The virally encoded NS5B RNA-dependent RNA polymerase has emerged as a prime target in the search for specific HCV antivirals. A series of benzimidazole 5-carboxamide compounds inhibit the cellular ...RNA replication of a HCV subgenomic replicon and we have advanced our understanding of this class of inhibitors through a combination of complementary approaches that include biochemical cross-linking experiments with a photoreactive analogue followed by mass spectrometry analysis of the enzyme. A novel binding site has been localized for these inhibitors at the junction of the thumb domain and the N-terminal finger loop. Furthermore, the isolation and characterization of resistant replicon mutants that co-localize to this region distinguished this class of compounds from other non-nucleoside NS5B inhibitors that bind to distinct allosteric sites. Resistant mutations that emerged with the benzimidazole 5-carboxamide and related compounds were found at three amino acid positions in the thumb domain: Pro495 with substitutions to Ser, Leu, Ala, or Thr; Pro496 substitutions to Ser or Ala; and a V499A substitution. Mutations at each of these positions conferred different levels of resistance to this drug class: the Pro495 changes provided the greatest shifts in compound potency, followed by moderate changes in potency with the Pro496 substitutions, and finally only minor shifts in potency with V499A. Combinations that include the benzimidazole 5-carboxamide polymerase inhibitors and compounds that bind other sites or other HCV targets, including HCV protease inhibitors, are complementary in cell culture models of HCV RNA replication at suppressing the emergence of resistant variants. This novel class of compounds and unique binding site expand the diversity of HCV antivirals currently under development and offer the potential to improve the treatment of chronic HCV infection.
A previously disclosed series of non-nucleoside allosteric inhibitors of the NS5B polymerase of the hepatitis C virus (HCV) was optimized to yield novel compounds with improved physicochemical ...properties and activity in cell-based assays. Replacement of ionizable carboxylic acids with neutral substituents in lead compounds produced inhibitors with cellular permeability and antiviral activity in a cell-based assay of subgenomic HCV RNA replication (replicon EC50 as low as 1.7 μM). The improvement in potency in this ex vivo model of HCV RNA replication validates, in part, the mechanism by which this class of allosteric benzimidazole derivatives inhibits the polymerase and represents a significant step forward in the discovery of novel HCV therapeutics.
Biobanking biological samples involve multiple handling, processing, and labeling steps. Each step may be a source of error, which if unnoticed or uncorrected may have consequences for research. We ...aimed to develop a simple and inexpensive genotyping method that would be valuable to detect such errors and confirm sample identity. For this purpose, seven variable number of tandem repeat (VNTR) loci were selected, analyzed by polymerase chain reaction (PCR) amplification, and organized in a PCR-based DNA profiling algorithm that proved useful to minimize the number of steps required for the procedure. Match probability calculations suggest that this method/algorithm has the potential to discriminate every participant of a biobank. As a proof of concept, the algorithm was applied on samples taken from the PROCURE Prostate Cancer Biobank. It was applied on 403 DNA samples from 101 randomly chosen patients who provided prostate tissues at surgery and blood at two to three different time points over a period of up to 7 years. A unique DNA profile requiring the analysis of no more than four VNTR loci (D16S83, D17S5, D1S80, D19S20) was successfully obtained for each of the 101 cases studied and led to the identification of two mismatches among the 403 samples evaluated (0.5% error rate). Further investigations using the same genotyping method revealed that one of the errors was due to tissue mishandling and that the other was due to tissue mislabeling. These errors, typical to the complex biobanking process, highlight the importance to implement a routine genotyping method as part of quality assurance in biobanking.
Benzimidazole-based allosteric inhibitors of the hepatitis C virus (HCV) NS5B polymerase were diversified to a variety of topologically related scaffolds. Replacement of the polar benzimidazole core ...by lipophilic indoles led to inhibitors with improved potency in the cell-based subgenomic HCV replicon system. Transposing the indole scaffold into a previously described series of benzimidazole–tryptophan amides generated the most potent inhibitors of HCV RNA replication in cell culture reported to date in this series (EC
50
∼
50
nM).
The hepatitis C virus (HCV) NS3 protease is essential for polyprotein maturation and viral propagation, and it has been proposed as a suitable target for antiviral drug discovery. An N-terminal ...hexapeptide cleavage product of a dodecapeptide substrate identified as a weak competitive inhibitor of the NS3 protease activity was optimized to a potent and highly specific inhibitor of the enzyme. The effect of this potent NS3 protease inhibitor was evaluated on replication of subgenomic HCV RNA and compared with interferon-α (IFN-α), which is currently used in the treatment of HCV-infected patients. Treatment of replicon-containing cells with the NS3 protease inhibitor or IFN-α showed a dose-dependent decrease in subgenomic HCV RNA that reached undetectable levels following a 14-day treatment. Kinetic studies in the presence of either NS3 protease inhibitor or IFN-α also revealed similar profiles in HCV RNA decay with half-lives of 11 and 14 h, respectively. The finding that an antiviral specifically targeting the NS3 protease activity inhibits HCV RNA replication further validates the NS3 enzyme as a prime target for drug discovery and supports the development of NS3 protease inhibitors as a novel therapeutic approach for HCV infection.
We analyzed molecular data on 2,579 tumors from The Cancer Genome Atlas (TCGA) of four gynecological types plus breast. Our aims were to identify shared and unique molecular features, clinically ...significant subtypes, and potential therapeutic targets. We found 61 somatic copy-number alterations (SCNAs) and 46 significantly mutated genes (SMGs). Eleven SCNAs and 11 SMGs had not been identified in previous TCGA studies of the individual tumor types. We found functionally significant estrogen receptor-regulated long non-coding RNAs (lncRNAs) and gene/lncRNA interaction networks. Pathway analysis identified subtypes with high leukocyte infiltration, raising potential implications for immunotherapy. Using 16 key molecular features, we identified five prognostic subtypes and developed a decision tree that classified patients into the subtypes based on just six features that are assessable in clinical laboratories.
•Integrated analysis finds molecular features characteristic of gynecologic tumors•Subtypes with high leukocyte infiltration, a marker for immune response, identified•Gene-lncRNA interaction network of ESR1, DKC1, and lncRNAs TERC, NEAT1, and TUG1 identified•Decision tree to group patients into clinically relevant prognostic subtypes proposed
By performing molecular analyses of 2,579 TCGA gynecological (OV, UCEC, CESC, and UCS) and breast tumors, Berger et al. identify five prognostic subtypes using 16 key molecular features and propose a decision tree based on six clinically assessable features that classifies patients into the subtypes.
To evaluate the International Society of Urological Pathology (ISUP) 5-tier grade grouping (GG) system of prostate cancers as well as previously proposed optimizations.
The PROCURE biobank is a ...prospective cohort study of patients with localized prostate cancer who underwent radical prostatectomy in Quebec province between 2005 and 2013. Surgical specimens were graded by experienced genitourinary pathologists using 2019 ISUP criteria. Follow-up was conducted until November 2021. The current 5-tier and a proposed 6-tier GG system were evaluated, the latter having two changes: 1) Gleason 3 + 4 and 4 + 3 tumors with minor/tertiary Gleason 5 patterns were upgraded to GG 3 and 4, respectively; and 2) patients in GG5 were separated based on primary Gleason pattern (4 or 5). Cox proportional hazards models and Harrell's concordance (C) indices were used for statistical analyses.
2003 patients were included (median follow-up: 8.7 years). The current 5-tier GG system predicted time to recurrence (hazard ratio HR 2.12, 95% confidence interval 95%CI 1.99–2.25, C 0.717), androgen-deprivation therapy (HR 2.58, 95%CI 2.38–2.80, C 0.790), metastasis (HR 2.48, 95%CI 2.17–2.83, C 0.806), castration-resistant prostate cancer (HR 2.67, 95%CI 2.28–3.13, C 0.829), and cancer-specific mortality (HR 2.80, 95%CI 2.27–3.44, C 0.835). Goodness-of-fit further improved with the proposed 6-tier GG system, with Harrell's C of 0.733, 0.807, 0.827, 0.853, and 0.853, respectively.
The 5-tier GG system predicted short- and long-term outcomes for patients with localized prostate cancer, and the proposed 6-tier GG system further improved its accuracy.
•PROCURE follows over 2000 men with prostate cancer after radical prostatectomies.•Median follow-up is currently 8.7 years, maximum follow-up 14.8 years.•Using PROCURE, we evaluated the 2019 ISUP Gleason grading (GG) system.•The system can be improved by separating GG5 based on primary Gleason pattern.•Men with a Gleason 3 + 4/4 + 3 and minor/tertiary Gleason 5 should be upgraded 1 GG.
We present an integromic analysis of gene alterations that modulate transforming growth factor β (TGF-β)-Smad-mediated signaling in 9,125 tumor samples across 33 cancer types in The Cancer Genome ...Atlas (TCGA). Focusing on genes that encode mediators and regulators of TGF-β signaling, we found at least one genomic alteration (mutation, homozygous deletion, or amplification) in 39% of samples, with highest frequencies in gastrointestinal cancers. We identified mutation hotspots in genes that encode TGF-β ligands (BMP5), receptors (TGFBR2, AVCR2A, and BMPR2), and Smads (SMAD2 and SMAD4). Alterations in the TGF-β superfamily correlated positively with expression of metastasis-associated genes and with decreased survival. Correlation analyses showed the contributions of mutation, amplification, deletion, DNA methylation, and miRNA expression to transcriptional activity of TGF-β signaling in each cancer type. This study provides a broad molecular perspective relevant for future functional and therapeutic studies of the diverse cancer pathways mediated by the TGF-β superfamily.
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•Genetic alterations in TGF-β pathway members observed in 39% of TCGA cases•GI cancers enriched with hotspot mutations in TGF-β pathway members•Gene alterations correlated with expression of metastasis genes and poor prognosis•TGF-β signaling silenced by miRNAs or DNA methylation in hematologic cancers
To date, there are no studies of the TGF-β superfamily of signaling pathways across multiple cancers. This study represents a key starting point for unraveling the role of this complex superfamily in 33 divergent cancer types from over 9,000 patients.
Objectives
To evaluate the five‐tier Gleason grade group (GG) scoring of prostate cancers adopted by the International Society of Urology Pathology (ISUP) in 2014, and to propose modifications to ...optimize its performance.
Patients and Methods
Data were obtained from PROCURE, a prospective cohort of patients with localized prostate cancer undergoing radical prostatectomy in Québec, 2006–2013. Surgical specimens were evaluated by genitourinary pathologists using 2014 ISUP criteria. Treatment failure was defined as biochemical recurrence and/or initiation of secondary, non‐adjuvant therapy. Analyses were conducted using Kaplan–Meier methods, log‐rank tests, Cox proportional hazards models and Harrell's concordance indices.
Results
A total of 1 917 patients were included, with a median follow‐up of 69 months. The 5‐year treatment failure rates were 9.6%, 23.5%, 43.1%, 52.6% and 84.3% in GG1–5, respectively (P < 0.001 when comparing GG2 with GG3). Treatment failure rates for patients in GG2 and GG3 with tertiary Gleason 5 pattern were higher than patients in the same group without a tertiary pattern (P < 0.001), but were similar to rates for patients in GGs 3 or 4 without a tertiary pattern (P > 0.3). Primary Gleason pattern (4/5) predicted treatment failure in GG5 (5‐year failure rates 82.3% vs 97.1%, respectively; P = 0.001). The five‐tier GG system had greater accuracy as a prognostic indicator compared with the four‐tier system (Harrell's concordance index 0.716 vs 0.676). When upgrading patients in GG2/3 with tertiary Gleason 5 pattern to patients in GG3/4, and separating patients in GG5 by primary Gleason pattern, the Harrell's concordance index increased to 0.730.
Conclusion
The five‐tier GG system increased accuracy for predicting treatment failure compared with the previous grading systems, but can be further improved.
Objective
The psychosocial impact of a prostate cancer diagnosis significantly affects a patient's quality of life. We studied patient communication at the time of diagnosis and its impact on ...psychosocial adjustment of patients.
Methods
This is a cross‐sectional data analysis from self‐administered questionnaires in the PROCURE biobank study, consisting of a cohort of patients with localized prostate cancer undergoing radical prostatectomy in Québec (Canada), 2006 to 2013. Odds ratios (OR) and their respective 95% confidence intervals (95% CI) were calculated using binary or ordered logistic regression models.
Results
Data from 1841 patients were analyzed. The median age of patients was 62 years (range 41‐80 years), the majority was French‐Canadian (68.3%) and married (79.6%). Most patients (90.1%) considered conversations with their treating physician a useful information source. Patients were dissatisfied on the communication when receiving their diagnosis by telephone (OR = 0.19, 95% CI, 0.11‐0.33). Younger patients were also more dissatisfied. Most patients preferred to receive information on prostate cancer (89.5%) and radical prostatectomy (88.0%) at the time of diagnosis, while only 58.8% and 52.4% of patients received this information at this stage. Patients who were dissatisfied with the communication of the diagnosis had more negative responses, such as increased worries and fear (P < 0.05). The five most useful coping mechanisms were physical activity (62.3%), breathing exercises (44.5%), music (32.8%), faith (30.3%), and muscle relaxation (30.1%), but varied by demographics.
Conclusions
This study highlights the importance of physicians communicating a prostate cancer diagnosis well to their patients. Patients may benefit from individually tailored interventions to facilitate their overall coping.
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