Citations

Abstract Chromosome 13 (Δ13) abnormalities are found in greater than 50% of patients with Multiple Myeloma (MM). MM is most commonly defined by chromosome 13 monosomy or 13q loss (85%). Interstitial deletions comprise the remaining 15%. Many studies have revealed that Δ13 in MM are associated with poor survival and reduced response to therapy. Genes mapping to chromosome 13 may be involved in pathogenesis and/or progression of the disease due to loss of function from gene mutation or from epigenetic effects such as haploinsufficiency. In this study, array-based comparative genomic hybridization coupled with microarray technology (aCGH) is used to detect gene copy number loss on chromosome 13 from nine MM patient samples. Whole genome long-oligo microarrays constructed by Agilent Technologies were used which contain 40,000 genes that span the human genome with an average spatial resolution of ~75 kb. Using genomic DNA isolated from MM patients with interstitial deletions on chromosome 13, DNA was amplified, labeled and hybridized with a differentially labeled normal DNA reference to determine gene/genomic copy number changes. Arrays were analyzed to search for the minimum region of loss based upon single copy loss for a series of nearby mapping transcripts. A common region of loss of 2.2 Mb, at 13q14.2 was detected. Additionally, we investigated the correlation between genomic copy number change and the expression level for MM patients in the13q region. From an independent gene expression data set whose expression measurements were conducted with Affymetrix HG-U133A v2 microarrays, data was selected that corresponded to the samples used for current aCGH. Expression values from MM samples were divided by the mean expression values from 12 normal bone marrow samples for each gene and the resulting values were treated as surrogate ratios between MM and normal samples. Probes from both microarrays were then aligned according to their chromosomal positions and merged if their chromosomal positions overlapped. Composite chromosomal maps were generated that displayed the expression levels and copy number changes. The maps were used to differentiate chromosomal regions in 13q where copy number changes and expression levels show high correlation and regions where such correlation was not observed. Although the number of probes sampled in the expression microarray was much smaller than those in aCGH microarray, a chromosomal region of great interest, that encompasses 13q14.2, arose naturally from this analysis. Although the mechanism by which loss of 13q effects tumorigenesis in MM could be a haploinsufficiency model, we are not ruling out the presence of a tumor suppressor gene in this region. We are evaluating candidate tumor suppressor genes in the region for loss of function by mutational analysis and hypermethylation studies.

Abstract Activation of NFkB has been noted in late B-cell malignancies, but no genetic basis for this activation has been shown except for rare mutations of the NFkB pathway in lymphoma and none have been described in MM. Bortezomib, highly tumoricidal in a subset of MM patients, inhibits NFkB suggesting it’s role as a therapeutic target. Here we show for the first time the critical importance of mutations that dysregulate this potential survival pathway in human myeloma cell lines (HMCL) and new diagnosis MM patients. We performed high-density oligonucleotide array CGH (Agilent 44k) on CD138+ selected MM cells from 68 patients and 42 unique HMCL. Initially we focused on small loci, bi-allelically deleted, as markers for inactivation of potential tumor suppressor genes. We next developed FISH probes for the identified loci to confirm the bi-allelic deletions seen by aCGH. We next sequenced all samples with monoallelic deletions, and additional unselected patients, and identified additional inactivating mutations. Multiple novel tumor suppressor genes (TSG) were identified and validated, whose loss of function (both in patients and HMCL) leads to activation of the non-canonical NFkB pathway including: TRAF2 (9q34), TRAF3 (14q32), BIRC2/BIRC3 (11q22) and CYLD (16q12). Functional studies showed that HMCL with deletion or mutations in these genes have markedly increased NFkB2 p52/p100 ratios relative to other HMCL (and for BIRC2/BIRC3 relative to an isogenic line that retains one copy of BIRC2/BIRC3), indicating genetic activation of the non-canonical NFkB pathway. Reintroduction of deleted TSG into HMCL inhibited cell growth and resulted in cell death (see data on abstract by J. Keats et al). We next focused our analysis (of combined aCGH and GEP data) on positive regulators of this pathway. Rare IgH translocations of NIK have recently been identified in MM. By aCGH we identified amplification and rearrangements of NIK. We identified dysregulated expression of TNF family receptors that activate the non-canonical pathway: CD40 (translocation), TACI (amplification) and LTBR. All of the HMCL with these mutations also showed increased NFkB2 p52/p100 ratios, consistent with activation of the non-canonical NFkB. These mutations correlate with a gene expression profile of NFkB activation that is detected in one half of patients. In summary, we have determined for the first time the genetic basis for constitutive NFkB activation - present in 19/42 HMCL, and we estimate in at least one quarter of newly diagnosed patients (approximately one half of those with evidence of NFkB activation by GEP). We propose a mechanism in which positive (TACI, CD40, LTBR) and negative regulators (TRAF2, TRAF3, BIRC2/BIRC3, CYLD) of the pathway converge on NIK to mediate the processing of NFKB2 p100 to p52. The preponderance of genetic evidence suggests that drugs that target the non-canonical NFkB pathway, will be most effective in treating the 50% of MM patients with NFkB activation.

Abstract Our understanding of the molecular pathogenesis of myeloma is largely based on observations made from the available human myeloma cell lines. Cell lines have proved invaluable to the characterization of the known immunoglobulin translocations, recurrent deletions and amplifications, and the development of novel therapies. However, it has long been perceived that the cell lines are not representative of patient samples as they often have complex genomes and not even a single cell line has been described with a typical hyperdiploid karyotype. The absence of a hyperdiploid model system is significant as conventional cytogenetic studies of myeloma patient samples has established that patients can be almost evenly split into two broad categories of hyperdiploid and non-hyperdiploid based on their chromosome counts, with the hyperdiploid patients having recurrent trisomies of chromosomes 3, 5, 7, 9, 11, 15, 19, and 21 plus periodic gains of 1q, 18, 20 and loss of 13. Though all of the cell lines have abnormal genomes none of the previously tested cell lines had the characteristic pattern of chromosomal gains seen in hyperdiploid patients and the majority have immunoglobulin translocations, which are more commonly associated with non-hyperdiploid patients. These observations have provided the basis for the assumption that the cell lines are only representative of the non-hyperdiploid patient population. Furthermore, even though very few cell lines have been directly compared to the patient sample from which they were derived it is widely believed that the cell line genomes are unstable and have diverged significantly from the patient samples from which they were derived. Therefore, we decided to compare patient-cell line pairs available from the Mayo Clinic using Agilent 244k array-based comparative genomic hybridization (aCGH) and Affymetrix U133Plus2.0 gene expression profiling and repeated the analysis of our previously studied 46 cell lines on the higher resolution Agilent 244k platform. To date we have completed the analysis of four patient cell line pairs (ALMC-1; ALMC-2; KP-6; KAS-6/1, KAS-6/2) and have repeated our entire cell line panel on the higher resolution array. Four additional patient-cell line pairs (DP-6, JMW-1, SPMC, and VPC-6) are currently being completed. The first compelling observation from this study was that the patient sample from which KP-6 was derived is a perfect match to the characteristic hyperdiploid karyotype with a CGH defined karyotype (51, XY, −1p, +1q, +3, +7, +11, −13, +15, −16q, −17p, +19, +21). The KP-6 cell line showed a similar aCGH defined karyotype (50, X, −Y, −1p, +1q, +3q, +7, −8p, +9p, +11, +15, −16q, −17p, +17q, +19, +21) with the most significant changes occurring on the trisomic chromosomes as many transitioned from trisomies to single arm gains. Therefore, KP-6 appears to be the first myeloma cell line derived from a patient with a characteristic hyperdiploid phenotype. The ALMC patient cell line series is comprised of patient samples at diagnosis and relapse and cell lines derived from both stages. The two patient-cell line pairs only show five and two aCGH definable changes, respectively. In comparison the two matched patient sample pairs have diverged at six regions in the genome. The KAS patient-cell line series is actually two cell lines derived from pre- (KAS-6/1) and post-transplant (KAS-6/2) samples and the KAS-6/2 matching post-transplant patient sample. The comparison of the paired patient sample and derived cell line shows only four aCGH detectable changes. Similarly, there are only three changes between the KAS-6/1 cell line and post-transplant patient sample suggesting that the evolution of this tumor in both the patient and tissue culture is very limited. In conclusion, this study has identified the first bona fide hyperdiploid cell line, thereby providing a valuable investigative tool to better understand the biological differences between the two broad genetic categories of myeloma. Moreover, we demonstrate that the genomes of myeloma cell lines are typically stable and highly representative of the patient sample that was placed into culture to establish the cell line thereby validating their use in the study of this disease.

Abstract Marginal zone B-cell lymphomas (MZL) represent a sub-group of indolent B-cell lymphomas, normally localized in the “marginal zone” of the secondary lymphoid follicles. Depending on the site of involvement, three distinct sub-types have been identified: extra nodal MZL of MALT type, splenic MZL (SMZL), and nodal MZL (NMZL). MALT lymphoma is the most frequent of the MZL subtypes, representing 70% of MZL and 7% to 8% of non-Hodgkin lymphomas. SMZL and NMZL comprise the remaining 20% and 10% of MZL, respectively, and account for less than 1% of NHL. The relative rarity of these lymphomas and difficulty in distinguishing them from other low-grade B-cell lymphoma subtypes like lymphoplasmacytic lymphomas (LPL), making therapeutic decisions difficult. The aim of this study was to perform a comprehensive high-resolution study to identify distinctive molecular markers in MZL and LPL, which would help to better define these lymphomas at genomic level and distinguish them from other types of low-grade B-cell lymphoma. We analyzed 119 patients, including 22 pulmonary MALT (pMALT), 20 non-pulmonary MALT (npMALT), 34 SMZL, 21 NMZL and 22 LPL (8 Waldenström’s Macroglobulinemia and 14 non-WM) cases. Human Agilent 244A platform was used by array-based comparative genomic hybridization (aCGH) analysis. Overall, 93% of patients have an altered genome. LPL had the highest amount of copy number abnormalities (median of 7.5 per patient; average of 11.7; range: 0–44), followed by npMALT (6.5; 7.6; 0–33), NMZL (5; 8.3; 0–31), SMZL (4; 7.1; 0–56) and pMALT (3.5; 4.3; 1–11). When the overall size of the abnormalities was considered, LPL was also the most affected disease with an average size of 245.15Mb included in copy number changes per patient, followed by NMZL (188.6Mb), npMALT (187.2Mb), SMZL (126.4Mb) and pMALT (109Mb). Deletions were more commonly observed than amplifications but the affected area was significantly smaller (average of 55.2Mb and 118.6Mb included in deletions and amplifications per genome, respectively). Partial or total gains of chromosome 3 and 18 were recurrently identified in all the entities, being the most common abnormalities in npMALT (60% and 50%, respectively) and pMALT (27% each). Trisomy 12 was also ubiquitously observed, ranging from 24% of NMZL to 9% of pMALT. Deletions in 6q were commonly identified in LPL (55%), npMALT (35%) and, in a less extent, in SMZL (12%) and NMZL (5%), but not in pMALT. Biallelic and focal monoallelic deletions at 6q23 clearly delineate a minimal deleted region (MDR) that includes TNFAIP3 as being the target gene of the abnormality. Deletions on 7q were found in SMZL and npMALT, thus delineating two MDR. Interstitial 11q deletions were found in LPL, NMZL and SMZL, but not in MALT. Chromosome 13 abnormalities were monosomies in NMZL and interstitial 13q14 deletions in LPL and SMZL, comprising MIRN15A and MIRN16-1 in the MDR. Partial X chromosome gains were common to all the entities but involving different areas: Xq27.3–q28 gains were recurrent events in LPL and NMZL, but not in SMZL and MALT, which were characterized by p arm gains or trisomies. Finally, some recurrent abnormalities were exclusive of specific entities: 1p deletions and 1q gains were only common in NMZL; a focal 2p gain including BCL11A and REL was found in npMALT and partial 8q gains were only identified in LPL. Trisomy 4 was only identified in the subgroup of LPL with WM, but not in the remaining LPL cases or in the remaining diseases. In this study we made a compendium of chromosomal abnormalities present in a group of related diseases, in which the molecular basis remains poorly defined. Using this high-resolution approach we were able to establish recurrent and disease-specific patterns of abnormalities and minimal deleted/amplified regions were redefined. Furthermore, TNFAIP3, a negative regulator of the NF-kB pathway, has been identified as being a commonly affected gene in MALT, LPL and NMZL, highlighting its potential role in pathogenesis.

Abstract The use of high-resolution aCGH allows for whole genome screening for copy number changes even in tumors that rarely produce metaphase spreads. The aim of this study was to characterize the aCGH findings in B-CLL, lung MALT lymphoma, Waldenström’s Macroglobulinemia (WM), Multiple Myeloma (MM) and human myeloma cell lines (HMCLs). This study includes 301 B-cell malignancy samples (19 B-CLL, 19 MALT, 20 WM, 48 HMCLs and 195 MM) and an additional 76 melanoma samples. We found MM to have the highest number of abnormalities per karyotype, with 15.8±7.5 (mean ± SD) and 20.6±17.0 in hyperdiploid (H) and non-hyperdiploid MM (NH), respectively. The remaining diseases have a significantly lower number of abnormalities: 5.5±4.5 in B-CLL, 3.5±1.96 in MALT and 4±3.5 in WM. Aneuploidy and biallelic deletions were rare events in these three diseases. B-CLL has two highly recurrent abnormalities involving 11q22-q23 (29%) and 13q14.3 (33%). A minimal deleted region (MDR) of ∼108Kb was identified at 11q comprising ACAT1, NPAT and ATM. In 13q, a 280Kb MDR was recognized, including TRIM13, KCNRG, mir-15a and mir-16. The subgroup of MALT patients with t(11;18) had very few abnormalities and the majority are a consequence of unbalanced translocations (MALT, BIRC2 and BIRC3 deletions). In the remaining MALT samples, trisomy 3 and 18q gain were the most common abnormalities (31% each). The 6q16.3-q26 deletion was the most common abnormality in WM (45%). In 4 of 9 patients with 6q deletion there was an associated 6p gain. The same observation was found in 2 of 3 patients with 8p loss and concomitant 8q gain. Interestingly, 6p and 8q gain were not identified in patients without 6q and 8p deletions. Deletion of 17p was the most common recurrent abnormality observed in our panel of B-cell cancers, being identified in MM, WM and B-CLL. In B-CLL and WM, small mono and biallelic deletions of the NF-kB negative regulators, TRAF3 and NFKBIA, were identified, suggesting a potential involvement of this pathway in the pathogenesis of these diseases. Hierarchical clustering of the aCGH data in MM identified 3 distinct groups, NH-MM, H-MM and MM with deletions of chromosome 13 and 14. Interestingly, MGUS and SMM were more commonly clustered with H-MM. Several sub-clusters were observed in the H-MM group, the most prominent being made up exclusively of patients from TC class D1. This cluster was characterized by the presence of trisomy 11 and 21. The 11q13 TC group clustered and was highly associated with 11q amplifications due to unbalanced t(11;14). The 6q deletion defined a cluster with WM, MM and Melanoma patient with that abnormality. In the case of B-CLL and MALT, the only identifiable clusters were observed in cases with 13q loss and trisomy 3, respectively. These results highlight both, the common and unique aCGH findings in several B-cell cancers. By hierarchical clustering, MM was significantly divergent from the rest of the B-cell diseases. Due to the limited number of abnormalities in B-CLL/MALT/WM, the clustering of these groups was exclusively based on the common abnormalities. The use of aCGH has refined the MDRs of 11q and 13q in B-CLL. Additionally, the identification of deletions affecting the NF-kB pathway in B-CLL and WM has prompted us to hypothesize on the importance of constitutive NF-κB activation in these diseases.

Abstract Risk stratification in Barrett's esophagus may allow aggressive management of those at “high risk” and reduction in surveillance in at “low” risk. Davison et al. report the results of the independent validation of a multibiomarker panel (TissueCypher assay) performed on biopsy tissue, in a case control study. “High-risk” patients progressed 5 times more than those at “low risk.” Sensitivity and specificity for “high-risk” patients were 29% and 86% with a positive predictive value of 23%. A negative predictive value of a “low-risk” score was 96%. These findings may allow more intensive surveillance in those at “high risk.” Despite some limitations, this assay is a potentially major advance in the management of Barrett's esophagus patients without dysplasia.

Abstract Introduction: Amplification of chromosome 9p24.1 encoding PDL1, PDL2, and JAK2 (the PDJ amplicon) has been detected in 5-25% of triplenegative breast cancers (TNBC), and is associated with poor outcome and activation of the JAK/STAT pathway. Here, we have developed a robust multiplexed fluorescence in situ hybridization (FISH) assay for detection of 9p24.1 amplification, and assessed the frequency and cellular distribution of the PDJ amplicon in a cohort of African American (AA) women with TNBC. Methods: The FISH assay combines three chromosome 9 probes to simultaneously target JAK2 and PD-L1 (9p24.1, PDJ), chromosome 9q22, and the 9q34.1 regions. This enables discrimination of PDJ amplicons from whole chromosome 9p arm gains and from chromosome 9 ploidies that occur in the background of genomic instability in aneuploid cancer genomes. Fifty cells were scored for each probe and the average copy number was obtained. We defined PDJ amplification as PDJ>4, PDJ/9q22 ratio≥2, and/or PDJ/9q34.1 ratio≥2. The assay was benchmarked to array CGH of flow sorted TNBC tissue from Mayo Clinic Arizona (n=14). Tissue microarrays from TNBC PDX tumors (n=20) and from African American women with TNBC (n=87) were assessed. Results: Using selected TNBC tissue with known CGH data, the FISH assay tightly correlated with PDJ copy number in 13/14 cases. The discordant case was negative by CGH on a biopsy with low tumor content, but FISH positive on tissue section (PDJ >7.5 and a PDJ/9q22 ratio=4). Of 20 TNBC PDX tumors, 5 were amplified by FISH. Twelve of 87 (14%) of tumors had PDJ amplification by FISH, of which ten were from breast tissue and two were from lymph node. Of these 12, PDJ>4 (n=0), PDJ/9q22 ratio≥2 (n=6), and PDJ/9q34.1 ratio≥2 (n=10). Significant intratumoral variation was observed with the presence of single cells with >10 PDJ copies in 8/17 (47%) amplified and 0/90 non-amplified total cases. Conclusion: 9p24.1 (PDJ) amplification encoding JAK2, PD-L1, and PD-L2 is detected by three-color FISH in 14% of TNBC from African American women. Individual cells with ≥10 copies of PDJ was seen exclusively in 8/17 amplified cases. We identified 5 PDX tumors which may provide valuable preclinical models for the amplicon. The association of this biomarker with clinical outcome will be presented. Citation Format: Karen S. Anderson, Tammey Naab, Lori K Koslosky, Megan Anderson, Michael Lewis, Yasmine Kanaan, Ali Afsari, Luisel Ricks-Santi, Barbara A. Pockaj, Michael T Barrett. Tissue prevalence and cellular heterogeneity of 9p24.1 amplification in TNBC in African American women [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P2-10-17.

1021 Background: At 5 years, AT did not improve disease free survival or overall survival and RS was a more accurate predictor of relapse than standard clinicopathologic characteristics for patients with hormone receptor (HR) positive tumors. Methods: A Phase III Intergroup trial tested adjuvant AT vs. AC. Women with 1-3 N + or N - and T-size > 1cm were randomized to 4 cycles of AT (60 mg/m2/60 mg/ m2) or AC (60 mg/m2/600 mg/m2) q 3 wk x 4. Patients(pts) with ER + and/ or PR + tumors received tam for 5 yrs. Pts were stratified by nodal, HR (ER+ PR+, ER+PR-, ER-PR+, ER-PR-, ER/PR unk) and menopausal status. The primary endpoint was DFS. A sample of 465 pts with HR + breast cancer with 0 to 3 positive axillary nodes who did (N =116) or did not have a recurrence had tumor tissue evaluated using the 21- gene assay. Grade and HR expression were evaluated locally and centrally. Results: 2952 pts were randomized between 7/30/98 and 1/21/00. 2883 were eligible and analyzable. Arms were balanced for age, HR, menopause, nodes, surgery, grade and T-size: median age 51; 64% ER +; 65% LN-; grade: 10% low, 38% int., 46% high; and median T-size - 2.0 cm. At a median follow-up of 11.5 years the DFS/OS results are shown in the table below. RS was a highly significant predictor of recurrence including node negative and node positive disease (P < .0001) and predicted recurrence more accurately than clinical variables. Conclusions: At 11.5 yrs. median follow-up, there remains no difference in DFS or OS, although there continue to be fewer events in the AT arm in the prespecified ER/PR negative subgroup. At 10 years, the RS continues to be a more accurate predictor of relapse than standard clinical features. [Table: see text]