Revisiting JC virus and progressive multifocal leukoencephalopathy.

Since its definition 65 years ago, progressive multifocal leukoencephalopathy (PML) has continued to devastate a growing population of immunosuppressed patients despite major advances in our understanding of the causative JC virus (JCV). Unless contained by the immune system, JCV lyses host oligodendrocytes collateral to its life cycle, leading to demyelination, neurodegeneration, and death. Novel treatments have stagnated in the absence of an animal model while current antiviral agents fail to address the now ubiquitous polyomavirus. In this review, we highlight the established pathogenesis by which JCV infection progresses to PML, highlighting major challenges that must be overcome to eliminate the underlying virus and, therefore, the debilitating disease.

Protein Quality Control in Glioblastoma: A Review of the Current Literature with New Perspectives on Therapeutic Targets.

Protein quality control allows eukaryotes to maintain proteostasis under the stress of constantly changing conditions. In this review, we discuss the current literature on PQC, highlighting flaws that must exist for malignancy to occur. At the nidus of PQC, the expression of BAG1-6 reflects the cell environment; each isoform directs proteins toward different, parallel branches of the quality control cascade. The sum of these branches creates a net shift toward either homeostasis or apoptosis. With an established role in ALP, Bag3 is necessary for cell survival in stress conditions including those of the cancerous niche (i.e., hypoxia, hypermutation). Evidence suggests that excessive Bag3-HSP70 activity not only sustains, but also propagates cancers. Its role is anti-apoptotic-which allows malignant cells to persist-and intercellular-with the production of infectious 'oncosomes' enabling cancer expansion and recurrence. While Bag3 has been identified as a key prognostic indicator in several cancer types, its investigation is limited regarding glioblastoma. The cochaperone HSP70 has been strongly linked with GBM, while ALP inhibitors have been shown to improve GBM susceptibility to chemotherapeutics. Given the highly resilient, frequently recurrent nature of GBM, the targeting of Bag3 is a necessary consideration for the successful and definitive treatment of GBM.

Perturbation of Critical Prolines in Gloeobacter violaceus Ligand-gated Ion Channel (GLIC) Supports Conserved Gating Motions among Cys-loop Receptors.

Gloeobacter violaceus ligand-gated ion channel (GLIC) has served as a valuable structural and functional model for the eukaryotic Cys-loop receptor superfamily. In Cys-loop and other receptors, we have previously demonstrated the crucial roles played by several conserved prolines. Here we explore the role of prolines in the gating transitions of GLIC. As conventional substitutions at some positions resulted in nonfunctional proteins, we used in vivo non-canonical amino acid mutagenesis to determine the specific structural requirements at these sites. Receptors were expressed heterologously in Xenopus laevis oocytes, and whole-cell electrophysiology was used to monitor channel activity. Pro-119 in the Cys-loop, Pro-198 and Pro-203 in the M1 helix, and Pro-299 in the M4 helix were sensitive to substitution, and distinct roles in receptor activity were revealed for each. In the context of the available structural data for GLIC, the behaviors of Pro-119, Pro-203, and Pro-299 mutants are consistent with earlier proline mutagenesis work. However, the Pro-198 site displays a unique phenotype that gives evidence of the importance of the region surrounding this residue for the correct functioning of GLIC.

Surrogate outcomes: experiences at the Common Drug Review.

BACKGROUND: Surrogate outcomes are a significant challenge in drug evaluation for health technology assessment (HTA) agencies. The research objectives were to: identify factors associated with surrogate use and acceptability in Canada's Common Drug Review (CDR) recommendations, and compare the CDR with other HTA or regulatory agencies regarding surrogate concerns. METHODS: Final recommendations were identified from CDR inception (September 2003) to December 31, 2010. Recommendations were classified by type of outcome (surrogate, final, other) and acceptability of surrogates (determined by the presence/absence of statements of concern regarding surrogates). Descriptive and statistical analyses examined factors related to surrogate use and acceptability. For thirteen surrogate-based submissions, recommendations from international HTA and regulatory agencies were reviewed for statements about surrogate acceptability. RESULTS: Of 156 final recommendations, 68 (44%) involved surrogates. The overall 'do not list' (DNL) rate was 48%; the DNL rate for surrogates was 41% (p = 0.175). The DNL rate was 64% for non-accepted surrogates (n = 28) versus 25% for accepted surrogates (odds ratio 5.4, p = 0.002). Clinical uncertainty, use of economic evidence over price alone, and a premium price were significantly associated with non-accepted surrogates. Surrogates were used most commonly for HIV, diabetes, rare diseases, cardiovascular disease and cancer. For the subset of drugs studied, other HTA agencies did not express concerns for most recommendations, while regulatory agencies frequently stated surrogate acceptance. CONCLUSIONS: The majority of surrogates were accepted at the CDR. Non-accepted surrogates were significantly associated with clinical uncertainty and a DNL recommendation. There was inconsistency of surrogate acceptability across several international agencies. Stakeholders should consider collaboratively establishing guidelines on the use, validation, and acceptability of surrogates.

Guidelines for health technologies: specific guidance for oncology products in Canada.

OBJECTIVE: Specific methodological challenges are often encountered during cancer-related economic evaluations. The objective of this study was to provide specific guidance to analysts on the methods for the conduct of high-quality economic evaluations in oncology by building on the Canadian Agency for Drugs and Technologies in Health Guidelines for the Economic Evaluation of Health Technologies (third edition). METHODS: Fifteen oncologists, health economists, health services researchers, and decision makers from across Canada identified sections in Canadian Agency for Drugs and Technologies in Health guidelines that would benefit from oncology-specific guidance. Fifteen sections of the guidelines were reviewed to determine whether 1) Canadian Agency for Drugs and Technologies in Health guidelines were sufficient for the conduct of oncology economic evaluations without further guidance specific for oncology products or 2) additional guidance was necessary. A scoping review was conducted by using a comprehensive and replicable search to identify relevant literature to inform recommendations. Recommendations were reviewed by representatives of academia, government, and the pharmaceutical industry in an iterative and formal review of the recommendations. RESULTS: Major adaptations for guidance related to time horizon, effectiveness, modeling, costs, and resources were required. Recommendations around the use of final outcomes over intermediate outcomes to calculate quality-adjusted life-years and life-years gained, the type of evidence, the source of evidence, and the use of time horizon and modeling were made. CONCLUSIONS: This article summarizes key recommendations for the conduct of economic evaluations in oncology and describes methods required to ensure that economic assessments in oncology are conducted in a standardized manner.

Inflammatory bowel disease: a Canadian burden of illness review.

BACKGROUND: Inflammatory bowel diseases (IBD) - Crohn's disease (CD) and ulcerative colitis (UC) - significantly impact quality of life and account for substantial costs to the health care system and society. OBJECTIVE: To conduct a comprehensive review and summary of the burden of IBD that encompasses the epidemiology, direct medical costs, indirect costs and humanistic impact of these diseases in Canada. METHODS: A literature search focused on Canadian data sources. Analyses were applied to the current 2012 Canadian population. RESULTS: There are approximately 233,000 Canadians living with IBD in 2012 (129,000 individuals with CD and 104,000 with UC), corresponding to a prevalence of 0.67%. Approximately 10,200 incident cases occur annually. IBD can be diagnosed at any age, with typical onset occurring in the second or third decade of life. There are approximately 5900 Canadian children <18 years of age with IBD. The economic costs of IBD are estimated to be $2.8 billion in 2012 (almost $12,000 per IBD patient). Direct medical costs exceed $1.2 billion per annum and are driven by cost of medications ($521 million), hospitalizations ($395 million) and physician visits ($132 million). Indirect costs (society and patient costs) total $1.6 billion and are dominated by long-term work losses of $979 million. Compared with the general population, the quality of life patients experience is low across all dimensions of health. CONCLUSIONS: The present review documents a high burden of illness from IBD due to its high prevalence in Canada combined with high per-patient costs. Canada has among the highest prevalence and incidence rates of IBD in the world. Individuals with IBD face challenges in the current environment including lack of awareness of IBD as a chronic disease, late or inappropriate diagnosis, inequitable access to health care services and expensive medications, diminished employment prospects and limited community-based support.

How do cost-effectiveness analyses inform reimbursement decisions for oncology medicines in Canada? The example of sunitinib for first-line treatment of metastatic renal cell carcinoma.

BACKGROUND: Canadian oncology decision-makers have reimbursed cancer drugs at incremental cost-effectiveness ratios (ICER) higher than those considered acceptable in other therapeutic areas. Sunitinib is a multitargeted receptor tyrosine kinase inhibitor, indicated for metastatic renal-cell carcinoma (MRCC) of clear cell histology. Canadian decision-makers evaluated sunitinib funding in the presence of important data limitations (including interim analysis of a surrogate outcome) and in the context of a high ICER. METHODS: First, a description was presented of the cost-effectiveness analysis submitted for sunitinib reimbursement decision-making in Canada before conclusive survival evidence had been available. Second, sunitinib access decisions and the oncology drug reimbursement literature were reviewed to explore the interpretation of sunitinib perceived value in the context of the decision-making framework in Canada. RESULTS: The economic evaluation yielded an ICER of $144K/quality-adjusted life-year gained for sunitinib compared with interferon-alfa. This high ratio was not an insurmountable barrier to access in Canada because all provinces now reimburse sunitinib for first-line treatment of MRCC. In this particular instance, payers were receptive to immature survival data but substantial progression-free gains, for patients with a relatively rare cancer and few treatment options. CONCLUSION: This demonstrates that the cost-effectiveness ratio is only one of many factors that affect an access decision in oncology.

The role of economic evidence in Canadian oncology reimbursement decision-making: to lambda and beyond.

OBJECTIVE: The overarching question addressed in this article is: what has been the impact of economic evidence to Canadian drug reimbursement decisions; within this, has an (explicit or implicit) threshold been identified for making such decisions; and is the impact or threshold different for oncology medications? METHODS: Three sequential strategies were employed: a literature search, a review of publicly available Canadian reimbursement recommendations, and a one-day key informant roundtable, held with a purposive sample of 13 individuals from across Canada to gain information not readily accessible from the public domain. RESULTS: Despite the formal requirement for structured economic evidence, the limited public information suggests that its uptake in the Canadian decision-making process has been tentative. Implicit economic thresholds have been published in Australia and the United Kingdom, but not in Canada. Based on reviews of reimbursement recommendations, thresholds specific to oncology medications may be higher than for nononcology medications, in Canada and elsewhere. Canadian reimbursement recommendations can appear inconsistent with respect to clinical evidence, economic evidence, and nonevidentiary factors, possibly because of a lack of transparency or context-sensitive interpretations. The key informant roundtable provided reasons for the inconsistent uptake of economic evidence: panelists were divided between those who found economic information useful and supportive to decision-making, and those who did not. Panelists generally agreed on the need for publicly defensible and ethical reimbursement restrictions. They suggested the following improvements: transparency of processes and decisions, dynamic formularies that can adapt with evolving treatment practices and clinical data, broader representation of expertise on review panels, greater use of ethics to resolve conflicts arising from different perspectives, and the development of an explicit Canadian weighting system for evidence and values. CONCLUSIONS: Economic evidence has been tentatively incorporated in reimbursement decision-making in Canada. Public reasons for recommendation indicate that this evidence is used primarily with respect to the attractiveness of an incremental cost-effectiveness ratio. Oncology drugs seem to be adopted at the highest thresholds of acceptability. Yet, decision-makers expressed a need to move beyond lambda, rejecting the simplicity of the incremental cost-effectiveness ratio and considering alternative strategies to improve decision-making, including formal guidance for weighting both evidence and values.

Activities of the pan-Canadian Pharmaceutical Alliance: An Observational Analysis.

BACKGROUND: The pan-Canadian Pharmaceutical Alliance (pCPA) was established in 2010 to negotiate confidential prices for drugs coming forward from Canada's centralized health technology assessment (HTA) agency reviews, on behalf of the participating public drug plans. OBJECTIVE:  To analyze the activities of the pCPA, to determine: alignment of HTA agency recommendations and pCPA negotiation decisions; the role of health economics in pCPA activities; and patterns of implicit prioritization. METHODS: The analysis was based on the archive of drugs handled through the pCPA, as posted on its website. The period of observation was from inception to August 31, 2017. HTA recommendations were sourced from the websites of the Common Drug Review (CDR) and the pan-Canadian Oncology Drug Review. Descriptive and statistical analyses were conducted. RESULTS: The dataset contained 206 drug-indication pairings. There was close but imperfect alignment between HTA agency recommendations and the pCPA's decisions to negotiate; deviations occurred only with CDR-reviewed drugs. The median incremental cost-effectiveness ratio of negotiated drugs was $168K/QALY for oncology drugs, but $70K/QALY for non-oncology drugs. The time to initiate negotiations was dramatically shorter for oncology versus non-oncology drugs (mean 54 versus 263 days), and also differed between therapeutic areas at CDR. The time required for PCPA activity was surprisingly similar for drugs recommended without a price condition and for those conditional on a price reduction. CONCLUSION: These findings revealed a strong alignment between HTA recommendations and pCPA negotiations, an implicit prioritization favouring oncology drug negotiations, and an evolving role for health economics in Canada's reimbursement process.

Transcriptional profiling of genes at the human common fragile site FRA1H in tumor-derived cell lines.

Common fragile sites (CFSs) are chromosome regions that exhibit gaps and breaks when the cells are exposed to replication stress and to some DNA-binding compounds. In cancer cells, the CFSs are frequently involved in recurrent chromosome rearrangements. Furthermore, altered expression of associated genes, known or potential oncogenes, and tumor-suppressor genes has often been observed. Seventeen of the 88 listed CFSs have been analyzed at the molecular level, but the basis of their fragility has not been clarified. In the present work, the nine genes TGFB2, IARS2, MARK1, TAF1A, TP53BP2, ADPRT, including a very large gene ESRRG and two microRNA genes, MIRN194-1 and MIRN215, localized in the fragile site FRA1H, were investigated by polymerase chain reaction (PCR) for homozygous deletions and by real-time PCR for modification or loss of gene expression in a panel of 19 cancer cell lines. The expression level of five (ESRRG, TGFB2, MIRN194-1, MIRN215, and MARK1) of the nine genes studied presented significant modifications in some of the 19 examined tumor-derived cell lines compared to their normal control tissues. Because of their function, these genes could have a role in neoplastic transformation.

Biallelic deletion and loss of expression analysis of genes at FRA2G common fragile site in tumor-derived cell lines.

Common fragile sites (CFS) are regions of chromosome instability that show gaps or breaks when cells are exposed to particular culture condition. Much evidence suggests that CFSs are causally related to cancer as breakpoints in recurrent chromosome mutations and as sites of viral integration. We investigated the FRA2G CFS (2q31) for biallelic deletions and loss of expression in a panel of 19 tumor-derived cell lines. We found that Burkitt lymphoma-derived cell line DAUDI has a biallelic deletion of eight of the nine analyzed genes. Moreover, we observed loss of expression (LOE) of the DHRS9 gene (alias RDHL), one of the deleted genes in the DAUDI cell line, in MOLT-14 and Raji cell lines derived from Burkitt lymphoma and from T-cell acute lymphoblastic leukemia, respectively. DHRS9 is involved in development and differentiation pathways.

Evolution of health technology assessment: best practices of the pan-Canadian Oncology Drug Review.

BACKGROUND: In 2007, Canada chose to develop a separate and distinct path for oncology drug health technology assessment (HTA). In 2013, the decision was made to transfer the pan-Canadian Oncology Drug Review (pCODR) to the Canadian Agency for Drugs and Technologies in Health (CADTH), to align the pCODR and CADTH Common Drug Review processes while building on the best practices of both. The objective of this research was to conduct an examination of the best practices established by the pCODR. METHODS: A qualitative research approach was taken to assess the policies, processes, and practices of the pCODR, based on internationally accepted best practice "principles" in HTA, with a particular focus on stakeholder engagement. Publicly available information regarding the approach of the pCODR was used to gauge the agency's performance against these principles. In addition, stakeholder observations and real-world experiences were gathered through key informant interviews to be inclusive of perspectives from patient advocacy groups, provincial and/or cancer agency decision-makers, community and academic oncologists, industry, expert committee members, and health economists. RESULTS: This analysis indicated that, through the pCODR, oncology stakeholders have had a voice in and have come to trust the quality and relevance of oncology HTA as a vital tool to ensure the best decisions for Canadians with cancer and their health care system. It could be expected that adoption of the principles and processes of the pCODR would bring a similar level of engagement and trust to other HTA organizations in Canada and elsewhere. CONCLUSION: The results of this research led to recommendations for improvement and potential extrapolation of these best practices to other HTA organizations worldwide, along with suggestions for continued evolution of the pCODR in conjunction with its integration into the CADTH. It is clear that the transition of the pCODR to CADTH provides an opportunity for practices initiated by the pCODR to become the standard for these newly amalgamated HTA agencies in Canada.

Cost-Effectiveness of Dolutegravir in HIV-1 Treatment-Naive and Treatment-Experienced Patients in Canada.

INTRODUCTION: The Antiretroviral Analysis by Monte Carlo Individual Simulation (ARAMIS) model was adapted to evaluate the cost-effectiveness of dolutegravir (DTG) in Canada in treatment-naive (TN) and treatment-experienced (TE) human immunodeficiency virus (HIV)-1 patients. METHODS: The ARAMIS-DTG model is a microsimulation model with a lifetime analytic time horizon and a monthly cycle length. Markov health states were defined by HIV health state (with or without opportunistic infection). DTG was compared to efavirenz (EFV), raltegravir (RAL), darunavir/ritonavir, rilpivirine (RPV), elvitegravir/cobicistat, atazanavir/ritonavir and lopinavir/ritonavir in TN patients and to RAL in TE patients. The initial cohort, the main efficacy data and safety data were derived from phase III clinical trials. Treatment algorithms were based on expert opinion. Costs normalized to the year 2013 included antiretroviral treatment cost, testing, adverse event, HIV and cardiovascular disease care and were derived from the literature. RESULTS: Dolutegravir was estimated to be the dominant strategy compared with all comparators in both TN and TE patients. Treatment with DTG was associated with additional quality-adjusted life-years that ranged from 0.17 (vs. RAL) to 0.47 (vs. EFV) in TN patients and was 0.60 in TE patients over a lifetime. Cost savings ranged from Can$1393 (vs. RPV) to Can$28,572 (vs. RAL) in TN patients and amounted to Can$3745 in TE patients. Sensitivity analyses demonstrated the robustness of the model. CONCLUSIONS: Dolutegravir is a dominant strategy in the management of TN and TE patients when compared to recommended comparators. This is mainly related to the high efficacy and high barrier to resistance. FUNDING: ViiV Healthcare.

Putting your money where your mouth is: willingness to pay for dental gel.

OBJECTIVES: To measure preferences and willingness to pay (WTP) for a novel anaesthetic (dental gel) versus existing anaesthetic options for periodontal maintenance visits. DESIGN: The study was conducted by developing and administering a survey, composed of a modified decision aid and a WTP instrument. The decision aid provided clinical information in layman's terms. Patients stated their anaesthetic preference; WTP elicited the hypothetical amount of money a subject would pay to have dental gel available for maintenance cleaning, should they require anaesthetic. PATIENTS: Periodontal recall patients (n = 97; 'recall') and participants from the general population (n = 196; 'general') from southwestern Ontario, Canada. RESULTS: The overwhelming majority of participants chose dental gel over injectable local anaesthetic or no anaesthetic as their first anaesthetic preference (general: 81.0%; recall: 82.5%). The median WTP for dental gel was 20.00 Canadian dollars (dollars Can) per visit for the general population and dollars Can10.00 for the recall population (1999 values). The majority of participants were willing to pay an insurance premium for dental gel, even if they did not personally prefer dental gel (general: 72.4%; recall: 73.2%). The median monthly premium to have dental gel available for any plan beneficiary requiring scaling and root planing (SRP) during maintenance was dollars Can2.00 per month for both groups. CONCLUSIONS: In this population, an alternative to traditional injectable local anaesthetic (i.e. dental gel) was overwhelmingly preferred by both general population participants and recall patients for maintenance cleaning procedures. Most participants were willing to pay to have dental gel available, either for themselves or for others.

Oncology drug health technology assessment recommendations: Canadian versus UK experiences.

BACKGROUND: CANADA HAS TWO HEALTH TECHNOLOGY ASSESSMENT (HTA) AGENCIES RESPONSIBLE FOR ONCOLOGY DRUG FUNDING RECOMMENDATIONS: the Institut National d'Excellence en Santé et Services Sociaux (INESSS) for the province of Québec and the pan-Canadian Oncology Drug Review for the rest of Canada. The objective of the research was to review and compare the recommendations of these two agencies alongside an international comparator - the National Institute for Health and Care Excellence (NICE) in the United Kingdom - with respect to their recommendations records and the influence of clinical and cost-effectiveness evidence on the recommendations. METHODS: Recommendations were identified from the three agencies from January 1, 2002 to June 1, 2013. Recommendations were limited to five cancer sites (lung, breast, colon, kidney, blood) and to metastatic/advanced settings. Descriptive analyses examined the frequency of positive recommendations and factors related to a positive recommendation. For each recommendation, only publicly available information posted on the agency website was used to abstract data. RESULTS: There was a wide variation in the rate of positive recommendations, ranging from 48% for NICE to 95% for Canada's national process (among the 74% of its recommendations that were publicly posted). Interagency agreement was low, with full agreement for only six of the 14 drugs commonly reviewed by all three agencies. Evidence of a survival gain was not necessary for a positive recommendation; progression-free survival was acceptable. Different approaches were taken when addressing unacceptable cost-effectiveness. NICE was most likely to yield a negative recommendation on these grounds, whereas Canada's national process was most likely to yield a positive recommendation with a required pricing arrangement. CONCLUSION: In this analysis, the primary reason for the observed divergence between agency recommendations appeared to be the availability of mechanisms in each jurisdiction to address cost-effectiveness subsequent to the HTA assessment process. Furthermore, caution is needed when interpreting cross-agency comparisons between HTA agencies, as recommendations may not correspond directly to subsequent funding decisions and actual patient access. This may be a concern, given the high international profile of assessments conducted by the reviewed HTA agencies.

Common Drug Review recommendations: an evidence base for expectations?

BACKGROUND: The Common Drug Review (CDR) was created to provide a single process to review the comparative clinical efficacy and cost effectiveness of new drugs, and then to make formulary listing recommendations to Canadian publicly funded drug benefit plans. OBJECTIVE: The objective was to conduct an in-depth analysis of Canadian Expert Drug Advisory Committee (CEDAC) recommendations to date, to explore predictors and possible explanatory factors associated with negative recommendations. METHODS: Final recommendations were identified from inception (September 2003) to 31 December 2009. Using only publicly available information, recommendations were analysed under the following categories: submission specifics, drug characteristics, clinical factors and economic factors. Descriptive analyses were conducted, followed by statistical analyses, to determine which factors independently predicted a 'do not list' (DNL) recommendation. RESULTS: The database consisted of 138 unique final recommendations. The overall DNL rate was 48%. Significant differences in DNL rates were observed between therapeutic areas, ranging from 0% for HIV antivirals up to 88% for analgesic drugs. In the univariate analysis, several factors were significantly associated with a DNL recommendation, including first-in-class drugs and use of clinical scales as an outcome. In the multivariate regression, four factors were significantly predictive of a DNL recommendation: clinical uncertainty (odds ratio [OR] 14), price higher than comparators (OR 9), request for reconsideration (OR 10) and price as the only economic evidence used (OR 18). Incremental cost-effectiveness thresholds were not predictive of recommendations. The hypothesis that economic factors did not impact recommendations when clinical factors were included first was supported by the analysis. CONCLUSIONS: This analysis documented an evidence-driven process that simultaneously weighted multiple factors. Clinical uncertainty and price considerations, but not economic results, had a strong impact on the recommendations. Insufficiency of clinical evidence may have resulted from the gap in evidence available at the time of product launch and the absence of demonstrated benefits to support innovative drugs.

Characterization of FRA7B, a human common fragile site mapped at the 7p chromosome terminal region.

Common fragile sites (CFS) are specific regions of the mammalian chromosomes that are particularly prone to gaps and breaks. They are a cause of genome instability, and the location of many CFS correlates with breakpoints of aberrations recurrent in some cancers. The molecular characterization of some CFS has not clarified the causes of their fragility. In this work, by using fluorescence in situ hybridization analysis with BAC and PAC clones, we determined the DNA sequence of the CFS FRA7B. The FRA7B sequence was then analyzed to identify coding sequences and some structural features possibly involved in fragility. FRA7B spans about 12.2 megabases, and is therefore one of the largest CFS analyzed. It maps at the 7p21.3-22.3 chromosome bands, therefore at the interface of G- and R-band regions that are probably difficult to replicate. A 90-kilobase long sequence that presents very high flexibility values was identified at the very beginning of the more fragile CFS region. Three large genes (THSD7A, SDK1, and MAD1L1) and two miRNA genes (MIRN589 and MIRN339) map in the fragile region. The chromosome band 7p22 is a recurrent breakpoint in chromosome abnormalities in different types of neoplasm. FRA7B is the first characterized CFS located in a chromosome terminal region.

Breakages at common fragile sites set boundaries of amplified regions in two leukemia cell lines K562 - Molecular characterization of FRA2H and localization of a new CFS FRA2S.

Genome amplification is often observed in human tumors. The breakage-fusion-bridge (BFB) cycle is the mechanism that often underlies duplicated regions. Some research has indicated common fragile sites (CFS) as possible sites of chromosome breakages at the origin of BFB cycles. Here we searched two human genome regions known as amplification hot spots for any DNA copy number amplifications by analyzing 21 cancer cell lines to investigate the relationship between genomic fragility and amplification. We identified a duplicated region on a chromosomes der(2) present in the karyotype of two analysed leukemia cell lines K562. The two duplicated regions are organized into large palindromes, which suggests that one BFB cycle has occurred. Our findings show that the three breakpoints are localized in the sequence of three CFSs: FRA2H (2q32.1-q32.2), which here has been characterized molecularly; FRA2S (2q22.3-q23.3), a newly localized aphidicolin inducible CFS; and FRA2G (2q24.3-q31).

Molecular characterization of the human common fragile site FRA1H.

The molecular basis of the fragility of common fragile sites (CFS) and their role in chromosome instability and in altered expression of associated genes in cancer cells have not yet been clarified. In the present work we analyzed the human CFS FRA1H. FRA1H is the first characterized CFS the expression of which is not induced by aphidicolin but instead by DAPI. 5-azaC, 5-azadC, and Ad12 induce a CFS with the same cytogenetic location. By using FISH analysis with BAC clones, we determined that this CFS extends for approximately 10 Mb, and is therefore one of the largest characterized CFSs. FRA1H maps to the chromosome bands 1q41 and 1q42.1 thus spanning an R-band/G-band boundary, a region considered difficult to duplicate. The FRA1H DNA sequence was analyzed to identify coding sequences, the AT content, the type and quantity of the DNA repeats, the CpG islands, the matrix attachment regions, and the number and distribution of high-flexibility regions. A 120 kb long sequence was identified that is very AT-rich (64.6%), has a very large number of flexibility peaks and that may be involved in inducing fragility in the surrounding regions. Among the other genes, two very large genes (USH2A, ESRRG) and two microRNA genes (MIRN194-1, MIRN215) map within the fragile region.

DNA methylation, histone H3 methylation, and histone H4 acetylation in the genome of a crustacean.

In this work, we used antibodies against histone H3 trimethylated at lysine 9 (H3K9m3); against histone H4 acetylated at lysines 5, 8, 12, and 16 (H4ac); and against DNA methylated at 5C cytosine (m5C) to study the presence and distribution of these markers in the genome of the isopod crustacean Asellus aquaticus. The use of these 3 antibodies to immunolabel spermatogonial metaphases yields reproducible patterns on the chromosomes of this crustacean. The X and Y chromosomes present an identical banding pattern with each of the antibodies. The heterochromatic telomeric regions and the centromeric regions are rich in H3K9m3, but depleted in m5C and H4ac. Thus, m5C does not seem to be required to stabilize the silence of these regions in this organism.