Wang, Xiaolin

AbstractBackgroundThe current risk stratification system defined by clinicopathological features does not identify the risk of recurrence in early-stage (stage I-II) colorectal cancer (CRC) with sufficient accuracy. We aimed to investigate whether DNA methylation could serve as a novel biomarker for predicting prognosis in early-stage CRC patients.MethodsWe analyzed the genome-wide methylation status of CpG loci using Infinium MethylationEPIC array run on primary tumor tissues and normal mucosa of early-stage CRC patients to identify potential methylation markers for prognosis. The machine-learning approach was applied to construct a DNA methylation–based prognostic classifier for early-stage CRC (MePEC) using the 4 gene methylation markers FAT3, KAZN, TLE4, and DUSP3. The prognostic value of the classifier was evaluated in 2 independent cohorts (n = 438 and 359, respectively).ResultsThe comprehensive analysis identified an epigenetic subtype with high risk of recurrence based on a group of CpG loci in the CpG-depleted region. In multivariable analysis, the MePEC classifier was independently and statistically significantly associated with time to recurrence in validation cohort 1 (hazard ratio = 2.35, 95% confidence interval = 1.47 to 3.76, P < .001) and cohort 2 (hazard ratio = 3.20, 95% confidence interval = 1.92 to 5.33, P < .001). All results were further confirmed after each cohort was stratified by clinicopathological variables and molecular subtypes.ConclusionsWe demonstrated the prognostic statistical significance of a DNA methylation profile in the CpG-depleted region, which may serve as a valuable source for tumor biomarkers. MePEC could identify an epigenetic subtype with high risk of recurrence and improve the prognostic accuracy of current clinical variables in early-stage CRC.

Background Tumor-infiltrating lymphocytes (TILs), especially CD8+ TILs, can be used for predicting immunotherapy responsiveness and survival outcome. However, the evaluation of CD8+ TILs currently relies on histopathological methodology with high variability. We therefore aimed to develop a DNA methylation signature for CD8+ TILs (CD8+ MeTIL) that could evaluate immune response and prognosis in colorectal cancer (CRC). Methods A CD8+ MeTIL signature score was constructed by using CD8+ T cell-specific differentially methylated positions (DMPs) that were identified from Illumina EPIC methylation arrays. Immune cells, colon epithelial cells, and two CRC cohorts (n=282 and 335) were used to develop a PCR-based assay for quantitative analysis of DNA methylation at single-base resolution (QASM) to determine CD8 + MeTIL signature score. Results Three CD8+ T cell-specific DMPs were identified to construct the CD8+ MeTIL signature score, which showed a dramatic discriminability between CD8+ T cells and other cells. The QASM assay we developed for CD8+ MeTIL markers could measure CD8+ TILs distributions in a fully quantitative, accurate, and simple manner. The CD8+ MeTIL score determined by QASM assay showed a strong association with histopathology-based CD8+ TIL counts and a gene expression-based immune marker. Furthermore, the low CD8+ MeTIL score (enriched CD8+ TILs) was associated with MSI-H tumors and predicted better survival in CRC cohorts. Conclusions This study developed a quantitative DNA methylation-based signature that was reliable to evaluate CD8+ TILs and prognosis in CRC. This approach has the potential to be a tool for investigations on CD8+ TILs and a biomarker for therapeutic approaches, including immunotherapy.

Abstract Background Imetelstat is a 13-mer lipid-conjugated oligonucleotide that targets the RNA template of human telomerase reverse transcriptase. A pilot study of imetelstat therapy in myelofibrosis showed the induction of complete (CR) or partial remissions, as well as molecular remissions, in a subset of patients (Blood. 2014;124:634). In the particular study, CR was significantly higher in patients with SF3B1 or U2AF1 spliceosome mutations, which provided the rationale for the current study; spliceosome mutations are closely associated with refractory anemia with ring sideroblasts with (RARS-T) or without (RARS) thrombocytosis (Leukemia. 2013;27:1826). Methods Diagnosis of RARS and RARS-T was according to WHO criteria (Blood. 2009;114:937). Study patients were treated with a 2-hour intravenous infusion of 7.5 mg/kg imetelstat (Janssen Biotech Inc., Horsham, PA, USA) every 4 weeks. Drug activity was monitored by both formal response criteria (Blood. 2006;108:419) and effect on spleen size, thrombocytosis and leukocytosis. Adverse events (AEs) were monitored by Common Terminology Criteria for Adverse Events (Version 4.03). Laboratory correlative studies included analysis of mutations. Results Accrual to this signal study is now complete and median time from study registration, as of 5/10/2015, was 17.1 months (range 16.1-20.1). Among the 9 study patients, 5 had RARS-T, 3 had RARS and one had "MDS/MPN overlap". Median age was 70 years (78% males). 8 (89%) patients were transfusion-dependent. One patient (RARS-T) had marked splenomegaly (palpable at 16 cm). Three patients each had leukocytosis and thrombocytosis. Seven (78%) patients had received prior treatments, including erythropoiesis stimulating agents in 6 (67%). Baseline international MDS prognostic scoring system scores were intermediate-1 (n=7) and intermediate-2 (n=2). Karyotype was normal in all but one patient with loss of Y chromosome. Drug activity Median duration of treatment with imetelstat was 13.7 months (range 6.6-17.9). Three (38%) patients achieved transfusion-independence (TI) during treatment, defined as not requiring transfusions for at least 8 weeks; 2 had RARS and one RARS-T. The median time to TI was 11 weeks (range 9-14) and the median TI duration was 28 weeks (range 9-37). One of the 3 "TI" patients also had resolution of leukocytosis and thrombocytosis. A 4th patient experienced >50% decrease in palpable spleen size as well as a decrease in transfusion need. In addition, imetelstat induced normalization of counts in two additional patients with thrombocytosis and leukocytosis. As of 5/10/2015, 4 (44%) patients remain on active treatment and one death had been recorded (deemed unrelated to imetelstat). The 5 treatment discontinuations were: death during active therapy, discovery of second malignancy, progression into acute leukemia and insufficient response (n=2). Safety Treatment-emergent grade 4 neutropenia and thrombocytopenia were seen in 2 (22%) and 1 (11%) patients, respectively; neutropenia, and thrombocytopenia were seen in 4 (44%), and 2 (22%) patients. Grade 3 anemia was seen in 6 (67%) of the patients, however baseline grade 2 anemia was noted in 2 (22%) and grade 3 in 3 (30%) patients. None of the grade ≥3 hematologic toxicities lasted ≥4 weeks.. The following grade 3 non-hematologic events occurred in 1 subject: aspiration, fatigue, and lipase increase and a patient with pre-existing cardiovascular disease history experienced a grade 5 heart failure. Treatment-emergent liver function test abnormalities affected: ALT (grade 1 56%/grade 2 11%), AST (grade 1 56%/grade 2 11%), ALP (grade 1 33%), and total bilirubin (grade 2 11%). For patients that discontinued treatment with imetelstat, these events were mostly reversible. Mutation studies Patients were screened for mutations involving JAK2, SF3B1, U2AF1 and SRSF2. Three patients were mutated for JAK2, 7 for SF3B1 (4 K700E, 2 H662Q, one K666N) and one for U2AF1 (Q157P). All three patients with "TI" (H662Q, K700E, K666N) and the 4th patient with spleen response (K700E) were SF3B1mutated. Post-treatment analysis showed no effect of imetelstat on mutations. Conclusions Treatment with imetelstat may offer clinical benefit in patients with RARS or RARS-T with generally acceptable safety profile and warrants further clinical investigation. Disclosures Al-Kali: Celgene: Research Funding. Wan:Janssen Research & Development: Employment, Equity Ownership.