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  • 1
    In: Blood, American Society of Hematology, Vol. 128, No. 22 ( 2016-12-02), p. 4365-4365
    Abstract: Immunoglobulins (Igs) are crucial for the defense against pathogens, but they are also important in many clinical and biotechnological applications. Their characteristics, and ultimately their function, depend on their three-dimensional (3D) structure; however, the procedures to experimentally determine it are extremely laborious and demanding. Hence, the ability to gain insight into the structure of Igs at large relies on the availability of tools and algorithms for producing accurate Ig structural models based on their primary sequence alone. These models can then be used to determine structural and eventually functional similarities between different Igs. An example of such a task is the clustering of Igs based on their structure to determine meaningful common features such as the possible existence of common molecular targets (antigens). Several approaches have been proposed in order to achieve an optimal solution to this task yet their results were hindered mainly due to the lack of efficient clustering methods based on the similarity of 3D structure descriptors. Here, we present a novel workflow for robust Ig 3D modeling and automated clustering. We validated our protocol in chronic lymphocytic leukemia (CLL), where the clonotypic Igs are critically implicated in the disease ontogeny and evolution. Indeed, immunogenetic studies on the clonotypic Igs have strongly implicated antigen selection in the pathogenesis of CLL, while also providing robust prognostic information. In the present study, we used the structure prediction tools PIGS and I-TASSER for creating the 3D models and the TM-align algorithm to superpose them. The innovation of the current methodology resides in the usage of methods adapted from 3D content-based search methodologies to determine the local structural similarity between the 3D models. The Fast Point Feature Histograms descriptors derived from the structurally aligned parts are used to compute a distance matrix, which is then used as input for the clustering procedure. Clustering analysis on the data is performed through the application of the agglomerative and density-based clustering approaches. The first method is unsupervised whereas the second belongs to the semi-supervised type, i.e. requires a predefined number of clusters. To evaluate the quality of the herein described workflow, we performed a supervised analysis of 125 Ig 3D models originating from 5 CLL stereotyped subsets i.e. subgroups sharing (quasi) identical IGs, namely subsets #1, #2, #4, #6, #8. The reasoning behind this choice was that (i) homologous Ig primary sequences can be reasonably anticipated to be reflected in overall similar 3D structures, hence providing a reference for evaluating the developed workflow; and, (ii) these subsets are well characterized at both the clinical and biological levels. Subset size distribution was as follows: subset #1 (IGHV clan I/IGKV1(D)-39), n=37; subset #2 (IGHV3-21/IGLV3-21), n=43; subset #4 (IGHV4-34/IGKV2-30), n=22; subset #6 (IGHV1-69/IGKV3-20), n=12; and, subset #8 (IGHV4-39/IGKV1(D)-39), n=11. Overall, we obtained a high level of clustering accuracy i.e. Ig 3D model clusters matched to a very high degree the subsets defined by Ig primary sequence similarity. In detail, 5 Ig 3D model clusters were produced by: (i) cluster 1 containing 37/37 (100%) subset #1 models and one (8.3%) subset #6 model, (ii) cluster 2 containing 43/43 (100%) subset #2 models, (iii) cluster 3 containing 21/22 (95.5%) subset #4 models, (iv) cluster 4 containing 11/12 (91.7%) #6 models, and, (v) cluster 5 containing 11/11 (100%) subset #8 models along with a single (4.5%) subset #4 model (subsets #4 and #8 concern IgG CLL, in itself a rarity for CLL). These findings support that the innovative workflow described here enables robust clustering of 3D models produced from Ig sequences from patients with CLL. Furthermore, they indicate that CLL classification based on stereotypy of Ig primary sequences is likely also verified at the Ig 3D structural level. Studies are ongoing for both addressing the minor discrepancies observed here and producing the unsupervised 3D clustering of the IGs from a large series of both stereotyped and non-stereotyped CLL cases. Disclosures Rosenquist: Gilead Sciences: Speakers Bureau. Stamatopoulos:Gilead: Consultancy, Honoraria, Research Funding; Abbvie: Honoraria, Other: Travel expenses; Janssen: Honoraria, Other: Travel expenses, Research Funding; Novartis: Honoraria, Research Funding.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2016
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  • 2
    In: The Journal of Pathology, Wiley, Vol. 247, No. 4 ( 2019-04), p. 416-421
    Abstract: The B cell receptor immunoglobulin (Ig) gene repertoires of marginal zone (MZ) lymphoproliferations were analyzed in order to obtain insight into their ontogenetic relationships. Our cohort included cases with MZ lymphomas ( n = 488), i.e. splenic (SMZL), nodal (NMZL) and extranodal (ENMZL), as well as provisional entities ( n = 76), according to the WHO classification. The most striking Ig gene repertoire skewing was observed in SMZL. However, restrictions were also identified in all other MZ lymphomas studied, particularly ENMZL, with significantly different Ig gene distributions depending on the primary site of involvement. Cross‐entity comparisons of the MZ Ig sequence dataset with a large dataset of Ig sequences (MZ‐related or not; n = 65 837) revealed four major clusters of cases sharing homologous (‘public’) heavy variable complementarity‐determining region 3. These clusters included rearrangements from SMZL, ENMZL (gastric, salivary gland, ocular adnexa), chronic lymphocytic leukemia, but also rheumatoid factors and non‐malignant splenic MZ cells. In conclusion, different MZ lymphomas display biased immunogenetic signatures indicating distinct antigen exposure histories. The existence of rare public stereotypes raises the intriguing possibility that common, pathogen‐triggered, immune‐mediated mechanisms may result in diverse B lymphoproliferations due to targeting versatile progenitor B cells and/or operating in particular microenvironments. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
    Type of Medium: Online Resource
    ISSN: 0022-3417 , 1096-9896
    URL: Issue
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    Language: English
    Publisher: Wiley
    Publication Date: 2019
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  • 3
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 72, No. 20 ( 2012-10-15), p. 5307-5316
    Abstract: Mantle cell lymphoma (MCL) is a heterogeneous disease with most patients following an aggressive clinical course, whereas others having an indolent behavior. We conducted an integrative and multidisciplinary analysis of 177 MCL to determine whether the immunogenetic features of the clonotypic B-cell receptors (BcR) may identify different subsets of tumors. Truly unmutated (100% identity) IGHV genes were found in 24% cases, 40% were minimally/borderline mutated (99.9%–97%), 19% significantly mutated (96.9%–95%), and 17% hypermutated ( & lt;95%). Tumors with high or low mutational load used different IGHV genes, and their gene expression profiles were also different for several gene pathways. A gene set enrichment analysis showed that MCL with high and low IGHV mutations were enriched in memory and naive B-cell signatures, respectively. Furthermore, the highly mutated tumors had less genomic complexity, were preferentially SOX11-negative, and showed more frequent nonnodal disease. The best cut-off of germline identity of IGHV genes to predict survival was 97%. Patients with high and low mutational load had significant different outcome with 5-year overall survival (OS) of 59% and 40%, respectively (P = 0.004). Nodal presentation and SOX11 expression also predicted for poor OS. In a multivariate analysis, IGHV gene status and SOX11 expression were independent risk factors. In conclusion, these observations suggest the idea that MCL with mutated IGHV, SOX11-negativity, and nonnodal presentation correspond to a subtype of the disease with more indolent behavior. Cancer Res; 72(20); 5307–16. ©2012 AACR.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2012
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  • 4
    In: Oncotarget, Impact Journals, LLC, Vol. 8, No. 41 ( 2017-09-19), p. 71234-71248
    Type of Medium: Online Resource
    ISSN: 1949-2553
    URL: Issue
    Language: English
    Publisher: Impact Journals, LLC
    Publication Date: 2017
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  • 5
    In: Blood Cells, Molecules, and Diseases, Elsevier BV, Vol. 41, No. 2 ( 2008-9), p. 215-218
    Type of Medium: Online Resource
    ISSN: 1079-9796
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2008
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  • 6
    In: Breathe, European Respiratory Society (ERS), Vol. 14, No. 4 ( 2018-12), p. e123-e127
    Type of Medium: Online Resource
    ISSN: 1810-6838 , 2073-4735
    Language: English
    Publisher: European Respiratory Society (ERS)
    Publication Date: 2018
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  • 7
    Online Resource
    Online Resource
    Elsevier BV ; 2013
    In:  Studies in Educational Evaluation Vol. 39, No. 4 ( 2013-12), p. 225-231
    In: Studies in Educational Evaluation, Elsevier BV, Vol. 39, No. 4 ( 2013-12), p. 225-231
    Type of Medium: Online Resource
    ISSN: 0191-491X
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2013
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  • 8
    In: Blood, American Society of Hematology, Vol. 124, No. 21 ( 2014-12-06), p. 2731-2731
    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 previously reported that the T-cell receptor (TR) gene repertoire in CIN is skewed, indicating antigen selection in CIN ontogeny. However, the analytical depth afforded by Sanger sequencing is limited, hindering definitive conclusions. In order to obtain a truly comprehensive view into the role of antigen drive in CIN, using next generation sequencing (NGS) we interrogated the TR repertoire of 13 patients (8 females, 5 males) included in our previous study as well as a healthy female. TRBV-TRBD-TRBJ gene rearrangements were amplified according to the BIOMED2 protocol on either genomic DNA or cDNA isolated from CD8+ cells of PB (n=4) or BM (n=10) samples. PCR products were used as a substrate for paired-end sample preparation (Illumina) and subjected to NGS on the MiSeq Illumina Platform. The raw NGS data were preprocessed with a dedicated pipeline for this purpose, including: (i) quality filtering of each read; (ii) merging of paired-end reads via local alignment; (iii) preparation of fasta files for submission to the IMGT/High V-QUEST tool; and, (iv) IMGT/High V-QUEST metadata analysis, interpretation and visualization. Overall, 6,196,980 TRBV-TRBD-TRBJ gene rearrangements were analyzed (130,020-1,037,680 /case) of which 5,317,609 were productive since they used functional TRBV genes and also carried in-frame CDR3. Rearrangements with identical TRBV gene usage and CDR3 sequence were defined as clonotypes. For repertoire analyses, clonotypes rather than single rearrangement sequences were considered. Overall, 553,145 unique clonotypes were identified (median 39,510; range 7,732-172,253/case), of which 408,744 represented singletons. All clonotypes from the Sanger analysis were detected by NGS as well. Among the 46 functional TRBV genes identified, the most frequent were: TRBV29-1 (13.9%), TRBV19 (6.7%), TRBV12-3 (5.6%), TRBV6-5 (5.4%), TRBV27 (4.9%) and TRBV6-1 (4.0%), collectively accounting for 40,5% of the TRBV repertoire; the TRBV29-1 gene predominated in 9/13 CIN cases. All CIN cases were found to carry distinct expanded clonotypes (median 10,314; range 2,279-40,245/case). The predominant clonotype ranged in frequency from 5.25 to 20.2% of the total clonotypes observed in each case. This contrasts significantly (p 〈 0.001) with a 0.47% frequency of the dominant clonotype in the healthy control. Cluster analysis of the sequences of all CIN cases identified 9034 different clonotypes shared by different patients and, thus, deemed as public. Notably, public clonotypes of a given CDR3 length could show high sequence similarity, further underscoring the restricted nature of the repertoire. As an example, 1632/2665 (61.2%) public clonotypes with 12 aminoacid-long CDR3 were grouped into 168 distinct communities, populated with 2-280 highly similar sequences, each linked with 1 aminoacid distance with at least another member of the community. Overall, the present study offers conclusive evidence that the TR repertoire in CIN is remarkably skewed. The finding of oligoclonal T-cell expansions and public clonotypes strongly indicates that antigen-driven immune responses are very likely implicated in the pathogenesis of CIN. Disclosures No relevant conflicts of interest to declare.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2014
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  • 9
    In: Blood, American Society of Hematology, Vol. 122, No. 21 ( 2013-11-15), p. 2999-2999
    Abstract: Immunogenetic studies have made seminal contributions towards understanding the pathogenesis of splenic marginal zone lymphoma (SMZL) by documenting a highly skewed immunoglobulin (IG) gene repertoire with molecular features strongly implicating selection by antigen(s) in disease ontogeny and evolution. Indeed, a major subset of SMZL, roughly 30% of the entire cohort, is defined by the expression of IG receptors with heavy variable domains (VH) utilizing the IGHV1-2*04 gene. These VH domains exhibit low-level, yet non-randomly targeted somatic hypermutation (SHM), carry long and often positively charged heavy complementarity-determining region 3 with restricted motifs, and also show biased associations with certain light IG genes, namely IGKV3-20, IGKV1-8 and IGLV2-14. We recently documented that the great majority of SMZL, especially IGHV1-2*04 cases, exhibit intraclonal diversification (ID) in IGHV genes, reflecting ongoing interactions with antigen(s). In this study we further extend the analysis of ID in SMZL focusing on IG light genes. To this end, we performed a comprehensive subcloning analysis of IGKV-IGKJ and IGLV-IGLJ gene rearrangements from 11 SMZL cases; two patients were studied at two different time-points. A total of 311 subcloned sequences (10-38/sample, median, 25) were obtained from 9 IGKV-IGKJ and 4 IGLV-IGLJ rearrangements. Multiple alignment of the subcloned sequences revealed that: (1) only one of 13 studied samples (7.8%) carried identical subclones (no ID); (2) 6/13 (46.1%) carried only unconfirmed mutations (UCMs, mutations in single subclones; unconfirmed ID); and, (3) 6/13 (46.1%) carried confirmed mutations (CMs, identical mutations in at least 2 subclones; confirmed ID). Both IGHV1-2*04 cases of the present series belonged to the confirmed ID category and both displayed intense ID with extensive subclone formation. Among cases positive for ID, the number of nucleotide substitutions introduced by ongoing SHM ranged from 1-21. A total of 66 unique substitutions were identified in 42 positions of the variable domain; 44 of these resulted in the replacement of the germline-encoded amino acid (R), while the remaining 22 were silent (S). The distribution of replacement and silent CMs and UCMs in CDRs and FRs was compatible with a canonical SHM process in that R/S ratios were higher in CDRs, except CDR2. In general, ID was more pronounced in IGKV-IGKJ versus IGLV-IGLJ rearrangements, regardless of the overall mutational load of each rearrangement. The analysis of the same rearrangement at different time-points revealed a consistent ID profile: one case carried only UCMs at both time-points, while the other (IGHV1-2*04 case) exhibited a dynamic pattern of appearing and disappearing CMs. Overall, the presence of mutations in the context of ID was independent of the mutational status, as ID was observed even in minimally mutated cases (98-99.9% germline identity). Moreover, in 3/6 cases with confirmed ID, subclones were classified in ≥2 main mutational groups, indicating early “branching” of the clonal population in subpopulations with distinct mutational profiles. In conclusion, the present study complements the immunogenetic profile of SMZL, offering novel molecular evidence for crosstalk with the microenvironment mediated through the clonotypic B-cell receptors. Furthermore, it underscores the significance of IG light chains in the immune pathogenesis of SMZL. Disclosures: No relevant conflicts of interest to declare.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2013
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  • 10
    In: Blood, American Society of Hematology, Vol. 126, No. 23 ( 2015-12-03), p. 1479-1479
    Abstract: B cells residing the marginal zone (MZ) provide a first line of defense against blood borne pathogens, producing the greater part of circulating natural antibodies conferring protection against infection. Dysregulated homeostasis and function of MZ B cells has been implicated in a wide range of B lymphoproliferations, encompassing the distinct MZ lymphomas recognized by the WHO Classification, the related provisional entities and even chronic lymphocytic leukemia (CLL), for which a MZ derivation has been proposed. Here, taking advantage of a large multi-institutional series, we aimed at obtaining insight into the ontogenetic relationship of MZ lymphoproliferations, related entities and CLL through cross-comparison of their B cell receptor immunoglobulin (BcR IG) gene repertoires. Our sequence dataset included 3660 unique IGHV-IGHD-IGHJ gene rearrangement sequences from our collaborative centers and/or public databases derived from: (1) MZ lymphomas: splenic (SMZL), n=379; nodal (NMZL), n=37; extranodal (ENMZL), n=95; (2) provisional entities of postulated MZ origin, including splenic diffuse red pulp lymphoma (SDRL, n=16) and clonal B cell lymphocytosis of MZ origin (CBL-MZ, n=60); (3) persistent polyclonal B cell lymphocytosis (PPBL), n=286 (from 2 cases); (4) MZ cells isolated from six spleen specimens free of neoplastic cells at histological inspection (non-malignant MZ), obtained at surgery for cancer, n=489; (5) autoimmune conditions, n=1243; (6) various types of normal B cells, n=1055. The most pronounced IG gene repertoire skewing was observed in SMZL with the IGHV1-2*04 gene accounting for 26% of cases. Restrictions, though less striking, were also identified in the other MZ lymphomas as well: (i) the IGHV4-34 gene predominated in NMZL (14.3%); and, (ii) the IGHV1-69 gene predominated in ENMZL (14.6%), albeit with significantly different distribution depending on the primary site of involvement, ranging from 38% in salivary ENMZL to 11% in gastric ENMZL to 4% in ocular adnexa ENMZL (p 〈 0.01). The vast majority of MZL cases showed at least some impact of somatic hypermutation (SHM), with the proportion of cases lacking any SHM ranging from 0% in salivary ENMZ to only 13% in SMZL. Following established bioinformatics approaches, we searched for stereotyped BcR IG sequences i.e. IGHV-IGHD-IGHJ gene rearrangements with restricted antigen-binding site sequence motifs. For the purposes of this analysis, the present sequence dataset was cross-compared to a large dataset of 20451 IGHV-IGHD-IGHJ gene rearrangement sequences from CLL patients from the IMGT/CLL-DB. Overall, 6437 different clusters with stereotyped BcR IG sequences were identified in the merged dataset, including from only 2 to more than 350 sequences. Two categories of clusters with stereotyped BcR IG were identified: disease-specific (n=4813) and 'mixed' (n=1624) i.e. comprised of cases with different diagnosis. The great majority of clusters in the former category concerned exclusively CLL and corresponded to well-established CLL stereotyped subsets, while only a small minority concerned exclusively MZ lymphomas, all with a diagnosis of SMZL. Mixed clusters were relatively small in size, with only 4 populated by more than 10 cases; of these, 2 utilized the IGHV1-69 gene, while the remaining 2 utilized the IGHV3-7 and IGHV4-59 gene, respectively. They comprised rearrangements from various entities, including SMZL, ENMZL (gastric, salivary gland, ocular adnexa), CLL, hepatitis C virus-associated diffuse large B cell lymphoma (DLBCL), but also rheumatoid factors and non-malignant spleen MZ cells. Notably, shared (recurrent) amino acid changes introduced by SHM (i.e. the same amino acid replacement at the same position) were identified in each mixed cluster. In conclusion, we document different immunogenetic signatures for MZ lymphomas, with limited overlap both amongst the various distinct and provisional WHO entities but also versus CLL. These findings indicate distinct antigen exposure histories and/or different (micro)environments underlying the ontogeny of MZ lymphomas. That said, the existence of rare public stereotypes raises the intriguing possibility that common, pathogen-triggered, immune-mediated mechanisms, may result in diverse B lymphoproliferations due to targeting versatile progenitor B cells and/or operating in particular microenvironments. Disclosures Ghia: Janssen Pharmaceuticals: Research Funding.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2015
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