Although transcriptome alteration is an essential driver of carcinogenesis, the effects of chromosomal structural alterations on the cancer transcriptome are not yet fully understood. Short-read transcript sequencing has prevented researchers from directly exploring full-length transcripts, forcing them to focus on individual splice sites. Here, we develop a pipeline for Multi-Sample long-read Transcriptome Assembly (MuSTA), which enables construction of a transcriptome from long-read sequence data. Using the constructed transcriptome as a reference, we analyze RNA extracted from 22 clinical breast cancer specimens. We identify a comprehensive set of subtype-specific and differentially used isoforms, which extended our knowledge of isoform regulation to unannotated isoforms including a short form TNS3. We also find that the exon–intron structure of fusion transcripts depends on their genomic context, and we identify double-hop fusion transcripts that are transcribed from complex structural rearrangements. For example, a double-hop fusion results in aberrant expression of an endogenous retroviral gene, ERVFRD-1, which is normally expressed exclusively in placenta and is thought to protect fetus from maternal rejection; expression is elevated in several TCGA samples with ERVFRD-1 fusions. Our analyses provide direct evidence that full-length transcript sequencing of clinical samples can add to our understanding of cancer biology and genomics in general.
Antiviral therapy is essential for HIV/AIDS patients, but many variables impede patients' adherence to therapy. To facilitate adherence, trained registered nurses in Japan provided consultation by phone at the AIDS Clinical Center. This study describes the process and content of this intervention and explores the predictors for length of time of phone consultations. The study was completed over 1 month using a time study, checklist, and medical record inquiry. A total of 175 consultations were described. Mean time was 4.8 +/- 3.8 min, and longer for patients with complications or comorbidity. Although the contents of conversations differed according to the phase of highly active antiretroviral therapy, major identified themes included need for medical consultation, symptom control, provision of information, and active listening. The results are useful for those trying to find ways to use telephone consultation effectively to reinforce adherence.
Colorectal cancer (CRC) is the second leading cause of cancer-related deaths in Japan (Vital Statistics Japan, Ministry of Health, Labor and Welfare, https://www. mhlw.go.jp/engli sh/datab ase/db-hw/vs01.html). While radical resection is the first line of treatment, postoperative adjuvant chemotherapy is usually administered to patients with stage III CRC. Although the postoperative recurrence rate of stage II CRC is approximately 15%, administration of chemotherapy in such cases is generally left to the discretion of the clinician, since its efficacy for stage II CRC is still unknown. [1][2][3] Extensive research has elucidated the landscape of genomic aberrations in CRC, 4-7 enabling the implementation of precision medicine through therapeutic stratification; however, the application of prognostic prediction based on mutational profiles remains limited. For
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