Cloning and Gene Mapping of the Chromosome 13q14 Region Deleted in Chronic Lymphocytic Leukemia

Frequent deletions and loss of heterozygosity in a segment of chromosome 13 (13q14) in cases of B-cell chronic lymphocytic leukemia (CLL) have suggested that this malignancy is caused by inactivation of an unknown tumor suppressor gene located in this region. Toward the identification of the putative CLL tumor suppressor, we have constructed a high-resolution physical map of YAC, PAC, and cosmid contigs covering 600 kb of the 13q14 genomic region. In addition to densely positioned genetic markers and STSs, this map was further annotated by localization of 32 transcribed sequences (ESTs) using a combination of exon trapping, direct cDNA selection, sample sequencing of cosmids and PACs, and homology searches. On the basis of these mapping data, allelic loss analyses at 13q14 using CLL tumor samples allowed narrowing of the genomic segment encompassing the putative CLL gene to <300 kb. Twenty-three ESTs located within this minimally deleted region are candidate exons for the CLL-associated tumor suppressor gene.     

A Yeast Artificial Chromosome Contig That Spans the RB1-D13S31 Interval on Human Chromosome 13 and Encompasses the Frequently Deleted Region in B-cell Chronic Lymphocytic Leukemia

Abnormalities involving chromosome 13 have been reported as the only cytogenetic change in B-cell chronic lymphocytic leukemia (BCLL). Deletions are the most common cytogenetic abnormality and always involve 13q14, but when translocations are seen, the consistent breakpoint is always in 13q14. It is now established that deletions, distal to the RB1 gene in 13q14, are invariably associated with these translocations. We have recently described the smallest such deletion from a series of rearrangements from these tumors isolated in somatic cell hybrids, which spans approximately 1 Mb. In this report, we present the results of a series of a chromosome walking experiments using YACs and have been able to span this small deletion, which must contain the gene that is frequently deleted in BCLL. Four probes from 13q14 (RBI-mgg15-D13S25-D13S31) were used to isolate corresponding YACs for each of the markers. The chromosomal location of these YACs was verified using FISH, which also demonstrated their nonchimeric nature. Vectorette end rescue was then used to demonstrate the overlap of the YACs and to isolate new clones to complete the contig. The extremes of the contig were shown to cross the chromosome 13 translocation breakpoints isolated in somatic cell hybrids that carry the derivatives of chromosome 13 involved in the smallest BCLL deletion. This YAC contig covers the entire deletion and will prove a valuable resource to begin isolating genes from this region. In addition, we have isolated YACs corresponding to the RB1 locus, which extends the contig over a 3.8-cM distance on the chromosome.     

Molecular Characterization of Chronic Lymphocytic Leukemia Patients with a High Number of Losses in 13q14

Background

Patients with chronic lymphocytic leukemia and 13q deletion as their only FISH abnormality could have a different outcome depending on the number of cells displaying this aberration. Thus, cases with a high number of 13q- cells (13q-H) had both shorter overall survival and time to first therapy. The goal of the study was to analyze the genetic profile of 13q-H patients.

Design and Methods:

A total of 102 samples were studied, 32 of which served as a validation cohort and five were healthy donors.

Results

Chronic lymphocytic leukemia patients with higher percentages of 13q- cells (>80%) showed a different level of gene expression as compared to patients with lower percentages (<80%, 13q-L). This deregulation affected genes involved in apoptosis and proliferation (BCR and NFkB signaling), leading to increased proliferation and decreased apoptosis in 13q-H patients. Deregulation of several microRNAs, such as miR-15a, miR-155, miR-29a and miR-223, was also observed in these patients. In addition, our study also suggests that the gene expression pattern of 13q-H cases could be similar to the patients with 11q- or 17p-.

Conclusions

This study provides new evidence regarding the heterogeneity of 13q deletion in chronic lymphocytic leukemia patients, showing that apoptosis, proliferation as well as miRNA regulation are involved in cases with higher percentages of 13q- cells.     

The Pathogenesis of Chronic Lymphocytic Leukemia

The pathogenesis of chronic lymphocytic leukemia was examined in a series of 88 cases observed during a 15-year period. In untreated cases the trend of the absolute lymphocyte counts followed two main patterns. In the type I trend, the counts rose throughout the observation period; in the type II trend, the tendency to rise ceased and the counts stabilized above and below a mean value, the stationary trend being maintained for months or years. The type II trend was associated with relatively benign disease. The development of lymphocytosis was correlated with the progression of lymphadenopathy. It is suggested that lymphocytosis may result from the physiological process of recirculation and that the accumulation of lymphocytes may result from the proliferation of a single slightly abnormal cell-line. The abnormal cells might survive an unusually long time because they are unable to respond to stimuli which cause normal lymphocytes to transform.     

Transcription map of the 13q14 region, frequently deleted in B-cell chronic lymphocytic leukemia patients]

Deletions in the region located between the STS markers D13S1168 and D13S25 on chromosome 13 are the most frequent genomic changes in patients with B-cell chronic lymphocytic leukemia (B-CLL). After sequencing of this region, two novel candidate genes were identified: C13orf1 (chromosome 13 open reading frame 1) and PLCC (putative large CLL candidate). Analysis of the repeat distribution revealed two subregions differing in composition of repetitious DNA and gene organization. The interval D13S1168-D13S319 contains 131 Alu repeats accounting for 24.8% of its length, whereas the interval GCT16C05-D13S25, which is no more than 180 kb away from the former one is extremely poor in Alu repeats (4.1% of the total length). Both intervals contain almost the same amount of the LINE-type repeats L1 and L2 (20.3 and 21.24%, respectively). In the chromosomal region studied, 29 Alu repeats were found to belong to the evolutionary young subfamily Y, which is still capable of amplifying. A considerable proportion of repeats of this type with similar nucleotide sequences may contribute to the recombinational activity of the chromosomal region 13q14.3, which is responsible for its rearrangements in some tumors in humans.     

聚焦慢性淋巴细胞白血病治疗药物

过去的10 年,慢性淋巴细胞白血病（CLL）的治疗策略已发生变化,其疗法已有长足进展,即从仅可治标性缓解病痛发展到能致病情完全缓解、最大限度根除疾患和提高存活率。Rituxan（rituximab）的开发及其在免疫化疗中的应用使抗CLL 疗法发生了改变,该药已成为目前用于小于65 岁患者的黄金标准治疗药物。然而,基于Rituxan 的免疫化疗仍仅局限用于两类常见CLL 病例——老年患者和具并发症及高危患者的治疗。再者,在为期两年的一线和二线治疗中,约有25% 和50% 的CLL 患者会复发,且已有数年缓解的患者对后续治疗的疗效较差。因此,对于CLL 的治疗,仍远不能满足需求。早期研究发现,B 细胞受体（BCR）信号通路与CLL 的发生和发展以及治疗后的高反应率与病情持续缓解有关联。鉴于此,靶向BCR信号通路的小分子药物得以快速发展。Imbruvic（ibrutinib）是首个口服Bruton 酪氨酸激酶（BTK）抑制剂,近期经快速审批上市,用于治疗复发/ 顽固性恶性淋巴瘤,但其长期生存率数据目前尚不成熟。眼下,新疗法面临着多个挑战：其需提供更高的反应率,特别是对老年患者和具并发症及高危患者,且需克服当前疗法造成的耐药性。目前,唯一的CLL 根治疗法是同种异体造血干细胞移植（HSCT）,但其并不适用于大多数CLL 患者。而目前CLL 的标准治疗方案是化学免疫疗法,适用于小于65 岁的患者,但老龄或高危患者的治疗选择是有限的。因此,最终的问题是针对CLL 的小分子疗法是否能达到根治目的,期望随着在鉴定与CLL 发病机制和预后相关的细胞遗传学及分子变化方面取得进展,能促进下一代靶向疗法的快速发展。新型靶向性小分子抑制剂,如Imbruvica 和idelablisib,已展现出对CLL 的显著治疗作用。综述CLL 治疗领域重大行业投资和研发的主要市场博弈者和交易亮点。     

High Mitochondrial DNA Stability in B-Cell Chronic Lymphocytic Leukemia

Background

Chronic Lymphocytic Leukemia (CLL) leads to progressive accumulation of lymphocytes in the blood, bone marrow, and lymphatic tissues. Previous findings have suggested that the mtDNA could play an important role in CLL.

Methodology/Principal Findings

The mitochondrial DNA (mtDNA) control-region was analyzed in lymphocyte cell DNA extracts and compared with their granulocyte counterpart extract of 146 patients suffering from B-Cell CLL; B-CLL (all recruited from the Basque country). Major efforts were undertaken to rule out methodological artefacts that would render a high false positive rate for mtDNA instabilities and thus lead to erroneous interpretation of sequence instabilities. Only twenty instabilities were finally confirmed, most of them affecting the homopolymeric stretch located in the second hypervariable segment (HVS-II) around position 310, which is well known to constitute an extreme mutational hotspot of length polymorphism, as these mutations are frequently observed in the general human population. A critical revision of the findings in previous studies indicates a lack of proper methodological standards, which eventually led to an overinterpretation of the role of the mtDNA in CLL tumorigenesis.

Conclusions/Significance

Our results suggest that mtDNA instability is not the primary causal factor in B-CLL. A secondary role of mtDNA mutations cannot be fully ruled out under the hypothesis that the progressive accumulation of mtDNA instabilities could finally contribute to the tumoral process. Recommendations are given that would help to minimize erroneous interpretation of sequencing results in mtDNA studies in tumorigenesis.     

Germline Allele-Specific Expression of DAPK1 in Chronic Lymphocytic Leukemia

We previously reported a rare germline variant (c.1-6531) that resulted in allele–specific expression (ASE) of death-associated protein kinase 1 (DAPK1) and predisposition to chronic lymphocytic leukemia (CLL). We investigated a cohort of CLL patients lacking this mutation for the presence of ASE of DAPK1. We developed a novel strategy that combines single-nucleotide primer extension (SNuPE) with MALDI-TOF mass spectrometry, and detected germline DAPK1 ASE in 17 out of 120 (14.2%) CLL patients associated with a trend towards younger age at diagnosis. ASE was absent in 63 healthy controls. Germline cells of CLL patients with ASE showed increased levels of DNA methylation in the promoter region, however, neither genetic nor further epigenetic aberrations could be identified in the DAPK1 5′ upstream regulatory region, within distinct exons or in the 3′-UTR. We identified B-lymphoid malignancy related cell line models harboring allelic imbalance and found that allele-specific methylation in DAPK1 is associated with ASE. Our data indicate that ASE at the DAPK1 gene locus is a recurrent event, mediated by epigenetic mechanisms and potentially predisposing to CLL.     

Alu-PCR Approach to Isolating NotI-Linking Clones from the 3p14-p21 Region Frequently Deleted in Renal Cell Carcinoma

In the mammalian genome CpG islands are associated with functional genes and cloning of these islands could be an alternative approach for cloning functional genes. Recently we have developed a new approach for cloning CpG islands and constructing NotI linking libraries. We have initiated the construction of a NotI restriction map for chromosome 3, especially focusing on the rearrangements in the 3p14-p21 region, which are associated with different malignancies. CpG islands from this region are useful for isolation of candidate tumor suppressor genes that map to this region and for isolating NotI-linking clones from 3p14-p21 for mapping purposes. Here we suggest a modification of Alu-PCR as an approach to isolating Not I sites (e.g., CpG islands) from defined regions of the chromosome. Instead of using whole chromosomal DNA for Alu-PCR, we have used representative NotI-linking libraries from hybrid cell lines containing either whole or deleted human chromosome 3 (MCH903.1 and MCH924.4, respectively). This decreases the complexity of the Alu-PCR products 10-100 times compared to the whole human genome. Using this modification, we can isolate NotI-linking clones, which are natural markers on the chromosome, rather than random genomic fragments. Among eight clones selected by this method, seven were from the region deleted in MCH924.4. The results clearly demonstrate the feasibility of Alu-PCR for isolating CpG islands from defined regions of the genome.     

Clinical and Biological Relevance of Genomic Heterogeneity in Chronic Lymphocytic Leukemia

Background

Chronic lymphocytic leukemia (CLL) is typically regarded as an indolent B-cell malignancy. However, there is wide variability with regards to need for therapy, time to progressive disease, and treatment response. This clinical variability is due, in part, to biological heterogeneity between individual patients’ leukemias. While much has been learned about this biological variation using genomic approaches, it is unclear whether such efforts have sufficiently evaluated biological and clinical heterogeneity in CLL.

Methods

To study the extent of genomic variability in CLL and the biological and clinical attributes of genomic classification in CLL, we evaluated 893 unique CLL samples from fifteen publicly available gene expression profiling datasets. We used unsupervised approaches to divide the data into subgroups, evaluated the biological pathways and genetic aberrations that were associated with the subgroups, and compared prognostic and clinical outcome data between the subgroups.

Results

Using an unsupervised approach, we determined that approximately 600 CLL samples are needed to define the spectrum of diversity in CLL genomic expression. We identified seven genomically-defined CLL subgroups that have distinct biological properties, are associated with specific chromosomal deletions and amplifications, and have marked differences in molecular prognostic markers and clinical outcomes.

Conclusions

Our results indicate that investigations focusing on small numbers of patient samples likely provide a biased outlook on CLL biology. These findings may have important implications in identifying patients who should be treated with specific targeted therapies, which could have efficacy against CLL cells that rely on specific biological pathways.     

C6-Ceramide Nanoliposomes Target the Warburg Effect in Chronic Lymphocytic Leukemia

Ceramide is a sphingolipid metabolite that induces cancer cell death. When C6-ceramide is encapsulated in a nanoliposome bilayer formulation, cell death is selectively induced in tumor models. However, the mechanism underlying this selectivity is unknown. As most tumors exhibit a preferential switch to glycolysis, as described in the “Warburg effect”, we hypothesize that ceramide nanoliposomes selectively target this glycolytic pathway in cancer. We utilize chronic lymphocytic leukemia (CLL) as a cancer model, which has an increased dependency on glycolysis. In CLL cells, we demonstrate that C6-ceramide nanoliposomes, but not control nanoliposomes, induce caspase 3/7-independent necrotic cell death. Nanoliposomal ceramide inhibits both the RNA and protein expression of GAPDH, an enzyme in the glycolytic pathway, which is overexpressed in CLL. To confirm that ceramide targets GAPDH, we demonstrate that downregulation of GAPDH potentiates the decrease in ATP after ceramide treatment and exogenous pyruvate treatment as well as GAPDH overexpression partially rescues ceramide-induced necrosis. Finally, an in vivo murine model of CLL shows that nanoliposomal C6-ceramide treatment elicits tumor regression, concomitant with GAPDH downregulation. We conclude that selective inhibition of the glycolytic pathway in CLL cells with nanoliposomal C6-ceramide could potentially be an effective therapy for leukemia by targeting the Warburg effect.     

54例慢性淋巴细胞白血病的临床回顾性分析

目的：本研究旨在探讨慢性淋巴细胞白血病（CLL）的实验室检查特点及特征性临床表现。方法：利用血细胞分析仪、流式细胞术、骨髓形态分析及R显带技术等对我院2002年4月．2012年4月收治的54例慢性淋巴细胞白血病患者的相关临床资料如血细胞计数、骨髓形态、染色体及免疫表型等进行检测并对结果进行回顾性分析。结果：CLL多发于老年患者,男性多见,中位年龄65岁（45．82岁）。大部分患者初诊时可出现典型的临床表现,37例（68％）患者初诊时淋巴结大,49例（91％）初诊时白细胞≥10×109、L,淋巴细胞绝对值≥5×109／L。13例（24％）初诊时肝脾或者脾大,17例（31％）初诊时乏力、消瘦。34（63％）例患者可见典型的CLL免疫表型,CD5、CDl9．CD23、CD20的阳性率分别为90％、87％、72％、67％。32例患者染色体检测结果表明：13q-2例,17p．2例,11q-1例,＋12有1例,6q-1例,t（14,16）1例。2例患者发生了自身免疫性溶血性贫血（AIHA）。1例患者发生了Richter转化,肿大淋巴结活检显示部分区域为弥漫性大B细胞淋巴瘤,其高表达CD20、CDl9、CD22。结论：慢性淋巴细胞白血病具有其典型的临床表现、免疫表型及遗传学改变,并且对诊断及治疗有重要意义。     

Role of CTLA4 in the Proliferation and Survival of Chronic Lymphocytic Leukemia

Earlier, we reported that CTLA4 expression is inversely correlated with CD38 expression in chronic lymphocytic leukemia (CLL) cells. However, the specific role of CTLA4 in CLL pathogenesis remains unknown. Therefore, to elucidate the possible role of CTLA4 in CLL pathogenesis, CTLA4 was down-regulated in primary CLL cells. We then evaluated proliferation/survival in these cells using MTT, ³H-thymidine uptake and Annexin-V apoptosis assays. We also measured expression levels of downstream molecules involved in B-cell proliferation/survival signaling including STAT1, NFATC2, c-Fos, c-Myc, and Bcl-2 using microarray, PCR, western blotting analyses, and a stromal cell culture system. CLL cells with CTLA4 down-regulation demonstrated a significant increase in proliferation and survival along with an increased expression of STAT1, STAT1 phosphorylation, NFATC2, c-Fos phosphorylation, c-Myc, Ki-67 and Bcl-2 molecules. In addition, compared to controls, the CTLA4-downregulated CLL cells showed a decreased frequency of apoptosis, which also correlated with increased expression of Bcl-2. Interestingly, CLL cells from lymph node and CLL cells co-cultured on stroma expressed lower levels of CTLA4 and higher levels of c-Fos, c-Myc, and Bcl-2 compared to CLL control cells. These results indicate that microenvironment-controlled-CTLA4 expression mediates proliferation/survival of CLL cells by regulating the expression/activation of STAT1, NFATC2, c-Fos, c-Myc, and/or Bcl-2.     

The Spectrum of Kidney Pathology in B-Cell Chronic Lymphocytic Leukemia / Small Lymphocytic Lymphoma: A 25-Year Multicenter Experience

Background

Chronic lymphocytic leukemia and small lymphocytic lymphoma are 2 different presentations of the most common B-cell neoplasm in western countries (CLL/SLL). In this disease, kidney involvement is usually silent, and is rarely reported in the literature. This study provides a clinicopathological analysis of all-cause kidney disease in CLL/SLL patients.

Methods

Fifteen CLL/SLL patients with kidney biopsy were identified retrospectively. Demographic, clinical, pathological and laboratory data were assessed at biopsy, and during follow-up.

Results

At biopsy 11 patients presented impaired renal function, 7 patients nephrotic syndrome, 6 patients dysproteinemia, and 3 patients cryoglobulinemia. Kidney pathology revealed CLL/SLL-specific monoclonal infiltrate in 10 biopsies, glomerulopathy in 9 biopsies (5 membranoproliferative glomerulonephritis, 2 minimal change disease, 1 glomerulonephritis with organized microtubular monoclonal immunoglobulin deposits, 1 AHL amyloidosis). Five patients presented interstitial granulomas attributed to CLL/SLL. After treatment of the hematological disease, improvement of renal function was observed in 7/11 patients, and remission of nephrotic syndrome in 5/7 patients. During follow-up, aggravation of the kidney disease systematically occurred in the absence of favorable response to hematological treatment.

Conclusions

A broad spectrum of kidney diseases is associated with CLL/SLL. In this setting, kidney biopsy can provide important information for diagnosis and therapeutic guidance.     

Assignment of 48 ESTs to Chromosome 13 Band q14.3 and Expression Pattern for ESTs Located in the Core Region Deleted in B-CLL

An expression map containing 48 ESTs was constructed to identify a tumor-suppressor gene involved in B-cell chronic lymphocytic leukemia (B-CLL), which was previously assigned to chromosome band 13q14.3 close to genetic markers D13S25 and D13S319. Thirty-nine of these 48 ESTs, together with 11 additional ones listed in databases, were initially assigned to chromosome 13q14 between markers D13S168 and D13S176. Nine others have recently been located in the D13S319 region. Our results indicate that 48 of the 59 ESTs analyzed belong to a YAC contig of chromosome 13 band q14, and 22 are contained on YAC 933e9, which encompasses the B-CLL critical region. Ten of these 22 ESTs were accurately assigned on a PAC, BAC, and cosmid contig encompassing the smallest minimal deletion area described so far in B-CLL, and 20 were tested for their expression on 27 normal or tumor tissues. One EST appears to be a likely candidate for the tumor-suppressor gene involved in B-CLL.     

Clustering of Expression Data in Chronic Lymphocytic Leukemia Reveals New Molecular Subdivisions

Although the identification of inherent structure in chronic lymphocytic leukemia (CLL) gene expression data using class discovery approaches has not been extensively explored, the natural clustering of patient samples can reveal molecular subdivisions that have biological and clinical implications. To explore this, we preprocessed raw gene expression data from two published studies, combined the data to increase the statistical power, and performed unsupervised clustering analysis. The clustering analysis was replicated in 4 independent cohorts. To assess the biological significance of the resultant clusters, we evaluated their prognostic value and identified cluster-specific markers. The clustering analysis revealed two robust and stable subgroups of CLL patients in the pooled dataset. The subgroups were confirmed by different methodological approaches (non-negative matrix factorization NMF clustering and hierarchical clustering) and validated in different cohorts. The subdivisions were related with differential clinical outcomes and markers associated with the microenvironment and the MAPK and BCR signaling pathways. It was also found that the cluster markers were independent of the immunoglobulin heavy chain variable (IGVH) genes mutational status. These findings suggest that the microenvironment can influence the clinical behavior of CLL, contributing to prognostic differences. The workflow followed here provides a new perspective on differences in prognosis and highlights new markers that should be explored in this context.     

Interstitial deletion of chromosome 13 involving the region 13q14

Summary A patient with an interstitial deletion 13q14 is described who has decreased erythrocyte esterase D activity and who has not developed a retinoblastoma.     

CD11c在慢性淋巴细胞白血病诊断中的意义

目的:探讨CD11c抗原在慢性淋巴细胞白血病(chronic lymphocytic leukemia,CLL)中的表达及在临床诊断中的价值,以及CD11c抗原表达与患者的遗传学异常及预后参数的相关性。方法:采用多参数流式细胞术(flow cytometry,FCM)检测200例CLL患者、49例套细胞淋巴瘤(mantle cell lymphoma,MCL)患者CD11c的表达率和平均荧光强度(mean fluorescence intensity,MFI);并比较CLL患者CD11c的表达与预后参数ZAP-70和CD38表达的关系;同时采用荧光原位杂交(fluorescence in situ hybridization,FISH)技术检测CLL患者的P53缺失、13q14缺失、ATM缺失、6q23缺失、+12以及IGH重排,比较CD11c~+CLL患者与CD11c~-CLL患者遗传学特点。结果:CLL患者中CD11c阳性率为49.5%(99/200),MFI中位值为2.06(1.00～7.34);而MCL患者中CD11c阳性率为6.12%(3/49),MFI中位值为2.00(1.97～2.54)。CD11c在CLL中的表达率明显高于MCL,(x~2=30.62,P0.05)。CD11c~+CLL患者的ZAP-70和CD38阳性率均明显高于CD11c~-CLL患者(x~2=15.472,P0.05;x~2=11.556,P0.05),差异有统计学意义。而CLL患者的CD11c表达率与P53缺失、13q14缺失、ATM缺失、6q23缺失、+12、IGH重排的结果均无统计学差异。结论:CD11c对于辅助诊断CLL有重要价值,尤其有助于CLL和MCL的诊断和鉴别诊断。