Front cover: High-sensitivity HLA class I peptidome analysis enables a precise definition of peptide motifs and the identification of peptides from cell lines and patients’ sera

Abstract We provide a comprehensive analysis of the antigenic landscape of glioblastoma using a multi-omics approach including ligandome mapping of the Human Leukocyte Antigen (HLA) ligandome, next generation sequencing (NGS) as well as an in-depth characterization of tumor-infiltrating lymphocytes (TIL) using mass cytometry and ultra-deep sequencing of the T-cell receptor (TCR). Tumor-exclusive HLA class I and class II ligands (immune precipitation and LC-MS/MS) of 24 isocitrate dehydrogenase 1 wild type glioblastoma samples and 10 autologous primary glioblastoma cell lines were defined in comparison to an HLA ligandome normal tissue reference database (n > 418). We found 11,496 glioblastoma exclusive HLA class I ligands (2,064 shared with cell lines; 3,754 on ≥ 2 glioblastoma samples). On the source protein level, 239 glioblastoma exclusive proteins were identified; among them 54 were also found in cell lines. For HLA class II ligands the analysis revealed 11,870 glioblastoma exclusive peptides (444 shared with cell lines; 3,420 on ≥ 2 glioblastoma samples) and 278 glioblastoma exclusive proteins; among which 18 were present also in cell lines. Moreover, whole-exome sequencing and whole RNA sequencing of 13 tumor samples was performed with the aim to predict neoantigens. On average 5,662 somatic missense effects were identified per patient (min: 4,258; max: 7,479). Candidate peptides are grouped into (i) in silico predicted neoepitopes, (ii) tumor-exclusivity on HLA, (iii) gene expression (e.g. cancer testis antigens). Top-ranking candidates from each group will be tested with regards to their immunogenicity in an autologous setting (TIL, peripheral blood mononuclear cells, patient derived tumor cells). Finally, the peptide and immunogenicity data is correlated with the immune phenotype of the TIL compartment as well as the TCR repertoire of the sample.

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Molecular definition of soluble HLA class I heavy chains

Human Immunology ◽

10.1016/0198-8859(93)90045-3 ◽

1993 ◽

Vol 36 (1) ◽

pp. 52

Author(s):

M. Drouet ◽

L. Aussel ◽

R. Fauchet

Keyword(s):

Hla Class I ◽

Class I ◽

Heavy Chains ◽

Soluble Hla ◽

Definition Of

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Abstract 3622: Total loss of HLA class I expression by two sarcomatoid hepatocellular carcinoma cell lines sHCC29 and sHCC63 was caused by a ∼49-kbp deletion at chromosome 15q15 across the β2m gene locus

10.1158/1538-7445.am2014-3622 ◽

2014 ◽

Author(s):

Wei-Yi Lei ◽

Chin-Hsuan Hsieh ◽

Chien-Chung Chang ◽

Shao-Hsuan Wen ◽

Chi-Tan Hu ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Cell Lines ◽

Gene Locus ◽

Carcinoma Cell ◽

Hla Class I ◽

Total Loss ◽

Class I ◽

Carcinoma Cell Lines ◽

Hepatocellular Carcinoma Cell

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HLA class I phenotype and genotype alterations in cervical carcinomas and derivative cell lines

Tissue Antigens ◽

10.1111/j.1399-0039.1998.tb03005.x ◽

1998 ◽

Vol 51 (6) ◽

pp. 623-636 ◽

Cited By ~ 37

Author(s):

L.A. Koopman ◽

A. Mulder ◽

W.E. Corver ◽

J.D.H. Anholts ◽

M.J. Giphart ◽

...

Keyword(s):

Cell Lines ◽

Hla Class I ◽

Class I ◽

Cervical Carcinomas

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HLA Influence on NK Cell Expansion

Blood ◽

10.1182/blood.v112.11.4924.4924 ◽

2008 ◽

Vol 112 (11) ◽

pp. 4924-4924

Author(s):

Jennifer Schellekens ◽

Anna Stserbakova ◽

Madis Tõns ◽

Hele Everaus ◽

Marcel GJ Tilanus ◽

...

Keyword(s):

Nk Cells ◽

Cell Lines ◽

Cell Expansion ◽

Nk Cell ◽

Killer Cell ◽

Hla Class I ◽

Class I ◽

Haematopoietic Stem Cell ◽

Specific Priming

Abstract Natural Killer (NK) cells are effector cells in the innate immune system. The anti-leukaemic capacities of NK cells in haematopoietic stem cell transplantation make these cells a potential treatment modality to improve clinical outcome. Immunotherapy with NK cells requires transfusion of large quantities, which obviates the need for an in vitro culture system for NK cells. The killer cell immunoglobulin-like receptors (KIR) on NK cells recognise defined groups of HLA class I alleles. To elucidate the influence of these interactions on proliferation, the peripheral blood mononuclear cells (PBMCs) of 29 patients and donors were cultured in CellGro SCGM with IL-2 and OKT3 antibody to expand the NK cell fraction. The killer cell immunoglobulin-like receptor (KIR) and HLA repertoire were determined by sequence specific priming and sequence based typing respectively. The percentage of NK cell expansion from the total PBMC fraction varied between 5.4% and 71.6%. A significantly better NK cell expansion was observed for individuals homozygous for HLA-C epitope group 2 (p<0.05). For evaluation of cytolytic competence of the cultured NK cells, specific killing of an HLA class I expression deficient LCL 721.221 cell line and three 721.221 cell lines transfected with different HLA-C alleles was determined. A significantly better NK cell-induced specific cytotoxicity was observed towards the untransfected 721.221 cells compared to the HLA-C transfected 721.221 cells. No significant differences were observed between killing of the three HLA-C transfected 721.221 cell lines. We have shown that cytolytic capacities of the cultured NK cells are maintained and in vitro expansion of NK cells is dependant on the presence of HLA-C alleles.

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α-interferon treatment induces quantitative modifications of HLA class I-associated peptides eluted from cultured cancer cell lines

Tissue Antigens ◽

10.1034/j.1399-0039.2000.550304.x ◽

2000 ◽

Vol 55 (3) ◽

pp. 212-218 ◽

Cited By ~ 3

Author(s):

G. Cangemi ◽

E. Millo ◽

G. Damonte ◽

C. Semino ◽

G. Pietra ◽

...

Keyword(s):

Cell Lines ◽

Cancer Cell ◽

Hla Class I ◽

Cancer Cell Lines ◽

Class I ◽

Interferon Treatment

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HDAC Inhibition Increases HLA Class I Expression in Uveal Melanoma

Cancers ◽

10.3390/cancers12123690 ◽

2020 ◽

Vol 12 (12) ◽

pp. 3690

Author(s):

Zahra Souri ◽

Aart G. Jochemsen ◽

Mieke Versluis ◽

Annemijn P.A. Wierenga ◽

Fariba Nemati ◽

...

Keyword(s):

Cell Surface ◽

Cell Lines ◽

Uveal Melanoma ◽

Hdac Inhibitor ◽

Mrna Level ◽

Hla Class I ◽

Class I ◽

In Vitro Tests ◽

Hla Class I Antigens

The treatment of uveal melanoma (UM) metastases or adjuvant treatment may imply immunological approaches or chemotherapy. It is to date unknown how epigenetic modifiers affect the expression of immunologically relevant targets, such as the HLA Class I antigens, in UM. We investigated the expression of HDACs and the histone methyl transferase EZH2 in a set of 64 UMs, using an Illumina HT12V4 array, and determined whether a histone deacetylase (HDAC) inhibitor and EZH2 inhibitor modified the expression of HLA Class I on three UM cell lines. Several HDACs (HDAC1, HDAC3, HDAC4, and HDAC8) showed an increased expression in high-risk UM, and were correlated with an increased HLA expression. HDAC11 had the opposite expression pattern. While in vitro tests showed that Tazemetostat did not influence cell growth, Quisinostat decreased cell survival. In the three tested cell lines, Quisinostat increased HLA Class I expression at the protein and mRNA level, while Tazemetostat did not have an effect on the cell surface HLA Class I levels. Combination therapy mostly followed the Quisinostat results. Our findings indicate that epigenetic drugs (in this case an HDAC inhibitor) may influence the expression of immunologically relevant cell surface molecules in UM, demonstrating that these drugs potentially influence immunotherapy.

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Characterization of Renal-Cell Carcinoma (RCC)-Reactive Cytotoxic T-Lymphocyte Responses Generated from Peripheral Blood of HLA-Matched Sibling and Unrelated Healthy Individuals in Vitro.

Blood ◽

10.1182/blood.v104.11.4971.4971 ◽

2004 ◽

Vol 104 (11) ◽

pp. 4971-4971

Author(s):

Mark Groene ◽

Sandra Kausche ◽

Elke Schnuerer ◽

Volker Lennerz ◽

Ralf G. Meyer ◽

...

Keyword(s):

Tumor Cell ◽

Cell Lines ◽

T Lymphocyte ◽

Peripheral Blood ◽

Cytotoxic T Lymphocyte ◽

Hla Class I ◽

Class I ◽

Healthy Individuals ◽

Allogeneic Cell Therapy ◽

Healthy Donors

Abstract Although current allo-transplantation therapy can induce considerable graft-versus-tumor (GvT) effects in RCC patients, it is also accompanied by severe, even life-threatening side effects, mainly due to graft-versus-host disease (GvHD). Efforts aiming to improve the specificity and efficiency of allogeneic cell therapy in this disease (e.g. specific donor lymphocyte infusion or vaccination) will certainly benefit from the identification of potential anti-tumor effector mechanisms and their corresponding target structures. We recently demonstrated that RCC-reactive cytotoxic T-lymphocyte (CTL) clones can be isolated from peripheral blood of healthy donors matched with the RCC stimulators for HLA-class I. These CTL were found to recognize a broad panel of RCC antigens with restricted or ubiquitous tissue expression (Doerrschuck A, et al., Blood July 1, 2004, Epub). We now extended our analyses on peripheral blood mononuclear cells (PBMC) of further HLA-matched healthy sibling (1) and unrelated individuals (4) and compared these results with available autologous patient PBMC. While mixed lymphocyte/tumor-cell culture (MLTC) responders derived from allogeneic donors showed a robust antigen-dependent proliferation over several weeks, a weak if any proliferative response was seen with autologous MLTC populations. By analysing the fine specificity of MLTC-derived clonal CTL the majority of allogeneic effectors recognized exclusively their RCC stimulators, but not corresponding lymphoblastoid-cell lines or natural killer target K562. These CTL were restricted by various HLA-A, -B or -C molecules. We further isolated CTL clones that exhibit an extraordinary strong recognition of RCC and various epithelial tumor-cell lines. Antibody blocking experiments provided clear evidence that these CTL are restricted by a not yet defined HLA-Ib molecule and, simultaneously, by a NKG2D-dependent mechanism. Other rapidly proliferating CD3+ CD8+ CTL clones were obtained that showed a non-HLA-restricted reactivity against RCC and a minor but consistent reactivity against targets with low or absent HLA-class I expression (e.g. K562). In conclusion, our results demonstrate that a heterogeneous panel of RCC-reactive HLA-Ia/Ib-restricted CTL can be isolated from PBMC of HLA-class I-matched healthy individuals. Alternatively, CTL recognizing RCC in a non-HLA restricted manner can be obtained. Our observations might reflect the superior ability to activate and expand RCC-directed T cells from PBMC of allogeneic healthy donors compared to the autologous setting. At this point, we cannot conclude whether these various CTL populations contribute to effective anti-RCC immune responses occurring in vivo. Answering this question will certainly require to identify further CTL-defined target structures at the molecular level. This would allow us to analyse the expression of candidate antigens and the frequency of specific CTL in RCC patients after allogeneic blood stem-cell transplantation, and to correlate these findings with clinical GvT and GvH events.

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