The Clonotypic BCR IG of CLL Patients Contain Predicted T-Cell Class I Epitopes with Shared Structural Properties

Targeted therapies have revolutionized the treatment of chronic lymphocytic leukemia (CLL) with remarkable overall response rates. Against that, however, CLL remains incurable, indicating a need for novel strategies towards disease control and eventual eradication, including reinvigoration of anti-tumor immune responses. T cells in CLL display an oligoclonal profile and appear selected by restricted antigens, with recent evidence suggesting that the selecting epitopes may lie within the clonotypic B-cell receptor immunoglobulins (BcR IG). Should this prove to be the case, such neoepitopes could be exploited as idiotypic targets for cellular therapy or for peptide vaccine design, aiming to augment response to current treatments. Here we performed ad hoc prediction of putative T-cell class I neoepitopes contained within the clonotypic BcR IGs of CLL patients, with an intended bias towards major stereotyped CLL subsets. We selected 27 patients to represent the full spectrum of CLL: (i) with mutated IGHV genes (M-CLL, n=5), (ii) with unmutated IGHV genes (U-CLL, n=5), (iii) assigned to major stereotyped subsets (subset #1, n=7; subset #2, n=5; subset #4, n=5). RT-PCR was performed for the heavy (H) and the light (K/L) IG chains using subgroup-specific Leader primers for the IGHV/IGK/LV gene and universal primers annealing to the constant domain (IGHG, IGHM, IGKC, IGLC), in order to produce the full-length V-(D)-J gene rearrangement sequence, plus the start of the constant domain. PCR products were subjected to direct double-strand Sanger sequencing with a quality-optimized protocol. The amino acid sequences were subsequently parsed in peptides and subjected to NetMHCpan. The rank score was calculated, considering the 4-digit HLA-A and -B typing for each individual patient. High- and medium-binding peptides (rank score <2%) were selected. Exact matches to germline and/or proteome databases were excluded. Overall, 1,007 predicted neoepitopes were identified. All patients had predicted CD8 + T-cell epitopes within the clonotypic BcR IG, either in the heavy chain (26/27 pts, n=632 epitopes) or the light chain (26/27 pts, n=375 epitopes). The majority of the peptides resulted from somatic hypermutations (SHMs) across the IGHV gene outside the complementarity-determining region 3 (CDR3; n=538, 53.4%). With the exception of few peptides located within the FR4 region (n=11, 0.1%), the remaining (n=458, 45.5%) involved (at least part of) the CDR3, which is particularly relevant given its small length (9-27 aa) within the full sequence (331-660 aa). There was no statistically significant difference in the rank score of peptides involving the CDR3 vs. all others. Peptide clustering assigned most of the predicted neoepitopes (970/1007, 96.3%) in 54 clusters of similar length and amino acid composition. Also, it revealed similar or identical predicted neoepitopes among different patients (30 clusters of two, 10 clusters of three, 8 clusters of four, 4 clusters of five, 1 cluster of six and 1 cluster of eight). Importantly, these clusters involved: (i) shared CDR3 patterns in patients assigned to the same stereotyped subset, but also (ii) subset-specific recurrent SHMs across the rearranged IGHV gene, e.g. G-to-E SHM at position 28 in the VH CDR1 of subset #4, a recurrent SHM in this subset. Also of note, the two most highly populated clusters involved peptides within the VL CDR3, and were biased towards specific subsets; the cluster of eight patients contained 4 patients assigned to subset #1 and the cluster of six patients included 4 patients assigned to subset #2. In conclusion, in silico prediction identified a significant number of putative T-cell class I neoepitopes contained within the clonotypic BcR IG of CLL patients. The majority of these neoepitopes can be assigned to clusters based on amino acid similarity and are shared among different patients. Many of them culminate from subset-specific ('stereotyped') CDR3 patterns or recurrent SHMs, suggesting that the targeted SHM which shapes the CLL BcR IG repertoire may produce immunogenic CD8 + T-cell epitopes. Their actual immunogenicity has to be tested in ex vivo studies, currently underway by our group. Disclosures Anagnostopoulos: Abbvie: Other: clinical trials; Sanofi: Other: clinical trials ; Ocopeptides: Other: clinical trials ; GSK: Other: clinical trials; Incyte: Other: clinical trials ; Takeda: Other: clinical trials ; Amgen: Other: clinical trials ; Janssen: Other: clinical trials; novartis: Other: clinical trials; Celgene: Other: clinical trials; Roche: Other: clinical trials; Astellas: Other: clinical trials . Chatzidimitriou: Abbvie: Honoraria, Research Funding; Janssen: Honoraria, Research Funding.

The Outcome of CLL Patients According to IGHV Mutational Status: An Israeli Perspective

Introduction: The prognostic significance of immunoglobulin heavy-chain variable region gene (IGHV) mutational status in chronic lymphocytic leukemia (CLL) is well established. Previous studies have shown that CLL patients with mutated IGHV (M-IGHV) have a better prognosis, manifested in a longer time-to first treatment (TTFT) and overall survival (OS). Here we present an analysis on the impact of IGHV mutational status in an Israeli cohort of patients with CLL. Methods: A total of 254 patients with CLL (diagnosed from 1991 to 2020), followed at the Tel-Aviv Sourasky Medical Center were included. The IGHV mutational status has been determined by next-generation sequencing (NGS) or cDNA Sanger. The sequences with a germline homology 98% or higher were considered unmutated, and those with a homology less than 98% as mutated CLL. IGHV subsets were analyzed using the ARResT/AssignSubsets website. All data were statistically analyzed by IBM SPSS Statistics 27 (IBM Corporation, Armonk, NY, USA), P-values were two-sided, and the significance level was determined at a<0.05 were considered significant. Results: Out of 254 patients, 132 (52.0%) had an unmutated IGHV gene (UM-IGHV), and 122 (48.0%) were mutated (M-IGHV). At diagnosis, most patients (Table 1) were ≤65 years of age (n=157, 61.8%), males (n=160, 63.0%) and had an absolute lymphocytic count equal to or less than (≤)15.0 x10 9/L (n=115, 52.5%). Advanced Binet stage was more commonly associated with UM-IGHV (n=44, 57.9%) (P=0.033). Among 240 patients (94.1%), the most frequently used VH gene segments (Figure 1) included; VH1-69 (n=35, 14.6%), VH4-34 (n=24, 10.0%), VH1-2 (n=17, 7.1%), and VH3-23 (n=16, 6.7%). Six major B-cell receptors (BCR) subsets (Figure 2) were identified in 21/180 of patients (11.7%), which most commonly included: CLL#1 (n=6, 28.6%), CLL#4 (n=5, 23.8%), and CLL#2(n=3, 14.3%). Patients with M-IGHV had a longer time to first treatment (TTFT) (P<0.001, hazard ratio (HR)=2.5, 95% confidence interval [1.8-3.5], Figure 3A) and a better overall survival (OS) (P=0.002, HR=2.7, [1.4-5.1]) compared to those with UM-IGHV gene (Figure 3B). In multivariate analyses of the entire cohort; for TTFT (Table 2A), males (P=0.002, HR=1.9, [1.3-2.9]), >65 years of age at diagnosis (P=0.008, HR=1.8, [1.2-2.7]), advanced Binet stage (P<0.001, HR=2.4, [1.5-3.8]) and UM-IGHV mutational status (P=<0.001, HR=2.0, [1.3-2.9]) were found to be significant predictors for shorter TTFT, while in a multivariate analysis for OS (Table 2B), only >65 years of age at diagnosis (P=0.010, HR=2.6, [1.3-5.5]) and UM-IGHV mutational status (P=0.004, HR=2.9, [1.4-5.9]) were found to be significant factors for shorter OS. In multivariate analyses performed separately for each IGHV mutational status group; males (P=0.021, HR=2.1, [1.1-4.0]), age >65 years (P=0.002, HR=3.2, [1.5-6.4]) and advanced Binet stage (P<0.001, HR=4.1, [1.9-8.7]) were found as independent predictors for a shorter TTFT in M-IGHV patients, while only males retained a statistically significance in UM-IGHV patients (P=0.017 HR=2.0, [1.1-3.5]). Furthermore, in a multivariate analysis for OS; age>65 years at diagnosis (P=0.039, HR=4.3, [1.1-17.0]) was the only independent predictor in M-IGHV patients, while no variable maintained its statistical significance in UM-IGHV cases. Conclusion: As previously studied, our cohort demonstrates that M-IGHV CLL patients have better TTFT and OS. However, the rate of BCR subsets in Israel appears to be lower than expected. A separated multivariate analysis for M-IGHV and UM-IGHV patients revealed different independent predictors for TTFT and OS to each of the IGHV mutational status groups. Further studies with larger cohorts are required to deeply study these differences and provide further clinical insight into the pathophysiology of CLL. Figure 1 Figure 1. Disclosures Joffe: AstraZeneca: Consultancy; Epizyme: Consultancy. Herishanu: AbbVie: Honoraria, Research Funding; Janssen: Honoraria; Roche: Honoraria; Medison: Honoraria.

CRIS: Complete Reconstruction of Immunoglobulin V-D-J Sequences from RNA-seq data

Motivation B-cells display remarkable diversity in producing B-cell receptors through recombination of immunoglobulin V-D-J genes. Somatic hypermutation of immunoglobulin heavy chain variable (IGHV) genes are used as a prognostic marker in B-cell malignancies. Clinically, IGHV mutation status is determined by targeted Sanger sequencing which is a resource intensive and low-throughput procedure. Here we describe a bioinformatic pipeline, CRIS (Complete Reconstruction of Immunoglobulin IGHV-D-J Sequences) that uses RNA sequencing (RNA-seq) datasets to reconstruct IGHV-D-J sequences and determine IGHV somatic hypermutation status. Results CRIS extracts RNA-seq reads aligned to immunoglobulin gene (Ig) loci, performs assembly of Ig-transcripts and aligns the resulting contigs to reference Ig sequences to enumerate and classify somatic hypermutations in the IGHV gene sequence. CRIS improves on existing tools that infer the B-cell receptor (BCR) repertoire from RNA-seq data using a portion IGHV gene segment by de novo assembly. We show that the somatic hypermutation status identified by CRIS using the entire IGHV gene segment is highly concordant with clinical classification in three independent chronic lymphocytic leukemia patient cohorts. Availability The CRIS pipeline is available under the MIT License from https://github.com/Rashedul/CRIS. Supplementary information Supplementary data are available at Bioinformatics Advances online.

IGHV-associated methylation signatures more accurately predict clinical outcomes of chronic lymphocytic leukemia patients than IGHV mutation load

Currently, no molecular biomarker indexes are used in standard care to make treatment decisions at diagnosis of chronic lymphocytic leukemia (CLL). We used Infinium MethylationEPIC array data from diagnostic blood samples of 114 CLL patients, and developed a patient stratification procedure based on methylation signatures associated with mutation load of the IGHV gene. This procedure allowed us to predict the time to treatment (TTT) with HR 8.34 (95% CI, 4.54-15.30), as opposed to HR 4.35 (95% CI, 2.60-7.28) for IGHV mutation status. Detailed evaluation of 17 discrepant cases between the two classification procedures showed that these cases were incorrectly classified using IGHV status. Moreover, methylation-based classification stratified patients with different overall survival (OS) (HR, 1.82; 95% CI, 1.07-3.09), which was not possible using IGHV status. Furthermore, we assessed the performance of the developed classification procedure using published HumanMethylation450 array data for 159 patients for which TTT, OS and relapse were available. Despite that 450K array methylation data did not contain all biomarkers used in our classification procedure, methylation signatures again stratified patients with significantly better accuracy than IGHV mutation load regarding all available clinical outcomes. Thus, stratification using IGHV-associated methylation signatures may provide improved prognostic power than IGHV mutation status.

Central Nervous System Involvement is Associated with Ibrutinib-Induced Severe Hyperleukocytosis and Controlled by the Combination of Intrathecal Chemotherapy in Chronic Lymphocytic Leukemia: A Case Report

Central nervous system involvement (CNSi) is a rare complication of chronic lymphocytic leukemia (CLL) with a very poor prognosis. Its diagnosis, predictive factors, and standard treatment remain elusive. Ibrutinib, an oral inhibitor of Bruton’s tyrosine kinase, has been approved to treat CLL, yet little is known of its effect on the occurrence and management of CNSi. Here, we report, for the first time, an elderly CLL patient with secondary CNSi following ibrutinib-induced severe hyperleukocytosis, characterized by subcutaneous lesions and unmutated IgHV gene. Ibrutinib combined with intrathecal chemotherapy induced a prompt and durable remission of CNSi. This case indicates that severe hyperleukocytosis caused by ibrutinib is associated with the emergence of CNSi, and a combined treatment with intrathecal chemotherapy is effective and safe in the treatment of CLL patient with CNSi.

The Traf2DNxBCL2-tg Mouse Model of Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma Recapitulates the Biased IGHV Gene Usage, Stereotypy, and Antigen-Specific HCDR3 Selection of Its Human Counterpart

Chronic lymphocytic leukemia (CLL)/Small lymphocytic lymphoma (SLL) is a heterogeneous disease consisting of at least two separate subtypes, based on the mutation status of the immunoglobulin heavy chain variable gene (IGHV) sequence. Exposure to antigens seems to play a role in malignant transformation and in the selection and expansion of more aggressive CLL clones. Furthermore, a biased usage of particular IGHV gene subgroups and the existence of stereotyped B-cell receptors (BCRs) are distinctive characteristics of human CLL. We have previously described that Traf2DN/BCL2 double-transgenic (tg, +/+) mice develop CLL/SLL with high incidence with aging. In this model, TNF-Receptor Associated Factor (TRAF)-2 deficiency cooperates with B cell lymphoma (BCL)-2 in promoting CLL/SLL in mice by specifically enforcing marginal zone (MZ) B cell differentiation and rendering B cells independent of BAFF for survival. In this report, we have performed the sequencing of the IGHV-D-J rearrangements of B cell clones from the Traf2DN/BCL2-tg+/+ mice with CLL/SLL. The results indicate that these mice develop oligoclonal and monoclonal B cell expansions. Allotransplantation of the oligoclonal populations into immunodeficient mice resulted in the preferential expansion of one of the parental clones. The analysis of the IGHV sequences indicated that 15% were mutated (M) and 85% unmutated (UM). Furthermore, while the Traf2DN/BCL2-tg-/- (wild-type), -/+ (BCL2 single-tg) and +/- (Traf2DNDN single-tg) littermates showed the expression of various IGHV gene subgroups, the CLL/SLL expanded clones from the Traf2DN/BCL2-tg+/+ (double-transgenic) mice showed a more restricted IGHV gene subgroup usage and an overrepresentation of particular IGHV genes. In addition, the HCDR3-encoded protein sequence indicates the existence of stereotyped immunoglobulin (Ig) in the BCRs and strong similarities with BCR recognizing autoantigens and pathogen-associated antigens. Altogether, these results highlight the remarkable similarities between the CLL/SLL developed by the Traf2DN/BCL2-tg+/+ mice and its human counterpart.

Discovery of 10,828 new putative human immunoglobulin heavy chain IGHV variants

The correct identification of immunoglobulin alleles in genome sequences is a challenge. Nevertheless, it can assist in the study of several human diseases associated with the antibody repertoire and in the development of new therapies using antibody engineering techniques. The advent of next-generation sequencing of human genomes and antibody repertoires enabled the development of several tools for the mapping and identification of new immunoglobulin (Ig) alleles. Some of these tools use 1,000 Genomes (G1K) data for new Ig alleles discovery. However, genome data from G1K present low coverage and variant call problems. Here, a computational screen of immunoglobulin alleles was carried out in the Genome Aggregation Database (gnomAD), the largest high-quality catalogue of variation from 125,748 exomes and 15,708 human genomes.A total of 10,909 putative IGHV alleles were identified, in which 10,828 of them are new and 2,024 appear at least in 6 different alleles from genomes/exomes. The IGHV2-70 was the IGHV gene segment with the largest number of variants described. The majority of the variants were found in the framework 3 and most of them are missense. Interestingly, a large number of variants were found to be population exclusive. A database integrated with a web platform was created (YGL-DB) to store and make accessible the likely new variants found.This available data can help the scientific community to validate new IGHV variants as well as it can shed light on the importance of variants in disease development and immunization protocols.

THE EXPRESSION OF THE MAIN AND ALTERNATIVE TRANSCRIPT (SORL1-Δ2) OF THE SORL1 GENE IN CHRONIC LYMPHOCYTIC LEUKEMIA PATIENTS AFFECTED BY THE CHORNOBYL ACCIDENT

Objective: to study clinical-hematological data and expression of the main and alternative transcripts of SORL1 gene in chronic lymphocytic leukemia (CLL) patients affected by the Chornobyl catastrophe. Methods. Analysis was performed in the main group of 34 CLL patients irradiated due to the Chornobyl NPP accident (30 clean-up workers, and 4 evacuees) and in the control group of 27 non-irradiated CLL patients. Groups of patients were comparable by age, sex, stage of disease, mutational status of IGHV genes. Expression of the main and alternative transcripts of SORL1 gene was evaluated by Quantitative Real-time polymerase chain reaction (PCR). The IGHV gene mutational status, TP53 and SF3B1 mutations were studied by PCR followed by direct sequencing. Data were analyzed with the SPSS software package, version 20.0. Results. Relative expression level of the main transcript of SORL1 gene was low (mean 1.71 ± 0.55, median 0.57), did not correlate with the IGHV gene mutational status, TP53 and SF3B1 mutations, stage of disease. The expression of B transcript was not detected, F transcript was expressed at a very low level in 9 patients. The average relative expression level of SORL1-Δ2 transcript was 14.1 ± 6.04 (median 3.48; range 0.01–90.51). The expression of SORL1-Δ2 transcript above the median was more frequent among patients on C stage (p = 0.001), and in patients with unmutated IGHV genes was associated with an extremely negative course of CLL (median of overall survival 9 months vs 61 months at low expression). Relative expression levels of the main and alternative transcripts of SORL1 gene in patients of the main and the control groups did not differ. Conclusions. Our preliminary data suggest that increased expression of SORL1-Δ2 transcript in CLL patients with unmutated IGHV genes can be considered as a negative prognostic marker. Key words: chronic lymphocytic leukemia, SORL1, SORL1-Δ2, Chornobyl NPP accident.

Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes in COVID-19 convalescent plasma

SUMMARYAlthough humoral immunity is essential for control of SARS-CoV-2, the molecular composition, binding epitopes and effector functions of the immunoglobulin G (IgG) antibodies that circulate in blood plasma following infection are unknown. Proteomic deconvolution of the circulating IgG repertoire (Ig-Seq1) to the spike ectodomain (S-ECD2) in four convalescent study subjects revealed that the plasma response is oligoclonal and directed predominantly (>80%) to S-ECD epitopes that lie outside the receptor binding domain (RBD). When comparing antibodies directed to either the RBD, the N-terminal domain (NTD) or the S2 subunit (S2) in one subject, just four IgG lineages (1 anti-S2, 2 anti-NTD and 1 anti-RBD) accounted for 93.5% of the repertoire. Although the anti-RBD and one of the anti-NTD antibodies were equally potently neutralizing in vitro, we nonetheless found that the anti-NTD antibody was sufficient for protection to lethal viral challenge, either alone or in combination as a cocktail where it dominated the effect of the other plasma antibodies. We identified in vivo protective plasma anti-NTD antibodies in 3/4 subjects analyzed and discovered a shared class of antibodies targeting the NTD that utilize unmutated or near-germline IGHV1-24, the most electronegative IGHV gene in the human genome. Structural analysis revealed that binding to NTD is dominated by interactions with the heavy chain, accounting for 89% of the entire interfacial area, with germline residues uniquely encoded by IGHV1-24 contributing 20% (149 Å2). Together with recent reports of germline IGHV1-24 antibodies isolated by B-cell cloning3,4 our data reveal a class of shared IgG antibodies that are readily observed in convalescent plasma and underscore the role of NTD-directed antibodies in protection against SARS-CoV-2 infection.

Genetic Lesions in Russian CLL Patients with the Most Common Stereotyped Antigen Receptors

Background: The features of the IGHV gene repertoire in CLL have been widely discussed in the last 20 years. In approximately 30% of cases of CLL, highly homologous "stereotyped" antigen receptors (SARs) are expressed, representing quasi identical amino acid sequences. Associations with age, disease severity, and cytogenetic aberrations have already been reported for certain SARs. It should be noted that the predictive value of certain SARs could be higher than that of IGHV mutation status. Several SAR subgroups have already been identified as independent prognostic factors in CLL (CLL#1, CLL#2, CLL#8 demonstrate an extremely aggressive course of the disease, CLL#4 - indolent). It was also shown that SAR subgroups may associate with distinct profiles of genetic lesions. Aim: To study the frequency of cytogenetic aberrations and mutations in the TP53, NOTCH1, and SF3B1 genes in CLL patients with the most common SARs in Russia. Methods: The study included 62 patients with CLL diagnosed and followed up from 2012 to 2020. Sequencing of the IGHV gene and SAR assignment were done according to the ERIC recommendations. NOTCH1 gene mutations (exon 34) were assessed by fragment analysis or by NGS using primers described by Campregher et al. TP53 gene mutations (exons 2-11) were determined using NGS according to Pavlova et al. SF3B1 gene mutations (exons 14-16) were studied in 26 patients by NGS. 51 patients underwent a FISH study for the presence of 17p13/TP53 deletions; 29 - additionally for 11q23/ATM and 13q14 deletions (Abbott, USA). Results: CLL#1, CLL#6, and CLL#3 are the most common SAR subsets in Russian CLL patients. Here we report data for 30 patients with CLL#1, 17 with CLL#6, and 15 with CLL#3. In CLL#1 group, 10 (33.3%) patients had mutations in the TP53 gene. In 7 cases, the mutation burden exceeded 35%, in three patients it was less than 10%. In 7 (23.3%) patients, mutations in the NOTCH1 gene were detected, in 5 - c.7544_7545delCT, in 1 - c.7558_7561delCTTC and in 1 - p.Q2444X. Simultaneous mutations in the NOTCH1 and TP53 genes were found in two patients. Deletion 17p13was found in 8 patients from 25 studied (32%). In 7 patients TP53 mutation and del17p13 were observed simultaneously. Deletion 11q23 was found in 6 out of 15 patients (40%). No cases with the simultaneous occurrence of del11q23 and del17p13 or mutations in the TP53 gene were observed. SF3B1 gene mutations in this group were not investigated. In the CLL#6 group, 6 (35.3%) patients had mutations in the TP53 gene (in two of them two clones with different TP53 mutations were observed). In one case, the mutation was less than 10%. In 4 (23.5%) patients NOTCH1 gene mutations (all c.7544_7545delCT) were detected, in two cases the mutation burden was less than 5%. Simultaneous NOTCH1 and TP53 gene mutations were found in two patients. Deletion 17p13 was found in 4 patients from 14 studied (28.5%). In 3 patients TP53 mutations and del17p13 were observed simultaneously. Deletion 11q23 was found in 1 patient out of 10. No SF3B1 gene mutations were found in this group (in 11 patients tested). In CLL#3 group, only 2 (13%) patients had mutations in the TP53 gene, with one having 2 different clones and the other having 4 (this patient also had del17p13, the only one in this group). Also, only 2 (13%) patients had c.7544_7545delCT deletion in the NOTCH1 gene. SF3B1 gene mutations were found in 8 (53.3%) patients. Conclusions: Our data show that in CLL#1, CLL#6, and CLL#3 subsets genetic lesions are much more common than in CLL patients in general. This is in part consistent with earlier European studies. However, in our sample, TP53 mutations and del17p13 are much more frequent in CLL#1 and CLL#6 groups. This may be due to a more sensitive approach (NGS) for mutation detection we used. Furthermore, our cohort included patients relapsed after the FCR treatment. The discrepancy in the detection rate of del11q23 in the CLL#1 subset can be explained by the small sample. Also, population differences in the development of the disease cannot be ruled out. Further studies of genetic lesions associated with certain SAR subgroups may improve diagnostics and therapy of CLL and impact the understanding of disease pathogenesis. Disclosures No relevant conflicts of interest to declare.