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Clinical Laboratories and Pathology Groups

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Cambridge Researchers in UK Develop ‘Unknome Database’ That Ranks Proteins by How Little is Known about Their Functions

Scientists believe useful new clinical laboratory assays could be developed by better understanding the huge number of ‘poorly researched’ genes and the proteins they build

Researchers have added a new “-ome” to the long list of -omes. The new -ome is the “unknome.” This is significant for clinical laboratory managers because it is part of an investigative effort to better understand the substantial number of genes, and the proteins they build, that have been understudied and of which little is known about their full function.

Scientists at the Medical Research Council Laboratory of Molecular Biology (MRC-LMB) in Cambridge, England, believe these genes are important. They have created a database of thousands of unknown—or “unknome” as they cleverly dubbed them—proteins and genes that have been “poorly understood” and which are “unjustifiably neglected,” according to a paper the scientist published in the journal PLOS Biology titled, “Functional Unknomics: Systematic Screening of Conserved Genes of Unknown Function.”

The Unknome Database includes “thousands of understudied proteins encoded by genes in the human genome, whose existence is known but whose functions are mostly not,” according to a news release.

The database, which is available to the public and which can be customized by the user, “ranks proteins based on how little is known about them,” the PLOS Biology paper notes.

It should be of interest to pathologists and clinical laboratory scientists. The fruit of this research may identify additional biomarkers useful in diagnosis and for guiding decisions on how to treat patients.

Sean Munro, PhD

“These uncharacterized genes have not deserved their neglect,” said Sean Munro, PhD (above), MRC Laboratory of Molecular Biology in Cambridge, England, in a press release. “Our database provides a powerful, versatile and efficient platform to identify and select important genes of unknown function for analysis, thereby accelerating the closure of the gap in biological knowledge that the unknome represents.” Clinical laboratory scientists may find the Unknome Database intriguing and useful. (Photo copyright: Royal Society.)

Risk of Ignoring Understudied Proteins

Proteomics (the study of proteins) is a rapidly advancing area of clinical laboratory testing. As genetic scientists learn more about proteins and their functions, diagnostics companies use that information to develop new assays. But did you know that researchers tend to focus on only a small fraction of the total number of protein-coding DNA sequences contained in the human genome?

The study of proteomics is primarily interested in the part of the genome that “contains instructions for building proteins … [which] are essential for development, growth, and reproduction across the entire body,” according to Scientific American. These are all protein-coding genes.

Proteomics estimates that there are more than two million proteins in the human body, which are coded for 20,000 to 25,000 genes, according to All the Science.

To build their database, the MRC researchers ranked the “unknome” proteins by how little is known about their functions in cellular processes. When they tested the database, they found some of these less-researched proteins important to biological functions such as development and stress resistance. 

“The role of thousands of human proteins remains unclear and yet research tends to focus on those that are already well understood,” said Sean Munro, PhD, MRC Laboratory of Molecular Biology in Cambridge, England, in the news release. “To help address this we created an Unknome database that ranks proteins based on how little is known about them, and then performed functional screens on a selection of these mystery proteins to demonstrate how ignorance can drive biological discovery.”

Munro created the Unknome Database along with Matthew Freeman, PhD, Head of England’s Sir William Dunn School of Pathology, University of Oxford.

In the paper, they acknowledged the human genome encodes about 20,000 proteins, and that the application of transcriptomics and proteomics has “confirmed that most of these new proteins are expressed, and the function of many of them has been identified.

“However,” the authors added, “despite over 20 years of extensive effort, there are also many others that still have no known function.”

They also recognized limited resources for research and that a preference for “relative safety” and “well-established fields” are likely holding back discoveries.

The researchers note “significant” risks to continually ignoring unexplored proteins, which may have roles in cell processes, serve as targets for therapies, and be associated with diseases as well as being “eminently druggable,” Genetic Engineering News reported.

Setting up the Unknome Database

To develop the Unknome Database, the researchers first turned to what has already come to fruition. They gave each protein in the human genome a “knownness” score based on review of existing information about “function, conservation across species, subcellular localization, and other factors,” Interesting Engineering reported.

It turns out, 3,000 groups of proteins (805 with a human protein) scored zero, “showing there’s still much to learn within the human genome,” Science News stated, adding that the Unknome Database catalogues more than 13,000 protein groups and nearly two million proteins. 

The researchers then tested the database by using it to determine what could be learned about 260 “mystery” genes in humans that are also present in Drosophila (small fruit flies).

“We used the Unknome Database to select 260 genes that appeared both highly conserved and particularly poorly understood, and then applied functional assays in whole animals that would be impractical at genome-wide scale,” the researchers wrote in PLOS Biology.

“We initially selected all genes that had a knownness score of ≤1.0 and are conserved in both humans and flies, as well as being present in at least 80% of available metazoan genome sequences. … After testing for viability, the nonessential genes were then screened with a panel of quantitative assays designed to reveal potential roles in a wide range of biological functions,” they added.

“Our screen in whole organisms reveals that, despite several decades of extensive genetic screens in Drosophila, there are many genes with essential roles that have eluded characterization,” the researchers conclude.

Clinical Laboratory Testing Using the Unknome Database

Future use of the Unknome Database may involve CRISPR technology to explore functions of unknown genes, according to the PLOS Biology paper.

Munro told Science News the research team may work with other research efforts aimed at understanding “mysterious proteins,” such as the Understudied Proteins Initiative.

The Unknome Database’s ability to be customized by others means researchers can create their own “knownness” scores as it applies to their studies. Thus, the database could be a resource in studies of treatments or medications to fight diseases, Chemistry World noted.

According to a statement prepared for Healthcare Dive by SomaLogic, a Boulder, Colorado-based protein biomarker company, diagnostic tests that measure proteins can be applied to diseases and conditions such as:

In a study published in Science Translational Medicine, SomaLogic’s SomaScan assay was reportedly successful in predicting the likelihood within four years of myocardial infarction, heart failure, stroke, and even death.

“The 27-protein model has potential as a ‘universal’ surrogate end point for cardiovascular risk,” the researchers wrote in Science Translational Medicine.

Proteomics definitely has its place in clinical laboratory testing. The development of MRC-LMB’s Unknome Database will help researchers’ increase their knowledge about the functions of more proteins which should in turn lead to new diagnostic assays for labs.

—Donna Marie Pocius

Related Information:

Mapping the ‘Unknome’ May Reveal Critical Genes Scientists Have Ignored

How Many Proteins Exist?

Unknome: A Database of Human Genes We Know Almost Nothing About

Functional Unknomics: Systematic Screening of Conserved Genes of Unknown Function

Unknome Database Ranks Proteins Based on How Little is Known about Them

How a New Database of Human Genes Can Help Discover New Biology

The Unknome Catalogs Nearly Two Million Proteins. Many are Mysterious

Into the Unknome: Scientists at MRC LMB in Cambridge Create Database Ranking Human Proteins by How Little We know About Them

Scientists Hope to Illuminate Unknown Human Proteins with New Public Database

Proteomic Tests Empower Precision Medicine

A Proteomic Surrogate for Cardiovascular Outcomes That is Sensitive to Multiple Mechanisms of Change in Risk

British Junior Doctors Stage Four-Day Walkout Demanding Increased Pay and Better Working Conditions

More than 10,000 doctors walked out for the second time in two months, further burdening an already overwhelmed NHS

On April 11, tens of thousands of junior doctors (similar to medical residents in the US) left their posts in British hospitals commencing a four-day walkout. The strike resulted in the cancellation of thousands of operations and appointments, as well as cancelling or delaying thousands of clinical laboratory tests and anatomic pathology readings associated with those healthcare visits and surgical procedures.

The walkout was spurred by pay concerns and working conditions and comes on the heels of a three-day strike last month. That strike had already weakened the UK’s frail National Health System (NHS), which has become inundated with appointment backlogs that predate the COVID-19 pandemic, and which has led to longer wait times to see a doctor, ABC News reported.

This latest strike was more perilous since the senior doctors who covered for their juniors during last month’s strike were previously on leave for a holiday weekend, United Press International (UPI) reported.

Matthew Taylor

“These strikes are going to have a catastrophic impact on the capacity of the NHS to recover,” Matthew Taylor (above), Chief Executive of the NHS Confederation, told Sky News. “The health service has to meet high levels of demand at the same time as making inroads into that huge backlog … That’s a tough thing to do at the best of times—it’s impossible to do when strikes are continuing.” (Photo copyright: Wikimedia Commons.)

Junior Docs Cite Injustice

Junior doctors who walked out are calling for a 35% pay raise to right the wrongs of 15 years of below-inflation raises, but the government continues to argue it cannot afford to increase pay, UPI noted.

“There is nothing ‘junior’ about the work I have done as a doctor. For an hour of work that I might save a life, I can be paid 19£ [$23.65],” said Jennifer Barclay, MD, a surgical junior doctor in the UK’s North West electoral zone, in a British Medical Association (BMA) press release.

“My dad, an electrician, tells me to quit and retrain in his footsteps. I’d be earning more, have less stress, less responsibility, better hours, and a better work-life balance after three years,” she added. “Surely, this life, this training, responsibility, debt, and crushing workload is worth more than 19£ per hour? I’ll be on the picket line this week because doctors believe that it is.”

According to the BMA, newly qualified junior doctors earn just over 14£ ($17.43) per hour, ABC News reported, which added, “The doctors’ union has asked for a 35% pay rise to bring junior doctor pay back to 2008 levels.”

However, their pay demands come in the midst of a cost-of-living crisis in the UK. Inflation has risen above 10%. Paired with increases in heating costs and food prices mean that decreased wages leave many struggling to pay bills, ABC news reports.

A hard-hitting BMA advertising campaign designed to shine light on these disparities depicts three junior doctors (with one-, seven-, and 10-years’ experience) removing an appendix. The video shows that the total the three would be paid for the hour-long operation would be 66.55£ ($82.84):

  • Doctor with one year experience: 14.09£ ($17.54).
  • Doctor with two years’ experience: 24.46£ ($30.45).
  • Doctor with three years’ experience: 28£ ($34.85).

And this for performing a potentially life-saving procedure, the BMA stated.

In the press release, BMA Junior Doctors Committee co-chairs Robert Laurenson and Vivek Trivedi said, “It is appalling that this government feels that paying three junior doctors as little as 66.55£ between them for work of this value is justified. This is highly skilled work requiring years of study and intensive training in a high-pressure environment where the job can be a matter of life or death.”

Patient Care is Affected

Lower salaries also affect patient care levels and have led to recruitment issues, with many doctors leaving the profession, the BBC reported. “This is not a situation where we are fixed in our position. We’re looking for negotiations and Steve Barclay (UK’s Secretary of State for Health and Social Care) isn’t even willing to talk to us. He hasn’t put any offer at all on the table … there has to be two sides in the discussion,” Emma Runswick, MD, a junior doctor and deputy chairwoman of the BMA, told the BBC.

But while the junior doctors battle for wages, the government’s initial focus has been on patient wellbeing. “There will be risks to patient safety, risks to patient dignity, as we are not able to provide the kind of care we want to,” NHS Confederation Chief Executive Matthew Taylor told UPI prior to the walkout.

The timing of the walkout also caused consternation with the NHS. “Not only will walkouts risk patient safety, but they have been timed to maximize disruption after the Easter break,” Health Secretary Barclay told UPI as the walkout was announced.

Barclay also claimed the amount sought by doctors was “unreasonable” and would cause raises above $25,000 per year, UPI reported. “If the BMA is willing to move significantly from this position and cancel strikes, we can resume confidential talks and find a way forward as we have done with other unions,” he stated.

It is important to note that doctors would be pulled from picket lines if immediate danger were present due to trade union laws that say life-and-limb coverage must be provided, the BMA told the BBC.

—Kristin Althea O’Connor

Related Information:

Junior Doctors’ Strike: Patient Care ‘On a Knife Edge’ as Up to 350,000 Appointments Could Be Cancelled During Four-Day Walkout

British Doctors Walk Out of Hospitals at Start of Crippling Four-Day Strike

Tens of Thousands of Doctors in Britain to Participate in 4-Day Walkout

Three Junior Doctors Would Earn Just 66£ Between Them for Taking Out Your Appendix, says BMA in New Advertising Campaign

English Docs Strike Could be Catastrophic, Officials Say”

Junior Doctors’ Strike Puts Patients at More Risk-Barclay

HSN Explains What a Junior Doctor Is

NHS System Explained

Why Is Britain’s Health Service, a Much-Loved National Treasure, Falling Apart?

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