Dual role of lipids for genome stability and pluripotency facilitates full potency of mouse embryonic stem cells

While Mek1/2 and Gsk3β inhibition ("2i") supports the maintenance of murine embryonic stem cells (ESCs) in a homogenous naïve state, prolonged culture in 2i results in aneuploidy and DNA hypomethylation that impairs developmental potential. Additionally, 2i fails to support derivation and culture of fully potent female ESCs. Here we find that mouse ESCs cultured in 2i/LIF supplemented with lipid-rich albumin (AlbuMAX) undergo pluripotency transition yet maintain genomic stability and full potency over long-term culture. Mechanistically, lipids in AlbuMAX impact intracellular metabolism including nucleotide biosynthesis, lipid biogenesis, and TCA cycle intermediates, with enhanced expression of DNMT3s that prevent DNA hypomethylation. Lipids induce a formative-like pluripotent state through direct stimulation of Erk2 phosphorylation, which also alleviates X chromosome loss in female ESCs. Importantly, both male and female "all-ESC" mice can be generated from de novo derived ESCs using AlbuMAX-based media. Our findings underscore the importance of lipids to pluripotency and link nutrient cues to genome integrity in early development.

Conventional and Spectral Karyotyping of Murine Cerebellar Granule Neuron Progenitors

Karyotyping remains an invaluable tool to researchers exploring the cause and consequence of genomic instability in biologic systems. It allows investigators to survey the entire chromosome complement in individual cells and in a single experiment, visualize, and measure different forms or features of instability such as aneuploidy, ongoing chromosomal instability, DNA damage/mis-repair, telomere erosion, chromosome mis-segregation, or defects in cell cycle progression. This chapter describes the combined use of conventional (DAPI-banding) and spectral karyotyping (SKY) to characterize genomic instability in murine cerebellar granule neuron progenitors (CGNPs), using CGNPs with conditional deletion of Atr as a positive control for chromosomal rearrangements. Protocols for preparing slides (metaphase spreads) from fixed cell suspension, DAPI-banding, and spectral karyotyping (SKY) are included. Pertinent aspects of image acquisition and analysis are detailed. These protocols can likely be adapted to other tissue types (murine or human).

Error-prone repair of stalled replication forks drives mutagenesis and loss of heterozygosity in haploinsufficient BRCA1 cells

Germline mutations in the BRCA genes are associated with a higher risk of carcinogenesis, which is linked to an increased mutation rate and loss of the second unaffected BRCA allele (loss of heterozygosity, LOH). However, the mechanisms triggering mutagenesis are not clearly understood. The BRCA genes contain high numbers of repetitive DNA sequences. We detected replication forks stalling, DNA breaks, and deletions at these sites in haploinsufficient BRCA cells, thus identifying the BRCA genes as fragile sites. Next, we found that stalled forks are repaired by error-prone pathways, such as microhomology-mediated break-induced replication (MMBIR) in haploinsufficient BRCA1 breast epithelial cells. We detected MMBIR mutations in BRCA1 tumor cells and noticed deletions-insertions (>50 bp) at the BRCA1 genes in BRCA1 patients. Altogether, these results suggest that under stress, error-prone repair of stalled forks is upregulated and induces mutations, including complex genomic rearrangements at the BRCA genes (LOH), in haploinsufficient BRCA1 cells.

EGFR Amplification in Metastatic Colorectal Cancer

BACKGROUND

EGFR amplification occurs in about 1% of metastatic colorectal cancers (mCRCs) but is not routinely tested as a prognostic or predictive biomarker for patients treated with anti-EGFR monoclonal antibodies (mAbs). Herein, we aimed to characterize the clinical and molecular landscape of EGFR-amplified metastatic colorectal cancer (mCRC).

METHODS

In this multinational cohort study, we compared clinical data of 62 patients with EGFR-amplified vs. 1459 EGFR non-amplified mCRC, as well as comprehensive genomic data of 35 EGFR-amplified vs. 439 EGFR non-amplified RAS/BRAF wild-type and microsatellite stable (MSS) tumor samples.

RESULTS

EGFR amplification was statistically significantly associated with left primary tumor sidedness and RAS/BRAF wild-type status. All EGFR-amplified tumors were MSS and HER2 non-amplified. Overall, EGFR-amplified samples had higher median fraction of genome altered compared to EGFR non-amplified, RAS/BRAF wild-type MSS cohort. Patients with EGFR-amplified tumors reported longer overall survival (OS) (median OS = 71.3 months; 95% confidence interval [CI] = 50.7-NA) vs. EGFR non-amplified ones (24.0 months; 95% CI = 22.8-25.6; hazard ratio [HR] = 0.30, 95% CI = 0.20-0.44, P<.001; adjusted HR = 0.46, 95%CI = 0.30-0.69, P<.001). In the subgroup of patients with RAS/BRAF wild-type mCRC exposed to anti-EGFR-based therapy, EGFR amplification was again associated with better OS (median OS = 54.0 months [95% CI = 35.2-NA] vs. 29.1 months [95% CI = 27.0-31.9], respectively; HR = 0.46, 95%CI = 0.28-0.76, P=.002).

CONCLUSION

Patients with EGFR-amplified mCRC represent a biologically defined subgroup and merit dedicated clinical trials with novel and more potent EGFR targeting strategies beyond single-agent monoclonal antibodies.

Novel insights into breast cancer copy number genetic heterogeneity revealed by single-cell genome sequencing

Copy number alterations (CNAs) play an important role in molding the genomes of breast cancers and have been shown to be clinically useful for prognostic and therapeutic purposes. However, our knowledge of intra-tumoral genetic heterogeneity of this important class of somatic alterations is limited. Here, using single-cell sequencing, we comprehensively map out the facets of copy number alteration heterogeneity in a cohort of breast cancer tumors. Ou/var/www/html/elife/12-05-2020/backup/r analyses reveal: genetic heterogeneity of non-tumor cells (i.e. stroma) within the tumor mass; the extent to which copy number heterogeneity impacts breast cancer genomes and the importance of both the genomic location and dosage of sub-clonal events; the pervasive nature of genetic heterogeneity of chromosomal amplifications; and the association of copy number heterogeneity with clinical and biological parameters such as polyploidy and estrogen receptor negative status. Our data highlight the power of single-cell genomics in dissecting, in its many forms, intra-tumoral genetic heterogeneity of CNAs, the magnitude with which CNA heterogeneity affects the genomes of breast cancers, and the potential importance of CNA heterogeneity in phenomena such as therapeutic resistance and disease relapse.

Cells in the body remain healthy by tightly preventing and repairing random changes, or mutations, in their genetic material. In cancer cells, however, these mechanisms can break down. When these cells grow and multiply, they can then go on to accumulate many mutations. As a result, cancer cells in the same tumor can each contain a unique combination of genetic changes.

This genetic heterogeneity has the potential to affect how cancer responds to treatment, and is increasingly becoming appreciated clinically. For example, if a drug only works against cancer cells carrying a specific mutation, any cells lacking this genetic change will keep growing and cause a relapse. However, it is still difficult to quantify and understand genetic heterogeneity in cancer.

Copy number alterations (or CNAs) are a class of mutation where large and small sections of genetic material are gained or lost. This can result in cells that have an abnormal number of copies of the genes in these sections. Here, Baslan et al. set out to explore how CNAs might vary between individual cancer cells within the same tumor.

To do so, thousands of individual cancer cells were isolated from human breast tumors, and a technique called single-cell genome sequencing used to screen the genetic information of each of them. These experiments confirmed that CNAs did differ – sometimes dramatically – between patients and among cells taken from the same tumor. For example, many of the cells carried extra copies of well-known cancer genes important for treatment, but the exact number of copies varied between cells. This heterogeneity existed for individual genes as well as larger stretches of DNA: this was the case, for instance, for an entire section of chromosome 8, a region often affected in breast and other tumors.

The work by Baslan et al. captures the sheer extent of genetic heterogeneity in cancer and in doing so, highlights the power of single-cell genome sequencing. In the future, a finer understanding of the genetic changes present at the level of an individual cancer cell may help clinicians to manage the disease more effectively.

Modeling Patient-Derived Glioblastoma with Cerebral Organoids

The prognosis of patients with glioblastoma (GBM) remains dismal, with a median survival of approximately 15 months. Current preclinical GBM models are limited by the lack of a "normal" human microenvironment and the inability of many tumor cell lines to accurately reproduce GBM biology. To address these limitations, we have established a model system whereby we can retro-engineer patient-specific GBMs using patient-derived glioma stem cells (GSCs) and human embryonic stem cell (hESC)-derived cerebral organoids. Our cerebral organoid glioma (GLICO) model shows that GSCs home toward the human cerebral organoid and deeply invade and proliferate within the host tissue, forming tumors that closely phenocopy patient GBMs. Furthermore, cerebral organoid tumors form rapidly and are supported by an interconnected network of tumor microtubes that aids in the invasion of normal host tissue. Our GLICO model provides a system for modeling primary human GBM ex vivo and for high-throughput drug screening.

Adult Human Glioblastomas Harbor Radial Glia-like Cells

Radial glia (RG) cells are the first neural stem cells to appear during embryonic development. Adult human glioblastomas harbor a subpopulation of RG-like cells with typical RG morphology and markers. The cells exhibit the classic and unique mitotic behavior of normal RG in a cell-autonomous manner. Single-cell RNA sequencing analyses of glioblastoma cells reveal transcriptionally dynamic clusters of RG-like cells that share the profiles of normal human fetal radial glia and that reside in quiescent and cycling states. Functional assays show a role for interleukin in triggering exit from dormancy into active cycling, suggesting a role for inflammation in tumor progression. These data are consistent with the possibility of persistence of RG into adulthood and their involvement in tumor initiation or maintenance. They also provide a putative cellular basis for the persistence of normal developmental programs in adult tumors.

Secretory carcinoma of the breast: clinicopathologic profile of 14 cases emphasising distant metastatic potential

AIMS

Secretory carcinoma of the breast (SCB) is a rare histological type of breast carcinoma with a generally indolent clinical behaviour. We aim to elucidate the clinical, pathological and molecular findings of SCB cases and identify characteristics associated with aggressive clinical courses.

METHODS AND RESULTS

Fourteen patients with SCB were identified, including 12 women and two men, with a median age of 56 years (range = 8-81 years). Clinical data, histological diagnosis, molecular findings and follow-up were reviewed. Eight patients presented with palpable masses and four patients with radiographic abnormalities. All cases were unilateral. Surgical procedures included excisional biopsies and ipsilateral mastectomies. In 10 cases, oestrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER2) results were obtained, with six cases positive for ER and three positive for PR. All cases lacked HER2 overexpression. Sentinel lymph node biopsy was performed in 10 cases, and two patients had axillary lymph node metastasis. Follow-up ranged from 21 to 212 months (median = 70 months). Two patients developed distant metastasis of SCB. Molecular analysis of these aggressive tumours revealed amplification of the 16p13.3 locus, a TERT promotor mutation and loss of 9p21.3 locus. Review of the literature for SCB cases with distant metastasis was performed.

CONCLUSIONS

Although SCBs are generally associated with a favourable prognosis, our study and review demonstrate that a subset of SCBs may develop distant metastases. Further studies are warranted to identify markers predictive of more aggressive clinical behaviour in this rare breast cancer subtype.

NOXA genetic amplification or pharmacologic induction primes lymphoma cells to BCL2 inhibitor-induced cell death

Although diffuse large B cell lymphoma (DLBCL) cells widely express the BCL2 protein, they rarely respond to treatment with BCL2-selective inhibitors. Here we show that DLBCL cells harboring PMAIP1/NOXA gene amplification were highly sensitive to BCL2 small-molecule inhibitors. In these cells, BCL2 inhibition induced cell death by activating caspase 9, which was further amplified by caspase-dependent cleavage and depletion of MCL1. In DLBCL cells lacking NOXA amplification, BCL2 inhibition was associated with an increase in MCL1 protein abundance in a BIM-dependent manner, causing a decreased antilymphoma efficacy. In these cells, dual inhibition of MCL1 and BCL2 was required for enhanced killing. Pharmacologic induction of NOXA, using the histone deacetylase inhibitor panobinostat, decreased MCL1 protein abundance and increased lymphoma cell vulnerability to BCL2 inhibitors in vitro and in vivo. Our data provide a mechanistic rationale for combination strategies to disrupt lymphoma cell codependency on BCL2 and MCL1 proteins in DLBCL.

Integrated Genomic Analysis of Hürthle Cell Cancer Reveals Oncogenic Drivers, Recurrent Mitochondrial Mutations, and Unique Chromosomal Landscapes

The molecular foundations of Hürthle cell carcinoma (HCC) are poorly understood. Here we describe a comprehensive genomic characterization of 56 primary HCC tumors that span the spectrum of tumor behavior. We elucidate the mutational profile and driver mutations and show that these tumors exhibit a wide range of recurrent mutations. Notably, we report a high number of disruptive mutations to both protein-coding and tRNA-encoding regions of the mitochondrial genome. We reveal unique chromosomal landscapes that involve whole-chromosomal duplications of chromosomes 5 and 7 and widespread loss of heterozygosity arising from haploidization and copy-number-neutral uniparental disomy. We also identify fusion genes and disrupted signaling pathways that may drive disease pathogenesis.

Abstract 4619: Integrated genomic analysis of Hurthle cell carcinoma reveals TMEM233/PRKAB1 fusion as a novel oncogenic driver

Background: Hurthle cell carcinoma (HCC) is an enigmatic malignancy of the thyroid that can behave in an aggressive fashion, sometimes lethal, yet its molecular foundations are poorly understood. Some HCC have a good prognosis (minimally invasive, HMIN) whereas others can be extremely aggressive (widely invasive, HWIDE), leading to metastasis and death. HCCs were not included in the TCGA thyroid cancer study, which focused solely on papillary thyroid carcinomas. To understand the development of HCC and unveil its molecular mechanism, we performed a comprehensive genomic characterization of 56 primary HCCs that span the spectrum of tumor behavior and investigated the role of TMEM233/PRKAB1 fusion as a critical driver of oncogenesis in HCC.

Methods: Tumor and matched normal specimens were obtained from 56 patients with primary HCC. Tumors were classified into minimally invasive ( n=24) or widely invasive subtype (n=32). Whole exome sequencing was used to identify somatic mutations. Copy number changes were identified using FACETS and validated by FISH. RNASeq was used to identify novel fusions genes and to identify differentially expressed genes. Genomic alterations associated with histological phenotype were identified. Genomic changes associated with recurrence and survival were identified by the Kaplan Meier method. Immortalized thyroid epithelial cell line, NTHY-ori 3.1 was used to express control and fusion gene for in vitro and in vivo experiments.

Results: We elucidate the mutational profile and driver mutations in HCC and reveal that they exhibit a diverse spectrum of recurrent mutations, most of which have not been previously associated with this cancer (EIF1AX, MADCAM1). Notably, HCC harbor an extremely high prevalence of disruptive mutations to both protein-coding and tRNA encoding regions of the mitochondrial genome. We reveal unique chromosomal landscapes that involve whole chromosomal duplications of chromosomes 5 and 7 and wide spread major loss of heterozygosity arising from haploidization and copy number neutral uniparental disomy. These chromosomal processes underlie genetic instability and are highly prevalent in aggressive forms of HCC. We also identify novel fusion genes such as TMEM233/PRKAB1 which expression resulted in a transformation, organoids formation and invasion phenotype in vitro and

tumorigenesis in vivo. These data suggested that TMEM233/PRKAB1 fusion plays as a critical driver and may serve as a therapeutic target for HCCs.

Conclusions: We performed integrated genomic analysis of hurthle cell carcinoma revealing novel oncogenic drivers, recurrent mitochondrial mutations and unique chromosomal landscapes, which will help guide development of new treatments for one of the most deadly types of thyroid cancer.

Citation Format: Yiyu Dong, Ian Ganly, Vladimir Makarov, Fengshen Kuo, Shyamprasad Deraje, Ed Reznik, Venkatraman Seshan, Gouri Nanjangud, Luc Morris, Nadeem Riaz, Eric Sherman, Ronald Ghossein, James Fagin, Timothy Chan. Integrated genomic analysis of Hurthle cell carcinoma reveals TMEM233/PRKAB1 fusion as a novel oncogenic driver [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4619.

Abstract NG03: Chromosomal instability promotes metastasis through a cytosolic DNA response

Chromosomal instability (CIN) is a hallmark of cancer and it results from ongoing errors in chromosome segregation during mitosis. While CIN is a major driver of tumor evolution, its role in metastasis has not been established. Here we show that CIN promotes metastasis by sustaining a tumor-cell autonomous response to cytosolic DNA. Errors in chromosome segregation create a preponderance of micronuclei whose rupture spills genomic DNA into the cytosol. This leads to the activation of the cGAS-STING cytosolic DNA-sensing pathway and downstream noncanonical NF-κB signaling. Genetic suppression of CIN significantly delays metastasis even in highly aneuploid tumor models, whereas inducing continuous chromosome segregation errors promotes cellular invasion and metastasis in a STING-dependent manner. Using single-cell RNA sequencing, we uncover a CIN-induced transcriptional switch from a proliferative and metabolically active state to a mesenchymal phenotype associated with inflammatory pathways, offering an opportunity to target chromosome segregation errors for therapeutic benefit. Our work reveals an unexpected link between CIN, cytosolic DNA sensing pathways, and metastasis. The use of an isogenic system has enabled us to dissect the role of CIN from that of aneuploidy. Importantly, while we do not discount the role of CIN in generating karyotypic heterogeneity that can serve as the substrate for natural selection, our work demonstrates that continuous chromosome missegregation is also required to replenish cytosolic DNA pools leading to chronic upregulation of inflammatory pathways. In non-transformed settings, cytosolic DNA sensing is incompatible with viability. Unlike normal cells, chromosomally unstable cells are awash with cytosolic DNA and have adapted to coexist with a chronically active cGAS-STING pathway by suppressing downstream type I interferon signaling and instead upregulating the alternative NF-κB pathway. Persistent STING activation mediates carcinogen-induced tumor formation and we now show that tumor cells co-opt this otherwise lethal program to spread to distant organs. The evolutionary benefit of the noncanonical pathway might justify the scarcity of inactivating mutations in cGAS and STING among human cancers. The emergence, and subsequent tolerance, of CIN represents an important bottleneck during tumor evolution. Our single-cell analysis revealed that CIN induces a transcriptional switch whereby cells shift from a proliferative and highly metabolic state, ideally suited for primary tumor growth, to a chromosomally unstable and mesenchymal state associated with upregulation of inflammatory pathways. These two largely mutually exclusive states likely account for the reversibility in chromosome missegregation rates seen in primary tumors and metastases, and provide an explanation for the negative effect of aneuploidy during early tumorigenesis. Interestingly, this mutual exclusivity was recently observed in a pan-cancer genomic analysis of metastatic tumors, and it leads us to suggest that CIN underlies the subset of metastases that are characterized by EMT and inflammation. By providing a mechanistic link between CIN and metastasis, our work opens new avenues to target chromosomally unstable tumors for therapeutic benefit.

Citation Format: Samuel F. Bakhoum, Bryon Ngo, Ashley L. Bakhoum, Julie-Ann Cavallo, Charles J. Murphy, Peter Ly, Pragya Shah, Roshan K. Sriram, Thomas B.k. Watkins, Neil K. Taunk, Mercedes Duran, Chantal Pauli, Christine Shaw, Kalyani Chadalavada, Vinagolu K. Rajasekhar, Giulio Genovese, Subramanian Venkatesan, Nicolai J. Birkbak, Nicholas McGranahan, Mark Lundquist, Quincy LaPlant, John H. Healey, Olivier Elemento, Christine H. Chung, Nancy Y. Lee, Marcin Imielinski, Gouri Nanjangud, Dana Pe'er, Don W. Cleveland, Simon N. Powell, Jan Lammerding, Charles Swanton, Lewis C. Cantley. Chromosomal instability promotes metastasis through a cytosolic DNA response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr NG03.

Low-Grade Astrocytoma Mutations in IDH1, P53, and ATRX Cooperate to Block Differentiation of Human Neural Stem Cells via Repression of SOX2

Low-grade astrocytomas (LGAs) carry neomorphic mutations in isocitrate dehydrogenase (IDH) concurrently with P53 and ATRX loss. To model LGA formation, we introduced R132H IDH1, P53 shRNA, and ATRX shRNA into human neural stem cells (NSCs). These oncogenic hits blocked NSC differentiation, increased invasiveness in vivo, and led to a DNA methylation and transcriptional profile resembling IDH1 mutant human LGAs. The differentiation block was caused by transcriptional silencing of the transcription factor SOX2 secondary to disassociation of its promoter from a putative enhancer. This occurred because of reduced binding of the chromatin organizer CTCF to its DNA motifs and disrupted chromatin looping. Our human model of IDH mutant LGA formation implicates impaired NSC differentiation because of repression of SOX2 as an early driver of gliomagenesis.

Intratumoral heterogeneity of ERBB2 amplification and HER2 expression in micropapillary urothelial carcinoma

Micropapillary urothelial carcinoma (MPUC) is a rare but an aggressive variant of urothelial carcinoma. MPUC has been shown to commonly exhibit ERBB2 amplification and HER2 protein overexpression, but the frequency and distribution of these findings within micropapillary (MP) and not otherwise specified (NOS) components of tumors with mixed histology have not been addressed. Therefore, we evaluated ERBB2 amplification and HER2 expression in 43 MPUC cases by fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC). Of the 35 tumors containing both MP and NOS components, ERBB2 amplification was present in both the MP and NOS components of 12 tumors (34.3%), in only the MP component of 11 tumors (31.4%), and exclusively in the NOS component of 4 tumors (11.4%). HER2 protein overexpression was significantly more commonly present in the MP component compared to the NOS component within the same tumor (68.6% versus 34.3%, P = .012). Overall, there was a moderately positive correlation between HER2 protein expression and ERBB2 amplification in both MP (ρ = 0.59, P < .001) and NOS (ρ = 0.70, P < .001) components. All MP/NOS areas with IHC score 3+ and none of MP/NOS areas with IHC score 0 were associated with ERBB2 amplification. We conclude that ERBB2 amplification and HER2 overexpression are preferentially but not exclusively identified in the MP component compared to the NOS component within the same tumor. Our findings identify the presence of intratumoral heterogeneity of ERBB2 amplification and HER2 expression in MPUC and provide grounds for further investigation into the mechanisms underlying the development of MPUC.

Concurrent deletion of BRCA2 and RB1 and aggressive prostate cancer

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Background: Pathogenic variants of BRCA2 have been observed in a substantial subset of men with metastatic castration resistance prostate cancer (mCRPC). Prostate cancer (PC) patients with germline mutations of BRCA2 experience more rapid progression of their localized PC to mCRPC. This stands in contrast to other cancers where BRCA2 alterations do not appear to be associated with a worse prognosis. We identified homozygous and hemizygous deletions of BRCA2 in a subset of primary PC, which had been previously unrecognized. BRCA2 deletion in PC more frequently co-exists with RB1 deletion rather than alone. BRCA2-RB1 co-deletion in primary PC (TCGA and Taylor cohort) is associated with a shorter disease free survival and increased genomic instability in patients, indicating that BRCA2-RB1 null tumors are likely very aggressive in nature. Methods: To determine the underlying molecular and genomic consequences of BRCA2- RB1 loss, we CRISPR/shRNA-out these genes from human PC cell lines and subjected them to various in vitro assays, RNA-seq and kinase arrays. We applied a 3-color FISH assay to identify the deletion of BRCA2 and RB1 in PC. Results: BRCA2-RB1 null LNCaP cells exhibit androgen independence as evidenced by relative resistance to enzalutamide, and increased growth in absence of androgen but show enhanced sensitivity towards PARPi or platinum. Moreover, the null cell induces an aggressive EMT like phenotype, which is associated with enhanced migration and invasion. RNA-seq and array results show significant activation of EMT related signaling pathways including an unexpected activation of WNK1 upon co-deletion of BRCA2-RB1. FISH assay revealed significant co-deletion of BRCA2-RB1 in ADT resistant aggressive PC tumor cells. More importantly these cells also show greater sensitivity towards PARPi or platinum. Conclusions: Our finding suggests that concurrent deletion of BRCA2-RB1 is most likely is a driver of therapy resistant aggressive PC rather than the consequence of exposure to therapy. We propose that screening for BRCA2-RB1 deletion early could be implemented to identify those at highest risk of aggressive PC and provide an opportunity for early intervention and alternative treatments.

Chromosomal instability drives metastasis through a cytosolic DNA response

Chromosomal instability is a hallmark of cancer that results from ongoing errors in chromosome segregation during mitosis. Although chromosomal instability is a major driver of tumour evolution, its role in metastasis has not been established. Here we show that chromosomal instability promotes metastasis by sustaining a tumour cell-autonomous response to cytosolic DNA. Errors in chromosome segregation create a preponderance of micronuclei whose rupture spills genomic DNA into the cytosol. This leads to the activation of the cGAS-STING (cyclic GMP-AMP synthase-stimulator of interferon genes) cytosolic DNA-sensing pathway and downstream noncanonical NF-κB signalling. Genetic suppression of chromosomal instability markedly delays metastasis even in highly aneuploid tumour models, whereas continuous chromosome segregation errors promote cellular invasion and metastasis in a STING-dependent manner. By subverting lethal epithelial responses to cytosolic DNA, chromosomally unstable tumour cells co-opt chronic activation of innate immune pathways to spread to distant organs.

Abstract B015: An approach to suppress the evolution of resistance in BRAFV600E-mutant cancer

Tumors evolve as they adapt to environmental cues. The principles governing evolution of tumors under the selective pressure of targeted therapy are not well understood. We aimed to evaluate the evolution of resistance and to identify therapeutic modalities that prevent this process in BRAFV600E-mutant tumors. We modeled the selection and propagation of BRAFV600E amplification (BRAFamp) in patient-derived tumor xenografts (PDX) treated with a direct ERK inhibitor. Single-cell sequencing and multiplex-fluorescence in situ hybridization mapped the emergence of extra-chromosomal amplification in multiple subclones of the same tumor shortly after treatment. The evolutionary selection of BRAFamp is determined by the fitness threshold, the barrier subclonal populations need to overcome to regain fitness in the presence of therapy. This differed for ERK signaling inhibitors, and single-cell sequencing of a melanoma PDX model showed that drugs of the same pathway do not necessarily select for the same subclones. These data suggest that sequential monotherapy is not optimal, but concurrent targeting of RAF, MEK, and ERK, however, imposes a sufficiently high fitness threshold to prevent the propagation of subclones with high-level amplification. Administered on an intermittent schedule, this treatment inhibited tumor growth without apparent toxicity in 11/11-lung cancer and melanoma PDX models with various additional alterations. Thus, gene amplification can be acquired and expanded through parallel evolution, enabling tumors to adapt while maintaining their intratumoral heterogeneity. Treatments that impose a high fitness threshold, such as our intermittent triple therapy, will likely prevent the evolution of resistance-causing alterations and merit testing in patients.

Citation Format: Yaohua Xue, Luciano Martelotto, Timour Baslan, Alberto Vides, Martha Solomon, Kalyani Chadalavada, Elisa DeStanchina, Gouri Nanjangud, Michael Berger, Scott Lowe, Jorge S. Reis-Filho, Neal Rosen, Piro Lito. An approach to suppress the evolution of resistance in BRAFV600E-mutant cancer [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr B015.

An approach to suppress the evolution of resistance in BRAFV600E-mutant cancer

The principles governing evolution of tumors exposed to targeted therapy are poorly understood. Here we modeled the selection and propagation of BRAF amplification (BRAF^amp) in patient-derived tumor xenografts (PDX) treated with a direct ERK inhibitor, alone or in combination with other pathway inhibitors. Single cell sequencing and multiplex-fluorescence in situ hybridization mapped the emergence of extra-chromosomal amplification in parallel evolutionary tracts, arising in the same tumor shortly after treatment. The evolutionary selection of BRAF^amp is determined by the fitness threshold, the barrier subclonal populations need to overcome to regain fitness in the presence of therapy. This differed for ERK signaling inhibitors, suggesting that sequential monotherapy is ineffective and selects for a progressively higher BRAF copy number. Concurrent targeting of RAF, MEK and ERK, however, imposes a sufficiently high fitness threshold to prevent the propagation of subclones with high-level amplification. Administered on an intermittent schedule, this treatment inhibited tumor growth in 11/11-lung cancer and melanoma PDX without apparent toxicity in mice. Thus, gene amplification can be acquired and expanded through parallel evolution, enabling tumors to adapt while maintaining their intratumoral heterogeneity. Treatments that impose the highest fitness threshold will likely prevent the evolution of resistance-causing alterations and merit testing in patients.

Intratumoral heterogeneity of ERBB2/HER2 expression in micropapillary urothelial carcinoma

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Background: Micropapillary urothelial carcinoma (MPUC) is a rare but an aggressive variant of urothelial carcinoma. Histologically, most of these tumors are associated with variable amounts of “not otherwise specified (NOS)” urothelial carcinoma. MPUC has been shown to be associated with ERBB2/HER2 amplification and protein overexpression. However, the status and distribution of these findings within the different components of tumors containing both MP and NOS urothelial carcinoma have not been addressed. Methods: We identified 44 cases of MPUC that had tissue available for FISH and IHC at our institute, of which an NOS component sufficient for both FISH and IHC was identified in 37 cases. We followed the updated ASCO/CAP Guidelines for breast cancer and as such amplification was defined by a HER2/CEP17 ratio of ≥ 2.0 or > 6 copies of the gene and HER2 overexpression was considered with IHC scores of 2+ and 3+. Results: In urothelial tumors with both MP and NOS components (n = 37), ERBB2 amplification in MP and NOS components was present in 25 and 16 cases respectively. ERBB2 amplification was significantly higher in the MP component compared to NOS component within the same tumor (67.57% vs. 43.24%, p = 0.049). HER2 overexpression in MP and NOS components was present in 25 and 13 cases respectively. HER2 overexpression was significantly higher in the MP component compared to NOS component within the same tumor (67.56% vs. 35.13%, p = 0.012). In addition, ERBB2 amplification strongly correlated with HER2 overexpression in both MP (rho = 0.65, p < 0.001) and NOS (rho = 0.74, p < 0.001) components. In this cohort (n = 44), tumor stage and lymph node status were significant predictors for overall survival (p = 0.01, < 0.001 respectively). However, ERBB2 amplification and HER2 overexpression in MP component were not associated with patients’ survival outcome (p = 1.00, 0.75 respectively). Conclusions: In MPUC, ERBB2 amplification and HER2 overexpression were preferentially but not exclusively identified in MP component compared to NOS component within the same tumor. Our findings provide evidence for intratumoral heterogeneity of ERBB2 amplification and HER2 expression in MPUC.

Whole-genome single-cell copy number profiling from formalin-fixed paraffin-embedded samples

A substantial proportion of tumors consist of genotypically distinct subpopulations of cancer cells. This intratumor genetic heterogeneity poses a substantial challenge for the implementation of precision medicine. Single-cell genomics constitutes a powerful approach to resolve complex mixtures of cancer cells by tracing cell lineages and discovering cryptic genetic variations that would otherwise be obscured in tumor bulk analyses. Because of the chemical alterations that result from formalin fixation, single-cell genomic approaches have largely remained limited to fresh or rapidly frozen specimens. Here we describe the development and validation of a robust and accurate methodology to perform whole-genome copy-number profiling of single nuclei obtained from formalin-fixed paraffin-embedded clinical tumor samples. We applied the single-cell sequencing approach described here to study the progression from in situ to invasive breast cancer, which revealed that ductal carcinomas in situ show intratumor genetic heterogeneity at diagnosis and that these lesions may progress to invasive breast cancer through a variety of evolutionary processes.

Abstract B14: Molecular characterization of mucinous ovarian carcinoma

Mucinous ovarian carcinoma (MOC) is a rare, chemoresistant tumor known to share pathologic features with tumors of the gastrointestinal and pancreaticobiliary tracts. To better understand the genomic and proteomic landscapes of invasive MOCs, we identified somatic mutations and proteins expression in a single institution cohort and compared these results with data from TCGA tumor projects.

Twenty-six tumors consistent with primary invasive MOC after expert pathology review and with available paired tumor and normal tissue were identified from institutional databases between July 2001 and July 2012. DNA extracted from FFPE or fresh frozen samples underwent next generation sequencing with a combination of a candidate gene assay (37 genes), the MSK-IMPACT assay (341 genes), transcriptome sequencing, and whole exome sequencing. Copy number alterations were identified using data from the MSK-IMPACT assay, whole exome sequencing or Affymetrix SNP 6.0 arrays. Immunohistochemistry (IHC) was performed using optimized antibodies for six proteins to confirm the diagnosis of MOC (ER, PR, CK7, CK20, CDX-2, PAX8) and seven proteins to correlate with mutation status and copy number alterations (p53, ARID1A[Baf250a], PTEN, PMS2, MSH6, HER2, p16). Mutation data for other TCGA tumor types was obtained from the cBio Cancer Genomics Portal (cbioportal.org).

The median age of the cohort was 58 years (range 20-86 years). Most (19/26, 73%) of the tumors were stage I. Somatic TP53 and KRAS mutations were the most common seen and were identified in 18 (69%) cases each, with a co-mutation rate of 50% (13/26). Other commonly mutated genes include ARID1A, PTEN, and PIK3CA. Homozygous deletions of CDKN2A were found in 27% (7/26). ERBB2 alterations were identified in 19% (5/26) and consisted of three amplifications and two mutations. Mutations in at least one potentially targetable gene were identified in 42% (11/26) of tumors. IHC was concordant with sequencing results in 154/182 (85%) of stained cases. Pancreatic, colorectal, lung adenocarcinoma, endometrial, and stomach cancers have the highest frequency of KRAS mutations. Co-mutations of KRAS and TP53 occur most commonly in pancreatic (59%) and colorectal (21%) carcinomas. CDKN2A homozygous deletions are also found at a similar frequency in pancreatic adenocarcinomas (28%). When evaluating the mutation rates of the five most commonly mutated genes in our MOC cohort with colorectal, pancreatic, gastric and high-grade serous ovarian carcinomas (HGSOC) in the TCGA datasets, pancreatic adenocarcinoma showed the most similarity. HGSOC showed little similarity to the MOCs.

KRAS and TP53 co-mutation are common in invasive MOCs. Other commonly mutated genes include ARID1A, PTEN, and PIK3CA. Potentially targetable ERBB2 alterations were identified in several cases. Despite anatomic distinctions, the mutational landscape of MOC shares similarities with that of pancreatic adenocarcinoma including frequent CDKN2A deletions and KRAS/TP53 co-mutation. The suggested shared molecular pattern with pancreatic adenocarcinoma offers potential to guide future developmental therapeutics.

Citation Format: Brooke Schlappe, Jennifer J. Mueller, Narciso Olvera, Fanny Dao, Cyriac Kandoth, Faina Bogomolniy, Agnes Viale, Kety Huberman, Gouri Nanjangud, Yaser Hussein, Barry Taylor, Robert Soslow, Douglas A. Levine. Molecular characterization of mucinous ovarian carcinoma. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: Exploiting Vulnerabilities; Oct 17-20, 2015; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(2 Suppl):Abstract nr B14.

Abstract 1103: Human tumorigenesis induced by endogenous DNA transposase

Recent cancer genome surveys have revealed extremely low rates of coding gene mutations in distinct tumor subtypes, suggesting that alternative mechanisms must contribute to their pathogenesis. Transposons are mobile genetic elements that are found in all living organisms, including humans where they occupy nearly half of the genome. Their mobilization can cause structural rearrangements in normal and cancer cells. However, it remains unknown whether transposition is a cause of cellular transformation or merely a bystander effect of dysregulated gene expression. Here, we report that PGBD5, a recently characterized human gene related to the piggyBac transposase from the cabbage looper moth, is aberrantly expressed in rhabdoid tumors, medulloblastoma, acute leukemias, and some sarcomas and carcinomas. Ectopic expression of PGBD5 in non-transformed primary human cells is sufficient to induce anchorage independence in vitro and penetrant tumor formation in immunodeficient mice in vivo. PGBD5 expression is sufficient to induce genomic mobilization of engineered DNA transposons in human cells, and purified recombinant PGBD5 exhibits transposase domain-dependent endonuclease activity in vitro. Flanking-sequence exponential anchored PCR and massively parallel sequencing of DNA transposon integrations revealed distinct activity on piggyBac-like inverted terminal repeats, and preference for specific euchromatic human genomic loci. This enables mapping of structural rearrangements of endogenous human transposable elements in primary human tumor genomes, some of which target genes involved in cellular transformation. We find that PGBD5 transposase-induced cell transformation is associated with morphologic de-differentiation, induction of distinct Polycomb gene expression programs and structural chromatin remodeling, consistent with its epigenetic control. These findings reveal an unanticipated mechanism of human tumorigenesis, genomic plasticity and structural alterations of non-coding regulatory genomic loci in human cancer.

Citation Format: Anton Henssen, Amy Eisenberg, Eileen Jiang, Elizabeth Henaff, Richard Koche, Melissa Burns, Julianne R. Carson, Gouri Nanjangud, Eric Still, Jorge Gandara, Paolo Cifani, Avantika Dhabaria, Xiaodong Huang, Elisa de Stanchina, Elizabeth Mullen, Hanno Steen, Elizabeth Perlman, Jeffrey Dome, Cristina Antonescu, Cedric Feschotte, Christopher E. Mason, Alex Kentsis. Human tumorigenesis induced by endogenous DNA transposase. [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 1103. doi:10.1158/1538-7445.AM2015-1103

Genomic imbalance defines three prognostic groups for risk stratification of patients with chronic lymphocytic leukemia

Array comparative genomic hybridization (aCGH) has yet to be fully leveraged in a prognostic setting in chronic lymphocytic leukemia (CLL). Genomic imbalance was assessed in 288 CLL specimens using a targeted array. Based on 20 aberrations in a hierarchical manner, all 228 treatment-naive specimens were classified into a group with poor outcome (20.6%) exhibiting at least one aberration that was univariately associated with adverse outcome (gain: 2p, 3q, 8q, 17q, loss: 7q, 8p, 11q, 17p, 18p), good outcome (32.5%) showing 13q14 loss without any of the other 10 aberrations (gain: 1p, 7p, 12, 18p, 18q, 19, loss: 4p, 5p, 6q, 7p) or intermediate outcome (remainder). The three groups were significantly separated with respect to time to first treatment and overall survival (p < 0.001), and validation of the stratification scheme was performed in two independent datasets. Gain of 3q and 8q, and 17p loss were determined to be independent unfavorable prognostic biomarkers. TP53, NOTCH1 and SF3B1 mutations correlated with the presence of one poor outcome aCGH marker, at a considerably higher frequency than when only considering poor risk aberrations routinely detected by fluorescence in situ hybridization (FISH). These data support genomic imbalance evaluation in CLL by aCGH to assist in risk stratification.

The Eph-receptor A7 is a soluble tumor suppressor for follicular lymphoma

Insights into cancer genetics can lead to therapeutic opportunities. By cross-referencing chromosomal changes with an unbiased genetic screen we identify the ephrin receptor A7 (EPHA7) as a tumor suppressor in follicular lymphoma (FL). EPHA7 is a target of 6q deletions and inactivated in 72% of FLs. Knockdown of EPHA7 drives lymphoma development in a murine FL model. In analogy to its physiological function in brain development, a soluble splice variant of EPHA7 (EPHA7(TR)) interferes with another Eph-receptor and blocks oncogenic signals in lymphoma cells. Consistent with this drug-like activity, administration of the purified EPHA7(TR) protein produces antitumor effects against xenografted human lymphomas. Further, by fusing EPHA7(TR) to the anti-CD20 antibody (rituximab) we can directly target this tumor suppressor to lymphomas in vivo. Our study attests to the power of combining descriptive tumor genomics with functional screens and reveals EPHA7(TR) as tumor suppressor with immediate therapeutic potential.

Effect of ischemic time, fixation time, and fixative type on HER2/neu immunohistochemical and fluorescence in situ hybridization results in breast cancer

Accurate determination of HER2/neu status in breast carcinoma is essential. Alteration of preanalytic variables is known to affect HER2/neu results. American Society of Clinical Oncology (ASCO) and the College of American Pathologists (CAP) issued guidelines to standardize fixation for increased HER2/neu accuracy. We studied the effects of changing preanalytic variables on HER2/neu immunohistochemical and fluorescence in situ hybridization (FISH) results in a known HER2/neu+ invasive carcinoma. The clinical specimen was processed according to ASCO/CAP guidelines, with remaining tumor stored fresh without any fixatives for 4 days at 4°C and cut into core biopsy-sized pieces. Each was fixed in 10% formalin, 15% formalin, Pen-Fix (Richard-Allan Scientific, Kalamazoo, MI), Bouin solution, Sakura molecular fixative (Sakura Tissue-Tek Xpress, Torrance, CA), or zinc formalin for 0 to 168 hours. Immunohistochemical studies and FISH were performed. Compared with the clinical specimen, the samples showed no tumor degradation or marked difference by immunohistochemical studies, except the 1-hour 10% formalin and Bouin samples, or FISH, except the Bouin-fixed samples. Our study demonstrates that HER2/neu results remain accurate beyond ASCO/CAP-recommended preanalytic variables, with the exception of Bouin solution for FISH analysis.

A classification model for distinguishing copy number variants from cancer-related alterations

BACKGROUND

Both somatic copy number alterations (CNAs) and germline copy number variants (CNVs) that are prevalent in healthy individuals can appear as recurrent changes in comparative genomic hybridization (CGH) analyses of tumors. In order to identify important cancer genes CNAs and CNVs must be distinguished. Although the Database of Genomic Variants (DGV) contains a list of all known CNVs, there is no standard methodology to use the database effectively.

RESULTS

We develop a prediction model that distinguishes CNVs from CNAs based on the information contained in the DGV and several other variables, including segment's length, height, closeness to a telomere or centromere and occurrence in other patients. The models are fitted on data from glioblastoma and their corresponding normal samples that were collected as part of The Cancer Genome Atlas project and hybridized to Agilent 244 K arrays.

CONCLUSIONS

Using the DGV alone CNVs in the test set can be correctly identified with about 85% accuracy if the outliers are removed before segmentation and with 72% accuracy if the outliers are included, and additional variables improve the prediction by about 2-3% and 12%, respectively. Final models applied to data from ovarian tumors have about 90% accuracy with all the variables and 86% accuracy with the DGV alone.

Array comparative genomic hybridization reveals genomic copy number changes associated with outcome in diffuse large B-cell lymphomas

To identify, in high-resolution regions of DNA, the copy number changes associated with outcome in patients with diffuse large B-cell lymphoma (DLBCL), a disease with an approximately 50% mortality rate, we performed array comparative genomic hybridization (array-CGH) on specimens from 64 patients with newly diagnosed DLBCL treated with anthracycline-based chemotherapy. For the entire cohort, 55 commonly gained/lost regions, ranging in size from less than 1 Mbp to entire chromosomes, were identified using 1- to 2-Mbp and 2- to 4-Mbp resolution BAC arrays. Copy number changes of 9 minimal regions significantly correlated with overall survival, of which 6 were 10 Mbp or smaller. On multivariate analysis, loss of chromosomes 2 (2.4-4.1 Mbp) and 16 (33.8-35.6 Mbp) were found to be prognostic indicators of poor survival, independent of clinical features routinely used to predict outcome. Loss of chromosome 1 (78.2-79.1 Mbp) was predictive of good outcome. For a subset of 55 specimens classified according to cell-of-origin expression signature subtype, gain of chromosome 12 (45.4-53.8 Mbp) was found to be significantly associated with the germinal center B-cell-like DLBCL subtype. Overall, array-CGH identified relatively small genomic regions associated with outcome, which, along with follow-up expression studies, may reveal target genes important in DLBCL clinical behavior.

Deregulation of the carbohydrate (chondroitin 4) sulfotransferase 11 (CHST11) gene in a B-cell chronic lymphocytic leukemia with a t(12;14)(q23;q32)

The t(12;14)(q23;q32) breakpoints in a case of B-cell chronic lymphocytic leukemia (B-CLL) were mapped by fluorescence in situ hybridization (FISH) and Southern blot analysis and cloned using an IGH switch-gamma probe. The translocation affected a productively rearranged IGH allele and the carbohydrate (chondroitin 4) sulfotransferase 11 (CHST11) locus at 12q23, with a reciprocal break in intron 2 of the CHST11 gene. CHST11 belongs to the HNK1 family of Golgi-associated sulfotransferases, a group of glycosaminoglycan-modifying enzymes, and is expressed mainly in the hematopoietic lineage. Northern Blot analysis of tumor RNA using CHST11-specific probes showed expression of two CHST11 forms of abnormal size. 5'- and 3'-Rapid Amplification of cDNA Ends (RACE) revealed IGH/CHST11 as well as CHST11/IGH fusion RNAs expressed from the der(14) and der(12) chromosomes. Both fusion species contained open reading frames making possible the translation of two truncated forms of CHST11 protein. The biological consequence of t(12;14)(q23;q32) in this case presumably is a disturbance of the cellular distribution of CHST11 leading to deregulation of a chondroitin-sulfate-dependent pathway specific to the hematopoietic lineage.

MUC-1 mucin protein expression in B-cell lymphomas

We have recently shown that MUC1, mapped to the chromosomal band 1q21, is rearranged or amplified in 15% of B-cell lymphomas and that rearrangement led to over-expression of MUC-1 mucin in a case of diffuse large B-cell lymphoma (DLBCL). To determine the incidence of MUC-1 mucin expression and its clinical significance in B-cell lymphomas, we investigated a panel of 113 cases by immunohistochemistry (IHC). MUC-1 mucin expression was detected in the majority of cases (92.9%), with moderate to high levels noted in 50.4% of all histologic subsets comprising DLBCL (82 cases), follicular lymphoma (FL) (15 cases), FL with transformation to DLBCL (4 cases), and other B-cell lymphomas (12 cases). No statistically significant correlation was found between MUC-1 mucin expression and MUC1 genomic status (amplification/rearrangement) evaluated by Southern blot analysis, and 1q21 abnormality by karyotypic analysis. For all cases, MUC-1 mucin expression correlated with a previous history of lymphoma (p=0.003).

Limited proliferation and telomere dysfunction following telomerase inhibition in immortal murine fibroblasts

Telomerase is a ribonucleoprotein enzyme that functions to maintain telomeres, the terminal DNA that protects chromosomal integrity, regulating cellular replicative life span. Telomerase is not expressed in most normal human somatic cells but is active in stabilizing telomeres of certain self-renewing cell populations and most malignant cells, making the enzyme an appealing target for anticancer therapy. We describe here a novel cross-species approach to telomerase inhibition. Ectopic expression of the human telomerase catalytic reverse transcriptase component in murine cells inhibited endogenous murine telomerase activity. Using this approach, telomerase inhibition in immortal murine fibroblasts resulted in critical telomere shortening, leading to slowed proliferation, abnormal morphology, altered cell cycle, and telomere dysfunction with cytogenetic instability, followed by apoptotic cell death. Subpopulations of two telomerase-inhibited clones escaped widespread apoptosis, showing proliferative recovery in culture despite persistently inhibited telomerase activity with progressive telomere shortening and dysfunction. This study, by targeting immortal murine cells for telomerase inhibition, demonstrates the importance of telomerase to murine cell immortalization and telomere maintenance. Moreover, the murine model used here should prove useful in further evaluating telomerase inhibition as an anticancer therapy.

Spectral karyotyping identifies new rearrangements, translocations, and clinical associations in diffuse large B-cell lymphoma

Diffuse large B-cell lymphoma (DLBCL), a histologically well-defined subset of non-Hodgkin lymphoma, is clinically and genetically heterogenous. By G-banding, most cases showed complex hyperdiploid karyotypes and diverse cytogenetic abnormalities that included recurring and nonrecurring translocations, deletions, duplications, and marker chromosomes. While G-banding provided valuable leads to identification of specific rearrangements that enabled gene discovery and clinical correlations, many aberrations remained uncharacterized because of their complexity. The molecular cytogenetic technique spectral karyotyping (SKY), on the other hand, enables complete characterization of all aberrations in a tumor cell karyotype and, hence, precise quantitation of chromosome instability. We report here, for the first time, SKY analysis of a panel of 46 DLBCL cases previously analyzed by G-banding, ascertained at the Memorial Sloan-Kettering Cancer Center. This analysis provided a cytogenetic profile of DLBCL that was characterized by a higher level of instability, qualitatively as well as quantitatively, compared with G-banding. Thus, 551 breakpoints were detected by SKY, in contrast to the 295 by G-banding. Several new recurring breakpoints, translocations, and regions of gain and loss were identified, which included 13 breakpoints not previously identified by G-banding, 10 breakpoints that were underrepresented by G-banding, and 4 previously unrecognized translocations: der(14)t(3;14)(q21;q32), t(1;13)(p32;q14), t(1;7)(q21;q22), and der(6)t(6;8)(q11;q11). We identified new clinical associations involving recurring breakpoints detected by SKY. These studies emphasize the value of SKY analysis for redefinition of chromosomal instability in DLBCL to enhance gene discovery as well as clinical correlation analysis.

Hypermutation of multiple proto-oncogenes in B-cell diffuse large-cell lymphomas

Genomic instability promotes tumorigenesis and can occur through various mechanisms, including defective segregation of chromosomes or inactivation of DNA mismatch repair. Although B-cell lymphomas are associated with chromosomal translocations that deregulate oncogene expression, a mechanism for genome-wide instability during lymphomagenesis has not been described. During B-cell development, the immunoglobulin variable (V) region genes are subject to somatic hypermutation in germinal-centre B cells. Here we report that an aberrant hypermutation activity targets multiple loci, including the proto-oncogenes PIM1, MYC, RhoH/TTF (ARHH) and PAX5, in more than 50% of diffuse large-cell lymphomas (DLCLs), which are tumours derived from germinal centres. Mutations are distributed in the 5' untranslated or coding sequences, are independent of chromosomal translocations, and share features typical of V-region-associated somatic hypermutation. In contrast to mutations in V regions, however, these mutations are not detectable in normal germinal-centre B cells or in other germinal-centre-derived lymphomas, suggesting a DLCL-associated malfunction of somatic hypermutation. Intriguingly, the four hypermutable genes are susceptible to chromosomal translocations in the same region, consistent with a role for hypermutation in generating translocations by DNA double-strand breaks. By mutating multiple genes, and possibly by favouring chromosomal translocations, aberrant hypermutation may represent the major contributor to lymphomagenesis.

Recurring chromosomal abnormalities in non-Hodgkin's lymphoma: biologic and clinical significance

Non-Hodgkin's lymphomas (NHLs) are a group of clinically important neoplasms with a complex biology that makes their classification and treatment difficult. Their incidence is increasing and they cause significant morbidity and mortality. NHLs result from transformation of B and T/natural killer (NK) cells. Their genetic hallmark is chromosomal translocations resulting from aberrant rearrangements of IG and TCR genes, which lead to inappropriate expression of genes at reciprocal breakpoints that regulate a variety of cellular functions, including gene transcription, cell cycle, apoptosis, and tumor progression. Cytogenetics followed by molecular genetic analysis of some of the recurring translocations continues to provide new insights into lymphomagenesis and cell biology. More recently, chromosomal and gene amplification and gene deletion have been recognized as frequent genetic changes that may play a role in lymphoma progression and clinical behavior. In this review, cytogenetic data pertaining to recurring chromosomal changes on lymphomas are reviewed and examined in relation to their relevance to lymphoma development, classification, and clinical behavior.

Translocation (11;14)(q13;q32) and overexpression of cyclin D1 protein in a CD23-positive low-grade B-cell neoplasm

We describe a case of low-grade B-cell neoplasm with features overlapping between B-chronic lymphocytic leukemia (CLL) and mantle cell lymphoma (MCL). The patient presented with a 10-year history of stable CLL without any treatment. The peripheral-blood picture was consistent with atypical mixed CLL (French-American-British criteria), whereas the lymph-node histology was more consistent with MCL. Neoplastic cells were strongly positive for surface immunoglobulin M, kappa, CD5, CD20, CD23, and cyclin D1. Expression of CD11c was weak. Translocation (11;14) and der(10)t(10;?)(p11;?) were the primary cytogenetic changes observed in both peripheral blood (47%) and lymph node (7%). Trisomy 12 was absent. Deletion 6q21 and rearrangements involving 1p/q, consistently associated with progression in lymphomas, also were noted in the peripheral blood but were nonclonal. The present case and similar cases with features overlapping between CLL and MCL most likely represent hybrids. In cases with features of typical CLL, t(11;14) is probably associated with gradual progression and may precede clinical and histologic transformation.

Karyotypic findings as an independent prognostic marker in chronic myeloid leukaemia blast crisis

Fifty-three patients with Ph positive chronic myeloid leukaemia in blastic phase were studied. Additional abnormalities were found in 29 (55%) patients and were more common in myeloid (64%) than lymphoid (45%) blast crisis. The most frequent were +Ph (32%), +8 (28%), +19 (19%), +20 (9%) and +21 (9%). i(17q) (9%) was associated with thrombocytopenia (5/5) and basophilia (2/5). The incidence of additional abnormalities was higher in patients treated with busulphan (70%) than hydroxyurea (44%). No significant differences were noted in the mean values of the clinical and haematological findings recorded at blast crisis between patients with only Ph positive (PP) cells and those with additional abnormalities (AP + AA). Univariate analysis identified karyotypic findings as an independent prognostic marker indicating its significance in assessing the response to therapy and survival after the onset of transformation.

High incidence of meningeal leukemia in lymphoid blast crisis of chronic myelogenous leukemia

Fifteen patients with lymphoid blast crisis of chronic myelogenous leukemia (LyBC-CML) and five patients with acute lymphoblastic leukemia converting to Philadelphia-positive (Ph+) chronic myeloid leukemia (ALL Ph + CML) were followed. Seven of 15 (46.7%) LyBC-CML patients developed meningeal leukemia within a median period of 6 months (range 2-11 months), while there was no medullary relapse. Five of these responded well to triple intrathecal therapy. In the ALL Ph + CML patients, in spite of central nervous system (CNS) prophylaxis with IT MTX and 18 Gy cranial radiation, two of five patients (40%) experienced meningeal leukemia, one isolated and the other with medullary relapse. The data confirm that LyBC-CML patients experience a high incidence of meningeal leukemia. The role of CNS prophylaxis is not very clear, but its use may delay development and reduce morbidity due to CNS disease.

T-lymphoid blast crisis in chronic myeloid leukemia

Chronic myeloid leukemia (CML) is considered to be a pleuripotential stem cell disorder with the capacity to differentiate into myeloid, erythroid, megakaryocytic, and lymphoid cell lines. Consequently, blast crisis (BC) involving each of the above lineages has been well described. Among lymphoblastic crises, differentiation frequently occurs along B-cell lineage. We report four patients of CML who terminated in T-cell extramedullary BC in lymph nodes after a variable duration of chronic phase. The T-lineage was established by characteristic cytochemical staining and reactivity with a panel of anti-T-cell monoclonal antibodies. All four cases were Philadelphia (Ph) chromosome positive and demonstrated the Ph chromosome and associated anomalies (extra Ph, +19) in the lymph nodes. Our data adds to the growing evidence that CML is a disorder of the common stem cell from which T, B, and myeloid precursors originate.

Chronic myeloid leukemia following radioactive iodine (131)I therapy of thyroid cancer

We describe a 51 years old female patient who developed Ph(1) positive chronic myeloid leukemia 7 years following radioactive iodine therapy for follicular carcinoma of thyroid. Until now, only two patients have been reported to have developed CML after this kind of therapy. The underlying mechanisms are discussed and the need to study such patients at cytogenetic, molecular biologic and cell kinetic levels is stressed.