Epigenomic mapping identifies a super-enhancer repertoire that regulates cell identity in bladder cancers through distinct transcription factor networks

Background: Muscle-invasive bladder cancer is a common aggressive disease with unmet clinical needs. Recent work established a set of consensus bladder cancer transcriptomic subtypes that distinguishes the cell identity of bladder cancers for improved diagnosis and treatment. However, how these distinct subtypes are regulated remains unclear. Given the link between super-enhancers and the regulation of cell identity, we hypothesized that epigenetic activation of distinct super-enhancers could drive the transcriptional programs of the various bladder cancer subtypes. Results: Through integrated RNA sequencing and epigenomic profiling of histone marks (H3K27ac, H3K27me3, H3K9me3) in a diverse panel of 15 primary bladder tumours, seven bladder cancer cell lines, and two primary cultures from normal human urothelia, we established the first integrated epigenetic map of bladder cancer and demonstrate the link between bladder cancer subtype and epigenetic control. Through H3K27ac analysis, we identify the repertoire of activated super-enhancers in bladder cancer that distinguish molecular subtypes. Building on these findings, we reveal the super-enhancer-regulated networks of candidate master transcription factors for Luminal and Basal bladder cancer subgroups. We find that FOXA1, a key pioneer factor in Luminal bladder cancers identified in our Luminal transcription factor network, binds subgroup-specific bladder super-enhancers and correlates with their activation. Furthermore, CRISPR-Cas9 inactivating mutation of FOXA1 triggers a shift from Luminal to Basal cell identity. This shift is accompanied by an overexpression of ZBED2, one of the newly identified transcriptional regulators in the Basal-specific transcription factor network. Finally, we show that both FOXA1 and ZBED2 play concordant roles in preventing inflammatory response in bladder cancer cells through STAT2 inhibition and promote cancer cell survival. Conclusions: Overall, our study provides new data for understanding epigenetic regulation of muscle-invasive bladder cancer and identifies a coregulated network of super-enhancers and associated transcription factors as new potential targets for the treatment of this aggressive disease.

Nocardia Endophthalmitis- Prophylactic Prevention with an Innovative Approach

Background: Nocardia is a common cause of endophthalmitis in southern India. It is an aggressive disease with a poor prognosis. Objective: This study was conducted using an amikacin antibiotic in the drip irrigation of balanced saline solution (BSS) during the surgery to prophylactically study the occurrence of Nocardia endophthalmitis and any subsequent toxic effects of the antibiotics used. Methods: Prospective study period was of 6 months, starting from July to December-2018. Preoperative and postoperative specular counts and macular thickness using Ocular Coherence Tomography (OCT) were compared with any incidence of Nocardia endophthalmitis. A total of 500 patients operated for manual SICS were randomly assigned into 2 groups. The first group of 250 patients received antibiotic amikacin added to the Balanced Saline Solution (BSS) irrigating solution throughout the course of the surgery. The second control group received no antibiotics. Manual SICS was performed on all 500 patients by a single surgeon and was found to be uneventful. Pre- and postoperative corneal endothelial cell density and mean macular thickness using OCT were taken and recorded of all the patients, respectively, and data obtained were statistically compared. Results: No incidence of Nocardia endophthalmitis among the cataract surgeries operated was found. There was no drug-related toxicity to the cornea or macula. Furthermore, no incidence of Nocardia endophthalmitis has been reported since 2018 after using antibiotics. Conclusion: A simple routine of adding amikacin in the drip prophylactically during the course of surgery helped us prevent Nocardia endophthalmitis with no side effects. Also, it will be an innovative technique that is economically feasible and effective in regions where Nocardia endophthalmitis is prevalent.

ROR1 is a novel putative druggable target for diffuse glioma

The cell surface receptor ROR1 is a therapeutic target of growing interest in oncology; however, its role in glioma has not been established thus far. This study analyzed associations between ROR1 mRNA expression and clinical outcomes, and histological and molecular subtypes in four independent glioma (grades II-IV) transcriptomic datasets (The Cancer Genome Atlas-GBMLGG, Chinese Glioma Genome Atlas, Repository for Molecular Brain Neoplasia, and GSE16011), encompassing a total of 2,388 cases. The data strongly suggests that ROR1 may be associated with poorer outcomes and more aggressive disease. Taken together, ROR1 should be further examined as a novel putative druggable target for glioma, a cancer that currently has very limited therapeutic options.

Therapeutic Targeting of Autophagy in Pancreatic Ductal Adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive disease characterized by early metastasis, late detection, and poor prognosis. Progress towards effective therapy has been slow despite significant efforts. Novel treatment approaches are desperately needed and autophagy, an evolutionary conserved process through which proteins and organelles are recycled for use as alternative energy sources, may represent one such target. Although incompletely understood, there is growing evidence suggesting that autophagy may play a role in PDAC carcinogenesis, metastasis, and survival. Early clinical trials involving autophagy inhibiting agents, either alone or in combination with chemotherapy, have been disappointing. Recently, evidence has demonstrated synergy between the MAPK pathway and autophagy inhibitors in PDAC, suggesting a promising therapeutic intervention. In addition, novel agents, such as ONC212, have preclinical activity in pancreatic cancer, in part through autophagy inhibition. We discuss autophagy in PDAC tumorigenesis, metabolism, modulation of the immune response, and preclinical and clinical data with selected autophagy modulators as therapeutics.

Reduced Zeb1 Expression in Prostate Cancer Cells Leads to an Aggressive Partial-EMT Phenotype Associated with Altered Global Methylation Patterns

Prostate cancer is the most common cancer in American men and the second leading cause of cancer-related death. Most of these deaths are associated with metastasis, a process involving the epithelial-to-mesenchymal (EMT) transition. Furthermore, growing evidence suggests that partial-EMT (p-EMT) may lead to more aggressive disease than complete EMT. In this study, the EMT-inducing transcription factor Zeb1 was knocked down in mesenchymal PC-3 prostate cancer cells (Zeb1KD) and resulting changes in cellular phenotype were assessed using protein and RNA analysis, invasion and migration assays, cell morphology assays, and DNA methylation chip analysis. Inducible knockdown of Zeb1 resulted in a p-EMT phenotype including co-expression of epithelial and mesenchymal markers, a mixed epithelial/mesenchymal morphology, increased invasion and migration, and enhanced expression of p-EMT markers relative to PC-3 mesenchymal controls (p ≤ 0.05). Treatment of Zeb1KD cells with the global de-methylating drug 5-azacytidine (5-aza) mitigated the observed aggressive p-EMT phenotype (p ≤ 0.05). DNA methylation chip analysis revealed 10 potential targets for identifying and/or targeting aggressive p-EMT prostate cancer in the future. These findings provide a framework to enhance prognostic and/or therapeutic options for aggressive prostate cancer in the future by identifying new p-EMT biomarkers to classify patients with aggressive disease who may benefit from 5-aza treatment.

Myelomatous Ascites and Pleural Effusion in Relapsed Multiple Myeloma

Extramedullary multiple myeloma is seen in advanced and aggressive disease and occurs due to plasma cell infiltration of sites other than the bone marrow. Myelomatous ascites or pleural effusion is seen in less than 1 % of cases and can be differentiated from infectious etiologies based on fluid cytology.

Two Distinct Clinical Courses and Outcomes in T-Cell Prolymphocytic Leukemia

Introduction: T-cell prolymphocytic leukemia (T-PLL) is a rare type of mature T-cell neoplasm with a poor prognosis. Up to 30% of patients initially present with indolent disease course that may be observed until progression to T-PLL with aggressive behavior. We aimed to compare the clinicopathologic characteristics and outcomes of patients with initially indolent versus aggressive disease. We hypothesized that patients with indolent disease have less cytogenetic abnormalities and a favorable overall survival (OS). Methods: We identified 65 patients diagnosed with T-PLL between 2004 and 2020 who were treated at Moffitt Cancer Center. Clinical presentation, laboratory parameters, and bone marrow biopsy at the time of diagnosis were retrospectively reviewed. Patients were categorized into two groups: indolent or aggressive disease type. Patients were considered indolent if they did not have symptoms requiring immediate treatment such as B symptoms or fatigue, symptomatic lymphadenopathy, symptomatic organomegaly, hyperlymphocytosis, organ dysfunction, or cytopenias requiring transfusions. Patients with 3 or more chromosomal abnormalities were considered to have complex cytogenetics. Clinicopathologic characteristics were compared using Chi-square test. OS and factors that are potential influencers of survival were compared using the Kaplan Meier curve as well as Cox Proportional Hazards regression. Results: Of the 65 patients with T-PLL, 32 (49%) presented with indolent disease and 33 (51%) presented with aggressive disease. The median age at diagnosis was 68 years (range 43-88 years). Patients with aggressive disease presented with a higher WBC compared to those with indolent disease, with median WBC 79.7 x 10 9/L and 22.9 x 10 9/L, respectively (p=<0.001). Patients with aggressive disease also presented with a higher absolute lymphocyte count (ALC), with median ALC 47.8 x 10 9/L and 15.4 x 10 9/L (p=<0.001) (Table 1). Extra-nodal, skin, and CNS involvement was not significantly different between disease types. Flow cytometry was similar between indolent and aggressive disease with the exception with the exception of CD56 and CD57 which were rare and only observed in aggressive disease. Patients with aggressive disease were more likely to have complex karyotype compared to patients with indolent disease (p=0.023). FISH results for inversion 14 and trisomy 8 were similar between disease types. Median time from diagnosis to initial treatment was 379 days for indolent and 44 days for those with aggressive disease. 36 (55%) patients were treated with Alemtuzumab as first line treatment. A total of 15 (23%) patients ultimately underwent allogeneic hematopoietic stem cell transplant (HSCT). The median OS for the entire cohort was 30 months. The median OS for indolent and aggressive disease was 44 and 24 months, respectively (p=0.015, Figure 1). The median OS for patients who underwent HSCT compared to those who did not was 99 and 24 months, respectively (p=0.002). Among patients with indolent disease, those who underwent HSCT had a significantly longer median OS of 153 compared to 34 months for those who did not (p=0.022). There was a trend toward improved OS in patients with aggressive disease who underwent HSCT compared to those that did not (35 vs 16 months; p=0.08). In addition, there was a trend toward improved OS with earlier treatment (<12 months) in the indolent group (383 versus 86 months, p= 0.155). On multivariate analysis (Table 2), factors that negatively affected overall survival were aggressive disease type (HR 3.0, p=0.018), presence of inversion 14 (HR 2.5, p=0.032), presence of B symptoms (HR 2.4, p=0.036), and absence of HSCT (HR 0.2, p=0.001). Conclusion: Patients with T-PLL who present with aggressive disease, inversion 14, B symptoms, and those who are unable to undergo bone marrow transplant have lower overall survival. Characteristics that predict a more aggressive disease phenotype at diagnosis are high WBC, high ALC, presence of B symptoms, and complex karyotype. Figure 1 Figure 1. Disclosures Saeed: Kite Pharma: Consultancy, Other: investigator; Other-TG therapeutics: Consultancy, Other: investigator; sano-aventis U.S.: Consultancy, Membership on an entity's Board of Directors or advisory committees; Other-Epizyme, Inc.: Consultancy; Bristol-Myers Squibb Company: Consultancy; Janssen Pharmaceutica Products, LP: Consultancy, Other: investigator; Celgene Corporation: Consultancy, Other: investigator; MEI Pharma Inc: Consultancy, Other: investigator; Nektar Therapeutics: Consultancy, Other: research investigator; MorphoSys AG: Consultancy, Membership on an entity's Board of Directors or advisory committees; Other-Secura Bio, Inc.: Consultancy; Seattle Genetics, Inc.: Consultancy, Membership on an entity's Board of Directors or advisory committees. Sokol: Dren Bio: Membership on an entity's Board of Directors or advisory committees; Kyowa-Kirin: Membership on an entity's Board of Directors or advisory committees.

Heterogeneity in Pancreatic Cancer Fibroblasts—TGFβ as a Master Regulator?

Pancreatic ductal adenocarcinoma is an aggressive disease for which there are very few available therapies. It is notable for its high degree of tumour complexity, with the tumour microenvironment often accounting for the majority of the tumour volume. Until recently, the biology of the stroma was poorly understood, particularly in terms of heterogeneity. Recent research, however, has shed light on the intricacy of signalling within the stroma and particularly the molecular and functional heterogeneity of the cancer associated fibroblasts. In this review, we summarise the recent improvements in our understanding of the different fibroblast populations within PDAC, with a focus on the role TGFβ plays to dictate their formation and function. These studies have highlighted some of the reasons for the failure of trials targeting the tumour stroma, however, there are still considerable gaps in our knowledge, and more work is needed to make effective fibroblast targeting a reality in the clinic.

Centrosome Aberrations as Drivers of Chromosomal Instability in Breast Cancer

Chromosomal instability (CIN), or the dynamic change in chromosome number and composition, has been observed in cancer for decades. Recently, this phenomenon has been implicated as facilitating the acquisition of cancer hallmarks and enabling the formation of aggressive disease. Hence, CIN has the potential to serve as a therapeutic target for a wide range of cancers. CIN in cancer often occurs as a result of disrupting key regulators of mitotic fidelity and faithful chromosome segregation. As a consequence of their essential roles in mitosis, dysfunctional centrosomes can induce and maintain CIN. Centrosome defects are common in breast cancer, a heterogeneous disease characterized by high CIN. These defects include amplification, structural defects, and loss of primary cilium nucleation. Recent studies have begun to illuminate the ability of centrosome aberrations to instigate genomic flux in breast cancer cells and the tumor evolution associated with aggressive disease and poor patient outcomes. Here, we review the role of CIN in breast cancer, the processes by which centrosome defects contribute to CIN in this disease, and the emerging therapeutic approaches that are being developed to capitalize upon such aberrations.