Biomarkers and the 'omics' Lec 1&2

Question 1

what are biomarkers

Answer 1

-biochemical features used to measure disease presence and progress, and treatment effect on disease
-substance present in or produced by a tumour or produced by host in response to a tumour
-found in low abundance in variety of fluids, tissues, and cell lines

Question 2

Primary Biomarkers

Answer 2

are tumour specific (more accurate than secondary)

Question 3

Secondary Biomarkers

Answer 3

are tumour non specific, a response to the presence of a tumour such as inflammation or an immune response

Question 4

what are the factors for an ideal serological (found in blood/serum) tumour marker

Answer 4

-produced by tumour cells then enter circulation
-present at low levels in healthy/benign individuals, increases substantially in cancer individuals even in early/preclinical stages
-easily quantifiable with an inexpensive assay (medical system under financial stress so expensive procedures wont be carried out as often as they should be)
-quantitative levels of marker reflect tumour burden
-high diagnostic sensitivity (few false negatives) and specificity (few false positives)

Question 5

Distal biofluids

Answer 5

-blood (fluid not in direct contact with site of disease)
-preferred material for final diagnostic test

Question 6

Proximal biofluids

Answer 6

-fluid in direct contact with the site of disease (saliva in head and neck cancer, pancreatic juice in pancreas cancer)
-local sinks for proteins and peptides secreted, shed, or leaked from diseased tissue meaning potential biomarkers of disease are enriched in proximal fluids

Question 7

what are the phases of biomarker discovery

Answer 7

-Experimental Design
-Discovery
-Qualification
-Verification
-Validation and Clinical assay development

Question 8

Experimental Design phase of biomarker discovery

Answer 8

phase 1, sample selection (proximal or distal fluid etc), collection processing and storage (strict adherence to protocols for accuracy), healthy/benign control samples (tumour tissue sample - control of surrounding non-cancerous tissue, biofluid sample - control of healthy/benign individuals from same body are, well matched ie. age and sex)

Question 9

Discovery phase of biomarker discovery

Answer 9

phase 2, identify potential biomarkers using 2D-DIGE, LC-MS/MS, SELDI-TOF, mass spectrometry, protein assays, immunodepletion uses antibodies to deplete blood samples of high abundant proteins enriches low abundant (disease) proteins making them more easily discovered

Question 10

Qualification phase of biomarker discovery

Answer 10

phase 3, confirm the differential abundance of potential biomarkers using LC-MS/MS, SELDI-TOF, high-throughput screening

Question 11

Verification phase of biomarker discovery

Answer 11

phase 4, begin to assess specificity and selectivity of potential biomarkers using LC-MS/MS, SELDI-TOF, high-throughput screening

Question 12

Validation and Clinical Assay Development phase of biomarker discovery

Answer 12

phase 5, establish sensitivity and specificity, and assay optimisation using radioimmunoassay(RIA), or enzyme-linked immunosorbent assay(ELISA)

Question 13

what is genomics

Answer 13

the study of a set of genes contained in the chromosomes

Question 14

what is transcriptomics

Answer 14

the study of a set of genes being expressed as mRNA molecules in a specific cell at a given time under specified conditions

Question 15

what is proteomics

Answer 15

the study of a set of proteins being expressed in a specific cell at a given time under specified conditions and the state of modification

Question 16

what is metabolomics

Answer 16

the study of the set of small molecules (fats, vitamins, sugars, amino acids etc), in a specific cell at a given time under specified conditions

Question 17

Expression proteomics

Answer 17

define all gene products present in a cell and their modifications

Question 18

Cell-Map proteomics

Answer 18

define the spatial and temporal positions of all proteins and interactions

Question 19

Functional proteomics

Answer 19

define the biological function of all proteins within their network and complexes

Question 20

Structural proteomics

Answer 20

determine the structure of all proteins, alone and in complexes

Question 21

Population proteomics

Answer 21

largescale version of expression proteomics for disease studies

Question 22

what are the post-translational modifications with examples

Answer 22

proteolytic cleavage (fragmenting protein) and addition of chemical groups (phosphorylation-activation and inactivation of enzymes, methylation-regulation of gene expression, ubiquitination-destruction signal)

Question 23

primary protein structure

Answer 23

proteins are linear polymers of amino acids, the sequence of which gives the protein its primary structure

Question 24

secondary protein structure

Answer 24

local folding structures such as alpha helices which is formed by the hydrogen bonding of the carbonyl of one amino acid to the amino H of an amino acid 4 down the chain, and beta pleated sheets which form when 2 or more segments of a polypeptide chain line up next to each other either parallel or antiparallel and form a sheet like structure held together by hydrogen bonds between the carbonyl and amino groups of the backbone

Question 25

tertiary protein structure

Answer 25

overall folding of the amino acid chain by interactions such as hydrogen bonding, ionic bonding, hydrophobic, and disulfide bonds

Question 26

quaternary protein structure

Answer 26

subunits composing functional protein, made up of multiple polypeptide chains, not all proteins have a quaternary structure

Question 27

Cystic Fibrosis - Gene mutations and CFTR protein

Answer 27

CFTR protein acts as a channel for movement of chloride ions in and out of cells which is important for salt and water balance on epithelial surfaces like lungs and pancreas, changes in the CFTR gene can affect the structure of the CFTR protein which is what occurs with Cystic Fibrosis with class 1, 2 and 3 mutations generally leading to complete loss of function and more severe disease while class 4 and 5 mutations are less severe disease causing only a reduction in function