Molecular mechanisms of lymphomagenesis through transcriptional disregulation by chromosome translocation

Targeted Locus Amplification as Marker Screening Approach to Detect Immunoglobulin (IG) Translocations in B-Cell Non-Hodgkin Lymphomas

Although MRD monitoring by the classic polymerase chain reaction (PCR) approach is a powerful outcome predictor, about 20% of mantle cell lymphoma (MCL) and 50% of follicular lymphoma (FL) patients still lack a molecular marker and are thus resulting not eligible for MRD monitoring. Targeted locus amplification (TLA), a new NGS technology, has been revealed as a feasible marker screening approach able to identify uncommon B-cell leukemia/lymphoma 1 (BCL1) and B-cell leukemia/lymphoma 2 (BCL2) rearrangements in MCL and FL cases defined as having "no marker" by the classic PCR approach.

Loss of Setd4 delays radiation-induced thymic lymphoma in mice

Radiation-induced lymphomagenesis results from a clonogenic lymphoid cell proliferation due to genetic alterations and immunological dysregulation. Mouse models had been successfully used to identify risk and protective factors for radiation-induced DNA damage and carcinogenesis. The mammalian SETD4 is a poorly understood putative methyl-transferase. Here, we report that conditional Setd4 deletion in adult mice significantly extended the survival of radiation-induced T-lymphoma. However, in Tp53 deficient mice, Setd4 deletion did not delay the radiation-induced lymphomagenesis although it accelerated the spontaneous T-lymphomagenesis in non-irradiated mice. The T-lymphomas were largely clonogenic in both Setd4^flox/flox and Setd4^Δ/Δ mice based on sequencing analysis of the T-cell antigen β receptors. However, the Setd4^Δ/Δ T-lymphomas were CD4⁺/CD8⁺ double positive, while the littermate Setd4^flox/floxtumor were largely CD8+ single positive. A genomic sequencing analysis on chromosome deletion, inversion, duplication, and translocation, revealed a larger contribution of inversion but a less contribution of deletion to the overall chromosome rearrangements in the in Setd4^Δ/Δ tumors than the Setd4^flox/flox tumors. In addition, the Setd4^flox/flox mice died more often from the large sizes of primary thymus lymphoma at earlier time, but there was a slight increase of lymphoma dissemination among peripheral organs in Setd4^Δ/Δ at later times. These results suggest that Setd4 has a critical role in modulating lymphomagenesis and may be targeted to suppress radiation-induced carcinogenesis.

Nonsense-mediated mRNA decay: The challenge of telling right from wrong in a complex transcriptome

The nonsense-mediated mRNA decay pathway selects and degrades its targets using a dense network of RNA-protein and protein-protein interactions. Together, these interactions allow the pathway to collect copious information about the translating mRNA, including translation termination status, splice junction positions, mRNP composition, and 3'UTR length and structure. The core NMD machinery, centered on the RNA helicase UPF1, integrates this information to determine the efficiency of decay. A picture of NMD is emerging in which many factors contribute to the dynamics of decay complex assembly and disassembly, thereby influencing the probability of decay. The ability of the NMD pathway to recognize mRNP features of diverse potential substrates allows it to simultaneously perform quality control and regulatory functions. In vertebrates, increased transcriptome complexity requires balance between these two functions since high NMD efficiency is desirable for maintenance of quality control fidelity but may impair expression of normal mRNAs. NMD has adapted to this challenge by employing mechanisms to enhance identification of certain potential substrates, while using sequence-specific RNA-binding proteins to shield others from detection. These elaborations on the conserved NMD mechanism permit more sensitive post-transcriptional gene regulation but can have severe deleterious consequences, including the failure to degrade pathogenic aberrant mRNAs in many B cell lymphomas. This article is categorized under: RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms.

hnRNP L-dependent protection of normal mRNAs from NMD subverts quality control in B cell lymphoma

The human nonsense-mediated mRNA decay pathway (NMD) performs quality control and regulatory functions within complex post-transcriptional regulatory networks. In addition to degradation-promoting factors, efficient and accurate detection of NMD substrates involves proteins that safeguard normal mRNAs. Here, we identify hnRNP L as a factor that protects mRNAs with NMD-inducing features including long 3'UTRs. Using biochemical and transcriptome-wide approaches, we provide evidence that the susceptibility of a given transcript to NMD can be modulated by its 3'UTR length and ability to recruit hnRNP L. Integrating these findings with the previously defined role of polypyrimidine tract binding protein 1 in NMD evasion enables enhanced prediction of transcript susceptibility to NMD. Unexpectedly, this system is subverted in B cell lymphomas harboring translocations that produce BCL2:IGH fusion mRNAs. CRISPR/Cas9 deletion of hnRNP L binding sites near the BCL2 stop codon reduces expression of the fusion mRNAs and induces apoptosis. Together, our data indicate that protection by hnRNP L overrides the presence of multiple 3'UTR introns, allowing these aberrant mRNAs to evade NMD and promoting BCL2 overexpression and neoplasia.

Abnormal AP-1 protein expression in primary cutaneous B-cell lymphomas

BACKGROUND

Primary cutaneous B-cell lymphoma (PCBCL) consists mainly of primary cutaneous marginal zone B-cell lymphoma (PCMZL), primary cutaneous follicle centre lymphoma (PCFCL) and primary cutaneous large B-cell lymphoma, leg type (PCLBCL-LT). The activator protein 1 (AP-1) transcription factor includes JUN, FOS and other family members.

OBJECTIVES

To assess the expression pattern of AP-1 transcription factors in PCBCL.

METHODS

We analysed paraffin tissue sections from nine cases of PCMZL, seven PCFCL, six PCLBCL-LT and two unspecified PCBCL cases by using immunohistochemistry with antibodies against c-JUN, JUNB, JUND, c-FOS, RAF1, alphaPAK, CD30 and CCND1.

RESULTS

A positive staining for JUND (++) was observed in six cases of PCFCL (86%), five PCLBCL-LT (83%) and five PCMZL (56%). Positive CCND1 protein expression was present in four cases of PCLBCL-LT (67%), four PCFCL (57%) and four PCMZL (44%), and the two unspecified PCBCL cases. Expression of alphaPAK protein was seen in three cases of PCLBCL-LT (50%), two PCMZL (22%) and one PCFCL. However, c-JUN, c-FOS and RAF1 protein were rarely expressed in the PCBCL cases analysed; JUNB and CD30 protein expression was absent in these cases.

CONCLUSIONS

These findings suggest that the presence of abnormal AP-1 protein expression is associated with upregulation of JUND, CCND1 and alphaPAK and downregulation of JUNB in PCBCL.

Presence of simian virus 40 in diffuse large B-cell lymphomas in Tunisia correlates with germinal center B-cell immunophenotype, t(14;18) translocation, and P53 accumulation

Previously we have reported the presence of simian virus 40 DNA in 56% of diffuse large B-cell lymphomas in Tunisia. Here, we investigated the relationship between the status of simian virus 40 and t(14;18) translocation, germinal center status, and P53 and BCL2 expression to assess the clinical and biological relevance of simian virus 40 presence in diffuse large B-cell lymphomas. Therefore, we evaluated by immunohistochemistry the expression patterns of CD10, BCL6, MUM1, BCL2, and P53 in 86 diffuse large B-cell lymphomas (48 simian virus 40-positive and 38 simian virus 40-negative cases). The t(14;18) translocation was investigated by polymerase chain reaction. Immunostaining patterns for CD10, BCL6, and MUM1 were used to subclassify diffuse large B-cell lymphoma cases as germinal center or non-germinal center phenotypes. Germinal center phenotype, t(14;18), P53, and BCL2 expression were found in 71, 30, 55, and 65% of cases, respectively. Interestingly, germinal center phenotype, t(14;18), and P53 accumulation were found to be more frequent in simian virus 40-positive cases than in simian virus 40-negative ones (81, 44, 69 vs 58, 13, 37%; P=0.018, 0.002, and 0.003, respectively). However, there were no correlations between the presence of simian virus 40 and the expression of CD10, BCL6, MUM1 and BCL2, patient's age and gender, clinical stage, or the International Prognosis Index. Multivariate logistic regression analyses revealed that the germinal center phenotype, P53 accumulation, and t(14;18) were independent factors for simian virus 40 association (P=0.029, 0.006, and 0.014, respectively). There were no significant differences in overall survival regarding P53, BCL2, or t(14;18) status. However, patients with germinal center phenotype or low International Prognosis Index scores displayed a significantly better survival than those with non-germinal center phenotype or high International Prognosis Index scores (P=0.003 and 0.0001, respectively). These two prognosis factors remain independent in multivariate analyses (P=0.001 and <0.0001, respectively). Interestingly, among patients with germinal center phenotype, simian virus 40-positive subgroup displayed a significantly shorter survival than simian virus 40-negative subgroup (P=0.034). In summary, these findings support a role of simian virus 40 in the pathogenesis of diffuse large B-cell lymphomas. On other hand, they suggest that a significant proportion of diffuse large B-cell lymphoma cases with germinal center phenotype may result from early transformation by simian virus 40, mainly those harboring the t(14;18). Modern Pathology (2008) 21, 282-296; doi:10.1038/modpathol.3800993; published online 28 December 2007.

Heterogeneous Abnormalities of CCND1 and RB1 in Primary Cutaneous T-Cell Lymphomas Suggesting Impaired Cell Cycle Control in Disease Pathogenesis

Upregulation of cyclin D1/B-cell leukemia/lymphoma 1 (CCND1/BCL1) is present in most mantle cell lymphomas with the t(11;14)(q13;q32) translocation. However, little is known about the abnormalities of CCND1 and its regulator RB1 in primary cutaneous T-cell lymphomas (CTCL). We analyzed CCND and RB status in CTCL using fluorescent in situ hybridization (FISH), immunohistochemistry (IHC), and Affymetrix expression microarray. FISH revealed loss of CCND1/BCL1 in five of nine Sézary syndrome (SS) cases but gain in two cases, and RB1 loss in four of seven SS cases. IHC showed absent CCND1/BCL1 expression in 18 of 30 SS, 10 of 23 mycosis fungoides (MF), and three of 10 primary cutaneous CD30+ anaplastic large-cell lymphoma (C-ALCL). Increased CCND1/BCL1 expression was seen in nine MF, seven C-ALCL, and six SS cases. Absent RB1 expression was detected in 8 of 12 MF and 7 of 9 SS cases, and raised RB1 expression in 7 of 8 C-ALCL. Affymetrix revealed increased gene expression of CCND2 in four of eight CTCL cases, CCND3 in three cases, and CDKN2C in two cases with a normal expression of CCND1 and RB1. These findings suggest heterogeneous abnormalities of CCND and RB in CTCL, in which dysregulated CCND and RB1 may lead to impaired cell cycle control.

Monoclonal B-cell hyperplasia and leukocyte imbalance precede development of B-cell malignancies in uracil-DNA glycosylase deficient mice

Ung-deficient mice have reduced class switch recombination, skewed somatic hypermutation, lymphatic hyperplasia and a 22-fold increased risk of developing B-cell lymphomas. We find that lymphomas are of follicular (FL) and diffuse large B-cell type (DLBCL). All FLs and 75% of the DLBCLs were monoclonal while 25% were biclonal. Monoclonality was also observed in hyperplasia, and could represent an early stage of lymphoma development. Lymphoid hyperplasia occurs very early in otherwise healthy Ung-deficient mice, observed as a significant increase of splenic B-cells. Furthermore, loss of Ung also causes a significant reduction of T-helper cells, and 50% of the young Ung(-/-) mice investigated have no detectable NK/NKT-cell population in their spleen. The immunological imbalance is confirmed in experiments with spleen cells where the production of the cytokines interferon gamma, interleukin 6 and interleukin 2 is clearly different in wild type and in Ung-deficient mice. This suggests that Ung-proteins, directly or indirectly, have important functions in the immune system, not only in the process of antibody maturation, but also for production and functions of immunologically important cell types. The immunological imbalances shown here in the Ung-deficient mice may be central in the development of lymphomas in a background of generalised lymphoid hyperplasia.

Long-term outcome of intractable ulcerating enterocolitis of infancy

BACKGROUND

Chronic enterocolitis is rare in infancy and accounts for less than 0.5% of all newly diagnosed inflammatory bowel disease (IBD) in the UK. Presentation at this young age is usually indicative of underlying immunodeficiency/immunodysregulation. A group of such infants suffer intractable ulcerating enterocolitis of infancy (IE) in which there is a pan-enteritis with marked oro-anal involvement and deep flask like mucosal ulcers throughout the colon.

METHODS

Retrospective review of presenting features, treatment and long-term outcome in a series of 8 children with typical IE.

RESULTS

The 8 children were aged between 1 and 4 weeks at onset (median 2 weeks, mean 2.3 weeks), of which 7 were followed up for 2-22 years (median 7.5 years, mean 11 years). All 8 children had an intractable disease course requiring a colectomy for control of symptoms. The median age at colectomy was 1.7 years (range 4 months-4 years). Three children developed a generalised lymphadenopathy due to uncontrolled EBV-related lymphoid proliferations (ages 4, 12, 18). These comprised a monomorphous B-lymphoycte lympho-proliferative disorder, a large pleomorphic follicular lymphoma, and a high grade pleomorphic B cell non-Hodgkin's lymphoma.

CONCLUSIONS

Infants with IE have a high risk of developing lymphomatous proliferations that appears to be related to the underlying immunodysregulation. Use of aggressive immunosuppression and acquisition of EBV infection appears to accelerate this process; hence we advocate early colectomy in confirmed cases. In children with IE screening for EBV and vigilance for abnormal lymphoid proliferations is paramount.