scholarly journals An innovative approach for HLA typing, molecular tumor testing and the validation of tumor exclusive antigens

2020 ◽  
Author(s):  
Michael Ghosh ◽  
Leon Bichmann ◽  
Jonas Scheid ◽  
Gizem Güler ◽  
Heiko Schuster ◽  
...  
Keyword(s):  
Machine Learning ◽  
Tumor Antigens ◽  
Internal Standard ◽  
Hla Class I ◽  
Hla Typing ◽  
Class I ◽  
Data Sets ◽  
Peptide Motifs ◽  
Versatile Tool ◽  
Specific Antigens

AbstractThe immunopeptidome, representing the point of contact between somatic and T cells, is key for adaptive immunity. Each presented peptide holds an abundance of information not yet well understood. Up to now, the scientific focus has been the definition of pathogenic or tumor derived epitopes and the deconvolution of HLA peptide motifs of the entire immunopeptidome. Here we go one step further and assess the properties of individual peptides to identify defined HLA allotype-specific and frequently presented peptides. Such allotypic peptides represent a versatile tool to determine HLA allotypes or serve as internal standard for characterization of cancer antigens and differentially processed antigens. Finally, individual tissue- and dignity-specific antigens were defined, and the latter were successfully implemented for molecular tumor testing.Using mass spectrometry based immunopeptidomics a database was generated consisting of ∼900 HLA-typed samples. The identified allotypic peptides enabled a HLA class I allotype determination, which was 95% correct in our in-house dataset and 98% in an external dataset. These abundant peptides were implemented as internal standard for a semi-quantitative investigation of established tumor antigens and antigens processed differentially in malignant and benign tissue. Defined dignity-specific antigens allowed a 87% correct tumor detection across numerous tumor types.In summary, we describe a machine learning approach for mining immunopeptidomic data in order to develop a classification method, allowing to differentiate HLA class I-allotypes of a sample or distinguish between healthy and malignant state of tissues. Furthermore, based on this method, we developed a procedure for the validation of tumor exclusive antigens. Our results support classification of immunopeptidomic data sets using machine learning and highlight their potential utility for biomarker development.

scholarly journals A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction

2020 ◽  
Vol 21 (4) ◽  
pp. 1119-1135 ◽  
Author(s):  
Shutao Mei ◽  
Fuyi Li ◽  
André Leier ◽  
Tatiana T Marquez-Lago ◽  
Kailin Giam ◽  
...  
Keyword(s):  
Machine Learning ◽  
T Cell ◽  
Peptide Binding ◽  
Hla Class I ◽  
Machine Learning Algorithms ◽  
Class I ◽  
Target Cells ◽  
Binding Prediction ◽  
Validation Data ◽  
Data Set

Abstract Human leukocyte antigen class I (HLA-I) molecules are encoded by major histocompatibility complex (MHC) class I loci in humans. The binding and interaction between HLA-I molecules and intracellular peptides derived from a variety of proteolytic mechanisms play a crucial role in subsequent T-cell recognition of target cells and the specificity of the immune response. In this context, tools that predict the likelihood for a peptide to bind to specific HLA class I allotypes are important for selecting the most promising antigenic targets for immunotherapy. In this article, we comprehensively review a variety of currently available tools for predicting the binding of peptides to a selection of HLA-I allomorphs. Specifically, we compare their calculation methods for the prediction score, employed algorithms, evaluation strategies and software functionalities. In addition, we have evaluated the prediction performance of the reviewed tools based on an independent validation data set, containing 21 101 experimentally verified ligands across 19 HLA-I allotypes. The benchmarking results show that MixMHCpred 2.0.1 achieves the best performance for predicting peptides binding to most of the HLA-I allomorphs studied, while NetMHCpan 4.0 and NetMHCcons 1.1 outperform the other machine learning-based and consensus-based tools, respectively. Importantly, it should be noted that a peptide predicted with a higher binding score for a specific HLA allotype does not necessarily imply it will be immunogenic. That said, peptide-binding predictors are still very useful in that they can help to significantly reduce the large number of epitope candidates that need to be experimentally verified. Several other factors, including susceptibility to proteasome cleavage, peptide transport into the endoplasmic reticulum and T-cell receptor repertoire, also contribute to the immunogenicity of peptide antigens, and some of them can be considered by some predictors. Therefore, integrating features derived from these additional factors together with HLA-binding properties by using machine-learning algorithms may increase the prediction accuracy of immunogenic peptides. As such, we anticipate that this review and benchmarking survey will assist researchers in selecting appropriate prediction tools that best suit their purposes and provide useful guidelines for the development of improved antigen predictors in the future.

Evidence for HLA-related susceptibility for stroke in children with sickle cell disease

Blood ◽  
2000 ◽  
Vol 95 (11) ◽  
pp. 3562-3567 ◽  
Author(s):  
Lori A. Styles ◽  
Carolyn Hoppe ◽  
William Klitz ◽  
Elliott Vichinsky ◽  
Bertram Lubin ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Cerebral Infarction ◽  
Sickle Cell ◽  
Hla Class I ◽  
Class Ii ◽  
Hla Typing ◽  
Class I ◽  
Increased Risk ◽  
Mri Scans ◽  
Comparison Of The Results

Abstract Cerebral infarction occurs in one quarter of all children with sickle cell anemia (SCA). There is an increased risk of stroke in siblings with SCA, suggesting genetic factors may influence risk of stroke. The authors investigated whether HLA type was associated with risk of stroke in children with SCA. Fifty-three patients with SCA underwent complete HLA typing at both HLA class I (HLA-A, B) and HLA class II (HLA-DR, DQ, DP) loci. Of the 53 patients, 22 had magnetic resonance imagining (MRI)–documented evidence of cerebral infarction, and the remaining 31 patients had negative MRI scans. Comparison of the results of HLA typing between the SCA patients with a positive and those with a negative MRI documented that the 2 groups differed with respect to the class I HLA-B (P = .012), and the class II HLA-DRB1 (P = .0008) and DQB1 (P = .029). Susceptibility associations at the HLA-DRB1 locus included both DR3 alleles, where DRB1*0301 and *0302 were both associated with an increased risk of stroke. Protective associations were found in the DR2 group, where DRB1*1501 was protective for stroke. DQB1*0201, which is in linkage disequilibrium with DRB1*0301, was also associated with stroke. Similarly, DQB1*0602, in linkage disequilibrium with DRB1*1501, was protective. Specific HLA alleles may influence the risk of stroke in children with SCA. HLA typing may prove useful in identifying SCA patients at higher risk for stroke.

scholarly journals Mislabeled units of umbilical cord blood detected by a quality assurance program at the transplantation center

Blood ◽  
2009 ◽  
Vol 114 (8) ◽  
pp. 1684-1688 ◽  
Author(s):  
Jeffrey McCullough ◽  
David McKenna ◽  
Diane Kadidlo ◽  
David Maurer ◽  
Harriett J. Noreen ◽  
...  
Keyword(s):  
Cord Blood ◽  
Umbilical Cord ◽  
Umbilical Cord Blood ◽  
Human Leukocyte ◽  
Hla Class I ◽  
Hla Typing ◽  
Class I ◽  
Quality Assurance Program ◽  
Cord Blood Unit ◽  
Transplantation Center

Abstract We instituted procedures to check the identity of cord blood unit provided for transplantation by carrying out ABO and human leukocyte antigen (HLA) typing of the thawed units before transplantation. ABO typing is done using standard techniques. Rapid HLA class I serology is with monoclonal antibody trays (One Lambda Inc) using standard incubations. One mislabeled umbilical cord blood (UCB) unit was detected on the day of intended transplantation by repeat ABO typing of the thawed unit at our transplantation center. Because ABO typing will not detect all labeling errors, the rapid serologic class I HLA typing procedure was done on thawed units just before transplantation for all units without an attached segment. This procedure identified a second mislabeled unit. In a 6-year period, 2 of 871 (0.2%) cord blood units sent to us for transplantation were mislabeled and potentially would have been transplanted incorrectly. This error rate of 1 per 249 (0.4%) patients could have potentially devastating consequences.

Generation of Antigen Specific Cytotoxic T Lymphocytes (CTL) by Dendritic Cells (DCs) Transfected with In Vitro Transcribed (IVT) SART-1 and WT-1 mRNA.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 3859-3859
Author(s):  
Anri Saito ◽  
Miwako Narita ◽  
Toshio Yano ◽  
Naoko Sato ◽  
Asuka Sekiguchi ◽  
...  
Keyword(s):  
Mhc Class I ◽  
Tumor Antigen ◽  
Hla Class I ◽  
Class Ii ◽  
Class I ◽  
Target Cells ◽  
Mhc Restriction ◽  
Specific Ctls ◽  
Specific Antigens

Abstract Transfection with tumor antigen RNA is one of the promising tools not only because of a possible sufficient amplification of tumor antigen RNA but also because of the absence of antigen peptides-associated MHC restriction. Several succeeded experiments about generation of CTLs using DCs transfeced in vitro transcribed (IVT) cancer specific antigen mRNA such as PSA, CEA, hTERT and MUC-1 have been reported in these a few years. In addition, recent reports about the simultaneous presentation of peptides in both MHC class I and class II molecules on DCs after mRNA electroporation show another superiority of mRNA transfection into DCs. In this presentation, we demonstrate successful generation of tumor antigen specific CTLs using with DCs transfected with IVT mRNA such as SART-1 and WT-1 by electroporation. This is the first report about the generation of SART-1 and WT-1 specific CTLs by using mRNA transfected DCs. [Methods] HLA-A24 positive human PB CD14+ cell-derived DCs were transfected with IVT mRNA (SART-1and WT-1) by electroporation. MRNA transfected DCs were co-cultured with autologous lymphocytes. The bulk co-cultures were re-stimulated several times with same DCs. CD8+ cells were separated and CTL activity was evaluated by 51chromium release assay. To determine whether the induced CTL cells could recognize the target cells in an HLA class I restricted manner, anti-HLA class I monoclonal antibodies were utilized to block the cytotoxicity of effectors. [Results] Electroporation of mRNA showed no effect on the surface phenotypes and antigen presenting ability of DCs. In addition to the demonstration of efficient transfection of M1 mRNA into DCs by using RT-PCR, which eliminated the amplification of transfected mRNA by the treatment with RNase before RNA extraction from the transfected cells, we identified the definite expression of WT-1 protein in the cytoplasm of DCs by using immunoblotting. CTL assay indicated that 1) DCs transfected with mRNA stimulated the generation of antigen-specific CTLs which are capable of lysing autologous DCs transfected with the same mRNA. 2) CTLs also demonstrated cytotoxic ability against cell lines such as KE-4 presenting SART-1 peptides on HLA-A24, MEGO1 presenting WT-1 peptides on MHC class I, and HLA-A24 cDNA transfected T2 which were used as target cells after co- incubation with 9 mer SART-1 peptides with strong affinity to HLA-A24. 3) Each cytotoxicities were markedly blocked after co-incubation of target cells with anti-MHC class I antibody and not inhibited with anti-MHC class II antibody. [Conclusion] Our results showed that IVT mRNA-transfected DCs which is constructed non-virally have a highly efficient ability to stimulate specific T-cell immunity against tumor. Unlike peptide- or tumor cells extract-pulsed DCs based vaccines, anti-tumor immunotherapy using the DCs transfected with antigen mRNA could be extended to a wide range of patients who have previously been excluded from clinical trials for the reason of the un-identification of tumor specific antigens, for the reason of the impossibility of obtaining sufficient tumor specimens, or for the reason of MHC restriction of the tumor specific antigens.

High Resolution HLA Typing by Sequencing for HLA-A, B, C, DR, DQ in 115 Unrelated Cord Blood/Patient Pairs- Does It Improve Outcomes after Cord Blood-Transplantation?.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 973-973 ◽  
Author(s):  
Gesine Koegler ◽  
Juergen Enczmann ◽  
Vanderson Rocha ◽  
Eliane Gluckman ◽  
Peter Wernet
Keyword(s):  
High Resolution ◽  
Cord Blood ◽  
Cord Blood Transplantation ◽  
Hla Class I ◽  
Hla Typing ◽  
Class I ◽  
Published Data ◽  
Number Of Patients ◽  
The Impact ◽  
Grade Iii

Abstract The CB Bank Düsseldorf has provided to date (July 2004) 224 CB units (216 unrelated and 8 related, 29% adults, 71% children) to transplant centers worldwide. Until now no correlation could be detected between the number of HLA-mismatches based on low resolution (LR) typing for HLA-A and-B and high resolution typing (HR) for DRB1 and the incidence of aGvHD as published previously by us and other groups. The lack of correlation between aGvHD occurrence and donor/recipient HLA diversity in patients given an unrelated CBT could be explained by the fact that some mismatches for HLA class I antigens (A, B and C) are not detected by LR typing. In order to determine the impact of HLA high resolution typing with outcomes, mainly aGvHD after UCBT we analysed DNA samples of 115 CB recipients (86 children; 29 adults; 66 male, 49 female; diagnosis ALL=43, AML=19, SecAL =1, MDS=5, CML=10, NHL=5, Hodgkin=1, AA=7, genetic and metabolic diseases= 24) and their unrelated CB grafts were HLA-typed for HLA-class I (A, B, C) and HLA-class II (DRB1 and DQB1) by sequencing. The transplant centers used their own protocols for GvHD prophylaxis, the most commonly used was the combination of CsA and steroids alone (60%), CsA alone (15%), or the combination with MTX (6%). 55 of 115 patients did not develop aGvHD (grade 0= 48%), 26 patients developed grade I (23%), 12 patients developed grade II (10%), 10 patients grade III (9%) and 12 patients grade IV (10%). When mismatches (MM) were analysed for HLA-A, B based on LR-typing and -DRB1 based on HR-typing in concordance with all published data so far, the following mismatch situation resulted: No MM (16 pairs, 13.9%), one MM (47 pairs, 40.9%), two MM (41 pairs, 35.7%), three MM (5 pairs, 4.3%), four MM (3 pairs, 2.6%). If the MM for A and B alleles detected by HR-typing were included, the situation was as follows: 0 MM (6 pairs, 5.2%), 1 MM (35 pairs, 30.4%), 2 MM (54 pairs, 47%), 3MM (14 pairs, 12.2%), 4 MM (5 pairs, 4.3%), 5 MM (1 pair, 0.9%). If analysing A, B, C, DR and DQ based on HR typing a high additional frequency of MM occurred: No MM (4 pairs, 3.5%), 1 MM (13 pairs, 11.3%), 2 MM (19 pairs, 16.5%), 3 MM (24 pairs, 20.9%), 4 MM (30 pairs, 26.1%), 5 MM (14 pairs, 12.2%), 6 MM (6 pairs, 5.2 %), 6 MM (6 pairs, 5.2%), 7 MM (3 pairs, 2.6%), 8 MM (2 pairs, 1.7%). There was no significant correlation between the number of MM (also analysed in GvHD or rejection direction) using high-resolution level for HLA-A, B and DRB1 as well as for HLA-A, B, C, DRB1 and DQB1 and the development of aGvHD grade III-IV. More interestingly, we have not found any significant correlation between numbers of MM with 2-year survival probability. Although the heterogeneity and number of patients analysed, it shows that the degree of mismatching is even higher than expected, also in comparison to unrelated BMT. It also shows that additional subtyping for HLA-A, B, C and DQ, not performed on a routine basis at present, does not improve the 2-year survival rate.

Product Attributes and Donor Factors in Reported Cases of Transfusion-Associated Graft Versus Host Disease: A Systematic Review

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 2883-2883
Author(s):  
Ilana Kopolovic ◽  
Jackie Ostro ◽  
Christine Cserti ◽  
Walter Sunny Dzik ◽  
Hidacki Tsubota ◽  
...  
Keyword(s):  
Storage Time ◽  
Hla Antigens ◽  
Hla Class I ◽  
Class Ii ◽  
Hla Typing ◽  
Class I ◽  
Blood Component ◽  
Blood Components ◽  
Donor Factors ◽  
Related Donor

Abstract INTRODUCTION: Transfusion-associated graft-vs-host disease (TA-GVHD) is a rare and often fatal complication of transfusion of cellular blood products. The relative contributions of product and donor factors to the risk of TA-GVHD remain uncertain. METHODS: Systematic review of all reported cases of TA-GVHD in the published literature prior to Oct 2013, without language restrictions. Cases attributed to granulocyte transfusions, passenger lymphocyte syndrome, or GVHD following stem-cell transplant (unless traced to blood components rather than the graft) were excluded. Data collected included patient demographics and health information, details of transfusion event(s) and blood component(s), clinicolaboratory features of the TA-GVHD presentation and outcome, and results of human leukocyte antigen (HLA) and chimerism studies. HLA typing was evaluated where reported for both donor (product) and recipient at either class I or class II loci. Donor/recipient pairs were categorized as D=0 when there were no identified donor HLA antigens foreign to the recipient, or D>0 when donor cells contained one or more HLA antigens not found in the recipient. This classification applied separately to HLA class I and class II loci for each case. RESULTS: After removing duplicates, 2130 citations discovered by the search were examined by two independent reviewers, with 394 identified as publications of interest for complete review. An additional 21 publications were found from the initial review, for a total of 415 publications. Of these, 195 publications described 348 unique cases for inclusion. Component: The component implicated in TA-GVHD was identified in 248 (71%) cases: Red cells (RBC) in 132 (38%); whole blood (WB) in 92 (26%); platelets in 20 (6%); buffy- coat product in 2 (0.6%); and plasma and plasma-reduced blood in one case each. In 100 (29%) cases, the blood component was either not specified or not identified among several potentially responsible components. Storage: Component storage time was reported in 158 (45%) cases. Of these, the implicated product was either described as “fresh” or </=10 days old in 148 (94%). 10 (6%) cases reported a storage time >10 days (maximum 14 days). Related donor: In 63 cases, the donor was either related (n=61) or deliberately HLA-matched (n=2) to the recipient, while in 113 cases the donor was unrelated. The remaining cases either reported a “possible” related donor or did not report the donor-recipient relationship. Leukoreduction/Irradiation: Leukoreduction status was reported in 135 (39%) cases. Of these, the implicated product was leukoreduced in 23 (17%) (10 bedside, 2 pre-storage, 11 not specified). The product was irradiated in 9 cases. HLA: HLA typing of recipient and donor, by serological or molecular techniques, was available for 84 cases (74 cases Class I, 62 Class II). Among patients with HLA data available, 20 (24%) had an underlying diagnosis warranting irradiation by current standards, while 64 (76%) did not. The category of D=0 was found in 47 (64%) of cases with reported class I typing; 44 (71%) of cases with reported class II typing; and 60 (71%) overall (Figure 1). There were 9 cases in which the category of D=0 could be ruled out for both HLA I and II. In the remaining 15 cases, the category of D=0 at either HLA I or II could not be definitively ruled in or out based on reported data. When considering those in whom the presence or absence of D=0 could be definitely determined, while D=0 at either HLA class I or class II was present in 55 of 57 (96%) of recipients without an indication for blood component irradiation, D=0 was present in only 5 of 12 (42%) of recipients with an indication for irradiation, p< 0.0001 (Table 1). CONCLUSIONS: The most common components implicated in TA-GVHD were WB and RBC. Most units were non-leukoreduced and stored for <10 days. Most cases of TA-GVHD occurred in recipients without a standard indication for irradiation. The absence of a foreign donor antigen at either HLA class I or class II occurred in a large majority of cases and was significantly more common in TA-GVHD among recipients without an indication for irradiation compared with those in whom irradiation would be indicated, suggesting that this donor-recipient relationship is the predominant risk factor in the development of TA-GVHD. Policies for irradiating cellular blood components based solely on the diagnosis of the recipient may fail to address all relevant risk factors for TA-GVHD. Figure 1 Figure 1. Table 1. Table 1. Disclosures No relevant conflicts of interest to declare.

Evidence for HLA-related susceptibility for stroke in children with sickle cell disease

Blood ◽  
2000 ◽  
Vol 95 (11) ◽  
pp. 3562-3567
Author(s):  
Lori A. Styles ◽  
Carolyn Hoppe ◽  
William Klitz ◽  
Elliott Vichinsky ◽  
Bertram Lubin ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Cerebral Infarction ◽  
Sickle Cell ◽  
Hla Class I ◽  
Class Ii ◽  
Hla Typing ◽  
Class I ◽  
Increased Risk ◽  
Mri Scans ◽  
Comparison Of The Results

Cerebral infarction occurs in one quarter of all children with sickle cell anemia (SCA). There is an increased risk of stroke in siblings with SCA, suggesting genetic factors may influence risk of stroke. The authors investigated whether HLA type was associated with risk of stroke in children with SCA. Fifty-three patients with SCA underwent complete HLA typing at both HLA class I (HLA-A, B) and HLA class II (HLA-DR, DQ, DP) loci. Of the 53 patients, 22 had magnetic resonance imagining (MRI)–documented evidence of cerebral infarction, and the remaining 31 patients had negative MRI scans. Comparison of the results of HLA typing between the SCA patients with a positive and those with a negative MRI documented that the 2 groups differed with respect to the class I HLA-B (P = .012), and the class II HLA-DRB1 (P = .0008) and DQB1 (P = .029). Susceptibility associations at the HLA-DRB1 locus included both DR3 alleles, where DRB1*0301 and *0302 were both associated with an increased risk of stroke. Protective associations were found in the DR2 group, where DRB1*1501 was protective for stroke. DQB1*0201, which is in linkage disequilibrium with DRB1*0301, was also associated with stroke. Similarly, DQB1*0602, in linkage disequilibrium with DRB1*1501, was protective. Specific HLA alleles may influence the risk of stroke in children with SCA. HLA typing may prove useful in identifying SCA patients at higher risk for stroke.

Determination of the immunogenetic risk of developing cancer.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e13132-e13132
Author(s):  
István Miklós ◽  
Eniko Rita Toke ◽  
Mónika Megyesi ◽  
Levente Molnar ◽  
József Tóth ◽  
...  
Keyword(s):  
T Cell ◽  
General Population ◽  
Cancer Risk ◽  
Tumor Antigens ◽  
Hla Class I ◽  
Class I ◽  
P Value ◽  
T Cell Epitopes ◽  
Risk Of Cancer

e13132 Background: Association between certain HLA types and cancer is well known. We hypothesized that the number of epitopes of tumor antigens presented by autologous HLAs characterizes a patient’s capacity to kill tumor cells. These CD8+ T cell epitopes are presented by 6 out of >13,000 known HLA class I alleles and induce extremely variable tumor-specific T-cell responses. Methods: We predicted HLA-binding epitopes from 48 frequently expressed tumor antigens in subjects characterized with 6 HLA class I alleles. To develop the “HLA Score” cancer risk predictor we used epitopes binding to multiple HLAs of a subject. The predictor was trained on 5,789 non-American subjects. To identify populations with high and low immunogenetic risk to develop cancer we compared the HLA Score of American cancer subjects to a general population of American subjects (1,400 subjects). The performance of the predictor was characterized with AUC and Risk Ratio. Due to Bonferroni correction, AUC values with p-value p<0.007 was accepted as significant. Results: “HLA Score” predictor significantly separated cancer patients from the general population in six out of the seven investigated cancer types. The Risk Ratios between the most protected and most at risk subpopulations ranged between 2.38 and 5.67 (Table). Cancer risk prediction with HLA Score. Conclusions: Subjects with certain HLA class I alleles have high risk of developing cancer. The novel “HLA Score” predictor we introduced here could complement current testing used for determination of the genetic risk of cancer.[Table: see text]

Sign in / Sign up

Export Citation Format

Share Document