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Clinical Laboratories and Pathology Groups

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Clinical Laboratories and Pathology Groups

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Might Proteomics Challenge the Cult of DNA-centricity? Some Clinical Laboratory Diagnostic Developers See Opportunity in Protein-Centered Diagnostics

Should greater attention be given to protein damage in chronic diseases such as Alzheimer’s and diabetes? One life scientist says “yes” and suggests changing how test developers view the cause of age-related and degenerative diseases

DNA and the human genome get plenty of media attention and are considered by many to be unlocking the secrets to health and long life. However, as clinical laboratory professionals know, DNA is just one component of the very complex organism that is a human being.

In fact, DNA, RNA, and proteins are all valid biomarkers for medical laboratory tests and, according to one life scientist, all three should get equal attention as to their role in curing disease and keeping people healthy.

Along with proteins and RNA, DNA is actually an “equal partner in the circle of life,” wrote David Grainger, PhD, CEO of Methuselah Health, in a Forbes opinion piece about what he calls the “cult of DNA-centricity” and its relative limitations.

Effects of Protein Damage

“Aging and age-related degenerative diseases are caused by protein damage rather than by DNA damage,” explained Grainger, a Life Scientist who studies the role proteins play in aging and disease. “DNA, like data, cannot by itself do anything. The data on your computer is powerless without apps to interpret it, screens and speakers to communicate it, keyboards and touchscreens to interact with it.”

“Similarly,” he continued, “the DNA sequence information (although it resides in a physical object—the DNA molecule—just as computer data resides on a hard disk) is powerless and ethereal until it is translated into proteins that can perform functions,” he points out.

According to Grainger, diseases such as cystic fibrosis and Duchenne Muscular Dystrophy may be associated with genetic mutation. However, other diseases take a different course and are more likely to develop due to protein damage, which he contends may strengthen in time, causing changes in cells or tissues and, eventually, age-related diseases.

“Alzheimer’s disease, diabetes, or autoimmunity often take decades to develop (even though your genome sequence has been the same since the day you were conceived); the insidious accumulation of the damaged protein may be very slow indeed,” he penned.

“But so strong is the cult of DNA-centricity that most scientists seem unwilling to challenge the fundamental assumption that the cause of late-onset diseases must lie somewhere in the genome,” Grainger concludes.

Shifting Focus from Genetics to Proteins

Besides being CEO of Methuselah Health, Grainger also is Co-Founder and Chief Scientific Advisor at Medicxi, a life sciences investment firm that backed Methuselah Health with $5 million in venture capital funding for research into disease treatments that focus on proteins in aging, reported Fierce CEO.

Methuselah Health, founded in 2015 in Cambridge, UK, with offices in the US, is reportedly using post-translational modifications for analysis of many different proteins.

“At Methuselah Health, we have shifted focus from the genetics—which tells you in an ideal world how your body would function—to the now: this is how your body functions now and this is what is going wrong with it. And that answer lies in the proteins,” stated Dr. David Grainger (above), CEO of Methuselah Health, in an interview with the UK’s New NHS Alliance. Click on this link to watch the full interview. [Photo and caption copyright: New NHS Alliance.]

How Does it Work?

This is how Methuselah Health analyzes damaged proteins using mass spectrometry, according to David Mosedale, PhD, Methuselah Health’s Chief Technology Officer, in the New NHS Alliance story:

  • Protein samples from healthy individuals and people with diseases are used;
  • Proteins from the samples are sliced into protein blocks and fed slowly into a mass spectrometer, which accurately weighs them;
  • Scientists observe damage to individual blocks of proteins;
  • Taking those blocks, proteins are reconstructed to ascertain which proteins have been damaged;
  • Information is leveraged for discovery of drugs to target diseases.

Mass spectrometry is a powerful approach to protein sample identification, according to News-Medical.Net. It enables analysis of protein specificity and background contaminants. Interactions among proteins—with RNA or DNA—also are possible with mass spectrometry.

Methuselah Health’s scientists are particularly interested in the damaged proteins that have been around a while, which they call hyper-stable danger variants (HSDVs) and consider to be the foundation for development of age-related diseases, Grainger told WuXi AppTec.

“By applying the Methuselah platform, we can see the HSDVs and so understand which pathways we need to target to prevent disease,” he explained.

For clinical laboratories, pathologists, and their patients, work by Methuselah Health could accelerate the development of personalized medicine treatments for debilitating chronic diseases. Furthermore, it may compel more people to think of DNA as one of several components interacting that make up human bodies and not as the only game in diagnostics.

—Donna Marie Pocius

Related Information:

The Cult of DNA-Centricity

Methuselah Health CEO David Grainger Out to Aid Longevity

VIDEO: Methuselah Health, Addressing Diseases Associated with Aging

Understanding and Slowing the Human Aging Clock Via Protein Stability

Using Mass Spectrometry for Protein Complex Analysis

 

 

Genomics and Proteomics and Interactomics, Oh, My! Researchers Conclude Metabolite-Protein Interactions are Important to Cellular Processes; Could New Omics Be Added to Clinical Laboratories’ Test Menus?

This potential new source of diagnostic biomarkers could give clinical labs a new tool to diagnose disease earlier and with greater accuracy

Clinical laboratories may soon have a new “omics” in their toolkit and vocabulary. In addition to genomics and proteomics, anatomic pathologists could also be using “interactomics” to diagnose disease earlier and with increased accuracy.

At least that’s what researchers at ETH Zurich (ETH), an international university for technology and natural sciences, have concluded. They published the results of their study in Cell.

“Here, we present a chemoproteomic workflow for the systematic identification of metabolite-protein interactions directly in their native environments,” the researchers wrote. “Our data reveal functional and structural principles of chemical communication, shed light on the prevalence and mechanisms of enzyme promiscuity, and enable extraction of quantitative parameters of metabolite binding on a proteome-wide scale.”

Interactomics address interactions between proteins and small molecules, according to an article published in Technology Networks. The terms “interactomics” and “omics” were inspired by research that described, for the first time, the interactions and relationships of all proteins and metabolites (A.K.A, small molecules) in the whole proteome.

Medical laboratories and anatomic pathologists have long understood the interactions among proteins, or between proteins and DNA or RNA. However, metabolite interactions with packages of proteins are not as well known.

These new omics could eventually be an important source of diagnostic biomarkers. They may, one day, contribute to lower cost clinical laboratory testing for some diseases, as well.

Metabolite-Protein Interactions are Key to Cellular Processes

The ETH researchers were motivated to explore the interplay between small molecules and proteins because they have important responsibilities in the body. These cellular processes include:

“Metabolite-protein interactions control a variety of cellular processes, thereby playing a major role in maintaining cellular homeostasis. Metabolites comprise the largest fraction of molecules in cells. But our knowledge of the metabolite-protein interaction lags behind our understanding of protein-protein or protein-DNA interactomes,” the researchers wrote in Cell.

Leveraging Limited Proteolysis and Mass Spectrometry

The researchers used limited proteolysis (LiP) technology with mass spectrometry to discover metabolite-protein interactions. Results aside, experts pointed out that the LiP technology itself is significant.

“It is one of the few methods that enables the unbiased and proteome-wide profiling of protein conformational changes resulting from interaction of proteins with compounds,” stated a Biognosys blog post.

Biognosys, a proteomics company founded in 2008, was originally part of a lab at ETH Zurich.

The ETH team focused on the E. coli bacterial cell in particular and how its proteins and enzymes interact with metabolites.

Paola Picotti PhD

“Although the metabolism of E. coli and associated molecules is already very well known, we succeeded in discovering many new interactions and the corresponding binding sites,” Paola Picotti, PhD, Professor of Molecular Systems Biology at ETH Zurich, who led the research, told Technology Networks. “The data that we produce with this technique will help to identify new regulatory mechanisms, unknown enzymes and new metabolic reactions in the cell,” she concluded. (Photo copyright: ETH Zurich.)

 

More than 1,000 New Interactions Discovered

The study progressed as follows, according to Technology Networks’ report:

  • “Cellular fluid, containing proteins, was extracted from bacterial cells;
  • “A metabolite was added to each sample;
  • “The metabolite interacted with proteins;
  • “Proteins were cut into smaller pieces by molecular scissors (A.K.A., CRISPR-Cas9);
  • “Protein structure was altered when it interacted with a metabolite;
  • “A different set of peptides emerged when the “molecular scissors” cut at different sites;
  • “Pieces of samples were measured with a mass spectrometer;
  • “Data were obtained, fed into a computer, and structural differences and changes were reconstructed;
  • “1,650 different protein-metabolite interactions were found;
  • “1,400 of those discovered were new.”

A Vast, Uncharted Metabolite-protein Interaction Network  

The research is a major step forward in the body of knowledge about interactions between metabolites and proteins and how they affect cellular processes, according to Balázs Papp, PhD, Principal Investigator, Biological Research Center of the Hungarian Academy of Sciences.

“Strikingly, more than 80% of the reported interactions were novel and about one quarter of the measured proteome interacted with at least one of the 20 tested metabolites. This indicates that the metabolite-protein interaction network is vast and largely uncharted,” Papp stated in an ETH Zurich Faculty of 1000 online article.

According to Technology Networks, “Picotti has already patented the method. The ETH spin-off Biognosys is the exclusive license holder and is now using the method to test various drugs on behalf of pharmaceutical companies.”

The pharmaceutical industry is reportedly interested in the approach as a way to ascertain drug interactions with cellular proteins and their effectiveness in patient care.

The ETH Zurich study is compelling, especially as personalized medicine takes hold and more medical laboratories and anatomic pathology groups add molecular diagnostics to their capabilities.

—Donna Marie Pocius 

Related Information:

The New “Omics”—Measuring Molecular Interactions

Map of Protein-Metabolite Interactions Reveals Principles of Chemical Communication

A New Study Maps Protein-Metabolite Interactions in an Unbiased Way

Cell Paper on Protein Metabolite Interactions Recommended in Faculty 1000 Twice

Metabolomics Promises to Provide New Diagnostic Biomarkers, Assays for Personalized Medicine and Medical Laboratories

Researchers are finding multiple approaches to metabolomic research and development involving disparate technology platforms and instrumentation

Human metabolome has been discovered to be a wealth of medical laboratory biomarkers for diagnosis, therapy, and patient monitoring. Because it can provide a dynamic phenotype of the human body, there are many potential clinical laboratory applications that could arise from metabolomics, the study of metabolites.

Researchers are discovering numerous ways the expanding field of metabolomics could transform the future of healthcare. However, to fully exploit the potential of human metabolome, developers must choose from various approaches to research.

“The metabolites we’re dealing with have vast differences in chemical properties, which means you need multi-platform approaches and various types of instrumentation,” James MacRae, PhD, Head of Metabolomics at the Francis Crick Institute in London, told Technology Networks. “We can either use an untargeted approach—trying to measure as much as possible, generating a metabolic profile—or else a more targeted approach where we are focusing on specific metabolites or pathways,” he added.

A multi-platform approach means different diagnostic technologies required to assess an individual’s various metabolomes, which, potentially, could result in multi-biomarker assays for medical laboratories.

Measuring All Metabolites in a Cell or Bio System

Metabolomics is the study of small molecules located within cells, biofluids, tissues, and organisms. These molecules are known as metabolites, and their functions within a biological system are cumulatively known as the metabolome.

Metabolomics, the study of metabolome, can render a real-time representation of the complete physiology of an organism by examining differences between biological samples based on their metabolite characteristics.

“Metabolomics is the attempt to measure all of the metabolites in a cell or bio system,” explained MacRae in the Technology Networks article. “You have tens of thousands of genes, of which tens of thousands will be expressed—and you also have the proteins expressed from them, which will then also be modified in different ways. And all of these things impact on a relatively small number of metabolites—in the thousands rather than the tens of thousands. Because of that, it’s a very sensitive output for the health or physiology of your sample.

“With that in mind, metabolomics has great potential for application in most, if not all, diseases—from diabetes, heart disease, cancer, HIV, autoimmune disease, parasitology, and host-pathogen interactions,” he added.

State-of-the-art metabolomic technologies

The graphic above is taken from a study published in the Journal of the American College of Cardiology (JACC). It notes, “State-of-the-art metabolomic technologies give us the ability to measure thousands of metabolites in biological fluids or biopsies, providing us with a metabolic fingerprint of individual patients. These metabolic profiles may serve as diagnostic and/or prognostic tools that have the potential to significantly alter the management of [chronic disease].” (Image and caption copyright:Journal of the American College of Cardiology.)

There are four major fields of study that are collectively referred to as the “omics.” In addition to metabolomics, the remaining three are:

•                  Genomics: the study of DNA and genetic information within a cell;

•                  Proteomics: the large-scale study of proteins; and,

•                  Transcriptomics: the study of RNA and differences in mRNA expressions.

Researchers caution that metabolomics should be used in conjunction with other methods to analyze data for the most accurate results.

“Taking everything together—metabolic profiling, targeted assays, label incorporation and computational models, and also trying to associate all of this with proteomics and

genomics and transcriptomic data—that’s really what encapsulates both the power and also the challenges of metabolomics,” MacRae explained.

Metabolome in Precision Medicine

Metabolomics may also have the ability to help researchers and physicians fine-tune therapies to meet the specific needs of individual patients.

“We know we’re all very different and we don’t respond to drugs in the same way, so we could potentially use metabolomics to help select the best treatment for each individual,” Warwick Dunn, PhD, Senior Lecturer in Metabolomics at the University of Birmingham, Director of Mass Spectrometry, Phenome Center Birmingham, and, Co-Director, Birmingham Metabolomics Training Center, UK, told Technology Networks.

“Our genome is generally static and says what might happen in the future. And the metabolome at the other end is the opposite—very dynamic, saying what just happened or could be about the happen,” Dunn explained. “So, we could apply it to identify prognostic biomarkers, for example, to predict if someone is at greater risk of developing diabetes five to ten years from now. And if you know that, you can change their lifestyle or environment to try and prevent it.”

Metabolomics continues to tap the many diagnostic possibilities posed by the human metabolome. And, the resulting human biomarkers derived from the research could result in a rich new vein of medical laboratory assays.

—JP Schlingman

Related Information:

Metabolomics and Health: On the Cusp of a Revolution

‘Metabolomics’ Distinguishes Pancreatic Cancer from Pancreatitis

Using Metabolomics to Prevent Colon Cancer

Applications of Metabolomics

The Emerging Role of Metabolomics in the Diagnosis and Prognosis of Cardiovascular Disease

Metabolomics Takes Another Step Forward as Methodology for Clinical Laboratory Testing with Development of an Assay for the Diagnosis of Concussion

 

Developments in MALDI Mass Spectrometry Could Lead to Advancements in Cancer Imaging Technologies for Anatomic Pathologists and Clinical Laboratories

This may especially benefit cancer research and treatment thanks to MALDI’s ability to provide pathologists with a view of the whole-tissue micro-environment

Though it may be years before Matrix-Assisted Laser Desorption Ionization (MALDI) mass spectrometry finds use in clinical applications, recent developments show medical laboratories and anatomic pathologists how one type of technology is being rapidly adapted for use in diagnosing cancers.

Richard Drake, PhD, Director of the Medical University of South Carolina (MUSC) Proteomics Center, notes the importance of MALDI to cancer research. “In the clinic, there has to be something that will facilitate looking at all this data—tools that will let the pathologists look at it as well as the mass spec person,” Drake told GenomeWeb.

“It has been known for decades that glycosylation changes on the cell surface promotes cancer progression and the way the immune system sees a tumor or doesn’t see a tumor,” he explained. “That’s the advantage of MALDI imaging. You’re looking at the whole tissue micro-environment, and particularly for cancer it turns out to be important.”

Imaging Mass Spectrometry Applications for Anatomic Pathology

MALDI uses mass spectrometry imaging technology to enable high-molecular identification and an overall view of tissue. It differs from liquid chromatography-mass spectrometry (LC-MS), which is a chemical analysis technique.

An article by News-Medical describes in detail how MALDI technology works:

“MALDI imaging works through the utilization of a matrix, an acidic aromatic molecule that absorbs energy of the same wavelength produced by the irradiating laser. The matrix transfers the substance being examined to the gas state, thereby producing ionization in a three-step process:

1.     “Thin sample sections on a metal slide are first covered with the matrix and the procedure for extracting molecules of interest from the tissue into the matrix begins. The matrix can be applied both manually and automatically.

2.     “The laser irradiates the sample only in the matrix layer, meaning the underlying tissue remains intact.

3.     “The released molecules are transferred to the gas state as the matrix absorbs the laser energy. Ions are formed due to the addition or removal of protons when in the gas state.

“The irons are required for further analysis via the mass spectrometer. The metal slide is placed into a MALDI mass spectrometer where the spatial distribution of the biological molecules is mapped. Within the mass spectrometer, the tissue specimen is raster scanned forming a mass spectrum for each spot measured. Image processing software is then required to import the data from the mass spectrometer to allow visualization of the image produced.”

 

The above schematic illustrates “the identification of bacteria and yeast by MALDI-TOF MS using the intact-cell method. Bacterial or fungal growth is isolated from plated culture media (or can be concentrated from broth culture by centrifugation in specific cases) and applied directly onto the MALDI test plate. Samples are then overlaid with matrix and dried. The plate is subsequently loaded into the MALDI-TOF MS instrument and analyzed by software associated with the respective system, allowing rapid identification of the organism.” (Caption and image copyright: Clinical Microbiology Reviews/American Society for Microbiology.)

MALDI in Clinical Laboratories

MALDI experts at MUSC worked with researchers at Bruker Corporation, a developer of scientific instruments and analytical diagnostic solutions for cell biology, preclinical imaging, clinical phenomics and proteomics research, clinical microbiology, and for molecular pathology research. Bruker is reportedly working with labs in Europe on MALDI-based assays for clinical use.

Developing MALDI applications for use in clinical laboratories and anatomic pathology groups could result in major improvements. Imaging mass spectrometry could:

  • make more molecular information available;
  • reduce pathology’s subjectivity and intra-observer nature;
  • enable more accuracy and ability to duplicate current pathology assays; and,
  • pave the way for new assays to be made.

“MALDI-IMS [imaging mass spectrometry] identifies the distributions of proteins, peptides, small molecules, lipids, and drugs and their metabolites in tissues, with high spatial resolution. This unique capacity to directly analyze tissue samples without the need for lengthy sample preparation reduces technical variability and renders MALDI-IMS ideal for the identification of potential diagnostic and prognostic biomarkers and disease gradation,” noted authors of a MALDI study published in the July 2017 edition of Biochimica et Biophysica Acta Proteins and Proteomics.

“You can take a slide of tissue and essentially do metabolomics on it so that you can look at the intricate nature of what metabolism is happening within a tissue,” James MacRae, PhD, Head of Metabolomics at the Francis Crick Institute in London, told Technology Networks, which described development of new mass spectrometry imaging technologies as “potentially game-changing.”

Mass Spectrometry in Clinical Laboratories

This is just the latest in a string of scientific developments involving mass spectrometry over the past decade that are potential boons to clinical laboratories. In “Is Mass Spectrometry Ready to Challenge ELISA for Medical Laboratory Testing Applications?Dark Daily reported on the development of a new technique from the Department of Energy’s Pacific Northwest National Laboratory that uses mass spectrometry to identify protein biomarkers associated with cancer and other diseases. Researchers dubbed the technique PRISM, which stands for Proteomics Research Information System and Management.

And in “Swiss Researchers Use New Mass Spectrometry Technique to Obtain Protein Data, Create Strategy That Could Lead to Clinical Laboratory Advances in Personalized Medicine,” Dark Daily reported on researchers at the Swiss Federal Institute of Technology in Lausanne and ETH Zurich who developed a new way to use mass spectrometry to explain why patients respond differently to specific therapies. The method potentially could become a useful tool for clinical laboratories that want to support the practice of precision medicine.

As mass spectrometry’s role in clinical laboratories continues to expand, MALDI technology development and research could eventually lead to tools and applications that enhance how anatomic pathologist view tissue specimens in the medical laboratory. Though the research is ongoing, the technology seems particularly suited to cancer research and treatment.

—Donna Marie Pocius

Related Information:

Technical Advances Position MALDI Imaging as Plausible Tool for Clinical Pathology

Bruker Introduces Novel Mass Spectrometry Solutions for MALDI Imaging, Metabolomics, Proteoform Profiling, and Toxicology at ASMS 2017

The Proteomics of Prostate Cancer Exosomes

MALDI Imaging

Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry: A Fundamental Shift in the Routine Practice of Clinical Microbiology

Metabolomics and Health – On the Cusp of a Revolution

Is Mass Spectrometry Ready to Challenge ELISA for Medical Laboratory Testing Applications?

Swiss Researchers Use New Mass Spectrometry Technique to Obtain Protein Data, Create Strategy That Could Lead to Clinical Laboratory Advances in Personalized Medicine

Precision Medicine Summit Feb. 21, 2018

National Institutes of Health Creates Partnership with Big Pharma to Improve Development Success of New Drugs and Diagnostics and Speed FDA Clearance

Pathology groups and clinical laboratories are among the beneficiaries if the Accelerating Medicines Partnership achieves its goals

Power players in healthcare are about to invest nearly a quarter of a billion dollars to accelerate the time it takes for new medical discoveries to gain regulatory approval and enter clinical use. The emphasis will be on both therapeutic drugs and diagnostics, making this an important development for in vitro diagnostics companies and medical laboratories.

Anchors to this new initiative are the National Institutes of Health (NIH) and the Food and Drug Administration (FDA). Their partners are 10 pharmaceutical companies and six nonprofit groups. The goal is to jumpstart research to find targets for new drugs and diagnostics, noted a Genomeweb.com article. (more…)

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