Why some genes are more popular with researchers than others – and how the IMPC can help

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By IMPC

Published 19th September 2018

New research finds that scientists are still studying the same 10% of human genes and ignoring the rest, highlighting the importance of international projects such as the IMPC.

Historical bias is a key reason why biomedical researchers continue to study the same 10 percent of all human genes while ignoring many genes known to play roles in disease, according to a study publishing in PLOS Biology. The researchers involved in this study suggest this bias is bolstered by research funding mechanisms and social forces. The International Mouse Phenotyping Consortium (IMPC) aims to address this issue by creating a platform that characterizes all 20,000 protein-coding mouse genes, which can then give valuable information into homologous genes in the human genome.

Recent studies have reported that researchers actively study only about 2,000 human protein-coding genes, so the researchers set out to find why. They compiled 36 distinct resources describing various aspects of biomedical research and analyzed the large database for answers. The team found that well-meaning policy interventions to promote exploratory or innovative research actually result primarily in additional work on the most established research topics — those genes first characterized in the 1980s and 1990s, before completion of the Human Genome Project. The researchers also discovered that postdoctoral fellows and Ph.D. students who focus on poorly characterized genes have a 50 percent lower chance of becoming an independent researcher.

The researchers applied a systems approach to the data — which included chemical, physical, biological, historical and experimental data — to uncover underlying patterns. In addition to explaining why some genes are not studied, they also explain the extent to which an individual gene is studied. And they can do that for approximately 15,000 genes.

The Human Genome Project — the identification and mapping of all human genes, completed in 2003 — promised to expand the scope of scientific study beyond the small group of genes scientists had studied since the 1980s. But the Northwestern researchers found that 30 percent of all genes have never been the focus of a scientific study and less than 10 percent of genes are the subject of more than 90 percent of published papers.

“The bias to study the exact same human genes is very high,” said Amaral, the Erastus Otis Haven Professor of Chemical and Biological Engineering and a co-author of the study. “The entire system is fighting the very purpose of the agencies and scientific knowledge which is to broaden the set of things we study and understand. We need to make a concerted effort to incentivize the study of other genes important to human health.”

The International Mouse Phenotyping Consortium

This new research highlights the need for projects such as the IMPC, in which the aim is to characterize approximately all 20,000 or so protein coding genes. To achieve this, genes in the mouse genome are switched off, or ‘knocked out’, then standardised physiological tests undertaken across a range of biological systems. This data is then made freely available to the research community. As well as completing large scale comparative studies, the overall aim of the project is to create a platform for this data where researchers/clinicians can search for genes or diseases of interest to help them understand human health and disease. Data for over 6,000 genes is now available on the IMPC website and the project should therefore help address some of the main issues outlined above.

“The IMPC is leveling the playing field by freely providing robust phenotype data for poorly characterized genes. Nothing pleases me more than helping researchers overcome these barriers and discover new research areas none of us have dreamed of. This will be lasting legacy of the IMPC and is why our global partners continue to generate and phenotype mutant mice every day.” said Terry Meehan, a member of IMPC, and the Mouse Informatics Coordinator at the European Bioinformatics Institute.

Lluis Montoliu, researcher at the National Center for Biotechnology (CNB-CSIC) and member of the IMPC said “In the scientific community we all know of ‘famous’ genes and genes that are not so. Fashions also prevail in the scientific community and, indeed, there are many very relevant genes that, due to their difficulty and scarce literature, remain largely unknown. For example, huntingtin, whose gene causes Huntington’s deadly neurodegenerative disease. The IMPC aims to generate and phenotype mutant mice for each and every one of the 20,000 genes, whether or not they are famous, in order to correlate the data obtained with their homologous genes in the human genome.”

PLOS Biology research article: https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2006643

More information on the IMPC: https://www.mousephenotypetest.org/what-is-the-impc/

 

Scientists at the Champalimaud Centre for the Unknown and the Instituto de Medicina Molecular, in Lisbon, Portugal, have discovered that neurons located at mucosal tissues can immediately detect an infection in the organism, promptly producing a substance that acts as an “adrenaline rush” for immune cells. Under the effect of this signal, immune cells rapidly become poised to fight the infection and repair the damage caused to surrounding tissues. These results have been published in the journal Nature. The research utilised the KOMP Repository for obtaining Nmur1 deleted mouse strains.

Most neurons in the body are located in the brain and its vicinity – the central nervous system -, with neurons projecting their axons to every tissue in the organism by way of the spinal cord. In turn, glial cells are neuron satellites ensuring the cohesion of the nervous tissue. Nevertheless, throughout the body there is a very abundant number of peripheral nervous cells. These are so numerous in the gut that they have collectively been dubbed “the second brain”.

Innate lymphocytes (in green) surround the gut (in red). Credit: Henrique Veiga-Fernandes

What do these peripheral nervous cells do? Experts are just beginning to understand that they are in fact extremely important for the organism to be able to mount adequate immune responses and preserve health.

In 2016, Henrique Veiga-Fernandes and his colleagues (then at the Institute for Molecular Medicine, in Lisbon) published, also in Nature, a study where they showed that glial cells in the gut can stimulate a type of immune cells, called ILC3, to produce substances against bacterial infections.

These immune cells that are being studied by Veiga-Fernandes – collectively called “innate lymphoid cells”, or ILC -, are also very special. We are born with them; they are not produced in response to an immunization, for instance through vaccination. “ILCs were discovered very recently, in 2010, but they are very ancient in evolutionary terms. Even lampreys have them!”, says Veiga-Fernandes. Lampreys belong to a very old animal lineage.

There are several types of these innate lymphocytes (white cells). In their 2016 study, the team had analyzed the behavior of ILC3s in the gut – and their “dialog” with their glial cell neighbours. In the new study, also led by Veiga-Fernandes, they focused on another type of innate lymphoid cells: ILC2s.

ILC2s produce substances that are essential to immune responses against parasites, such as worms. “These cells are normally abundant at barrier sites, such as the gut, lungs and skin”, which serve as physical forteresses to the body”, Veiga-Fernandes explains.

Now, the team showed that these immune cells would not be able to develop their protective actions against infections without establishing a “dialog” with neurons residing at those sites.

The study brings “two big novelties”, says Veiga-Fernandes. The first, he explains, “is that neurons define the immune cells’ function. Nobody could have imagined that the nervous system coordinates, commands and controls the immune response throughout the whole organism.” Second, he adds, “it’s one of the fastest and most powerful immune reactions we have ever seen”. Comparatively, the newly discovered neuronal stimulus induces an immune response in a few minutes, while the immune response following vaccination typically takes several weeks to mount.

How did the scientists discover this neuro-immune “tandem”? “What happened was that we observed, in high-resolution microphotographs of the lungs and gut of mice, that ILC2s were placed along the axons of neurons residing in these mucosa, a bit like pearls on a string”, replies Veiga-Fernandes. “So we asked ourselves if these two distinct tissues could productively ‘talk’ to each other.”

To test this hypothesis, the team started by analyzing the whole genome of a series of immune cells – ILC1s, ILC2s, ILC3s, T-cells, etc. -, “searching for genes that code molecules that may act as receivers of neuronal signals”, says Veiga-Fernandes. They found that only ILC2s possessed a defined “receptor” (membrane molecules that act as antennae) for nervous signals.

Notably, the authors discovered that ILC2s have receptors to a neuronal messenger called neuromedin U (NMU). Since neurons are the only cells that produce abundant levels of NMU, this indicated that only neurons could be sending this signal to ILC2s.

Later, they used a rodent parasite, Nippostrongylus brasiliensis (a sort of hookworm) to infect “normal” control mice and mutant mice whose ILC2s had been stripped of their NMU receptors. In the first group of animals, the innate immune cells immediately triggered a response to neutralize the parasite and repair damaged tissue. In the second group, the mice were unable to fight the infection and the damage caused by the parasite – including the internal bleeding of the lungs due to N. brasiliensis.

The researchers also showed that neurons are able to detect the products secreted by parasites that infect the organism – and that, when this happens, they rapidly produce NMU. In turn, NMU acts vigorously on ILC2s, thus generating a protective response in a few minutes.

Could these results be extrapolated to humans? “Maybe. In humans, ILC2s also have NMU receptors”, replies Veiga-Fernandes. “But we are still very far from understanding how we could safely use this neuro-immunological ‘bomb’; for now, we are at the fundamental research level”, he adds.

Research Article: Neuronal regulation of type 2 innate lymphoid cells via neuromedin U

Nerve cells in the gut play a crucial role in the body’s ability to marshal an immune response to infection, according to a new study from Weill Cornell Medicine scientists.

The study, published in Nature, shows that the immune system and nervous system have co-evolved to respond to infectious threats. This means that scientists looking for ways to treat diseases like inflammatory bowel disease or asthma that involve an excessive immune system response may also have to address the nervous system’s role.

“The immune system and neuronal system don’t act independently,” said senior author Dr. David Artis, director of the Jill Roberts Institute for Research in Inflammatory Bowel Disease and the Michael Kors Professor of Immunology at Weill Cornell Medicine. “They are working together.”

“These guys are dancing like a tango,” Dr. Klose said. The lining of the gut is home to many immune system cells, which serve as a defense against parasites and other infections. It is also loaded with nerve cells. Lead author Dr. Christoph Klose, a postdoctoral associate at the Roberts Institute, found that immune system cells in the gut, called group 2 innate lymphoid cells (ILC2s), are intertwined with nerve cells called cholinergic neurons.

The intestinal barrier. Color-enhanced image of the intestinal lining, which serves as a barrier and limits dissemination of the microbiota. Credit: Greg Sonnenberg and David Artis, Weill Cornell Medicine.

The cells’ close proximity led the researchers to wonder if they may be communicating. That’s when they discovered that the ILC2 cells had a receptor for a protein called neuromedin U (NMU), which acts as a messenger for the nerve cells. In laboratory experiments, the investigators found that exposing ILC2 cells to NMU causes the ILC2 cells to rapidly multiply and secrete chemicals called cytokines that may help trigger an immune response or cause inflammation.

Administering NMU to mice infected with a gut parasite triggered inflammation and a powerful immune response that helped the mice more quickly expel the parasites. Conversely, mice genetically engineered to lack receptors for NMU were more susceptible to the parasites, allowing them to multiply rapidly in the rodents’ gut. The study shows that the NMU-producing nerve cells help prime the ILC2 cells, enabling them to rapidly and effectively respond to infection.

“Where we are most excited is thinking about multiple chronic inflammatory diseases that might be related to this neuronal-immune axis and where we might be able to intervene,” Dr. Artis said. The findings may have important implications for scientists studying inflammatory diseases, including asthma, food allergies and inflammatory bowel disease (IBD). Dr. Artis said it was too soon to say whether NMU itself or its receptors could be treatment targets, but he said studying these pathways might lead to potential new therapies for these diseases.

 

Research article: The neuropeptide neuromedin U stimulates innate lymphoid cells and type 2 inflammation

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By IMPC

Published 6th July 2018

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