Pan-cancer analysis reveals multifaceted roles of retrotransposon-fusion RNAs.

Transposon-derived transcripts are abundant in RNA sequences, yet their landscape and function, especially for fusion transcripts derived from unannotated or somatically acquired transposons, remains underexplored. Here, we developed a new bioinformatic tool to detect transposon-fusion transcripts in RNA-sequencing data and performed a pan-cancer analysis of 10,257 cancer samples across 34 cancer types as well as 3,088 normal tissue samples. We identified 52,277 cancer-specific fusions with ~30 events per cancer and hotspot loci within transposons vulnerable to fusion formation. Exonization of intronic transposons was the most prevalent genic fusions, while somatic L1 insertions constituted a small fraction of cancer-specific fusions. Source L1s and HERVs, but not Alus showed decreased DNA methylation in cancer upon fusion formation. Overall cancer-specific L1 fusions were enriched in tumor suppressors while Alu fusions were enriched in oncogenes, including recurrent Alu fusions in EZH2 predictive of patient survival. We also demonstrated that transposon-derived peptides triggered CD8+ T-cell activation to the extent comparable to EBV viruses. Our findings reveal distinct epigenetic and tumorigenic mechanisms underlying transposon fusions across different families and highlight transposons as novel therapeutic targets and the source of potent neoantigens.

Deciphering the DNA methylation landscape of colorectal cancer in a Korean cohort.

Aberrant DNA methylation plays a pivotal role in the onset and progression of colorectal cancer (CRC), a disease with high incidence and mortality rates in Korea. Several CRC-associated diagnostic and prognostic methylation markers have been identified; however, due to a lack of comprehensive clinical and methylome data, these markers have not been validated in the Korean population. Therefore, in this study, we aimed to obtain the CRC methylation profile using 172 tumors and 128 adjacent normal colon tissues of Korean patients with CRC. Based on the comparative methylome analysis, we found that hypermethylated positions in the tumor were predominantly concentrated in CpG islands and promoter regions, whereas hypomethylated positions were largely found in the open-sea region, notably distant from the CpG islands. In addition, we stratified patients by applying the CpG island methylator phenotype (CIMP) to the tumor methylome data. This stratification validated previous clinicopathological implications, as tumors with high CIMP signatures were significantly correlated with the proximal colon, higher prevalence of microsatellite instability status, and MLH1 promoter methylation. In conclusion, our extensive methylome analysis and the accompanying dataset offers valuable insights into the utilization of CRC-associated methylation markers in Korean patients, potentially improving CRC diagnosis and prognosis. Furthermore, this study serves as a solid foundation for further investigations into personalized and ethnicity-specific CRC treatments. [BMB Reports 2023; 56(10): 569-574].

Evaluation of a GC-MS method for benzyl chloride content in processed food, meats, and marine products distributed in Korea.

Benzyl chloride is a harmful chemical that contaminates air, water, and food. A static headspace GC-MS method for determining benzyl chloride in food was developed and validated. Two food matrices (fat/oil and chicken) were used for method validation. Sample preparation involved ultrasonication extraction and purification (syringe filtration). Linearity (R 2) was > 0.99, accuracy ranged from 86.91% to 110%, the limit of detection was 0.04-0.17 mg/kg, and the limit of quantification was 0.13-0.52 mg/kg. Recovery varied from 88.19% to 111.77%, and precision ranged from 0.10% to 1.17% in intraday and interday analyses. Among 102 food items (oils, fats, meat, marine, and egg products) distributed in Korea, benzyl chloride was only detected in six of the marine products. The validated analytical method can be used for routine monitoring of benzyl chloride residues in food and thereby prevent the human health risks associated with the consumption of food contaminated with this chemical.

Combination of gabapentin and ramosetron for the prevention of postoperative nausea and vomiting after gynecologic laparoscopic surgery: a prospective randomized comparative study.

BACKGROUND: As a drug originally introduced for its anticonvulsant effects, gabapentin has been recently shown to be effective in the treatment of nausea and vomiting in various clinical settings. This study compared the antiemetic efficacy of oral gabapentin, intravenous ramosetron and gabapentin plus ramosetron in patients receiving fentanyl-based patient-controlled analgesia after laparoscopic gynecologic surgery. METHODS: One hundred and thirty two patients undergoing laparoscopic gynecologic surgery under general anesthesia were allocated randomly into three groups: group G received 300 mg oral gabapentin 1 h before anesthesia, group R received 0.3 mg intravenous ramosetron at the end of surgery, and group GR received a combination of 300 mg oral gabapentin 1 h before anesthesia and 0.3 mg intravenous ramosetron at the end of surgery. Postoperative nausea, retching, vomiting, rescue antiemetic drug use, pain, rescue analgesic requirements and adverse effects were assessed at 0-2, 2-24 and 24-48 h after surgery. Postoperative nausea and vomiting (PONV) was defined as the presence of nausea, retching or vomiting. RESULTS: The incidence of complete response (no PONV and no rescue antiemetics up to 48 h postoperatively) was significantly higher in group GR (26/40, 65%) than group G (16/40, 40%; P = 0.025) and group R (18/44, 41%; P = 0.027), whereas there was no significant difference between group G and group R (P = 0.932). There were no significant between-group differences in the incidence of emetic episodes, use of rescue antiemetics, severe emesis, use of rescue analgesics or any adverse effects. Postoperative pain scores were also similar among groups. CONCLUSIONS: The combination with gabapentin and ramosetron is superior to either drug alone for prevention of PONV after laparoscopic gynecologic surgery. TRIAL REGISTRATION: ClinicalTrials.gov NCT02617121 , registered November 25, 2015.