Dysregulation of PRMT5 in chronic lymphocytic leukemia promotes progression with high risk of Richter's transformation

Richter's Transformation (RT) is a poorly understood and fatal progression of chronic lymphocytic leukemia (CLL) manifesting histologically as diffuse large B-cell lymphoma. Protein arginine methyltransferase 5 (PRMT5) is implicated in lymphomagenesis, but its role in CLL or RT progression is unknown. We demonstrate herein that tumors uniformly overexpress PRMT5 in patients with progression to RT. Furthermore, mice with B-specific overexpression of hPRMT5 develop a B-lymphoid expansion with increased risk of death, and Eµ-PRMT5/TCL1 double transgenic mice develop a highly aggressive disease with transformation that histologically resembles RT; where large-scale transcriptional profiling identifies oncogenic pathways mediating PRMT5-driven disease progression. Lastly, we report the development of a SAM-competitive PRMT5 inhibitor, PRT382, with exclusive selectivity and optimal in vitro and in vivo activity compared to available PRMT5 inhibitors. Taken together, the discovery that PRMT5 drives oncogenic pathways promoting RT provides a compelling rationale for clinical investigation of PRMT5 inhibitors such as PRT382 in aggressive CLL/RT cases.

Prognostic gene expression signature for high-grade serous ovarian cancer

BACKGROUND

Median overall survival (OS) for women with high-grade serous ovarian cancer (HGSOC) is ∼4 years, yet survival varies widely between patients. There are no well-established, gene expression signatures associated with prognosis. The aim of this study was to develop a robust prognostic signature for OS in patients with HGSOC.

PATIENTS AND METHODS

Expression of 513 genes, selected from a meta-analysis of 1455 tumours and other candidates, was measured using NanoString technology from formalin-fixed paraffin-embedded tumour tissue collected from 3769 women with HGSOC from multiple studies. Elastic net regularization for survival analysis was applied to develop a prognostic model for 5-year OS, trained on 2702 tumours from 15 studies and evaluated on an independent set of 1067 tumours from six studies.

RESULTS

Expression levels of 276 genes were associated with OS (false discovery rate < 0.05) in covariate-adjusted single-gene analyses. The top five genes were TAP1, ZFHX4, CXCL9, FBN1 and PTGER3 (P < 0.001). The best performing prognostic signature included 101 genes enriched in pathways with treatment implications. Each gain of one standard deviation in the gene expression score conferred a greater than twofold increase in risk of death [hazard ratio (HR) 2.35, 95% confidence interval (CI) 2.02-2.71; P < 0.001]. Median survival [HR (95% CI)] by gene expression score quintile was 9.5 (8.3 to -), 5.4 (4.6-7.0), 3.8 (3.3-4.6), 3.2 (2.9-3.7) and 2.3 (2.1-2.6) years.

CONCLUSION

The OTTA-SPOT (Ovarian Tumor Tissue Analysis consortium - Stratified Prognosis of Ovarian Tumours) gene expression signature may improve risk stratification in clinical trials by identifying patients who are least likely to achieve 5-year survival. The identified novel genes associated with the outcome may also yield opportunities for the development of targeted therapeutic approaches.

Large-Scale Drug Screen Identifies FDA-Approved Drugs for Repurposing in Sickle-Cell Disease

Sickle-cell disease (SCD) is a debilitating hematological disorder with very few approved treatment options. Therapeutic reactivation of fetal hemoglobin (HbF) is one of the most pursued methods for ameliorating the systemic manifestations of SCD. Despite this, very few pharmacological agents have advanced to clinical trials or marketing for use. In this study, we report the development of an HbF in situ intracellular immunoblot assay coupled to a high-throughput drug screen to identify Food and Drug Administration (FDA) approved drugs that can be repurposed clinically for treatment of SCD. Using this assay we evaluated the National Institute of Health (NIH) Clinical Collection (NCC), a publicly available library of 725 small molecules, and found nine candidates that can significantly re-express HbF in erythroid cell lines as well as primary erythroblasts derived from SCD patients. Furthermore, we show the strong effects on HbF expression of these candidates to occur with minimal cytotoxicity in 7 of the 9 drugs. Given these data and their proven history of use for other indications, we hypothesize that several of these candidate drugs warrant further investigation for use in SCD.

BRD4 Profiling Identifies Critical Chronic Lymphocytic Leukemia Oncogenic Circuits and Reveals Sensitivity to PLX51107, a Novel Structurally Distinct BET Inhibitor

Bromodomain and extra-terminal (BET) family proteins are key regulators of gene expression in cancer. Herein, we utilize BRD4 profiling to identify critical pathways involved in pathogenesis of chronic lymphocytic leukemia (CLL). BRD4 is overexpressed in CLL and is enriched proximal to genes upregulated or de novo expressed in CLL with known functions in disease pathogenesis and progression. These genes, including key members of the B-cell receptor (BCR) signaling pathway, provide a rationale for this therapeutic approach to identify new targets in alternative types of cancer. Additionally, we describe PLX51107, a structurally distinct BET inhibitor with novel in vitro and in vivo pharmacologic properties that emulates or exceeds the efficacy of BCR signaling agents in preclinical models of CLL. Herein, the discovery of the involvement of BRD4 in the core CLL transcriptional program provides a compelling rationale for clinical investigation of PLX51107 as epigenetic therapy in CLL and application of BRD4 profiling in other cancers.Significance: To date, functional studies of BRD4 in CLL are lacking. Through integrated genomic, functional, and pharmacologic analyses, we uncover the existence of BRD4-regulated core CLL transcriptional programs and present preclinical proof-of-concept studies validating BET inhibition as an epigenetic approach to target BCR signaling in CLL. Cancer Discov; 8(4); 458-77. ©2018 AACR.This article is highlighted in the In This Issue feature, p. 371.

Abstract 4471: Novel SF3B1 deletion mutations result in aberrant RNA splicing in CLL patients

Recurrent heterozygous mutations in SF3B1, a component of the U2snRNP complex involved in branchsite recognition during the first step of splicing catalysis, are found in various solid tumors and hematologic cancers including myelodysplastic syndromes (MDS) and chronic lymphocytic leukemia (CLL). To provide broader insight into the effects of SF3B1 mutations on RNA splicing in CLL, RNAseq was performed on 215 CLL patient samples with unknown SF3B1 mutation status. 37 patients (17%) demonstrated cryptic 3’ splice site usage we and others have previously reported in patients with known SF3B1 hotspot mutations. Interestingly, 3 patient samples harbored previously unreported in-frame deletions in SF3B1 around K700, the most common amino acid mutated in hematologic cancers with SF3B1 mutations. In particular, 2 patient sequences contained 6 nucleotide (nt) deletions (c.2186 to c.2191) resulting in replacement of Q698, Q699 and K700 with Q (p.Q698_K700delinsQ: “p.Q698del”) and 1 patient sequence had a 3 nt deletion (c.2192 to c.2194) resulting in replacement of K700 and V701 with N (p.K700_V701delinsN: “p.K700del”) in SF3B1. The variant allele fraction (VAF) of these deletions was 20-40%. Targeted resequencing of DNA confirmed presence of these mutations at similar VAFs. Differential splicing analysis across patients with wild-type SF3B1, mutant SF3B1 and our novel deletions revealed similar alternative 3’ splice site patterns. To study the mechanism of alternative 3’ splice site selection induced by these novel p.Q698del and p.K700del in-frame deletions we used our ZDHHC16 minigene system with modifications in the canonical and cryptic 3’ splice sites and respective branchsites. After confirming expression of these deletion mutants and their incorporation in the SF3b complex by qPCR and co-immunoprecipitation, we demonstrated that recognition of both canonical 3’ splice site and alternate branchsite are important for aberrant splicing. This observation is identical to the intronic features required for aberrant splicing that we previously reported for the p.K700E SF3B1 hotspot mutation in CLL and MDS. By comparing the recent cryo-electron microscopy and X-ray crystal structures of SF3b complexes (PDB: 5GM6 and 5IFE, respectively), it is evident that the K700 present at the edge of heat repeat domain 6 is important for pre-mRNA interactions. Both the in-frame deletions and substitution mutations at K700 perturb SF3B1 charge, likely affecting a side-chain interaction with pre-mRNA, thus altering splice-site recognition through a mechanism that is still not well understood. Together, these data indicate that small in-frame deletions in SF3B1 around K700 offer a novel mechanism to induce aberrant splicing in patients with CLL. The common mechanism of action of these mutations and deletions suggest that they should also be sensitive to splicing modulators.

Citation Format: Anant A. Agrawal, Michael Seiler, Lindsey Brinton, Rose Mantel, Rosa Lapalombella, Jennifer A. Woyach, Amy J. Johnson, Lihua Yu, John C. Byrd, Peter G. Smith, James S. Blachly*, Silvia Buonamici*. Novel SF3B1 deletion mutations result in aberrant RNA splicing in CLL patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4471. doi:10.1158/1538-7445.AM2017-4471

Abstract 4147: T cell targeted peptides for monitoring immune response in melanoma

Melanoma develops the ability to evade immune recognition through multiple mechanisms, despite being highly immunogenic. This is demonstrated by the effective and additive response checkpoint blockade therapies have had during combination clinical trials in melanoma [1]. While the results of these trials have been promising, large portions of patients do not respond to treatment [1,2]. Additionally, many responders take months to show a response using standard criteria. In order to monitor patient response and understand the limitations of immunotherapy, we performed phage display to discover peptides targeted to tumor infiltrating lymphocytes (TILs) in melanoma tumors.

To improve phage library characterization, we developed a method to deep sequence phage with the Ilumina MiSeq platform. Phage screens using PhD7 library (NEB) performed on HUVECS and on TILs, naïve and effector T cells, and B cells harvested from mice. The phage libraries generated from these screens were deep sequenced using the Illumina MiSeq system. The sequencing data was analyzed with an efficient, custom MATLAB script, which arranges sequences by frequency determining peptide frequencies for each library. Peptide frequency was normalized to a reference library generated by amplifying an unscreened phage library. T cell screens were compared with B cell and endothelial cell screens in sequence frequency matrices. Top TIL targeting sequences were cloned into phage, and then fluorescently labeled along with insert-less control phage. Labeled phage were incubated with TILs, or effector T cells and analyzed for specificity using flow cytometry. Four phage clones were identified with at least four fold increased binding for TILs over effector T cells isolated from the spleen. Interestingly, only subsets of the TILs were bound by the targeted phage.

We have identified and validated peptides that demonstrate specificity for CD8 TILs. These peptide sequences represent candidates for development into companion diagnostic imaging agents for use with checkpoint therapies. We are currently evaluating these peptides in an in vivo tumor model to further validate their specificity and to determine their biodistributions. Peptides that validate in vivo could be developed into useful imaging agents. After peptide sequences have been validated in vivo, we will determine the phage binding partner using a phage based pulldown. The peptide binding partners discovered through this approach will provide insight into the subset of TILs bound by the phage.

[1] Wolchok, J. D. et al., N Engl J Med 2013; 369:122-133.

[2] Drake, CG. et al., Clin Cancer Res November 15, 201117.

Citation Format: Dustin Bauknight, Andrew Buckner, Lindsey Brinton, Timothy Bullock, Kimberly Kelly. T cell targeted peptides for monitoring immune response in melanoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4147.

Registered report: Wnt activity defines colon cancer stem cells and is regulated by the microenvironment

The Reproducibility Project: Cancer Biology seeks to address growing concerns about reproducibility in scientific research by replicating selected results from a substantial number of high-profile papers in the field of cancer biology. The papers, which were published between 2010 and 2012, were selected on the basis of citations and Altmetric scores (Errington et al., 2014). This Registered report describes the proposed replication plan of key experiments from ‘Wnt activity defines colon cancer stem cells and is regulated by the microenvironment’ by Vermeulen and colleagues, published in Nature Cell Biology in 2010 (Vermeulen et al., 2010). The key experiments that will be replicated are those reported in Figures 2F, 6D, and 7E. In these experiments, Vermeulen and colleagues utilize a reporter for Wnt activity and show that colon cancer cells with high levels of Wnt activity also express cancer stem cell markers (Figure 2F; Vermeulen et al., 2010). Additionally, treatment either with conditioned medium derived from myofibroblasts or with hepatocyte growth factor restored clonogenic potential in low Wnt activity colon cancer cells in vitro (Figure 6D; Vermeulen et al., 2010) and in vivo (Figure 7E; Vermeulen et al., 2010). The Reproducibility Project: Cancer Biology is a collaboration between the Center for Open Science and Science Exchange and the results of the replications will be published in eLife.

DOI:http://dx.doi.org/10.7554/eLife.07301.001

Menopausal estrogen and estrogen-progestin replacement therapy and breast cancer risk

CONTEXT

Whether menopausal hormone replacement therapy using a combined estrogen-progestin regimen increases risk of breast cancer beyond that associated with estrogen alone is unknown.

OBJECTIVE

To determine whether increases in risk associated with the estrogen-progestin regimen are greater than those associated with estrogen alone.

DESIGN

Cohort study of follow-up data for 1980-1995 from the Breast Cancer Detection Demonstration Project, a nationwide breast cancer screening program.

SETTING

Twenty-nine screening centers throughout the United States.

PARTICIPANTS

A total of 46355 postmenopausal women (mean age at start of follow-up, 58 years).

MAIN OUTCOME MEASURE

Incident breast cancers by recency, duration, and type of hormone use.

RESULTS

During follow-up, 2082 cases of breast cancer were identified. Increases in risk with estrogen only and estrogen-progestin only were restricted to use within the previous 4 years (relative risk [RR], 1.2 [95% confidence interval [CI], 1.0-1.4] and 1.4 [95% CI, 1.1-1.8], respectively); the relative risk increased by 0.01 (95% CI, 0.002-0.03) with each year of estrogen-only use and by 0.08 (95% CI, 0.02-0.16) with each year of estrogen-progestin-only use among recent users, after adjustment for mammographic screening, age at menopause, body mass index (BMI), education, and age. The P value associated with the test of homogeneity of these estimates was .02. Among women with a BMI of 24.4 kg/m2 or less, increases in RR with each year of estrogen-only use and estrogen-progestin-only use among recent users were 0.03 (95% CI, 0.01-0.06) and 0.12 (95% CI, 0.02-0.25), respectively. These associations were evident for the majority of invasive tumors with ductal histology and regardless of extent of invasive disease. Risk in heavier women did not increase with use of estrogen only or estrogen-progestin only.

CONCLUSION

Our data suggest that the estrogen-progestin regimen increases breast cancer risk beyond that associated with estrogen alone.

Molar pregnancy and risk for cancer in women and their male partners

OBJECTIVE

It was our aim to evaluate the hypothesis that molar pregnancy is a marker of increased risk for cancer.

STUDY DESIGN

This was a nationwide cohort study of 1520 women, identified from the Danish National Register of Patients, in whom a molar pregnancy was diagnosed during the period 1977-1992 and of 1295 male partners of these women, traced in the Danish Central Population Register.

RESULTS

Linkage of the female roster with the Danish Cancer Registry through 1994 revealed 19 cases of gestational choriocarcinoma, whereas 0.04 was expected from the rates for the general population. Twenty cases of cancers of other types were observed with 24.9 expected (standardized incidence ratio, 0.8; 95% confidence interval, 0.5-1.2), but no specific type of cancer other than gestational choriocarcinoma occurred at a rate significantly different from that expected. Among the 1295 male partners notified in the Central Population Register, a total of 22 cancers were observed with 21.9 expected (standardized incidence ratio, 1.0; 95% confidence interval, 0.7-1.5).

CONCLUSION

Molar pregnancy is not associated with an increased risk for cancer other than gestational carcinoma.

Endometrial cancer chemoprevention: implications of diverse pathways of carcinogenesis

Endometrial cancers may be divided into two groups, reflecting differences in clinical behavior and pathogenesis. Endometrioid adenocarcinoma, which accounts for the majority of endometrial cancers, typifies the group of endometrial carcinomas that develop from atypical endometrial hyperplasia in the setting of excess estrogenic stimulation. In contrast, serous carcinomas are representative of endometrial tumors that occur in older women who have endometrial atrophy and lack the typical endometrial cancer risk factors reflecting unopposed estrogen exposure. Serous carcinomas are frequently associated with p53 abnormalities and appear to develop from a surface lesion termed endometrial intraepithelial carcinoma. Although serous carcinomas are rare, these highly aggressive tumors account for a disproportionate number of endometrial cancer deaths. Further delineation of the estrogen-dependent and estrogen-independent pathways of endometrial carcinogenesis may be useful in developing comprehensive chemopreventive approaches for endometrial cancer.

Regional distribution of human papillomavirus DNA and other risk factors for invasive cervical cancer in Panama

A population-based national cancer registry has documented strikingly different regional incidence rates of cervical cancer in the Republic of Panama. Such regional differences in disease rates could represent regional differences in the occurrence of risk factors, in particular, human genital papillomaviruses (HPV). This study enrolled newly diagnosed invasive cancer patients in the Republic of Panama over an 18-mo period. Behavioral risk factors were measured by interviewing cases and matched controls. In addition, DNA extracted from biopsies of the cancers was tested for HPV sequences. Early age at first coitus, multiple pregnancies, and nonparticipation in Pap smear screening programs were significant risk factors for cervical cancer in this population. These factors and low levels of education occurred more frequently among women residing in regions with higher cancer rates than women residing in the region with lower cancer rates. HPV DNA was detected most frequently (70%) among cases from the region with the lowest cancer rate (30 of 100,000) and least frequent (54%) among cases where the cancer rate was the highest (51 of 100,000). The observations suggest that risk factors other than HPV contribute to the differences in cervical cancer rates among women residing in various regions of Panama.