Prognosis and immunotherapy efficacy in dMMR&MSS colorectal cancer patients and an MSI status predicting model.

The inconsistency between mismatch repair (MMR) protein immunohistochemistry (IHC) and microsatellite instability PCR (MSI-PCR) methods has been widely reported. We aim to investigate the prognosis and the effect of immunotherapy in dMMR by IHC but MSS by MSI-PCR (dMMR&MSS) colorectal cancer (CRC) patients. A microsatellite instability (MSI) predicting model was established to help find dMMR&MSS patients. MMR and MSI states were detected by the IHC and MSI-PCR in 1622 CRC patients (ZS6Y-1 cohort). Logistic regression analysis was used to screen clinical features to construct an MSI-predicting nomogram. We propose a new nomogram-based assay to find patients with dMMR&MSS, in which the MSI-PCR assay only detects dMMR patients with MSS predictive results. We applied the new strategy to a random cohort of 248 CRC patients (ZS6Y-2 cohort). The consistency of MMR IHC and MSI-PCR in the ZS6Y-1 cohort was 95.7% (1553/1622). Both pMMR&MSS and dMMR&MSS groups experienced significantly shorter overall survival (OS) than those in dMMR by IHC and MSI-H by MSI-PCR (dMMR&MSI-H) group (hazard ratio [HR] = 2.429, 95% confidence interval [CI]: 1.89-3.116, p < .01; HR = 21.96, 95% CI: 7.24-66.61, p < .01). The dMMR&MSS group experienced shorter OS than the pMMR&MSS group, but the difference did not reach significance (log rank test, p = .0686). In the immunotherapy group, the progression-free survival of dMMR&MSS patients was significantly shorter than that of dMMR&MSI-H patients (HR = 13.83, 95% CI: 1.508-126.8, p < .05). The ZS6Y-MSI-Pre nomogram (C-index = 0.816, 95% CI: 0.792-0.841, already online) found 66% (2/3) dMMR&MSS patients in the ZS6Y-2 cohort. There are significant differences in OS and immunotherapy effect between dMMR&MSI-H and dMMR&MSS patients. Our prediction model provides an economical way to screen dMMR&MSS patients.

Testing region selection and prognostic analysis of MLH1 promoter methylation in colorectal cancer in China.

Background: MLH1 promoter methylation analysis is recommended in screening for Lynch syndrome (LS) in patients with MLH1-deficient colorectal cancer (CRC). The study aims to identify specific methylation regions in the MLH1 promoter and to evaluate the clinicopathologic characteristics of and prognosis for patients with MLH1 methylation. Methods: A total of 580 CRC cases were included. The DNA mismatch repair (MMR) protein expression was assessed by using immunohistochemistry (IHC). The methylation status of the Regions A, B, C, D, and E in the MLH1 promoter was tested by using bisulfite sequencing PCR. The specificities of the five regions were calculated. Associations between MLH1 methylation and clinicopathologic characteristics were evaluated. Kaplan-Meier analyses for overall survival (OS) were carried out. Results: In 580 CRC cases, the specificities of the methylation test in Regions D and E were both 97.8%. In the MLH1-deficient CRCs, the frequencies of MLH1 methylation and BRAFV600E mutation were 52.6% and 14.6%, respectively; BRAFV600E mutation occurred in 27.7% of patients with MLH1-methylated CRC. In the MMR-deficient patients, compared with MLH1 unmethylation, MLH1 methylation was more common in patients who were aged ≥50 years, female, had no family history of LS-related tumors, and had tumors located at the right colon. In the MMR-deficient patients, the MLH1-methylated cases had lower OS rates than the unmethylated cases with a family history of LS-related tumors (P = 0.047). Conclusions: Regions D and E in the MLH1 promoter are recommended for determining the MLH1 methylation status in screening for LS in MLH1-deficient CRC. In MMR-deficient patients, the MLH1-methylated cases had a worse OS than the unmethylated cases with a family history of LS-related cancer.

Head-to-head comparative study: evaluating three panels for MSI-PCR testing in patients with colorectal and gastric cancer.

AIMS: Due to the lack of large clinical cohorts in the Chinese populations with colorectal cancer (CRC) and gastric cancer (GC), there is no consensus among the preferred panel for microsatellite instability (MSI)-PCR testing. This study aims to evaluate a more appropriate panel. METHODS: We tested the MSI status of 2572 patients with CRC and GC using the NCI panel and 2 mononucleotide panels (5 and 6 mononucleotide panels). Immunohistochemistry (IHC) was employed to perform mismatch repair protein testing in 1976 samples. RESULTS: We collected 2572 patients with CRC and GC. The National Cancer Institute (NCI) panel failed to detect 13 cases. Of the 2559 cases that received results from all three panels, 2544 showed consistent results. In the remaining 15 cases, 9 showed discrepancies between MSI-H and MSI-L, and 6 showed discrepancies between MSI-L and microsatellite stability (MSS). The misdiagnosis rate of MSI-L was significantly lower in two mononucleotide panels than in the NCI panel (12.5% vs 87.5%, p=0.010) in CRC. In patients with GC, only the NCI panel detected three MSI-L cases, while the results of the two mononucleotide panels were one MSI-H and two MSS. Based on their IHC results, the MSI-L misdiagnosis rate of the NCI panel was 33.3%. Furthermore, compared with two mononucleotide panels, the NCI panel had a much lower rate of all loci instability in CRC (90.8% and 90.3% vs 25.2%) and GC (89.5% and 89.5% vs 12.0%). CONCLUSION: In Chinese patients with CRC and GC, the five and six mononucleotide panels have advantages for detecting MSI over the NCI panel.

The Spectrum, Tendency and Predictive Value of PIK3CA Mutation in Chinese Colorectal Cancer Patients.

BACKGROUND: PIK3CA is a high-frequency mutation gene in colorectal cancer, while its prognostic value remains unclear. This study evaluated the mutation tendency, spectrum, prognosis power and predictive power in cetuximab treatment of PIK3CA in Chinese CRC cohort. METHODS: The PIK3CA exon 9 and 20 status of 5763 CRC patients was detected with Sanger sequencing and a high-resolution melting test. Clinicopathological characteristics of 5733 patients were analyzed. Kaplan-Meier method and nomogram were used to evaluate the overall survival curve and disease recurrence, respectively. RESULTS: Fifty-eight types of mutations in 13.4% (771/5733) of the patients were detected. From 2014 to 2018, the mutation rate of PIK3CA increased from 11.0% to 13.5%. At stage IV, exon 20 mutated patients suffered shorter overall survival time than wild-type patients (multivariate COX regression analysis, HR = 2.72, 95% CIs = 1.47-5.09; p-value = 0.012). At stage III, PIK3CA mutated patients were more likely to relapse (multivariate Logistic regression analysis, exon 9: OR = 2.54, 95% CI = 1.34-4.73, p = 0.003; exon 20: OR = 3.89, 95% CI = 1.66-9.10, p = 0.002). The concordance index of the nomogram for predicting the recurrence risk of stage III patients was 0.685. After cetuximab treatment, the median PFS of PIK3CA exon 9 wild-type patients (n = 9) and mutant patients (n = 5) did not reach a significant difference (3.6 months vs. 2.3 months, Log-rank test, p-value = 0.513). CONCLUSIONS: We found that PIK3CA mutation was an adverse predictive marker for the overall survival of stage IV patients and recurrence of stage III patients, respectively. Further more, we suggested that PIK3CA exon 9 mutations are not negative predictors of cetuximab treatment in KRAS, NRAS, and BRAF wild-type mCRC patients.

Complete plastome sequence of Erythropalum scandens (Erythropalaceae), an edible and medicinally important liana in China.

Erythropalum scandens (Erythropalaceae, Santalales) is a large liana distributed in alluvial and riparian forests of Southeast Asia. Here we report and characterize the complete plastid genome sequence of E. scandens in an effort to provide genomic resources useful for developing its medicinal and edible value. The complete plastome is 156,154 bp in length and contains the typical structure and gene content of angiosperm plastomes, including two Inverted Repeat (IR) regions of 26,394 bp, a large single-copy (LSC) region of 84,799 bp and a small single-copy (SSC) region of 18,567 bp. The plastome contains 112 genes, consisting of 79 unique protein-coding genes, 29 unique tRNA genes and four unique rRNA genes. The overall A/T content in the plastome of E. scandens is 62.01%. Phylogenetic analyses were performed using the entire plastome, including genes, spacers and introns, which recovered E. scandens as sister to remaining Santalales with complete plastome sequences.

Complete chloroplast genome sequence of Heritiera angustata (Malvaceae): an endangered plant species.

Heritiera angustata (Malvaceae) is an evergreen tree distributed in the Chinese provinces of Hainan and Yunnan and in Cambodia. In China, it is listed as 'Endangered' (EN) China Red List of Higher Plants, although it is not protected by law. The complete chloroplast (cp) genome sequence of this threatened species is reported in this study, based on high-throughput sequencing (Illumina). The complete cp genome is 168, 953 bp in length, containing a pair of inverted repeat regions (IRs) of 34,491 bp, a large single copy (LSC) region of 89,054 bp, and a small single copy (SSC) region of 10,917 bp. The cp genome contains 129 genes, consisting of 85 protein-coding genes, 36 tRNA genes and eight rRNA genes. The overall AT content in the cp genome of H. angustata is 63.2%. The phylogenetic analyses indicate that there is a close relationship between H. angustata and Firmiana pulcherrima.

The complete chloroplast genome sequence of Melastoma candidum (Melastomataceae).

The plant genus Melastoma is comprised of members estimated to have formed through recent species radiation. Natural hybridization among member species further complicates taxonomy within the genus. Herein, we report the complete chloroplast genome of M. candidum, assembled from partial data obtained from a parallel whole-genome Illumina paired-end sequencing effort on the species. The chloroplast genome was 156,682 bp in length, with a large single-copy (LSC) region of 86,084 bp, a small single-copy (SSC) region of 17,094 bp, separated by two inverted repeat (IR) regions of 26,752 bp each. It was predicted to contain a total of 129 genes, with an overall GC content of 37.17%. Phylogenetic analysis placed M. candidum in the same clade as species within the Melastomeae tribe of Melastomataceae.

The complete chloroplast genome sequence of Barthea barthei (Melastomataceae), a shrub endemic to southern China.

The plant genus Barthea is monotypic, comprising of only a single species (Barthea barthei), and is endemic to southern China. In this study, we report the complete chloroplast genome of B. barthei, assembled from whole-genome high-throughput sequencing data, as a resource for future studies on the taxonomy and evolution of Barthea. The chloroplast genome was 155,951 bp in length, with a large single-copy (LSC) region of 85,882 bp, a small single-copy (SSC) region of 16,445 bp, separated by two inverted repeat (IR) regions of 26,812 bp each. It was predicted to contain a total of 130 genes, with an overall GC content of 36.99%. Phylogenetic analysis placed B. barthei closest to Opisthocentra sp. in Melastomataceae.