CCND1 Locus Research Articles

Abstract 3412: Liquid biopsy for t(11;14)/blc2 identification in multiple myeloma

Abstract Background: Multiple myeloma (MM) is a spatially heterogeneous plasma cell malignancy of the bone marrow (BM). Venetoclax is a potent inhibitor of the anti-apoptotic protein BCL2 with evidence in MM that t(11;14) and high BCL2 expression confers greater sensitivity to venetoclax. BM biopsy is required for fluorescent in-situ hybridisation (FISH) detection of t(11;14) and the evaluation of MM cell BCL2 expression, with success being entirely dependent on the quality of the BM sample procured. We hypothesised that a liquid biopsy strategy to enable interrogation of cell-free circulating tumour (ct)DNA and extra-cellular (ex)RNA would represent a more practical and less invasive alternative strategy to BM biopsy for the detection of t(11;14) and the determination of MM cell BCL2 expression, respectively. Methods: Blood and BM were obtained from 24 FISH characterised MM patients - normal karyotype (n=9), t(11;14) (n=11) and t(4;14) (n=4). Plasma derived ctDNA and exRNA was extracted utilising the QIAamp circulating nucleic acid kit and matched PBMC DNA was obtained for germ line controls. BM CD138+ MM cells for DNA and RNA extraction were selected with Miltenyi Biotec CD138 microbeads. A low density custom panel of unique capture probes (SSEL XT HS2, SureSelect Custom Tier 2, Agilent Technology), spanning approximately 10% of the CCND1 and IGH loci involved in t(11;14), was used for sequencing with approximately 5 million reads per sample with adapter sequences trimmed from the reads and aligned to the hg38 using bwa mem algorithm. Structural variant caller, Lumpy was used for identifying translocations, with low confidence reads excluded with a defined Z-score threshold. Droplet digital PCR (ddPCR) for BCL2 was performed on exRNA. Results: The low-density capture seq identified t(11;14) in 6 of 11 (55%) of the CD138+ BM samples, but not in paired germ-line samples nor in the non-t(11;14) cohort BM samples. Interrogation of ctDNA identified t(11;14) in 1 of 11 samples but also in ctDNA from a patient labelled as being t(4;14) positive raising questions about the validity of the FISH attribution. We are now utilising a modification of the assay using ultra-high density capture probes with coverage approaching 100% of the IGH region and higher ctDNA input to detect translocations involving the IGH region on chromosome 14 with any partner chromosome, including translocations undetectable by FISH. BCL2 exRNA transcripts were detected in all patients with a range of 2-120 copies/ml of plasma with 79% of patients classified as ‘high’ BCL2 expression (>40 copies/ml of plasma) compared to 59% of the matched CD138+ BM samples. Conclusion: We provide proof-of-concept of the potential of ctDNA and exRNA for t(11;14) detection and ddPCR quantitation of BCL2 expression, respectively, providing a rationale for further exploration of ctDNA and exRNA liquid biopsy testing as a strategy for identifying patients with t(11;14) and/or high BCL2. Citation Format: Andrew Spencer, Sridurga Mithraprabhu, Jaynish Shah, Kawa Choi, Ashley George, Carlos Hader, Tiffany Khong. Liquid biopsy for t(11;14)/blc2 identification in multiple myeloma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3412.

Single Time Frame Overview of the Genetic Changes in Conjunctival Melanoma from Intraepithelial Disease to Invasive Melanoma: A Study of 4 Exenteration Specimens Illustrating the Potential Role of Cyclin D1

Introduction: Despite advances in the understanding of the molecular pathogenesis of cutaneous melanoma, relatively little is known about the genetic changes that occur in the progression of conjunctival melanocytic intraepithelial lesions to invasive conjunctival melanoma. Methods: We exposed 4 exenteration specimens that each contained varying grades of intraepithelial conjunctival melanocytic neoplasia and invasive neoplasia to a combination of various techniques, including array comparative genomic hybridization (aCGH), ribonucleic acid sequencing (RNA-seq), fluorescence in situ hybridization (FISH), and immunohistochemistry. Results: Three out of 4 of the invasive melanomas showed gains in 11q13 (CCND1 locus) by aCGH. FISH demonstrated CCND1 gain in invasive melanoma and in conjunctival melanocytic intraepithelial lesions (CMILs) of all grades (low-grade CMILs and in situ melanoma), and this was paralleled by increased expression of Cyclin D1 protein within the atypical melanocytes by immunohistochemistry, using a double-staining method with a red end point for Melan A cytoplasmic staining and a brown end point for nuclear Cyclin D1 expression. Higher grades of melanocytic intraepithelial lesions showed more cells expressing Cyclin D1 than lower grade melanocytic intraepithelial lesions. The Cyclin D1 protein expression was in the same location as the amplified CCND1 signal by FISH. One out of 3 of these cases also showed the amplification of the 12q13-15 locus corresponding to MDM2 and FISH confirmed gains in the conjunctival melanocytic intraepithelial neoplasia and invasive melanoma. The remaining fourth case showed a homozygous deletion of 9p21 (CDKN2A) by aCGH only, with immunohistochemistry showing clonal loss of p16 protein expression in the invasive and conjunctival melanocytic intraepithelial lesion. Two out of 4 of the invasive melanomas harboured classical driver mutations in NRAS and NF-1, respectively. None of the cases showed mutations in BRAF, KIT, and TERT mutations. RNA-seq data showed secondary mutations in ARAF, PLCB4, MET, EZH2, MAP2K2, CTNNB1, CIITA, NF2, TP53, and MEN1, some of which are implicated in the MAPK pathway. Conclusion: CMILs harbour amplifications of CCND1 (3 cases), MDM2 (1 case), and loss of CDKN2A (1 case), which are also present when the lesion progresses to invasive melanoma, implicating these amplifications in the early pathogenesis of CMILs. This study represents the first attempt to capture the mutational landscape of all stages of conjunctival melanoma in a single tissue excision.

Integrated Epigenetic and Transcriptional Single Cell Analysis of t(11;14) Myeloma and Its BCL2 Dependency

Multiple myeloma is characterized by recurrent chromosomal translocations that involve the immunoglobulin gene enhancers and partners such as the cyclin D genes (CCND1, CCND2 or CCND3) or other genes like WHSC1 and MAF. t(11;14) results in upregulation of CCND1 with unique morphological, phenotypic markers, and drug sensitivity profiles with exquisite sensitivity to BCL2 inhibitors. It is evident now that this unique sensitivity profile is driven by the BH3-proapoptotic protein priming of BCL2 with high BCL2/MCL1 or BCL2/BCL2L1 ratios. However, the epigenetic mechanisms associated with t(11;14) and their impact on genes regulation and clinical response to venetoclax remains elusive. In the present study we compared the transcriptomics (scRNA-seq) and chromatin accessibility (scATAC-seq) of single plasma cells of MM patients with and without t(11;14) as well as pre- and post-venetoclax exposure in order to establish the epigenomic signature of t(11;14) and/or BCL2-sensitivity in myeloma.Serial BM aspirates (n=24) were collected from 15 relapsed or refractory myeloma patients (RRMM); harboring t(11;14) (n=6 pairs) and 9 without this translocation prior to initiation of salvage therapy and at time of relapse. All t(11;14) MM patients were treated with venetoclax. Unbiased chromatin accessibility and mRNA profiling of CD138 pos cells were performed using the chromium single cell ATAC and RNA-Seq 3‘ solution (10x Genomics), respectively. Cell Ranger, Seurat and ArchR were used for sample de-multiplexing, barcode processing, single-cell 3‘ gene, peaks counting, and data analysis.We first compared the scATAC-seq and scRNA-seq profiles found in CD138 pos MM cell isolated from patients harboring t(11;14) with the one obtained in patients without this translocation. As expected, t(11:14) patients had high chromatin accessibility at the CCND1 locus and high mRNA expression. Differentially accessible chromatin analysis identified 147518 peaks that were specific to t(11;14) patients. Of interest, motifs enrichment analysis of accessible peaks identified a “B cell-like” motifs signature with enriched TFs motifs such as TCF4 and PAX5 in t(11;14) patients compared to non t(11:14) enriched for IRF and STAT family of motifs. The integration of the scATAC-seq and scRNA-seq data confirmed the B cell signature of t(11;14) patients with upregulation of B cell markers such as MS4A1, VPREB3, CD79A, CD19, and down-regulation of plasma cell markers such as TDO2, EFEMP1, CD28, SLAMF7, and IL6R. Additionally, we found PAX1, PAX5, TCF3, TCF5, and SPI1 transcription factors to be highly expressed in t(11;14) while the non t(11:14) were enriched for IRF1-9 transcription factors. Of interest, the clustering analysis performed on scATAC-seq data identified 3 non t(11;14) patients with a chromatin accessibility profile similar to that of t(11;14) patients. They expressed B cell markers (PAX5, VPREB3 or FCRLA), overexpressed BCL2 and we are currently examining whether this B cell-like epigenetic signature determines sensitivity to venetoclax.In order to define the epigenetic contribution to the acquired resistance to venetoclax in t(11;14) myeloma, we compared the chromatin accessibility profiles of t(11;14) patients pre- vs. post-venetoclax treatment. Enriched motifs within accessible peaks differed significantly between pre- and post-venetoclax with RELA, REL, RELB and EGR1 motifs predominantly enrichmed in the pre-samples in contrast to JUN, JUNB, JUND and FOSL1/L2 motifs enrichment in the post-samples. Of note, integration analysis of scRNAseq (differentially expressed genes) and ATACseq data (differentially accessible peaks) identified MCL1 and ENSA (a gene 60 Kb centromeric to MCL1 on chr1q) as the top enriched genes and peaks in resistant samples suggesting that copy number gain at the MCL1 locus (which we confirmed by single cell CNV analysis) rather than epigenetic modifications is likely the main determinant of acquired resistant to venetoclax in t(11;14) MM.In the current study we have defined the epigenetic regulome and transcriptome associated with t(11;14) myeloma and its relatedness to B cell rather than plasma cell biology. Our studies also suggest that acquired resistance to venetoclax is largely driven by copy number gain at the MCL1 locus. DisclosuresBahlis: Karyopharm: Consultancy, Honoraria; Amgen: Consultancy, Honoraria; Takeda: Consultancy, Honoraria; Sanofi: Consultancy, Honoraria; Abbvie: Consultancy, Honoraria; Janssen: Consultancy, Honoraria; BMS/Celgene: Consultancy, Honoraria; GlaxoSmithKline: Consultancy, Honoraria; Genentech: Consultancy; Pfizer: Consultancy, Honoraria. Neri: BMS: Consultancy, Honoraria; Janssen: Consultancy, Honoraria; Sanofi: Consultancy, Honoraria; Amgen: Consultancy, Honoraria.

Landscape of copy number aberrations in esophageal squamous cell carcinoma from a high endemic region of South Africa

BackgroundEsophageal squamous cell carcinoma (ESCC) is an aggressive cancer with one of the highest world incidences in the Eastern Cape region of South Africa. Several genome wide studies have been performed on ESCC cohorts from Asian countries, North America, Malawi and other parts of the world but none have been conducted on ESCC tumors from South Africa to date, where the molecular pathology and etiology of this disease remains unclear. We report here tumor associated copy number changes observed in 51 ESCC patients’ samples from the Eastern Cape province of South Africa.MethodsWe extracted tumor DNA from 51 archived ESCC specimens and interrogated tumor associated DNA copy number changes using Affymetrix® 500 K SNP array technology. The Genomic Identification of Significant Targets in Cancer (GISTIC 2.0) algorithm was applied to identify significant focal regions of gains and losses. Gains of the top recurrent cancer genes were validated by fluorescence in situ hybridization and their protein expression assessed by immunohistochemistry.ResultsTwenty-three significant focal gains were identified across samples. Gains involving the CCND1, MYC, EGFR and JAG1 loci recapitulated those described in studies on Asian and Malawian cohorts. The two most significant gains involved the chromosomal sub-bands 3q28, encompassing the TPRG1 gene and 11q13.3 including the CTTN, PPFIA1and SHANK2 genes. There was no significant homozygous loss and the most recurrent hemizygous deletion involved the B3GAT1 gene on chromosome 11q25. Focal gains on 11q13.3 in 37% of cases (19/51), consistently involved CTTN and SHANK2 genes. Twelve of these cases (23,5%), had a broader region of gain that also included the CCND1, FGF19, FGF4 and FGF3 genes. SHANK2 and CTTN are co-amplified in several cancers, these proteins interact functionally together and are involved in cell motility. Immunohistochemistry confirmed both Shank2 (79%) and cortactin (69%) protein overexpression in samples with gains of these genes. In contrast, cyclin D1 (65%) was moderately expressed in samples with CCND1 DNA gain.ConclusionsThis study reports copy number changes in a South African ESCC cohort and highlights similarities and differences with cohorts from Asia and Malawi. Our results strongly suggest a role for CTTN and SHANK2 in the pathogenesis of ESCC in South Africa.

Microglandular adenosis is an advanced precursor breast lesion with evidence of molecular progression to matrix-producing metaplastic carcinoma

Microglandular adenosis (MGA) is a rare breast lesion reported to be associated with invasive carcinoma in up to 20% to 30% of cases and has been proposed as a nonobligate precursor to basal-like breast cancers. We identified a case of matrix-producing metaplastic carcinoma with morphologic and immunohistochemical evidence of progression from MGA to atypical MGA, carcinoma in situ, and invasive carcinoma. We performed whole-exome sequencing of each component (MGA, atypical MGA, carcinoma in situ, and cancer) to characterize the mutational landscape of these foci. There was a significant copy number overlap between all foci, including a segmental amplification of the CCND1 locus (partial chromosome 11 trisomy) and MYC (8q24.12-13). Using a bioinformatics approach, we were able to identify 3 putative mutational clusters and recurrent, stop-gain nonsynonymous mutations in both ZNF862 and TP53 that were shared across all foci. Finally, we identified a novel deleterious splice-acceptor site mutation of chr5:5186164 G>T (chromosome 5p15) encoding the gene, ADAMTS16, in the invasive component.

New susceptibility loci for cutaneous melanoma risk and progression revealed using a porcine model

Despite major advances, it is estimated that a large part of melanoma predisposing genes remains to be discovered. Animal models of spontaneous diseases are valuable tools and experimental crosses can be used to identify and fine-map new susceptibility loci associated with melanoma. We performed a Genome-Wide Association Study (GWAS) of melanoma occurrence and progression (clinical ulceration and presence of metastasis) in a porcine model of spontaneous melanoma, the MeLiM pig. Five loci on chromosomes 2, 5, 7, 8 and 16 showed genome-wide significant associations (p < 5 × 10–6) with either one of these phenotypes. Suggestive associations (p < 5 × 10–5) were also found at 16 additional loci. Moreover, comparison of the porcine results to those reported by human melanoma GWAS indicated shared association signals notably at CDKAL1 and TERT loci but also nearby CCND1, FTO, PLA2G6 and TMEM38B-RAD23B loci. Extensive search of the literature revealed a potential key role of genes at the identified porcine loci in tumor invasion (DST, PLEKHA5, CBY1, LIMK2 and ETV5) and immune response modulation (ETV5, HERC3 and DICER1) of the progression phenotypes. These biological processes are consistent with the clinico-pathological features of MeLiM tumors and can open new routes for future melanoma research in humans.

SP8 Transcriptional Regulation of Cyclin D1 During Mouse Early Corticogenesis.

Multiple signals control the balance between proliferation and differentiation of neural progenitor cells during corticogenesis. A key point of this regulation is the control of G1 phase length, which is regulated by the Cyclin/Cdks complexes. Using genome-wide chromatin immunoprecipitation assay and mouse genetics, we have explored the transcriptional regulation of Cyclin D1 (Ccnd1) during the early developmental stages of the mouse cerebral cortex. We found evidence that SP8 binds to the Ccnd1 locus on exon regions. In vitro experiments show SP8 binding activity on Ccnd1 gene 3′-end, and point to a putative role for SP8 in modulating PAX6-mediated repression of Ccnd1 along the dorso-ventral axis of the developing pallium, creating a medialLow-lateralHigh gradient of neuronal differentiation. Activation of Ccnd1 through the promoter/5′-end of the gene does not depend on SP8, but on βcatenin (CTNNB1). Importantly, alteration of the Sp8 level of expression in vivo affects Ccnd1 expression during early corticogenesis. Our results indicate that Ccnd1 regulation is the result of multiple signals and that SP8 is a player in this regulation, revealing an unexpected and potentially novel mechanism of transcriptional activation.

Detection of CCND1 Gene Copy Number Variations Using Multiplex Ligation-Dependent Probe Amplification and Fluorescence In Situ Hybridization Methods.

The CCND1 locus is located in 11q13 and encodes the G1-S regulatory protein, cyclin D1. Cyclin D1 is frequently amplified in various types of cancers, and is an attractive potential therapeutic target. Multiplex ligation-dependent probe amplification (MLPA) is a new, high-resolution method for the detection of amplification of numerous genes including CCND1 in small amounts of DNA fragments derived from formalin-fixed, paraffin-embedded material in a single reaction. This approach is, however, based on PCR and averages many different cells, so validation by morphological methods such as fluorescence in situ hybridization (FISH) is theoretically mandatory. Here we describe detection of CCND1 gene copy number variations by commercially available MLPA kits and FISH using a bacterial artificial chromosome (BAC) probe.

Detection of CCND1 Locus Amplification by Fluorescence In Situ Hybridization.

It is well known that chromosomal aberrations of tumors are associated with the initiation and progression of malignancy. Fluorescence in situ hybridization (FISH) is a powerful, rapid method to detect chromosome copy number and structural alterations in tissue sections, chromosome, or interphase cellular preparations via hybridization of complementary probe sequences. The technique is based on the complementary nature of DNA double strands, which allows fluorescently labeled DNA probes to be used as probes to label the complementary sequences of target cells, chromosomes, and tissues. FISH technique has many applications, including basic gene mapping, used in pathological diagnosis to detect chromosome and gene copy number aberrations, translocations, microdeletions, and duplications. For the recognition of gene amplifications and deletions, locus-specific probes that are collections of one or a few cloned DNA sequences are routinely used. Multiplex-FISH (M-FISH) technique visualizes all chromosomes with different colors using spectrally distinct fluorophores for each chromosome in one experiment to detect numerical and structural alterations of chromosomes obtained from tumor cells. Recently many of the gene-specific probes are commercially available.

Nuclear localization of translocation partners in differentiating B-cells.

We studied the nuclear localization and relative position in the nuclear space of malignant translocation partner genes c-Myc, CCND1, and IGH locus in naive and differentiating B cells. We have shown that, during B-cell maturation, c-Myc and IGH loci become closer to each other. In differentiating lymphocytes, those alleles of c-Myc and IGH that are in close spatial proximity to each other are closer to the nucleolus. For the CCND1 locus, no correlation between the proximity of loci and nuclear localization was found. These data suggest that the close spatial proximity of c-Myc and IGH loci during B-cell maturation increase the probability of malignant translocation.

Abstract 3745: Comprehensive integrative characterization of hepatocellular carcinoma: The TCGA HCC project

Abstract Background: Hepatocellular carcinomas (HCCs) are heterogenous primary liver cancers with pleomorphic histologic features. We present a comprehensive genetic, genomic, transcriptomic and proteomic analysis of 203 HCCs in The Cancer Genome Atlas Program (TCGA) on behalf of the TCGA Liver analysis working group to provide a deeper understanding of the molecular features of HCCs, to classify them in a clinically-relevant manner, and to provide a public resource that identifies potential targets for emerging therapies.Results: Mutation analyses confirmed the presence of TERT promoter mutations in 40% of HCCs. The analysis also revealed the first reported germline mutation in the TERT promoter in a 30 year old male, possibly reflecting an inherited predisposition to HCC. TERT promoter mutations were enriched in hepatitis C virus infected subjects. Analyses of hepatitis B virus (HBV)-induced HCCs demonstrated recurrent integrations of HBV in the TERT locus. Thus, HBV integration may substitute for TERT promoter mutations as an alternate mechanism of telomerase activation. Other tumor suppressor genes inactivated by mutation included the cell cycle genes TP53 (32% of cases), RB1 (8%), and PTEN (3%), the Wnt/beta catenin pathway gene AXIN1 (4%), and the chromatin remodeling genes ARID1A (9%), BAP1 (6%), ARID1B (4%), ARID2 (4%), and PBRM1 (3%). The oncogene CTNNB1 was mutated in 27% of HCCs. Mutations were also found in the MTOR pathway genes, MTOR (4%), TSC2 (4%) and TSC1 (3%). The patterns of mutational signatures observed included signatures characteristic of the known carcinogens aristolochic acid and aflatoxin B1. Clustering of mRNA, miRNA, or protein expression, DNA hypermethylation and DNA copy number profiles identified five, four, two, five and three clusters, respectively. Analysis of mRNA expression data identified five groups. In particular, Group 1 was associated with Asian race, higher histologic grade, and micro- and macrovascular invasion. Integrated clustering showed a grouping of HCCs into three superclusters: iCluster 1 had a low frequency of CDKN2A silencing, lack of CTNNB1 mutation, a normal-like methylation pattern, and overexpression of proliferation marker genes; iClusters 2 and 3 had a high frequency of CDKN2A silencing, CTNNB1 mutation, and overexpression of oxidative response genes; iCluster 3 tumors had a higher degree of chromosomal instability, high frequency of 17p loss, and a highly altered methylation profile. Copy number aberrations included gains in the MYC, VEGFA, CCND1, TERT, and MET loci and losses in the TP53, RB1, ERFFI1, CDKN2A, ARID1A and PTEN loci. Discussion: Based on integrated analysis of genome, transcriptome, methylome and proteome we showed that HCCs naturally separate into three to five distinct groups with associated molecular and clinical characteristics. Importantly, we identified a novel germline mutation in the TERT promoter that may be associated with an inherited risk for HCC. Note: This abstract was not presented at the meeting. Citation Format: Lewis R. Roberts, David A. Wheeler. Comprehensive integrative characterization of hepatocellular carcinoma: The TCGA HCC project. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3745. doi:10.1158/1538-7445.AM2015-3745

Genomic high-resolution profiling of single CKpos/CD45neg flow-sorting purified circulating tumor cells from patients with metastatic breast cancer.

Circulating tumor cells (CTCs) are promising surrogate markers for systemic disease, and their molecular characterization might be relevant to guide more individualized cancer therapies. To enable fast and efficient purification of individual CTCs, we developed a work flow from CellSearch(TM) cartridges enabling high-resolution genomic profiling on the single-cell level. Single CTCs were sorted from 40 CellSearch samples from patients with metastatic breast cancer using a MoFlo XDP cell sorter. Genomes of sorted single cells were amplified using an adapter-linker PCR. Amplification products were analyzed by array-based comparative genomic hybridization, a gene-specific quantitative PCR (qPCR) assay for cyclin D1 (CCND1) locus amplification, and genomic sequencing to screen for mutations in exons 1, 9, and 20 of the phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha (PIK3CA) gene and exons 5, 7, and 8 of the tumor protein p53 (TP53) gene. One common flow-sorting protocol was appropriate for 90% of the analyzed CellSearch cartridges, and the detected CTC numbers correlated positively with those originally detected with the CellSearch system (R(2) = 0.9257). Whole genome amplification was successful in 72.9% of the sorted single CTCs. Over 95% of the cells displayed chromosomal aberrations typical for metastatic breast cancers, and amplifications at the CCND1 locus were validated by qPCR. Aberrant CTCs from 2 patients harbored mutations in exon 20 of the PIK3CA gene. This work flow enabled effective CTC isolation and provided insights into genomic alterations of CTCs in metastatic breast cancer. This approach might facilitate further molecular characterization of rare CTCs to increase understanding of their biology and as a basis for their molecular screening in the clinical setting.

Unusual concomitant rearrangements of Cyclin D1 and MYC genes in blastoid variant of mantle cell lymphoma: Case report and review of literature

We report herein a case of blastoid variant mantle cell lymphoma (MCL) with both aberrant phenotype and unusual genetics. Unexpectedly, lymphoma cells were CD5− and CD10+. Standard karyotype and FISH techniques showed that tumor cells carried two distinct translocations which had not been reported together in a same tumor. The first translocation juxtaposed the immunoglobulin lambda light chain locus with CCND1 locus, leading to Cyclin D1 overexpression. The second translocation revealed MYC rearrangement with a non-immunoglobulin gene partner located on the short arm of chromosome 4. The interpretation of the case on tissue sections alone could have been challenging. Indeed, the lack of CD5 and expression of CD10 associated with MYC rearrangement detected on interphasic nuclei could support the diagnosis of diffuse large B-cell lymphoma or Burkitt lymphoma. This distinction is also especially important as these lymphoma subtypes require specific treatment.

Mantle cell lymphoma with intrafollicular growth pattern

Mantle cell lymphoma (MCL) can show diffuse, nodular and mantle zone growth patterns. We report on two cases of MCL with an unusual intrafollicular growth pattern and discuss the differential diagnosis. The first case was a small lymph node biopsy from a patient with a history of MCL in remission for 6 years. The lymph node showed a preserved architecture but with cyclin D1-positive cells exclusively confined to follicle centers, thus representing an unusual in situ pattern of recurrent disease. The second case was a lymph node biopsy infiltrated with classical diffuse MCL but with areas of intrafollicular growth pattern. Both cases exhibited the classical immunophenotype of MCL with CD20 positivity and co-expression of CD5, cyclin D1, BCL2, and SOX11. Proliferation rate, as assessed by Mib-1 immunostaining was <10% within the infiltrated follicle centers. Fluorescence in situ hybridization analysis demonstrated a break in the CCND1 locus indicative of the t(11;14)(q13;q32), whereas the BCL2 gene locus was intact. Both patients followed a relatively indolent clinical course as compared with classical MCL. It is important to recognize this particular pattern in MCL, since it may occur as minimal lymph node involvement and may also lead to confusion with follicular lymphoma.

Non-MTC IGH-CCND1 Breakpoints in Mantle Cell Lymphoma Are Associated with CpG Sites and AID Hotspots

Abstract 398Most t(11;14)(q13;q32) breakpoints in mantle cell lymphoma (MCL) are scattered across a large genomic region centromeric to the CCND1 gene on chromosome 11q13. However, few t(11;14) breakpoints outside the major translocation cluster (MTC) have been sequenced. We report our analysis of 56 IGH-CCND1 fusion sequences from 32 non-MTC cases of MCL. Our analysis reveals remarkable breakpoint diversity at both CCND1 and IGH loci. The CCND1 breakpoints are located from 2 kb to 331 kb from the CCND1 gene, including 12 breakpoints (38%) in the 220kb region centromeric to the MTC, which is itself located 110 kb centromeric to the CCND1 gene. Twenty-one cases had a JH coding end breakpoint on the der(14) chromosome and a DH coding end breakpoint on the der(11). Two cases had der(14) and der(11) breakpoints derived from the coding and signal ends of the same JH or DH gene segment; one case had a JH/DH breakpoint on the der(14) and a VH breakpoint on the der(11); and one case had a breakpoint in the JH region located >100 bases from the nearest RSS motif, suggesting a RAG-independent break at IGH. No der(11) breakpoint could be amplified in eight cases. In sixteen cases (50%), one or both CCND1 breakpoints were within 4 bases of a CpG dinucleotide, a feature characteristic of translocation breakpoints in many human B cell lymphomas. Three CpG-associated “microclusters” were identified, i.e. breakpoints in two different tumors located at or near the same CpG site. Breakpoints in the sixteen (50%) “non-CpG” cases showed a significant association with AID hotspot motifs at the CCND1 locus. In addition, the non-CpG breakpoints were more likely to: 1) be located telomeric to the MTC, 2) involve 3’ JH and 5’ DH gene segments, and 3) be associated with immunoglobulin lambda light chain restriction; features that suggest occurrence at a late stage of pre-B cell maturation. In contrast, the CpG-associated breakpoints were: 1) more likely to be centromeric to the MTC, 2) not biased in their JH or DH segment usage, and 3) associated with kappa light chain restriction; features suggesting occurrence in an earlier pre-B cell or pro-B cell. Our results implicate AID in chromosomal breakage at both CpG and non-CpG sites within the CCND1 locus and suggest that AID and RAG collude to generate the chromosomal breaks underlying the t(11;14). Our findings also suggest that IGH-CCND1 rearrangements can occur at different stages of pre-B cell maturation. This study provides novel insights into the mechanism and developmental timing of the t(11;14) in human MCL, features that are likely to be relevant to a broad range of human lymphomas. Disclosures:Greisman:Signature Genomics, LLC: Patents & Royalties. Yi:Signature Genomics, LLC: Patents & Royalties.

Pediatric Follicular Lymphoma: A Report of the First 3 Cases From Taiwan and Literature Review

Follicular lymphoma (FL) is a common lymphoma entity in adults but is rare in children. As opposed to adult cases, pediatric FL is characterized by a high-grade histology, low-stage disease, a lower frequency of both bcl-2 protein expression and BCL2 gene rearrangement, and a more favorable prognosis. During the authors’ previous study of pediatric Burkitt lymphoma, they identified 3 cases of pediatric FL. Here the authors present the first series of pediatric FL from Taiwan. The patients were 2 boys and 1 girl, aged from 7 to 14. The presentation sites were cervical lymph node in 2 and tonsil in 1. All cases showed large neoplastic nodules comprising sheets of centroblasts, corresponding to grade 3b FL. Two of the 3 tumors weakly expressed bcl-2 protein. Fluorescence in situ hybridization for IGH, BCL2, BCL6, CCND1, and MYC loci showed that the only chromosomal translocation was rearranged IGH in 1 case. Two patients were at stage I, and 1 at stage III. All were treated with combination chemotherapy and achieved long-term complete remission. Literature review including the current cases showed that 45% cases of pediatric FL expressed bcl-2 protein and 9% cases carried BCL2 gene rearrangement, suggesting an alternate molecular pathogenesis of pediatric FL as compared to their adult counterparts.

FISH reveals chromosomal abnormalities in 41 Patients with Systemic Amyloidosis (AL).

AbstractAbstract 1197Over the past fifteen years FISH has considerably improved our ability to reveal consistent chromosomal changes in M-GUS, MM and plasma cell leukaemia (PCL), providing evidence of common genetic disease mechanisms and parameters to guide therapeutic decisions. In contrast, this information is still limited in AL due to the rarity of the disease, the low burden and the low proliferative index of clonal PCs. However, recent studies have suggested that in AL FISH, either combined with cytoplasmic staining of specific IgL (cIg-FISH) or performed on immuno-selected PCs, can reveal aneuploidies and translocations involving the immunoglobulin heavy chain locus (IGH). Based on these data we applied FISH to study 41 consecutive AL patients in order to establish the incidence of chromosomal abnormalities and their possible correlation with clinical parameters and outcome. In addition, since in every patient FISH was carried out on immuno-selected and immuno-stained PCs a comparison between these two FISH methods ((iFISH and cIg-FISH respectively) was made. The diagnosis of primary AL was based on the demonstration of amyloid deposits in tissues and organs, the identification of a monoclonal protein in serum or urine, the predominance of a monoclonal k or λ plasma cell population in the bone marrow. iFISH and cIg-FISH were carried out with the FGFR3/IGH [t(4;14)] dual color dual fusion, the CCND1/IGH [t(11;14)] dual color dual fusion, the IgH/c-MAF [t(14;16)] dual color dual fusion, the CEP7, the CEP9, the LSI D13S319+LSI 13q34, the LSI ATM+CEP11, the LSI p53+CEP17 probes (Vysis, Downers Grove, IL, USA) and with the ON MM 1q21/8p21.1 and the 4q21 tricolor probes (Kreated, Amsterdam, The Netherlands). Probes cut-off values were calculated by applying a one tail binomial distribution with a 95% confidence interval to the results obtained from the analysis of 1500 nuclei from five normal controls. For monosomies cut-off values were fixed at 8.3%, for trisomies at 3%, for translocations at 10%. The Mann Whitney U test and the Fisher exact test were used to make statistical comparisons. A 2-sided p-value <0.05 was considered statistically significant. Karyotype defects had an incidence of 87.8% on iFISH and of 80.4% on cIg-FISH. An insufficient PCs number in cytospin preparation was the major drawback of cIg-FISH. However, the two FISH approaches revealed similar percentages of abnormal cells. IGH rearrangements were the most frequent karyotype alterations and their incidence was 51.2%. The CCND1 locus was the most common IGH partner being involved in 41.5% of patients and was followed by the c-MAF locus involved in two patients (4.8%). No patient with the t(11;14) translocation presented a FISH pattern suggestive of a 11q13 (CCND1 locus) gain which, instead, was observed in ten t(11;14) negative patients. Monosomy 13/13q deletion and 1q21 amplification were revealed in 34.1% and 31.7% of patients respectively. Hyperdiploidy had a frequency of 24.4%. The t(11;14) was rare in patients with major peripheral nervous system involvement (p=0.027) and was not correlated with cardiac involvement (p=0.5). Moreover, t(11;14) positive patients presented a median bone marrow PCs percentage similar to that of patients with amp1q21 and higher than that of 13q-/-13 patients. No defect correlated with an increased bone marrow PCs infiltration. In conclusion: i) iFISH and cIg-FISH provided very similar results; ii) chromosomal defects had an incidence of 80–88%; iii) the t(11;14) was significantly correlated with absence of peripheral nervous system involvement; iv) no chromosomal defect was associated with a significant increase of median BM PCs infiltration. Our data confirm the relevant role of CCDN1 in AL pathogenesis. Disclosures:Merlini:Millennium: Honoraria; Ortho-Biotech: Honoraria.

Somatic alterations in the melanoma genome: A high‐resolution array‐based comparative genomic hybridization study

We performed DNA microarray-based comparative genomic hybridization to identify somatic alterations specific to melanoma genome in 60 human cell lines from metastasized melanoma and from 44 corresponding peripheral blood mononuclear cells. Our data showed gross but nonrandom somatic changes specific to the tumor genome. Although the CDKN2A (78%) and PTEN (70%) loci were the major targets of mono-allelic and bi-allelic deletions, amplifications affected loci with BRAF (53%) and NRAS (12%) as well as EGFR (52%), MITF (40%), NOTCH2 (35%), CCND1 (18%), MDM2 (18%), CCNE1 (10%), and CDK4 (8%). The amplified loci carried additional genes, many of which could potentially play a role in melanoma. Distinct patterns of copy number changes showed that alterations in CDKN2A tended to be more clustered in cell lines with mutations in the BRAF and NRAS genes; the PTEN locus was targeted mainly in conjunction with BRAF mutations. Amplification of CCND1, CDK4, and other loci was significantly increased in cell lines without BRAF-NRAS mutations and so was the loss of chromosome arms 13q and 16q. Our data suggest involvement of distinct genetic pathways that are driven either through oncogenic BRAF and NRAS mutations complemented by aberrations in the CDKN2A and PTEN genes or involve amplification of oncogenic genomic loci and loss of 13q and 16q. It also emerges that each tumor besides being affected by major and most common somatic genetic alterations also acquires additional genetic alterations that could be crucial in determining response to small molecular inhibitors that are being currently pursued.

Cyclin D1 expression in typical chronic lymphocytic leukaemia

Demonstration of cyclin D1 expression by immunohistochemistry in a CD5-positive small B-cell proliferation is extremely helpful in the diagnosis of mantle cell lymphoma in tissue samples, including bone marrow trephine biopsies (BMTB) and in differentiating them from chronic lymphocytic leukaemia (CLL). Following the identification of cyclin D1 expression in one case of CLL on BMTB, 64 additional cases, which included 25 lymph nodes, one tonsillar lesion, one skin lesion and 37 BMTBs were systematically reviewed for presence of cyclin D1 overexpression. Overall, in seven of 65 samples (approximately 10%) of CLL, a minority of the leukaemic cells in the proliferation centres expressed cyclin D1. Cytogenetic analysis had been performed in three of seven cases and there was no evidence of translocation involving CCND1 locus. Our findings suggest that a small subset of CLL overexpresses cyclin D1 in amounts that can be demonstrated by immunohistochemistry. Our observation has impact on the diagnosis of small B-cell lymphomas in BMTB and other tissue samples.

CCND1 rearrangements and cyclin D1 overexpression in renal oncocytomas: frequency, clinicopathologic features, and utility in differentiation from chromophobe renal cell carcinoma

Renal oncocytoma is a benign tumor occurring singly or as multiple synchronous lesions. The histologic features of renal oncocytoma may overlap with those of chromophobe renal cell carcinoma. Chromosomal translocations involving the CCND1 locus at 11q13 and overexpression of cyclin D1 occur in a subset of renal oncocytomas. We evaluated a series of 63 renal oncocytomas and 36 chromophobe renal cell carcinomas and assessed the clinical features, cyclin D1 overexpression by immunohistochemistry, and alterations of the CCND1 gene by fluorescence in situ hybridization. All 36 chromophobe renal cell carcinomas were negative for cyclin D1 overexpression and alterations of CCND1. Of the 63 renal oncocytomas, 21 (33%) showed cyclin D1 overexpression. Of 21 renal oncocytomas with cyclin D1 overexpression, a CCND1 rearrangement was detected in 12 (57%). A CCND1 rearrangement was also identified in 1 (2%) of the 42 renal oncocytomas without cyclin D1 overexpression. Of 42 renal oncocytomas without cyclin D1 overexpression, 16 (38%) were from patients with multiple renal oncocytomas at nephrectomy. Of 21 renal oncocytomas with cyclin D1 overexpression, only 1 (5%) patient had multiple renal oncocytomas (P = .006). Of the 25 patients whose original tumor showed no cyclin D1 overexpression, 8 (32%) developed a subsequent renal oncocytoma. None of 15 patients whose original tumor showed cyclin D1 overexpression had a subsequent renal oncocytoma (P = .016). The findings of this study suggest that renal oncocytomas lacking cyclin D1 overexpression may be associated with the development of multiple renal oncocytomas and that these patients are more likely to develop subsequent renal oncocytomas suggesting the need for more frequent clinical for these patients and little need for follow-up in patients with renal oncocytomas overexpressing cyclin D1. The data also show that cyclin D1 overexpression and CCND1 rearrangements by fluorescence in situ hybridization are absent in chromophobe renal cell carcinoma, suggesting that these are useful when differentiating between renal oncocytoma and chromophobe renal cell carcinoma.