relase-sequencing-all-24-human-chromosomes-uncovers-rare-disorders/
 

Vitamin C may “tell” faulty stem cells in the bone marrow to mature and die normally, instead of multiplying to cause blood cancers.
Certain genetic changes are known to reduce the ability of an enzyme called tet methylcytosine dioxygenase 2, or TET2, to encourage stem cells to become mature blood cells, which eventually die, in many patients with certain kinds of leukemia, say the authors. The new study found that vitamin C activated TET2 function in mice engineered to be deficient in the enzyme.
“We’re excited by the prospect that high-dose vitamin C might become a safe treatment for blood diseases caused by TET2-deficient leukemia stem cells, most likely in combination with other targeted therapies,” says corresponding study author Benjamin G. Neel, MD, PhD, professor in the Department of Medicine and director of Perlmutter Cancer Center.
Changes in the genetic code, or mutations, that reduce TET2 function are found in 10 percent of patients with acute myeloid leukemia (AML), 30 percent of those with a form of preleukemia called myelodysplastic syndrome, and in nearly 50 percent of patients with chronic myelomonocytic leukemia. Such cancers cause anemia, infection risk, and bleeding as abnormal stem cells multiply in the bone marrow until they interfere with blood cell production, with the number of cases increasing as the population ages.
Along with these diseases, new tests suggest that about 2.5 percent of all United States cancer patients—or about 42,500 new patients each year—may develop TET2 mutations, including some with lymphomas and solid tumours, say the authors.
The study results revolve around the relationship between TET2 and cytosine, one of the four nucleic acid “letters” that comprise the DNA code in genes. Every cell type has the same genes, but each gets different instructions to turn on only those needed in a given cellular context. These “epigenetic” regulatory mechanisms include DNA methylation, the attachment of a small molecule termed a methyl group to cytosine bases that shuts down the action of a gene containing them.
The back-and-forth attachment and removal of methyl groups also fine tunes gene expression in stem cells, which can mature, specialize, and multiply to become muscle, bone, nerve, or other cell types. This happens as the body first forms, but the bone marrow also keeps pools of stem cells on hand into adulthood, ready to become replacement cells as needed. In leukemia, signals that normally tell a blood stem cell to mature malfunction, leaving it to endlessly multiply and “self-renew” instead of producing normal white blood cells needed to fight infection.
The enzyme studied in this report TET2, enables a change in the molecular structure, or oxidation, of methyl groups that is needed for them to be removed from cytosines. This “demethylation” turns on genes that direct stem cells to mature, and to start a countdown toward self-destruction as part of normal turnover. This serves as an anti-cancer safety mechanism, one that is disrupted in blood cancer patients with TET2 mutations, says Dr. Neel.
To determine the effect of mutations that reduce TET2 function in abnormal stem cells, the research team genetically engineered mice such that the scientists could switch the TET2 gene on or off.
Similar to the naturally occurring effects of TET2 mutations in mice or humans, using molecular biology techniques to turn off TET2 in mice caused abnormal stem cell behaviour. Remarkably, these changes were reversed when TET2 expression was restored by a genetic trick. Previous work had shown that vitamin C could stimulate the activity of TET2 and its relatives TET1 and TET3. Because only one of the two copies of the TET2 gene in each stem cell is usually affected in TET2-mutant blood diseases, the authors hypothesized that high doses of vitamin C, which can only be given intravenously, might reverse the effects of TET2 deficiency by turning up the action of the remaining functional gene.
Indeed, they found that vitamin C did the same thing as restoring TET2 function genetically. By promoting DNA demethylation, high-dose vitamin C treatment induced stem cells to mature, and also suppressed the growth of leukemia cancer stem cells from human patients implanted in mice.
NYU Langone Healthhttp://tinyurl.com/y8pvrxso

Over the past decade, mutations in more than 60 different genes have been linked with autism spectrum disorder, including de novo mutations, which occur spontaneously and aren’t inherited. But much of autism still remains unexplained.
A new study of nearly 6,000 families implicates a hard-to-find category of de novo mutations: those that occur after conception and therefore affect only a subset of cells.
De novo mutations can occur in a parent’s sperm or egg. Alternately, they can occur after egg and sperm meet, arising in an embryonic cell. These are known as somatic mutations or post-zygotic mutations (PZMs).
If a PZM happens very early, when the embryo has just a handful of cells, the mutation will show up in most of the mature organism’s cells. But the later PZMs occur during embryonic development, the fewer cells will carry them, making them harder to detect.
“If the mutation is in a very small fraction of all cells, it will be missed by whole-exome sequencing,” said Elaine Lim, a postdoctoral fellow in the lab of Christopher A. Walsh, the Bullard Professor of Pediatrics and Neurology at Harvard Medical School and Boston Children’s Hospital. Lim is first author of the study; Walsh is the senior investigator.
To identify PZMs, Lim, Walsh and colleagues obtained whole-exome sequencing data previously gathered from 5,947 families, usually through blood tests, courtesy of the Simons Foundation Autism Research Initiative Simplex Collection, the Autism Sequencing Consortium and Autism Speaks. They then re-sequenced some of the DNA from these children using three independent sequencing technologies in parallel.
Based on their findings, they classified 7.5 percent of autism spectrum disorder subjects’ de novo mutations as PZMs. Of these, 83 percent had not been picked up in the original analysis of their genome sequence.
Some PZMs affected genes already known to be linked to autism or other neurodevelopmental disorders (such as SCN2A, HNRNPU and SMARCA4) but sometimes affected these genes in different ways. Many other PZMs occurred in genes known to be active in brain development (such as KLF16 and MSANTD2) but not previously associated with autism spectrum disorder.
The connection of these genes to autism may have been missed because the earlier studies focused on mutations that knocked down gene function, the authors said.
“Some of the postzygotic mutations we found represented a gain of function, not a loss of function,” said Lim, who is also affiliated with the Wyss Institute for Biologically Inspired Engineering.
Lim, Walsh and colleagues then brought in another huge data set: gene expression data from the BrainSpan project. These publicly available data came from autopsies of brain samples from deceased patients of different ages, from prenatal through adult.
Comparing these with the genomic sequencing data, based mostly on blood DNA samples, allowed the researchers to estimate the timing of the PZMs and the brain regions they affected.
“By overlapping the data, we can start to map where in the brain these genes are expressed and when the mutations occurred during development,” said Lim. These analyses showed that PZMs in the subjects with autism spectrum disorder occur disproportionately in genes expressed in the amygdala.
“This was exciting to us, in that the amygdala has been proposed as an important region of the brain in autism,” said Lim.
Overall, the work adds to the evidence that complex brain disorders, such as epilepsy, intellectual disability, schizophrenia and brain malformations, can arise from non-inherited mutations that occur at some point during prenatal development.
Harvard Medical Schoolhttp://tinyurl.com/yb2lpxd7