Dynamics of magnetization at infinite temperature in a Heisenberg spin chain

Understanding universal aspects of quantum dynamics is an unresolved problem in statistical mechanics. In particular, the spin dynamics of the one-dimensional Heisenberg model were conjectured as to belong to the Kardar-Parisi-Zhang (KPZ) universality class based on the scaling of the infinite-temperature spin-spin correlation function. In a chain of 46 superconducting qubits, we studied the probability distribution of the magnetization transferred across the chain's center, [Formula: see text]. The first two moments of [Formula: see text] show superdiffusive behavior, a hallmark of KPZ universality. However, the third and fourth moments ruled out the KPZ conjecture and allow for evaluating other theories. Our results highlight the importance of studying higher moments in determining dynamic universality classes and provide insights into universal behavior in quantum systems.

Insights on E1-like enzyme ATG7: functional regulation and relationships with aging-related diseases

Autophagy is a dynamic self-renovation biological process that maintains cell homeostasis and is responsible for the quality control of proteins, organelles, and energy metabolism. The E1-like ubiquitin-activating enzyme autophagy-related gene 7 (ATG7) is a critical factor that initiates classic autophagy reactions by promoting the formation and extension of autophagosome membranes. Recent studies have identified the key functions of ATG7 in regulating the cell cycle, apoptosis, and metabolism associated with the occurrence and development of multiple diseases. This review summarizes how ATG7 is precisely programmed by genetic, transcriptional, and epigenetic modifications in cells and the relationship between ATG7 and aging-related diseases.

Stable quantum-correlated many-body states through engineered dissipation

Engineered dissipative reservoirs have the potential to steer many-body quantum systems toward correlated steady states useful for quantum simulation of high-temperature superconductivity or quantum magnetism. Using up to 49 superconducting qubits, we prepared low-energy states of the transverse-field Ising model through coupling to dissipative auxiliary qubits. In one dimension, we observed long-range quantum correlations and a ground-state fidelity of 0.86 for 18 qubits at the critical point. In two dimensions, we found mutual information that extends beyond nearest neighbors. Lastly, by coupling the system to auxiliaries emulating reservoirs with different chemical potentials, we explored transport in the quantum Heisenberg model. Our results establish engineered dissipation as a scalable alternative to unitary evolution for preparing entangled many-body states on noisy quantum processors.

ATM-CHK2-TRIM32 axis regulates ATG7 ubiquitination to initiate autophagy under oxidative stress

Oxidative stress-induced autophagy helps to prevent cellular damage and to maintain homeostasis. However, the regulatory pathway that initiates autophagy remains unclear. We previously showed that reactive oxygen species (ROS) function as signaling molecules to activate the ATM-CHK2 pathway and promote autophagy. Here, we find that the E3 ubiquitin ligase TRIM32 functions downstream of ATM-CHK2 to regulate ATG7 ubiquitination. Under metabolic stress, ROS induce ATM phosphorylation at S1981, which in turn phosphorylates CHK2 at T68. We show that CHK2 binds and phosphorylates TRIM32 at the S55 site, which then mediates K63-linked ubiquitination of ATG7 at the K45 site to initiate autophagy. In addition, Chk2-/- mice show an aggravated infarction phenotype and reduced phosphorylation of TRIM32 and ubiquitination of ATG7 in a stroke model. We propose a molecular mechanism for autophagy initiation by ROS via the ATM-CHK2-TRIM32-ATG7 axis to maintain intracellular homeostasis and to protect cells exposed to pathological conditions from stress-induced tissue damage.

Measurement-induced entanglement and teleportation on a noisy quantum processor

Measurement has a special role in quantum theory1: by collapsing the wavefunction, it can enable phenomena such as teleportation2 and thereby alter the 'arrow of time' that constrains unitary evolution. When integrated in many-body dynamics, measurements can lead to emergent patterns of quantum information in space-time3-10 that go beyond the established paradigms for characterizing phases, either in or out of equilibrium11-13. For present-day noisy intermediate-scale quantum (NISQ) processors14, the experimental realization of such physics can be problematic because of hardware limitations and the stochastic nature of quantum measurement. Here we address these experimental challenges and study measurement-induced quantum information phases on up to 70 superconducting qubits. By leveraging the interchangeability of space and time, we use a duality mapping9,15-17 to avoid mid-circuit measurement and access different manifestations of the underlying phases, from entanglement scaling3,4 to measurement-induced teleportation18. We obtain finite-sized signatures of a phase transition with a decoding protocol that correlates the experimental measurement with classical simulation data. The phases display remarkably different sensitivity to noise, and we use this disparity to turn an inherent hardware limitation into a useful diagnostic. Our work demonstrates an approach to realizing measurement-induced physics at scales that are at the limits of current NISQ processors.

Tumor Cell-Intrinsic PD-L1 Effects on Radiation-Induced Locoregional Antitumor Immunity

PURPOSE/OBJECTIVE(S)

Targeting PD-L1 is a beneficial strategy to reinvigorate antitumor immunity, however variable response and resistance are challenging and suggest the need for multimodality approaches. Tumor cell-intrinsic PD-L1 signals also regulate non-canonical pathogenic pathways that may impact treatment resistance. Ionizing radiation (IR) can induce antitumor immunity and has demonstrated therapeutic synergy with immunotherapy in some cases, however tumor-driven immunologic mechanisms affecting clinical outcomes remain incompletely understood. In this study, we investigated the impact of tumor cell-intrinsic PD-L1 signals on IR-induced locoregional immune response and tumor control.

MATERIALS/METHODS

We used orthotopic B16-F10 melanoma (WT-B16) and 4T1 triple negative breast cancer (WT-4T1) murine tumor models, as well as PD-L1 disabled variants (KO) generated by CRISPR/Cas9, implanted bilaterally. IR (10 Gy) was targeted at one tumor alone to evaluate both direct and indirect IR effects based on tumor PD-L1 status. We evaluated response by tumor volume (TV) measurements, flow cytometry of tumor-infiltrating lymphocytes (TILs) and tumor draining lymph nodes (TDLNs) in both irradiated and unirradiated compartments, and granzyme B (GZB) PET imaging to assess functional in vivo changes. Chemokine-based multiplex assays were used to assess cell lines receiving IR (4Gy) and ex vivo tumor lysates and serum.

RESULTS

IR-induced local tumor control was not significantly affected based on tumor PD-L1 status, however deactivation of tumor cell PD-L1 enhanced IR-induced regional tumor control. Unirradiated WT tumors in mice harboring irradiated KO but not irradiated WT tumors demonstrated a significant mean reduction in TV with instances of complete distant tumor regression. PET imaging demonstrated a nearly 2-fold higher concentration of GZB in KO versus WT tumors, in line with known locally immunosuppressive effects of tumor PD-L1. Remarkably, GZB levels were >1.5-fold higher in unirradiated WT tumors in mice harboring an irradiated KO versus WT tumor, which correlated with a 50% increase in PD-1+CD8+ T cells. Higher levels of CD62+CD44- naïve CD4+ (4-fold) and CD8+ (2-fold) memory T cells were seen in TDLNs of irradiated KO versus WT tumors. Cytokine levels positively correlated with immune recruitment and activation status, as CXCL10, CCL2 and CCL5 were significantly upregulated in PD-L1 KO versus WT tumors cells.

CONCLUSION

Results from this study demonstrate cell-intrinsic PD-L1 inhibits IR-induced locoregional immune activation and frequency of regional tumor control, with clinical implications including therapeutic targeting of tumor cell-intrinsic PD-L1 signals to enhance IR-induced immunogenicity, utility of IR based on tumor PD-L1 status particularly in the metastatic setting, and immunotherapy combinations. Future studies investigating mechanisms of resistance to IR-induced immune activation to enhance responsiveness are warranted.

Expression and regulatory network of E3 ubiquitin ligase NEDD4 family in cancers

NEDD4 family represent an important group of E3 ligases, which regulate various cellular pathways of cell proliferation, cell junction and inflammation. Emerging evidence suggested that NEDD4 family members participate in the initiation and development of tumor. In this study, we systematically investigated the molecular alterations as well as the clinical relevance regarding NEDD4 family genes in 33 cancer types. Finally, we found that NEDD4 members showed increased expression in pancreas cancer and decreased expression in thyroid cancer. NEDD4 E3 ligase family genes had an average mutation frequency in the range of 0-32.1%, of which HECW1 and HECW2 demonstrated relatively high mutation rate. Breast cancer harbors large amount of NEDD4 copy number amplification. NEDD4 family members interacted proteins were enriched in various pathways including p53, Akt, apoptosis and autophagy, which were confirmed by further western blot and flow cytometric analysis in A549 and H1299 lung cancer cells. In addition, expression of NEDD4 family genes were associated with survival of cancer patients. Our findings provide novel insight into the effect of NEDD4 E3 ligase genes on cancer progression and treatment in the future.

Non-Abelian braiding of graph vertices in a superconducting processor

Indistinguishability of particles is a fundamental principle of quantum mechanics¹. For all elementary and quasiparticles observed to date-including fermions, bosons and Abelian anyons-this principle guarantees that the braiding of identical particles leaves the system unchanged^2,3. However, in two spatial dimensions, an intriguing possibility exists: braiding of non-Abelian anyons causes rotations in a space of topologically degenerate wavefunctions^4-8. Hence, it can change the observables of the system without violating the principle of indistinguishability. Despite the well-developed mathematical description of non-Abelian anyons and numerous theoretical proposals^9-22, the experimental observation of their exchange statistics has remained elusive for decades. Controllable many-body quantum states generated on quantum processors offer another path for exploring these fundamental phenomena. Whereas efforts on conventional solid-state platforms typically involve Hamiltonian dynamics of quasiparticles, superconducting quantum processors allow for directly manipulating the many-body wavefunction by means of unitary gates. Building on predictions that stabilizer codes can host projective non-Abelian Ising anyons^9,10, we implement a generalized stabilizer code and unitary protocol²³ to create and braid them. This allows us to experimentally verify the fusion rules of the anyons and braid them to realize their statistics. We then study the prospect of using the anyons for quantum computation and use braiding to create an entangled state of anyons encoding three logical qubits. Our work provides new insights about non-Abelian braiding and, through the future inclusion of error correction to achieve topological protection, could open a path towards fault-tolerant quantum computing.

De-ubiquitination of SAMHD1 by USP7 promotes DNA damage repair to overcome oncogenic stress and affect chemotherapy sensitivity

Oncogenic stress induces DNA damage repair (DDR) that permits escape from mitotic catastrophe and allows early precursor lesions during the evolution of cancer. SAMHD1, a dNTPase protecting cells from viral infections, has been recently found to participate in DNA damage repair process. However, its role in tumorigenesis remains largely unknown. Here, we show that SAMHD1 is up-regulated in early-stage human carcinoma tissues and cell lines under oxidative stress or genotoxic insults. We further demonstrate that de-ubiquitinating enzyme USP7 interacts with SAMHD1 and de-ubiquitinates it at lysine 421, thus stabilizing SAMHD1 protein expression for further interaction with CtIP for DDR, which promotes tumor cell survival under genotoxic stress. Furthermore, SAMHD1 levels positively correlates with USP7 in various human carcinomas, and is associated with an unfavorable survival outcome in patients who underwent chemotherapy. Moreover, USP7 inhibitor sensitizes tumor cells to chemotherapeutic agents by decreasing SAMHD1 in vitro and in vivo. These findings suggest that de-ubiquitination of SAMHD1 by USP7 promotes DDR to overcome oncogenic stress and affect chemotherapy sensitivity.

Ultra-high-resolution observations of persistent null-point reconnection in the solar corona

Magnetic reconnection is a key mechanism involved in solar eruptions and is also a prime possibility to heat the low corona to millions of degrees. Here, we present ultra-high-resolution extreme ultraviolet observations of persistent null-point reconnection in the corona at a scale of about 390 km over one hour observations of the Extreme-Ultraviolet Imager on board Solar Orbiter spacecraft. The observations show formation of a null-point configuration above a minor positive polarity embedded within a region of dominant negative polarity near a sunspot. The gentle phase of the persistent null-point reconnection is evidenced by sustained point-like high-temperature plasma (about 10 MK) near the null-point and constant outflow blobs not only along the outer spine but also along the fan surface. The blobs appear at a higher frequency than previously observed with an average velocity of about 80 km s^-1 and life-times of about 40 s. The null-point reconnection also occurs explosively but only for 4 minutes, its coupling with a mini-filament eruption generates a spiral jet. These results suggest that magnetic reconnection, at previously unresolved scales, proceeds continually in a gentle and/or explosive way to persistently transfer mass and energy to the overlying corona.

Formation of robust bound states of interacting microwave photons

Systems of correlated particles appear in many fields of modern science and represent some of the most intractable computational problems in nature. The computational challenge in these systems arises when interactions become comparable to other energy scales, which makes the state of each particle depend on all other particles1. The lack of general solutions for the three-body problem and acceptable theory for strongly correlated electrons shows that our understanding of correlated systems fades when the particle number or the interaction strength increases. One of the hallmarks of interacting systems is the formation of multiparticle bound states2-9. Here we develop a high-fidelity parameterizable fSim gate and implement the periodic quantum circuit of the spin-½ XXZ model in a ring of 24 superconducting qubits. We study the propagation of these excitations and observe their bound nature for up to five photons. We devise a phase-sensitive method for constructing the few-body spectrum of the bound states and extract their pseudo-charge by introducing a synthetic flux. By introducing interactions between the ring and additional qubits, we observe an unexpected resilience of the bound states to integrability breaking. This finding goes against the idea that bound states in non-integrable systems are unstable when their energies overlap with the continuum spectrum. Our work provides experimental evidence for bound states of interacting photons and discovers their stability beyond the integrability limit.

Short period-administration of myo-inositol and metformin on hormonal and glycolipid profiles in patients with polycystic ovary syndrome: a systematic review and updated meta-analysis of randomized controlled trials

OBJECTIVE

This meta-analysis aims to perform an updated meta-analysis to evaluate myo-inositol (myo-ins) and the classical insulin sensitizer metformin in terms of efficacy and safety for treating women with polycystic ovary syndrome (PCOS).

MATERIALS AND METHODS

A comprehensive literature search was performed using PubMed, Web of Science, EMBASE, Cochrane Library, PhRMA Clinical Study Results, Wan Fang, and CNKI databases; the database was searched from inception to June 2021. The random effects model was chosen to synthesize the effect sizes of individual trails. The registration number is CRD42021239786.

RESULTS

Nine randomized controlled trials (RCTs) and 612 patients were included in the analysis. Compared with metformin, myo-ins might be more effective in lowering triglycerides (TG) levels (SMD -0.49, 95% CI -0.74 to -0.24, p=0.0001, I2 = 0%) and avoiding side effects (RR=0.14, 95% CI 0.08-0.24, p<0.00001, I2 = 2%), while no significant differences were observed in other relevant indexes, such as total testosterone (TT) and sex-hormone binding globulin (SHBG).

CONCLUSIONS

Compared with metformin, the suitable supplemental dosage of myo-ins may be helpful in lowering levels of TG and avoiding adverse events (AEs).

[Interventional effect of asiaticosdide on rats exposed to silica dust]

Objective: To investigate the effect of asiaticoside for fibrosis in lung tissues of rats exposed to silica and to explore its possible mechanism. Methods: 144 SD male rats were randomly divided into control group, model group, positive drug control group, asiaticoside high-dose group, medium-dose group and low-dose group, each group included 24 rats. Rats in the control group were perfused with 1.0 ml of normal saline, and the other groups were given 1.0 ml 50 mg/ml SiO(2) suspension. Gavage of herbal was given from the next day after model establishment, once a day. Rats in the positive drug control group were administration with 30 mg/kg tetrandrine and rats in the low-dose group, medium-dose group and high-dose group were given 20 mg/kg, 40 mg/kg and 60 mg/kg asiaticoside for fibrosis respectively. Rats in the control group and the model group were given 0.9% normal saline. The rats were sacrificed in on the 14th, 28th and 56th day after intragastric administration and collect the lung tissues to detect the content of hydroxyproline, TGF-β(1) and IL-18, observe the pathological changes of the lung tissues by HE and Masson staining and determine the expressions of Col-I, a-SMA, TGF-β in lung tissues by Western Blot. Results: On the 14th day, 28th day and 56th day after model establishment, the lung tissues of rats in the model group showed obvious inflammatory response and accumulation of collagen fibers, and the degree of inflammation and fibrosis increased with time. The intervention of asiaticoside could effectively inhibit the pathological changes of lung tissues. The contents of hydroxyproline, IL-18 and TGF-β1 in lung tissues of model group were higher than those in the control group (P<0.05) , while the level of hydroxyproline, IL-18 and TGF-β1 in asiaticoside groups were significantly decreased, and the difference was statistically signicant (P<0.05) . Compared with the control group, the expression levels of Col-I, TGF-β1and α-SMA in lung tissue of model group were increased (P<0.05) , while the expression level of Col-I, TGF-β1 and α-SMA were decreased after the intervention of asiaticoside, and the difference was statistically signicant (P<0.05) . Conclusion: Asiaticoside can inhibit the increase of Col-I, TGF-β1 and α-SMA content in the SiO(2)-induced lung tissues of rats, reduce the release of TGF-β1 and IL-18 inflammatory factors in lung tissue, and then inhibit the synthesis and deposition of extracellular matrix in rat lung tissue, and improve silicosis fibrosis.

Comprehensive analysis of ceRNA network of ERCC4 in colorectal cancer

Objective

ERCC4 is one of the most significant molecules of Nucleotide Excision Repair (NER), which has been researched due to its high expression in colorectal cancer (CRC). This study aimed to find out the ceRNA (competitive endogenous RNA) network of ERCC4 in CRC.

Methods and Materials

Pan cancer mRNA expression of ERCC4 was evaluated using TCGA database. The protein expression of ERCC4 was evaluated based on the Human Protein Atlas (HPA). We screened DElncRNAs and DEmiRNAs in two groups of ERCC4^high and ERCC4^low expression in CRC. Then a lncRNA-miRNA-ERCC4 regulatory network was constructed based on DElncRNAs and DEmiRNAs using Starbase database and visualized by Cytoscape software. Kaplan-Meier analysis was performed to evaluate the prognostic value of the ceRNA network. Further, RT-PCR was performed to validate the expression of the representative molecules in the ceRNA network in CRC and normal tissues. The relationship between drug sensitivity and these molecules were also evaluated using RNAactDrug database.

Results

ERCC4 was overexpressed in a variety of tumors at mRNA levels, including CRC. High expression of ERCC4 was also observed on protein level in CRC. A total of 1,885 DElncRNAs and 68 DEmiRNAs were identified from CRC samples in ERCC4^high and ERCC4^low expression groups. Predicted by the Starbase database, we got interacting miRNAs and lncRNAs of ERCC4 from the DEmiRNAs and DElncRNAs, and a lncRNA-miRNA-ERCC4 regulatory network was constructed. Kaplan-Meier survival curves results showed that miR-200c-3p (hazard ratio [HR] = 0.62, P = 0.032), MALAT1 (HR = 1.54, P = 0.016), and AC005520.2 (hazard ratio [HR] = 1.75, P = 0.002) were significantly associated with the prognosis of CRC. After validation by RT-PCR, we found that ERCC4 and MALAT1 were up-regulated in CRC compared with normal tissues, while miR-200c-3p was down-regulated. A strong negative correlation was observed between MALAT1 and miR-200c-3p. Drug sensitivity analysis showed that ERCC4, miR-200c and MALAT1 were all associated with Cisplatin.

Conclusion

We constructed a ceRNA network of ERCC4 in CRC, of which the MALAT1-miR-200c-3p-ERCC4 axis may be involved in the development, prognosis and chemotherapy sensitivity of CRC. These findings might provide novel clues and insights on the molecular mechanisms of ERCC4 and NER pathway in CRC.

The Involvement of TRIB3 and FABP1 and Their Potential Functions in the Dynamic Process of Gastric Cancer

Background: Dysregulated expression of TRIB3 and FABP1 have been previously observed in human cancer tissues. However, there are little information as to their expression change in dynamic gastric diseases and the functional roles.

Methods: Tissues from a total of 479 patients, including 89 GS, 102 IM-GA, 144 EGC, and 144 AGC were collected. The protein expressions of TRIB3 and FABP1 were detected by immunohistochemical staining. Meanwhile, the potential functions of TRIB3 and FABP1 in GC were further analyzed by R software and some internet public databases, such as TCGA and DAVID.

Results: During this multi-stage process that go through GS to EGC, the expression trend of TRIB3 and FABP1 protein was GS > IM-GA > EGC. Besides, the expression of TRIB3 protein continued to decrease in AGC, while the expression of FABP1 was abnormally increased. Hp infection was significantly associated with the decreased expression of TRIB3 and FABP1. In addition, the diagnostic efficiency of the combination of these two indicators to diagnose EGC was higher than that of a single indicator. Survival analysis showed that higher expression of TRIB3 or FABP1 could indicate a better prognosis of GC. The protein expressions of TRIB3 and FABP1 were significantly positively correlated. Moreover, CEACAM5 and PRAP1 were positively correlated with both TRIB3 and FABP1 expressions, while GABRP and THBS4 were negatively correlated. The macrophages M0 infiltration was positively correlated with both TRIB3 and FABP1 expressions.

Conclusion: The protein expressions of TRIB3 and FABP1 gradually decreased with the gastric disease progress, and was positively correlated. Hp infection may reduce the protein expression of TRIB3 and FABP1. Combing TRIB3 and FABP1 expressions can improve the diagnostic efficiency for EGC. Either a high expression of TRIB3 or FABP1 indicates a better prognosis for GC. TRIB3 and FABP1 may interact with CEACAM5, PRAP1, GABRP and THBS4, and affect tumor immune microenvironment by regulating immune cells, and participate in the development and progression of GC.

Interleukin 20 receptor A expression in colorectal cancer and its clinical significance

Background

Interleukin 20 receptor A (IL20RA) has been shown to play a role in the establishment and progression of multiple tumors. However, the expression of this protein in colorectal cancer (CRC) and its correlation with the clinicopathological parameters of CRC have remained unclear.

Methods

A total of 323 paraffin sections including CRC tissues and adjacent normal tissues after surgery were collected. IL20RA protein expression was detected by immunohistochemical staining. The difference expression of IL20RA mRNA between CRC and normal tissues was also explored in the Oncomine and GEO databases. In addition, the IL20RA-related differentially expressed genes were analyzed in TCGA database and enrichment analysis was conducted to explore the cell functions and pathways related to IL20RA expression.

Results

There was increased IL20RA expression in CRC compared with that in normal tissues. High IL20RA expression was associated with greater tumor diameter, lymph node metastasis, and poor TNM stage in CRC, while also being suggestive of poor prognosis. The main pathways of IL20RA-related differentially expressed genes in TCGA were protein heterodimerization activity, oxygen binding, oxygen transporter activity, hormone activity, and lipid transporter activity. Meanwhile, IL20RA-related differentially expressed genes were mainly enriched in peroxidase, nucleotide stimulant repair, fatty acid metabolism, basal transcription factor, and RNA degradation.

Conclusions

IL20RA might have a role as a biomarker for CRC. Its upregulation might contribute to an aggressive phenotype in CRC. IL20RA’s involvement in the development and progression of CRC might occur through it affecting fatty acid metabolism, oxygen binding, oxygen transport, and hormone activity.

Integrative analysis of somatic mutations and differential expression profiles in glioblastoma based on aging acceleration

BACKGROUND

Glioblastoma (GBM) is an aggressive brain tumor and the mechanisms of progression are very complex. Accelerated aging is a driving factor of GBM. However, there has not been thorough research about the mechanisms of GBM progression based on aging acceleration.

METHODS

The aging predictor was modeled based on normal brain samples. Then an aging acceleration background network was constructed to explore GBM mechanisms.

RESULTS

The accelerated aging-related mechanisms provided an innovative way to study GBM, wherein integrative analysis of somatic mutations and differential expression revealed key pathologic characteristics. Moreover, the influence of the immune system, the nervous system and other critical factors on GBM were identified. The survival analysis also disclosed crucial GBM markers.

CONCLUSION

An integrative analysis of multi-omics data based on aging acceleration identified new driving factors for GBM.

MiR-1539 and Its Potential Role as a Novel Biomarker for Colorectal Cancer

Purpose

We investigated microRNA (miR) 1539 as a potential biomarker for predicting the risk and pathobiological behavior of colorectal cancer (CRC).

Methods

Our strategy consisted of analyzing 100 serum samples from 51 CRC patients, 49 healthy controls (HCs), and another 56 CRC tissue and matched normal adjacent to tumor (NAT) samples. The relative expression levels of miR-1539 in exosomes, serum and tissues were detected and compared in the different groups, using reverse transcription-polymerase chain reaction (RT-qPCR). The diagnostic value and potential function of miR-1539 were investigated using clinicopathological data combined with bioinformatics analysis.

Results

MiR-1539 expression was significantly up-regulated in exosomes (p = 0.003) and cancer tissue (p < 0.001) from CRC patients. MiR-1539 expression levels in serum varied according to different tumor sites (right-sided vs. left-sided, p = 0.047; left-side CRC vs. HCs, p = 0.031). In terms of diagnostic efficacy, miR-1539 expression in exosomes may help distinguish CRC cases from HCs with a sensitivity of 92.2%, and miR-1539 expression in serum may improve the specificity to 96.6% for left-sided CRC diagnosis. When combined with clinicopathological data, serum miR-1539 levels were positively associated with vascular endothelial growth factor (VEGF) expression (p = 0.028), whilst levels in CRC tissue were positively associated with increased Ki-67 levels (p = 0.035). Poorer pathologic differentiation was potentially related to an increased tendency of miR-1539 expression in CRC tissue (p = 0.071). Based on our bioinformatics analysis, miR-1539 may have a significant mechanistic influence on CRC genesis and progression.

Conclusions

Circulating or tissue based miR-1539 may be used as a novel potential biomarker for CRC screening, and a predictor of poor clinicopathological behavior in tumors.

XPF expression and its relationship with the risk and prognosis of colorectal cancer

BACKGROUND

XPF (xeroderma pigmentosum complementation group F) is a key factor contributing to DNA damage excision of nucleotide excision repair pathway. The relationship between XPF expression and the risk and prognosis of colorectal cancer (CRC) is unclear.

METHODS

In this experiment, a total of 824 cases of colorectal tissue were collected. XPF protein expression was detected by immunohistochemical staining. We conducted a Mann-Whitney U test in order to explore the differential expression of XPF between CRC and non-cancer controls, and the correlation between XPF expression and CRC clinicopathological parameters. Univariate and multivariate Cox regression analyses were conducted to investigate the relationship between XPF expression and CRC prognosis. The Java based software GSEA as well as STRING, David, GO, KEGG were used to explore the function and regulation network of XPF.

RESULTS

The results demonstrated that the XPF expression in CRC was significantly up-regulated compared with non-tumor controls (P < 0.001) and adenoma tissue (P < 0.001). XPF protein was increased in the dynamic sequence of anal diseases to adenoma tissue to CRC. Expression of XPF was related to tumor location (P = 0.005) and tumor growth pattern (P = 0.009). The results of prognosis analysis suggested that in patients with stage T1-T2, XPF low expression may be significantly associated with better overall survival (HR = 7.978, 95% CI 1.208-52.673, P = 0.031). XPF and its interacting genes played a vital role in different processes of nucleotide excision repair pathway. XPF expression was related with Ubiquitin like protein specific protease activity.

CONCLUSIONS

XPF might be a promising biomarker for CRC risk, and also showed potential as a prognostic predictor in CRC patients.

Community diversity and abundance of ammonia-oxidizing archaea and bacteria in shrimp pond sediment at different culture stages

AIMS

Ammonia oxidation is a significant process of nitrogen cycles in a lot of ecosystems sediments while there are few studies in shrimp culture pond (SCP) sediments. This paper attempted to explore the community diversity and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in SCP sediments at different culture stages.

METHODS AND RESULTS

We collected SCP sediments and analysed the community diversity and abundance of AOA and bacteria in shrimp pond sediment at different culture stages using the ammonia monooxygenase (amoA) gene with quantitative PCR (qPCR) and 16S rRNA gene sequencing. The AOB-amoA gene abundance was showed higher than AOA-amoA gene abundance in SCP sediments on Day 50 and Day 60 after shrimp larvae introducing into the pond, and the diversity of AOA in SCP sediments was higher than that of AOB. The phylogenetic tree revealed that the most of AOA were the member of Nitrosopumilus and Nitrososphaera, and the majority of AOB sequences were clustered into Nitrosospira, Nitrosomonas clusters 6a and 7. The AOA community has close relationship with total organic carbon (TOC), pH, total phosphorus (TP), nitrate reductase, urease, acid phosphatase and β-glucosidase. The AOB community was related to TOC, C/N and nitrate reductase.

CONCLUSIONS

AOA and AOB play the different ecological roles in SCP sediments at different culture stages.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our results suggested that the different community diversity and abundance of AOA and AOB in SCP sediments, which may improve our ecological cognition of shrimp culture stages in SCP ecosystems.

Joint analysis of lncRNA m6A methylome and lncRNA/mRNA expression profiles in gastric cancer

Background

N ⁶-methyladenosine (m⁶A) modification might be closely associated with the genesis and development of gastric cancer (GC). Currently, the evidence established by high-throughput assay for GC-related m⁶A patterns based on long non-coding RNAs (lncRNAs) remains limited. Here, a joint analysis of lncRNA m⁶A methylome and lncRNA/mRNA expression profiles in GC was performed to explore the regulatory roles of m⁶A modification in lncRNAs.

Methods

Three subjects with primary GC were enrolled in our study and paired sample was randomly selected from GC tissue and adjacent normal tissue for each case. Methylated RNA Immunoprecipitation NextGeneration Sequencing (MeRIP-Seq) and Microarray Gene Expression Profiling was subsequently performed. Then co-expression analysis and gene enrichment analysis were successively conducted.

Results

After data analysis, we identified 191 differentially m⁶A-methylated lncRNAs, 240 differentially expressed lncRNAs and 229 differentially expressed mRNAs in GC. Furthermore, four differentially m⁶A-methylated and expressed lncRNAs (dme-lncRNAs) were discovered including RASAL2-AS1, LINC00910, SNHG7 and LINC01105. Their potential target genes were explored by co-expression analysis. And gene enrichment analysis suggested that they might influence the cellular processes and biological behaviors involved in mitosis and cell cycle. The potential impacts of these targets on GC cells were further validated by CCLE database and literature review.

Conclusions

Four novel dme-lncRNAs were identified in GC, which might exert regulatory roles on GC cell proliferation. The present study would provide clues for the lncRNA m⁶A methylation-based research on GC epigenetic etiology and pathogenesis.

Identification of novel monoclonal antibodies targeting the outer membrane protein C and lipopolysaccharides for Escherichia coli O157:H7 detection

AIMS

To identify and evaluate the application of two novel monoclonal antibody (mAb) 2G12 against outer membrane protein (Omp) C and mAb 12B1 targeting the O chain of the lipopolysaccharides (LPS) of Escherichia coli O157:H7 (ECO157).

METHODS AND RESULTS

The sensitivity and specificity of these two antibodies were evaluated with eight ECO157 strains and 68 untargeted strains. mAb 2G12 and 12B1 had no detectable binding with any of the non-O157 strains at 6·0 log₁₀ CFU per ml, while its high specificity and affinity remained with all ECO157 strains. When a higher level (8·0 log₁₀ CFU per ml) was tested, 2G12 and 12B1 did not react with 82·35 and 97·06% of the non-O157 strains respectively. Based on the pair of two antibodies, the sandwich enzyme-linked immunosorbent assay detected 100% (8/8) of ECO157 strains and none of the non-ECO157 strains. The detection limit of ECO157 strains in pure culture were 4·2 ± 0·2 log₁₀ CFU per ml. When the developed test was applied to artificially inoculated beef samples, the detection limit was 6·0 log₁₀ CFU per gram without enrichment and 1·0 log₁₀ CFU per gram after 12 h of enrichment.

CONCLUSIONS

The two novel antibodies identified in this study served as great candidates for the recovery, and detection of ECO157 from different environmental and food samples.

SIGNIFICANCE AND IMPACT OF THE STUDY

ECO157-specific detection was improved by a combination of the novel OmpC mAb and LPS mAb with defined target antigen and good specificity.

Analysis of the nanoscale phase characteristics of bitumen and bitumen in mastics and mixtures via AFM

A peak force quantitative nanomechanical mode (PF-QNM) can be used to simultaneously measure the topographical and nanomechanical property maps of samples. Currently, few studies used this mode to investigate the phase characteristics of bitumen in mastics and mixtures. The present study adopted hot-bitumen-pouring methods to prepare base bitumen surface samples and further used frozen-storage and low-temperature-cutting methods to prepare the internal samples of base bitumen in mastics and mixtures. Then, the atomic force microscopy (AFM) PF-QNM mode was used to collect data on the topographical and nanomechanical properties of bitumen and bitumen in mastics and mixtures. The results indicated that a typical bee structure only appeared on the bitumen surface. In contrast to the bitumen surface, the bitumen interior showed two phases, A- and B-phase, which were close in some properties to the periphase and paraphase of the bitumen surface, respectively. Furthermore, the addition of mineral aggregates affected the phase characteristics of the free bitumen interior. With an increase in the mineral aggregate surface area, the proportion of A-phase decreased and that of B-phase increased in the free bitumen interior. LAY DESCRIPTION: Bitumen is a complex mixture of hydrocarbons primarily applied for pavement materials. In the pavement industry, the bituminous mixture is a multilevel system, in which bitumen acts as a binder binding the aggregates and fillers to form bituminous mixture. Currently, atomic force microscopy (AFM), which is an advanced microscopy technology, has been used to investigate bitumen surface phase characteristics at the nanoscale. However, few studies have directly explored the nanoscale phase characteristics of bitumen in mastics or mixtures. Recently, with the progress of technology, a peak-force-quantitative-nanomechanical mode (PF-QNM) can be used to simultaneously measure the topographical and nanomechanical property maps of samples. Relying on this advanced mode, this study analyzed the nanoscale phase characteristics of the bitumen surface and interior, and further explored the effect of mineral aggregates on bitumen interior phase characteristics. In detail, we used hot-bitumen-pouring methods to prepare bitumen surface samples and adopted frozen-storage and low-temperature-cutting methods to prepare the internal samples of bitumen in mastics and mixtures. Subsequently, AFM PF-QNM mode was used to collect topographical and nanomechanical property maps of bitumen and bitumen in mastics and mixtures. The results indicated that the bitumen interior only consisted of two phases, where the A-phase presented low adhesion, deformation, and dissipation, while the B-phase presented high adhesion, deformation, and dissipation. A-phase and B-phase of the bitumen interior were close to the periphase and paraphase of the bitumen surface, respectively. Furthermore, the addition of mineral aggregates significantly affected the bitumen interior phase characteristics.

RNF8 induces β-catenin-mediated c-Myc expression and promotes colon cancer proliferation

DNA damage signals transducer RING finger protein 8 (RNF8) is involved in maintaining genomic stability by facilitating the repair of DNA double-strand breaks (DSB) via ubiquitin signaling. By analyzing the TCGA database and colon cancer tissue microarrays, we found that the expression level of RNF8 was positively correlated with that of c-Myc in colon cancer, which were closely associated with poor survival of colon cancer patients. Furthermore, overexpressing and knocking down RNF8 increased and decreased the expression of c-Myc in colon cancer cells, respectively. In addition, RNF8 interacted with β-catenin and facilitated its nuclear translocation by conjugating K63 polyubiquitination on it. These observations suggested a de novo role of RNF8 in promoting the progression of colon cancer by inducing β-catenin-mediated c-Myc expression.

Prognostic evaluation of colorectal cancer using three new comprehensive indexes related to infection, anemia and coagulation derived from peripheral blood

Background: Many indicators of peripheral blood in routine blood test (BRT) results of colorectal cancer (CRC) patients are related to prognosis. Currently, indexes such as NLR (Neutrophil-to- Lymphocyte Ratio), PLR (Platelet-to-Lymphocyte Ratio) and LMR (Lymphocyte-to-Monocyte ratio) evaluate the survival risk of patients by assessing the inflammatory - immune status of CRCs. These indexes are more comprehensive and accurate than independent estimates. We hope to design more effective indexes through fully considering the correlation and significance between BRT indicators and prognosis, so as to play a guiding role in clinical malignant estimation of CRCs.

Methods: 701 CRCs in training set and 256 CRCs in test set were included in the study samples, and their clinical data, tumor pathology results and peripheral blood routine results were collected. The prognosis, progression, and survival status of all patients were determined after follow-up. Above data were used for statistical analysis and designing new indexes.

Results: It was found that high NE, MONO, RDW-CV/SD and PLT in peripheral blood indicated poor prognosis of DFS and OS. Conversely, CRCs with postoperative tumor progression or death had lower LY, EO, RBC, HGB, HCT, MCV, MCH, MCHC, PDW, and P-LCR. IRR, ARR and CRR related to infection, anemia and coagulation were designed respectively using the largest AUC indicators (P<0.05) selected by ROC curve. The formula: IRR= (NE*MONO)/(LY*EO); ARR= (HGB*MCHC)/RDW-CV; CRR=PLT/PDW. Results of Kaplan‑Meier survival analysis and multivariate COX proportional hazard analysis adjusted for age, gender, TNM stage, infiltration, adhesion showed IRR, ARR, CRR were all able to be used as the evaluation standard of survival of CRC. The result was also authenticated in the test set.

Conclusion: We designed three different prognostic indexes of colorectal cancer, IRR, ARR and CRR, which could be used as risk indicators of CRC prognosis, tumor progression and survival.

Gm6377 suppressed SP 2/0 xenograft tumor by down-regulating Myc transcription

PURPOSE

Disturbed process of B-cell differentiation into plasmablasts (PBs)/plasma cells (PCs) is involved in multiple myeloma (MM). New strategies will be required to eliminate the MM cell clone for a long-term disease control. Because of its PB-like characteristics, the mus musculus myeloma SP 2/0 cell line was used in this study to search novel targets for PBs/PCs.

METHODS/PATIENTS

Affymetrix microarrays and RNA-sequencing assays were used to search a novel different molecule (Gm6377) between PBs/PCs and mature B cells. Cell counting kit-8 (CCK8), flow cytometry (FACS), xenograft mouse model, and the luciferase reporter system were used to assess the effect of Gm6377 on SP 2/0 cell proliferation, cell cycle, tumor growth, and Myc promoter activation, respectively.

RESULTS

We found that B cells expressed a high level of Gm6377 mRNA, whereas Gm6377 mRNA was decreased in PCs. In addition, SP 2/0 cells also expressed low levels of Gm6377 mRNA. Critically, Gm6377 overexpression suppressed SP 2/0 cell proliferation but not cell cycle. Furthermore, Gm6377 overexpression suppressed tumor progression in the SP 2/0 xenograft mouse model. Finally, we found that Gm6377 suppressed SP 2/0 cell proliferation by reducing the activation of the Myc promoter.

CONCLUSIONS

These results suggest that Gm6377 suppresses myeloma SP 2/0 cell growth by suppressing Myc. Thus, modulation of Gm6377 may be a potential therapeutic way to treat MM.

p53 protein expression affected by TP53 polymorphism is associated with the biological behavior and prognosis of low rectal cancer

Low rectal cancer is a subtype of colorectal cancer at a special anatomic site with distinct biological behavior. TP53 is one of the most important cancer suppressor genes, and its structural variation and abnormal expression has been revealed to be associated with multiple cancer types. However, to the best of our knowledge, the association of p53 protein expression with its gene polymorphism, biological behavior and prognosis in low rectal cancer has not been clarified. Therefore, the current study aimed to explore these associations. In the present study, 347 patients with low rectal cancer and 353 controls were enrolled. Kompetitive Allele-Specific Polymerase Chain Reaction was used to detect five polymorphic sites of the TP53 gene (rs1042522, rs12947788, rs1625895, rs2909430 and rs12951053), while immunohistochemistry was used to detect the protein expression of TP53. The associations between p53 protein expression and TP53 polymorphism, biological behavior and prognosis in low rectal cancer were systematically analyzed. In low rectal cancer, p53 protein expression was markedly higher in TP53 rs1042522 mutant carriers compared with that in other genotypes where expression was higher in poorly differentiated, III-IV phase and T3-4 phase tumors, and in III-IV phase female patients. The survival time of patients with low p53 protein expression was evidently longer in females, non-smokers and patients >60 years old. In summary, p53 protein expression was identified to be affected by TP53 rs1042522 polymorphism, and was associated with the biological behavior and prognosis of low rectal cancer. TP53 rs1042522 and the associated protein expression could be used as indicators for biological behavior and prognosis in low rectal cancer.

MiR-205 enhances cisplatin sensitivity of glioma cells by targeting E2F1

OBJECTIVE

miR-205 has been previously identified as a diagnostic and prognostic factor in glioma. However, its exact functions in glioma remain unclear. The current research aimed to decipher the role of miR-205 in the development of cisplatin resistance in glioma cells.

MATERIALS AND METHODS

miR-205 expressions in both cisplatin sensitive and resistant cell lines were compared by the Real-time PCR method. The dose-response to cisplatin of U87/DDP cells was determined by MTT assay. Cell cycle and apoptosis were determined by flow cytometry, caspase 3/7 activity assay and Western blot assay. The direct repression of E2F1 by miR-205 was confirmed by luciferase assay and Western blot assay.

RESULTS

miR-205 expression was decreased in cisplatin resistant glioma cell lines, and cisplatin treatment led to a decrease of miR-205 in glioma cells. Overexpression of miR-205 in U87/DDP restored its cisplatin sensitivity by enhancing apoptosis and G1/S cell cycle arrest; notably, all these effects were then partially abrogated by E2F1 overexpression. Luciferase assay and Western blot assay confirmed E2F1 as the direct target of miR-205 in U87/DDP cells.

CONCLUSIONS

These findings suggest that down-regulation of miR-205 confers the cisplatin resistance in glioma cells via upregulation of E2F1. It might serve as a candidate for glioma therapy.

Epigenetic Alternations of MicroRNAs and DNA Methylation Contribute to Liver Metastasis of Colorectal Cancer

BACKGROUND

Liver metastasis is a major cause of mortality in colorectal cancer (CRC). Epigenetic alternations could serve as biomarkers for cancer diagnosis and prognosis. In this study, we analyzed microarray data in order to identify core genes and pathways which contribute to liver metastasis in CRC under epigenetic regulations.

MATERIALS AND METHODS

Data of miRNAs (GSE35834, GSE81582), DNA methylation (GSE90709, GSE77955), and mRNA microarrays (GSE68468, GSE81558) were downloaded from GEO database. Differentially expressed genes (DEGs), differentially expressed miRNAs (DEMs), and differentially methylated genes (DMGs) were obtained by GEO2R. The target genes of DEMs were predicted by miRWalk. Functional and enrichment analyses were conducted by DAVID database. Protein-protein interaction (PPI) network was constructed in STRING and visualized using Cytoscape.

RESULTS

In liver metastasis, miR-143-3p, miR-10b-5p, miR-21-5p, and miR-518f-5p were down-regulated, while miR-122-5p, miR-885-5p, miR-210-3p, miR-130b-5p, miR-1275, miR-139-5p, miR-139-3p, and miR-1290 were up-regulated compared with primary CRC. DEGs targeted by altered miRNAs were enriched in pathways including complement, PPAR signaling, ECM-receptor interaction, spliceosome, and focal adhesion. In addition, aberrant DNA methylation-regulated genes showed enrichment in pathways of amino acid metabolism, calcium signaling, TGF-beta signaling, cell cycle, spliceosome, and Wnt signaling.

CONCLUSION

Our study identified a series of differentially expressed genes which are associated with epigenetic alternations of miRNAs and DNA methylation in colorectal liver metastasis. Up-regulated genes of SLC10A1, MAPT, SHANK2, PTH1R, and C2, as well as down-regulated genes of CAB39, CFLAR, CTSC, THBS1, and TRAPPC3 were associated with both miRNA and DNA methylation, which might become promising biomarker of colorectal liver metastasis in future.

Five P53 SNPs Involved in Low Rectal Cancer Risk and Prognosis in a Chinese Population

Although the impact and potential mechanisms of p53 polymorphisms on human malignancies have been intensively studied, analyses for association between p53 polymorphisms and colorectal cancer (CRC) risk were still limited to some common variants. Moreover, the majority of previous studies did not classify the specimens of CRC based on tumor location. This case-control study aimed to evaluate the association of five p53 polymorphisms (rs1042522, rs12947788, rs1625895, rs2909430 and rs12951053) with the risk of low rectal cancer (LRC) and investigate the prognostic significance. A total of 347 cases and 353 controls from a Chinese population were recruited and genotyped using KASP assay. Individuals carrying the variant rs12947788 A allele were observed to associate with an increased risk of LRC. After stratification for clinicopathological parameters, rs12947788 was significantly co-related with the histological type of LRC under a dominant model. Although none of the selected p53 polymorphisms was significantly associated with patient prognosis in total population, significant associations with the overall survival were revealed in the heterozygosis carriers vs. wild type carriers model through subgroup analyses based on clinical characteristics. Moreover, haplotype analyses showed that C-A-G-A-A haplotype was associated with a significantly higher LRC risk as compared to the other haplotypes. In low rectal cancer, P53 protein expression was obviously higher in p53 rs1042522 mutant carriers than in other genotypes. Our study further proves the involvement of p53 polymorphisms in pathogenesis of LRC and may provide potential therapeutic implications.

Genetic Polymorphisms of DNA Repair Pathways in Sporadic Colorectal Carcinogenesis

DNA repair systems play a critical role in maintaining the integrity and stability of the genome, which mainly include base excision repair (BER), nucleotide excision repair (NER), mismatch repair (MMR) and double-strand break repair (DSBR). The polymorphisms in different DNA repair genes that are mainly represented by single-nucleotide polymorphisms (SNPs) can potentially modulate the individual DNA repair capacity and therefore exert an impact on individual genetic susceptibility to cancer. Sporadic colorectal cancer arises from the colorectum without known contribution from germline causes or significant family history of cancer or inflammatory bowel disease. In recent years, emerging studies have investigated the association between polymorphisms of DNA repair system genes and sporadic CRC. Here, we review recent insights into the polymorphisms of DNA repair pathway genes, not only individual gene polymorphism but also gene-gene and gene-environment interactions, in sporadic colorectal carcinogenesis.

Combining Red Blood Cell Distribution Width (RDW-CV) and CEA Predict Poor Prognosis for Survival Outcomes in Colorectal Cancer

Background: Colorectal cancer is one of the common tumors that seriously threaten human health worldwide. Serum tumor markers, including CEA and CA19-9, have become the focus of research on colorectal cancer in recent years. As one of the classic blood test results, RDW is related to the pathological features, diagnosis and prognosis of various cancers in recent studies. We hope to search the correlation between RDW and the pathological features of colorectal cancer through the following studies, explore the potential relationship between RDW and the prognosis of colorectal cancer, and find a more effective prognostic evaluation method by combining other blood markers.

Methods: We retrospectively analyzed 168 patients with colorectal cancer included in this study, collected their clinical data, tumor pathological features and their preoperative blood test results including RDW value and tumor markers, and grouped them. After 3 and 5 years of follow-up, the recurrence and survival status were defined, and the above data were statistically analyzed.

Results: The distribution frequency/rate of abnormal RDW-CV in colorectal cancer patients was significantly increased in the elderly (>62), colon cancer, serosal permeability, lymph node metastasis, stage III and IV, peripheral adhesion (P < 0.05). Furthermore, RDW-CV was significantly positively correlated with abnormal high values of tumor serum markers CEA and CA19-9 (P < 0.05). More importantly, ROC curve analysis found that the abnormal increase in RDW-CV in colorectal cancer was associated with the shortening of DFS and OS in patients who were followed up for 3 and 5 years (P < 0.05). Further combined with CEA, it was found that the prognosis and survival of patients with colorectal cancer in 3 and 5 years were more accurate and effective than independent prediction (AUC of DFS in 3/5years=0.630/0.635, AUC of OS in 3/5 years=0.692/0.652).

Conclusion: RDW-CV is correlated with the pathological features of colorectal cancer, indicating a worse malignant tendency of tumor. RDW-CV can independently evaluate the prognosis of colorectal cancer patients, and combined with the high value of CEA, it can effectively indicate the adverse recurrence and survival prognosis.

Expression of DDB2 Protein in the Initiation, Progression, and Prognosis of Colorectal Cancer

BACKGROUND

Damage-specific DNA binding protein 2 (DDB2) is implicated in the recognition of DNA damage and the initiation of nucleotide excision repair process. The aim of this study was to explore the role of DDB2 in the initiation, progression, and prognosis of colorectal cancer (CRC).

METHODS

Totally tissues of 300 CRC and 300 adjacent, 267 colorectal adenoma (CRA) and 214 normal (NOR) were collected. The expression of DDB2 protein was detected by immunohistochemical staining.

RESULTS

DDB2 protein was highly expressed in CRC and CRA compared with NOR (P < 0.001, respectively) in the dynamic sequence of NOR → CRA → CRC; CRC tissue demonstrated increased DDB2 expression compared with non-tumor adjacent tissues (P < 0.001). DDB2 expression was higher in T1-T2 than that in T3-T4 in CRC (P = 0.023); cloddy/nested CRC demonstrated increased DDB2 expression than infiltrative CRC (P = 0.007). Survival analysis showed that high DDB2 expression was associated with favorable survival in colon cancer (adjusted HR 0.20, 95% CI 0.06-0.72, P = 0.014) and female CRC patients (adjusted HR 0.27, 95% CI 0.08-0.92, P = 0.036).

CONCLUSION

DDB2 protein expression was associated with the initiation, progression, and prognosis of CRC, and might function as a tumor biomarker for the diagnosis and prognosis of CRC.

SNP interactions of PGC with its neighbor lncRNAs enhance the susceptibility to gastric cancer/atrophic gastritis and influence the expression of involved molecules

Multidimensional interactions of multiple factors are more important in promoting cancer initiation. Gene-gene interactions between protein-coding genes have been paid great attention, while rare studies refer to the interactions between encoding and noncoding genes. Our research group previously found encoding gene PGC polymorphisms could affect the susceptibility to atrophic gastritis (AG) and gastric cancer (GC). Interestingly, several SNPs in long noncoding RNA (lncRNA) genes, just adjacent to PGC, were found to be associated with AG risk and GC prognosis afterward. This study aims to explore the SNP interactions between PGC and its neighbor lncRNAs on the risk of AG and GC. Genotyping for seven PGC SNPs and seven lncRNA SNPs was conducted using Sequenom MassARRAY platform in a total of 2228 northern Chinese subjects, including 536 GC cases, 810 AG cases, and 882 controls. We found 15 pairwise PGC-lncRNAs SNPs had interactions: Five pairs were associated with AG risk, and ten pairs were associated with GC risk. Moreover, two GC-related interactions PGC rs6939861 with lnc-C6orf-132-1 rs7749023 and rs7747696 survived the Bonferroni correction (P_correction  = 0.049 and 0.007, respectively). Several combinations showed obvious epistasis and cumulative effects on disease risk. Some three-way interactions of SNPs with smoking and drinking could also be observed. Besides, a few interacting SNPs showed correlations with the expression levels of PGC protein and related lncRNAs in serum. Our study would provide research clues for further screening combination biomarkers uniting both protein-coding and noncoding genes with the potential in prediction of the susceptibility to GC and its precursor.

The Src homology and collagen A (ShcA) adaptor protein may participate in the pathogenesis of membranous lupus nephritis

The Src homology and collagen A (ShcA) adaptor protein that binds to tyrosine kinase receptors. ShcA plays a role in insulin signaling, stress resistance and energy metabolism. The 66-kDa Src homology 2 domain-containing protein (p66shc) belongs to the ShcA family and has been associated with reactive oxygen species (ROS); increased ROS is involved in the pathology of lupus nephritis (LN). However, whether ShcA can act as a biomarker for oxidative injury in LN is unknown. This study is aimed to investigate the ShcA expression in kidney tissues from patients presenting with LN and the association between ShcA expression and clinical parameters. Renal biopsy tissues were obtained from 62 LN, 20 primary membranous nephropathy (MN) and 10 other secondary MN patients. ShcA was measured by immunofluorescence. The expression of ShcA in the membranous lupus nephritis (class V) group showed a higher trend but there were no significant differences compared with pure mesangial disease (class II) and proliferative (Class III/IV) lupus nephritis. ShcA deposits were negative in primary and other secondary MN. ShcA might act as a new biomarker and a diagnostic tool to identify membranous lupus nephritis with other MN.

High expression of microRNA‑31 and its host gene LOC554202 predict favorable outcomes in patients with colorectal cancer treated with oxaliplatin

The expression levels of microRNA‑31 (miR‑31) and LOC554202 have been previously investigated in colorectal cancer (CRC) and their oncogenic and/or tumor suppressive roles have been described. The aim of the present study was to examine the role of miR‑31 and its host gene LOC554202 in the prognosis of patients with CRC. Patients with CRC treated with oxaliplatin‑based chemotherapy between June 2005 and March 2010 were recruited to the First Affiliated Hospital of China Medical University. Tumor and adjacent mucosal tissues were collected. The detection of miR‑31 and/or LOC554202 was performed with probe hybridization targeting. Correlation analysis was performed among the expression levels of miR‑31, LOC554202, and their association with clinicopathological parameters and/or survival rates. miR‑31 and LOC554202 were expressed at high levels in CRC (P<0.01) compared with adjacent intestinal mucosa. A linear correlation was noted for the two markers in CRC tissues (P<0.01). The expression of miR‑31 was significantly higher in adenocarcinoma than in the adjacent intestinal mucosa (P<0.01), whereas the expression of LOC554202 was significantly higher in the adenocarcinoma and the rectal cancer tissue regions (P<0.01). The high expression levels of miR‑31 and LOC554202 were associated with high disease‑free survival (DFS) and overall survival (OS) rates (P<0.05). Associations between the increase in DFS and OS and the elevated expression levels of miR‑31 and LOC554202 were present in patients with colon cancer but not in patients with rectal cancer (P<0.05). These data indicated that miR‑31 and LOC554202 may be potential markers for evaluation of the prognosis of patients treated with oxaliplatin‑based chemotherapy.

DNA repair protein XPA is differentially expressed in colorectal cancer and predicts better prognosis

As an indispensable factor in DNA damage recognition step of nucleotide excision repair, XPA interacts with a series of proteins to initiate repair process. The expression characteristics of XPA in colorectal cancer (CRC) and its influence on CRC prognosis remain elusive. Tissue specimens of CRC and nontumor adjacent tissues from 283 patients were collected. XPA protein expressions were detected by immunohistochemistry staining. Nonparametric test was used to investigate the difference of XPA expression between CRC and nontumor adjacent tissues, as well as the correlation between XPA expression and clinicopathological parameters of CRC. Univariate and multivariate Cox proportional hazards models were applied to estimate the relationship between XPA expression and CRC prognosis. Meanwhile, we analyzed TCGA data to investigate the relation between XPA mRNA expression and survival of CRC. XPA protein expression was significantly decreased in CRC tissues compared with nontumor adjacent tissues (P = 0.001). Subgroup analysis indicated consistently significant down-regulation of XPA in CRC tissues in age > 60 (P = 0.026), age ≤ 60 (P = 0.008), colon cancer (P = 0.009), and rectal cancer (P = 0.015) patients and males (P = 0.004). For clinicopathological parameters, CRC patients with drinking habits revealed XPA overexpression than nondrinkers (P = 0.032). For prognosis, CRC patients with high XPA protein expression had longer overall survival (OS) (HR = 0.62, 95%CI: 0.39-0.97, P = 0.037). Stratified analysis suggested a better prognosis in relation to high XPA protein expression in patients over 60 years (adjusted HR = 0.48, P = 0.021), with rectal cancer (HR = 0.56, P = 0.037), without distant metastasis (HR = 0.58, P = 0.033), without tumor deposits (HR = 0.40, P = 0.006; adjusted HR = 0.44, P = 0.028), and with tumor diameter over 4 cm (HR = 0.49, P = 0.023). DNA repair protein XPA is significantly decreased in colorectal cancer tissues than in adjacent nontumor tissues. High expression of XPA protein showed significant relationship with better survival of CRC, especially rectal cancer. XPA might be a novel biomarker but might not be an independent factor to predict prognosis of CRC patients.

Copy number variation and high expression of DNA topoisomerase II alpha predict worse prognosis of cancer: a meta-analysis

Background: Increasing numbers of literatures have investigated the association between TOP2A and cancer prognosis. But the results of the relationship between the two were inconclusive. The aim of this meta-analysis was to elucidate whether TOP2A could predict prognosis of cancer. Materials and Methods: A systematically searching for potentially valuable literature was conducted through electronic databases containing PubMed and Web of Science. Hazard Ratio (HR) and their 95% confidence interval (CI) were used to assess the strength of association between TOP2A and cancer prognosis. Results: Finally twenty-five studies were included in this meta-analysis. High expression of TOP2A was associated with shorter disease free survival (DFS) of cancer prognosis compared with low expression of TOP2A (HR= 1.36, 95% CI= 1.18-1.57, P<0.001). Amplification of TOP2A gene showed no significant association with overall survival (OS), disease free survival (DFS) or relapse free survival (RFS) compared with non-amplification of TOP2A (OS: HR= 0.96, 95%CI= 0.75-1.22, P= 0.735; DFS: HR= 0.93, 95%CI= 0.70-1.23, P= 0.621; RFS: HR= 0.97, 95%CI= 0.71-1.34, P= 0.867). In the subgroup of regions, TOP2A amplification was associated with longer overall survival (HR= 0.66, 95%CI= 0.46-0.96, P= 0.029) in Australia. Alteration (amplification or deletion) of TOP2A gene demonstrated shorter survival according to OS and RFS compared with those with normal TOP2A status (OS: HR= 1.37, 95%CI= 1.22-1.55, P<0.001; RFS: HR= 1.26, 95%CI= 1.12-1.41, P<0.001). Conclusion: High TOP2A expression suggested significant relationship with worse cancer prognosis. Alteration (amplification or deletion) of TOP2A gene was also significantly related to shorter survival of cancer patients. Therefore, TOP2A might be used as an indicator for poor prognosis of cancer in the future.

Alternative splicing events implicated in carcinogenesis and prognosis of colorectal cancer

Background: Emerging evidence suggested that aberrant alternative splicing (AS) is pervasive event in development and progression of cancer. However, the information of aberrant splicing events involved in colorectal carcinogenesis and progression is still elusive. Materials and Methods: In this study, splicing data of 499 colon adenocarcinoma cases (COAD) and 176 rectum adenocarcinoma (READ) with clinicopathological information were obtained from The Cancer Genome Atlas (TCGA) to explore the changes of alternative splicing events in relation to the carcinogenesis and prognosis of colorectal cancer (CRC). Gene interaction network construction, functional and pathway enrichment analysis were performed by multiple bioinformatics tools. Results: Overall, most AS patterns were more active in CRC tissues than adjacent normal ones. We detected altogether 35391 AS events of 9084 genes in COAD and 34900 AS events of 9032 genes in READ, some of which were differentially spliced between cancer tissues and normal tissues including genes of SULT1A2, CALD1, DTNA, COL12A1 and TTLL12. Differentially spliced genes were enriched in biological process including muscle organ development, cytoskeleton organization, actin cytoskeleton organization, biological adhesion, and cell adhesion. The integrated predictor model of COAD showed an AUC of 0.805 (sensitivity: 0.734; specificity: 0.756) while READ predictor had an AUC of 0.738 (sensitivity: 0.614; specificity: 0.900). In addition, a number of prognosis-associated AS events were discovered, including genes of PSMD2, NOL8, ALDH4A1, SLC10A7 and PPAT. Conclusion: We draw comprehensive profiles of alternative splicing events in the carcinogenesis and prognosis of CRC. The interaction network and functional connections were constructed to elucidate the underlying mechanisms of alternative splicing in CRC.

Expression of Minichromosome Maintenance Proteins (MCM) and Cancer Prognosis: A meta-analysis

Minichromosome maintenance proteins (MCM) played a critical role in replication and cell cycle progression. However, their prognostic roles in cancer remain controversial. Therefore, we performed a meta-analysis to investigate the prognostic value of MCMs in cancers. Totally 31 eligible articles with 7653 cancer patients were included in this meta-analysis. We evaluated the relationship between MCMs expression and overall survival (OS) in various cancer patients by using pooled hazard ratios (HRs) and risk ratios (RRs) with 95% confidence intervals (CIs). The meta-analysis showed that carriers with high expression of MCM5 and MCM7 were significantly associated with short OS for pooled HR (HR=1.04, 95% CI=1.01-1.08, P=0.020, HR=1.78, 95% CI=1.04-3.02, P=0.035, respectively). For pooled RR, individuals with increased MCM2 and MCM7 expression were significantly correlated with poor OS (RR=2.30, 95% CI=1.14-4.63, P=0.019; RR=3.52, 95% CI=2.01-6.18, P<0.001, respectively). The findings suggest that high expression of MCM2, MCM5 and MCM7 might serve as predictive biomarkers for poor prognosis in cancers.