Proteomics: an evolving technology in laboratory medicine
Internet Journal of Medical Update 2010 January;5(1):35-41
Internet Journal of Medical Update
Journal home page: http://www.akspublication.com/ijmu
Review Article
Proteomics: an evolving technology in Laboratory Medicine
Dr. Javed Akhter*Ψ PhD, Dr. Waleed Al Tamimi* PhD, Dr. Abubaker El Fatih*
FRCPath and Dr. D J Venter† MD
*Department of Pathology and Laboratory Medicine, King Abdulaziz Medical
City, Riyadh, Saudi Arabia
†Department of Pathology and Laboratory Medicine, Mater Health, Brisbane,
Australia
(Received 23 February 2009 and accepted 12 April 2009)
ABSTRACT: The rapid developments in both genomics and proteomics
will allow scientists to define the molecular pathways in normal and
diseased cells. With these models, researchers will have the ability to
predict previously unknown interactions and verify such predictions
experimentally. Novel proteins, cellular functions, and pathways will also
be unravelled. It is hoped that understanding the connections between
cellular pathways and the ability to identify their associated biomarkers
will greatly reduce the suffering and loss of life due to diseases.
KEY WORDS: Proteomics; Laboratory medicine
INTRODUCTIONΨ
different proteins. On average, however, a
gene produces five to ten different proteins4.
Completion of the Human Genome Project
Genomics is the systematic use of information
was a pivotal first step to revolutionize
on the expression, regulation and structural
medicine in the 21st century1. The completed
association of genes. It is used in genetic
human genome was found to contain between
analysis, measurement of gene expression and
30,000 and 35,000 genes, far less than the
determination of gene function5. As genomics
100,000 genes predicted when the project
has proven inadequate to predict the structure
commenced in the mid-1990s2. Subsequently it
and dynamic properties of all proteins, a new
was found that one gene can produce more
field of protein study termed proteomics has
than one protein, each with a different
developed. This is the large-scale study of
functional capability. The generation of
protein expression, structure and function. It
multiple proteins from a single gene can occur
aims to correlate the structural and functional
as a result of alternate splicing where a single
diversity of proteins with underlying biological
DNA template can produce several different
processes, including disease processes6.
messenger RNAs, each of which is then used
Proteomics has created opportunities to
to make different proteins3. In addition, the
identify, investigate and target proteins that are
protein may undergo modification by cellular
differentially expressed in health and disease.
processes after it is created (termed post-
Clinical medicine is poised to benefit
translational modification). The result is that
enormously with the potential to develop better
one gene can produce as many as 1,000
diagnostic and prognostic tests, to identify new therapeutic targets and ultimately to allow patient-individualized therapy. Finding the
protein or proteins (biomarker) associated with
ΨCorrespondence at: Department of
a disease or adverse event will lead to a much
Pathology and Laboratory Medicine, King
earlier identification of disease, potentially
Abdulaziz Medical City, Riyadh 11426, Saudi
prior to the onset of symptoms7.
Email: [email protected]
Copyrighted by Dr. Arun Kumar Agnihotri. All right reserved
Akhter et al/ Proteomics: an evolving technology in Laboratory Medicine
24 atoms, which represents an immense
scientific challenge to amplify precisely.
The first high resolution protein separations
Hence, proteins are studied using a synergistic
were achieved by two-dimensional gel
combination of electrophoresis, mass
electrophoresis in 1975; this was followed by
spectrometry, multidimensional liquid
the first computerised 2-D gel image analysis
chromatography and bioinformatics11.
platform to quantify changes in 2-D gel protein
2D gel electrophoresis is a suitable technique
spot levels8. However there was a lack of
for asking, "Where do differences arise
useful tools to identify proteins of interest.
amongst the proteins in two similar samples?"
Furthermore, the lack of reproducibility
For example, closely matched samples from
hindered the expansion of the technique until
diseased and healthy cells can be compared.
the introduction of immobilized pH gradients
Differences in protein abundance or covalent
(IPGs) in the 80s. This has coincided with the
modification (e.g. phosphorylation,
development of mass spectrometry ionization
glycosylation and acylation) can provide
techniques for peptides, allowing protein
important clues to the pathogenesis, progress
identification and characterization on a large
and treatment of a disease. Once a protein has
scale9. However, it was not until the mid-90s
been isolated and digested, the mass
that mass spectrometry became a mainstream
spectrometer (ICP-MS, MALDI-TOF) is a
technique for protein identification, mostly
suitable tool for asking, "What is this
replacing Edman sequencing10.
protein?", "Which residues are modified?",
Currently, there is no diagnostic amplification
and "What is the modification?" By taking 3-D
technique for proteins as there is for
pictures of proteins, X-ray Tomography allows
amplifying genes. It is therefore not possible to
researchers to see biomolecules in their cellular
make copies of proteins that are present in very
context. Tomograms provide insights into the
small amounts. Another challenge is that
conformation and flexibility of functional
amino acids are very small, ranging from 7 to
targets and their environment (Table 1).
Table 1: Technologies used in proteomics
Technology Uses
2-D Gel electrophoresis
Used to identify low abundance proteins in complex biological samples such as blood, urine and oral fluid.
Tandem mass spectrometry
Used to separate ions based on a sample's electronic mass, to study inborn errors of metabolism and metabolic profiles, and to identify therapeutic drugs, drugs of abuse, disease markers and toxic compounds.
Mass spectrometry MALDI-TOF (Matrix Deals with thermolabile, non-volatile organic Assisted Laser Desorption Ionisation-Time compounds and those of high molecular mass. It is used Of Flight)
in for the analysis of proteins, peptides, glycoproteins, oligosaccharides and oligonucleotides.
ICP-MS (Inductively Coupled Plasma- Involves the formation of gas containing electrons, ions Mass Spectrometry )
and neutral particles from Argon gas. Technology is used for ultrasensitive quantification of proteins and peptides down to low attomole range.
X-ray Tomography
Used to determine the location of labelled proteins or protein complexes in an intact cell. Frequently correlated with images of cells from light based microscopes.
Microarray ‘chips'
These are matrix-support surfaces for binding selected
proteins and allowing high-throughput screening for disease associated proteins.
These methods are used for detection of drug-protein,
1. Affinity chromatography
hormone-protein, protein-protein, DNA-protein,
2. Yeast two hybrid techniques
carbohydrate-protein, and lipid-protein interactions.
3. Fluorescence Resonance Energy
4. Surface Plasmon Resonance (SPR)
Copyrighted by Dr. Arun Kumar Agnihotri. All right reserved
Akhter et al/ Proteomics: an evolving technology in Laboratory Medicine
CLINICAL APPLICATIONS
nearly two million people each year. More than
50% of TB cases occur in the largest Asian
The potential applications of proteomics in the
countries (India, China, Indonesia,
laboratory revolve around: identifying
Bangladesh, Philippines and Pakistan). Sub-
components of the proteome; comparing the
Saharan Africa has the highest incidence rate
expression of proteins between normal and
(approximately 300/100,000 population/year).
diseased organs at certain stages of disease;
Even though TB has declined steadily in
bioinformational analysis to determine how
Western Europe and North America, the global
proteins interact with each other in vivo;
TB burden appears on the rise, especially in
identification and characterization of proteins
the former Soviet Union, Eastern Europe, and
post-translationally; study the structure and
Africa15.
function of protein complexes to understand
A serum or saliva-based screening test that
the organization of cells at the molecular level.
could detect pre-clinical infection would allow
The goal of clinical proteomics and molecular
early treatment, potentially reducing
medicine is to assist in the study of
transmission, and have widespread application.
characterization of the cellular components and
Proteomic techniques have identified proteins
cellular networks to be used in the
secreted in vitro by common clinical isolates.
understanding of the pathology of disease
Two of these (rRv3369 and rRv3874) have
process, diagnosis and patient management.
shown great potential as serodiagnostic
The translational nature of this technology
antigens, with sensitivity of 60%–74% and
provides unique challenges and boundless
specificity of 96%–97% in clinical studies.
opportunities that promise to transform the
These proteins are potential candidates for a
way disease is diagnosed, treated and
kit-based serum screening test.
managed12. It has many clinical applications
including the following:
Diagnosis of Severe Acute Respiratory
• Translational pathology and Syndrome: The pathogenesis of severe acute
immunohistochemistry applied to protein
respiratory syndrome (SARS) is not well
biomarkers in tissue
understood, and a specific diagnostic method is
• Bioinformatics tools including pattern
critical for the management and control of this
recognition, artificial intelligence and
disease. Proteomic analysis of sera from
computer learning algorithms
patients with SARS has identified potential
• Biomarker discovery and validation from
biomarkers. These are truncated forms of α
clinical samples
(1)-Antitrypsin, which were consistently found
• Signal transduction pathways profiling in
in higher concentrations in the sera of SARS
clinical tissue samples
patients compared with healthy controls. These
• Discovery of new drug targets from
markers may prove useful as diagnostic tools
clinical samples
and therapeutic targets. Moreover, studies of
the protein structure of the SARS virus may
Use of proteomic technologies in the drug development pipeline
reveal potential vaccine targets16.
Use of proteomic technologies to monitor prognosis, therapeutic end points, toxicity
PROTEOMIC AND CANCER
Many studies using proteomic techniques have
Clinical trials using proteomic monitoring
been performed on biomarkers to investigate
Some of the major areas in which clinical
potentials of early cancer diagnosis17.
proteomics are utilized include cancer,
cardiovascular disease, Alzheimer's disease,
Ovarian Cancer: Ovarian cancer represents
infectious diseases, infertility, obstetrics and
the sixth most commonly diagnosed cancer
immune rejection following transplantation13.
among women in the world, and causes more
deaths per year than any other cancer of the
TARGETED MODALITIES OF female reproductive system. Ovarian cancer is
PROTEOMIC CLINICAL
more common in Northern European and
North American countries. Ovarian cancer is a
major focus of early biomarker discovery
Diagnosis of infectious diseases: Tuberculosis
because it is usually diagnosed at an advanced
(TB) affects millions of people around the
stage with a median five-year survival rate of
globe with many drug-resistant
about 20 percent18. To evaluate the potential
Mycobacterium tuberculosis strains spreading
use of proteomics as a diagnostic tool, a group
worldwide14. Among the communicable
of researchers from the National Cancer
diseases, TB is the second leading cause of
Institute (NCI) in Bethesda, MD, collected
death worldwide after HIV-AIDS, killing
Copyrighted by Dr. Arun Kumar Agnihotri. All right reserved
Akhter et al/ Proteomics: an evolving technology in Laboratory Medicine
serum from 50 ovarian cancer patients and 50
cancer harbour microscopic metastasis at the
controls and used a computer algorithm to
time of diagnosis. It is now well established
search for the protein patterns that
that adjuvant systemic therapy improves
distinguished cancer cells from non-cancer
survival in patients with early-stage breast
cells. They have shown that with a set of
cancer. Recent technical advances in mass
blinded serum samples, the test pattern
spectrometry, such as matrix-assisted laser
correctly identified all 50 patients with cancer,
desorption/ionisation time-of-flight mass
and was able to discriminate them from 63 out
spectrometry (MALDI-TOF MS) and its
of 66 patients without cancer or had benign
variant surface-enhanced laser
disease. Using the same approach, two other
desorption/ionisation time-of-flight mass
groups reported similar results19,20.
spectrometry (SELDI-TOF MS), have enabled
high-throughput proteome analysis26,27.
Prostate cancer: The worldwide incidence of
A multitude of molecules involved in breast
prostate cancer (PCa) ranks third among
cancer biology have been studied as potential
cancers in men. The highest incidence of
prognostic markers. In one study a
prostate cancer in the world is found in
combination of three candidate proteins in the
American black men, who have approximately
blood were found to be useful in
a 9.8% lifetime risk of developing this cancer
discriminating between 169 patients at various
compared to the 8% lifetime risk for American
stages of breast cancer compared to women
white men. The Japanese and mainland
with benign breast disease and healthy
Chinese populations have the lowest rates of
controls28. In other studies, nipple aspirate
prostate cancer21. Since the advent of prostate
fluid was used to identify tumor marker
specific antigen (PSA) screening, a significant
candidates29. Proteomic analysis of breast
number of men have had a PSA test performed
nipple aspirate fluid (NAF) holds promise as a
and this has led to a significant increase in the
non-invasive, low cost method to identify
number of diagnosed cases22. However, the
markers of breast cancer. These protein
PSA lacks sensitivity and therefore, evaluating
molecules when secreted, they represent the
multiple proteins will be essential to
final processed form of the marker protein,
establishing signature proteomic patterns that
which makes proteomic analyses less
distinguish cancer from non-cancer as well as
ambiguous to provide clues to changes in
identify all genetic subtypes of the cancer and
protein translational rates, post-translational
their biological activity.
modification, sequestration, and degradation
In one study, proteomic analysis of prostate
that lead to disease. Many of the proteins that
cancer patients versus healthy controls was
have been identified in the NAF proteome
carried out by looking for differences in
could potentially be markers of disease,
protein patterns between the two groups. Using
including ras-related protein; metastasis-
blood samples from 167 prostate cancer
associated protein; BCL2, which has been
patients, 77 patients with benign prostate
implicated in the suppression of cell death;
hyperplasia and 82 healthy men, protein
CD5, which is reported to play a role in the
patterns developed as a classification system
inhibition of apoptosis; retinol-binding protein,
had correctly classified 96 percent of the
which has recently been shown to suppress
samples as either prostate cancer or non-cancer
breast cancer cell survival and has been shown
(benign prostate hyperplasia/healthy men)23. A
to be down-regulated in a subset of breast
further proteomic approach is to determine
cancer; clusterin, which has been associated
whether the changes in specific
with cell death and apoptosis; and transferrin,
phosphoproteins believed to be involved in
which has been assigned a role in cell
cellular signalling events and cancer
progression in prostate cancer patients have
been speculated to serve as a biomarker of
Bladder Cancer: Bladder cancer incidence
early disease24.
varies widely throughout the world. Belgium
and Italy, have the highest recorded incidence
Breast Cancer: Breast cancer is the most
rates in Europe (42.5/100,000 and 41/100,000
common malignancy among women in the
population respectively), much more than in
Western world and constitutes 18% of all
the United States with an incidence of
cancers in women25. Traditional prognostic
24.1/100,000 and an estimated 61,160 newly
factors include the axillary lymph node status,
diagnosed cases in 2007. However,, cancer
the tumor size, the nuclear grade and the
registries in Slovenia, Croatia, and Switzerland
histologic grade. Interest in novel prognostic
have reported even lower European bladder
markers is based on the fact that a significant
cancer incidence (10.1/100,000, 11.7/100,000
number of patients with early-stage breast
and 12.0/100,000 respectively) with the lowest
Copyrighted by Dr. Arun Kumar Agnihotri. All right reserved
Akhter et al/ Proteomics: an evolving technology in Laboratory Medicine
rates found in Asian and South American
resistance. Proteomics technologies are playing
countries. Bladder cancer affects men four
a major role in identifying potential therapeutic
times more often than women. The risk of
targets in Plasmodium species, as well as host-
bladder cancer increases with age with over 70
pathogen interactions and protein-drug
percent of people diagnosed are older than 65
interactions. Advances to date include the
years31,32.
identification of differences between
Biological characteristics of urothelial
Plasmodium species, identification of immune
carcinomas range from benign, superficial,
targets for vaccination and immune protection,
low-grade, non-life threatening, papillary
better understanding of the cellular target(s) of
lesions, that respond well to resection and
chloroquine and the mechanisms of
adjuvant treatment but are prone to recurrence
chloroquine resistance36.
to highly invasive malignant carcinomas with
Development of new Therapeutic Agents
Several laboratories have successfully
demonstrated that specific protein patterns can
Proteomics as an evolving science is expected
be detected from tumor tissue and these could
to have a major impact on drug development in
discriminate adequately between diseased and
the near future. It has been shown that some
healthy tissue. In the case of bladder cancer,
proteins which are differentially expressed by
proteomics analysis has identified several
microorganisms, and that differ primarily in
keratin proteins that are expressed in different
thier tertiary structure from related proteins in
amounts as the disease progresses from the
the host have now become potential
early transitional epithelium stage to full
therapeutic drug targets. These can be tested
blown squamous cell carcinoma. The
against commercially available libraries of
measurement of keratin levels in bladder
chemical agents to identify lead compounds -
cancer biopsies can therefore be used to
compounds with in vitro activity that can be
monitor the progression of the disease.
used to target these protein markers and to
Another protein, psoriasin, is found in the
represent potential new therapies. Exploitation
urine of bladder cancer patients and can be
of these scientific findings could assist to
used as an early diagnostic marker for the
develop improved therapeutic agents to
disease. The study and utilization of these
challenge the complexity of various clinical
novel markers support the notion that
proteomics, but not DNA arrays, can be used
in cancer diagnosis. Urine, in common with
FUTURE DEVELOPMENTS
most bodily fluids, contains proteins but no
RNA33,34.
At present, it is fairly premature to utilize
many of the newly discovered biomarkers
PROTEOMICS AND THERAPEUTICS
using proteomics analyses as screening or
diagnostic tools. However, these exploratory
Drug Resistance
studies point to the promise of proteomics as
an investigatory tool to be used to screen or
Drug resistance represents a major clinical
diagnose many disease entities using newly
obstacle in the management of many infectious
discovered biomarkers.
diseases, and, in many cases, the mechanism is
Applied research in medical diagnostics is
unknown. Genetic and protein-sequence data
being developed and continues on several
for many microorganisms is now available and
metabolic, inherited, infectious and malignant
provides tools for understanding their
disease entities with construction of proteomic
resistance to drugs and for identifying novel
maps of many serum and body fluids
agents for treating drug-resistant disease, such
as azole resistance in Candida albicans which
These include amniotic fluid biomarkers which
has been linked with differential expression of
are being studied for the complex
proteins such as Erg10p, a protein involved in
determination of fetal pathology biomarkers.
the ergosterol biosynthesis pathway. This has
Moreover, based on dynamics of specific
been shown as a potential drug target for the
biomarkers' alterations, special attention has
treatment of resistant disease35.
been given to elucidation of the pathogenesis
and the etiology of female infertility, and of
Chloroquine resistance: Chloroquine has been
recurrent miscarriages with the elaboration of
one of the most successful drugs used to treat
clinical algorithms for the management of
malaria but has been rendered virtually
these conditions
ineffective in many parts of the world by the
Further research is needed to examine specific
widespread emergence of chloroquine
features of posttranslational modification of
Copyrighted by Dr. Arun Kumar Agnihotri. All right reserved
Akhter et al/ Proteomics: an evolving technology in Laboratory Medicine
peptide hormones that could as markers of
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