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The mortality-to-incidence ratio (MIR) is a marker that reflects the clinical outcome of cancer treatment. MIR as a prognostic marker is more accessible when compared with long-term follow-up survival surveys. Theoretically, countries with good health care systems would have favorable outcomes for cancer; however, no report has yet demonstrated an association between gallbladder cancer MIR and the World’s Health System ranking.
We used linear regression to analyze the correlation of MIRs with the World Health Organization (WHO) rankings and total expenditures on health/gross domestic product (e/GDP) in 57 countries selected according to the data quality.
The results showed high crude rates of incidence/mortality but low MIR in more developed regions. Among continents, Europe had the highest crude rates of incidence/mortality, whereas the highest age-standardized rates (ASR) of incidence/mortality were in Asia. The MIR was lowest in North America and highest in Africa (0.40 and 1.00, respectively). Furthermore, favorable MIRs were correlated with good WHO rankings and high e/GDP (p = 0.01 and p = 0.030, respectively).
The MIR variation for gallbladder cancer is therefore associated with the ranking of the health system and the expenditure on health.
Electronic supplementary material
The online version of this article (10.1186/s12889-019-7160-z) contains supplementary material, which is available to authorized users.
Gallbladder cancer, Mortality, Incidence, Mortality-to-incidence ratio, Expenditure
Favorable gallbladder cancer mortality-to-incidence ratios of countries with good ranking of world’s health system and high expenditures on health
Chi-Chih Wang, Ming-Chang Tsai, Shao-Chuan Wang, Cheng-Ming Peng, Hsiang-Lin Lee, Hsuan-Yi Chen, Tzu-Wei Yang, Chun-Che Lin, Wen-Wei Sung
Second generation RNA sequencing technology (RNA-seq) offers the potential to interrogate genome-wide differential RNA splicing in cancer. However, since short RNA reads spanning spliced junctions cannot be mapped contiguously onto to the chromosomes, there is a need for methods to profile splicing from RNA-seq data. Before the invent of RNA-seq technologies, microarrays containing probe sequences representing exon-exon junctions of known genes have been used to hybridize cellular RNAs for measuring context-specific differential splicing. Here, we extend this approach to detect tumor-specific splicing in prostate cancer from a RNA-seq dataset.
A database, SPEventH, representing probe sequences of under a million non-redundant splice events in human is created with exon-exon junctions of optimized length for use as virtual microarray. SPEventH is used to map tens of millions of reads from matched tumor-normal samples from ten individuals with prostate cancer. Differential counts of reads mapped to each event from tumor and matched normal is used to identify statistically significant tumor-specific splice events in prostate.
We find sixty-one (61) splice events that are differentially expressed with a p-value of less than 0.0001 and a fold change of greater than 1.5 in prostate tumor compared to the respective matched normal samples. Interestingly, the only evidence, EST (BF372485), in the public database for one of the tumor-specific splice event joining one of the intron in KLK3 gene to an intron in KLK2, is also derived from prostate tumor-tissue. Also, the 765 events with a p-value of less than 0.001 is shown to cluster all twenty samples in a context-specific fashion with few exceptions stemming from low coverage of samples.
We demonstrate that virtual microarray experiments using a non-redundant database of splice events in human is both efficient and sensitive way to profile genome-wide splicing in biological samples and to detect tumor-specific splicing signatures in datasets from RNA-seq technologies. The signature from the large number of splice events that could cluster tumor and matched-normal samples into two tight separate clusters, suggests that differential splicing is yet another RNA phenotype, alongside gene expression and SNPs, that can be exploited for tumor stratification.
Genome-wide Profiling of RNA splicing in prostate tumor from RNA-seq data using virtual microarrays
Subhashini Srinivasan, Arun H Patil, Mohit Verma, Jonathan L Bingham, Raghunathan Srivatsan
Ascoviruses (family Ascoviridae) are double-stranded DNA viruses with circular genomes that attack lepidopterans, where they produce large, enveloped virions, 150 by 400 nm, and cause a chronic, fatal disease with a cytopathology resembling that of apoptosis. After infection, host cell DNA is degraded, the nucleus fragments, and the cell then cleaves into large virion-containing vesicles. These vesicles and virions circulate in the hemolymph, where they are acquired by parasitic wasps during oviposition and subsequently transmitted to new hosts. To develop a better understanding of ascovirus biology, we sequenced the genome of the type species Spodoptera frugiperda ascovirus 1a (SfAV-1a). The genome consisted of 156,922 bp, with a G+C ratio of 49.2%, and contained 123 putative open reading frames coding for a variety of enzymes and virion structural proteins, of which tentative functions were assigned to 44. Among the most interesting enzymes, due to their potential role in apoptosis and viral vesicle formation, were a caspase, a cathepsin B, several kinases, E3 ubiquitin ligases, and especially several enzymes involved in lipid metabolism, including a fatty acid elongase, a sphingomyelinase, a phosphate acyltransferase, and a patatin-like phospholipase. Comparison of SfAV-1a proteins with those of other viruses showed that 10% were orthologs of Chilo iridescent virus proteins, the highest correspondence with any virus, providing further evidence that ascoviruses evolved from a lepidopteran iridovirus. The SfAV-1a genome sequence will facilitate the determination of how ascoviruses manipulate apoptosis to generate the novel virion-containing vesicles characteristic of these viruses and enable study of their origin and evolution.
Genomic Sequence of Spodoptera frugiperda Ascovirus 1a, an Enveloped, Double-Stranded DNA Insect Virus That Manipulates Apoptosis for Viral Reproduction
Dennis K. Bideshi, Marie-Veronique Demattei, Florence Rouleux-Bonnin, Karine Stasiak, Yeping Tan, Sylvie Bigot, Yves Bigot, Brian A. Federici