LM - Antibodies - eBOOK - JL V3
LM - Antibodies - eBOOK - JL V3
❱ Antibody Generation
and Validation
❱ Efficiency, Reliability,
and Possible Danger in
Protein Quantification
ASSAYS, REAGENTS,
AND ANTIBODIES
RESOURCE GUIDE
Assays, Reagents, and Antibodies Resource Guide
Questions to • Does the assay, kit, or reagent work well with the existing
lab equipment?
Ask When • Does the assay, kit, or reagent reduce lab work time to
implement?
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Assays, Reagents, and Antibodies Resource Guide
Your Antibodies
Antibodies can be used to label a variety of biomole-
cules. Western blot is a technique that is used to detect the
presence and compare relative amounts of a target protein in a
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Assays, Reagents, and Antibodies Resource Guide
Check for host species and clonality cies, and cross-species reactivity unless there are proprietary
reasons. Bordeaux et al. reported three levels of antibody
Antibodies are typically used in pairs: the primary antibody validation efforts from companies. The first is “low/no
binds to the antigen of interest, such as a protein, and the validation” where there is minimal information except for a
fluorescent molecule- or enzyme-conjugated secondary anti- brief description of the target and recommended applications,
body binds to the primary antibody for signal detection and without examples of references that have successfully used
amplification. The host species of the primary and second- the antibodies. The second is “moderate validation” where
ary antibody should be different from the antigen species to manufacturers include at least one example of the antibody
prevent cross-reactivity and unwanted background staining being used to correctly identify targets through western
or interference. blots. The third is “high validation” where companies include
western blot data for multiple cell sources with high batch-to-
The antibody clonality is also an important factor. Monoclo- batch consistency. Users should try to find suppliers that share
nal antibodies are more specific as they bind only to a single antibody manufacturing and quality analysis data, which is
antigen, but they cannot be used across multiple species. On useful in troubleshooting.
the other hand, polyclonal antibodies bind to multiple epi-
topes with greater tolerance of antigen changes (such as those Adopt good techniques to handle antibodies
unintentionally induced by sample treatment and prepara-
tion), but they suffer from greater batch-to-batch variability. Being proteins, antibodies are vulnerable to extreme envi-
ronmental conditions like heat and acidity that can cause
Talk to other users denaturation and affect binding specificity to targets. Some
malpractices include repeated freezing and thawing of the
Before attempting to perform antibody-related experiments, same antibody samples. Users should aliquot the antibodies
it pays to read scientific literature to check which antibodies into smaller quantities and thaw only when needed. Users can
are being used by researchers in the same field. While there also read protocols from suppliers and publishers to know the
is a possibility that everyone might be using a non-specific ideal temperature to handle antibodies, duration for incuba-
antibody, the pooled risk is lower. Users can also consider tion with antibodies, and various troubleshooting tips.
attending webinars by The Antibody Society to learn tips on
choosing antibodies. Incorporate experimental controls
Purchase validated antibodies As much as possible, users should include positive and
negative controls in their experiments to validate antibodies.
Different manufacturers can adopt widely different standards Positive controls can be lysate or recombinant proteins that
for antibody manufacturing, which affect material quality. It are known to bind to the specific antibody. Negative controls
is advisable to check databases of validated antibodies such can include genetic knockout samples that no longer pro-
as Antibodypedia, which contains data on 19,000 human duce the antigens. Users can also omit a primary antibody to
protein targets (~95 percent of human genes). It is also recom- understand whether secondary antibody can cause unwanted
mended to read the guidelines by the International Working background interference.
Group for Antibody Validation on techniques to validate
antibodies and outline which applications each antibody is Antibodies are popular and valuable materials in labs and for
suitable for. use in clinics. Nevertheless, how they are manufactured and
handled can lead to poor reproducibility. To fully optimize
Scrutinize quality analysis documents from antibodies for use, tips such as sharing and learning from your
manufacturers peer community, choosing only reliable manufacturers, and
incorporating good handling practices will greatly benefit the
Reputable manufacturers will provide detailed information science done in your lab.
about their antibodies, such as the antigen sample, host spe-
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Assays, Reagents, and Antibodies Resource Guide
Validation
of conjugated antibodies for fluorescence flow cytometry
and cytometry by time-of-flight (CyTOF) applications is
also explored.
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Assays, Reagents, and Antibodies Resource Guide
B cells while B cells with a shorter life span perish. The cell This technique relies on a primary antibody that targets spe-
population is then diluted to one cell per well plate and as the cific antigens binding with a secondary antibody conjugated
antibodies in a well are produced by the same B cell cone, with fluorescence tags. The secondary antibody specifically
they recognize the same epitope, and are monoclonal. binds to the heavy chain (Fc) region of the primary antibody.
As an example, the primary antibody binds to antigen X and
Besides this method, advances in genetic sequencing have also is produced in a rabbit. Then a suitable secondary antibody
given rise to recombinant antibody technology. Rather than should bind to the Fc region of a rabbit immunoglobin and be
using animals, the gene responsible for producing the target tagged with a fluorescence label (antirabbit-fluorescence). It
antibody is identified and cloned into an appropriate vector should also come from a non-rabbit source and preferably an
before being introduced into a host cell like Chinese hamster animal that shares little homology.
ovarian cell. The genetically-engineered host cell produces
the monoclonal antibody, which can then be purified using An emerging flow cytometry technique is cytometry by
methods like affinity chromatography. time of flight (CyTOF). This technique overcomes spectral
overlaps in fluorescence flow cytometry, and it enables the
Validating antibodies detection of more antigens at a single time (approximate-
ly 100 antigens, compared to 40 antigens using traditional
Reduced antibody specificity, due to batch-to-batch vari- methods). In CyTOF, antibodies targeting antigens of interest
ability, or antibodies that bind the wrong targets lead to poor are conjugated with metals instead of fluorescence tags.
experimental reproducibility and can result in data misinter- Antibody-bound cells are then sent through an argon plasma,
pretation and wasted resources. It is, therefore, important to which ionizes the metal-conjugated antibodies, and the metal
check that the antibody is specific to its target antigen. signals are analyzed by a time-of-flight mass spectrometer.
CyTOF is becoming a popular way to label intracellular
There are a few simple ways to validate antibodies. First, labs proteins such as cytokines involved in complex signaling
should request characterization information of the same anti- pathways that involve many proteins.
body batch being purchased from the manufacturer. Second,
seek assistance and peer review from the community. If you Antibodies are an indispensable tool in biology. Although
are using an antibody that has been reported in a publication, the technology to manufacture them is established, antibody
it may be valuable to reach out to authors in that paper about validation remains poorly standardized. Before using antibod-
their experience using the antibody. Initiatives like Antibody- ies in experiments like flow cytometry, users should always
pedia and The Antibody Registry also list user-validated perform a few extra steps to ensure they are validated.
antibody information for reference. Third, perform simple
lab tests using positive and negative controls. Some examples
include using cells with a knock-out gene expressing the anti-
gen of interest or using siRNA to block the mRNA translation
of the target antigen.
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The Incucyte® instrument, proprietary assays, and
reagents provide you with the ability to gain new
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quantitative analysis of live cells.
Assays, Reagents, and Antibodies Resource Guide
Efficiency, Ease of use and reliability have been the keywords in subse-
quent variations on protein assays since the days of Lowry
Reliability,
et al. Most modern assays rely on colorimetric evaluation
of a solution via its linear change in absorbance at a given
visible-spectrum wavelength when exposed to a pro-
and Possible
tein-binding reagent. One way the Lowry method retains
an advantage over contemporary procedures is that it is an
“end-point” assay; in other words, the reaction between
in Protein
used repeatedly to calibrate sample concentrations across
multiple experiments.
Quantification
In other commonly used assays, color continues to deepen
indefinitely, and a new standard curve must be generated
every time. This is achieved by measuring absorbance
across a range of known concentrations in serial dilution of
Biochemical assays are dependent on the bovine serum albumin or immunoglobulin and calculating
fidelity with which one can quantify the relative the concentrations of experimental samples from the equa-
concentrations of proteins in solution tion generated by the standard curve. If it sounds tedious
to repeat this procedure every time you run a protein gel,
by Brandoch Cook, PhD
that’s because it is.
Biochemical assays are powerful tools in laboratory Improvements in reliability and throughput
biomedical science, and they can often answer questions
clearly and digitally in ways other procedures cannot. Tedium aside, where Lowry is deficient compared with newer
However, their accuracy is wholly dependent on the fidelity assays is in almost every other aspect relevant to modern
with which one can quantify the relative concentrations of biochemical techniques. Therefore, when the BCA assay re-
proteins in solution. placed the Folin-Ciocalteau reagent with bicinchoninic acid,
the throughput and reliability of copper-chelate protein quan-
To give an idea of the importance of protein quantification, tification improved dramatically. The BCA assay proceeds
the top three most-cited articles in the history of scientific in one easy step, making it more amenable to simultaneous
publication describe techniques for measurement or prepa- measurement of many samples, in terms of both time and re-
ration of protein samples. The all-time champion is the agent usage. Moreover, the detection reagent is more stable in
1951 paper (with over 305,000 citations!) in which its lead an alkaline solution, with less interference from components
author, Oliver Lowry, introduced an eponymous procedure typical of many protein-containing cell lysates, including
for protein quantification. detergents, Tris, cations, EDTA, and reducing agents.
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Assays, Reagents, and Antibodies Resource Guide
Assay Comparison Table for 'Efficiency, Reliability, and Possible Danger in Protein Quantification'
Number of reagents 2 2 1 3
Number of steps 2 1 1 3
Temperature of
Ambient / 4°C 37°C / Ambient Ambient / 4°C Ambient / -21°C
reaction/storage
Accuracy ++ ++ + +++
Value ++ ++ +++ +
Incompatibilities Tris, cations, EDTA, Reducing agents, thiols, Low molecular weight Tris, glycine, ammonium
detergents, reducing lipids samples, detergents ions
agents
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Assays, Reagents, and Antibodies Resource Guide
Therapeutic
increasing efficiency, consistency, and sterility.
Predefined Specificity
Monoclonal In 1975, Georges Köhler and César Milstein were the first to
Antibody
describe the creation of hybridomas for monoclonal antibody
production. In an early study, they fused mouse myeloma and
spleen cells from an immunized donor to produce cell lines
Development
that secreted anti-sheep red blood cell antibodies. The hy-
bridoma technique is still used to develop cell lines for mAb
production. Dr. David Fox is a professor of internal medicine
in the Division of Rheumatology and the director of the
Advances in automation eliminate the tedious, Hybridoma Core at the University of Michigan. The Core
time-consuming aspects of cell culture and offers antibody development services for preclinical antibody
cell line development research and investigation, using the same process involved in
therapeutic mAb development. Dr. Fox explains this process:
by Michelle Dotzert, PhD
“We receive the antigen from the person who wishes to devel-
op a monoclonal antibody. We then immunize mice and test
An astonishing 38 percent of men and women are diagnosed the serum to determine if the mouse is mounting an immune
with cancer at some point during their lives, according to the response. Once there is sufficient antibody titer in the serum,
National Cancer Institute at the National Institutes of Health. the spleen is removed to create hybridomas by fusing spleen
While this statistic is disheartening, it is important to note that cells with a cell line. Supernatant [fluid] is taken from the
the fight against cancer is not a losing battle. Between 1991 hybridomas, and the investigator screens for the monoclonal
and 2015, the overall cancer death rate in the United Sates was antibody of interest that will recognize a specific antigen and
reduced by 26 percent. Early-detection strategies and cut- is appropriate for their application.”
ting-edge treatments are continuously evolving as a result of
ongoing research. Therapeutic monoclonal antibodies (mAbs), Humanization techniques are required for antibodies destined
for example, have emerged as a promising treatment strategy. for therapeutic use in humans. “Once they are considered a
Numerous mAbs have been approved for clinical use, and therapeutic lead, these mouse antibodies must be humanized
dozens more are under investigation as potential cancer ther- (by genetic engineering) unless they are made in a humanized
apeutics. The use of mAbs for cancer treatment began in 1997, mouse, which allows more rapid progress to a potential drug
when rituximab was the first mAb approved by the U.S. Food stage,” explains Dr. Thomas Moran, a professor of microbiolo-
and Drug Administration (FDA) for treatment of some forms
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Assays, Reagents, and Antibodies Resource Guide
gy at the Icahn School of Medicine at Mount Sinai and the di- pipette tips for each cell line and noncontact liquid dispens-
rector of the Center for Therapeutic Antibody Development. ing reduce the risk of cross-contamination. Automation,
by design, reduces the amount of human interaction with
Targeting Cancer cell cultures, thereby eliminating various opportunities for
contamination. Automated systems range in capability, with
Humanization techniques have moved mAbs into the clinic, sophisticated systems enabling automated media changes,
and several are FDA-approved for use as cancer therapeu- passage, harvesting, and monitoring when integrated with
tics. mAbs are used to target and bind tumor cells expressing plate readers and imaging devices.
cancer-specific antigens and induce cell death. Individual an-
tibodies exhibit unique mechanisms of action. “Monoclonals Working with an automated system has contributed to more
can be used directly to bind to surface proteins on cancer cells than just increased productivity for Dr. Moran and his col-
to kill or inhibit their growth,” explains Dr. Moran. Trastu- leagues. “The traditional method was to test and then identify
zumab (Herceptin), for example, targets the HER2 protein the clones through a laborious replating and retesting step. An
on the surface of breast and stomach cells. “[They] can work automated system is more accurate, automated, and less prone
by recruiting immune elements, delivering toxins, producing to contamination,” he notes.
CAR-T cells, or as bispecific antibodies that recruit T or NK
cells to kill the cancer cells.” Tositumomab is used in the Challenges Remain
treatment of some B-cell non-Hodgkin lymphomas and is an
example of a monoclonal antibody used to deliver toxins, as While mAbs are a promising line of investigation in the
some of the antibody delivers a linked radioactive substance search for cancer treatments, their development is not without
to the B-cells. Bispecific antibodies consist of two different challenges. Cell culture contamination from chemicals, bacte-
monoclonals capable of binding to separate proteins simul- ria, yeasts, viruses, and even cross-contamination with other
taneously. Blinatumomab is a bispecific T cell engager that cell lines can have severe consequences, including destruction
binds to the CD19 protein on leukemia and lymphoma cells of the culture and even the cell line. Practicing good aseptic
and CD3 proteins on T cells to direct an immune response techniques and implementing automated cell culture technol-
toward the cancerous cells. The unique targets and mecha- ogies can dramatically reduce the risk of contamination.
nism of action of each mAb enable a highly specific approach
to cancer treatment compared with other treatments such Another methodological challenge is to “make antibodies
as chemotherapy. As a result, they are often associated with that bind to native molecules as they appear on the surface of
fewer side effects among patients. cells,” says Dr. Moran. “Often, synthesized proteins produced
to simulate the real protein are not folded the same way and
The Automation Advantage antibodies made against them do not bind effectively to the
‘real protein.’” It is extremely difficult to predict if an anti-
Antibody development on a small scale is often done without body developed with a specific protein will effectively rec-
automated devices. “For the scale of culture we work with, we ognize the protein on the cell surface. Immunogenicity also
mainly use in vitro bioreactor flask systems,” says Elizabeth poses challenges. Genetically engineering the antibodies to
Smith, assistant director of the Core. Sterility is critical for render them more human has shown some success; however,
all cell culture applications, and smaller-scale mAb produc- even fully human antibodies can elicit a negative immune
tion may not require highthroughput equipment. “I like the reaction. Scalability, yield, and cost are also considerations in
control that I have over the sterility of what I’m doing when the development of mAbs.
I’m handling the liquids myself,” says Smith.
Given their highly specific nature, monoclonal antibodies
However, for large-scale production of therapeutic mAbs, are promising cancer therapeutics. Their development relies
automating cell culture can offer numerous advantages, heavily on cell culture techniques, which can be laborious,
including reducing time-consuming, repetitive tasks for time-consuming, and prone to contamination. Automated cell
laboratory staff and enhancing throughput. Automated culture technologies ensure greater accuracy and precision,
liquid-handling systems eliminate hours spent pipetting and reduce the risk of contamination, and alleviate scientists of
ensure highly accurate volumes. Systems that offer dedicated tedious and time-consuming tasks.
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Assays, Reagents, and Antibodies Resource Guide
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