Variable Gene Segments Research Articles

Constitutively active CaMKII Drives B lineage acute lymphoblastic leukemia/lymphoma in tp53 mutant zebrafish.

Acute lymphoblastic leukemia/lymphoma (ALL) is the most common pediatric cancer and is a malignancy of T or B lineage lymphoblasts. Dysregulation of intracellular Ca2+ levels has been observed in patients with ALL, leading to improper activation of downstream signaling. Here we describe a new zebrafish model of B ALL, generated by expressing human constitutively active CaMKII (CA-CaMKII) in tp53 mutant lymphocytes. In this model, B cell hyperplasia in the kidney marrow and spleen progresses to overt leukemia/lymphoma, with only 29% of zebrafish surviving the first year of life. Leukemic fish have reduced productive genomic VDJ recombination in addition to reduced expression and improper splicing of ikaros1, a gene often deleted or mutated in patients with B ALL. Inhibiting CaMKII in human pre-B ALL cells induced cell death, further supporting a role for CaMKII in leukemogenesis. This research provides novel insight into the role of Ca2+-directed signaling in lymphoid malignancy and will be useful in understanding disease development and progression.

Uncovering the diversity and distribution of biosynthetic gene clusters of prochlorosins and other putative RiPPs in marine Synechococcus strains.

Genome mining studies have revealed the remarkable combinatorial diversity of ribosomally synthesized and post-translationally modified peptides (RiPPs) in marine bacteria, including prochlorosins. However, mining strategies also prove valuable in investigating the genomic landscape of associated genes within biosynthetic gene cluster (BGC) specific to targeted RiPPs of interest. Our study contributes to the enrichment of knowledge regarding prochlorosin diversity. It offers insights into potential mechanisms involved in their biosynthesis and modification, such as hyper-modification, which may give rise to active lantibiotics. Additionally, our study uncovers putative novel promiscuous post-translational enzymes, thereby expanding the chemical space explored within the Synechococcus genus. Moreover, this research extends the applications of mining techniques beyond the discovery of new RiPP-like clusters, allowing for a deeper understanding of genomics and diversity. Furthermore, it holds the potential to reveal previously unknown functions within the intriguing RiPP families, particularly in the case of prochlorosins.

Atypical Stem Cell, Pre-B-Cell, T-Cell and Myeloid Gene Expression Characterizes Early Waldenstrom's Macroglobulinemia Clones Which Diminishes with Advancing Disease and Has Therapeutic Implications

Background: In previous studies using multi-omic data for 253 treatment-naive patients with Waldenstrom's Macroglobulinemia (WM), we identified three subtypes of WM: B-cell like (BCL), Plasma cell like (PCL), and an intermediate clone enriched for early/smoldering WM from which the other two evolved (Hunter et al, ASH 2022). The BCL and PCL subtypes show distinct mutation and transcriptional signatures, as well as clinical characteristics. Diffusion pseudo-time (DPT) analysis suggests all patient tumors, regardless of subtype have a shared evolutionary path and can be divided into Early and Late DPT determined stages that mirror disease progression. Additional analysis of DPT suggests it represents a continuous process akin to clonal evolution. We therefore sought to further characterize the DPT signal in MYD88 mutated WM. Methods: RNASeq was performed on CD19-selected bone marrow (BM) samples from 249 of the 253 treatment-naive WM patients who were MYD88 mutated, as well as 13 paired CD19+CD27- and CD19+CD27+ selected healthy donor (HD) peripheral blood samples. Whole exome sequencing of CD19-selected BM cells along with CD19-depleted peripheral blood mononuclear controls was also performed for 215 of the WM samples. To assess BM histology, slides from 66 BM paraffin blocks from these WM patients were analyzed. Results: WM patients had median age of 66 (range 31-95 years), BM involvement of 50% (5-95%) and serum IgM level of 3,162 (104-10,321 mg/dL). The median follow-up for the study cohort was 8.8 (range 0.2 - 33.8 years). Patients were stratified into 5 cohorts by DPT values. Analysis of BM involvement by DPT cohorts revealed a stepwise increase with the median involvement rising from 20% in the lowest to 80% in the highest cohort (p<0.0001). Increasing DPT predicted for shorter time from biopsy to first therapy (p=0.0003) but was not predictive of time from diagnosis to first therapy consistent with DPT alignment by stage of WM development. RNASeq analysis revealed high expression of genes atypical of mature B-cells that diminished with increasing DPT ( Figure 1). Among these were the myeloid chemo-attractants CXCL1, CXCL8 and CXCL12 which fell from a median of 4.4, 67.2 and 41.1 to 0.1, 3.6 and 0.8 transcripts per million (TpM) in the lowest and highest DPT cohorts, respectively (p<0.0001). Accordingly, all the top 20 gene ontology (GO) terms associated with DPT were related to activation, degranulation, and migration of myeloid cells and leukocytes. Pathological review of the 66 BM slides ranked by DPT, showed increased early myeloid cells and eosinophils clustering near small lymphoid aggregates, and as DPT increased, increased lymphocytes and mast cells with decreased myeloid cell involvement was observed. By RNASeq, pre-B-cell genes including MYB, the VDJ recombination genes RAG1, RAG2 and DNTT as well as the surrogate light chain genes IGLL1 and VPREB1 fell from 22.5, 10, 13.5, 61.1, 144 and 38.3 to 2.2, 1, 1.1, 9.1, 12.2 and 4.3 TpM, respectively (p<0.0001). T-cell and myeloid genes including CD4, CD8A, FCGR3A (CD16), CD14 and CD33 also decreased with increased DPT from 67.6, 7.1, 80.5, 200, and 23.2 to 2.4, 0.9, 1.7, 3.6 and 0.7 TpM, respectively (p<0.0005). A subclonal stem cell signature was also detected, including CD34 and KIT (CD117), which fell from 1.67 and 0.64 to 0.15 and 0.06 TpM, respectively (0<0.0001). CD34, KIT, preBCR, CD4, CD8A, FCGR3A, CEACAM8 (CD66b), and CD33 expression was confirmed by CD19+ light chain restricted flow cytometry in WM but not in HD samples. In addition, the MB and plasma blast genes PRDM1 and XBP1 were elevated in all samples regardless of DPT, consistent with a putative memory B-cell origin. Progression free survival (PFS) in response to proteasome inhibitors revealed strong stratification by subtype (p=0.001), as well as inferior PFS with BTK-inhibitors in low DPT patients (p= 0.044; Figure 2), suggesting less BTK dependence in the early DPT clones. Consistent with this finding, gene set enrichment identified increased BCR signaling with increased DPT. Conclusions: This analysis suggests that stem cell program reactivation and atypical marker expression characterize early WM clones that are ultimately replaced by clones exhibiting more typical B-cell markers with disease progression. The findings may be relevant to treatment selection and provide a framework for investigating subtype and early/late evolutionary staging in the treatment approach to WM.

Novel bimodal TRBD1-TRBD2 rearrangements with dual or absent D-region contribute to TRB V-(D)-J combinatorial diversity.

T-cell receptor (TR) diversity of the variable domains is generated by recombination of both the alpha (TRA) and beta (TRB) chains. The textbook process of TRB chain production starts with TRBD and TRBJ gene rearrangement, followed by the rearrangement of a TRBV gene to the partially rearranged D-J gene. Unsuccessful V-D-J TRB rearrangements lead to apoptosis of the cell. Here, we performed deep sequencing of the poorly explored pool of partial TRBD1-TRBD2 rearrangements in T-cell genomic DNA. We reconstructed full repertoires of human partial TRBD1-TRBD2 rearrangements using novel sequencing and validated them by detecting V-D-J recombination-specific byproducts: excision circles containing the recombination signal (RS) joint 5'D2-RS - 3'D1-RS. Identified rearrangements were in compliance with the classical 12/23 rule, common for humans, rats, and mice and contained typical V-D-J recombination footprints. Interestingly, we detected a bimodal distribution of D-D junctions indicating two active recombination sites producing long and short D-D rearrangements. Long TRB D-D rearrangements with two D-regions are coding joints D1-D2 remaining classically on the chromosome. The short TRB D-D rearrangements with no D-region are signal joints, the coding joint D1-D2 being excised from the chromosome. They both contribute to the TRB V-(D)-J combinatorial diversity. Indeed, short D-D rearrangements may be followed by direct V-J2 recombination. Long D-D rearrangements may recombine further with J2 and V genes forming partial D1-D2-J2 and then complete V-D1-D2-J2 rearrangement. Productive TRB V-D1-D2-J2 chains are present and expressed in thousands of clones of human antigen-experienced memory T cells proving their capacity for antigen recognition and actual participation in the immune response.

The immunogenicity of human-origin therapeutic antibodies are associated with V gene usage.

Therapeutic antibodies can elicit unwanted immune responses in a subset of patients, which leads to the production of anti-drug antibodies (ADA). Some of these ADAs have been reported to effect the pharmacokinetics, efficacy and/or safety of the therapeutic antibodies. The sequence diversity of antibodies are generated by VDJ recombination and mutagenesis. While the antibody generation process can create a large candidate pool for identifying high-affinity antibodies, it also could produce sequences that are foreign to the human immune system. However, it is not clear how VDJ recombination and mutagenesis impact the clinical ADA rate of therapeutic antibodies. In this study, we identified a positive correlation between the clinical ADA rate and the number of introduced mutations in the antibody sequences. We also found that the use of rare V alleles in human-origin antibody therapeutics is associated with higher risk of immunogenicity. The results suggest that antibody engineering projects should start with frameworks that contain commonly used V alleles and prioritize antibody candidates with low number of mutations to reduce the risk of immunogenicity.

A dual function for the chromatin organizer Special A-T rich Binding Protein 1 in B-lineage cells.

SATB1 (Special A-T rich Binding protein 1) is a cell type-specific factor that regulates the genetic network in developing T cells and neurons. In T cells, SATB1 is required for lineage commitment, VDJ recombination, development and maturation. Considering that its expression varies during B-cell differentiation, the involvement of SATB1 needs to be clarified in this lineage. Using a KO mouse model in which SATB1 was deleted from the pro-B-cell stage, we examined the consequences of SATB1 deletion in naive and activated B-cell subsets. Our model indicates first, unlike its essential function in T cells, that SATB1 is dispensable for B-cell development and the establishment of a broad IgH repertoire. Second, we show that SATB1 exhibits an ambivalent function in mature B cells, acting sequentially as a positive and negative regulator of Ig gene transcription in naive and activated cells, respectively. Third, our study indicates that the negative regulatory function of SATB1 in B cells extends to the germinal center response, in which this factor limits somatic hypermutation of Ig genes.

Exploiting big data survival information to unify risk-stratification related, adaptive immune receptor parameters for multiple myeloma.

With the improvement of treatment options, multiple myeloma related life expectancy has been prolonged, but the disease remains largely incurable. Immunotherapy is a growing field that shows promise in advancements for treatment, and recent work has demonstrated an opportunity to use immune receptor, complementarity determining region-3 (CDR3)-candidate antigen chemical complementarity scores to identify survival distinctions among subgroups of patients. Here, we have applied the complementarity scoring algorithm to identify multiple myeloma related, CDR3-cancer testis antigen (CTA) relationships associated with survival distinctions. Furthermore, we have overlapped these immune receptor features with a previous study that showed a dramatic survival distinction based on T-cell receptor, V- and J-gene segment usage, HLA allele combinations, whereby 100% of the patients in certain combination groups had no mortality related to multiple myeloma, during the study period. This overlap evaluation was consistent with the idea that there are likely considerable constraints on productive TRB-antigen-HLA combinations but more flexibility, and unpredictability, for the TRA-antigen-HLA combinations. Also, the approaches in this reported indicated the potential importance of the CTA, IGSF11, as a multiple myeloma antigen, an antigen previously, independently considered as a vaccine candidate in other settings.

The recombinase activating genes: architects of immune diversity during lymphocyte development.

The mature lymphocyte population of a healthy individual has the remarkable ability to recognise an immense variety of antigens. Instead of encoding a unique gene for each potential antigen receptor, evolution has used gene rearrangements, also known as variable, diversity, and joining gene segment (V(D)J) recombination. This process is critical for lymphocyte development and relies on recombination-activating genes-1 (RAG1) and RAG2, here collectively referred to as RAG. RAG serves as powerful genome editing tools for lymphocytes and is strictly regulated to prevent dysregulation. However, in the case of dysregulation, RAG has been implicated in cases of cancer, autoimmunity and severe combined immunodeficiency (SCID). This review examines functional protein domains and motifs of RAG, describes advances in our understanding of the function and (dys)regulation of RAG, discuss new therapeutic options, such as gene therapy, for RAG deficiencies, and explore in vitro and in vivo methods for determining RAG activity and target specificity.

Evolution of immunogenetic components encoding ultralong CDR H3.

The genomes of most vertebrates contain many V, D, and J gene segments within their Ig loci to construct highly variable CDR3 sequences through combinatorial diversity. This nucleotide variability translates into an antibody population containing extensive paratope diversity. Cattle have relatively few functional VDJ gene segments, requiring innovative approaches for generating diversity like the use of ultralong-encoding IGHV and IGHD gene segments that yield dramatically elongated CDR H3. Unique knob and stalk microdomains create protracted paratopes, where the antigen-binding knob sits atop a long stalk, allowing the antibody to bind both surface and recessed antigen epitopes. We examined genomes of twelve species of Bovidae to determine when ultralong-encoding IGHV and IGHD gene segments evolved. We located the 8-bp duplication encoding the unique TTVHQ motif in ultralong IGHV segments in six Bovid species (cattle, zebu, wild yak, domestic yak, American bison, and domestic gayal), but we did not find evidence of the duplication in species beyond the Bos and Bison genera. Additionally, we analyzed mRNA from bison spleen and identified a rich repertoire of expressed ultralong CDR H3 antibody mRNA, suggesting that bison use ultralong IGHV transcripts in their host defense. We found ultralong-encoding IGHD gene segments in all the same species except domestic yak, but again not beyond the Bos and Bison clade. Thus, the duplication event leading to this ultralong-encoding IGHV gene segment and the emergence of the ultralong-encoding IGHD gene segment appears to have evolved in a common ancestor of the Bos and Bison genera 5-10 million years ago.

Function and Evolution of the Loop Extrusion Machinery in Animals.

Structural maintenance of chromosomes (SMC) complexes are essential proteins found in genomes of all cellular organisms. Essential functions of these proteins, such as mitotic chromosome formation and sister chromatid cohesion, were discovered a long time ago. Recent advances in chromatin biology showed that SMC proteins are involved in many other genomic processes, acting as active motors extruding DNA, which leads to the formation of chromatin loops. Some loops formed by SMC proteins are highly cell type and developmental stage specific, such as SMC-mediated DNA loops required for VDJ recombination in B-cell progenitors, or dosage compensation in Caenorhabditis elegans and X-chromosome inactivation in mice. In this review, we focus on the extrusion-based mechanisms that are common for multiple cell types and species. We will first describe an anatomy of SMC complexes and their accessory proteins. Next, we provide biochemical details of the extrusion process. We follow this by the sections describing the role of SMC complexes in gene regulation, DNA repair, and chromatin topology.

A Cre-LoxP-based approach for combinatorial chromosome rearrangements in human HAP1 cells.

Alterations of human karyotype caused by chromosomal rearrangements are often associated with considerable phenotypic effects. Studying molecular mechanisms underlying these effects requires an efficient and scalable experimental model. Here, we propose a Cre-LoxP-based approach for the generation of combinatorial diversity of chromosomal rearrangements. We demonstrate that using the developed system, both intra- and inter-chromosomal rearrangements can be induced in the human haploid HAP1 cells, although the latter is significantly less effective. The obtained genetically modified HAP1 cell line can be used to dissect genomic effects associated with intra-chromosomal structural variations.

Enhancer-instructed epigenetic landscape and chromatin compartmentalization dictate a primary antibody repertoire protective against specific bacterial pathogens.

Antigen receptor loci are organized into variable (V), diversity (D) and joining (J) gene segments that rearrange to generate antigen receptor repertoires. Here, we identified an enhancer (E34) in the murine immunoglobulin kappa (Igk) locus that instructed rearrangement of Vκ genes located in a sub-topologically associating domain, including a Vκ gene encoding for antibodies targeting bacterial phosphorylcholine. We show that E34 instructs the nuclear repositioning of the E34 sub-topologically associating domain from a recombination-repressive compartment to a recombination-permissive compartment that is marked by equivalent activating histone modifications. Finally, we found that E34-instructed Vκ-Jκ rearrangement was essential to combat Streptococcus pneumoniae but not methicillin-resistant Staphylococcus aureus or influenza infections. We propose that the merging of Vκ genes with Jκ elements is instructed by one-dimensional epigenetic information imposed by enhancers across Vκ and Jκ genomic regions. The data also reveal how enhancers generate distinct antibody repertoires that provide protection against lethal bacterial infection.

DNA repair defects and inborn errors of immunity: why we need to fix what is broken

DNA damage is part and parcel of the life of a cell and an organism. Cells respond to DNA damage by initiating DNA damage response (DDR) pathways that allow for removal of the damaged DNA and subsequent repair. At least five major pathways of DNA repair operate in humans – base excision repair (BER), nucleotide excision repair (NER), mismatch repair (MMR) and DNA double-strand break repair (DSB), which involves homologous recombination (HR) and non-homologous end-joining (NHEJ). This talk will focus on DNA DSB repair, which is most commonly used in the immune system. Genetic diversity, through VDJ recombination, class-switch recombination and somatic hypermutation are essential in T and B cells, and are managed by numerous DNA repair pathways, but most prominently DNA DSB repair. Genetic defects in genes associated with DNA DSB repair are associated with syndromic immunodeficiencies (e.g., ataxia telangiectasia, Nijmegen Breakage Snydrome) or radiosensitive forms of severe combined immunodeficiency (rs-SCID), e.g., Artemis SCID, DNA ligase IV defects, Cernunnos deficiency, DNA-PKcs defects among others. These conditions are collectively called XCIND (X-ray/radiation sensitivity, cancer susceptibility, immunodeficiency, neurological development defects). This talk will provide an overview of DNA DSB repair defects and discuss a new flow cytometry assay, which is used for the diagnosis of these disorders in the clinical laboratory.

Pathological characteristics of light chain crystalline podocytopathy

Monoclonal immunoglobulin light chain (LC) crystalline inclusions within podocytes are rare, poorly characterized entities. To provide more insight, we now present the first clinicopathologic series of LC crystalline podocytopathy (LCCP) encompassing 25 patients (68% male, median age 56 years). Most (80%) patients presented with proteinuria and chronic kidney disease, with nephrotic syndrome in 28%. Crystalline keratopathy and Fanconi syndrome were present in 22% and 10%, respectively. The hematologic condition was monoclonal gammopathy of renal significance (MGRS) in 55% and multiple myeloma in 45%. The serum monoclonal immunoglobulin was IgG κappa in 86%. Histologically, 60% exhibited focal segmental glomerulosclerosis (FSGS), often collapsing. Ultrastructurally, podocyte LC crystals were numerous with variable effacement of foot processes. Crystals were also present in proximal tubular cells as light chain proximal tubulopathy (LCPT) in 80% and in interstitial histiocytes in 36%. Significantly, frozen-section immunofluorescence failed to reveal the LC composition of crystals in 88%, requiring paraffin-immunofluorescence or immunohistochemistry, with identification of kappa LC in 87%. The LC variable region gene segment, determined by mass spectrometry of glomeruli or bone marrow plasma cell sequencing, was IGKV1-33 in four and IGKV3-20 in one. Among 21 patients who received anti-plasma cell-directed chemotherapy, 50% achieved a kidney response, which depended on a deep hematologic response. After a median follow-up of 36 months, 26% progressed to kidney failure and 17% died. The mean kidney failure-free survival was 57.6 months and was worse in those with FSGS. In sum, LCCP is rare, mostly associates with IgG κappa MGRS, and frequently has concurrent LCPT, although Fanconi syndrome is uncommon. Paraffin-immunofluorescence and electron microscopy are essential to prevent misdiagnosis as primary FSGS since kidney survival depends on early diagnosis and subsequent clone-directed therapy.

A Hands-on Activity for V(D)J Recombination in an Undergraduate Immunology Class.

This learning activity teaches the difficult concept of V(D)J recombination as it occurs in B cells. Following the traditional lecture, this hands-on activity uses pipe cleaners of various colors representing variable, joining, and diversity gene segments and recombination signal sequences. Students are provided with instructions for using the pipe cleaners to assemble specific light and heavy immunoglobulin chains. Students each assemble their own light and heavy chains and compare the products made by classmates. This activity uses materials that are easy and affordable to acquire and provides a tactile approach to reinforcing concepts that students often struggle to visualize and master from lecture and textbook material alone.

Improved Quantitative Approach for Monitorization of Gangliosides Structural Diversity in Fungal Cell Factories by LC-MS/MS

Gangliosides are glycolipids occurring in higher animals, with a sphingoid core in the form of ceramide, bound to a glycan moiety including several units of sialic acid. Gangliosides are involved in important (patho)-physiological processes as components of cell membranes in humans, which has led to intensive study and interest in production strategies. Their structural variability depends on the combination of a sphingoid base, a fatty acyl chain, and an attached oligosaccharide. The combinatorial diversity differs and grows exponentially in synthetic biology approaches, e.g., use of microbial cell factories. A specific analytical platform accounting for this complexity is not available to date. However, quantification of the intermediates of the whole biosynthetic route is needed to boost projects on biotechnological ganglioside production. In this study, a fast high-throughput quantitative LC-MS/MS methodology was developed to cover analysis of gangliosides, with a wider structural perspective adapted to fungal organisms. This work was achieved using metabolically engineered strains that further allowed to test detection in biological complex matrixes. Ganglioside backbones—hitherto uncharacterized—with the five most common fungal sphingoid bases and both simple and hydroxylated fatty acids were subjected to characterization. The addition of glycans to the polar head was also successfully monitored with up to 4 units—corresponding to GD3 which bears two sialic acid units and furthermore represents the common precursor for the whole ganglio-series. This platform represents an improved methodology to study the biochemical diversity associated to gangliosides for natural and metabolically engineered biosynthetic pathways.

Intergenic Non-Switch Immunoglobulin Translocations Are Frequently Observed in Genomically Unstable MM

Multiple myeloma (MM) is a B cell malignancy involving terminally differentiated plasma cells that is often initially driven by translocations of the IGHgene at 14q32 (tIGH, observed in ~35% of patients). It is believed that the main cause of tIGH is activation-induced cytidine deaminase (AID), which is a protein that mediates antibody class switching. This is based on data from MM cell lines, where tIGH is located most often in breakpoints in the switch regions. However, it can also be in the VDJ regions, which implicates dysregulated VDJ recombination. To fully understand the mechanisms behind tIGH, we must first fully catalog the spectrum of these translocations and assess their association with other genomic features. Here, we analyzed deep whole-genome sequencing from 1257 newly diagnosed patients enrolled in the IFM or DFCI trials as well as the MMRF cohort. In addition, targeted sequencing data were collected from 4078 patients in the IFM network. tIGH breakpoints were classified according to their overlap with the switch, 3' regulatory (3'RR) or VDJ regions. If a breakpoint did not overlap with any of these regions, it was considered "intergenic". Overall, we identified tIGH in 38% of patients, and among all tIGH breakpoints, switch region translocations were the most frequent (59.5%) followed by 24.8% in the VDJ regions, 12% in intergenic regions and 3.7% in the 3'RR. We next looked at how common translocations in MM were related to various breakpoint locations. t(4;14) occurred almost exclusively in switch regions (95.7%, 95% CI 92.7-97.7%, p value < 2.2e-16). For other translocations (t(6;14), t(11;14), t(14;16), t(14;20)), tIGH tended to be in the switch regions (max 62%) but they were also present in VDJ regions (range 12.6 to 30.9%). On the other hand, for MYC-targeting translocations (t[8;14]), the most common breakpoints were in intergenic (37.8%, 95%CI 28.1-48.4%, p value = 9.5e-11) regions and the 3'RR. To investigate the mechanisms that translocate IGHto intergenic regions, we first searched for homology and found that intergenic breakpoint hotspots have a high sequence similarity between each other and IgHG1/2/3/4 (cosine distance > 0.80) unlike IgHA and IgHM. Because AID is involved in somatic hypermutation, we next investigated the mutational load of tIGH and found a significant increase in mutations (Kruskal-Wallis p value = 0.03) from VDJ to switch to intergenic patients. However, the intergenic group had significantly lower AID-related mutations on both an absolute (t test p value = 0.007) and normalized (t test p value = 0.002) scale. In addition, the intergenic group had increased genomic instability, as assessed by CNA segmentation and the percentage of the genome that was either amplified or deleted (Wilcoxon p value = 0.048). Furthermore, genes involved in genome instability and class switch-associated genes, like BLM and TP53BP1, were only mutated in the intergenic group. There were no KRAS mutations in the intergenic group (p value = 0.011), whereas BRAFmutations were much more common (p value=0.008, OR=17.3). Overall, our study indicates that multiple factors contribute to tIGH and these factors correlate to MM subgroups. tIGH in patients with t(4;14) is clearly associated with faulty class switching, likely caused by AID, whereas patients with other translocations appear to have multiple potential mechanisms. Interestingly, even within the MM subgroups, those patients with tIGH in an intergenic region have increased hypodiploidy frequency, implicating a mechanism that also plays a role in genomic stability.

I-FISH Guided Cytogenetic Study of Non-Hodgkin Lymphomas in Children and Adolescents: Correlation with Etiology and Outcome

Introduction: Pediatric non-Hodgkin lymphomas (NHLs) comprise approximately 10% of all childhood cancers. The diagnosis requires extensive workup with multiple ancillary studies. Genetic testing using fluorescence in situ hybridization (FISH) is a cytogenetic approach that is often utilized in pediatric NHL. Patients and Methods: Our study included 146 children (113 boys-33 girls), aged 0.33-17.8 years (median 9.16 years), with NHL diagnosis based on histopathology (table 1). The histological diagnosis was based on the complete microscopic and immunohistochemical study of infiltrated tissue. Touch imprints from the diagnostic biopsy samples were further investigated with i-FISH (table 2). Results: In all BL cases MYC gene rearrangement was identified. At least one additional chromosomal aberration was also found in 47 patients. Six hyperdiploid cases were identified among 72 children (8.3%), with at least 3 chromosomes involved. Interestingly, there were no cases of refractory disease, relapse, or death among hyperdiploid patients, and their overall survival (OS) was comparable to that of MYC rearrangement subgroup, a unique finding. Among LBL patients, a high frequency of 9p21 region deficiency was found, as in Acute Lymphoblastic Leukemia (ALL). Also, the chromosomes most frequently involved in hyperdiploid B-LBL (X,17,21) were identical to chromosomes commonly overrepresented in ALL. In contrast, the absence of cases positive for ETV6/RUNX1 hybrid gene is surprising. Possibly, the incidence of the most common cytogenetic atypias is different between leukemia and lymphoma. Of note, the two patients with KMT2A rearrangement achieved complete remission after first-line therapy. Finally, we identified cases with a normal karyotype but existing cytogenetic atypia demonstrable by i-FISH exclusively in LBLs. ALK gene rearrangement was found in all ALCL patients while no MYC gene rearrangement was found. At least one additional atypia was identified in 6/12 patients. Interestingly, ALCL patients had proportionally more recurrences than any other histological category, but without a corresponding increase in mortality. Among DLBCL group we found the highest rate of hyperdiploidy (22.2%). Only two (non-hyperdiploid) patients with BCL6 gene rearrangement were found. The single patient who relapsed had an IGL gene rearrangement, suggesting activation of an oncogene in the context of reciprocal chromosomal translocation involving the 22q11 region. No MYC or BCL2 gene rearrangements were found among DLBCL cases. In hyperdiploid patients, overrepresentation of chromosome 8 was found, along with overrepresentation of chromosome 3 (and, in addition, 18 in one of the two cases). This combination of atypias apparently leads to supernumerary copies of MYC gene, simultaneously with the presence of supernumerary alleles of BCL6 (or BCL2, respectively). Regarding findings in FL, MZL and PTLD, due to the small number of patients in these subgroups, any observation is of limited value. Absence of BCL2 gene rearrangement in childhood FL was confirmed. In the study's only patient with MZL, the identification of trisomy 3 may not be accidental, since this atypia is common in the corresponding adult disease. Of particular interest is the one patient with PTLD. Although monomorphic Burkitt-type PTLD was diagnosed and B-clonality documented based on VDJ recombination of IGH gene, marrow karyotyping and thorough i-FISH screening revealed no chromosomal atypia. The phenomenon has been highlighted in the literature and indicates that PTLD's aggressive clinical course is not necessarily associated with genomic instability and damage. In our study no patient met double-hit lymphoma criteria. We might wonder whether, in our series, the hyperdiploid patients with supernumerary copies of intact MYC, BCL2 and/or BCL6 genes constitute a subgroup of the "alternative" double hit lymphomas. With a median follow-up time of 61.5 months (range 7-123 months), 20 patients succumbed, yielding: 3-year and 5-year progression free survival (PFS) in all patients 84.5% και 82.5% respectively, and 3-year and 5-year OS in all patients 86.7%. Conclusions: This extensive i-FISH investigation provides clinically meaningful information on the genetic profile of NHLs, raises new questions, and points to directions for further investigation within the field of childhood lymphoproliferation. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Clonal Diversity As an Alternative Measure for Hematopoietic Reserve in Bone Marrow Failure

Fanconi anemia (FA) is the most common inherited bone marrow failure syndrome, typically presenting in early childhood. The pace of progression from diagnosis to symptomatic failure requiring therapy varies widely between patients, but peripheral blood cell counts, bone marrow cellularity and progenitor frequency measurement have proved poor predictors for the residual regenerative potential. Declining hematopoietic output in the context of aging or experimental stress leads to a decrease in clonal diversity. Here, we hypothesized that clonal diversity may also be an alternative measure for the residual hematopoietic functional reserve and developed an experimental platform to test our hypothesis. We crossed the previously described Confetti mouse model (Ganuza et al, NCB 2017) with a hematopoietic stem cell selective hSclCreERT Cre driver and the Fancc model of FA. We first optimized the clonal calculation formula to achieve an improved fit (R2: original 0.75, optimized: 0.96). We then performed a transplantation experiment with defined numbers of transplantable clones to directly validate performance (predicted: 250; original formula: 558, optimized formula: 354). Next, to determine homeostatic clonal diversity, we induced Confetti expression either in embryos at E14.5, or in adult mice at 2-month-old (n=30-, and ~60 mice, respectively) using the Confetti/hSclCreERT cross (no Fancc). In these cohorts we then measured the clonal diversity in peripheral blood myeloid and lymphoid subpopulations. We found that the number of B-cell clones marked by fetal induction was relatively stable before three-month of age (~7700 clones), followed by a decline to ~2700 clones at 7 months old. In contrast, T-cell clonal diversity marked by fetal induction was relatively stable for the observation period (~5100 to ~8000 clones). The number of granulocytes and myeloid clones at 7-month post-birth also decreased compared to that measured at one-month old (~6300 clones at one-month old; ~3600 clones at 7 months old). By contrast, clonal diversity and dynamics after adult induction differed substantially from fetal induction. Here we observed relatively greater clonal diversity at one-month post-induction in granulocytes and myeloid cells, which gradually declined to a stable level at 4-months post-induction. In contrast, clonal output measured from T-cell or B-cell was relatively stable throughout. We also examined the clonal diversity of stem and progenitor cells in the bone marrow (BM) at six months post-adult induction. In the adult induction cohort, we also found that the clonal diversity of granulocytes and myeloid cells in the peripheral blood was comparable with the clonal diversity of their progenitors in the BM (GMP and MPP3), suggesting peripheral blood clonal diversity as a reflection of the clonal diversity of the progenitors in the BM. Interestingly, we detected ~4500 clones in pre-pro-B cells, while only ~1300 clones in pro-B cells. This clonal contraction coincided with the stage when B-cell starts VDJ recombination. As a more conventional measure of residual activity, we next compared the frequency of stem and progenitor cell subpopulations in the BM with their clonal diversity and found that clonal diversity did not correlate with frequency. As an example, the frequency-to-clonal-diversity ratio of MPP2 progenitors is as low as LT-HSC even though MPP2 are much more highly proliferative, consistent with the notion that they contribute to downstream progenitor expansion, but are unable to symmetrically expand, thereby keeping their frequency low. Altogether, we have validated a system to measure clonal diversity and temporal dynamics in PB- and BM compartments. This provides us with reference metrics for clonal diversity studies in triple cross Confetti/hSclCreERT/Fancc-/- mice currently underway. We predict our approach will reveal reduced clonality in Fancc-/- mice and propose clonal diversity as a more accurate metric for functional reserve in BMF syndromes.

A double-negative thymocyte-specific enhancer augments Notch1 signaling to direct early T cell progenitor expansion, lineage restriction and β-selection.

T cell differentiation requires Notch1 signaling. In the present study, we show that an enhancer upstream of Notch1 active in double-negative (DN) mouse thymocytes is responsible for raising Notch1 signaling intrathymically. This enhancer is required to expand multipotent progenitors intrathymically while delaying early differentiation until lineage restrictions have been established. Early thymic progenitors lacking the enhancer show accelerated differentiation through the DN stages and increased frequency of B, innate lymphoid (IL) and natural killer (NK) cell differentiation. Transcription regulators for T cell lineage restriction and commitment are expressed normally, but IL and NK cell gene expression persists after T cell lineage commitment and T cell receptor β VDJ recombination, Cd3 expression and β-selection have been impaired. This Notch1 enhancer is inactive in double-positive (DP) thymocytes. Its aberrant reactivation at this stage in Ikaros mutants is required for leukemogenesis. Thus, the DN-specific Notch1 enhancer harnesses the regulatory architecture of DN and DP thymocytes to achieve carefully orchestrated changes in Notch1 signaling required for early lineage restrictions and normal T cell differentiation.