Multilevel prioritization of gene regulators associated with consensus molecular subtypes of colorectal cancer.

Consensus molecular subtypes (CMSs) are emerging as critical factor for prognosis and treatment of colorectal cancer. Gene regulators, including chromatin regulator, RNA-binding protein and transcriptional factor, are critical modulators of cancer hallmark, yet little is known regarding the underlying functional mechanism in CMSs. Herein, we identified a core set of 235 functional gene regulators (FGRs) by integrating genome, epigenome, transcriptome and interactome of CMSs. FGRs exhibited significant multi-omics alterations and impacts on cell lines growth, as well as significantly enriched cancer driver genes and pathways. Moreover, common FGRs played different roles in the context of CMSs. In accordance with the immune characteristics of CMSs, we found that the anti-tumor immune pathways were mainly activated by FGRs (e.g. STAT1 and CREBBP) in CMS1, while inhibited by FGRs in CMS2-4. FGRs mediated aberrant expression of ligands, which bind to receptor on immune cells, and modulated tumor immune microenvironment of subtypes. Intriguingly, systematic exploration of datasets using genomic and transcriptome co-similarity reveals the coordinated manner in FGRs act in CMSs to orchestrate their pathways and patients' prognosis. Expression signatures of the FGRs revealed an optimized CMS classifier, which demonstrated 88% concordance with the gold-standard classifier, but avoiding the influence of sample composition. Overall, our integrative analysis identified FGRs to regulate core tumorigenic processes/pathways across CMSs.

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 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.

SnO2 nanoparticle-coated ZnO nanotube arrays for high-performance electrochemical sensors.

Novel 1D nanostructures offer new opportunities for improving the performance of electrochemical sensors. In this study, highly ordered 1D nanostructure array electrodes composed of SnO2 nanoparticle-coated ZnO (SnO2 @ZnO) nanotubes are designed and fabricated. The composite nanotube array architecture not only endows the electrochemical electrodes with large surface areas, but also allows electrons to be quickly transferred along the nanotubes. Modifying the SnO2 @ZnO nanotube arrays with negatively charged polymer film and employing them as a working electrode, sensitive and selective electrochemical detection of an important neurotransmitter, i.e., dopamine, is realized via the cycle voltammetry (CV) and differential pulse voltammetry (DPV) techniques. Interference from ascorbic acid can be successfully eliminated. The oxidative peak currents recorded from CV linearly depend on the dopamine concentrations from 0.1 to 100 µM with a sensitivity of 2.16 × 10(-7) A µM(-1) cm(-2) and detection limit of 45.2 nM. Using the DPV technique, an improved sensitivity and detection limit of 1.94 × 10(-6) A µM(-1) cm(-2) and 17.7 nM are respectively achieved. Moreover, the SnO2 @ZnO nanotube array electrodes can be reused through simple ultrasonical cleaning and no obvious deterioration is observed in the performance.

YAP/Aurora A-mediated ciliogenesis regulates ionizing radiation-induced senescence via Hedgehog pathway in tumor cells.

Primary cilia are antenna-like organelles that play critical roles in sensing and responding to various signals. Nevertheless, the function of primary cilia in cellular response to ionizing radiation (IR) in tumor cells remains unclear. Here, we show that primary cilia are frequently expressed in tumor cells and tissues. Notably, IR promotes cilia formation and elongation in time- and dose-dependent manners. Mechanistic study shows that the suppression of YAP/Aurora A pathway contributes to IR-induced ciliogenesis, which is diminished by Aurora A overexpression. The ciliated tumor cells undergo senescence but not apoptosis in response to IR and the abrogation of cilia formation is sufficient to elevate the lethal effect of IR. Furthermore, we show that IR-induced ciliogenesis leads to the activation of Hedgehog signaling pathway to drive senescence and resist apoptosis, and its blockage enhances cellular radiosensitivity by switching senescence to apoptosis. In summary, this work shows evidence of primary cilia in coordinating cellular response to IR in tumor cells, which may help to supply a novel sensitizing target to improve the outcome of radiotherapy.

Structural variation and introgression from wild populations in East Asian cattle genomes confer adaptation to local environment.

BACKGROUND: Structural variations (SVs) in individual genomes are major determinants of complex traits, including adaptability to environmental variables. The Mongolian and Hainan cattle breeds in East Asia are of taurine and indicine origins that have evolved to adapt to cold and hot environments, respectively. However, few studies have investigated SVs in East Asian cattle genomes and their roles in environmental adaptation, and little is known about adaptively introgressed SVs in East Asian cattle. RESULTS: In this study, we examine the roles of SVs in the climate adaptation of these two cattle lineages by generating highly contiguous chromosome-scale genome assemblies. Comparison of the two assemblies along with 18 Mongolian and Hainan cattle genomes obtained by long-read sequencing data provides a catalog of 123,898 nonredundant SVs. Several SVs detected from long reads are in exons of genes associated with epidermal differentiation, skin barrier, and bovine tuberculosis resistance. Functional investigations show that a 108-bp exonic insertion in SPN may affect the uptake of Mycobacterium tuberculosis by macrophages, which might contribute to the low susceptibility of Hainan cattle to bovine tuberculosis. Genotyping of 373 whole genomes from 39 breeds identifies 2610 SVs that are differentiated along a "north-south" gradient in China and overlap with 862 related genes that are enriched in pathways related to environmental adaptation. We identify 1457 Chinese indicine-stratified SVs that possibly originate from banteng and are frequent in Chinese indicine cattle. CONCLUSIONS: Our findings highlight the unique contribution of SVs in East Asian cattle to environmental adaptation and disease resistance.

Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing.

Indicine cattle, also referred to as zebu (Bos taurus indicus), play a central role in pastoral communities across a wide range of agro-ecosystems, from extremely hot semiarid regions to hot humid tropical regions. However, their adaptive genetic changes following their dispersal into East Asia from the Indian subcontinent have remained poorly documented. Here, we characterize their global genetic diversity using high-quality whole-genome sequencing data from 354 indicine cattle of 57 breeds/populations, including major indicine phylogeographic groups worldwide. We reveal their probable migration into East Asia was along a coastal route rather than inland routes and we detected introgression from other bovine species. Genomic regions carrying morphology-, immune-, and heat-tolerance-related genes underwent divergent selection according to Asian agro-ecologies. We identify distinct sets of loci that contain promising candidate variants for adaptation to hot semi-arid and hot humid tropical ecosystems. Our results indicate that the rapid and successful adaptation of East Asian indicine cattle to hot humid environments was promoted by localized introgression from banteng and/or gaur. Our findings provide insights into the history and environmental adaptation of indicine cattle.

Whole-Genome Sequencing of Endangered Dengchuan Cattle Reveals Its Genomic Diversity and Selection Signatures.

Dengchuan cattle are the only dairy yellow cattle and endangered cattle among Yunnan native cattle breeds. However, its genetic background remains unclear. Here, we performed whole-genome sequencing of ten Dengchuan cattle. Integrating our data with the publicly available data, Dengchuan cattle were observed to be highly interbred than other cattle in the dataset. Furthermore, the positive selective signals were mainly manifested in candidate genes and pathways related to milk production, disease resistance, growth and development, and heat tolerance. Notably, five genes (KRT39, PGR, KRT40, ESR2, and PRKACB) were significantly enriched in the estrogen signaling pathway. Moreover, the missense mutation in the PGR gene (c.190T > C, p.Ser64Pro) showed a homozygous mutation pattern with higher frequency (83.3%) in Dengchuan cattle. In addition, a large number of strong candidate regions matched genes and QTLs related to milk yield and composition. Our research provides a theoretical basis for analyzing the genetic mechanism underlying Dengchuan cattle with excellent lactation and adaptability, crude feed tolerance, good immune performance, and small body size and also laid a foundation for genetic breeding research of Dengchuan cattle in the future.

Genomics, Origin and Selection Signals of Loudi Cattle in Central Hunan.

Due to the geographical, cultural and environmental variability in Xiangxi, China, distinctive indigenous cattle populations have formed. Among them, Loudi cattle and Xiangxi cattle are the local cattle in Hunan, and the environment in Loudi is relatively more enclosed and humid than that in Xiangxi. To study the genome and origin of Loudi cattle in hot and humid environments, 29 individuals were collected and sequenced by whole-genome resequencing. In addition, genomic data were obtained from public databases for 96 individuals representing different cattle breeds worldwide, including 23 Xiangxi cattle from western Hunan. Genetic analysis indicated that the genetic diversity of Loudi cattle was close to that of Chinese cattle and higher than that of other breeds. Population structure and ancestral origin analysis indicated the relationship between Loudi cattle and other breeds. Loudi has four distinctive seasons, with a stereoscopic climate and extremely rich water resources. Selective sweep analysis revealed candidate genes and pathways associated with environmental adaptation and homeostasis. Our findings provide a valuable source of information on the genetic diversity of Loudi cattle and ideas for population conservation and genome-associated breeding of local cattle in today's extreme climate environment.

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.

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.

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.

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 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.

Effects of Ginkgo biloba on Early Decompression after Spinal Cord Injury.

Spinal cord injury (SCI) is a severe trauma of the central nervous system characterized by high disability and high mortality. Clinical progress has been achieved in understanding the pathological mechanism of SCI and its early treatment, but the results are unsatisfactory. In China, increasing attention has been paid to the role of traditional Chinese medicine in the treatment of SCI. In particular, extracts from the leaves of Ginkgo biloba (maidenhair tree), which have been reported to exert anti-inflammatory and antioxidant properties and repair a variety of active cellular damage, have been applied therapeutically for centuries. In this study, we established a rat SCI model to investigate the effects of Ginkgo biloba leaves on decompression at different stages of SCI. The application of Ginkgo biloba leaves during the decompression of SCI at different time points, the neurological recovery of SCI, and the underlying molecular mechanism were explored. The findings provide reliable experimental data that reveal the mechanism of GBI (Ginkgo biloba injection) in the clinical treatment of SCI.

miR-185 enhances the inhibition of proliferation and migration induced by ionizing radiation in melanoma.

Melanoma is an aggressive malignancy that is increasingly common and exhibits a poor patient survival rate. Radiotherapy is the primary option for patients with melanoma, particularly those who are not candidates for surgery; however, the therapeutic effect is limited due to the relative radioresistance of melanoma to ionizing radiation (IR). It has been reported that microRNAs (miRNAs) serve a vital role in determining the radiosensitivity of tumors; however, little is known concerning the radiosensitization of melanoma using miRNA. In the present study, the radiosensitization effect of miRNA 185 (miR-185), which has been demonstrated to reduce renal cancer radioresistance, was investigated in B16 cells, a skin melanoma cell line derived from C57/BL mice, was investigated. Cell proliferation and scratch wound healing assays were used to determine the proliferative and migratory abilities of B16 cells. Annexin V/propidium iodide double staining was used to determine the apoptosis induced by IR. A tumor formation assay was performed to determine the radiosensitization effect of miR-185 on melanoma cells in vivo. Proliferation marker protein Ki-67, and hematoxylin and eosin staining were used to assess the proliferative activity and histological changes, respectively. The results of the present study demonstrated that miR-185 suppresses cellular proliferation and migration, and enhances IR-induced apoptosis, and the inhibition of proliferation and migration, in vitro and in vivo, which provides an insight into understanding the radiosensitization of melanoma using miRNA.