Circular RNA as a source of neoantigens for cancer vaccines.

BACKGROUND: The effectiveness of somatic neoantigen-based immunotherapy is often hindered by the limited number of mutations in tumors with low to moderate mutation burden. Focusing on microsatellite-stable colorectal cancer (CRC), this study investigates the potential of tumor-associated circular RNAs (circRNAs) as an alternative source of neoepitopes in CRC. METHODS: Tumor-associated circRNAs in CRC were identified using the MiOncoCirc database and ribo-depletion RNA sequencing of paired clinical normal and tumor samples. Candidate circRNA expression was validated by quantitative real-time PCR (RT-qPCR) using divergent primers. TransCirc database was used for translation prediction. Human leukocyte antigen binding affinity of open reading frames from potentially translatable circRNA was predicted using pVACtools. Strong binders from messenger RNA-encoded proteins were excluded using BlastP. The immunogenicity of the candidate antigens was functionally validated through stimulation of naïve CD8+ T cells against the predicted neoepitopes and subsequent analysis of the T cells through enzyme-linked immunospot (ELISpot) assay, intracellular cytokine staining (ICS) and granzyme B (GZMB) reporter. The cytotoxicity of T cells trained with antigen peptides was further tested using patient-derived organoids. RESULTS: We identified a neoepitope from circRAPGEF5 that is upregulated in CRC tumor samples from MiOncoCirc database, and two neoepitopes from circMYH9, which is upregulated across various tumor samples from our matched clinical samples. The translation potential of candidate peptides was supported by Clinical Proteomic Tumor Analysis Consortium database using PepQuery. The candidate peptides elicited antigen-specific T cells response and expansion, evidenced by various assays including ELISpot, ICS and GZMB reporter. Furthermore, T cells trained with circMYH9 peptides were able to specifically target and eliminate tumor-derived organoids but not match normal organoids. This observation underscores the potential of circRNAs as a source of immunogenic neoantigens. Lastly, circMYH9 was enriched in the liquid biopsies of patients with CRC, thus enabling a detection-to-vaccination treatment strategy for patients with CRC. CONCLUSIONS: Our findings underscore the feasibility of tumor-associated circRNAs as an alternative source of neoantigens for cancer vaccines targeting tumors with moderate mutation levels.

A functional personalised oncology approach against metastatic colorectal cancer in matched patient derived organoids.

Globally, colorectal cancer (CRC) is the third most frequently occurring cancer. Progression on to an advanced metastatic malignancy (metCRC) is often indicative of poor prognosis, as the 5-year survival rates of patients decline rapidly. Despite the availability of many systemic therapies for the management of metCRC, the long-term efficacies of these regimens are often hindered by the emergence of treatment resistance due to intratumoral and intertumoral heterogeneity. Furthermore, not all systemic therapies have associated biomarkers that can accurately predict patient responses. Hence, a functional personalised oncology (FPO) approach can enable the identification of patient-specific combinatorial vulnerabilities and synergistic combinations as effective treatment strategies. To this end, we established a panel of CRC patient-derived organoids (PDOs) as clinically relevant biological systems, of which three pairs of matched metCRC PDOs were derived from the primary sites (ptCRC) and metastatic lesions (mCRC). Histological and genomic characterisation of these PDOs demonstrated the preservation of histopathological and genetic features found in the parental tumours. Subsequent application of the phenotypic-analytical drug combination interrogation platform, Quadratic Phenotypic Optimisation Platform, in these pairs of PDOs identified patient-specific drug sensitivity profiles to epigenetic-based combination therapies. Most notably, matched PDOs from one patient exhibited differential sensitivity patterns to the rationally designed drug combinations despite being genetically similar. These findings collectively highlight the limitations of current genomic-driven precision medicine in guiding treatment strategies for metCRC patients. Instead, it suggests that epigenomic profiling and application of FPO could complement the identification of novel combinatorial vulnerabilities to target synchronous ptCRC and mCRC.

Preoperative Quality of Life and Mental Health Can Predict Postoperative Outcomes and Quality of Life after Colorectal Cancer Surgery.

Background and Objectives: It remains unclear which domains of preoperative health-related quality of life (HRQOL) and mental health are predictive of postoperative clinical and patient-reported outcomes in colorectal cancer (CRC) patients. Materials and Methods: A prospective cohort of 78 CRC patients undergoing elective curative surgery was recruited. The EORTC QLQ-C30 and HADS questionnaires were administered preoperatively and one month after surgery. Results: Preoperative cognitive functioning scores (95% CI 0.131-1.158, p = 0.015) and low anterior resection (95% CI 14.861-63.260, p = 0.002) independently predicted poorer 1-month postoperative global QOL. When postoperative complications were represented using the comprehensive complication index (CCI), poorer preoperative physical function scores were associated with higher CCI scores (B = -0.277, p = 0.014). Preoperative social function score (OR = 0.925, 95% CI 0.87 to 0.99; p = 0.019) was an independent predictor for 30-day readmission, while physical functioning score (OR = -0.620, 95% CI -1.073--0.167, p = 0.008) was inversely related to the length of hospitalization. The overall regressions for 1-month postoperative global QOL (R2: 0.546, F: 1.961, p = 0.023) and 30-day readmission (R2: 0.322, χ2: 13.129, p < 0.001) were statistically significant. Conclusions: Various QLQ-C30 domains were found to be predictive of postoperative outcomes, including complications, readmission, and length of hospitalization. Preoperative cognitive dysfunction and low AR were independent predictors of poorer postoperative global QOL. Future research should seek to examine the efficacy of targeting specific baseline QOL domains in improving clinical as well as patient-reported outcomes after CRC surgery.

MiR-138 is a potent regulator of the heterogenous MYC transcript population in cancers.

3'UTR shortening in cancer has been shown to activate oncogenes, partly through the loss of microRNA-mediated repression. This suggests that many reported microRNA-oncogene target interactions may not be present in cancer cells. One of the most well-studied oncogenes is the transcription factor MYC, which is overexpressed in more than half of all cancers. MYC overexpression is not always accompanied by underlying genetic aberrations. In this study, we demonstrate that the MYC 3'UTR is shortened in colorectal cancer (CRC). Using unbiased computational and experimental approaches, we identify and validate microRNAs that target the MYC coding region. In particular, we show that miR-138 inhibits MYC expression and suppresses tumor growth of CRC and hepatocellular carcinoma (HCC) cell lines. Critically, the intravenous administration of miR-138 significantly impedes MYC-driven tumor growth in vivo. Taken together, our results highlight the previously uncharacterized shortening of the MYC 3'UTR in cancer, and identify miR-138 as a potent regulator of the heterogenous MYC transcript population.

Early surgery after bridge-to-surgery stenting for malignant bowel obstruction is associated with better oncological outcomes.

BACKGROUND: Placement of self-expanding metal stents has been increasingly adopted as a bridge to surgery in patients presenting with obstructed left-sided colorectal cancers. The optimal bridging time has yet to be widely established, hence this retrospective study aims to determine the optimal bridging time to elective surgery post endoluminal stenting. PATIENTS AND METHODS: All patients who underwent colorectal stenting for large bowel obstruction in a single, tertiary hospital in Singapore between January 2003 and December 2017 were retrospectively identified. Patients' baseline demographics, tumour characteristics, stent-related complications, intra-operative details, post-operative complications and oncological outcomes were analysed. RESULTS: Of the 53 patients who successfully underwent colonic stenting for malignant left sided obstruction, 33.96% of patients underwent surgery within two weeks of stent placement while 66.04% of patients underwent surgery after 2 weeks of stent placement. Univariate analysis between both groups did not demonstrate significant differences in postoperative complications and stoma formation. Significant differences were observed between both groups for stent complications (38.89% vs 8.57%, p = 0.022), on-table decompression (38.89% vs 2.86%, p = 0.001) and systemic recurrence (11.11% vs 40.00%, p = 0.030). Increased bridging interval to surgery (OR 13.16, CI 1.37-126.96, p = 0.026) was a significant risk factor for systemic recurrence on multivariate analysis. CONCLUSIONS: Patients undergoing definitive surgery within 2 weeks of colonic stenting may have better oncological outcomes without compromising on postoperative outcomes. Further prospective studies are required to compare outcomes between emergency surgery and different bridging intervals.

Are hemoglobin levels really lower in faecal immunochemical test positive patients with colorectal cancer?

INTRODUCTION: Faecal immunochemical test (FIT) is advocated in many colorectal cancer-screening programs. A positive FIT translates to the need for a colonoscopy. However, waiting times for diagnostic colonoscopy is long. The aim of our study is to determine the correlation of hemoglobin levels in patients with a positive FIT who were subsequently diagnosed with colorectal cancer, and to compare them with patients with only colonic adenomas and those with normal colonoscopy with the intention of determining if hemoglobin levels could be used to stratify the urgency of colonoscopy. METHODOLOGY: This is a matched case-control study of patients who were FIT positive and subsequently underwent colonoscopy at the National University Hospital, Singapore. Newly diagnosed colorectal cancers formed the case group. The patients with colorectal cancers were then matched for age, gender and ethnicity at a 1:1 ratio to patients with colonic adenomas and then those in whom colonoscopy was normal. RESULTS: Fifteen patients met the inclusion criteria and formed the case group. The differences between the groups were not statistically significant in terms of age, gender and ethnicity. The median hemoglobin level for the patients in the case group compared to the control group was (12.4 vs 14.5, p = 0.002) for the group with adenomas and (12.4 vs 14.4, p = 0.007) for the group with normal colonoscopy. CONCLUSION: Colorectal cancer patients presenting with a positive FIT are more likely to be anemic. A test to identify those patients who have a positive FIT that are anemic could enable earlier colonoscopic evaluation.

Early weight loss after laparoscopic sleeve gastrectomy predicts midterm weight loss in morbidly obese Asians.

BACKGROUND: Laparoscopic sleeve gastrectomy (SG) is a popular bariatric procedure in morbidly obese Asians. OBJECTIVES: To investigate the effect of initial weight loss on midterm weight maintenance and remission of co-morbidities after laparoscopic SG in morbidly obese Asians. SETTING: University Hospital, Singapore. METHODS: Data of patients who underwent laparoscopic SG were analyzed. Change in body mass index (BMI), percentage of total weight loss (%WL), and of excess weight loss (%EWL) was calculated and remission of obesity-related co-morbidities was examined. Linear regression analysis was performed to determine the effect of initial weight loss on successful weight maintenance. Receiver operative characteristic curve analysis was used to define optimal cutoff values. RESULTS: Two hundred and seventy-two patients were included in this study. Mean preoperative weight and BMI were 115.4±25.5 kg and 42.5±8.0 kg/m2, respectively. Mean follow-up duration was 27.6±16.4 months. Successful weight loss of>50% EWL was achieved by 65.7%, 65.5%, and 50.8% of patients at 1, 2, and 3 years, postoperatively. There was a significant correlation of %EWL at 3 months with %EWL up to 3 years (P≤.005). Receiver operative characteristic analysis showed initial EWL of 35% at 3 months best predicted successful weight loss at 1 year (sensitivity 73.1%, specificity 81.4%). Patients achieving>35% EWL were significantly more likely to achieve remission of co-morbidities (P≤.005) at 1 year after surgery. CONCLUSION: Early weight loss at 3 months predicts weight maintenance up to 3 years and remission of co-morbidities at 1 year after laparoscopic SG in Asians.