Monitoring of postoperative neutrophil-to-lymphocyte ratio, D-dimer, and CA153 in: Diagnostic value for recurrent and metastatic breast cancer

ObjectiveThis stydy aims to assess the value of monitoring of postoperative neutrophil-to-lymphocyte ratio (NLR), D-dimer, and carbohydrate antigen 153 (CA153) for diagnosis of breast cancer (BC) recurrence and metastasis.Materials/MethodsA cohort of 252 BC patients who underwent surgery at the First Affiliated Hospital of Anhui Medical University between August 2008 and August 2018 were enrolled in this retrospective study. All patients were examined during outpatient follow-ups every 3 months for 5 years postoperation and every 6 months thereafter. Recurrence or metastasis was recorded for 131 patients but not for the remaining 121. Retrospective analysis of hematological parameters and clinicopathological characteristics allowed comparison between the two groups and evaluation of these parameters for the recurrent and metastatic patients.ResultsLymph node metastasis, higher tumor node metastasis (TNM) staging, and higher histological grade correlated with BC recurrence and metastasis (p < 0.05). Statistical differences were found in absolute neutrophil count (ANC), absolute lymphocyte count (ALC), CEA, CA153, D-dimer, NLR, platelet-to-lymphocyte ratio (PLR), and monocyte-to-lymphocyte ratio (MLR) between the recurrent and metastatic and control groups (p < 0.05). Logistic regression analysis showed that CA153, D-dimer, NLR, and TNM staging were risk factors for BC recurrence and metastasis (p < 0.05). Combined values for the NLR, D-dimer, and CA153 had good diagnostic values, giving the highest area under the curve (AUC) of 0.913. High NLR, D-dimer, and CA153 values were significantly associated with recurrence and metastasis at multiple sites, lymph node metastasis, and higher TNM staging (p < 0.05). Patients with high CA153 were more likely to have bone metastases (p < 0.05), and those with high D-dimer were prone to lung metastasis (p < 0.05). With the increasing length of the postoperative period, the possibility of liver metastases gradually decreased, while that of chest wall recurrence gradually increased (p < 0.05).ConclusionMonitoring postoperative NLR, D-dimer, and CA153 is a convenient, practical method for diagnosing BC recurrence and metastasis. These metrics have good predictive value in terms of sites of recurrence and metastasis and the likelihood of multiple metastases

Assessing the clinical utility of cancer genomic and proteomic data across tumor types

Molecular profiling of tumors promises to advance the clinical management of cancer, but the benefits of integrating molecular data with traditional clinical variables have not been systematically studied. Here we retrospectively predict patient survival using diverse molecular data (somatic copy-number alteration, DNA methylation and mRNA, miRNA and protein expression) from 953 samples of four cancer types from The Cancer Genome Atlas project. We found that incorporating molecular data with clinical variables yielded statistically significantly improved predictions (FDR < 0.05) for three cancers but those quantitative gains were limited (2.2–23.9%). Additional analyses revealed little predictive power across tumor types except for one case. In clinically relevant genes, we identified 10,281 somatic alterations across 12 cancer types in 2,928 of 3,277 patients (89.4%), many of which would not be revealed in single-tumor analyses. Our study provides a starting point and resources, including an open-access model evaluation platform, for building reliable prognostic and therapeutic strategies that incorporate molecular data

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

BM-Map: an efficient software package for accurately allocating multireads of RNA-sequencing data

Abstract Background RNA sequencing (RNA-seq) has become a major tool for biomedical research. A key step in analyzing RNA-seq data is to infer the origin of short reads in the source genome, and for this purpose, many read alignment/mapping software programs have been developed. Usually, the majority of mappable reads can be mapped to one unambiguous genomic location, and these reads are called unique reads. However, a considerable proportion of mappable reads can be aligned to more than one genomic location with the same or similar fidelities, and they are called "multireads". Allocating these multireads is challenging but critical for interpreting RNA-seq data. We recently developed a Bayesian stochastic model that allocates multireads more accurately than alternative methods (Ji et al. Biometrics 2011). Results In order to serve a greater biological community, we have implemented this method in a stand-alone, efficient, and user-friendly software package, BM-Map. BM-Map takes SAM (Sequence Alignment/Map), the most popular read alignment format, as the standard input; then based on the Bayesian model, it calculates mapping probabilities of multireads for competing genomic loci; and BM-Map generates the output by adding mapping probabilities to the original SAM file so that users can easily perform downstream analyses. The program is available in three common operating systems, Linux, Mac and PC. Moreover, we have built a dedicated website, http://bioinformatics.mdanderson.org/main/BM-Map, which includes free downloads, detailed tutorials and illustration examples. Conclusions We have developed a stand-alone, efficient, and user-friendly software package for accurately allocating multireads, which is an important addition to our previous methodology paper. We believe that this bioinformatics tool will greatly help RNA-seq and related applications reach their full potential in life science research.</p

Expression of Vitis amurensis VaERF20 in Arabidopsis thaliana Improves Resistance to Botrytis cinerea and Pseudomonas syringae pv. Tomato DC3000

Ethylene response factor (ERF) transcription factors play important roles in regulating immune responses in plants. In our study, we characterized a member of the ERF transcription factor family, VaERF20, from the Chinese wild Vitis genotype, V. amurensis Rupr “Shuangyou”. Phylogenetic analysis indicated that VaERF20 belongs to group IXc of the ERF family, in which many members are known to contribute to fighting pathogen infection. Consistent with this, expression of VaERF20 was induced by treatment with the necrotrophic fungal pathogen Botrytis cinerea (B. cinerea) in “Shuangyou” and V. vinifera “Red Globe”. Arabidopsis thaliana plants over-expressing VaERF20 displayed enhanced resistance to B. cinerea and the bacterium Pseudomonas syringae pv. tomato (Pst) DC3000. Patterns of pathogen-induced reactive oxygen species (ROS) accumulation were entirely distinct in B. cinerea and PstDC3000 inoculated plants. Examples of both salicylic acid (SA) and jasmonic acid/ethylene (JA/ET) responsive defense genes were up-regulated after B. cinerea and PstDC3000 inoculation of the VaERF20-overexpressing transgenic A. thaliana plants. Evidence of pattern-triggered immunity (PTI), callose accumulation and stomatal defense, together with increased expression of PTI genes, was also greater in the transgenic lines. These data indicate that VaERF20 participates in various signal transduction pathways and acts as an inducer of immune responses

Non-thermal plasma-treated melatonin inhibits the biological activity of HCC cells by increasing intracellular ROS levels and reducing RRM2 expression

Non-thermal plasma (NTP) is thought to have a cytotoxic effect on tumor cells. Although its application in cancer therapy has shown considerable promise, the current understanding of its mechanism of action and cellular responses remains incomplete. Furthermore, the use of melatonin (MEL) as an adjuvant anticancer drug remains unexplored. In this study, we found that NTP assists MEL in promoting apoptosis, delaying cell cycle progression, and inhibiting cell invasion and migration in hepatocellular carcinoma (HCC) cells. This mechanism may be associated with the regulation of intracellular reactive oxygen species levels and ribonucleotide reductase regulatory subunit M2 expression. Our findings confirm the pharmacological role of MEL and the adjuvant value of NTP, emphasizing their potential in combination therapy for HCC. Our study may have important implications for the development of new approaches for HCC treatment