Prevalence and analysis of t(14;18) and t(11;14) chromosomal translocations in healthy Indian population

Mutations at BCL11B Exon 4 Associated with T Cell Acute Lymphoblastic Leukemia Are Facilitated by AID and Formation of Non-B DNA Conformations

One of the primary reasons behind the pathogenesis of T cell acute lymphoblastic leukemia (T-ALL) is the deregulation of the transcription factor BCL11B. The exon 4 of BCL11B harbors several driver mutations, which abolishes its DNA-binding ability. The high frequency of C > T or G > A conversion in close vicinity of AID (Activation-induced cytidine deaminase)-hotspot motifs in the deregulated gene prompted us to investigate the role of AID in BCL11B mutagenesis. Our results reveal that AID is expressed in T-ALL patient-derived cells, binds to BCL11B fragile region (FR) in exon 4 of T cells in vivo, and generates a signature mutation pattern in this region. The mutation frequency in BCL11B FR could be modulated upon overexpression of the AID gene in the knockout background, further suggesting the involvement of AID in BCL11B mutagenesis. Importantly, various lines of experimentation reveal that BCL11B FR could fold into parallel G-quadruplex, triplex, and hairpin structures, which could act as a replication/transcription block, causing mutagenesis. Thus, our results suggest that AID binds to BCL11B exon 4 due to non-B DNA formation, causing U:G mismatches or replication blocks, which, when repaired erroneously, generates deleterious mutations, resulting in loss of functionality of BCL11B, and thus becomes the cause of T-ALL.

Evaluation of potential role of R-loop and G-quadruplex DNA in the fragility of c-MYC during chromosomal translocation associated with Burkitt's lymphoma

t(8;14) translocation is the hallmark of Burkitt's lymphoma and results in c-MYC deregulation. During the translocation, c-MYC gene on chromosome 8 gets juxtaposed to the Ig switch regions on chromosome 14. Although the promoter of c-MYC has been investigated for its mechanism of fragility, little is known about other c-MYC breakpoint regions. We have analyzed the translocation break points at the exon 1/intron 1 of c-MYC locus from patients with Burkitt's lymphoma. Results showed that the breakpoint region, when present on a plasmid, could fold into an R-loop confirmation in a transcription-dependent manner. Sodium bisulfite modification assay revealed significant single-strandedness on chromosomal DNA of Burkitt's lymphoma cell line, Raji, and normal lymphocytes, revealing distinct R-loops covering up to 100 bp region. Besides, ChIP-DRIP analysis reveals that the R-loop antibody can bind to the breakpoint region. Further, we show the formation of stable parallel intramolecular G-quadruplex on non-template strand of the genome. Finally, incubation of purified AID in vitro or overexpression of AID within the cells led to enhanced mutation frequency at the c-MYC breakpoint region. Interestingly, anti-γH2AX can bind to DSBs generated at the c-MYC breakpoint region within the cells. The formation of R-loop and G-quadruplex was found to be mutually exclusive. Therefore, our results suggest that AID can bind to the single-stranded region of the R-loop and G4 DNA, leading to the deamination of cytosines to uracil and induction of DNA breaks in one of the DNA strands, leading to double-strand break, which could culminate in t(8;14) chromosomal translocation.

Precursory or early lesions of follicular lymphoma: clinical features, pathology, and genetics

Follicular lymphoma (FL) is an indolent B-cell lymphoma with a germinal center (GC) B cell phenotype that typically harbors t(14;18)(q32;q21). t(14;18) juxtaposes IGH on 14q32 and BCL2 on 18q21, resulting in overexpression of the anti-apoptotic BCL2 protein. However, t(14;18) is also found in the peripheral blood or lymphoid nodes (LNs) of otherwise healthy individuals. Moreover, overt FL has several additional gene alterations involved in epigenetic modification, JAK/STAT signaling, immune modulation, and NF-κB signaling, indicating multi-step lymphomagenesis in FL. There are two early or precursory lesions of FL: t(14;18)-positive cells in the peripheral blood of otherwise healthy individuals and in situ follicular B-cell neoplasm (ISFN). t(14;18)-positive cells are found in 10%-50% of healthy populations, and their incidence and frequency increase with age. The detection of t(14;18) in peripheral blood is a predictive factor for an increased risk of overt FL development. In contrast, ISFN is a histopathologically recognizable precursory lesion, in which t(14;18)-positive cells are confined to the GC of otherwise reactive LNs. ISFN is usually detected incidentally, with an incidence ranging from 2.0% to 3.2%. Occasional ISFN cases have concurrent or metachronous clonally related overt FL or aggressive B-cell lymphoma of a GC phenotype. t(14;18)-positive cells in peripheral blood and isolated ISFN, by themselves, are asymptomatic with limited clinical significance; however, investigations of t(14;18)-positive precursory or early lesions offer meaningful insights into the pathogenesis of FL. This review summarizes the epidemiology, clinical features, pathology, and genetics of precursory or early lesions of FL.

Quantitative analysis of cell-free DNA by droplet digital PCR reveals the presence of EGFR mutations in non-malignant lung pathologies

Tyrosine kinase inhibitors (TKIs) targeting epidermal growth factor receptor (EGFR) are effectively used in treatment of non-small cell lung cancer (NSCLC). Mutation profile of tyrosine kinase domain of EGFR determines the eligibility of the patients for tyrosine kinase inhibitor (TKI) therapy. Liquid biopsy, which relies on circulating tumor-derived nucleic acids, has emerged as an effective tool in lung cancer management with proven diagnostic, prognostic and predictive applications. We screened 100 subjects, suspected to have lung malignancy, for four hotspot mutations including three activating (G719S, Ex19del E746-A750 and L858R) and one acquired (T790M, de novo) in EGFR gene by droplet digital PCR (ddPCR). While 97 subjects were subsequently confirmed to have lung malignancy based on histo/cytopathological studies, three cases turned out to be non-malignant lung pathologies that were completely cured by antibiotic therapy. Intriguingly, ddPCR revealed the presence of EGFR mutations in these non-malignant subjects. Two cases showed the presence of G719S and T790M mutations respectively and another had compound mutations (T790M and L858R). The detection of EGFR mutations in non-malignant pulmonary conditions opens up a new area of research.

Prevalence of BCL-2/J(H) Translocation in Healthy African Americans

The translocation t(14;18)(q32;q21) (BCL-2/J(H)) is present in over 80 % of all follicular lymphomas and is detectable in peripheral blood lymphocytes (PBL) of healthy individuals. The prevalence of this translocation has not been studied in African Americans (AAs). Given the higher incidence of follicular lymphomas in whites compared to AAs in the United States (USA), we hypothesized that the translocation prevalence in the blood of AAs would be lower. DNA was isolated from PBL from blood samples collected from participants from FL. Polymerase chain reaction was performed on the BCL-2/J(H) major (MBC) and minor breakpoint cluster (mBC) regions. Eight of the 77 (10.4 %) blood samples from AA participants were positive for MBC (95 % CI, 4.6-19.5 %), and three (3.9 %) were positive for mBC (95 % CI, 0.81-10.97 %) of BCL-2/J(H), with a total of 11 (14.3 %) participants with positive samples (95 % CI, 7.35-24.13 %). In 167 white patient samples, 22 (13.2 %; 95 % CI, 8.44-19.26 %) were positive for MBC, and five (3.0 %; 95 % CI, 0.98-6.85 %) were positive for mBC, with a total of 25 (15 %) participants with positive samples (CI, 9.93-21.30 %). The prevalence of t(14;18)(q32;q21) is not significantly different among AAs and whites from the USA. The lower prevalence of follicular lymphomas in AAs compared with whites is likely a result of differences in secondary molecular alterations involved in follicular lymphoma development. This study is the first report of prevalence of t(14;18) in an AA cohort.

Homology and enzymatic requirements of microhomology-dependent alternative end joining

Nonhomologous DNA end joining (NHEJ) is one of the major double-strand break (DSB) repair pathways in higher eukaryotes. Recently, it has been shown that alternative NHEJ (A-NHEJ) occurs in the absence of classical NHEJ and is implicated in chromosomal translocations leading to cancer. In the present study, we have developed a novel biochemical assay system utilizing DSBs flanked by varying lengths of microhomology to study microhomology-mediated alternative end joining (MMEJ). We show that MMEJ can operate in normal cells, when microhomology is present, irrespective of occurrence of robust classical NHEJ. Length of the microhomology determines the efficiency of MMEJ, 5 nt being obligatory. Using this biochemical approach, we show that products obtained are due to MMEJ, which is dependent on MRE11, NBS1, LIGASE III, XRCC1, FEN1 and PARP1. Thus, we define the enzymatic machinery and microhomology requirements of alternative NHEJ using a well-defined biochemical system.

Influence of reproductive history and exogenous hormone use on prevalence and frequency of circulating t(14;18)-positive cells in a population-based cross-sectional study

Purpose

The t(14;18) translocation might represent an intermediate step in the pathogenesis of follicular lymphoma (FL), one of the most common subtypes of non-Hodgkin lymphoma. Circulating t(14;18)-positive cells can also be detected in 30–60 % of healthy individuals at low frequencies. Some studies found a negative association between reproductive factors or use of menopausal hormone therapy (MHT) with FL. The objective of this study was to evaluate whether there is an association between number of frequencies, oral contraceptive (OC) use, menopausal status and MHT, and t(14;18) prevalence and frequency in a representative population analysis based on an epidemiologic study in the northeastern part of Germany.

Methods

The analysis is based on results of buffy coat samples from 1,981 women of the Study of Health in Pomerania (SHIP-0) and data obtained in standardized face-to-face interviews. For prevalence, odds ratios (OR) and 95 % confidence intervals (CI) were calculated using unconditional logistic regression. Frequency data were analyzed using negative binomial regression. The multivariable models included age, number of pregnancies, menopausal status (premenopausal, natural, medical/surgical menopause), OC use and MHT as a measure for exogenous hormone exposure use.

Results

We found no association between reproductive history and combined exogenous hormone use on the prevalence of circulating t(14;18)-positive cells. Modeling MHT and OC use separately in a sensitivity analysis, the MHT parameter yielded statistical significance [OR 1.37 (95 % CI 1.04;1.81)]. t(14;18) frequency was associated with use of OC [incidence rate ratio (IRR) for ever use 3.18 (95 % CI 1.54;6.54)], current use [IRR 3.86 (1.56;9.54)], >10 years use [IRR 3.93 (1.67;9.23)] and MHT [restricted to postmenopausal women; IRR 2.63 (95 % CI 1.01;6.85)] in bivariate age-adjusted analyses. In the multivariable model, medical/surgical menopause [IRR 2.46 (1.11;5.44)] and the category ever use of OC and MHT were statistically significant [IRR 2.41 (1.09;5.33)].

Conclusions

Exogenous hormone use might be a risk factor for t(14;18) frequency rather than for t(14;18) prevalence. Further research on healthy individuals carrying a t(14;18) translocation and possible risk factors for malignant lymphoma is necessary to determine the additional molecular or immunological events that have to occur to develop FL.

Electronic supplementary material

The online version of this article (doi:10.1007/s10552-015-0525-4) contains supplementary material, which is available to authorized users.

Methylation of the nonhomologous end joining repair pathway genes does not explain the increase of translocations with aging

Chromosome translocations are especially frequent in human lymphomas and leukemias but are insufficient to drive carcinogenesis. Indeed, several of the so-called tumor specific translocations have been detected in peripheral blood of healthy individuals, finding a higher frequency of some of them with aging. The inappropriate repair of DNA double strand breaks by the nonhomologous end joining (NHEJ) pathway is one of the reasons for a translocation to occur. Moreover, fidelity of this pathway has been shown to decline with age. Although the mechanism underlying this inefficacy is unknown, other repair pathways are inactivated by methylation with aging. In this study, we analyzed the implication of NHEJ genes methylation in the increase of translocations with the age. To this aim, we determined the relationship between translocations and aging in 565 Spanish healthy individuals and correlated these data with the methylation status of 11 NHEJ genes. We found higher frequency of BCL2-JH and BCR-ABL (major) translocations with aging. In addition, we detected that two NHEJ genes (LIG4 and XRCC6) presented age-dependent promoter methylation changes. However, we did not observe a correlation between the increase of translocations and methylation, indicating that other molecular mechanisms are involved in the loss of NHEJ fidelity with aging.

Chromosomal translocations among the healthy human population: implications in oncogenesis

Chromosomal translocations are characteristic features of many cancers, especially lymphoma and leukemia. However, recent reports suggest that many chromosomal translocations can be found in healthy individuals, although the significance of this observation is still not clear. In this review, we summarize recent studies on chromosomal translocations in healthy individuals carried out in different geographical areas of the world and discuss the relevance of the observation with respect to oncogenesis.

An inhibitor of nonhomologous end-joining abrogates double-strand break repair and impedes cancer progression

DNA Ligase IV is responsible for sealing of double-strand breaks (DSBs) during nonhomologous end-joining (NHEJ). Inhibiting Ligase IV could result in amassing of DSBs, thereby serving as a strategy toward treatment of cancer. Here, we identify a molecule, SCR7 that inhibits joining of DSBs in cell-free repair system. SCR7 blocks Ligase IV-mediated joining by interfering with its DNA binding but not that of T4 DNA Ligase or Ligase I. SCR7 inhibits NHEJ in a Ligase IV-dependent manner within cells, and activates the intrinsic apoptotic pathway. More importantly, SCR7 impedes tumor progression in mouse models and when coadministered with DSB-inducing therapeutic modalities enhances their sensitivity significantly. This inhibitor to target NHEJ offers a strategy toward the treatment of cancer and improvement of existing regimens.

Molecular Evaluation of t(14;18)(bcl-2/IgH) Translocation in Follicular Lymphoma at Diagnosis Using Paraffin-Embedded Tissue Sections

Objective: Follicular lymphoma (FL) is one of the most common lymphomas, and is characterized by t(14;18)(q32;q21) in more than 80% of patients. The aim of this study was to determine the rate of t(14;18) positivity based onthe detection of mbr or mcr in paraffin-embedded tissue samples.

Material and Methods: The study included 32 paraffin-embedded tissue samples collected from 32 consecutive FL patients that were diagnosed and followed-up at our hospital between 1999 and 2006. The MBR breakpoint wasidentified based on real-time PCR using a LightCycler v.2.0 t(14;18) Quantification Kit (MBR), multiplex PCR, and seminestedPCR. To identify the mcr breakpoint, real-time PCR was performed using specific primers and the FastStart DNAMaster SYBR Green I Kit. To detect t(14;18) via fluorescence in situ hybridization (FISH) nuclei from paraffin-embeddedtissue sections were extracted and used together with LSI IgH (immunoglobulin heavy chain) (spectrum green)/bcl-2(B-cell leukemia-lymphoma 2) (spectrum orange) probes.

Results: The DNA and nuclei isolation success rate for B5 formalin-fixed, paraffin-embedded tissue sections (n = 12)was 42% and 33%, respectively, versus 95% and 60%, respectively, for 20 tissue sections fixed in formalin only. In all,24 paraffin-embedded tissue sections were analyzed and mbr positivity was observed in the DNA of 82.14% via seminested PCR, in 53.57% via multiplex PCR, and in 28.57% via real-time PCR. We did not detect mcr rearrangementin any of the samples. In all, 15 of 16 patients (93.75%) whose nuclei were successfully isolated were observed to bet(14;18) positive via the FISH method.

Conclusion: Semi-nested PCR and FISH facilitated the genetic characterization of FL tumors. As such, FISH and PCR complement each other and are both essential for detecting t(14;18) translocation.

[Leukemia- and lymphoma-associated flow cytometric, cytogenetic, and molecular genetic aberrations in healthy individuals]

Most leukemia and lymphoma cases are characterized by specific flow cytometric, cytogenetic and molecular genetic aberrations, which can also be detected in healthy individuals in some cases. The authors review the literature concerning monoclonal B-cell lymphocytosis, and the occurrence of chromosomal translocations t(14;18) and t(11;14), NPM-ALK fusion gene, JAK2 V617F mutation, BCR-ABL1 fusion gene, ETV6-RUNX1(TEL-AML1), MLL-AF4 and PML-RARA fusion gene in healthy individuals. At present, we do not know the importance of these aberrations. From the authors review it is evident that this phenomenon has both theoretical and practical (diagnostic, prognostic, and therapeutic) significance.

How does DNA break during chromosomal translocations?

Chromosomal translocations are one of the most common types of genetic rearrangements and are molecular signatures for many types of cancers. They are considered as primary causes for cancers, especially lymphoma and leukemia. Although many translocations have been reported in the last four decades, the mechanism by which chromosomes break during a translocation remains largely unknown. In this review, we summarize recent advances made in understanding the molecular mechanism of chromosomal translocations.