V Proteome=PROTEin complement to a

genOME
V The qualitative and quantitative
comparison of proteomes under
different conditions to further unravel
biological processes
V Refers to all the proteins produced by an
organism, much like the genome is the
entire set of genes
PROTEIN SYNTHESIS
V Oenome = constant for an organism
V Proteins secreted can vary widely
V Proteins undergo post translational
modification
¾ Phosphorylation
¾ Ubiquitination
¾ methylation, acetylation, glycosylation, oxid
ation, nitrosylation
V mRNA assessment does not correlate
with protein content
V ˜ Oel Electrophoresis
V S S-PAOE (Sodium odecyl
Sulfate Polyacrylamide Oel Electrophoresis)
V PROTOMAP (PRotein TOpography and
Migration Analysis Platform)
V MAL I (Matrix-assisted laser
desorption/ionization )
V Tissue microarrays
V Nanotechnology driven assays
V ELISA
V ëiomarkers
V Proteomic pattern analysis
V Pharmacoproteomics
V A substance used as an indicator of a
biological state
V Characteristic that is objectively
measured and evaluated as
an indicator of normal biological
processes, pathogenic processes,
or pharmacologic responses to
a therapeutic intervention
V diagnostic biomarkers
V staging of disease biomarkers
V disease prognosis biomarkers
V Also classified as
¾ Type 0 u Natural History markers
¾ Type 1 u rug Activity markers
¾ Type ˜ u Surrogate markers
0Oncology
0Infectious diseases
0Renal disorders
0Endocrinology
0Neurosciences
0Cardiovascular medicine
0Autoimmune diseases
V evelopment of more sensitive
screening techniques
V Tumor markers
V Highly sensitive immunohistochemistry
technology
V etermining cellular sensitivity to
antineoplastic agents
V Lung adenocarcinomas u £ k a pI
ÿ
V ëreast cancer u 14-£-£ DD
V Prostate cancer
¾ NE
, Calponin, Folistatin related protein
are not found in malignant cells
¾ Cytokeratin 1, Annexin I are specific to tumor
cells
V Renal Cell Ca u ubiquinol cytochrome c
reductase is absent in tumor cells
V Traditional tumor markers
¾ PSA, ǂ-FP, ǃ-HCO
V Limitations
¾ Low specificity, low sensitivity
¾ High false positive rate
¾ Only detectable when in large quantities
V Proteomics enable quantitative analysis
of proteins produced in malignant states
V Antibodies to tumor antigens have been
studied in
¾ Lung cancer uProtein Oene Product 9
,
annexin I,II
¾ ëreast cancer u IgO Ab to SUM-44, RS/ -1
¾ Renal cell Ca u Smooth muscle protein ˜˜-ü



 
V Approach limited to those malignancies
that do not trigger autoimmune
responses
V Similar to measuring the effect of
antibiotics on bacteriae
V Proteomic analysis of tumor cell lines are
conducted
V Yeast cells are used as models for
identification of factors conferring
sensitivity or resistance and the
mechanism of action of protein targeted
drugs
V Structural and functional studies of
microoganisms at the cellular level
V The proteome of a microbe is called its
infectome
V The infectomic changes including mRNA
and protein expression profiles in an
infected host are believed to be
patterned and stereotyped
V ëasic research ² pathogenic and virulence
factors and host responses
V iagnostic infectomics
¾ Infectomes of the pathogens and the hosts can
be used for diagnosis eg
P
falciparum
detection in serum by HRP-˜ analysis
V Preventive and therapeutic proteomics
¾ Assessment of the Proteome of commensals
¾ Vaccine development
¾ iscovery of new drug targets eg
Protease
inhibitors in HIV
V Physiology
¾ Proteins specific to cortex and medulla
identified from serum and biopsy specimens
¾ Tubular physiology studied by urinanalysis
¾ Ion transporters eg
ëumetanide sensitive Na-
K-˜Cl cotransporter, Thiazide sensitive Na-Cl
cotransporter have been identified
¾ Proteins regulating sodium handling
identified
¾ Proteome map of normal urine is being
generated
V Pathophysiology
¾ Hypertension u Kallistatin and ü

   o
ë˜-bradykinin receptor expression 



 

  
¾ iabetic nephropathy u † unique proteins have
been identified involved in apoptosis, vascular
thrombosis and remodelling, glomerulopathy
and fibrogenesis
¾ Nephrotoxicity u First used to study CsA related
nephrotoxicity, Calbindin- levels Ņ
Also being
used to study lead and radiocontrast
nephropathy
V Olomerular diseases u No reference
available at present

V Urological Malignancies u Psoriasin has
been isolated from patients with
Squamous cell malignancies
Other
markers are being assessed
V Traditional endocrinology u Using a
known hormone to identify its effects
and its pathways
V Reverse endocrinology u Using a
genomic analysis to identify new
hormones, receptors and pathways via
proteomic analysis
V Orphan Nuclear receptors u Retinoid
acid X receptors leading to discovery of
9-cis retinoic acid, PPAR ü   

V CSF markers of Alzheimers disesase u
Amyloid ǃ4˜, total and phosphorylated
Tau protein
V Parkinsons u ǂ Synuclein, symphylin,
parkin, neurofilament proteins
V Neurodegenerative diseases u
apolipoprotein E, presenilin ˜, Tau
protein

V A c-NTP detection in CSF and urine as
a screening test
V ilated cardiomyopathy
¾ Cytoskeletal and myofibrillar proteins eg
Alpha
Actin, esmin, MLC 1,˜
¾ Proteins associated with mitochondria and
energy production eg
ihydrolipoamide
dehydrogenase, Creatine kinase M-chain,
Aconitate hydratase, Lactate dehydrogenase,
Phospholamban
¾ Proteins associated with stress responses eg
HSP
0, †0, ˜, Serum albumin, i-terminal fragment
V Atherosclerosis
¾ Endothelial smooth muscle cell proteins
V Hypertension
V Oxidation status of 1-Cys peroxiredoxin
(PRX †) is a surrogate marker for oxidative
stress in cardiovascular tissues
V high sensitivity C-reactive protein (hsCRP)
V Creatine Kinase isoforms, Troponins
V Interleukin †,
, fibrinogen isoforms,
Amyloid A protein
V Protein biomarkers for autoimmune
conditions eg
Autoimmune hepatitis
(Heterogenous nuclear
ribonucleoprotein A˜/ë1)
V Chemokine assessment in Rheumatoid
arthritis treated with infliximab
V Assessment of disease severity using
proteomic analysis of inflammation
related proteins in synovial tissue, serum
V Computer assisted model
V Computer attempts to fit millions of
molecules to various sites on a target
protein
V The computer rates the quality of ´fitµ
according to the effect on the protein
with respect to amplifying or disabling
the proteins activity
V Method used to identify protease
inhibitors in HIV ² 1 proteome
V Process of covalent attachment of
Polyethylene glycol chains to another
molecule
V Advantages
¾ ecreases immunogenicity and antigenicity
¾ Increases hydrodynamic size enabling
decreased renal clearance and prolonged
circulating levels
¾ Increases solubility of hydrophobic compounds
V Examples ² PEOylated interferon,
oxorubicin, L-Asparaginase, O-CSF
V Major fraction of proteome in humans is
albumin, globulins u markers are in
minute quantities
V No tool exists to amplify proteins (no
proteomic analogue of PCR in
genomics)
V Proteomes are dynamic
V Protein levels do not correlate with
protein activity
V The Human Proteome Organisation (HUPO) u
edicated to the human proteome mapping
V Human Protein Reference atabase (HPR ) u
Collaboration between National Institute of
ëioinformantics (ëangalore) and ohns Hopkins
University (ëaltimore) u creating a freely
available protein database
V Application of proteomic technologies to
clinical practice outside laboratories
V More rapid and specific diagnostic tools
V Specific ´designerµ pharmaceuticals tailored
to patient·s proteome