A particular location in DNA, called the Dlk1-Gtl2 locus, plays a critical role in protecting hematopoietic, or blood-forming, stem cells–a discovery revealing a critical role of metabolic control in adult stem cells, and providing insight for potentially diagnosing and treating cancer, according to researchers from the Stowers Institute for Medical Research.

In their study, Stowers Investigator Linheng Li, Ph.D., and first author Pengxu Qian, Ph.D., along with other collaborators, reveal how the mammalian imprinted Gtl2, located on mouse chromosome 12qF1, protects adult hematopoietic stem cells by restricting metabolic activity in the cells’ mitochondria.

The research focused on imprinted genes–genes ‘stamped’ according to whether they are inherited from the mother or father. With imprinted genes, one working copy, or allele, is inherited instead of two. Either the copy from the mother or father is inactivated or ‘silenced.’ Typically, the paternally inherited allele’s expression promotes growth, while the maternally inherited allele’s expression suppresses it.

The researchers found that when the Gtl2 locus is expressed from the maternally inherited allele, it produces non-coding RNAs to curb metabolic activity. Mechanistically, Gtl2’s ‘megacluster’ of microRNA, the largest cluster of microRNA in the mammalian genome, suppresses the mTOR signaling pathway and downstream mitochondrial biogenesis and metabolism, thus blocking mitochondrial-associated byproducts called reactive oxygen species (ROS) that can damage adult stem cells.

‘Reactive oxygen species are like the potentially harmful by-products that come from industrial manufacturing,’ says Li. ‘ROS are unavoidable derivatives of the mitochondrial metabolic process and need to be managed by the cell,’ he explains.

Hematopoietic stems cells renew themselves and differentiate into other cells, including white blood cells, red blood cells, and platelets, constantly renewing the body’s blood supply in a process called hematopoiesis. Because of their extraordinary transformative qualities, the transplantation or transfusion of isolated human hematopoietic stem cells has been used in the treatment of anemia, immune deficiencies, and other diseases, including cancer.

While hematopoietic stem cells have gained attention in research, it remains largely unknown how cell metabolic states are controlled. The new findings shed light on the delicate metabolic control required to balance hematopoietic stem cell maintenance and action and the associated healthy hematopoiesis.

An upset in that balance can cause cells to grow abnormally and lead to disease. Abnormalities in the Gtl2 locus on human chromosome 14q32.2 are associated with uniparental disomy in which an individual receives two copies of a chromosome from one parent and no copy from the other parent. Uniparental disomy may cause delayed development, mental retardation, or other medical problems. Differences in gene expression at the Gtl2 locus have also been linked to fetal alcohol exposure disorder.

But when working properly, the Gtl2 locus acts as a great protector of cells.

‘Most of the non-coding RNAs at the Gtl2 locus have been documented to function as tumor suppressors to maintain normal cell function,’ Qian says.

Li’s team zeroed in on Gtl2 by studying hematopoietic stem cells in mice with support from Stowers core centers including cytometry, bioinformatics, histology and electron microscopy, molecular biology, and tissue culture. Other collaborators included researchers from the University of Kansas; the University of Kansas Medical Center; Tianjin Medical University, China; Christian Medical College, Vellore, India; Tokyo University of Agriculture, Japan; and University of Cambridge, United Kingdom.

Over the three-year study, investigators used transcriptome profiling to analyze 17 hematopoietic cell types and found that non-coding RNAs expressed from the Gtl2 locus are predominantly located in a subset of the cell types, including adult ‘long-term’ hematopoietic stem cells which have long-term self-renewal capacity. In subsequent experiments, deleting the locus from the maternally inherited allele in hematopoietic stem cells increased mitochondrial biogenesis and subsequent metabolic activity as well as increased ROS levels, with the latter inducing cell death.

The finding opens the possibility for Gtl2 to be used as a biomarker because it could help label dormant (or reserve) stem cells in normal or potentially cancerous stem cell populations, Li says. The addition of a fluorescent tag to the Gtl2 locus could allow researchers to mark other adult stem cells in the gut, hair follicle, muscle, and neural systems. EurekAlert

Scientists who analysed the genes involved in 10 autoimmune diseases that begin in childhood have discovered 22 genome-wide signals shared by two or more diseases. These shared gene sites may reveal potential new targets for treating many of these diseases, in some cases with existing drugs already available for non-autoimmune disorders.

Autoimmune diseases, such as type 1 diabetes, Crohn’s disease and juvenile idiopathic arthritis, collectively affect 7 to 10 percent of the population in the Western Hemisphere.

Dr. Hakonarson“Our approach did more than finding genetic associations among a group of diseases,” said study leader, Hakon Hakonarson, MD, PhD, director of the Center for Applied Genomics at The Children’s Hospital of Philadelphia (CHOP). “We identified genes with a biological relevance to these diseases, acting along gene networks and pathways that may offer very useful targets for therapy.”

The international study team performed a meta-analysis, including a case-control study of 6,035 subjects with automimmune disease and 10,700 controls, all of European ancestry. The study’s lead analyst, Yun (Rose) Li, an MD/PhD graduate student at the University of Pennsylvania and the Center for Applied Genomics, mentored by Hakonarson and his research team, applied highly innovative and integrative approaches in supporting the study of pathogenic roles of the genes uncovered across multiple diseases.

The research encompassed 10 clinically distinct autoimmune diseases with onset during childhood: type 1 diabetes, celiac disease, juvenile idiopathic arthritis, common variable immunodeficiency disease, systemic lupus erythematosus, Crohn’s disease, ulcerative colitis, psoriasis, autoimmune thyroiditis and ankylosing spondylitis.

Because many of these diseases run in families and because individual patients often have more than one autoimmune condition, clinicians have long suspected these conditions have shared genetic predispositions. Previous genome-wide association studies have identified hundreds of susceptibility genes among autoimmune diseases, largely affecting adults.

The current research was a systematic analysis of multiple paediatric-onset diseases simultaneously. The study team found 27 genome-wide loci, including five novel loci, among the diseases examined. Of those 27 signals, 22 were shared by at least two of the autoimmune diseases, and 19 of them were shared by at least three of them.

Many gene signals found on biological pathways linked to cell activation, proliferation and signalling

Many of the gene signals the investigators discovered were on biological pathways functionally linked to cell activation, cell proliferation and signalling systems important in immune processes. One of the five novel signals, near the CD40LG gene, was especially compelling, said Hakonarson, who added, “That gene encodes the ligand for the CD40 receptor, which is associated with Crohn’s disease, ulcerative colitis and celiac disease. This ligand may represent another promising drug target in treating these diseases.”

Gene signals have biological relevance to autoimmune disease processes, opportunities to better target gene networks and pathways

Many of the 27 gene signals the investigators uncovered have a biological relevance to autoimmune disease processes, Hakonarson said. “Rather than looking at overall gene expression in all cells, we focused on how these genes upregulated gene expression in specific cell types and tissues, and found patterns that were directly relevant to specific diseases. For instance, among several of the diseases, we saw genes with stronger expression in B cells. Looking at diseases such as lupus or juvenile idiopathic arthritis, which feature dysfunctions in B cells, we can start to design therapies to dial down over-expression in those cells.”

He added that “the level of granularity the study team uncovered offers opportunities for researchers to better target gene networks and pathways in specific autoimmune diseases, and perhaps to fine tune and expedite drug development by repurposing existing drugs, based on our findings.” The Children’s Hospital of Philadelphia

An improved gene therapy treatment can cure mice with cystic fibrosis (CF). Cell cultures from CF patients, too, respond well to the treatment. Those are the encouraging results of a study presented by the KU Leuven Laboratory for Molecular Virology and Gene Therapy.

Cystic fibrosis or mucoviscidosis is a genetic disorder that makes the mucus in the body thick and sticky, which in turn causes clogging in, for instance, the airways and the gastrointestinal tract. The symptoms can be treated, but there is no cure for the disorder.

Cystic fibrosis is caused by mutations in the CFTR gene. This gene contains the production code for a protein that functions as a channel through which chloride ions and water flow out of cells. In the cells of CF patients, these chloride channels are dysfunctional or even absent, so that thick mucus starts building up.

“A few years ago, a new drug was launched that can repair dysfunctional chloride channels”, Professor Zeger Debyser explains. “Unfortunately, this medicine only works in a minority of CF patients. As for the impact of gene therapy, previous studies suggested that the treatment is safe, but largely ineffective for cystic fibrosis patients. However, as gene therapy has recently proven successful for disorders such as haemophilia and congenital blindness, we wanted to re-examine its potential for cystic fibrosis”.

That is why lead authors Dragana Vidović and Marianne Carlon examined an improved gene therapy treatment based on inserting the genetic material for chloride channels – coded by the CFTR gene – into the genome of a recombinant AAV viral vector, which is derived from the relatively innocent AAV virus. The researchers then used this vector to ‘smuggle’ a healthy copy of the CFTR gene into the affected cells.

Both in mice with cystic fibrosis and in gut cell cultures from CF patients, this approach yielded positive results. “We administered the rAAV to the mice via their airways. Most of the CF mice recovered. In the patient-derived cell cultures, chloride and fluid transport were restored”.

There is still a long way to go before gene therapy can be used to treat cystic fibrosis patients, Debyser clarifies: “We must not give CF patients false hope. Developing a treatment based on gene therapy will take years of work. For one thing, our study did not involve actual human beings, only mice and patient-derived cell cultures. Furthermore, we still have to examine how long the therapy works. Repeated doses might be necessary. But gene therapy clearly is a promising candidate for further research towards a cure for cystic fibrosis”. KU Leuven

Humans evolved unique gene variants that protect older adults from neurodegenerative disease, thus preserving their valuable contributions and delaying dependency

Many human gene variants have evolved specifically to protect older adults against neurodegenerative and cardiovascular diseases, thus preserving their contributions to society, report University of California, San Diego School of Medicine researchers.

“We unexpectedly discovered that humans have evolved gene variants that can help protect the elderly from dementia,” said Ajit Varki, MD, Distinguished Professor of Medicine and Cellular and Molecular Medicine at UC San Diego School of Medicine, adjunct professor at the Salk Institute for Biological Studies and co-director of the UC San Diego/Salk Center for Academic Research and Training in Anthropogeny (CARTA). “Such genes likely evolved to preserve valuable and wise grandmothers and other elders, as well as to delay or prevent the emergence of dependent individuals who could divert resources and effort away from the care of the young.” Varki led the study, along with Pascal Gagneux, PhD, associate professor of pathology and associate director of CARTA.

The standard model of natural selection predicts that once the age of reproduction ends, individuals die. That’s because selection early in life strongly favours variants that benefit reproductive success, even at the cost of negative consequences late in life — one major reason we age. This is indeed the case in almost all vertebrates. Humans (and certain whales) are an exception to this rule, living decades beyond reproductive age. Such elders contribute to the fitness of younger individuals by caring for grandchildren and also by passing down important cultural knowledge. Age-related cognitive decline compromises these benefits, and eventually burdens the group with the need to care for dependent older members.

In this first-of-its kind discovery, Varki, Gagneux and their teams initially focused on the gene that encodes the CD33 protein. CD33 is a receptor that projects from the surface of immune cells, where it keeps immune reactions in check, preventing “self” attack and curtailing unwanted inflammation. Previous studies suggested that a certain form of CD33 suppresses amyloid beta peptide accumulation in the brain. Amyloid beta accumulation is thought to contribute to late-onset Alzheimer’s disease, a post-reproductive condition that uniquely affects humans and is aggravated by inflammation and cerebral vascular disease.

The researchers compared CD33 regulation in humans and our closest living relatives, chimpanzees. They found that levels of the CD33 variant that protects against Alzheimer’s are four-fold higher in humans than chimpanzees.

They also found human-specific variations in many other genes involved in the prevention of cognitive decline, such as APOE. The ancestral form of the gene, APOE4, is a notorious risk factor for Alzheimer’s and cerebral vascular disease. But this study finds that variants APOE2 and APOE3 seem to have evolved to protect from dementia. All of these protective gene variants are present in Africa, and thus predate the origin of our species. This finding is in keeping with the valuable role of the elderly across human societies.

“When elderly people succumb to dementia, the community not only loses important sources of wisdom, accumulated knowledge and culture, but elders with even mild cognitive decline who have influential positions can harm their social groups by making flawed decisions,” Gagneux said. “Our study does not directly prove that these factors were involved in the selection of protective variants of CD33, APOE and other genes, but it is reasonable to speculate about the possibility. After all, inter-generational care of the young and information transfer is an important factor for the survival of younger kin in the group and across wider social networks or tribes.” San Diego School of Medicine