Current prognostic and predictive factors in follicular lymphoma

Follicular lymphoma (FL) is generally considered an indolent disorder. With modern day treatments, long remissions are often achieved both in the front-line and relapsed setting. However, a subset of patients has a more aggressive course and a worse outcome. Their identification is the main purpose of modern day prognostic tools. In this review, we attempt to summarize the evidence concerning prognostic and predictive factors in FL, including (1) pre-treatment factors, from baseline clinical characteristics and imaging tests to histological grade, the microenvironment and genomic abnormalities; (2) post-treatment factors, i.e., depth of response, measured both by imaging tests and minimal residual disease; (3) factors at relapse and duration of response; and (4) prognostic factors in histological transformation. We conclude that, despite the existence of numerous tools, the availability of some of them is still limited; they generally suffer from notable downsides, and most have unproven predictive value, thus having scarce bearing on the choice of regimen at present. However, with the technological and scientific developments of the last few years, the potential for these prognostic factors is promising, particularly in combination, which will probably, in time, help guide therapeutic decisions.

Identification of a novel distal regulatory element of the human Neuroglobin gene by the chromosome conformation capture approach

Neuroglobin (NGB) is predominantly expressed in the brain and retina. Studies suggest that NGB exerts protective effects to neuronal cells and is implicated in reducing the severity of stroke and Alzheimer's disease. However, little is known about the mechanisms which regulate the cell type-specific expression of the gene. In this study, we hypothesized that distal regulatory elements (DREs) are involved in optimal expression of the NGB gene. By chromosome conformation capture we identified two novel DREs located -70 kb upstream and +100 kb downstream from the NGB gene. ENCODE database showed the presence of DNaseI hypersensitive and transcription factors binding sites in these regions. Further analyses using luciferase reporters and chromatin immunoprecipitation suggested that the -70 kb region upstream of the NGB gene contained a neuronal-specific enhancer and GATA transcription factor binding sites. Knockdown of GATA-2 caused NGB expression to drop dramatically, indicating GATA-2 as an essential transcription factor for the activation of NGB expression. The crucial role of the DRE in NGB expression activation was further confirmed by the drop in NGB level after CRISPR-mediated deletion of the DRE. Taken together, we show that the NGB gene is regulated by a cell type-specific loop formed between its promoter and the novel DRE.

Meta-analysis of genome-wide association studies identifies two loci associated with circulating osteoprotegerin levels

Osteoprotegerin (OPG) is involved in bone homeostasis and tumor cell survival. Circulating OPG levels are also important biomarkers of various clinical traits, such as cancers and atherosclerosis. OPG levels were measured in serum or in plasma. In a meta-analysis of genome-wide association studies in up to 10 336 individuals from European and Asian origin, we discovered that variants >100 kb upstream of the TNFRSF11B gene encoding OPG and another new locus on chromosome 17q11.2 were significantly associated with OPG variation. We also identified a suggestive locus on chromosome 14q21.2 associated with the trait. Moreover, we estimated that over half of the heritability of OPG levels could be explained by all variants examined in our study. Our findings provide further insight into the genetic regulation of circulating OPG levels.

Sensitivity and reproducibility of conventional qualitative and quantitative PCR assays for detection of the t(14;18)(q32;q21) chromosomal translocation in biopsy material from patients with follicular lymphoma

Follicular lymphoma (FL) is characterized by the t(14;18)(q32;q21) chromosomal translocation which can be detected by polymerase chain reaction (PCR) in approximately 70% of cases. The aim of our retrospective study was to evaluate the sensitivity and the reproducibility of both conventional qualitative and quantitative PCR assays for detection of the t(14;18)(q32;q21) chromosomal translocation in biopsy material. Fifty-seven formalin-fixed, paraffin-embedded tumor lymph node (LN) specimens from 50 patients with FL were included in the study. Qualitative PCR was performed with primer sets specific for the MBR, far3'-MBR and the mcr regions, respectively. Quantitative PCR was performed using the LightCycler instrument and the LightCycler - t(14;18) Quantification Kit (MBR). The overall detection rate of the t(14;18) in our study (52.6%) was in accordance with the literature. Of the t(14;18)-positive cases, 49.1% had breakpoints within the MBR and only 3.5% had breakpoints within the mcr. The most sensitive method was LightCycler-based PCR with a detection rate of 47.4%, followed by MBR1,2 assay (43.9%). We observed good agreement between qualitative MBR1,2 and quantitative LightCycler-based assay with a slightly higher detection rate of the quantitative method. The sensitivities of both methods were in accordance with results from other studies. Since LightCycler-based assay detects only breakpoints within the MBR, qualitative PCR should be employed in routine diagnostic settings for detection of breakpoints within the mcr and far3'-MBR regions.

A DA/DAPI positive human 14p heteromorphism defined by fluorescence in-situ hybridisation using chromosome 15-specific probes D15Z1 (satellite III) and p-TRA-25 (alphoid)

We have investigated the use of the satellite III probe, D15Z1, as an alternative to DA/DAPI staining in the identification of chromosome 15-derived markers. The probe hybridises to the short arm of chromosome 15 under high stringency conditions. We have screened 100 randomly selected patients, by fluorescence in-situ hybridisation (FISH), using co-hybridisation experiments with D15Z1 and a whole chromosome library, pBS-15. 88 individuals showed the expected pattern of two D15Z1 signals on the p-arm of both homologues of chromosome 15, whereas 12 individuals showed an additional signal on a third acrocentric D-group chromosome. Sequential GTC banding and D15Z1 hybridisation revealed that in each case it was one homologue of chromosome 14 that was D15Z1 positive. This pattern always correlated with positive DA/DAPI staining. In contrast, the 15 centromere-specific alphoid probe, pTRA-25, gave the expected two signals on both homologues of chromosome 15 in every case. Thus, D15Z1 and DA/DAPI signals co-localize while pTRA-25 is 15 centromere-specific and should be applied for unequivocal identification of chromosome 15-derived markers in clinical studies. The chromosome 14 heteromorphism, as identified by D15Z1, and defined by pTRA-25, may have arisen by intrachromosomal amplification or interchromosomal exchange.

Molecular response of follicular lymphoma to cyclophosphamide, doxorubicin, vincristine, prednisone C(H)OP or COP-based therapy as measured by polymerase chain reaction evidence of translocation (14;18)(q32;q21)

PURPOSE

Existing data suggest that conventional C(H)OP (cyclophosphamide, doxorubicin, vincristine, prednisone) regimen may not be intensive enough to achieve molecular response, as measured by polymerase chain reaction (PCR) evidence of translocation (14;18)(q32:q21) for follicular lymphoma. This study was undertaken to study the molecular response rate of follicular lymphoma to C(H)OP-based therapy and to analyze prognostic factors for molecular response.

PATIENTS AND METHODS

Twenty patients with pretreatment PCR evidence of t(14;18)(q32; q21) and at least one posttreatment PCR analysis after the initiation of the treatment with C(H)OP with or without radiation therapy constituted the basis for this analysis. The random effects logistic model was used to analyze the data. The following factors were investigated for their relationship to molecular response: gender, age, beta2-microglobulin, use of radiation therapy, Ann Arbor stage, and international Prognostic Index for malignant lymphoma.

RESULTS

Median follow-up was 56 months (range, 23-153 months). A total of 135 PCR results were available, 33 from bone marrow and 102 from peripheral blood. Overall, there was a clear and steady decreasing trend toward loss of PCR positivity with increasing time aftertreatment. By univariate analysis, stage > or = 3, stage = 4, International Prognostic Index > or = 2, and no radiation therapy were adverse factors for molecular response. On multivariate analysis, Ann Arbor stage IV and no radiation therapy were independent risk factors for PCR positivity, both for the peripheral blood data analyzed alone and for all data combined.

DISCUSSION

It is possible to achieve molecular response with C(H)OP with or without radiation therapy in patients with follicular lymphoma. Response rate depends on the Ann Arbor stage and radiation therapy.

The genes for human brain factor 1 and 2, members of the fork head gene family, are clustered on chromosome 14q

Brain factor-1 (BF-1) is a member of the fork head gene family which shows expression restricted to the neurons of the developing telencephalon in rodents and man. We have isolated a second human gene (HBF-2), which is also strongly expressed in embryonic brain and has very high homology to both the rat and human brain factor-1 genes and the retroviral oncogene qin. The HBF-2 cDNA was isolated from a human fetal brain expression library and contains a putative open reading frame of 479 amino acids. The HBF-2 gene is strongly expressed in fetal brain and also with lower levels of expression in several adult tissues. At the genomic level the gene for HBF-1 contains an 500 bp intron situated between the DNA binding domain II and the fork head domain while that of HBF-2 is intronless. The two genes are clustered on human chromosome 14q11-13.

Quantitation of follicular non-Hodgkin's lymphoma cells carrying t(14;18) by competitive polymerase chain reaction

A competitive polymerase chain reaction (PCR) technique was developed to quantify residual malignant cells in the peripheral blood and bone marrow of patients with low-grade follicular non-Hodgkin's lymphoma carrying a translocation between chromosomes 14 and 18. Artificial segments were constructed imitating a translocation between chromosome 14 and 18. These artificial translocation segments were used as competitor molecules in the quantitative PCR. Serial dilutions of a known amount of patient-derived translocation segments were coamplified with a fixed number of competitor molecules, and a patient specific calibration curve was constructed. Several patient samples were coamplified with an equal number of competitor molecules and the number of t(14;18) translocations within the samples was calculated by comparison with the calibration curve. The method was demonstrated on samples of four follicular non-Hodgkin's lymphoma (NHL) patients. In a patient transplanted with allogeneic bone marrow declining numbers of residual lymphoma cells were observed. We conclude that the method is accurate, relatively fast and the general principle of this method can be applied to all malignancies with characteristic abnormalities on DNA or RNA level that are detectable by PCR.

Chromosomal organization of the human VH4 gene family. Location of individual gene segments

To investigate the organization and evolution of VH gene segments, we characterized the elements belonging to the VH4 gene family from the germline of a single subject. One hundred sixty VH4-carrying lambda-phage clones were isolated from a genomic library. A combination of hybridization and sequence analysis yielded 13 distinct VH4 clones. Six of these elements had one or more nucleotide substitutions that distinguished them from previously identified VH4 genes, whereas seven elements were identical to previously described VH4 genes. In four of the six new sequences, nucleotide substitutions resulted in amino acid replacements. One pseudogene was identified. On the basis of sequence-specific hybridization using oligonucleotide probes corresponding to these sequences, each of the elements could be assigned to a specific band in a BglII digest. Since the VH4-carrying BglII bands have been mapped in genomic DNA, it was also possible to assign chromosomal locations to the specific VH4 elements. The results indicate that the majority of VH4 elements are located in a region of approximately 500 kb, extending from approximately 500 to 1000 kb 5' of the JH locus. The distribution of shared structural motifs among the VH4 elements indicates that the VH4 gene family has evolved through repeated duplication and gene conversion events.

Characterization of chromosome 11 translocation breakpoints at the bcl-1 and PRAD1 loci in centrocytic lymphoma

The chromosome 11q13 bcl-1 locus is rearranged in the majority of centrocytic lymphomas, a CD5-positive B-cell non-Hodgkins lymphoma, as a result of reciprocal translocation with the 14q32 immunoglobulin heavy chain genes. Although several 11q13 bcl-1 breakpoint sites have been characterized, a postulated bcl-1 oncogene was not identified. Recently, however, a gene encoding cyclin D1, designated PRAD1, was proposed as a candidate bcl-1 oncogene; accumulated evidence now indicates this gene is bcl-1. To further characterize 11q13 breakpoints in B-cell neoplasms, we analyzed 26 centrocytic lymphomas and 68 other B-cell cancers by Southern blot using a panel of breakpoint probes spanning 110 kilobases of the bcl-1 and PRAD1 loci. Nineteen centrocytic cases (73%) showed rearrangement, 15 at bcl-1 breakpoint sites and 5 at PRAD1 sites. One case was rearranged at both bcl-1 and PRAD1 loci. All but the latter case showed comigration of rearranged bcl-1 or PRAD1 bands and immunoglobulin heavy chain joining gene bands, consistent with the t(11;14). bcl-1 rearrangement was present in only one of 68 noncentrocytic B-cell neoplasms; none showed PRAD1 rearrangement. Thus, bcl-1 and PRAD1 rearrangement is strongly associated with centrocytic lymphoma, providing a useful molecular marker for classifying this subtype of lymphoma and suggesting an important role for PRAD1 cyclin D1 in the pathogenesis of this neoplasm.

A chromosome 14-specific human satellite III DNA subfamily that shows variable presence on different chromosomes 14

We describe a new subfamily of satellite III DNA (pTRS-63), which, by a combination of in situ hybridization to human metaphase chromosomes and analysis of a panel of somatic cell hybrids, is shown to be specific for human chromosome 14. This DNA has a basic 5-bp repeating unit of diverged GGAAT which is tandemly repeated and organized into either one of two distinct higher-order structures of 5 kb (designated the "L" form) or 4.8 kb (designated the "S" form). In addition, a third (Z) form, representing no detectable levels of this satellite III subfamily, is found. Results from five somatic cell hybrid lines and from a number of informative human individuals suggest that, on any one chromosome 14, only one of the three forms may exist. Subchromosomally, this sequence has been mapped to the p11 region and is distal to the domain occupied by another previously described satellite III subfamily (pTRS-47) found on chromosome 14. The pTRS-63 sequence described adds to the understanding of the structural organization of the short arm of human chromosome 14 and should be useful for the investigation of the molecular etiology of the frequently occurring t(13q14q) and t(14q21q) Robertsonian translocations.

Identification of DNA sequences flanking the breakpoint of human t(14q21q) Robertsonian translocations

We have employed molecular probes and in situ hybridization to investigate the DNA sequences flanking the breakpoint of a group of t(14q21q) Robertsonian translocations. In all the families studied, the probands were patients with Down syndrome who carried a de novo t(14q21q) translocation. The DNA probes used were two alphoid sequences, alphaRI and alphaXT, which are specific for the centromeres of chromosomes 13 and 21 and of chromosomes 14 and 22, respectively; a satellite III sequence, pTRS-47, which is specific for the proximal p11 region of chromosomes 14 and 22; and a newly defined satellite III DNA, pTRS-63, which is specific for the distal p11 region of chromosome 14. The two alphoid probes detected approximately the same amount of autoradiographic signal on the translocated chromosomes as was expected for chromosomes 14 and 21 of the originating parent, suggesting that there has been no loss of these centromeric sequences during the translocation events. Results with the two satellite III probes indicated that the domain corresponding to pTRS-47 was retained in the translocated chromosomes, whereas the domain for pTRS-63 was lost. These results have allowed us to place the translocation breakpoint between the pTRS-47 and pTRS-63 domains within the p11 region of chromosome 14.

Correlation of chromosome abnormalities with laboratory features and clinical course in B-cell chronic lymphocytic leukaemia

141 patients with B-cell chronic lymphocytic leukaemia (B-CLL) have been studied for a minimum of 12 months and a maximum of 25 years. 30 of 133 patients (32.5%) had greater than 10% FMC7 positive peripheral blood lymphocytes and 19 of 131 patients (14.5%) had a serum or urinary paraprotein. At presentation 88 patients were stage A0, 18 A1, 18 A2, 11 B and six C. 44 (31%) had progressive disease and 42 (30%) died during the study period. 63 patients had a normal karyotype, 75 a clonal abnormality and in three no metaphases were obtained. The finding of a complex karyotypic abnormality was significantly associated with lambda surface phenotype (P less than 0.01), the presence of greater than 10% FMC7 positive cells (P less than 0.025), and the presence of a paraprotein (P = 0.025). Patients whose leukaemic cells had a complex karyotype and those with structural abnormalities of chromosomes 14 and 6 required treatment earlier than those with a normal karyotype.

Sequence analysis of amplified t(14;18) chromosomal breakpoints in B-cell lymphomas

We have explored different strategies for sequencing of major breakpoint (mbr) junctional regions in t(14;18) chromosomal translocations--the most frequent chromosomal abnormality observed in B-cell lymphomas. We demonstrate that coupling of the preparation of single-stranded DNA by asymmetric polymerase chain reaction (PCR) and direct sequencing is the method of choice for the rapid and precise determination of clone-specific bcl-2/JH fusion gene sequences. The rapidity, relative ease, and accuracy of the technique, described for the nucleotide sequence analysis of mbr t(14;18) breakpoints, permits the analysis of a relatively large number of samples and should be considered as part of the clinical evaluation of lymphoma patients. Furthermore, by providing sequence information of clone-specific DNA regions, the procedure should reduce the risk of false-positive results from PCR.