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Journal articles on the topic 'Repertoire profiling'

Author: Grafiati

Published: 4 June 2021

Last updated: 5 February 2022

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1

D'Angelo, Sara, Flavio Mignone, Cecilia Deantonio, et al. "Profiling celiac disease antibody repertoire." Clinical Immunology 148, no. 1 (2013): 99–109. http://dx.doi.org/10.1016/j.clim.2013.04.009.

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2

Pashova, Shina, Christoph Schneider, Stephan von Gunten, and Anastas Pashov. "Antibody repertoire profiling with mimotope arrays." Human Vaccines & Immunotherapeutics 13, no. 2 (2016): 314–22. http://dx.doi.org/10.1080/21645515.2017.1264786.

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3

Mulder, David T., Etienne R. Mahé, Mark Dowar, et al. "CapTCR-seq: hybrid capture for T-cell receptor repertoire profiling." Blood Advances 2, no. 23 (2018): 3506–14. http://dx.doi.org/10.1182/bloodadvances.2017014639.

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Abstract Mature T-cell lymphomas consisting of an expanded clonal population of T cells that possess common rearrangements of the T-cell receptor (TCR) encoding genes can be identified and monitored using molecular methods of T-cell repertoire analysis. We have developed a hybrid-capture method that enriches DNA sequencing libraries for fragments encoding rearranged TCR genes from all 4 loci in a single reaction. We use this method to describe the TCR repertoires of 63 putative lymphoma clinical isolates, 7 peripheral blood mononuclear cell (PBMC) populations, and a collection of tumor infiltr

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4

Bolotin, Dmitriy A., Stanislav Poslavsky, Alexey N. Davydov, et al. "Antigen receptor repertoire profiling from RNA-seq data." Nature Biotechnology 35, no. 10 (2017): 908–11. http://dx.doi.org/10.1038/nbt.3979.

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5

Lo, Ken C., Eric Sullivan, Ryan M. Bannen, et al. "Comprehensive Profiling of the Rheumatoid Arthritis Antibody Repertoire." Arthritis & Rheumatology 72, no. 2 (2019): 242–50. http://dx.doi.org/10.1002/art.41089.

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6

Su, L. "Profiling the t cell repertoire in rheumatoid arthritis." Annals of the Rheumatic Diseases 69, Suppl 2 (2010): A75. http://dx.doi.org/10.1136/ard.2010.129668z1.

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7

Somers, V., C. Govarts, N. Hellings, R. Hupperts, and P. Stinissen. "Profiling the autoantibody repertoire by serological antigen selection." Journal of Autoimmunity 25, no. 3 (2005): 223–28. http://dx.doi.org/10.1016/j.jaut.2005.09.023.

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8

Liu, Xinyue, Qiang Hu, Song Liu, et al. "Serum Antibody Repertoire Profiling Using In Silico Antigen Screen." PLoS ONE 8, no. 6 (2013): e67181. http://dx.doi.org/10.1371/journal.pone.0067181.

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9

Ayoglu, Burcu, Anna Gundberg, Mohsen Khademi, et al. "Proteomic profiling of the autoimmunity repertoire in multiple sclerosis." New Biotechnology 29 (September 2012): S20. http://dx.doi.org/10.1016/j.nbt.2012.08.049.

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10

Jiang, Ning, Alexandra A. Schonnesen, and Ke-Yue Ma. "Ushering in Integrated T Cell Repertoire Profiling in Cancer." Trends in Cancer 5, no. 2 (2019): 85–94. http://dx.doi.org/10.1016/j.trecan.2018.11.005.

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11

Khan, Tarik A., Simon Friedensohn, Arthur R. Gorter de Vries, Jakub Straszewski, Hans-Joachim Ruscheweyh, and Sai T. Reddy. "Accurate and predictive antibody repertoire profiling by molecular amplification fingerprinting." Science Advances 2, no. 3 (2016): e1501371. http://dx.doi.org/10.1126/sciadv.1501371.

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High-throughput antibody repertoire sequencing (Ig-seq) provides quantitative molecular information on humoral immunity. However, Ig-seq is compromised by biases and errors introduced during library preparation and sequencing. By using synthetic antibody spike-in genes, we determined that primer bias from multiplex polymerase chain reaction (PCR) library preparation resulted in antibody frequencies with only 42 to 62% accuracy. Additionally, Ig-seq errors resulted in antibody diversity measurements being overestimated by up to 5000-fold. To rectify this, we developed molecular amplification fi

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12

Raybould, Matthew I. J., Claire Marks, Aleksandr Kovaltsuk, Alan P. Lewis, Jiye Shi, and Charlotte M. Deane. "Public Baseline and shared response structures support the theory of antibody repertoire functional commonality." PLOS Computational Biology 17, no. 3 (2021): e1008781. http://dx.doi.org/10.1371/journal.pcbi.1008781.

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The naïve antibody/B-cell receptor (BCR) repertoires of different individuals ought to exhibit significant functional commonality, given that most pathogens trigger an effective antibody response to immunodominant epitopes. Sequence-based repertoire analysis has so far offered little evidence for this phenomenon. For example, a recent study estimated the number of shared (‘public’) antibody clonotypes in circulating baseline repertoires to be around 0.02% across ten unrelated individuals. However, to engage the same epitope, antibodies only require a similar binding site structure and the pres

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13

Levy, Eric, Pamela Milani, Gabor Bartha, et al. "67 B-cell receptor heavy chain repertoire profiling using an augmented transcriptome." Journal for ImmunoTherapy of Cancer 8, Suppl 3 (2020): A72. http://dx.doi.org/10.1136/jitc-2020-sitc2020.0067.

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BackgroundComprehensive profiling of the tumor and tumor microenvironment (TME) is a critical tool for furthering our understanding of tumor progression and response to treatment, including immunotherapies. To address this challenge, we developed an augmented, immuno-oncology-optimized exome/transcriptome platform, ImmunoID NeXTTM, which provides a more comprehensive view of the tumor and TME from limited FFPE tumor biopsies. We have recently added the ability to profile the B-cell receptor (BCR) heavy chain. Here, we show that ImmunoID NeXT is now able to accurately and reproducibly profile a

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14

Mancini, Arturo, Charlotte Avet, Billy Breton, et al. "Profiling the Signaling Repertoire of One Hundred Therapeutically‐Relevant Human GPCRs." FASEB Journal 34, S1 (2020): 1. http://dx.doi.org/10.1096/fasebj.2020.34.s1.05196.

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15

Murray, D., Hayden Pearce, Wayne Croft, Chris Yau, Paul Moss, and Julia Scarisbrick. "Single-cell RNA sequencing with TCR repertoire profiling of mycosis fungoides." European Journal of Cancer 119 (2019): S7. http://dx.doi.org/10.1016/s0959-8049(19)30528-3.

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16

Zhang, Michael, Stephanie Hilz, Michael Martin, et al. "IMMU-11. SPATIOTEMPORAL IMMUNOGENOMIC ANALYSIS OF THE T-CELL REPERTOIRE IN IDH-MUTANT LOWER GRADE GLIOMAS." Neuro-Oncology 21, Supplement_6 (2019): vi121. http://dx.doi.org/10.1093/neuonc/noz175.505.

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Abstract The design and evaluation of immunotherapies in IDH-mutant lower grade gliomas (LGG) is hindered by a poor understanding of the LGG T-cell repertoire. We present data on the temporal evolution, intratumoral spatial distribution, and prognostic value of the T-cell repertoire in IDH-mutant LGGs. We performed immunogenomic profiling using T-cell receptor beta-chain sequencing of 163 glioma and peripheral blood samples from 33 immunotherapy-naive glioma patients (22 astrocytomas, 11 oligodendrogliomas). T-cell repertoire evolution was analyzed in a subset of 26 patients (69 samples) with

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17

Spatola, Bradley N., Joseph A. Murray, Martin Kagnoff, Katri Kaukinen, and Patrick S. Daugherty. "Antibody Repertoire Profiling Using Bacterial Display Identifies Reactivity Signatures of Celiac Disease." Analytical Chemistry 85, no. 2 (2012): 1215–22. http://dx.doi.org/10.1021/ac303201d.

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18

Chang, Che-Mai, Yu-Wen Hsu, Henry Sung-Ching Wong, Hsien-Tzung Liao, and Wei-Chiao Chang. "Profiling of T-cell Repertoire in biologic-treated patients with rheumatoid arthritis." Proceedings for Annual Meeting of The Japanese Pharmacological Society WCP2018 (2018): PO4–10–27. http://dx.doi.org/10.1254/jpssuppl.wcp2018.0_po4-10-27.

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19

Freeman, J. D., R. L. Warren, J. R. Webb, B. H. Nelson, and R. A. Holt. "Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing." Genome Research 19, no. 10 (2009): 1817–24. http://dx.doi.org/10.1101/gr.092924.109.

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20

Minervina, Anastasia, Mikhail Pogorelyy, and Ilgar Mamedov. "T‐cell receptor and B‐cell receptor repertoire profiling in adaptive immunity." Transplant International 32, no. 11 (2019): 1111–23. http://dx.doi.org/10.1111/tri.13475.

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21

Yang, Huaxia, Zhongxing Bing, Lei Cao, et al. "Genetic profiling and TCR repertoire feature of synchronous multiple primary lung carcinomas." Journal of Clinical Oncology 38, no. 15_suppl (2020): e21031-e21031. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.e21031.

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e21031 Background: The incidence and detection rates of multiple primary lung cancer are increasing, as a result of the advances in lung cancer screening techniques. However, the molecular and immune mechanisms of their carcinogenesis were little known, which may have important diagnostic, prognostic and therapeutic implications. Methods: We retrospective analyzed 10 patients (pts) with clinically designated synchronous multiple primary lung cancers (sMPLC). 28 different tumor lesions were included and mutation profiles were analyzed using 1021 genes panel based next-generation sequencing (NGS

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22

Li, Yang, Cheng-qiang Li, Shu-juan Guo, et al. "Longitudinal serum autoantibody repertoire profiling identifies surgery-associated biomarkers in lung adenocarcinoma." EBioMedicine 53 (March 2020): 102674. http://dx.doi.org/10.1016/j.ebiom.2020.102674.

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23

Jakobi, Tobias, Lisa F. Czaja-Hasse, Richard Reinhardt, and Christoph Dieterich. "Profiling and Validation of the Circular RNA Repertoire in Adult Murine Hearts." Genomics, Proteomics & Bioinformatics 14, no. 4 (2016): 216–23. http://dx.doi.org/10.1016/j.gpb.2016.02.003.

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24

Zivraj, K. H., Y. C. L. Tung, M. Piper, et al. "Subcellular Profiling Reveals Distinct and Developmentally Regulated Repertoire of Growth Cone mRNAs." Journal of Neuroscience 30, no. 46 (2010): 15464–78. http://dx.doi.org/10.1523/jneurosci.1800-10.2010.

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25

Liu, Hongxing, Fang Wang, Wen Teng, et al. "Mutaome Profiling and Retrospective Mutaome Profiling Using Archived Bone Marrow Smear In AML." Blood 122, no. 21 (2013): 4983. http://dx.doi.org/10.1182/blood.v122.21.4983.4983.

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Abstract Background Acute myeloid leukemia (AML) is a heterogeneous disease with respect to presentation and clinical outcome. In recent years, more and more somatic mutations and their clinical significance were identified in AML. Most AML patients carry multiple gene mutations and the repertoire of mutations changing during the disease process, which determine the patient's unique clinical manifestations. Herein we recommend using the novel word ”mutaome¡± for representing the repertoire of somatic gene mutations in a specific tumor tissue, and aimed to establish a panel of mutation profilin

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26

Vardi, Anna, Evangelia Stalika, Athanasios Gkoufas, et al. "High-Throughput T-Cell Receptor Gene Repertoire Profiling in Chronic Lymphocytic Leukemia Reveals a Molecular Signature of Antigen Selection." Blood 124, no. 21 (2014): 1950. http://dx.doi.org/10.1182/blood.v124.21.1950.1950.

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Abstract The role of antigen(s) in shaping the T-cell repertoire in chronic lymphocytic leukemia (CLL) is largely unexplored, though highly relevant in light of the interactions of the CLL B cells with T cells, effectively inducing tolerance to the latter. Our recent classic subcloning/Sanger sequencing studies of the T-cell receptor beta chain (TRB) gene repertoire in CLL indicated repertoire restriction, pointing to antigenic selection. However, due to the inherent limitations of low-throughput analysis, definitive conclusions were not possible. Here, we sought to advance the analytical dept

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27

Alié, Alexandre, Tetsutaro Hayashi, Itsuro Sugimura, et al. "The ancestral gene repertoire of animal stem cells." Proceedings of the National Academy of Sciences 112, no. 51 (2015): E7093—E7100. http://dx.doi.org/10.1073/pnas.1514789112.

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Stem cells are pivotal for development and tissue homeostasis of multicellular animals, and the quest for a gene toolkit associated with the emergence of stem cells in a common ancestor of all metazoans remains a major challenge for evolutionary biology. We reconstructed the conserved gene repertoire of animal stem cells by transcriptomic profiling of totipotent archeocytes in the demosponge Ephydatia fluviatilis and by tracing shared molecular signatures with flatworm and Hydra stem cells. Phylostratigraphy analyses indicated that most of these stem-cell genes predate animal origin, with only

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28

Warnatz, Hans-Jörg, Rita I. Azevedo, Maria G. D. Soares, et al. "Profiling T Cell Receptor Repertoires in Phase I/II Clinical Trials of Donor Treg Infusion for the Treatment of Chronic Graft-Versus-Host Disease." Blood 132, Supplement 1 (2018): 4563. http://dx.doi.org/10.1182/blood-2018-99-111866.

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Abstract Introduction Under the auspices of the EC-Horizon 2020 project "TREGeneration", we are conducting five clinical phase I/II trials investigating the safety and efficacy of donor regulatory T cell (Treg) infusion in patients with chronic Graft-versus-Host Disease (cGvHD), a serious complication following hematopoietic stem cell transplantation (HSCT). Workpackage 4 evaluates T cell receptor (TCR) repertoire changes by high-throughput sequencing following the infusion of donor Tregs. Methods For repertoire analysis, four different T cell subsets (Treg, conventional CD4 T cells - Tcon, to

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29

Chang, Che-Mai, Yu-Wen Hsu, Henry Sung-Ching Wong, et al. "Characterization of T-Cell Receptor Repertoire in Patients with Rheumatoid Arthritis Receiving Biologic Therapies." Disease Markers 2019 (July 7, 2019): 1–12. http://dx.doi.org/10.1155/2019/2364943.

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Rheumatoid arthritis (RA) is a systematic autoimmune disease, predominantly causing chronic polyarticular inflammation and joint injury of patients. For the treatment of RA, biologic disease-modifying antirheumatic drugs (bDMARDs) have been used to reduce inflammation and to interfere with disease progression through targeting and mediating the immune system. Although the therapeutic effects of bDMARDs in RA patients have been widely reported, whether these drugs also play important roles in T-cell repertoire status is still unclear. We therefore designed the study to identify the role of T-ce

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Lin, Kai-Rong, Fei-Wen Deng, Ya-Bin Jin, et al. "T cell receptor repertoire profiling predicts the prognosis of HBV-associated hepatocellular carcinoma." Cancer Medicine 7, no. 8 (2018): 3755–62. http://dx.doi.org/10.1002/cam4.1610.

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31

Bolotin, Dmitry A., Ilgar Z. Mamedov, Olga V. Britanova, et al. "Next generation sequencing for TCR repertoire profiling: Platform-specific features and correction algorithms." European Journal of Immunology 42, no. 11 (2012): 3073–83. http://dx.doi.org/10.1002/eji.201242517.

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32

Hogan, Sabrina A., Anaïs Courtier, Phil F. Cheng, et al. "Peripheral Blood TCR Repertoire Profiling May Facilitate Patient Stratification for Immunotherapy against Melanoma." Cancer Immunology Research 7, no. 1 (2018): 77–85. http://dx.doi.org/10.1158/2326-6066.cir-18-0136.

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33

Shukla, Navika D., Alexander F. M. Craig, Brian Sworder, et al. "Profiling T-Cell Receptor Diversity and Dynamics during Lymphoma Immunotherapy Using Cell-Free DNA (cfDNA)." Blood 136, Supplement 1 (2020): 49–50. http://dx.doi.org/10.1182/blood-2020-141655.

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Background: Characterization of T-cell receptor (TCR) diversity and dynamics is increasingly critical to understanding therapeutic immune responses targeting tumors. Current TCR profiling methods generally require invasive tissue biopsies that capture a single snapshot of immune activity or are limited by the sheer diversity of the circulating TCR repertoire. In theory, T-cells with the greatest turnover could best reflect pivotal immune dynamics from both circulating and tissue-derived compartments, including non-circulating tissue-resident memory T-cells (Trm). To noninvasively capture such

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34

Rosati, Elisa, Mikhail V. Pogorelyy, C. Marie Dowds, et al. "Identification of Disease-associated Traits and Clonotypes in the T Cell Receptor Repertoire of Monozygotic Twins Affected by Inflammatory Bowel Diseases." Journal of Crohn's and Colitis 14, no. 6 (2019): 778–90. http://dx.doi.org/10.1093/ecco-jcc/jjz179.

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Abstract Background and Aims Intestinal inflammation in inflammatory bowel diseases [IBD] is thought to be T cell mediated and therefore dependent on the interaction between the T cell receptor [TCR] and human leukocyte antigen [HLA] proteins expressed on antigen presenting cells. The collection of all TCRs in one individual, known as the TCR repertoire, is characterised by enormous diversity and inter-individual variability. It was shown that healthy monozygotic [MZ] twins are more similar in their TCR repertoire than unrelated individuals. Therefore MZ twins, concordant or discordant for IBD

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35

Chen, Si-Yi, Tao Yue, Qian Lei, and An-Yuan Guo. "TCRdb: a comprehensive database for T-cell receptor sequences with powerful search function." Nucleic Acids Research 49, no. D1 (2020): D468—D474. http://dx.doi.org/10.1093/nar/gkaa796.

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Abstract T cells and the T-cell receptor (TCR) repertoire play pivotal roles in immune response and immunotherapy. TCR sequencing (TCR-Seq) technology has enabled accurate profiling TCR repertoire and currently a large number of TCR-Seq data are available in public. Based on the urgent need to effectively re-use these data, we developed TCRdb, a comprehensive human TCR sequences database, by a uniform pipeline to characterize TCR sequences on TCR-Seq data. TCRdb contains more than 277 million highly reliable TCR sequences from over 8265 TCR-Seq samples across hundreds of tissues/clinical condi

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36

Skowronska, Magdalena, Monica M. Schaller, and Johanna A. Kremer Hovinga Strebel. "Profiling the Autoantibody Repertoire of Acquired Thrombotic Thrombocytopenic Purpura (aTTP) Patients By Single Cell Sorting and Deep Sequencing of Splenic B-Cells." Blood 126, no. 23 (2015): 108. http://dx.doi.org/10.1182/blood.v126.23.108.108.

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Abstract Introduction: Antibodies are the primary effector molecules in the humoral immune system. To create a diversity of receptors-antibodies B-cells undergo V(D)J gene recombination and somatic hypermutation. This allows the recognition of most of pathogens but also sometimes of self-antigen, which can lead to autoimmune diseases. Autoantibodies (Abs) neutralizing and/or accelerating the clearance of ADAMTS13 are present in nearly all acquired thrombotic thrombocytopenic purpura (aTTP) patients with severe ADAMTS13 activity (<5%). As increasing evidence points at the spleen as a major r

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37

Britanova, Olga V., Ekaterina V. Putintseva, Mikhail Shugay, et al. "Age-Related Decrease in TCR Repertoire Diversity Measured with Deep and Normalized Sequence Profiling." Journal of Immunology 192, no. 6 (2014): 2689–98. http://dx.doi.org/10.4049/jimmunol.1302064.

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38

Cowell, Lindsay G. "The Diagnostic, Prognostic, and Therapeutic Potential of Adaptive Immune Receptor Repertoire Profiling in Cancer." Cancer Research 80, no. 4 (2019): 643–54. http://dx.doi.org/10.1158/0008-5472.can-19-1457.

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39

Dombrovsky, A., L. Arthaud, T. N. Ledger, S. Tares, and A. Robichon. "Profiling the repertoire of phenotypes influenced by environmental cues that occur during asexual reproduction." Genome Research 19, no. 11 (2009): 2052–63. http://dx.doi.org/10.1101/gr.091611.109.

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40

Fortier, Marie-Hélène, Étienne Caron, Marie-Pierre Hardy, et al. "The MHC class I peptide repertoire is molded by the transcriptome." Journal of Experimental Medicine 205, no. 3 (2008): 595–610. http://dx.doi.org/10.1084/jem.20071985.

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Under steady-state conditions, major histocompatibility complex (MHC) I molecules are associated with self-peptides that are collectively referred to as the MHC class I peptide (MIP) repertoire. Very little is known about the genesis and molecular composition of the MIP repertoire. We developed a novel high-throughput mass spectrometry approach that yields an accurate definition of the nature and relative abundance of unlabeled peptides presented by MHC I molecules. We identified 189 and 196 MHC I–associated peptides from normal and neoplastic mouse thymocytes, respectively. By integrating our

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41

Bouslimani, Amina, Alexey V. Melnik, Zhenjiang Xu, et al. "Lifestyle chemistries from phones for individual profiling." Proceedings of the National Academy of Sciences 113, no. 48 (2016): E7645—E7654. http://dx.doi.org/10.1073/pnas.1610019113.

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Imagine a scenario where personal belongings such as pens, keys, phones, or handbags are found at an investigative site. It is often valuable to the investigative team that is trying to trace back the belongings to an individual to understand their personal habits, even when DNA evidence is also available. Here, we develop an approach to translate chemistries recovered from personal objects such as phones into a lifestyle sketch of the owner, using mass spectrometry and informatics approaches. Our results show that phones’ chemistries reflect a personalized lifestyle profile. The collective re

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Hassel, Jessica Cecile, Michael Flossdorf, Sonja Hänzelmann, et al. "Investigation of the immune infiltrate of melanoma metastases under immune checkpoint inhibition." Journal of Clinical Oncology 35, no. 15_suppl (2017): 9570. http://dx.doi.org/10.1200/jco.2017.35.15_suppl.9570.

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9570 Background: Tumor infiltrating lymphocytes (TIL) play a crucial role in the therapeutic impact of immune checkpoint blockers. Methods: We investigated metastases from 56 melanoma patients before and during treatment with immune checkpoint blockers (i) immunohistochemically, (ii) with TCR repertoire profiling and (iii) analysis of the transcriptome. The patients were treated with ipilimumab (n = 25) or pembrolizumab (n = 23) or ipilimumab/nivolumab (n = 7); half of them had a disease control, the other half progressed as best response to treatment. Results: In contrast to previous reports

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Gao, Shouguo, Zhijie Wu, Carrie Diamond, et al. "Single Cell RNA Sequencing and V(D)J Profiling of T-Cell Large Granular Lymphocytosis." Blood 132, Supplement 1 (2018): 2404. http://dx.doi.org/10.1182/blood-2018-99-115166.

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Abstract Introduction . T-cell large granular lymphocytosis (T-LGL) is a low grade lymphoproliferative disorder, often clinically manifest as bone marrow failure. Treatment with immunosuppressive therapies is effective, but the dominant clone may persist even in responding patients. The pathogenesis of T-LGL has not been fully elucidated. In this study, we performed single cell RNA sequencing (sc-RNA seq) and V(D)J profiling to discern clonotypes and gene expression patterns of T lymphocytes from T-LGL patients who were sampled before and after treatment. Methods. Blood was obtained from patie

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44

Breden, Felix. "486 iReceptor plus: a data integration platform to share, compare and analyze adaptive immune receptor repertoire (AIRR-seq) data from antibody/B- and T-cell repertoires." Journal for ImmunoTherapy of Cancer 8, Suppl 3 (2020): A522. http://dx.doi.org/10.1136/jitc-2020-sitc2020.0486.

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BackgroundOver the past few years, next-generation sequencing technologies have been developed to characterize ‘adaptive immune receptor repertoires’ (i.e., antibody/B-cell and T-cell receptor repertoires or AIRRs) in exquisite detail. AIRR sequencing (AIRR-seq) has enormous promise for understanding the dynamics of the immune repertoire in vaccinology, infectious diseases, autoimmunity, and cancer biology. While AIRR-seq data is important, it is also very large, complex, and requires specialized tools and services to curate, analyze, and share. In response to these challenges, The AIRR Commun

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45

Sherwood, Anna, Harlan Robins, Jonathan R. Fromm, et al. "Detection Of Recurrent/Persistent Disease By T-Cell Receptor Repertoire Profiling In Patients With Mature T-Cell Neoplasm." Blood 122, no. 21 (2013): 2614. http://dx.doi.org/10.1182/blood.v122.21.2614.2614.

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Abstract Identification of recurrent or persistent disease in T-cell neoplasms is important for individualized patient care. While patients with T-cell lineage lymphomas and leukemias are a small subset of all lymphoma and leukemia patients, the incidence of refractory disease in these patients can be higher than patients with B-cell lineage neoplasms. We recently developed a method to sequence the diversity of the TCR CDR3 rearrangements (Blood. 2009; 114(19): 4099-107) that exploits the capacity of high-throughput sequencing (HTS) to document the diverse repertoire of TCRB CDR3 chains simult

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46

Looney, Timothy, Jianping Zheng, Denise Topacio-Hall, Geoffrey Lowman, and Fiona Hyland. "Peripheral blood TCRB chain convergence and clonal expansion following cytomegalovirus infection: Implications for the biomarker use of TCR-seq." Journal of Clinical Oncology 37, no. 8_suppl (2019): 134. http://dx.doi.org/10.1200/jco.2019.37.8_suppl.134.

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134 Background: Human cytomegalovirus (CMV) is a common immune-evasive herpes family virus leading to lifelong asymptomatic infection in 50 to 80% of humans. The effect of CMV infection on the T cell repertoire may be relevant given interest in identifying T cell repertoire features predictive of response to checkpoint blockade immunotherapy (CPI) for cancer. Here we sought to identify features of CMV infection using TCRB profiling of peripheral blood (PBL) total RNA. Methods: Total RNA from PBL was obtained from 35 blood donors of known CMV status, then used for TCRB sequencing via the Oncomi

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47

Stalika, Evangelia, Anastasia Hadzidimitriou, Athanasios Gkoufas, et al. "High-Throughput Profiling of the T-Cell Receptor Gene Repertoire Supports Antigen Drive in the Pathogenesis of Chronic Idiopathic Neutropenia." Blood 124, no. 21 (2014): 2731. http://dx.doi.org/10.1182/blood.v124.21.2731.2731.

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Abstract Chronic idiopathic neutropenia (CIN) is an acquired disorder of granulopoiesis characterized by prolonged neutropenia, mainly affecting middle-age females of the HLA-DRB1*1302 type. The defective hematopoiesis in CIN can be mainly attributed to accelerated Fas-mediated death of the CD34+/CD33+ granulocytic progenitors, secondary to an inflammatory bone marrow (BM) microenvironment. Crucial to CIN pathogenesis are the increased numbers of activated T cells identified in both peripheral blood (PB) and BM of CIN patients, supporting an immune pathogenesis. Using Sanger sequencing, we pre

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Schmidt, W. M., M. Kalipciyan, E. Dornstauder, et al. "Gene expression profiling of colon cancer reveals a broad molecular repertoire in 5-fluorouracil resistance." Int. Journal of Clinical Pharmacology and Therapeutics 41, no. 12 (2003): 624–25. http://dx.doi.org/10.5414/cpp41624.

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Li, Dengrui, Guanju Gao, Zhihui Li, et al. "Profiling the T-cell receptor repertoire of patient with pleural tuberculosis by high-throughput sequencing." Immunology Letters 162, no. 1 (2014): 170–80. http://dx.doi.org/10.1016/j.imlet.2014.08.012.

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Spence, Allyson, Whitney Purtha, Janice Tam, et al. "Revealing the specificity of regulatory T cells in murine autoimmune diabetes." Proceedings of the National Academy of Sciences 115, no. 20 (2018): 5265–70. http://dx.doi.org/10.1073/pnas.1715590115.

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Abstract:

Regulatory T cells (Tregs) control organ-specific autoimmunity in a tissue antigen-specific manner, yet little is known about their specificity in a natural repertoire. In this study, we used the nonobese diabetic (NOD) mouse model of autoimmune diabetes to investigate the antigen specificity of Tregs present in the inflamed tissue, the islets of Langerhans. Compared with Tregs present in spleen and lymph node, Tregs in the islets showed evidence of antigen stimulation that correlated with higher proliferation and expression of activation markers CD103, ICOS, and TIGIT. T cell receptor (TCR) r

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