Genome-wide identification and characterization of the AP2/ERF gene family in loblolly pine (Pinus taeda L.).

The loblolly pine (Pinus taeda L.) is one of the most profitable forest species worldwide owing to its quick growth, high wood yields, and strong adaptability. The AP2/ERF gene family plays a widespread role in the physiological processes of plant defense responses and the biosynthesis of metabolites. Nevertheless, there are no reports on this gene family in loblolly pine (P. taeda). In this study, a total of 303 members of the AP2/ERF gene family were identified. Through multiple sequence alignment and phylogenetic analysis, they were classified into four subfamilies, including AP2 (34), RAV (17), ERF (251), and Soloist (1). An analysis of the conservation domains, conserved motifs, and gene structure revealed that every PtAP2/ERF transcription factor (TF) had at least one AP2 domain. While evolutionary conservation was displayed within the same subfamilies, the distribution of conserved domains, conserved motifs, and gene architectures varied between subfamilies. Cis-element analysis revealed abundant light-responsive elements, phytohormone-responsive elements, and stress-responsive elements in the promoter of the PtAP2/ERF genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of potential target genes showed that the AP2/ERF gene family might play a critical role in plant growth and development, the response to environmental stresses, and metabolite biosynthesis. Utilizing quantitative real-time PCR (qRT-PCR), we examined the expression patterns of 10 randomly selected genes from Group IX after 6 h of treatments with mechanical injury, ethephon (Eth), and methyl jasmonate (MeJA). The AP2/ERF gene family in the loblolly pine was systematically analyzed for the first time in this study, offering a theoretical basis for exploring the functions and applications of AP2/ERF genes.

Decoding the specificity of m6A RNA methylation and its implication in cancer therapy.

N6-methyladenosine (m6A) is the most abundant endogenous modification in eukaryotic RNAs. It plays important roles in various biological processes and diseases, including cancers. More and more studies have revealed that the deposition of m6A is specifically regulated in a context-dependent manner. Here, we review the diverse mechanisms that determine the topology of m6A along RNAs and the cell-type-specific m6A methylomes. The exon junction complex (EJC) as well as histone modifications play important roles in determining the topological distribution of m6A along nascent RNAs, while the transcription factors and RNA-binding proteins, which usually bind specific DNAs and RNAs in a cell-type-specific manner, largely account for the cell-type-specific m6A methylomes. Due to the lack of specificity of m6A writers and readers, there are still challenges to target the core m6A machinery for cancer therapies. Therefore, understanding the mechanisms underlying the specificity of m6A modifications in cancers would be important for future cancer therapies through m6A intervention.

Experimental study on failure characteristics and rheological properties of pillar-like rock samples with different shapes.

The stability of coal pillar is extremely important to the control of rock strata movement and surface subsidence. It is of great significance for mining design to analyze the stability and failure characteristics of coal and rock pillars left after mining and to study the failure characteristics and rheological properties of coal and rock with different shapes. In this paper, based on uniaxial compression and rheological tests on rock samples, the rheological properties of rock samples with different shapes were discussed by using the nonlinear theoretical mechanics and damage theory, and the rheological mechanical characteristics of coarse yellow sandstone samples under the action of different free surface areas and the same loading contact area were investigated by means of experimental research, theoretical analysis and numerical simulation. The following conclusions were drawn: the failure characteristics and dynamic change process of rock samples with different shapes under the same loading contact area are obtained by uniaxial compression test and multi-stage rheological loading. The uniaxial compressive strengths of rock samples with the same loading contact surface area and different free surface areas are inversely proportional to their free surface areas. For the round sample, the stress level in the rheological test is obviously lower than the instantaneous peak uniaxial compression strength, while for the other samples, the stress level in the rheological test is close to the instantaneous peak uniaxial compression strength. For rock all these samples, both the ratio of steady-state rheological time to final failure time and the deformation degree decrease with the increase of free surface area.

Green coal mining under buildings by overburden grout injection for coalmine sustainable development of central China.

Coal will occupy the main position in China's energy structure for a long time, and the negative externalities of its exploitation have a serious impact on the ground surface and its appurtenances. With the proposal of the dual carbon strategy, the coal-based energy determines that green and safe coal mining should be the priority direction of China's energy development. Taking Xinyi coalmine, which is mined in unstable coal seams with large mining depth, as the research area, the surface response characteristic and subsidence law under the different mining degrees were clarified. Meanwhile, the damage mechanism of buildings was revealed, which was from no obvious damage to Grade Ⅳ under the extremely insufficient mining to subcritical mining. Based on the sustainable development and green production in coalmines, the overburden grout injection technique under buildings that does not affect the normal production was proposed, and its technical principle was described. A weighted grey relational analysis model was established, and obtained that the panel width was the main factor affecting the overburden failure height under subcritical mining. According to the definition of overburden failure degree proposed by the author, the feasibility of overburden grout injection technique under buildings was analyzed and the key parameters, such as slurry diffusion radius, borehole position and depth, grouting system and technology, were determined and successfully applied. The engineering application shows that the maximum surface subsidence after grouting is 253 mm, and the building damage is within the Grade I. Meanwhile, 5.82 Mt of coal resources under the buildings have been liberated, which realizes high quality coal mining, low environmental damage, green and low-carbon, and also provides a reference for the sustainable development of coal enterprises, especially for the exhausted coalmines that recover coal pillars.

Stiffness of gangue backfilling body in goaf and its influence mechanism on rock strata control and stress evolution in gangue backfill mining.

To study the influence mechanism of gangue backfilling material (GBM) with different particle sizes on overburden deformation, the particle movement characteristics and the mechanism of stiffness difference with different particle sizes of GBM were analysed by physical compression and particle flow numerical simulations. Then, combined with a similar material simulation method, the deformation characteristics of roof overburden and the evolution process of floor stress in backfill mining with backfilling bodies of different stiffness levels were studied. The results indicate that the subsidence decreased monotonously with a decrease in the particle size, and the stiffness of the GBM increased significantly under the same vertical load. The small-particle gangue moved downward in the layered law under the same load conditions, while the large-particle gangue moved downward through rotation, rubbing, crushing, and filling interaction processes. In the treatment of goaf by the backfilling method, the entire process of overlying strata movement mainly experienced bending, micro-fracture, separation, compaction, and new fracture, and the anti-deformation capacity of the backfilling body directly determined the deformation and movement of the overburden strata in a goaf. In the backfilling method, the greater the stiffness of the filling body, the smaller the advanced support pressure, and the more effective it was to inhibit pressure relief from the floor.

Plasma cell subtypes analyzed using artificial intelligence algorithm for predicting biochemical recurrence, immune escape potential, and immunotherapy response of prostate cancer.

Background: Plasma cells as an important component of immune microenvironment plays a crucial role in immune escape and are closely related to immune therapy response. However, its role for prostate cancer is rarely understood. In this study, we intend to investigate the value of a new plasma cell molecular subtype for predicting the biochemical recurrence, immune escape and immunotherapy response in prostate cancer. Methods: Gene expression and clinicopathological data were collected from 481 prostate cancer patients in the Cancer Genome Atlas. Then, the immune characteristics of the patients were analyzed based on plasma cell infiltration fractions. The unsupervised clustering based machine learning algorithm was used to identify the molecular subtypes of the plasma cell. And the characteristic genes of plasma cell subtypes were screened out by three types of machine learning models to establish an artificial neural network for predicting plasma cell subtypes. Finally, the prediction artificial neural network of plasma cell infiltration subtypes was validated in an independent cohort of 449 prostate cancer patients from the Gene Expression Omnibus. Results: The plasma cell fraction in prostate cancer was significantly decreased in tumors with high T stage, high Gleason score and lymph node metastasis. In addition, low plasma cell fraction patients had a higher risk of biochemical recurrence. Based on the differential genes of plasma cells, plasma cell infiltration status of PCa patients were divided into two independent molecular subtypes(subtype 1 and subtype 2). Subtype 1 tends to be immunosuppressive plasma cells infiltrating to the PCa region, with a higher likelihood of biochemical recurrence, more active immune microenvironment, and stronger immune escape potential, leading to a poor response to immunotherapy. Subsequently, 10 characteristic genes of plasma cell subtype were screened out by three machine learning algorithms. Finally, an artificial neural network was constructed by those 10 genes to predict the plasma cell subtype of new patients. This artificial neural network was validated in an independent validation set, and the similar results were gained. Conclusions: Plasma cell infiltration subtypes could provide a potent prognostic predictor for prostate cancer and be an option for potential responders to prostate cancer immunotherapy.

Dynamic Landscapes of tRNA Transcriptomes and Translatomes in Diverse Mouse Tissues.

Although the function of tRNA in the translational process is well established, it remains controversial whether tRNA abundance is tightly associated with translational efficiency (TE) in mammals. Moreover, how critically the expression of tRNAs contributes to the establishment of tissue-specific proteomes in mammals has not been well addressed. Here, we measured both tRNA expression using demethylase-tRNA sequencing (DM-tRNA-seq) and TE of mRNAs using ribosome-tagging sequencing (RiboTag-seq) in the brain, heart, and testis of mice. Remarkable variation in the expression of tRNA isodecoders was observed among different tissues. When the statistical effect of isodecoder-grouping on reducing variations is considered through permutating the anticodons, we observed an expected reduction in the variation of anticodon expression across all samples, an unexpected smaller variation of anticodon usage bias, and an unexpected larger variation of tRNA isotype expression at amino acid level. Regardless of whether or not they share the same anticodons, the isodecoders encoding the same amino acids are co-expressed across different tissues. Based on the expression of tRNAs and the TE of mRNAs, we find that the tRNA adaptation index (tAI) and TE are significantly correlated in the same tissues but not between tissues; and tRNA expression and the amino acid composition of translating peptides are positively correlated in the same tissues but not between tissues. We therefore hypothesize that the tissue-specific expression of tRNAs might be due to post-transcriptional mechanisms. This study provides a resource for tRNA and translation studies, as well as novel insights into the dynamics of tRNAs and their roles in translational regulation.

Efficient resin production using stimulant pastes in Pinus elliottii × P. caribaea families.

To address the increasing labor cost of resin tapping, more efficient methods for resin tapping need to be developed. This study aimed to evaluate the features of resinosis as affected by stimulant pastes in Pinus elliottii × P. caribaea, which is also one of the predominant resin-producing species hybrids in South China. The resin yields and resin compositions were assessed in 33 P. elliottii × P. caribaea F1 families, with the application of four kinds of chemical stimulants, potassium (K2SO4) paste, naphthalene acetic acid (NAA) paste, benzoic acid (BA) paste and 2-chloroethylphosphonic acid (CEPA) paste. Our results showed that all four pastes significantly increased the resin yield by at least 20% at each tapping, and 3- to fivefold increases were detected at the beginning of each year. The correlations between resin yield and growth at each tapping ranged from uncorrelated to moderately positively correlated, indicating that resin yield was mostly but not always determined by tree size. The concentration of each resin component did not change with the stimulant applications. In P. elliottii × P. caribaea, selecting a larger tree diameter at breast height and employing the chemical stimulants at the first several tapping rounds are efficient tapping procedures. Moreover, the K2SO4-based stimulant can be recommended considering its promoting effects on resin yield and the low cost of the chemicals required to produce it.

Comprehensive signature analysis of drug metabolism differences in the White, Black and Asian prostate cancer patients.

The drug response sensitivity and related prognosis of prostate cancer varied from races, while the original mechanism remains rarely understood. In this study, the comprehensive signature including transcriptomics, epigenome and single nucleotide polymorphisms (SNPs) of 485 PCa cases- including 415 Whites, 58 Blacks and 12 Asians from the TCGA database were analyzed to investigate the drug metabolism differences between races. We found that Blacks and Whites had a more prominent drug metabolism, cytotoxic therapy resistance, and endocrine therapy resistance than Asians, while Whites were more prominent in drug metabolism, cytotoxic therapy resistance and endocrine therapy resistance than Blacks. Subsequently, the targeted regulation analysis indicated that the racial differences in cytotoxic therapy resistance, endocrine therapy resistance, might originate from drug metabolisms, and 19 drug metabolism-related core genes were confirmed in the multi-omics network for subsequent analysis. Furthermore, we verified that CYP1A1, CYP3A4, CYP2B6, UGT2B17, UGT2B7, UGT1A8, UGT2B11, GAS5, SNHG6, XIST significantly affected antineoplastic drugs sensitivities in PCa cell lines, and these genes also showed good predictive efficiency of drug response and treatment outcomes for PCa in this cohort of patients. These findings revealed a comprehensive signature of drug metabolism differences for the Whites, Blacks and Asians, and it may provide some evidence for making individualized treatment strategies.

Prediction Model Combining Clinical and MR Data for Diagnosis of Lymph Node Metastasis in Patients With Rectal Cancer.

BACKGROUND: Determining the status of lymph node (LN) metastasis in rectal cancer patients preoperatively is crucial for the treatment option. However, the diagnostic accuracy of current imaging methods is low. PURPOSE: To develop and test a model for predicting metastatic LNs of rectal cancer patients based on clinical data and MR images to improve the diagnosis of metastatic LNs. STUDY TYPE: Retrospective. SUBJECTS: In all, 341 patients with histologically confirmed rectal cancer were divided into one training set (120 cases) and three validation sets (69, 103, 49 cases). FIELD STRENGTH/SEQUENCE: 3.0T, axial and sagittal T2 -weighted turbo spin echo and diffusion-weighted imaging (b = 0 s/mm2 , 800 s/mm2 ) ASSESSMENT: In the training dataset, univariate logistic regression was used to identify the clinical factors (age, gender, and tumor markers) and MR data that correlated with LN metastasis. Then we developed a prediction model with these factors by multiple logistic regression analysis. The accuracy of the model was verified using three validation sets and compared with the traditional MRI method. STATISTICAL TESTS: Univariate and multivariate logistic regression. The area under the curve (AUC) value was used to quantify the diagnostic accuracy of the model. RESULTS: Eight factors (CEA, CA199, ADCmean, mriT stage, mriN stage, CRM, EMVI, and differentiation degree) were significantly associated with LN metastasis in rectal cancer patients (P<0.1). In the training set (120) and the three validation sets (69, 103, 49), the AUC values of the model were much higher than the diagnosis by MR alone (training set, 0.902 vs. 0.580; first validation set, 0.789 vs. 0.743; second validation set, 0.774 vs. 0.573; third validation set, 0.761 vs. 0.524). DATA CONCLUSION: For the diagnosis of metastatic LNs in rectal cancer patients, our proposed logistic regression model, combining clinical and MR data, demonstrated higher diagnostic efficiency than MRI alone. LEVEL OF EVIDENCE: 4 TECHNICAL EFFICACY STAGE: 2.

An absolute human stemness index associated with oncogenic dedifferentiation.

The progression of cancer is accompanied by the acquisition of stemness features. Many stemness evaluation methods based on transcriptional profiles have been presented to reveal the relationship between stemness and cancer. However, instead of absolute stemness index values-the values with certain range-these methods gave the values without range, which makes them unable to intuitively evaluate the stemness. Besides, these indices were based on the absolute expression values of genes, which were found to be seriously influenced by batch effects and the composition of samples in the dataset. Recently, we have showed that the signatures based on the relative expression orderings (REOs) of gene pairs within a sample were highly robust against these factors, which makes that the REO-based signatures have been stably applied in the evaluations of the continuous scores with certain range. Here, we provided an absolute REO-based stemness index to evaluate the stemness. We found that this stemness index had higher correlation with the culture time of the differentiated stem cells than the previous stemness index. When applied to the cancer and normal tissue samples, the stemness index showed its significant difference between cancers and normal tissues and its ability to reveal the intratumor heterogeneity at stemness level. Importantly, higher stemness index was associated with poorer prognosis and greater oncogenic dedifferentiation reflected by histological grade. All results showed the capability of the REO-based stemness index to assist the assignment of tumor grade and its potential therapeutic and diagnostic implications.

A Qualitative Transcriptional Signature for Predicting CpG Island Methylator Phenotype Status of the Right-Sided Colon Cancer.

A part of colorectal cancer which is characterized by simultaneous numerous hypermethylation CpG islands sites is defined as CpG island methylator phenotype (CIMP) status. Stage II and III CIMP-positive (CIMP+) right-sided colon cancer (RCC) patients have a better prognosis than CIMP-negative (CIMP-) RCC treated with surgery alone. However, there is no gold standard available in defining CIMP status. In this work, we selected the gene pairs whose relative expression orderings (REOs) were associated with the CIMP status, to develop a qualitative transcriptional signature to individually predict CIMP status for stage II and III RCC. Based on the REOs of gene pairs, a signature composed of 19 gene pairs was developed to predict the CIMP status of RCC through a feature selection process. A sample is predicted as CIMP+ when the gene expression orderings of at least 12 gene pairs vote for CIMP+; otherwise the CIMP-. The difference of prognosis between the predicted CIMP+ and CIMP- groups was more significantly different than the original CIMP status groups. There were more differential methylation and expression characteristics between the two predicted groups. The hierarchical clustering analysis showed that the signature could perform better for predicting CIMP status of RCC than current methods. In conclusion, the qualitative transcriptional signature for classifying CIMP status at the individualized level can predict outcome and guide therapy for RCC patients.

A Qualitative Transcriptional Signature for Predicting Prognosis and Response to Bevacizumab in Metastatic Colorectal Cancer.

Bevacizumab is the molecular-targeted agent used for the antiangiogenic therapy of metastatic colorectal cancer. But some patients are resistant to bevacizumab, it needs an effective biomarker to predict the prognosis and responses of metastatic colorectal cancer (mCRC) to bevacizumab therapy. In this work, we developed a qualitative transcriptional signature to individually predict the response of bevacizumab in patients with mCRC. First, using mCRC samples treated with bevacizumab, we detected differentially expressed genes between response and nonresponse groups. Then, the gene pairs, consisting of at least one differentially expressed gene, with stable relative expression orderings in the response samples but reversal stable relative expression orderings in the nonresponse samples were identified, denoted as pairs-bevacizumab. Similarly, we screened the gene pairs significantly associated with primary tumor locations, donated as pairs-LR. Among the overlapped gene pairs between the pairs-bevacizumab and pairs-LR, we adopted a feature selection process to extract gene pairs that reached the highest F-score for predicting bevacizumab response status in mCRC as the final gene pair signature (GPS), denoted as 64-GPS. In two independent datasets, the predicted response group showed significantly better overall survival than the nonresponse group (P = 6.00e-4 in GSE72970; P = 0.04 in TCGA). Genomic analyses showed that the predicted response group was characterized by frequent copy number alternations, whereas the nonresponse group was characterized by hypermutation. In conclusion, 64-GPS was an objective and robust predictive signature for patients with mCRC treated with bevacizumab, which could effectively assist in the decision of clinical therapy.

Qualitative Ras pathway signature for cetuximab therapy reveals resistant mechanism in colorectal cancer.

Cetuximab therapy, which heavily relies on the activation of Ras pathway, has been used in KRAS, NRAS, BRAF, and PIK3CA wild-type colorectal cancer (CRC) (Ras-normal). However, the response rate only reached 60%, due to false-negative mutation detection and mutation-like transcriptome features in wild-type patients. Herein, by integrating RNA-seq, microarray, and mutation data, we developed a Ras pathway signature by characterizing KRAS/NRAS/BRAF/PIK3CA mutations to identify the hidden nonresponders from the Ras-normal patients by mutation detection. Using public and in-house data of CRC patients treated with cetuximab, discovery of the signature could identify cetuximab-resistant samples from the Ras-normal samples. Cetuximab resistance-related genes, such as PTEN, were significantly and frequently mutated in the identified Ras-activated samples, whereas two cetuximab sensitivity-related genes, APC and TP53, showed comutation and significantly higher mutation frequencies in the remaining Ras-normal samples. Furthermore, all the NF1- and BCL2L1-mutated samples were identified as Ras-activated from the Ras-normal samples by the Ras pathway signature with significantly under-regulated expression. Genes co-expressed with the two genes were both involved in Ras signaling pathway, the out-of-control of which could be attributed by the genes' loss-of-function mutations. To improve the treatment of cetuximab in CRC, NF1 and BCL2L1 could be used as complementary detection technique to those applied in clinical. In conclusion, the proposed Ras pathway signature could identify the hidden CRC patients resistant to cetuximab therapy and help to reveal resistance mechanisms.

An Exon Signature to Estimate the Tumor Mutational Burden of Right-sided Colon Cancer Patients.

The clinical applicability of the whole-exome sequencing (WES) in estimating tumor mutational burden (TMB) is currently limited by high cost, time-consuming and tissue availability. And given to the differences in the mutational landscapes among different types of cancer, we aimed to develop a cancer-specific signature to estimate TMB for right-sided colon cancer patients (RCC). Using WES data of 315 RCC patients, we identified the exons in which the number of mutational sites of the coding DNA sequences associated with TMB through linear regression analysis. Then, among these exons, we extracted a signature composed by 102 exons (~0.13 Mbp) through a heuristic selection procedure. The TMB estimated by the signature was highly correlated with those calculated by WES in the discovery dataset (R2=0.9869) and three independent validation datasets (R2=0.9351, R2=0.8063 and R2=0.9527, respectively). And the performance of the signature was superior to a colorectal-specific TMB estimation model contained 22 genes (~0.24 Mbp). Moreover, between TMB-high and TMB-low RCC patients, there were significantly differences in the frequencies of microsatellite instability status, CpG island methylator phenotype, BRAF, KRAS and POLE/POLD1 mutation status (p<0.01). However, the performances of the signature in other types of cancer were dramatically degraded (left-sided colon cancer, R2=0.7849 and 0.9407, respectively; rectum, R2=0.5955 and R2=0.965, respectively; breast cancer, R2=0.8444; lung cancer, R2=0.5963), suggesting that it was necessary to develop cancer-specific TMB estimated signatures to estimate precisely the TMB in different types of cancer. In summary, we developed an exon signature that can accurately estimate TMB in RCC patients, and the cost and time required for the assessment of TMB can be considerably decreased, making it more suitable for blood and/or biopsy samples.

Predictive value of cadherin-11 for subsequent recurrence and progression in non-muscle invasive bladder cancer.

BACKGROUND: Cadherin-11 (CDH11) is a type II cadherin and reported to function as an oncogene in various cancers. Our present study aims to investigate the role of CDH11 in bladder cancer (BCA). METHODS: Bioinformatics analysis was performed in four independent microarray data including 56 non-muscle-invasive bladder cancer (NMIBC) and 132 muscle-invasive bladder cancer (MIBC) tissues from Gene Expression Omnibus to screen out differentially expressed genes. Next, we detected CDH11 expression in BCA specimens and cell lines by qPCR and western blotting assays. Immunohistochemical analyses were performed in 209 paraffin-embedded BCA samples and 30 adjacent normal bladder tissues. RESULTS: Bioinformatics analysis revealed that CDH11 had a higher expression level in MIBC tissues than in NMIBC, which was consistent with our clinical BCA specimens and cell lines at both mRNA and protein levels. Immunohistochemical analysis demonstrated that over-expression of CDH11 was closely related to the histological grade, pT status, tumour size and poor outcomes of BCA patients. What's more, CDH11 (area under curve (AUC) = 0.673 and 0.735) had a better predictive value than E-cadherin (AUC = 0.629 and 0.629) and a similar discrimination with the European Organization for Research and Treatment of Cancer (EORTC) score system (AUC = 0.719 and 0.667) in evaluating potential recurrence and progression of NMIBC. Moreover, combination of CDH11 and EORTC score system was the best predictive model in predicting recurrence of NMIBC (AUC = 0.779) among the three models. CONCLUSIONS: CDH11 was a reliable therapeutic target in BCA and a useful index to predict the possibilities of recurrence and progression in NMIBC patients.

Optimal Starting Age and Baseline Level for Repeat Tests: Economic Concerns of PSA Screening for Chinese Men - 10-Year Experience of a Single Center.

OBJECTIVE: To investigate the optimal age for the baseline serum prostate-specific antigen (PSA) test and for repeat screening and its economic burden in a single center in China. MATERIALS AND METHODS: 35,533 men with PSA screening were retrospectively enrolled in this study. Follow-ups were conducted in 1,586 men with PSA >4 ng/mL, and receiver-operating characteristic (ROC) curves were employed to investigate the optimal cutoffs. RESULTS: ROC analysis indicated that the optimal age for initial PSA screening was 57.5 years (AUC = 0.84), 62.5 years (AUC = 0.902), 60.5 years (AUC = 0.909), and 61.5 years (AUC = 0.890) for individuals with PSA >4 and >10 ng/mL, a diagnosis of prostate cancer (PCa), and clinically significant PCa defined as the focus events, respectively. For Chinese men aged 50-59, 60-69, and >70 years, the initial PSA levels of 1.305 ng/mL (AUC = 0.699), 1.975 ng/mL (AUC = 0.711), and 2.740 ng/mL (AUC = 0.720) might have a PSA velocity >0.75 ng/mL per year during the follow-up. In addition, the total cost amounts to CNY 13,609,260 in these cases, but only 60 of the 35,533 (0.17%) men gained benefit from PSA screening. CONCLUSION: In our opinion, the optimal starting age for initial PSA testing was 57.5 years. The necessity for repeat screening should be based on the first PSA level depending on age. A cost--benefit analysis should be included in population-based screening.

A qualitative transcriptional signature for determining the grade of colorectal adenocarcinoma.

Histological grading (HG) is an important prognostic factor of colorectal adenocarcinoma (CRAC): the high-grade CRAC patients have poorer prognosis after tumor resection. Especially, the high-grade stage II CRAC patients are recommended to receive adjuvant chemotherapy. Due to the subjective nature of HG assessment, it is difficult to achieve consistency among pathologists, which brings patients uncertain grading outcomes and inappropriate treatments. We developed a qualitative transcriptional signature based on the within-sample relative expression orderings (REOs) of gene pairs to discriminate high-grade and low-grade CRAC. Using the stage II-III CRAC samples, we detected gene pairs with stable REOs in the high-grade samples and reversal stable REOs in the low-grade samples, and retained the gene pairs whose specific REO patterns were significantly associated with the disease-free survival of patients by univariate Cox regression model. Then, we used a forward-backward searching procedure to extract gene pairs with the highest concordance index as the final grading signature. Finally, 9 gene pairs (9-GPS) were developed to divide CRAC patients into high-grade and low-grade groups. With the signature, there were more differential expression characteristics between reclassified high-grade and low-grade groups. Significant difference of prognosis between the classified two group patients could be seen in four independent datasets. Additionally, genomic analyses showed that the classified high-grade groups were characterized by hypermutation while classified low-grade groups were characterized by frequent copy number alternations. In conclusion, the 9-GPS can provide an objective and robust grading assessment for CRAC patients, which could assist clinical treatment decision.

Correction: A qualitative transcriptional signature for determining the grade of colorectal adenocarcinoma.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

A qualitative transcriptional signature for predicting microsatellite instability status of right-sided Colon Cancer.

BACKGROUND: Microsatellite instability (MSI) accounts for about 15% of colorectal cancer and is associated with prognosis. Today, MSI is usually detected by polymerase chain reaction amplification of specific microsatellite markers. However, the instability is identified by comparing the length of microsatellite repeats in tumor and normal samples. In this work, we developed a qualitative transcriptional signature to individually predict MSI status for right-sided colon cancer (RCC) based on tumor samples. RESULTS: Using RCC samples, based on the relative expression orderings (REOs) of gene pairs, we extracted a signature consisting of 10 gene pairs (10-GPS) to predict MSI status for RCC through a feature selection process. A sample is predicted as MSI when the gene expression orderings of at least 7 gene pairs vote for MSI; otherwise the microsatellite stability (MSS). The classification performance reached the largest F-score in the training dataset. This signature was verified in four independent datasets of RCCs with the F-scores of 1, 0.9630, 0.9412 and 0.8798, respectively. Additionally, the hierarchical clustering analyses and molecular features also supported the correctness of the reclassifications of the MSI status by 10-GPS. CONCLUSIONS: The qualitative transcriptional signature can be used to classify MSI status of RCC samples at the individualized level.