Name: personalized peptide arrays for detection of hla alloantibodies in organ transplantation
Uploaded: 2017-09-06T15:00:00
Description: Watch this Scientific Journal Video about Personalized Peptide Arrays for Detection of HLA Alloantibodies in Organ Transplantation at JoVE.com

We thank Drs. Shawn Li and Xing Li of Western University in Canada for their kind assistance with SPOT array production. We are grateful to the staff members at the Histocompatibility Core and at the Comprehensive Transplant Center of Northwestern University for providing sample services. This work has been partly supported by the Auxiliary Board of Northwestern Memorial Hospital, and by a faculty startup fund provided by Northwestern University to J.J..

All methods described here have been approved by the Northwestern University Institutional Review Board (IRB protocol#: STU00104680). An overall workflow of the protocol is illustrated in Figure 1.
1. Bioinformatic Analysis of Donor and Recipient HLA Sequences
<ol>
	<li>Retrieve sequences from IMGT/HLA database15.
	<ol>
		<li>Obtain HLA typing reports of both the organ donor and his/her recipient. 
		NOTE: Ensure proper procedures to pro...

<ol>
	<li>Bradshaw, R. A., Dunn, P. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Unambiguous+high+resolution+genotyping+of+human+leukocyte+antigens.">Unambiguous high resolution genotyping of human leukocyte antigens.</a> J Immunol Methods. , (2017).</li><li>Robinson, J., Halliwell, J. A., McWilliam, H., Lopez, R., Marsh, S. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=IPD--the+Immuno+Polymorphism+Database.">IPD--the Immuno Polymorphism Database.</a> Nucleic Acids Res. 41, D1234-D1240 (2013).</li><li>Tait, B. 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A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=HLA+antibody+detection+with+solid+phase+assays:+great+expectations+or+expectations+too+great?.">HLA antibody detection with solid phase assays: great expectations or expectations too great?.</a> Am J Transplant. 14 (9), 1964-1975 (2014).</li><li>Horton, R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Gene+map+of+the+extended+human+MHC.">Gene map of the extended human MHC.</a> Nat Rev Genet. 5 (12), 889-899 (2004).</li><li>Duquesnoy, R. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=HLAMatchmaker:+a+molecularly+based+algorithm+for+histocompatibility+determination+I.+Description+of+the+algorithm.">HLAMatchmaker: a molecularly based algorithm for histocompatibility determination I. Description of the algorithm.</a> Hum Immunol. 63 (5), 339-352 (2002).</li><li>Duquesnoy, R. J., Marrari, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=HLAMatchmaker-based+definition+of+structural+human+leukocyte+antigen+epitopes+detected+by+alloantibodies.">HLAMatchmaker-based definition of structural human leukocyte antigen epitopes detected by alloantibodies.</a> Curr Opin Organ Transplant. 14 (4), 403-409 (2009).</li><li>Wedel, J., Bruneau, S., Kochupurakkal, N., Boneschansker, L., Briscoe, D. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chronic+allograft+rejection:+a+fresh+look.">Chronic allograft rejection: a fresh look.</a> Curr Opin Organ Transplant. 20 (1), 13-20 (2015).</li><li>Rostaing, L. P., Malvezzi, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=HLA-Incompatible+Kidney+Transplantation--Worth+the+Risk?.">HLA-Incompatible Kidney Transplantation--Worth the Risk?.</a> N Engl J Med. 374 (10), 982-984 (2016).</li><li>Gebel, H. M., Bray, R. A., Nickerson, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Pre-transplant+assessment+of+donor-reactive,+HLA-specific+antibodies+in+renal+transplantation:+contraindication+vs.+risk.">Pre-transplant assessment of donor-reactive, HLA-specific antibodies in renal transplantation: contraindication vs. risk.</a> Am J Transplant. 3 (12), 1488-1500 (2003).</li><li>Haas, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+updated+Banff+schema+for+diagnosis+of+antibody-mediated+rejection+in+renal+allografts.">An updated Banff schema for diagnosis of antibody-mediated rejection in renal allografts.</a> Curr Opin Organ Transplant. 19 (3), 315-322 (2014).</li><li>Cecka, J. M., Reed, E. F., Zachary, A. 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H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=HLA+epitopes+as+viewed+by+antibodies:+what+is+it+all+about?.">HLA epitopes as viewed by antibodies: what is it all about?.</a> Am J Transplant. 15 (5), 1148-1154 (2015).</li><li>Robinson, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+IPD+and+IMGT/HLA+database:+allele+variant+databases.">The IPD and IMGT/HLA database: allele variant databases.</a> Nucleic Acids Res. 43, D423-D431 (2015).</li><li>Gabriel, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=HLA+typing+by+next-generation+sequencing+-+getting+closer+to+reality.">HLA typing by next-generation sequencing - getting closer to reality.</a> Tissue Antigens. 83 (2), 65-75 (2014).</li><li>Liu, P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+Novel+Method+for+Anti-HLA+Antibody+Detection+Using+Personalized+Peptide+Arrays.">A Novel Method for Anti-HLA Antibody Detection Using Personalized Peptide Arrays.</a> Transplant Direct. 2 (11), (2016).</li><li>Frank, R., Overwin, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=SPOT+synthesis.+Epitope+analysis+with+arrays+of+synthetic+peptides+prepared+on+cellulose+membranes.">SPOT synthesis. Epitope analysis with arrays of synthetic peptides prepared on cellulose membranes.</a> Methods Mol Biol. 66, 149-169 (1996).</li><li>Frank, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+SPOT-synthesis+technique.+Synthetic+peptide+arrays+on+membrane+supports--principles+and+applications.">The SPOT-synthesis technique. Synthetic peptide arrays on membrane supports--principles and applications.</a> J Immunol Methods. 267 (1), 13-26 (2002).</li><li>Amartely, H., Iosub-Amir, A., Friedler, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identifying+protein-protein+interaction+sites+using+peptide+arrays.">Identifying protein-protein interaction sites using peptide arrays.</a> J Vis Exp. (93), (2014).</li><li>Kudithipudi, S., Kusevic, D., Weirich, S., Jeltsch, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Specificity+analysis+of+protein+lysine+methyltransferases+using+SPOT+peptide+arrays.">Specificity analysis of protein lysine methyltransferases using SPOT peptide arrays.</a> J Vis Exp. (93), e52203 (2014).</li><li>Hilpert, K., Winkler, D. F., Hancock, R. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Peptide+arrays+on+cellulose+support:+SPOT+synthesis,+a+time+and+cost+efficient+method+for+synthesis+of+large+numbers+of+peptides+in+a+parallel+and+addressable+fashion.">Peptide arrays on cellulose support: SPOT synthesis, a time and cost efficient method for synthesis of large numbers of peptides in a parallel and addressable fashion.</a> Nat Protoc. 2 (6), 1333-1349 (2007).</li><li>McBride, R., Head, S. R., Ordoukhanian, P., Law, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Low-Cost+Peptide+Microarrays+for+Mapping+Continuous+Antibody+Epitopes.">Low-Cost Peptide Microarrays for Mapping Continuous Antibody Epitopes.</a> Methods Mol Biol. 1352, 67-83 (2016).</li><li>Li, S. S., Wu, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Using+peptide+array+to+identify+binding+motifs+and+interaction+networks+for+modular+domains.">Using peptide array to identify binding motifs and interaction networks for modular domains.</a> Methods Mol Biol. 570, 67-76 (2009).</li><li>Kaczmarek, I., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Donor-specific+HLA+alloantibodies:+long-term+impact+on+cardiac+allograft+vasculopathy+and+mortality+after+heart+transplant.">Donor-specific HLA alloantibodies: long-term impact on cardiac allograft vasculopathy and mortality after heart transplant.</a> Exp Clin Transplant. 6 (3), 229-235 (2008).</li><li>Claas, F. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Clinical+relevance+of+circulating+donor-specific+HLA+antibodies.">Clinical relevance of circulating donor-specific HLA antibodies.</a> Curr Opin Organ Transplant. 15 (4), 462-466 (2010).</li><li>Brown, N. K., Kheradmand, T., Wang, J., Marino, S. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+and+characterization+of+novel+HLA+alleles:+Utility+of+next-generation+sequencing+methods.">Identification and characterization of novel HLA alleles: Utility of next-generation sequencing methods.</a> Hum Immunol. 77 (4), 313-316 (2016).</li><li>Cino, E. A., Choy, W. Y., Karttunen, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Conformational+Biases+of+Linear+Motifs.">Conformational Biases of Linear Motifs.</a> Journal of Physical Chemistry B. 117 (50), 15943-15957 (2013).</li><li>Duquesnoy, R. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Human+leukocyte+antigen+epitope+antigenicity+and+immunogenicity.">Human leukocyte antigen epitope antigenicity and immunogenicity.</a> Curr Opin Organ Transplant. 19 (4), 428-435 (2014).</li><li>Lavinder, J. 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The design of the SPOT array described here is for experimental study of alloantibody specificity in transplantation against an organ donor's HLA antigens. In contrast to the existing SAB assay broadly used in clinic, the antigen array method has a major advantage in its flexible design that can accommodate the true HLA sequences of the individual donor. The new platform exploits the potentials of the rapidly advancing DNA sequencing technology that will soon be able to produce accurate HLA allelic sequence readings with...

Organ replacement therapy that is routinely conducted across the world has saved millions of lives. Solid organ transplantation occurs in approximately 100 patients per million people in the USA annually, while a greater number still are on waitlists to receive donor organs due to a severe shortage of supply (according to information provided by the Organ Procurement and Transplantation Network - OPTN/UNOS: optn.transplant.hrsa.gov). Organ transplant is highly regulated in order to reduce organ waste and save lives, but the scientific tools used to inform these regulations are limited in effectiveness. For instance, the scientific community fully recognizes the highly polymorphic states of HLA molecules and accurate genetic tests of DNA using high-resolution typing and sequence-based typing (SBT) have been developed in recent years1,2. However, alloantibody testing methods have not yet been able to produce the vast variety of individual HLA sequences as antigen probes. The standard test nowadays uses an invariable panel of ~100 allelic antigens that are comprised of common variants of HLA, A, B, C, DQ, DP and DR sequences in human populations3,4,5,6. Frequently, the actual donor&#39;s HLA sequences are not included in the test panel, forcing transplant physicians and surgeons to infer donor-specific reactivity based on shared similarities between donor&#39;s actual sequences and corresponding &#34;standards&#34; in the test set7,8. Consequently, it is sometimes challenging to make a reliable estimation of rejection risk based on antibody test results9,10,11,12. Therefore, new personally customizable tests for alloantibodies are urgently needed13,14.
The HLA genes encode the major histocompatibility complex (MHC) receptors that have a key function in immune responses6. HLA genes are known to be the most polymorphic genes of the human genome6. Due to the rapid advancements in DNA sequencing strategies for the HLA genes, new allelic variants (or simply referred to as alleles) are being discovered at an explosive rate15,16. By March 2017, 16,755 validated alleles had been deposited to the IMGT/HLA Database (http://www.ebi.ac.uk/ipd/index.html), of which 12,351 were of class I and 4,404 were of class II groups. In stark contrast, only a little over 100 distinct alleles are represented in the standard single-antigen beads (SAB) assay, which is routinely used to detect alloantibodies in organ transplantation. The SAB method is built on a Luminex platform using flow cytometry. Since the assay utilizes an invariable set of antigens, apart from minor batch to batch variabilities in production, the antiserum test can be robustly standardized across individuals and across laboratories5. However, this test is unable to capture all alloantibodies developed specifically against the donor alleles, particularly when the donor sequences are absent from the SAB set. Although custom production of donors&#8217; antigens based on true sequences are desirable, there remain technical challenges in streamlining the necessary production and testing procedures.
We recently described an alternative methodology in a feasibility study of renal transplant subjects17. The method used peptide antigens in an array format for probing pre- and post-transplant sera of individual subjects. Each array was custom built using the SPOT synthesis method18,19,20,21,22,23 that produces peptide antigens, each 15 amino acids in length, entirely based on the respective organ donor&#39;s HLA alleles of A, B, C, DQA1, DQB1 and DRB1. SPOT synthesis is operated on a cellulose membrane using standard Fmoc-chemistry22 and can produce hundreds of custom peptides in parallel with a fully automated robotic system19,21. The membrane array can withstand multiple rounds of stripping and reprobing cycles. In our retrospective study17, we detected changes in antigen patterns with stored transplant antisera collected in a time series (i.e., before and after transplantation). Herein we describe the technical protocol for the workflow including array design, manufacturing, antiserum probing and result analysis. The method is intended for detecting alloantibodies against specific linear epitopes on transplant donors&#39; HLA molecules.

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			<td height="40" style="height:40px;width:167px;">Peptide array</td>
			<td style="width:141px;">INTAVIS Bioanalytical Instruments</td>
			<td style="width:115px;"></td>
			<td style="width:155px;"></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:167px;">Ethanol</td>
			<td style="width:141px;">Sigma-Aldrich</td>
			<td style="width:115px;">E7023</td>
			<td style="width:155px;"></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:167px;">Ponceau S solution</td>
			<td style="width:141px;">Sigma-Aldrich</td>
			<td style="width:115px;">P7170</td>
			<td style="width:155px;"></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:167px;">Non-fat milk</td>
			<td style="width:141px;">Bio Rad Laboratories</td>
			<td style="width:115px;">1706404</td>
			<td style="width:155px;"></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:167px;">TBST</td>
			<td style="width:141px;">Santa Cruz Biotechnology</td>
			<td style="width:115px;">10711454001</td>
			<td style="width:155px;"></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:167px;">Goat anti-human IgG&#8211;HRP&#160;</td>
			<td style="width:141px;">ThermoFisher Scientific</td>
			<td style="width:115px;">A18811</td>
			<td style="width:155px;"></td>
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			<td height="40" style="height:40px;width:167px;">Clarity Western ECL Substrate</td>
			<td style="width:141px;">Bio Rad Laboratories</td>
			<td style="width:115px;">1705061</td>
			<td style="width:155px;"></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:167px;">Restore Western Blot Stripping Buffer</td>
			<td style="width:141px;">Thermo Scientifics</td>
			<td style="width:115px;">21059</td>
			<td style="width:155px;"></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:167px;">ChemiDoc gel imaging system</td>
			<td style="width:141px;">Bio Rad Laboratories</td>
			<td style="width:115px;">1708265&#160;</td>
			<td style="width:155px;"></td>
		</tr>
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personalized peptide arrays for detection of hla alloantibodies in organ transplantation

In organ transplantation, the function and longevity of the graft critically rely on the success of controlling immunological rejection reactivity against human leukocyte antigens (HLA). Histocompatibility guidelines are based on laboratory tests of anti-HLA immunity, which presents either as pre-existing or de novo generated HLA antibodies that constitute a major transplantation barrier. Current tests are built on a single-antigen beads (SAB) platform using a fixed set of ~100 preselected recombinant HLA antigens to probe transplant sera. However, in humans there exist a far greater variety of HLA types, with no two individuals other than identical twins who can share the same combination of HLA sequences. While advanced technologies for HLA typing and direct sequencing can precisely capture any mismatches in DNA sequence between a donor's and recipient's HLA, the SAB assay, due to its limited variety in sequence representation, is unable to precisely detect alloantibodies specifically against the donor HLA mismatches. We sought to develop a complementary method using a different technology to detect and characterize anti-donor HLA antibodies on a personalized basis. The screening tool is a custom peptide array of donor HLA-derived sequences for probing post-transplant sera of the organ recipient to assess the risk for antibody-mediated rejection. On a single array for one donor-recipient pair, up to 600 unique peptides are made based on the donor's HLA protein sequences, each peptide carrying at least one mismatched residue in a 15-amino acid sequence. In our pilot experiments to compare antigen patterns for pre- and post-transplant sera on these arrays, we were able to detect anti-HLA signals with the resolution that also allowed us to pinpoint the immune epitopes involved. These personalized antigen arrays allow high-resolution detection of donor-specific HLA epitopes in organ transplantation.

In the original study using the array screening method17, we enrolled a total of 5 kidney transplant subjects. We obtained the HLA typing results of our cohort and of their respective donors. Their medical history and allelic antibody titers from SAB tests were also available to us. In our pilot study of these 5 patients, we devised two different methodologies: a standard array comprised of a fixed panel of peptides and personalized arrays that were custom made for...

Watch this Scientific Journal Video about Personalized Peptide Arrays for Detection of HLA Alloantibodies in Organ Transplantation at JoVE.com

Personalized Peptide Arrays for Detection of HLA Alloantibodies in Organ Transplantation

Mismatches in human leukocyte antigen (HLA) sequences between organ donor and recipient pairs are the major cause of antibody-mediated rejection in organ transplantation. Here we present the use of custom antigen arrays that are based on individual donors' HLA sequences to probe anti-donor HLA alloantibodies in organ recipients.

In organ transplantation, the function and longevity of the graft critically rely on the success of controlling immunological rejection reactivity against ...

The overall goal of this custom array method for alloantibody detection is to delineate humane leukocyte antigen or HLA epitopes in organ transplantation. This method can help answer key questions in the organ transplantation field about the specific immune epitopes involved in transplant rejection. The main advantage of this technique is that it's fully customizable, allowing incorporation of personalized antigen sets that can reflect individual organ donors'HLA sequences.The technique has the potential to detect specific HLA epitopes for alloantibodies. To retrieve sequences from the International Immunogenetics Project human leukocyte antigen project database, in the ambiguous allele combinations page, open the database allele query form and input the subject's first allele name into the search for box. Click Search for Alleles Now and locate the matching allele name displayed on the screen.Click Allele and copy and paste the protein sequence into a text document under an allele name header line to arrange the allele name in sequence in a FASTA format. When all of the sequences have been identified, copy and paste the sequences from the FASTA format into the enter your input sequences box on the Cluster Omega website and click submit your job using the standard parameter settings. Then click submit.An alignment of the sequences will be displayed. To mark the donor-specific mismatches, copy and paste the alignment text into a new text document and use a distinguishing font color to mark each mismatched donor-specific residue within the aligned sequences that belong uniquely to the donor. Underline all of the letters in the donor sequences that extend 14 residues up and downstream of the marked donor-specific mismatches and use the underlined sequences as templates to sequentially derive short 15 amino acid sequences in a series that overlap by four residues between any two immediately adjacent sequences in the series.Copy and paste these 15 amino acid sequences into a spreadsheet in a column format accompanied by notation columns that include the corresponding names of the donor alleles. To design a custom array layout, generate a spreadsheet of peptide sequences with corresponding allele callings with 20 rows and 30 columns. Then input the sequences into each of the array cells and use the spot synthesizer to run an automated peptide array synthesis.When designing an array, it is critical to use individual donors'HLA sequences as a template for deriving the antigen set. When the arrays have been synthesized, block the membranes with 20 milliliters of 5%nonfat milk dissolved in Tris-buffered saline with 0.1%tween 20 or TBST for the appropriate incubation period with rocking. Next, wash the membrane three times with 20 milliliters of fresh TBST for five minutes per wash followed by incubation with 20 microliters of crude-recipient serum in 2.5%milk in TBST for two to three hours at room temperature.At the end of the incubation, wash the membrane three times for 10 minutes per wash and incubate the membranes with goat anti-human horse radish peroxidase conjugated IgG secondary antibody for two hours. Remove the unbound secondary antibody with three 10-minute washes in TBST and develop the membranes in five milliliters of freshly-prepared luminol solution plus five milliliters of peroxide solution. After one minute, visualize the enhanced chemiluminescence signals on a suitable imager.After saving the developed images, incubate the membranes with 20 milliliters of commercial stripping buffer at 37 degrees Celsius for 20 minutes followed by three 10-minute washes in TBST. Then block, re-probe, and visualize the membranes as just demonstrated with a serum sample from the same patient obtained at a different time point. To manually annotate the positive antigen peptides, locate the spots with positive antibody signals in the saved developed image files and determine each of their grid positions.Then retrieve the peptide sequences from the master worksheet to identify any potentially shared epitope sequences based on their overlapping segments of reactive peptides. To structurally model antigen epitopes, obtain prototype HLA crystal structures from the protein data bank and display the prototype HLA structure in Pymol. Highlight the reactive peptide sequences to map the discovered anti-donor epitopes to the 3D structures of the prototype HLA.Then click Display and Background and select White, saving the data as a PNG file. After sequencing multiple alignments of this representative donor patient's alleles as just demonstrated, an alignment file was obtained for each of the alleles. The template sequences of the donor that were sufficiently long enough to cover all of the mismatched residues were then identified and underlined and three series of 15-mer peptides were derived for the first allele.After all of the donor's alleles were analyzed, a total of 202 peptides were loaded into an array for the specific probing of the donor's post-transplant serum. Comparing the results with those obtained from a subsequent re-probing of the donor's pre-transplant serum revealed the antibody signals associated with the post-transplant specimen of which several donor-specific residues mismatched from the recipient appeared to be involved in inciting antibody reactivity. When the antibody reactive epitopes on HLA-DQA1 and DQB1 were modeled to a co-crystal heterodimer structure, a prominent segment of the structure known as the beta one strand was identified as a hotspot that had a much higher chance of being targeted by alloantibodies among the transplant subjects in a representative five-case cohort.Once mastered, the technique can be completed in seven to eight hours if it is performed properly. After its development, the technique paved the way for researchers in the field of transplant rejection to explore the personalized detection of donor-specific alloantibodies.

Research

JoVE Journal

Biochemistry

Automated Acoustic Dispensing for the Serial Dilution of Peptide Agonists in Potency Determination Assays

As with small molecule drug discovery, screening for peptide agonists requires the serial dilution of peptides to produce concentration-response curves. ...

Easy Manipulation of Architectures in Protein-based Hydrogels for Cell Culture Applications

Hydrogels are recognized as promising materials for cell culture applications due to their ability to provide highly hydrated cell environments. The field ...

Analysis of Histone Antibody Specificity with Peptide Microarrays

Post-translational modifications (PTMs) on histone proteins are widely studied for their roles in regulating chromatin structure and gene expression. The ...

Electrochemical Detection of Deuterium Kinetic Isotope Effect on Extracellular Electron Transport in Shewanella oneidensis MR-1

Electrochemical Detection of Deuterium Kinetic Isotope Effect on Extracellular Electron Transport in Shewanella oneidensis MR-1

Direct electrochemical detection of c-type cytochrome complexes embedded in the bacterial outer membrane (outer membrane c-type cytochrome complexes; OM ...

Isolation of Tissue Extracellular Vesicles from the Liver

Extracellular vesicles (EVs) can be released from many different cell types and detected in most, if not all, body fluids. EVs can participate in ...

A Fluorogenic Peptide Cleavage Assay to Screen for Proteolytic Activity: Applications for coronavirus spike protein activation

Enveloped viruses such as coronaviruses or influenza virus require proteolytic cleavage of their fusion protein to be able to infect the host cell. Often ...

Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry

The posttranslational modification of proteins by the small protein ubiquitin is involved in many cellular events. After tryptic digestion of ...

Study on the Metabolism of Six Systemic Insecticides in a Newly Established Cell Suspension Culture Derived from Tea (Camellia Sinensis L.) Leaves

Study on the Metabolism of Six Systemic Insecticides in a Newly Established Cell Suspension Culture Derived from Tea Camellia Sinensis L. Leaves

A platform for studying insecticide metabolism using in vitro tissues of tea plant was developed. Leaves from sterile tea plantlets were induced to form ...

Kinase Inhibitor Screening In Self-assembled Human Protein Microarrays

The screening of kinase inhibitors is crucial for better understanding properties of a drug and for the identification of potentially new targets with ...

Transplantation of Neonatal Mouse Cardiac Macrophages into Adult Mice

In an injured neonatal myocardium, macrophages facilitate cardiomyocyte proliferation and angiogenesis and promote heart regeneration. The present study ...