Relapse Timing Is Associated With Distinct Evolutionary Dynamics in Diffuse Large B-Cell Lymphoma.

PURPOSE: Diffuse large B-cell lymphoma (DLBCL) is cured in more than 60% of patients, but outcomes remain poor for patients experiencing disease progression or relapse (refractory or relapsed DLBCL [rrDLBCL]), particularly if these events occur early. Although previous studies examining cohorts of rrDLBCL have identified features that are enriched at relapse, few have directly compared serial biopsies to uncover biological and evolutionary dynamics driving rrDLBCL. Here, we sought to confirm the relationship between relapse timing and outcomes after second-line (immuno)chemotherapy and determine the evolutionary dynamics that underpin that relationship. PATIENTS AND METHODS: Outcomes were examined in a population-based cohort of 221 patients with DLBCL who experienced progression/relapse after frontline treatment and were treated with second-line (immuno)chemotherapy with an intention-to-treat with autologous stem-cell transplantation (ASCT). Serial DLBCL biopsies from a partially overlapping cohort of 129 patients underwent molecular characterization, including whole-genome or whole-exome sequencing in 73 patients. RESULTS: Outcomes to second-line therapy and ASCT are superior for late relapse (>2 years postdiagnosis) versus primary refractory (<9 months) or early relapse (9-24 months). Diagnostic and relapse biopsies were mostly concordant for cell-of-origin classification and genetics-based subgroup. Despite this concordance, the number of mutations exclusive to each biopsy increased with time since diagnosis, and late relapses shared few mutations with their diagnostic counterpart, demonstrating a branching evolution pattern. In patients with highly divergent tumors, many of the same genes acquired new mutations independently in each tumor, suggesting that the earliest mutations in a shared precursor cell constrain tumor evolution toward the same genetics-based subgroups at both diagnosis and relapse. CONCLUSION: These results suggest that late relapses commonly represent genetically distinct and chemotherapy-naïve disease and have implications for optimal patient management.

RUNX1 colludes with NOTCH1 to reprogram chromatin in T cell acute lymphoblastic leukemia.

Runt-related transcription factor 1 (RUNX1) is oncogenic in diverse types of leukemia and epithelial cancers where its expression is associated with poor prognosis. Current models suggest that RUNX1 cooperates with other oncogenic factors (e.g., NOTCH1, TAL1) to drive the expression of proto-oncogenes in T cell acute lymphoblastic leukemia (T-ALL) but the molecular mechanisms controlled by RUNX1 and its cooperation with other factors remain unclear. Integrative chromatin and transcriptional analysis following inhibition of RUNX1 and NOTCH1 revealed a surprisingly widespread role of RUNX1 in the establishment of global H3K27ac levels and that RUNX1 is required by NOTCH1 for cooperative transcription activation of key NOTCH1 target genes including MYC, DTX1, HES4, IL7R, and NOTCH3. Super-enhancers were preferentially sensitive to RUNX1 knockdown and RUNX1-dependent super-enhancers were disrupted following the treatment of a pan-BET inhibitor, I-BET151.

Genetic subdivisions of follicular lymphoma defined by distinct coding and noncoding mutation patterns.

Follicular lymphoma (FL) accounts for ∼20% of all new lymphoma cases. Increases in cytological grade are a feature of the clinical progression of this malignancy, and eventual histologic transformation (HT) to the aggressive diffuse large B-cell lymphoma (DLBCL) occurs in up to 15% of patients. Clinical or genetic features to predict the risk and timing of HT have not been described comprehensively. In this study, we analyzed whole-genome sequencing data from 423 patients to compare the protein coding and noncoding mutation landscapes of untransformed FL, transformed FL, and de novo DLBCL. This revealed 2 genetically distinct subgroups of FL, which we have named DLBCL-like (dFL) and constrained FL (cFL). Each subgroup has distinguishing mutational patterns, aberrant somatic hypermutation rates, and biological and clinical characteristics. We implemented a machine learning-derived classification approach to stratify patients with FL into cFL and dFL subgroups based on their genomic features. Using separate validation cohorts, we demonstrate that cFL status, whether assigned with this full classifier or a single-gene approximation, is associated with a reduced rate of HT. This implies distinct biological features of cFL that constrain its evolution, and we highlight the potential for this classification to predict HT from genetic features present at diagnosis.

Relapse timing is associated with distinct evolutionary dynamics in DLBCL.

Diffuse large B-cell lymphoma (DLBCL) is cured in over 60% of patients, but outcomes are poor for patients with relapsed or refractory disease (rrDLBCL). Here, we performed whole genome/exome sequencing (WGS/WES) on tumors from 73 serially-biopsied patients with rrDLBCL. Based on the observation that outcomes to salvage therapy/autologous stem cell transplantation are related to time-to-relapse, we stratified patients into groups according to relapse timing to explore the relationship to genetic divergence and sensitivity to salvage immunochemotherapy. The degree of mutational divergence increased with time between biopsies, yet tumor pairs were mostly concordant for cell-of-origin, oncogene rearrangement status and genetics-based subgroup. In patients with highly divergent tumors, several genes acquired exclusive mutations independently in each tumor, which, along with concordance of genetics-based subgroups, suggests that the earliest mutations in a shared precursor cell constrain tumor evolution. These results suggest that late relapses commonly represent genetically distinct and chemotherapy-naïve disease.

Super-enhancer hypermutation alters oncogene expression in B cell lymphoma.

Diffuse large B cell lymphoma (DLBCL) is the most common B cell non-Hodgkin lymphoma and remains incurable in around 40% of patients. Efforts to sequence the coding genome identified several genes and pathways that are altered in this disease, including potential therapeutic targets1-5. However, the non-coding genome of DLBCL remains largely unexplored. Here we show that active super-enhancers are highly and specifically hypermutated in 92% of samples from individuals with DLBCL, display signatures of activation-induced cytidine deaminase activity, and are linked to genes that encode B cell developmental regulators and oncogenes. As evidence of oncogenic relevance, we show that the hypermutated super-enhancers linked to the BCL6, BCL2 and CXCR4 proto-oncogenes prevent the binding and transcriptional downregulation of the corresponding target gene by transcriptional repressors, including BLIMP1 (targeting BCL6) and the steroid receptor NR3C1 (targeting BCL2 and CXCR4). Genetic correction of selected mutations restored repressor DNA binding, downregulated target gene expression and led to the counter-selection of cells containing corrected alleles, indicating an oncogenic dependency on the super-enhancer mutations. This pervasive super-enhancer mutational mechanism reveals a major set of genetic lesions deregulating gene expression, which expands the involvement of known oncogenes in DLBCL pathogenesis and identifies new deregulated gene targets of therapeutic relevance.

Elucidating the importance and regulation of key enhancers for human MEIS1 expression.

Myeloid ecotropic virus insertion site 1 (MEIS1) is essential for normal hematopoiesis and is a critical factor in the pathogenesis of a large subset of acute myeloid leukemia (AML). Despite the clinical relevance of MEIS1, its regulation is largely unknown. To understand the transcriptional regulatory mechanisms contributing to human MEIS1 expression, we created a knock-in green florescent protein (GFP) reporter system at the endogenous MEIS1 locus in a human AML cell line. Using this model, we have delineated and dissected a critical enhancer region of the MEIS1 locus for transcription factor (TF) binding through in silico prediction in combination with oligo pull-down, mass-spectrometry and knockout analysis leading to the identification of FLI1, an E-twenty-six (ETS) transcription factor, as an important regulator of MEIS1 transcription. We further show direct binding of FLI1 to the MEIS1 locus in human AML cell lines as well as enrichment of histone acetylation in MEIS1-high healthy and leukemic cells. We also observe a positive correlation between high FLI1 transcript levels and worse overall survival in AML patients. Our study expands the role of ETS factors in AML and our model constitutes a feasible tool for a more detailed understanding of transcriptional regulatory elements and their interactome.

Evaluation of Adverse Effects of Topical Glaucoma Medications on Trabeculectomy Outcomes Using the Glaucoma Medications Intensity Index.

INTRODUCTION: Trabeculectomy is commonly performed for glaucoma when medications are unable to control disease progression or have intolerable adverse effects. Previous studies have suggested that a higher number of and/or longer treatment duration with preoperative topical glaucoma medications are associated with a higher risk of trabeculectomy failure, but most of these studies lack quantification of exposure. The aim of this study was to investigate the relationship between preoperative exposure to topical glaucoma medications and trabeculectomy outcome, using a new method for quantifying accumulated exposure. METHODS: Consecutive patients with primary open-angle glaucoma (POAG) or normal-tension glaucoma (NTG) who underwent primary trabeculectomy between 2013 and 2017 were retrospectively reviewed. The Glaucoma Medications Intensity Index (GMII) was calculated for each eye by multiplying the number of drops per week by duration of use (in years). The relationship between the GMII and postoperative outcome in terms of 1- and 2-year success rates and survival time was analyzed. RESULTS: A total of 55 eyes from 40 subjects were analyzed, all with follow-up > 6 months (mean 2.72 ± 1.46 years). The GMII for eyes with successful (n = 41) and failed (n = 14) outcome at last visit was 111.71 ± 78.59 and 167.41 ± 85.04, respectively, and significantly higher in failed eyes (P = 0.03). Univariate regression analysis of age, gender, cup-disc ratio, previous phacoemulsification, diabetes, hypertension, dyslipidemia, preoperative number of glaucoma medications/treatment duration/intraocular pressure (IOP), and GMII showed age and GMII to be possible predictors of treatment failure. On subsequent multivariate analysis, only GMII was correlated with failure (odds ratio 1.021, 95% confidence interval 1.00-1.05; P = 0.05). When GMII ≥ 80, the postoperative survival time was shorter (P = 0.02), the 1-year IOP, number of glaucoma medications, and number of needlings performed were higher (P = 0.03, P < 0.01, P < 0.03, respectively), and reduction in glaucoma medication was less (P = 0.02). CONCLUSION: The GMII can be used to predict eyes at higher risk for trabeculectomy that may benefit from additional perioperative intervention or treatment. It can also help the surgeon time the surgery before the GMII becomes too high, thereby optimizing the patient's postoperative outcome.

Use of Chronic Prescription Medications and Prevalence of Polypharmacy in Survivors of Childhood Cancer.

BACKGROUND: As survivors of childhood cancer age, development of cancer treatment-related chronic health conditions often occur. This study aimed to describe the pattern of chronic prescription medication use and identify factors associated with polypharmacy among survivors of childhood cancer. METHODS: This was a retrospective study conducted at the pediatric oncology long-term follow-up clinic in Hong Kong. Eligible subjects included survivors who were (1) diagnosed with cancer before 18 years old, (2) were at least 3 years post-cancer diagnosis and had completed treatment for at least 30 days, and (3) receiving long-term follow-up care at the study site between 2015 and 2018. Dispensing records of eligible survivors were reviewed to identify medications taken daily for ≥30 days or used on an "as needed" basis for ≥6 months cumulatively within the past 12-month period. Polypharmacy was defined as the concurrent use of ≥5 chronic medications. Multivariable log-binomial modeling was conducted to identify treatment and clinical factors associated with medication use pattern and polypharmacy. RESULTS: This study included 625 survivors (mean current age = 17.9 years, standard deviation [SD] = 7.2 years) who were 9.2 [5.2] years post-treatment. Approximately one-third (n = 219, 35.0%) of survivors were prescribed at least one chronic medication. Frequently prescribed medication classes include systemic antihistamines (26.5%), sex hormones (19.2%), and thyroid replacement therapy (16.0%). Overall prevalence of polypharmacy was 5.3% (n = 33). A higher rate of polypharmacy was found in survivors of CNS tumors (13.6%) than in survivors of hematological malignancies (4.3%) and other solid tumors (5.3%) (P = .0051). Higher medication burden was also observed in survivors who had undergone cranial radiation (RR = 6.31; 95% CI = 2.75-14.49) or hematopoietic stem-cell transplantation (HSCT) (RR = 3.53; 95% CI = 1.59-7.83). CONCLUSION: Although polypharmacy was observed in a minority of included survivors of childhood cancer, chronic medication use was common. Special attention should be paid to survivors of CNS tumors and survivors who have undergone HSCT or cranial radiation. These individuals should be monitored closely for drug-drug interactions and adverse health outcomes that may result from multiple chronic medications, particularly during hospitalization in an acute care setting.

Prevalence and Causes of Visual Impairment and Blindness among Adult Chinese in Hong Kong - The Hong Kong Eye Study.

PURPOSE: To investigate the prevalence, associations, and causes of visual impairment and blindness in the adult population of Hong Kong. METHODS: This cross-sectional population-based study included 2018 (870, 43% male) randomly selected adults with a mean age 52 ± 16 years (range 18-90 years) in Hong Kong. Each participant underwent comprehensive ophthalmic examinations. Presenting visual acuity (PVA) and best-corrected visual acuity (BCVA) of each eye was recorded. Prevalence of visual impairment and blindness was calculated using both World Health Organization (WHO) and United States (US) definitions, based on BCVA and PVA. RESULTS: Visual acuity measurements were available for 1952 (96.8%) participants. The prevalence of visual impairment, based on BCVA value, using WHO and US definition, was 1.0 ± 0.1% and 2.7 ± 0.4%, respectively. The prevalence of visual impairment, based on PVA value, was 5.1 ± 0.5% and 14.0 ± 0.8%, using WHO and US definition, respectively. Multivariate analysis demonstrated the presence of visual impairment (PVA, WHO definition) increased significantly with older age (odds ratio 1.039, P < .001) and thinner central cornea thickness (odds ratio 0.994, P = .014), but not significantly associated with other socioeconomic, systemic or ocular parameters after adjusting for age and central corneal thickness. Under-correction of refractive error was the most common reason for presenting visual impairment. Causes of impaired BCVA were cataract (37%), age-related macular degeneration (26%), diabetic macular edema (11%), glaucoma (11%), epiretinal membrane (5%), and unknown (11%). CONCLUSION: The prevalence of visual impairment in Hong Kong increased significantly with older age and thinner central corneal thickness. The major causes for impairment were under-correction of refractive error, cataract, and age-related macular degeneration.

Epidemiology of E. coli in Cystic Fibrosis Airways Demonstrates the Capacity for Persistent Infection but Not Patient-Patient Transmission.

Escherichia coli is frequently isolated from the respiratory secretions of cystic fibrosis (CF) patients yet is not considered a classical CF pathogen. Accordingly, little is known about the natural history of this organism in the CF airways, as well as the potential for patient-to-patient transmission. Patients attending the Calgary Adult CF Clinic (CACFC) between January 1983 and December 2016 with at least one E. coli-positive sputum culture were identified by retrospective review. Annual E. coli isolates from the CACFC biobank from each patient were typed by pulsed-field gel electrophoresis (PFGE) and isolates belonging to shared pulsotypes were sequenced. Single nucleotide polymorphism (SNP) and phylogenetic analysis were used to investigate the natural history of E. coli infection and identify potential transmission events. Forty-five patients with E. coli-positive sputum cultures were identified. Most patients had a single infection episode with a single pulsotype, while replacement of an initial pulsotype with a second was observed in three patients. Twenty-four had E. coli recovered from their sputum more than once and 18 patients had persistent infections (E. coli carriage >6 months with ≥3 positive cultures). Shared pulsotypes corresponded to known extraintestinal pathogenic E. coli strains: ST-131, ST-73, and ST-1193. Phylogenetic relationships and SNP distances among isolates within shared pulsotypes were consistent with independent acquisition of E. coli by individual patients. Most recent common ancestor date estimates of isolates between patients were inconsistent with patient-to-patient transmission. E. coli infection in CF is a dynamic process that appears to be characterized by independent acquisition within our patient population and carriage of unique sets of strains over time by individual patients.

Amphiphilic additives in silicone oil tamponade and emulsification: an eye-on-a-chip study.

AIMS: Recently, chemically modified silicone oil has been demonstrated as a reservoir for sustained release of intraocular drugs, many of which might be amphiphilic in nature. In this work, we study the effect of amphiphilic additives in silicone oil on emulsification under eye-like movements. METHODS: Three silicone-oil-soluble surfactants, namely DC749, MQ1640 and FZ2233, were used as model amphiphilic additives. The change of viscosity was measured by a rheometer in the cone-and-plate geometry. The interfacial tension (IFT) between silicone oil and model aqueous phase was measured by pendant drop tensiometry. Emulsification of silicone oil was induced by simulated saccadic eye movements on a cell-coated eye-on-a-chip platform for 4 days. The number of emulsified silicone oil droplets observed in the aqueous phase was assessed daily by optical microscopy. RESULTS: Significantly more emulsified droplets were formed in silicone oil with DC749 or MQ1640 (P < 0.05). However, such increase was not directly related to the change in IFT nor viscosity. Moreover, water droplets were also found in the silicone oil, but not in the control silicone oil without additive. CONCLUSIONS: The amphiphilic substances in silicone oil promoted emulsification. Besides typical oil-in-water drops that normally affect the eye, water-in-oil drops were also formed. Before silicone oil could be considered as a vehicle for drug delivery, the nature of the drug and its possible effect on emulsification and therefore on the pharmacokinetics needs to be investigated. An additional concern is that water-in-oil droplets in the eye would affect the optical clarity of silicone oil and might cause visual symptoms.

Needlescopic video-assisted thoracic surgery for reversal of thoracic sympathectomy.

Thoracic sympathectomy is a commonly performed surgical procedure for the treatment of palmar hyperhidrosis. However, one major complication of such a procedure is compensatory truncal hyperhidrosis. We describe an extreme case of compensatory truncal hyperhidrosis and anhidrosis over the head and neck region which led to a heatstroke. Bilateral reoperative needlescopic video-assisted thoracic surgery was performed for the reversal of thoracic sympathectomy with an interposition intercostal nerve graft. The patient's truncal hyperhidrosis resolved gradually over 1 month following the reversal procedure.