Proteomic 'Lght-Bites'

Proteomic news & views to share





CRISPR gene editing can cause hundreds of unintended mutations

Kellie A. Schafer (Stanford University), Wen-Hsuan Wu (Columbia University Medical Center), and Diana G. Colgan (Iowa) et. al - Nature Methods, May 29, 2017  

As CRISPR-Cas9 starts to move into clinical trials, a new study published in Nature Methods has found that the gene-editing technology can introduce hundreds of unintended mutations into the genome.  CRISPR-Cas9 editing technology—by virtue of its speed and unprecedented precision—has been a boon for scientists trying to understand the role of genes in disease. The technique has also raised hope for more powerful gene therapies that can delete or repair flawed genes, not just add new genes.

But even though CRISPR can precisely target specific stretches of DNA, it sometimes hits other parts of the genome. Most studies that search for these off-target mutations use computer algorithms to identify areas most likely to be affected and then examine those areas for deletions and insertions.  These predictive algorithms seem to do a good job when CRISPR is performed in cells or tissues in a dish, but whole genome sequencing has not been employed to look for all off-target effects in living animals.

​In this new study, the researchers sequenced the entire genome of mice that had undergone CRISPR gene editing in the team's previous study and looked for all mutations, including those that only altered a single nucleotide.  Researchers who aren't using whole genome sequencing to find off-target effects may be missing potentially important mutations.


The power of tears: how tear proteomics research could revolutionize the clinic

Lei Zhou and Roger W. Beuerman - EXPERT REVIEW OF PROTEOMICS, VOL. 14, NO. 3, 189–191, 2017

Tear ‘omics’ research over the past decade has demonstrated the future applications of tear biomarkers for patient stratification or what is now often referred to as precision medicine. Tear collection is fast, safe, and noninvasive and offers a chance to determine the local pathology close to the disease site. The relatively simple chemical composition and sample preparation procedures make tear fluid an ideal source for diagnosis and prognosis. Proteomic studies can easily be translated into antibody-based assays for clinical use.  It is hoped that a ‘tear test’ that will eventually become like a ‘blood test’ or ‘urine test’ used in eye clinics in the near future.  Its application could also be extrapolated to other areas of proteomic and precision medicine.


Neuro-inflammation, neuro-protection and microglial activation

Understanding of microglial-induced neuro-inflammation is a key to understanding various neurological diseases.  Microglia are the brain's resident immune cells, transitioning from resting to activation state upon sensing damage or a foreign substance. Activated microglia release a wave of chemical mediators, including chemokines, cytokines, and proteases, all of which promote the neuroinflammatory milieu. Understanding how microglia trigger 'neuro-microglial induced neuro-inflammation' may help understand the disease process, progression and the role of:

  • Factors that induce microglial activation in neurodegenerative diseases
  • Better understanding of ‘neuro- protection’ in the brain


Y. J. Choi et al., “Deficiency of microRNA miR-34a expands cell fate potential in pluripotent stem cells,” Science, doi:10.1126/science.aag1927, 2017. 

Pluripotent stem cells are capable of generating all embryonic cell lineages but, until now, scientists could seldom manipulate induced pluripotent stem cells (iPSCs) and embryonic stem cells (ESCs) to generate extra-embryonic cell types, such as placental cells. A study published rcently (12th January,2017) in Science has now shown that removing one particular microRNA—miR-34a—from a stem cell can kick off a molecular pathway that induces endogenous retroviruses and, at the same time, enables iPSCs and ESCs to consistently form extra-embryonic cells in a dish.

The results suggest that a particular class of noncoding RNA works in concert with the latent viral elements of the genome work to limit stem cell potential, and that removing a key miRNA can lift this limitation—at least in vitro.  Although stem cells can give rise to virtually any cell type inside the embryo, they have limited potential to give rise to extra-embryonic cell types. They are now trying to understand how the body restricts iPSC and ESC potential.




Exosomes encapsulate and transport a wide variety of molecules generated by their ‘cell-of-origin’, a process now thought to be a form of cellular signalling. Exosome signalling is common across cell types and species, but it is of particular interest in diseases with an inflammatory component. While exosome isolation and analysis is useful to understanding the mechanisms behind these multifaceted diseases, exosomes may also be exploited for their therapeutic potential.  Scientists are reviewing the current knowledge on exosomes in inflammation, and exploring the potential for exosome-based therapeutics with reference to:

  • The exosomal cargoes released during inflammation, and their potential as therapeutic targets
  • How inflammatory diseases are uniquely suited to exosome analysis


The Cancer Genome Atlas (TCGA) project

Building on data from The Cancer Genome Atlas (TCGA) project, a multi-institutional team of scientists has completed the first large-scale "proteogenomic" study of breast cancer, linking DNA mutations to protein signaling and helping pinpoint the genes that drive cancer. Conducted by members of the National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC), including Baylor College of Medicine, Broad Institute of MIT and Harvard, Fred Hutchinson Cancer Research Center, New York University Langone Medical Center, and Washington University School of Medicine, the study takes aim at proteins, the workhorses of the cell, and their modifications to better understand cancer. Appearing in the Advance Online Publication of Nature on May 25, 2016 the study illustrates the power of integrating genomic and proteomic data to yield a more complete picture of cancer biology than either analysis could do alone.



Systems biology, functional genomics and high-throughput proteomics efforts have massively expedited gene-product annotation and characterization. However, identifying affinity reagents suitable for secondary analyses of proteins can pose a challenge. While antibodies are widely used, their efficacy in different biological systems and experimental applications often varies depending on their immunogen or the organism in which they were produced. In fact, the likelihood that an antibody will function in a novel application or cell/ tissue type depends heavily on its affinity for the antigen and the type of epitope recognized, as well as on the antigen's concentration, folding status and post-translational modifications. Without detailed understanding of the properties of both the antibody and the biological system in which it will be used, antibody selection can require guesswork.

Antibodypedia is a searchable database of antibodies against human proteins. It aims to provide the research community with information on the effectiveness of specific antibodies in specific applications—to help scientists select the right antibody for the right application.

The Antibodypedia database was originally developed within the 6th framework EU program Proteome Binders and the project is part of the Human Antibody Initiative.

Antibodypedia contains information about publicly available antibodies generated by academic or commercial providers and directed against human protein targets; we hope to extend coverage to a range of model organisms in the near future. The database is organized in a ‘gene-centric’ manner to provide users with an overview of all antibodies available against a particular target. All antibody pages link directly to the provider for ease of access and use of the database is free-of-charge.


Precision medicine

The influence of gut microbiota on human health has been well documented, particularly in the case of metabolic disorders, such as type 1 and type 2 diabetes. In light of the strong association between the composition of one’s microbiome and human health, researchers have begun to develop targeted therapies that restore optimal balance among microbial populations.  For a detailed look at the state of the microbiome and its role in precision medicine, researchers are examining:

  • The human microbiome’s influence on health
  • The challenges of translating microbiome studies into precision medicine therapies


A drug that heals broken bones faster and better

Author: Victoria White - Southampton University, UK

These esearchers are developing a new type of drug that may help bones heal faster and better.


Colony of human bone stem cells

Using bone samples from people undergoing hip replacement surgery, the researchers were able to show that the drug – a protein that activates a molecular pathway called the ‘Wnt’ pathway – causes stem cells found within bones to divide and to turn into more bone cells. The Wnt plays a fundamental role in animal development and disease. It is involved in controlling the growth of stem cells, which are ‘master cells’ that help restore tissues after injury. One example of this is in amphibians like salamanders. If these animals lose a leg, they can just regrow a new one.

Regenerative effect reverses if Wnt pathway switched on too long

Dr Nick Evans, Associate Professor in Bioengineering at the University of Southampton and lead author of the study, says: “Bone fractures are a big problem in society, especially in older people. It is getting worse as more people get older and their risk of fracture increases. Most fractures heal completely by themselves, but a surprising number, around 10 per cent, take over six months to heal, or never heal at all. In the worst cases this can lead to several surgical operations, or even amputation.

“Through our research, we are trying to find ways to chemically stimulate Wnt signaling using drugs. To achieve this, we selectively deliver proteins and other molecules that change Wnt signalling specifically to stem cells, particularly in the bone. This may help us find cures for many diseases, including bone disease, and speed up bone healing after fracture.”


Tumor microenvironment in tumorigenesis

The tumor milieu is the site of complex interactions between immune cells, tumor cells, and the surrounding tissue. Innovative technologies and strategies are being employed to characterize these interactions to understand the role of the tumor microenvironment in tumorigenesis and metastasis. Scientists are discussing advances in understanding of the tumor microenvironment and how this knowledge is being harnessed to develop targeted therapies with reference to:

  • The role of the immune system as a mediator of the tumor microenvironment
  • Modulation of the tumor microenvironment as a means of inhibiting tumor growth and suppressing metastasis


Power of microRNAs as Research Tools

microRNA (miRNA) expression provide valuable insight into disease-related transcripts, both protective and predisposing. Therapeutic design based on these data sets has enabled both supplementation with protective miRNAs such as miRNA mimics, and silencing of predisposing miRNAs using complementary RNAs.  Disease-specific miRNA profiles and miRNA-based therapeutic approaches is helping researchers to understand:

  • The various roles of miRNAs in disease progression and recovery
  • Steps for developing miRNA-based therapeutics



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