Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability

Whole-genome sequencing using massively parallel sequencing technologies enables accurate detection of somatic rearrangements in cancer. Pinpointing large numbers of rearrangement breakpoints to base-pair resolution allows analysis of rearrangement microhomology and genomic location for every sample. Here we analyze 95 tumor genome sequences from breast, head and neck, colorectal, and prostate carcinomas, and from melanoma, multiple myeloma, and chronic lymphocytic leukemia. We discover three genomic factors that are significantly correlated with the distribution of rearrangements: replication time, transcription rate, and GC content. The correlation is complex, and different patterns are observed between tumor types, within tumor types, and even between different types of rearrangements. Mutations in the APC gene correlate with and, hence, potentially contribute to DNA breakage in late-replicating, low %GC, untranscribed regions of the genome. We show that somatic rearrangements display less microhomology than germline rearrangements, and that breakpoint loci are correlated with local hypermutability with a particular enrichment for C ↔ G transversions

Trust and reputation policy-based mechanisms for self-protection in autonomic communications

Currently, there is an increasing tendency to migrate the management of communications and information systems onto the Web. This is making many traditional service support models obsolete. In addition, current security mechanisms are not sufficiently robust to protect each management system and/or subsystem from web-based intrusions, malware, and hacking attacks. This paper presents research challenges in autonomic management to provide self-protection mechanisms and tools by using trust and reputation concepts based on policy-based management to decentralize management decisions. This work also uses user-based reputation mechanisms to help enforce trust management in pervasive and communications services. The scope of this research is founded in social models, where the application of trust and reputation applied in communication systems helps detect potential users as well as hackers attempting to corrupt management operations and services. These so-called “cheating services” act as “attacks”, altering the performance and the security in communication systems by consumption of computing or network resources unnecessarily

Discovery and saturation analysis of cancer genes across 21 tumor types

Summary While a few cancer genes are mutated in a high proportion of tumors of a given type (>20%), most are mutated at intermediate frequencies (2–20%). To explore the feasibility of creating a comprehensive catalog of cancer genes, we analyzed somatic point mutations in exome sequence from 4,742 tumor-normal pairs across 21 cancer types. We found that large-scale genomic analysis can identify nearly all known cancer genes in these tumor types. Our analysis also identified 33 genes not previously known to be significantly mutated, including genes related to proliferation, apoptosis, genome stability, chromatin regulation, immune evasion, RNA processing and protein homeostasis. Down-sampling analysis indicates that larger sample sizes will reveal many more genes, mutated at clinically important frequencies. We estimate that near-saturation may be achieved with 600–5000 samples per tumor type, depending on background mutation rate. The results help guide the next stage of cancer genomics

AXL modulates extracellular matrix protein expression and is essential for invasion and metastasis in endometrial cancer

The receptor tyrosine kinase AXL promotes migration, invasion, and metastasis. Here, we evaluated the role of AXL in endometrial cancer. High immunohistochemical expression of AXL was found in 76% (63/83) of advanced-stage, and 77% (82/107) of high-grade specimens and correlated with worse survival in uterine serous cancer patients. In vitro, genetic silencing of AXL inhibited migration and invasion but had no effect on proliferation of ARK1 endometrial cancer cells. AXL-deficient cells showed significantly decreased expression of phospho-AKT as well as uPA, MMP-1, MMP-2, MMP-3, and MMP-9. In a xenograft model of human uterine serous carcinoma with AXL-deficient ARK1 cells, there was significantly less tumor burden than xenografts with control ARK1 cells. Together, these findings underscore the therapeutic potentials of AXL as a candidate target for treatment of metastatic endometrial cancer

Insufficient Impact: Limited Implementation of Federal Regulatory Changes to Methadone and Buprenorphine Access in Arizona During COVID-19

Introduction: This study examined the impact of federal regulatory changes on methadone and buprenorphine treatment during COVID-19 in Arizona. Methods: A cohort study of methadone and buprenorphine providers from September 14, 2021 to April 15, 2022 measured the proportion of 6 treatment accommodations implemented at 3 time periods: before COVID-19, during Arizona's COVID-19 shutdown, and at the time of the survey completion. Accommodations included (1) telehealth, (2) telehealth buprenorphine induction, (3) increased multiday dosing, (4) license reciprocity, (5) home medications delivery, and (6) off-site dispensing. A multilevel model assessed the association of treatment setting, rurality, and treatment with accommodation implementation time. Results: Over half (62.2%) of the 74-provider sample practiced in healthcare settings not primarily focused on addiction treatment, 19% practiced in methadone clinics, and 19% practiced in treatment clinics not offering methadone. Almost half (43%) were unaware of the regulatory changes allowing treatment accommodation. Telehealth was most frequently reported, increasing from 30% before COVID-19 to 80% at the time of the survey. Multiday dosing was the only accommodation substantially retracted after COVID-19 shutdown: from 41% to 23% at the time of the survey. Providers with higher patient limits were 2.5–3.2 times as likely to implement telehealth services, 4.4 times as likely to implement buprenorphine induction through telehealth, and 15.2–20.9 times as likely to implement license reciprocity as providers with lower patient limits. Providers of methadone implemented 12% more accommodations and maintained a higher average proportion of implemented accommodations during the COVID-19 shutdown period but were more likely to reduce the proportion of implemented accommodations (a 17-percentage point gap by the time of the survey). Conclusions: Federal regulatory changes are not sufficient to produce a substantive or sustained impact on provider accommodations, especially in methadone medical treatment settings. Practice change interventions specific to treatment settings should be implemented and studied for their impact

Opportunities and Challenges: Hepatitis C Testing and Treatment Access Experiences Among People in Methadone and Buprenorphine Treatment During COVID-19, Arizona, 2021

Introduction: The purpose of this study was to characterize hepatitis C virus screening and treatment access experiences among people in treatment for opioid use disorder in Arizona during COVID-19. Methods: Arizonans receiving treatment for opioid use disorder from methadone clinics and buprenorphine providers during COVID-19 were interviewed about hepatitis C virus testing, curative treatment, and knowledge about screening recommendations. Interviews were conducted with 121 people from August 4, 2021 to October 10, 2021. Qualitative data were coded using the categories of hepatitis C virus testing, knowledge of screening recommendations, diagnosis, and experiences seeking curative treatment. Data were also quantitated for bivariate testing with outcome variables of last hepatitis C virus test, diagnosis, and curative treatment process. Findings were arrayed along an adapted hepatitis C virus cascade framework to inform program and policy improvements. Results: Just over half of the sample reported ever having tested for hepatitis C virus (51.2%, n=62) and of this group, 58.1% were tested in the past 12 months. Among those who were ever tested, 54.8% reported a hepatitis C virus diagnosis and 16.1% reported either being in treatment or having been declared cured of the hepatitis C virus. Among those who were diagnosed with hepatitis C, 14.7% indicated that they unsuccessfully tried to access curative treatment and would not attempt to again. Reasons cited for not accessing or receiving curative treatment included beliefs about treatment safety, barriers created by access requirements, natural resolution of the infection, and issues with healthcare coverage and authorization. Conclusions: Structural barriers continue to prevent curative hepatitis C virus treatment access. Given that methadone and buprenorphine treatment providers serve patients who are largely undiagnosed or treated for hepatitis C virus, opportunities exist for them to screen their patients regularly and provide support for and/or navigation to hepatitis C virus curative treatment

A novel totivirus and piscine reovirus (PRV) in Atlantic salmon (Salmo salar) with cardiomyopathy syndrome (CMS)

<p>Abstract</p> <p>Background</p> <p>Cardiomyopathy syndrome (CMS) is a severe disease affecting large farmed Atlantic salmon. Mortality often appears without prior clinical signs, typically shortly prior to slaughter. We recently reported the finding and the complete genomic sequence of a novel piscine reovirus (PRV), which is associated with another cardiac disease in Atlantic salmon; heart and skeletal muscle inflammation (HSMI). In the present work we have studied whether PRV or other infectious agents may be involved in the etiology of CMS.</p> <p>Results</p> <p>Using high throughput sequencing on heart samples from natural outbreaks of CMS and from fish experimentally challenged with material from fish diagnosed with CMS a high number of sequence reads identical to the PRV genome were identified. In addition, a sequence contig from a novel totivirus could also be constructed. Using RT-qPCR, levels of PRV in tissue samples were quantified and the totivirus was detected in all samples tested from CMS fish but not in controls. <it>In situ </it>hybridization supported this pattern indicating a possible association between CMS and the novel piscine totivirus.</p> <p>Conclusions</p> <p>Although causality for CMS in Atlantic salmon could not be proven for either of the two viruses, our results are compatible with a hypothesis where, in the experimental challenge studied, PRV behaves as an opportunist whereas the totivirus might be more directly linked with the development of CMS.</p

Liminal Roles as a Source of Creative Agency in Management: The Case of Knowledge-Sharing Communities

Studies suggest that the experience of liminality – of being in an ambiguous, ‘betwixt and between’ position – has creative potential for organizations. We contribute to theory on the link between liminality and creative agency through a study of the coordinators of ‘knowledge-sharing communities’; one of the latest examples of a ‘neo-bureaucratic’ practice that seeks to elicit innovative responses from employees while intensifying control by the organization. Through a role-centred perspective, our study found that both the structural and interpretive aspects of coordinators’ role enactments promoted a degree of creative agency. ‘Front-stage’ and ‘back-stage’ activities were developed to meet the divergent expectations posed by senior management and community members, and the ambiguity of their roles prompted an array of different role interpretations. Our findings contribute to theory by showing how the link between liminality and creative agency is not confined to roles and spaces (consultancy work, professional expertise) that are positioned across organizational boundaries, or free from norms and expectations, but may also apply to roles that are ambiguously situated within organizational contexts and which are subject to divergent expectations. This shows how neo-bureaucratic forms may be both reproduced and renewed through the creative responses of individual managers

Gastrointestinal adenocarcinomas of the esophagus, stomach, and colon exhibit distinct patterns of genome instability and oncogenesis

A more detailed understanding of the somatic genetic events that drive gastrointestinal adenocarcinomas is necessary to improve diagnosis and therapy. Using data from high-density genomic profiling arrays, we conducted an analysis of somatic copy-number aberrations in 486 gastrointestinal adenocarcinomas including 296 esophageal and gastric cancers. Focal amplifications were substantially more prevalent in gastric/esophageal adenocarcinomas than colorectal tumors. We identified 64 regions of significant recurrent amplification and deletion, some shared and others unique to the adenocarcinoma types examined. Amplified genes were noted in 37% of gastric/esophageal tumors, including in therapeutically targetable kinases such as ERBB2, FGFR1, FGFR2, EGFR, and MET, suggesting the potential use of genomic amplifications as biomarkers to guide therapy of gastric and esophageal cancers where targeted therapeutics have been less developed compared with colorectal cancers. Amplified loci implicated genes with known involvement in carcinogenesis but also pointed to regions harboring potentially novel cancer genes, including a recurrent deletion found in 15% of esophageal tumors where the Runt transcription factor subunit RUNX1 was implicated, including by functional experiments in tissue culture. Together, our results defined genomic features that were common and distinct to various gut-derived adenocarcinomas, potentially informing novel opportunities for targeted therapeutic interventions