Molecular characterization of the region 7q22.1 in splenic marginal zone lymphomas

New Insights into the Biology and Diagnosis of Splenic Marginal Zone Lymphomas

Splenic marginal zone lymphoma (SMZL) is a small B-cell lymphoma, which has been recognized as a distinct pathological entity since the WHO 2008 classification. It classically presents an indolent evolution, but a third of patients progress rapidly and require aggressive treatments, such as immuno-chemotherapy or splenectomy, with all associated side effects. In recent years, advances in the comprehension of SMZL physiopathology have multiplied, thanks to the arrival of new devices in the panel of available molecular biology techniques, allowing the discovery of new molecular findings. In the era of targeted therapies, an update of current knowledge is needed to guide future researches, such as those on epigenetic modifications or the microenvironment of these lymphomas.

Establishment and characterization of HBV-associated B lymphocytes with an immortalization potential

Emerging evidences indicate that hepatitis B virus (HBV) infection is associated with non-Hodgkin lymphoma (NHL), but the mechanisms of HBV-induction lymphomagenesis remain unclear. In this report, retrospective analysis of the prevalence of hepatitis B surface antigen (HBsAg) among NHL cases demonstrated significantly higher HBsAg carrier rate among B-cell NHL cases than controls (other cancers except primary liver cancer) (adjusted odds ratio, 1.56; 95% confidence interval, 1.13–2.16). Furthermore, cells with an immortalization potential existed in the peripheral blood of 4 patients with chronic HBV infection. Characterization of these cells showed their immunophenotypes similar to that of the majority of HBsAg-positive B-cell NHL patients. Immunoglobulin (Ig) gene rearrangements confirmed the clonal Ig gene rearrangements. Cytogenetic analysis revealed abnormal karyotypes of these cells with an immortalization potential. Compared with cells with an immortalization potential that we previously found in B-cell NHL patients by the same way, these cells showed many similar features. In conclusion, cells with an immortalization potential existed in the part of patients with chronic HBV infection before lymphoma development and showed some malignant features. They may be the cellular basis of HBV-associated lymphomagenesis.

Deciphering splenic marginal zone lymphoma pathogenesis: the proposed role of microRNA

Splenic marginal zone lymphoma (SMZL) is a malignancy of mature B-cells that primarily involves the spleen, but can affect peripheral organs as well. Even though SMZL is overall considered an indolent malignancy, the majority of cases will eventually progress to be more aggressive. In recent years, the gene expression profile of SMZL has been characterized in an effort to identify: 1) the etiology of SMZL, 2) biological consequences of SMZL, and 3) putative therapeutic targets. However, due to the vast heterogeneity of the malignancy, no conclusive target(s) have been deciphered. However, the role of miRNA in SMZL, much as it has in chronic lymphocytic leukemia, may serve as a guiding light. As a result, we review the comprehensive expression profiling in SMZL to-date, as well as describe the miRNA (and potential mechanistic roles) that may play a role in SMZL transformation, particularly within the 7q region.

TRIM56-mediated monoubiquitination of cGAS for cytosolic DNA sensing

Intracellular nucleic acid sensors often undergo sophisticated modifications that are critical for the regulation of antimicrobial responses. Upon recognition of DNA, the cytosolic sensor cyclic GMP-AMP (cGAMP) synthase (cGAS) produces the second messenger cGAMP, which subsequently initiates downstream signaling to induce interferon-αβ (IFNαβ) production. Here we report that TRIM56 E3 ligase-induced monoubiquitination of cGAS is important for cytosolic DNA sensing and IFNαβ production to induce anti-DNA viral immunity. TRIM56 induces the Lys335 monoubiquitination of cGAS, resulting in a marked increase of its dimerization, DNA-binding activity, and cGAMP production. Consequently, TRIM56-deficient cells are defective in cGAS-mediated IFNαβ production upon herpes simplex virus-1 (HSV-1) infection. Furthermore, TRIM56-deficient mice show impaired IFNαβ production and high susceptibility to lethal HSV-1 infection but not to influenza A virus infection. This adds TRIM56 as a crucial component of the cytosolic DNA sensing pathway that induces anti-DNA viral innate immunity.

The protein cGAS responds to the presence of cytosolic DNA by producing the second messenger cGAMP, which triggers antiviral interferon responses. Here, Seo et al. show that ubiquitination by the E3 ligase TRIM56 enhances cGAS activity and is important for the immune response against DNA viruses.

Molecular pathogenesis of splenic and nodal marginal zone lymphoma

Genomic studies have improved our understanding of the biological basis of splenic (SMZL) and nodal (NMZL) marginal zone lymphoma by providing a comprehensive and unbiased view of the genes/pathways that are deregulated in these diseases. Consistent with the physiological involvement of NOTCH, NF-κB, B-cell receptor and toll-like receptor signaling in mature B-cells differentiation into the marginal zone B-cells, many oncogenic mutations of genes involved in these pathways have been identified in SMZL and NMZL. Beside genetic lesions, also epigenetic and post-transcriptional modifications contribute to the deregulation of marginal zone B-cell differentiation pathways in SMZL and NMZL. This review describes the progress in understanding the molecular mechanism underlying SMZL and NMZL, including molecular and post-transcriptional modifications, and discusses how information gained from these efforts has provided new insights on potential targets of diagnostic, prognostic and therapeutic relevance in SMZL and NMZL.

Chromothripsis Is a Recurrent Genomic Abnormality in High-Risk Myelodysplastic Syndromes

To explore novel genetic abnormalities occurring in myelodysplastic syndromes (MDS) through an integrative study combining array-based comparative genomic hybridization (aCGH) and next-generation sequencing (NGS) in a series of MDS and MDS/myeloproliferative neoplasms (MPN) patients. 301 patients diagnosed with MDS (n = 240) or MDS/MPN (n = 61) were studied at the time of diagnosis. A genome-wide analysis of DNA copy number abnormalities was performed. In addition, a mutational analysis of DNMT3A, TET2, RUNX1, TP53 and BCOR genes was performed by NGS in selected cases. 285 abnormalities were identified in 71 patients (23.6%). Three high-risk MDS cases (1.2%) displayed chromothripsis involving exclusively chromosome 13 and affecting some cancer genes: FLT3, BRCA2 and RB1. All three cases carried TP53 mutations as revealed by NGS. Moreover, in the whole series, the integrative analysis of aCGH and NGS enabled the identification of cryptic recurrent deletions in 2p23.3 (DNMT3A; n = 2.8%), 4q24 (TET2; n = 10%) 17p13 (TP53; n = 8.5%), 21q22 (RUNX1; n = 7%), and Xp11.4 (BCOR; n = 2.8%), while mutations in the non-deleted allele where found only in DNMT3A (n = 1), TET2 (n = 3), and TP53 (n = 4). These cryptic abnormalities were detected mainly in patients with normal (45%) or non-informative (15%) karyotype by conventional cytogenetics, except for those with TP53 deletion and mutation (15%), which had a complex karyotype. In addition to well-known copy number defects, the presence of chromothripsis involving chromosome 13 was a novel recurrent change in high-risk MDS patients. Array CGH analysis revealed the presence of cryptic abnormalities in genomic regions where MDS-related genes, such as TET2, DNMT3A, RUNX1 and BCOR, are located.

NF-κB deregulation in splenic marginal zone lymphoma

Splenic marginal zone lymphoma is a rare mature B-cell malignancy involving the spleen, bone marrow and blood. Over the past years, the rapid expansion of sequencing technologies allowing the genome-wide assessment of genomic, epigenetic and transcriptional changes has revolutionized our understanding of the biological basis of splenic marginal zone lymphoma by providing a comprehensive and unbiased view of the genes/pathways that are deregulated in this disease. NF-κB is a family of transcription factors that plays critical roles in development, survival, and activation of B lymphocytes. Consistent with the physiological involvement of NF-κB signalling in proliferation and commitment of mature B-cells to the marginal zone of the spleen, many oncogenic mutations involved in constitutive activation of the NF-κB pathway were recently identified in splenic marginal zone lymphoma. This review describes the progress in understanding the mechanism of NF-κB activation in splenic marginal zone lymphoma, including molecular, epigenetic and post-transcriptional modifications of NF-κB genes and of upstream pathways, and discusses how information gained from these efforts has provided new insights on potential targets of diagnostic, prognostic and therapeutic relevance for splenic marginal zone lymphoma.

Splenic marginal zone lymphoma: from genetics to management

Splenic marginal zone lymphoma (SMZL) is a rare B-cell malignancy involving the spleen, bone marrow, and frequently the blood. SMZL lymphomagenesis involves antigen and/or superantigen stimulation and molecular deregulation of genes (NOTCH2 and KLF2) involved in the physiological differentiation of spleen marginal zone B cells. Diagnosis requires either spleen histology or, alternatively, the documentation of a typical cell morphology and immunophenotype on blood cells coupled with the detection of intrasinusoidal infiltration by CD20+ cells in the bone marrow. Among B-cell tumors, deletion of 7q and NOTCH2 mutations are almost specific lesions of SMZL, thus representing promising diagnostic biomarkers of this lymphoma. Although the majority of SMZLs show an indolent course with a median survival of approximately 10 years, nearly 30% of patients experience a poor outcome. No randomized trials are reported for SMZL, and few prospective trials are available. A watch-and-wait approach is advisable for asymptomatic patients. Treatment options for symptomatic patients ranges from splenectomy to rituximab alone or combined with chemotherapy. In some geographic areas, a subset of patients with SMZL associates with hepatitis C virus infection, prompting virus eradication as an effective lymphoma treatment. It would be worthwhile to explore deregulated cellular programs of SMZL as therapeutic targets in the future; improved clinical and biological prognostication will be essential for identifying patients who may benefit from novel approaches.

Whole exome sequencing of microdissected splenic marginal zone lymphoma: a study to discover novel tumor-specific mutations

Background

Splenic marginal zone lymphoma (SMZL) is an indolent B-cell non-Hodgkin lymphoma and represents the most common primary malignancy of the spleen. Its precise molecular pathogenesis is still unknown and specific molecular markers for diagnosis or possible targets for causal therapies are lacking.

Methods

We performed whole exome sequencing (WES) and copy number analysis from laser-microdissected tumor cells of two primary SMZL discovery cases. Selected somatic single nucleotide variants (SNVs) were analyzed using pyrosequencing and Sanger sequencing in an independent validation cohort.

Results

Overall, 25 nonsynonymous somatic SNVs were identified, including known mutations in the NOTCH2 and MYD88 genes. Twenty-three of the mutations have not been associated with SMZL before. Many of these seem to be subclonal. Screening of 24 additional SMZL for mutations at the same positions found mutated in the WES approach revealed no recurrence of mutations for ZNF608 and PDE10A, whereas the MYD88 L265P missense mutation was identified in 15 % of cases. An analysis of the NOTCH2 PEST domain and the whole coding region of the transcription factor SMYD1 in eight cases identified no additional case with a NOTCH2 mutation, but two additional cases with SMYD1 alterations.

Conclusions

In this first WES approach from microdissected SMZL tissue we confirmed known mutations and discovered new somatic variants. Recurrence of MYD88 mutations in SMZL was validated, but NOTCH2 PEST domain mutations were relatively rare (10 % of cases). Recurrent mutations in the transcription factor SMYD1 have not been described in SMZL before and warrant further investigation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12885-015-1766-z) contains supplementary material, which is available to authorized users.

Whole-exome sequencing in splenic marginal zone lymphoma reveals mutations in genes involved in marginal zone differentiation

Splenic marginal zone lymphoma (SMZL) is a B-cell neoplasm whose molecular pathogenesis remains fundamentally unexplained, requiring more precise diagnostic markers. Previous molecular studies have revealed 7q loss and mutations of nuclear factor κB (NF-κB), B-cell receptor (BCR) and Notch signalling genes. We performed whole-exome sequencing in a series of SMZL cases. Results confirmed that SMZL is an entity distinct from other low-grade B-cell lymphomas, and identified mutations in multiple genes involved in marginal zone development, and others involved in NF-κB, BCR, chromatin remodelling and the cytoskeleton.

Unusual Course of Splenic Marginal Zone Lymphoma

A 53-year-old woman was diagnosed with splenic marginal zone lymphoma by pathological examination on left submandibular lymph node and bone marrow biopsies and markedly enlarged spleen. Four cycles of Rituximab chemotherapy were given. Seven months after finishing Rituximab chemotherapy, she developed left upper extremity swelling without evidence of deep venous thrombosis. Repeat PET/CT scan demonstrated multiple left axillary lymph nodes extending to left retroclavicular region and a new lymph node posterior to the left scapula. Biopsy of the lymph node demonstrated marginal zone lymhoma pattern with increased numbers of large cells, but not outright diffuse large B-cell lymphoma. Despite resuming rituximab, patient had persistent leukocytosis and severe anemia. Restaging PET/CT showed 3 new left anterior cervical lymph nodes and 1 new right axillary lymph node. Spleen has further enlarged. R-CHOP chemotherapy was started, which improved leukocytosis.After 4 cycles of R-CHOP, PET/CT showed new metabolic activity within right inguinal and abdominal lymph nodes. Patient was given one cycle of Bendamustine. She developed a possible “hematoma” in right medial elbow. However, MRI study revealed a subcutaneous deposit of the lymphoma. Patient needs consistently blood transfusion and she deteriorated quickly. Our patient had an aggressive course of splenic marginal zone lymphoma, not responding to four trials of chemotherapy although SMZL is well-known to be an indolent low grade lymphoma. This case report emphasizes the importance to individualize the treatment in SMZL patients and repeat bone marrow biopsy if the disease recurs.

Comparative outcomes of rituximab-based systemic therapy and splenectomy in splenic marginal zone lymphoma

Despite diagnostic and therapeutic advances, the majority of patients with splenic marginal zone lymphoma (SMZL) are still treated with splenectomy. We analyzed survival outcomes after surgery or rituximab-based systemic therapy in the Surveillance Epidemiology and End Results-Medicare database, using inverse probability of treatment weighting to minimize treatment selection bias. From the 657 recorded cases diagnosed between 2000 and 2007, with a median age of 77 years, we selected 227 eligible patients treated with splenectomy (68 %), rituximab alone (23 %), or in combination with chemotherapy (9 %) within 2 years from diagnosis. No significant difference between the groups was observed in the cumulative incidence of lymphoma-related death (LRD) at 3 years (19.6 % with systemic therapy and 17.3 % with splenectomy; hazard ratio [HR], 1.04; 95 % confidence interval [CI], 0.56-1.92; P = 0.90) or in the overall survival (HR, 1.01; 95 % CI, 0.66-1.55; P = 0.95). The 90-day mortality after splenectomy was 7.1 %. The rates of hospitalizations, infections, transfusions, and cardiovascular or thromboembolic events were higher after combination chemoimmunotherapy than after splenectomy. Conversely, there was no significant difference in most complications between groups treated with splenectomy or rituximab alone. The cumulative incidence of LRD after single-agent rituximab at 3 years was 18.7 % (95 % CI, 8.6-31.7). In conclusion, in SMZL patients over the age of 65 years, the risk of LRD and overall survival are similar with systemic therapy or splenectomy as initial therapy. Single-agent rituximab may offer the most favorable risk/benefit ratio in this population.

Copy number variation in ACHE/EPHB4 (7q22) and in BCHE/MME (3q26) genes in sporadic breast cancer

Gene amplifications and deletions are common changes in human cancer cells. Previous studies indicate that the regions, where the ACHE (7q22) and BCHE (3q26.1-q26.2) genes are localized, are suffering such structural modifications in breast cancer. Therefore, the products of these genes, acetylcholinesterase and butyrylcholinesterase, respectively, are related to the process of cell differentiation and proliferation, as well as apoptosis. This study also included two other genes involved in tumorigenesis, the EPHB4 (7q22.1) and MME (3q21-27). The aim of this study was to verify amplification and/or deletion in the ACHE, BCHE, EPHB4 and MME genes in 32 samples of sporadic breast cancer. The gene alterations were detected using real-time PCR and determined by relative quantification with the standard curve method. All samples presented genetic alterations, showing a higher tendency for amplification of the ACHE (62.5% vs. 37.5%; p>0.1) and EPHB4 (53.13% vs. 46.88%; p>0.5) genes, and for deletions of the BCHE and MME genes (56.25% vs. 43.75% for both; p>0.5). A positive correlation was found between alterations in ACHE-EPHB4 and BCHE-MME pairs (r(s) = 0.5948; p = 0.0004; r(s) = 0.3581; p = 0.0478, respectively) indicating that these changes comprise a wide region. In conclusion, the results suggest that these genomic regions may contain important genes for this pathology, such as the oncogenes MET (7q31) and PIK3CA (3q26), and thus being interesting targets for future studies in breast cancer research.

The coding genome of splenic marginal zone lymphoma: activation of NOTCH2 and other pathways regulating marginal zone development

Splenic marginal zone lymphoma (SMZL) is a B cell malignancy of unknown pathogenesis, and thus an orphan of targeted therapies. By integrating whole-exome sequencing and copy-number analysis, we show that the SMZL exome carries at least 30 nonsilent gene alterations. Mutations in NOTCH2, a gene required for marginal-zone (MZ) B cell development, represent the most frequent lesion in SMZL, accounting for ∼20% of cases. All NOTCH2 mutations are predicted to cause impaired degradation of the NOTCH2 protein by eliminating the C-terminal PEST domain, which is required for proteasomal recruitment. Among indolent B cell lymphoproliferative disorders, NOTCH2 mutations are restricted to SMZL, thus representing a potential diagnostic marker for this lymphoma type. In addition to NOTCH2, other modulators or members of the NOTCH pathway are recurrently targeted by genetic lesions in SMZL; these include NOTCH1, SPEN, and DTX1. We also noted mutations in other signaling pathways normally involved in MZ B cell development, suggesting that deregulation of MZ B cell development pathways plays a role in the pathogenesis of ∼60% SMZL. These findings have direct implications for the treatment of SMZL patients, given the availability of drugs that can target NOTCH, NF-κB, and other pathways deregulated in this disease.