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M. Weerakoon-Ratnayake K, Vaidyanathan S, Larkey N, Dathathreya K, Hu M, Jose J, Mog S, August K, K. Godwin A, L. Hupert M, A. Witek M, A. Soper S. Microfluidic Device for On-Chip Immunophenotyping and Cytogenetic Analysis of Rare Biological Cells. Cells 2020; 9:E519. [PMID: 32102446 PMCID: PMC7072755 DOI: 10.3390/cells9020519] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/10/2020] [Accepted: 02/18/2020] [Indexed: 01/09/2023] Open
Abstract
The role of circulating plasma cells (CPCs) and circulating leukemic cells (CLCs) as biomarkers for several blood cancers, such as multiple myeloma and leukemia, respectively, have recently been reported. These markers can be attractive due to the minimally invasive nature of their acquisition through a blood draw (i.e., liquid biopsy), negating the need for painful bone marrow biopsies. CPCs or CLCs can be used for cellular/molecular analyses as well, such as immunophenotyping or fluorescence in situ hybridization (FISH). FISH, which is typically carried out on slides involving complex workflows, becomes problematic when operating on CLCs or CPCs due to their relatively modest numbers. Here, we present a microfluidic device for characterizing CPCs and CLCs using immunofluorescence or FISH that have been enriched from peripheral blood using a different microfluidic device. The microfluidic possessed an array of cross-channels (2-4 µm in depth and width) that interconnected a series of input and output fluidic channels. Placing a cover plate over the device formed microtraps, the size of which was defined by the width and depth of the cross-channels. This microfluidic chip allowed for automation of immunofluorescence and FISH, requiring the use of small volumes of reagents, such as antibodies and probes, as compared to slide-based immunophenotyping and FISH. In addition, the device could secure FISH results in <4 h compared to 2-3 days for conventional FISH.
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Affiliation(s)
- Kumuditha M. Weerakoon-Ratnayake
- Department of Chemistry, The University of Kansas, Lawrence, KS 66047, USA; (K.M.W.-R.); (K.D.); (S.M.)
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66045, USA; (S.V.); (N.L.); (M.H.); (J.J.)
| | - Swarnagowri Vaidyanathan
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66045, USA; (S.V.); (N.L.); (M.H.); (J.J.)
- Bioengineering, The University of Kansas, Lawrence, KS 66045, USA
| | - Nicholas Larkey
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66045, USA; (S.V.); (N.L.); (M.H.); (J.J.)
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA;
| | - Kavya Dathathreya
- Department of Chemistry, The University of Kansas, Lawrence, KS 66047, USA; (K.M.W.-R.); (K.D.); (S.M.)
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66045, USA; (S.V.); (N.L.); (M.H.); (J.J.)
| | - Mengjia Hu
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66045, USA; (S.V.); (N.L.); (M.H.); (J.J.)
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA;
| | - Jilsha Jose
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66045, USA; (S.V.); (N.L.); (M.H.); (J.J.)
| | - Shalee Mog
- Department of Chemistry, The University of Kansas, Lawrence, KS 66047, USA; (K.M.W.-R.); (K.D.); (S.M.)
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66045, USA; (S.V.); (N.L.); (M.H.); (J.J.)
| | - Keith August
- Children’s Mercy Hospital, Kansas City, MO 64108, USA;
| | - Andrew K. Godwin
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA;
| | - Mateusz L. Hupert
- Biofluidica Inc., BioFluidica Research Laboratory, Lawrence, KS 66047, USA
| | - Malgorzata A. Witek
- Department of Chemistry, The University of Kansas, Lawrence, KS 66047, USA; (K.M.W.-R.); (K.D.); (S.M.)
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66045, USA; (S.V.); (N.L.); (M.H.); (J.J.)
| | - Steven A. Soper
- Department of Chemistry, The University of Kansas, Lawrence, KS 66047, USA; (K.M.W.-R.); (K.D.); (S.M.)
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66045, USA; (S.V.); (N.L.); (M.H.); (J.J.)
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA;
- Biofluidica Inc., BioFluidica Research Laboratory, Lawrence, KS 66047, USA
- Department of Mechanical Engineering, The University of Kansas, Lawrence, KS 66045, USA
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Zhu W, He QY, Lu C, Fu CY, Zhou JH, Liu S, Tao YG, Xiao DS. Detection of immunoglobulin and T-cell receptor gene rearrangements in angioimmunoblastic T-cell lymphoma. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2018; 11:2642-2653. [PMID: 31938379 PMCID: PMC6958285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 02/12/2018] [Indexed: 06/10/2023]
Abstract
Objective: To assess the value of immunoglobulin and T-cell receptor gene rearrangements in the diagnosis and differential diagnosis of angioimmunoblastic T-cell lymphoma. Methods: We selected 55 cases of angioimmunoblastic T-cell lymphoma confirmed by histopathology and 15 cases of reactive lymph node hyperplasia. Using the IdentiClone gene rearrangement detection kit, BIOMED-2 primer system, and GeneScanning analysis, we tested for immunoglobulin and T-cell receptor gene rearrangements. Results: Among all 55 angioimmunoblastic T-cell lymphoma cases, 1 (2%) displayed the first type of angioimmunoblastic T-cell lymphoma, which has an intact lymphoid follicle structure. Five cases (9%) displayed the second type, which has an intact segmental lymphatic follicular structure. Forty-nine cases (89%) displayed the third type, which is characterized by a complete obliteration of the lymphatic follicular structure. Fifty-two cases (95%) had tumor cells that were positive for CD3, 50 cases (91%) were positive for CD4, 33 cases (60%) were positive for Bcl-6, 20 cases (36%) were positive for CD10, 44 cases (80%) were positive for CXCL13 to different degrees, and 53 cases (96%) showed a strong positive expression of CD21. Ki67 expression intensity was 30-80% in tumor T cells. Clonal gene rearrangements were identified in 48 of the 55 angioimmunoblastic T-cell lymphoma cases (87%), of which 30 (55%) displayed IG gene rearrangements, including IGHA (7 cases; 13%), IGHB (6 cases; 11%), IGHC (2 cases; 4%), IGKA (22 cases; 40%), IGKB (6 cases; 11%), and IGL (20 cases; 36%). TCR gene rearrangements were observed in 32 cases (58%), including TCRBA (6 cases; 11%), TCRBB (5 cases; 9%), TCRBC (10 cases; 18%), TCRD (7 cases; 13%), TCRGA (22 cases; 40%), and TCRGB (16 cases; 29%). IG and TCR gene rearrangements were concurrently observed in 14 cases (25%). Immunoglobulin or TCR clonal gene rearrangements were not detected in the 15 cases of reactive hyperplasia. Conclusions: Angioimmunoblastic T-cell lymphomas may be positive for immunoglobulin or T-cell receptor clone gene rearrangements or may express double rearrangements. The assessment of clonal gene rearrangements is valuable for the diagnosis and differential diagnosis of angioimmunoblastic T-cell lymphoma.
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Affiliation(s)
- Wei Zhu
- Department of Pathology, Xiangya Hospital, Central South UniversityChangsha, Hunan, China
- Cancer Research Institute, School of Basic Medicine, Central South UniversityChangsha, Hunan, China
| | - Qiu-Yan He
- Department of Pathology, Xiangya Hospital, Central South UniversityChangsha, Hunan, China
- Cancer Research Institute, School of Basic Medicine, Central South UniversityChangsha, Hunan, China
| | - Can Lu
- Department of Pathology, Xiangya Hospital, Central South UniversityChangsha, Hunan, China
- Cancer Research Institute, School of Basic Medicine, Central South UniversityChangsha, Hunan, China
| | - Chun-Yan Fu
- Department of Pathology, Xiangya Hospital, Central South UniversityChangsha, Hunan, China
- Cancer Research Institute, School of Basic Medicine, Central South UniversityChangsha, Hunan, China
| | - Jian-Hua Zhou
- Department of Pathology, Xiangya Hospital, Central South UniversityChangsha, Hunan, China
- Cancer Research Institute, School of Basic Medicine, Central South UniversityChangsha, Hunan, China
| | - Shuang Liu
- Department of Pathology, School of Basic Medicine, Central South UniversityChangsha, Hunan, China
| | - Yong-Guang Tao
- Center for Medicine Research, Xiangya Hospital, Central South UniversityChangsha, Hunan, China
- Department of Pathology, School of Basic Medicine, Central South UniversityChangsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion (Central South University), Ministry of EducationHunan, China
- Key Laboratory of Carcinogenesis (Central South University), Ministry of HealthHunan, China
| | - De-Sheng Xiao
- Department of Pathology, Xiangya Hospital, Central South UniversityChangsha, Hunan, China
- Cancer Research Institute, School of Basic Medicine, Central South UniversityChangsha, Hunan, China
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3
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Jensen-Jarolim E, Bax HJ, Bianchini R, Crescioli S, Daniels-Wells TR, Dombrowicz D, Fiebiger E, Gould HJ, Irshad S, Janda J, Josephs DH, Levi-Schaffer F, O'Mahony L, Pellizzari G, Penichet ML, Redegeld F, Roth-Walter F, Singer J, Untersmayr E, Vangelista L, Karagiannis SN. AllergoOncology: Opposite outcomes of immune tolerance in allergy and cancer. Allergy 2018; 73:328-340. [PMID: 28921585 PMCID: PMC6038916 DOI: 10.1111/all.13311] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2017] [Indexed: 12/11/2022]
Abstract
While desired for the cure of allergy, regulatory immune cell subsets and nonclassical Th2-biased inflammatory mediators in the tumour microenvironment can contribute to immune suppression and escape of tumours from immunological detection and clearance. A key aim in the cancer field is therefore to design interventions that can break immunological tolerance and halt cancer progression, whereas on the contrary allergen immunotherapy exactly aims to induce tolerance. In this position paper, we review insights on immune tolerance derived from allergy and from cancer inflammation, focusing on what is known about the roles of key immune cells and mediators. We propose that research in the field of AllergoOncology that aims to delineate these immunological mechanisms with juxtaposed clinical consequences in allergy and cancer may point to novel avenues for therapeutic interventions that stand to benefit both disciplines.
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Affiliation(s)
- E Jensen-Jarolim
- The Interuniversity Messerli Research Institute, University of Veterinary Medicine Vienna, Medical University Vienna, University Vienna, Vienna, Austria
- Centre of Pathophysiology, Infectiology & Immunology, Institute of Pathophysiology & Allergy Research, Medical University Vienna, Vienna, Austria
| | - H J Bax
- St. John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
- School of Cancer & Pharmaceutical Sciences, King's College London, Guy's Hospital, London, UK
| | - R Bianchini
- The Interuniversity Messerli Research Institute, University of Veterinary Medicine Vienna, Medical University Vienna, University Vienna, Vienna, Austria
| | - S Crescioli
- St. John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - T R Daniels-Wells
- Division of Surgical Oncology, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - D Dombrowicz
- INSERM, CHU Lille, European Genomic Institute of Diabetes, Institut Pasteur de Lille, U1011 - Recepteurs Nucleaires, Maladies Cardiovasculaires et Diabete, Universite de Lille, Lille, France
| | - E Fiebiger
- Division of Gastroenterology, Hepatology and Nutrition Research, Department Medicine Research, Childrens' University Hospital Boston, Boston, MA, USA
| | - H J Gould
- Randall Division of Cell and Molecular Biophysics, King's College London, London, UK
| | - S Irshad
- St. John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
- Breast Cancer Now Unit, School of Cancer & Pharmaceutical Sciences, King's College London, Guy's Cancer Centre, London, UK
| | - J Janda
- Faculty of Science, Charles University, Prague, Czech Republic
| | - D H Josephs
- St. John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
- School of Cancer & Pharmaceutical Sciences, King's College London, Guy's Hospital, London, UK
| | - F Levi-Schaffer
- Faculty of Medicine, Pharmacology and Experimental Therapeutics Unit, The Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - L O'Mahony
- Molecular Immunology, Swiss Institute of Allergy and Asthma Research, Davos, Switzerland
| | - G Pellizzari
- St. John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
- School of Cancer & Pharmaceutical Sciences, King's College London, Guy's Hospital, London, UK
| | - M L Penichet
- Division of Surgical Oncology, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, CA, USA
| | - F Redegeld
- Faculty of Science, Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
| | - F Roth-Walter
- The Interuniversity Messerli Research Institute, University of Veterinary Medicine Vienna, Medical University Vienna, University Vienna, Vienna, Austria
- Centre of Pathophysiology, Infectiology & Immunology, Institute of Pathophysiology & Allergy Research, Medical University Vienna, Vienna, Austria
| | - J Singer
- Centre of Pathophysiology, Infectiology & Immunology, Institute of Pathophysiology & Allergy Research, Medical University Vienna, Vienna, Austria
| | - E Untersmayr
- Centre of Pathophysiology, Infectiology & Immunology, Institute of Pathophysiology & Allergy Research, Medical University Vienna, Vienna, Austria
| | - L Vangelista
- Department of Biomedical Sciences, Nazarbayev University School of Medicine, Astana, Kazakhstan
| | - S N Karagiannis
- St. John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
- Breast Cancer Now Unit, School of Cancer & Pharmaceutical Sciences, King's College London, Guy's Cancer Centre, London, UK
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Ward C, Rettig TA, Hlavacek S, Bye BA, Pecaut MJ, Chapes SK. Effects of spaceflight on the immunoglobulin repertoire of unimmunized C57BL/6 mice. LIFE SCIENCES IN SPACE RESEARCH 2018; 16:63-75. [PMID: 29475521 PMCID: PMC5826609 DOI: 10.1016/j.lssr.2017.11.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 11/20/2017] [Accepted: 11/27/2017] [Indexed: 05/25/2023]
Abstract
Spaceflight has been shown to suppress the adaptive immune response, altering the distribution and function of lymphocyte populations. B lymphocytes express highly specific and highly diversified receptors, known as immunoglobulins (Ig), that directly bind and neutralize pathogens. Ig diversity is achieved through the enzymatic splicing of gene segments within the genomic DNA of each B cell in a host. The collection of Ig specificities within a host, or Ig repertoire, has been increasingly characterized in both basic research and clinical settings using high-throughput sequencing technology (HTS). We utilized HTS to test the hypothesis that spaceflight affects the B-cell repertoire. To test this hypothesis, we characterized the impact of spaceflight on the unimmunized Ig repertoire of C57BL/6 mice that were flown aboard the International Space Station (ISS) during the Rodent Research One validation flight in comparison to ground controls. Individual gene segment usage was similar between ground control and flight animals, however, gene segment combinations and the junctions in which gene segments combine was varied among animals within and between treatment groups. We also found that spontaneous somatic mutations in the IgH and Igκ gene loci were not increased. These data suggest that space flight did not affect the B cell repertoire of mice flown and housed on the ISS over a short period of time.
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Affiliation(s)
- Claire Ward
- Division of Biology, Kansas State University, 1717 Claflin Rd, 116 Ackert Hall, Manhattan, KS 66502, United States
| | - Trisha A Rettig
- Division of Biology, Kansas State University, 1717 Claflin Rd, 116 Ackert Hall, Manhattan, KS 66502, United States
| | - Savannah Hlavacek
- Division of Biology, Kansas State University, 1717 Claflin Rd, 116 Ackert Hall, Manhattan, KS 66502, United States
| | - Bailey A Bye
- Division of Biology, Kansas State University, 1717 Claflin Rd, 116 Ackert Hall, Manhattan, KS 66502, United States
| | - Michael J Pecaut
- Department of Basic Sciences, Division of Radiation Research, Loma Linda University, 11021 Campus St. Rm 101, Loma Linda, CA 92350, United States
| | - Stephen K Chapes
- Division of Biology, Kansas State University, 1717 Claflin Rd, 116 Ackert Hall, Manhattan, KS 66502, United States.
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Bozekowski JD, Graham AJ, Daugherty PS. High-titer antibody depletion enhances discovery of diverse serum antibody specificities. J Immunol Methods 2018; 455:1-9. [PMID: 29360471 DOI: 10.1016/j.jim.2018.01.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 12/26/2017] [Accepted: 01/16/2018] [Indexed: 12/15/2022]
Abstract
The human antibody repertoire is a unique repository of information regarding infection, inflammation, and autoimmunity of the past, present, and future. However, antibodies can span vast ranges of concentrations with varying affinities and the repertoire is often heavily polarized by a few species. These complexities lead to difficulties detecting and characterizing low abundance antibody species that may be relevant to disease. We therefore developed a method to selectively remove antibodies from a sample in proportion to the titer of the species prior to analysis, referred to as high-titer depletion (HTD). Peptides from a large random peptide display library were enriched towards binding high-titer antibody species and utilized as binding reagents to deplete the corresponding species from the specimen. HTD enabled the discovery of antibody binding specificities using random peptide library screening with reduced cross-reactivity and background signal and improved coverage of low abundance species. With HTD, three monoclonal antibody species were detected at concentrations at least an order of magnitude lower than without HTD. Additionally, 92 serum antibody specificities were readily discovered from an individual specimen using HTD compared to only 25 specificities without HTD. Parameters affecting the extent of depletion such as the concentration of depleted serum were also adjusted to reproducibly improve the coverage of antibody specificities. These results demonstrate that HTD could be employed for the discovery of rare specificities related to disease and enable extensive characterization of the antibody repertoire. Moreover, the strategy of depletion in proportion to titer could be extended to other applications with complex biological samples to improve discovery.
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Affiliation(s)
- Joel D Bozekowski
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Austin J Graham
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Patrick S Daugherty
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA..
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6
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The value of detecting immunoglobulin gene rearrangements in the diagnosis of B-cell lymphoma. Oncotarget 2017; 8:77009-77019. [PMID: 29100365 PMCID: PMC5652759 DOI: 10.18632/oncotarget.20330] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 06/29/2017] [Indexed: 11/28/2022] Open
Abstract
Objective To discuss the clinical value of immunoglobulin gene rearrangements in the diagnosis of B-cell lymphoma. Methods A total of 209 cases of B-cell lymphomas and 35 cases of reactive lymphoid hyperplasia were selected for DNA extraction and PCR amplification using the BIOMED-2 primer system. Gel electrophoresis of heteroduplexes was used to analyze immunoglobulin gene rearrangements. Results A total of 209 cases of B-cell lymphoma, including 69 extranodal marginal zone B-cell lymphomas of mucosa-associated lymphoid tissue, 63 diffuse large B-cell lymphomas, 39 follicular lymphomas, 15 small lymphocytic lymphomas, 6 plasmacytomas, 6 mantle cell lymphomas, 7 nodal marginal zone B-cell lymphomas, and 4 lymphoplasmacytoid lymphomas, were examined. Immunoglobulin gene rearrangements were found in all 209 cases, with 93 IGHA, 122 IGHB, 98 IGHC, 167 IGK, 100 IGL, 167 IGHA/B/C, 204 IGH/IGK, 209 IGH/IGK/IGL, 129 IGH+IGK, 81 IGH+IGL, 83 IGK+IGL and 68 IGH+IGK+IGL gene rearrangements. Immunoglobulin gene rearrangements were not found in the 35 cases of reactive lymphoid hyperplasia. IGH and IGK gene rearrangements were mainly found in mantle cell lymphomas, small lymphocytic lymphomas, extranodal marginal zone B-cell lymphomas of mucosa-associated lymphoid tissue and diffuse large B-cell lymphomas. The IGH gene rearrangement was mainly found in lymphoplasmacytoid lymphomas and follicular lymphomas. IGK and IGL gene rearrangements were mainly found in plasmocytoma, and the IGK gene rearrangement was mainly found in nodal marginal zone B-cell lymphomas. Conclusions The BIOMED-2 standardized immunoglobulin gene rearrangement detection system is an important tool in B-cell lymphoma diagnosis. Analysis of IGH, IGK and IGL gene rearrangements is valuable in confirming the classification of B-cell NHL.
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7
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Wu GC, Cheung NKV, Georgiou G, Marcotte EM, Ippolito GC. Temporal stability and molecular persistence of the bone marrow plasma cell antibody repertoire. Nat Commun 2016; 7:13838. [PMID: 28000661 PMCID: PMC5187582 DOI: 10.1038/ncomms13838] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 11/04/2016] [Indexed: 12/15/2022] Open
Abstract
Plasma cells in human bone marrow (BM) are thought to be responsible for sustaining lifelong immunity, but its underlying basis is controversial. Here we use high-throughput sequence analysis of the same individual across 6.5 years to show that the BM plasma cell immunoglobulin heavy chain repertoire is remarkably stable over time. We find a nearly static bias in individual and combinatorial gene usage across time. Analysis of a second donor corroborates these observations. We also report the persistence of numerous BM plasma cell clonotypes (∼2%) identifiable at all points assayed across 6.5 years, supporting a model of serological memory based upon intrinsic longevity of human plasma cells. Donors were adolescents who completely recovered from neuroblastoma prior to the start of this study. Our work will facilitate differentiation between healthy and diseased antibody repertoires, by serving as a point of comparison with future deep-sequencing studies involving immune intervention.
Longevity of antibody responses has been attributed to persistence of plasma cells in mice. Here the authors provide human data in support of this model by immunoglobulin sequencing bone marrow sections from two human donors over 6.5 years to show temporal stability of plasma cell clonotypes, but not other B cells.
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Affiliation(s)
- Gabriel C Wu
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Nai-Kong V Cheung
- Department of Pediatrics, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - George Georgiou
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA.,Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, USA.,Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, USA.,Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Edward M Marcotte
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, USA.,Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA.,Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Gregory C Ippolito
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
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Turchaninova MA, Davydov A, Britanova OV, Shugay M, Bikos V, Egorov ES, Kirgizova VI, Merzlyak EM, Staroverov DB, Bolotin DA, Mamedov IZ, Izraelson M, Logacheva MD, Kladova O, Plevova K, Pospisilova S, Chudakov DM. High-quality full-length immunoglobulin profiling with unique molecular barcoding. Nat Protoc 2016; 11:1599-616. [DOI: 10.1038/nprot.2016.093] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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9
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Robust estimates of overall immune-repertoire diversity from high-throughput measurements on samples. Nat Commun 2016; 7:11881. [PMID: 27302887 PMCID: PMC4912625 DOI: 10.1038/ncomms11881] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 05/09/2016] [Indexed: 01/10/2023] Open
Abstract
The diversity of an organism's B- and T-cell repertoires is both clinically important and a key measure of immunological complexity. However, diversity is hard to estimate by current methods, because of inherent uncertainty in the number of B- and T-cell clones that will be missing from a blood or tissue sample by chance (the missing-species problem), inevitable sampling bias, and experimental noise. To solve this problem, we developed Recon, a modified maximum-likelihood method that outputs the overall diversity of a repertoire from measurements on a sample. Recon outputs accurate, robust estimates by any of a vast set of complementary diversity measures, including species richness and entropy, at fractional repertoire coverage. It also outputs error bars and power tables, allowing robust comparisons of diversity between individuals and over time. We apply Recon to in silico and experimental immune-repertoire sequencing data sets as proof of principle for measuring diversity in large, complex systems. Diversity of an organism's B- and T-cell repertoires is clinically important, but difficult to estimate due to uncertainty in the number of clones in a sample, sampling bias and experimental noise. Here Kaplinsky and Arnaout present Recon, a method that reconstructs the distribution of the overall repertoire from sample measurements.
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10
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Cowan G, Weston-Bell NJ, Bryant D, Seckinger A, Hose D, Zojer N, Sahota SS. Massive parallel IGHV gene sequencing reveals a germinal center pathway in origins of human multiple myeloma. Oncotarget 2015; 6:13229-40. [PMID: 25929340 PMCID: PMC4537010 DOI: 10.18632/oncotarget.3644] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 03/24/2015] [Indexed: 12/14/2022] Open
Abstract
Human multiple myeloma (MM) is characterized by accumulation of malignant terminally differentiated plasma cells (PCs) in the bone marrow (BM), raising the question when during maturation neoplastic transformation begins. Immunoglobulin IGHV genes carry imprints of clonal tumor history, delineating somatic hypermutation (SHM) events that generally occur in the germinal center (GC). Here, we examine MM-derived IGHV genes using massive parallel deep sequencing, comparing them with profiles in normal BM PCs. In 4/4 presentation IgG MM, monoclonal tumor-derived IGHV sequences revealed significant evidence for intraclonal variation (ICV) in mutation patterns. IGHV sequences of 2/2 normal PC IgG populations revealed dominant oligoclonal expansions, each expansion also displaying mutational ICV. Clonal expansions in MM and in normal BM PCs reveal common IGHV features. In such MM, the data fit a model of tumor origins in which neoplastic transformation is initiated in a GC B-cell committed to terminal differentiation but still targeted by on-going SHM. Strikingly, the data parallel IGHV clonal sequences in some monoclonal gammopathy of undetermined significance (MGUS) known to display on-going SHM imprints. Since MGUS generally precedes MM, these data suggest origins of MGUS and MM with IGHV gene mutational ICV from the same GC B-cell, arising via a distinctive pathway.
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Affiliation(s)
- Graeme Cowan
- Institute of Immunology and Infection Research, Centre for Immunity, Infection and Evolution, University of Edinburgh, UK
| | - Nicola J. Weston-Bell
- Tumour Immunogenetics Group, Cancer Sciences Academic Unit, Faculty of Medicine, University of Southampton, UK
| | - Dean Bryant
- Tumour Immunogenetics Group, Cancer Sciences Academic Unit, Faculty of Medicine, University of Southampton, UK
| | - Anja Seckinger
- Medizinische Klinik V, Universitätsklinikum Heidelberg, Heidelberg, Germany
| | - Dirk Hose
- Medizinische Klinik V, Universitätsklinikum Heidelberg, Heidelberg, Germany
| | - Niklas Zojer
- Center for Oncology and Hematology, 1st Department of Medicine, Wilhelminenspital, Vienna, Austria
| | - Surinder S. Sahota
- Tumour Immunogenetics Group, Cancer Sciences Academic Unit, Faculty of Medicine, University of Southampton, UK
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11
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Abstract
The B cell receptor (BCR) repertoire is highly diverse. Repertoire diversity is achieved centrally by somatic recombination of immunoglobulin (Ig) genes and peripherally by somatic hypermutation and Ig heavy chain class-switching. Throughout these processes, there is selection for functional gene rearrangements, selection against gene combinations resulting in self-reactive BCRs, and selection for BCRs with high affinity for exogenous antigens after challenge. Hence, investigation of BCR repertoires from different groups of B cells can provide information on stages of B cell development and shed light on the etiology of B cell pathologies. In most instances, the third complementarity determining region of the Ig heavy chain (CDR-H3) contributes the majority of amino acids to the antibody/antigen binding interface. Although CDR-H3 spectratype analysis provides information on the overall diversity of BCR repertoires, this fairly simple technique analyzes the relative quantities of CDR-H3 regions of each size, within a range of approximately 10-80 bp, without sequence detail and thus is limited in scope. High-throughput sequencing (HTS) techniques on the Roche 454 GS FLX Titanium system, however, can generate a wide coverage of Ig sequences to provide more qualitative data such as V, D, and J usage as well as detailed CDR3 sequence information. Here we present protocols in detail for CDR-H3 spectratype analysis and HTS of human BCR repertoires.
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Affiliation(s)
- Yu-Chang Wu
- Randall Division of Cell and Molecular Biophysics, King's College London School of Biomedical Science, London, UK
| | - David Kipling
- Department of Pathology, Cardiff University, Cardiff, UK
| | - Deborah Dunn-Walters
- Department of Immunobiology, King's College London School of Medicine, Strand, London, SE1 9RT, UK.
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12
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Lavinder JJ, Horton AP, Georgiou G, Ippolito GC. Next-generation sequencing and protein mass spectrometry for the comprehensive analysis of human cellular and serum antibody repertoires. Curr Opin Chem Biol 2014; 24:112-20. [PMID: 25461729 DOI: 10.1016/j.cbpa.2014.11.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 11/08/2014] [Accepted: 11/10/2014] [Indexed: 12/19/2022]
Abstract
Recent developments of high-throughput technologies are enabling the molecular-level analysis and bioinformatic mining of antibody-mediated (humoral) immunity in humans at an unprecedented level. These approaches explore either the sequence space of B-cell receptor repertoires using next-generation deep sequencing (BCR-seq), or the amino acid identities of antibody in blood using protein mass spectrometry (Ig-seq), or both. Generalizable principles about the molecular composition of the protective humoral immune response are being defined, and as such, the field could supersede traditional methods for the development of diagnostics, vaccines, and antibody therapeutics. Three key challenges remain and have driven recent advances: (1) incorporation of innovative techniques for paired BCR-seq to ascertain the complete antibody variable-domain VH:VL clonotype, (2) integration of proteomic Ig-seq with BCR-seq to reveal how the serum antibody repertoire compares with the antibody repertoire encoded by circulating B cells, and (3) a demand to link antibody sequence data to functional meaning (binding and protection).
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Affiliation(s)
- Jason J Lavinder
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712-1062, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712-1062, USA
| | - Andrew P Horton
- Center for Systems & Synthetic Biology, University of Texas at Austin, Austin, TX 78712-1062, USA; Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712-1062, USA
| | - George Georgiou
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712-1062, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712-1062, USA; Center for Systems & Synthetic Biology, University of Texas at Austin, Austin, TX 78712-1062, USA; Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712-1062, USA; Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712-1062, USA
| | - Gregory C Ippolito
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712-1062, USA.
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13
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DHH-RHEBL1 fusion transcript: a novel recurrent feature in the new landscape of pediatric CBFA2T3-GLIS2-positive acute myeloid leukemia. Oncotarget 2014; 4:1712-20. [PMID: 24127550 PMCID: PMC3858557 DOI: 10.18632/oncotarget.1280] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Childhood Acute Myeloid Leukemia (AML) is a clinically and genetically heterogeneous malignant disease. Despite improvements in outcome over the past decades, the current survival rate still is approximately 60-70%. Cytogenetic, recurrent genetic abnormalities and early response to induction treatment are the main factors predicting clinical outcome. While the majority of children carry recurrent chromosomal translocations, 20% of patients do not show any recognizable cytogenetic alteration and are defined to have cytogenetically normal AML (CN-AML). This subset of patients is characterized by a significant heterogeneity in clinical outcome, which is influenced by factors only recently started to be identified. In this respect, genome-wide analyses have been used with the aim of defining the full array of genetic lesions in CN-AML. Recently, through whole-transcriptome massively parallel sequencing of seven cases of pediatric CN-AML, we identified a novel recurrent CBFA2T3-GLIS2 fusion, predicting poorer outcome. However, since the expression of CBFA2T3-GLIS2 fusion in mice is not sufficient for leukemogenesis, we speculated that further unknown abnormalities could contribute to both cancer transformation and response to treatment. Thus, we analyzed, by whole-transcriptome sequencing, 4 CBFA2T3-GLIS2-positive patients, as well as 4 CN-AML patients. We identified a new fusion transcript in the CBFA2T3-GLIS2 -positive patients, involving Desert Hedgehog (DHH), a member of Hedgehog family, and Ras Homologue Enrich in Brain Like 1 (RHEBL1), a gene coding for a small GTPase of the Ras family. Through the screening of a validation cohort of 55 additional pediatric AML patients, we globally detected DHH-RHEBL1 fusion in 8 out of 20 (40%) CBFA2T3-GLIS2- rearranged patients. Gene expression analysis performed on RNA-seq data revealed that DHH-RHEBL1 –positive patients exhibited a specific signature. These 8 patients had an 8-year overall survival worse than that of the remaining 12 CBFA2T3-GLIS2- rearranged patients not harboring DHH-RHEBL1 fusion (25% vs 55%, respectively, P =0.1). Taken together, these findings are unprecedented and indicate that the DHH-RHEBL1 fusion transcript is a novel recurrent feature in the changing landscape of CBFA2T3-GLIS2 -positive childhood AML. Moreover, it could be instrumental in the identification of a subgroup of CBFA2T3-GLIS2 -positive patients with a very poor outcome.
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14
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The promise and challenge of high-throughput sequencing of the antibody repertoire. Nat Biotechnol 2014; 32:158-68. [PMID: 24441474 PMCID: PMC4113560 DOI: 10.1038/nbt.2782] [Citation(s) in RCA: 471] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 12/04/2013] [Indexed: 12/16/2022]
Abstract
Georgiou and colleagues discuss rapidly evolving methods for high-throughput sequencing of the antibody repertoire, and how the resulting data may be applied to answer basic and translational research questions. Efforts to determine the antibody repertoire encoded by B cells in the blood or lymphoid organs using high-throughput DNA sequencing technologies have been advancing at an extremely rapid pace and are transforming our understanding of humoral immune responses. Information gained from high-throughput DNA sequencing of immunoglobulin genes (Ig-seq) can be applied to detect B-cell malignancies with high sensitivity, to discover antibodies specific for antigens of interest, to guide vaccine development and to understand autoimmunity. Rapid progress in the development of experimental protocols and informatics analysis tools is helping to reduce sequencing artifacts, to achieve more precise quantification of clonal diversity and to extract the most pertinent biological information. That said, broader application of Ig-seq, especially in clinical settings, will require the development of a standardized experimental design framework that will enable the sharing and meta-analysis of sequencing data generated by different laboratories.
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15
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Tschumper RC, Dispenzieri A, Abraham RS, Henderson KJ, Jelinek DF. Molecular analysis of immunoglobulin genes reveals frequent clonal relatedness in double monoclonal gammopathies. Blood Cancer J 2013; 3:e112. [PMID: 23599024 PMCID: PMC3641320 DOI: 10.1038/bcj.2013.12] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Monoclonal gammopathies (MGs) are hematological diseases characterized by high levels of a monoclonal immunoglobulin (Ig) or M-protein. Within this group are patients with more than one M-protein, referred to as double MGs (DMGs). The M-proteins in DMG patients may have different heavy chain (HC) isotypes that are associated with different light chains (LCs), or different HCs that are LC matched. In this study, we examined the clonal relatedness of the M-proteins in the latter type in a cohort of 14 DMG patients. By using PCR, we identified 7/14 DMG patients that expressed two Ig HC isotypes with identical Ig HC variable (IGHV), diversity (IGHD), joining (IGHJ), and complementarity determining region (HCDR3) sequences. Two additional DMG patients had two Ig transcripts using the same IGHV, IGHD and IGHJ genes but with slight differences in variable region or HCDR3 mutations. LC analysis confirmed that a single LC was expressed in 3/7 DMG patients with identical HC transcripts and in the two DMGs with highly similar transcripts. The PCR findings were confirmed by immunofluorescence for HC and LC expression. Clonally related HC-dissimilar/LC-matched DMGs may occur often and defines a new subtype of MG that may serve as a tool for studies of disease pathogenesis.
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Affiliation(s)
- R C Tschumper
- Department of Immunology, Mayo Clinic, Rochester, MN, USA
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16
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Larsen PA, Smith TPL. Application of circular consensus sequencing and network analysis to characterize the bovine IgG repertoire. BMC Immunol 2012; 13:52. [PMID: 22978666 PMCID: PMC3500647 DOI: 10.1186/1471-2172-13-52] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 09/04/2012] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Vertebrate immune systems generate diverse repertoires of antibodies capable of mediating response to a variety of antigens. Next generation sequencing methods provide unique approaches to a number of immuno-based research areas including antibody discovery and engineering, disease surveillance, and host immune response to vaccines. In particular, single-molecule circular consensus sequencing permits the sequencing of antibody repertoires at previously unattainable depths of coverage and accuracy. We approached the bovine immunoglobulin G (IgG) repertoire with the objective of characterizing diversity of expressed IgG transcripts. Here we present single-molecule real-time sequencing data of expressed IgG heavy-chain repertoires of four individual cattle. We describe the diversity observed within antigen binding regions and visualize this diversity using a network-based approach. RESULTS We generated 49,945 high quality cDNA sequences, each spanning the entire IgG variable region from four Bos taurus calves. From these sequences we identified 49,521 antigen binding regions using the automated Paratome web server. Approximately 9% of all unique complementarity determining 2 (CDR2) sequences were of variable lengths. A bimodal distribution of unique CDR3 sequence lengths was observed, with common lengths of 5-6 and 21-25 amino acids. The average number of cysteine residues in CDR3s increased with CDR3 length and we observed that cysteine residues were centrally located in CDR3s. We identified 19 extremely long CDR3 sequences (up to 62 amino acids in length) within IgG transcripts. Network analyses revealed distinct patterns among the expressed IgG antigen binding repertoires of the examined individuals. CONCLUSIONS We utilized circular consensus sequencing technology to provide baseline data of the expressed bovine IgG repertoire that can be used for future studies important to livestock research. Somatic mutation resulting in base insertions and deletions in CDR2 further diversifies the bovine antibody repertoire. In contrast to previous studies, our data indicate that unusually long CDR3 sequences are not unique to IgM antibodies in cattle. Centrally located cysteine residues in bovine CDR3s provide further evidence that disulfide bond formation is likely of structural importance. We hypothesize that network or cluster-based analyses of expressed antibody repertoires from controlled challenge experiments will help identify novel natural antigen binding solutions to specific pathogens of interest.
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Affiliation(s)
- Peter A Larsen
- Genetics and Breeding Unit, United States Meat Animal Research Center, ARS, USDA, Clay Center, NE, USA
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