HiChIP-Based Epigenomic Footprinting Identifies a Promoter Variant of UXS1 That Confers Genetic Susceptibility to Gastroesophageal Cancer.

Genome-wide association studies (GWAS) have identified more than a hundred single nucleotide variants (SNV) associated with the risk of gastroesophageal cancer (GEC). The majority of the identified SNVs map to noncoding regions of the genome. Uncovering the causal SNVs and genes they modulate could help improve GEC prevention and treatment. Herein, we used HiChIP against histone 3 lysine 27 acetylation (H3K27ac) to simultaneously annotate active promoters and enhancers, identify the interactions between them, and detect nucleosome-free regions (NFR) harboring potential causal SNVs in a single assay. The application of H3K27ac HiChIP in GEC relevant models identified 61 potential functional SNVs that reside in NFRs and interact with 49 genes at 17 loci. The approach led to a 67% reduction in the number of SNVs in linkage disequilibrium at these 17 loci, and at 7 loci, a single putative causal SNV was identified. One SNV, rs147518036, located within the promoter of the UDP-glucuronate decarboxylase 1 (UXS1) gene, seemed to underlie the GEC risk association captured by the rs75460256 index SNV. The rs147518036 SNV creates a GABPA DNA recognition motif, resulting in increased promoter activity, and CRISPR-mediated inhibition of the UXS1 promoter reduced the viability of the GEC cells. These findings provide a framework that simplifies the identification of potentially functional regulatory SNVs and target genes underlying risk-associated loci. In addition, the study implicates increased expression of the enzyme UXS1 and activation of its metabolic pathway as a predisposition to gastric cancer, which highlights potential therapeutic avenues to treat this disease. Significance: Epigenomic footprinting using a histone posttranslational modification targeted 3D genomics methodology elucidates functional noncoding sequence variants and their target genes at cancer risk loci.

CCT-Unet: A U-Shaped Network Based on Convolution Coupled Transformer for Segmentation of Peripheral and Transition Zones in Prostate MRI.

The accurate segmentation of prostate region in magnetic resonance imaging (MRI) can provide reliable basis for artificially intelligent diagnosis of prostate cancer. Transformer-based models have been increasingly used in image analysis due to their ability to acquire long-term global contextual features. Although Transformer can provide feature representations of the overall appearance and contour representations at long distance, it does not perform well on small-scale datasets of prostate MRI due to its insensitivity to local variation such as the heterogeneity of the grayscale intensities in the peripheral zone and transition zone across patients; meanwhile, the convolutional neural network (CNN) could retain these local features well. Therefore, a robust prostate segmentation model that can aggregate the characteristics of CNN and Transformer is desired. In this work, a U-shaped network based on the convolution coupled Transformer is proposed for segmentation of peripheral and transition zones in prostate MRI, named the convolution coupled Transformer U-Net (CCT-Unet). The convolutional embedding block is first designed for encoding high-resolution input to retain the edge detail of the image. Then the convolution coupled Transformer block is proposed to enhance the ability of local feature extraction and capture long-term correlation that encompass anatomical information. The feature conversion module is also proposed to alleviate the semantic gap in the process of jumping connection. Extensive experiments have been conducted to compare our CCT-Unet with several state-of-the-art methods on both the ProstateX open dataset and the self-bulit Huashan dataset, and the results have consistently shown the accuracy and robustness of our CCT-Unet in MRI prostate segmentation.

Four-quadrant fast compressive tracking of breast ultrasound videos for computer-aided response evaluation of neoadjuvant chemotherapy in mice.

BACKGROUND AND OBJECTIVE: Neoadjuvant chemotherapy (NAC) is a valuable treatment approach for locally advanced breast cancer. Contrast-enhanced ultrasound (CEUS) potentially enables the assessment of therapeutic response to NAC. In order to evaluate the response accurately, quantitatively and objectively, a method that can effectively compensate motions of breast cancer in CEUS videos is urgently needed. METHODS: We proposed the four-quadrant fast compressive tracking (FQFCT) approach to automatically perform CEUS video tracking and compensation for mice undergoing NAC. The FQFCT divided a tracking window into four smaller windows at four quadrants of a breast lesion and formulated the tracking at each quadrant as a binary classification task. After the FQFCT of breast cancer videos, the quantitative features of CEUS including the mean transit time (MTT) were computed. All mice showed a pathological response to NAC. The features between pre- (day 1) and post-treatment (day 3 and day 5) in these responders were statistically compared. RESULTS: When we tracked the CEUS videos of mice with the FQFCT, the average tracking error of FQFCT was 0.65 mm, reduced by 46.72% compared with the classic fast compressive tracking method (1.22 mm). After compensation with the FQFCT, the MTT on day 5 of the NAC was significantly different from the MTT before NAC (day 1) (p = 0.013). CONCLUSIONS: The FQFCT improves the accuracy of CEUS video tracking and contributes to the computer-aided response evaluation of NAC for breast cancer in mice.

A predominant enhancer co-amplified with the SOX2 oncogene is necessary and sufficient for its expression in squamous cancer.

Amplification and overexpression of the SOX2 oncogene represent a hallmark of squamous cancers originating from diverse tissue types. Here, we find that squamous cancers selectively amplify a 3' noncoding region together with SOX2, which harbors squamous cancer-specific chromatin accessible regions. We identify a single enhancer e1 that predominantly drives SOX2 expression. Repression of e1 in SOX2-high cells causes collapse of the surrounding enhancers, remarkable reduction in SOX2 expression, and a global transcriptional change reminiscent of SOX2 knockout. The e1 enhancer is driven by a combination of transcription factors including SOX2 itself and the AP-1 complex, which facilitates recruitment of the co-activator BRD4. CRISPR-mediated activation of e1 in SOX2-low cells is sufficient to rebuild the e1-SOX2 loop and activate SOX2 expression. Our study shows that squamous cancers selectively amplify a predominant enhancer to drive SOX2 overexpression, uncovering functional links among enhancer activation, chromatin looping, and lineage-specific copy number amplifications of oncogenes.

The effects of acceptance and commitment therapy on the psychological and physical outcomes among cancer patients: A meta-analysis with trial sequential analysis.

OBJECTIVE: The current study used meta-analysis and trial sequential analysis to estimate the effects of Acceptance and Commitment Therapy (ACT) on the psychological and physical distress of cancer patients, and to identify potential moderators in this body of research. METHODS: A search of multiple databases in February 2020 identified 25 independent trials (17 randomized controlled trials, 8 non-randomized controlled trials; 2256 participants) on the effects of ACT among cancer patients. Trial sequential analysis (TSA) was used to determine whether the available evidence is sufficient to draw strong conclusions. RESULTS: ACT significantly reduced cancer patients' psychological distress (g = 0.88), and improved psychological flexibility (g = 0.58), quality of life (g = 1.19), and sense of hope (g = 2.17). TSA showed that there was sufficient evidence to obtain stable estimates of the effect of ACT on psychological distress and quality of life. Effect sizes for psychological distress were larger in studies conducted in eastern countries, in younger samples, and when therapy was of longer duration. CONCLUSION: Acceptance and Commitment Therapy can effectively improve the mental health of cancer patients, and can be applied to clinical practice as an effective psychological intervention. Researchers are encouraged to take into account stage and trajectory of cancer in future studies.

A single intranasal administration of virus-like particle vaccine induces an efficient protection for mice against human respiratory syncytial virus.

Human respiratory syncytial virus (RSV) is an important pediatric pathogen causing acute viral respiratory disease in infants and young children. However, no licensed vaccines are currently available. Virus-like particles (VLPs) may bring new hope to producing RSV VLP vaccine with high immunogenicity and safety. Here, we constructed the recombinants of matrix protein (M) and fusion glycoprotein (F) of RSV, respectively into a replication-deficient first-generation adenoviral vector (FGAd), which were used to co-infect Vero cells to assemble RSV VLPs successfully. The resulting VLPs showed similar immunoreactivity and function to RSV virion in vitro. Moreover, Th1 polarized response, and effective mucosal virus-neutralizing antibody and CD8+ T-cell responses were induced by a single intranasal (i.n.) administration of RSV VLPs rather than intramuscular (i.m.) inoculation, although the comparable RSV F-specific serum IgG and long-lasting RSV-specific neutralizing antibody were detected in the mice immunized by both routes. Upon RSV challenge, VLP-immunized mice showed increased viral clearance but decreased signs of enhanced lung pathology and fewer eosinophils compared to mice immunized with formalin-inactivated RSV (FI-RSV). In addition, a single i.n. RSV VLP vaccine has the capability to induce RSV-specific long-lasting neutralizing antibody responses observable up to 15 months. Our results demonstrate that the long-term and memory immune responses in mice against RSV were induced by a single i.n. administration of RSV VLP vaccine, suggesting a successful approach of RSV VLPs as an effective and safe mucosal vaccine against RSV infection, and an applicable and qualified platform of FGAd-infected Vero cells for VLP production.

Push Force Analysis of Anchor Block of the Oil and Gas Pipeline in a Single-Slope Tunnel Based on the Energy Balance Method.

In this paper, a single-slope tunnel pipeline was analysed considering the effects of vertical earth pressure, horizontal soil pressure, inner pressure, thermal expansion force and pipeline-soil friction. The concept of stagnation point for the pipeline was proposed. Considering the deformation compatibility condition of the pipeline elbow, the push force of anchor blocks of a single-slope tunnel pipeline was derived based on an energy method. Then, the theoretical formula for this force is thus generated. Using the analytical equation, the push force of the anchor block of an X80 large-diameter pipeline from the West-East Gas Transmission Project was determined. Meanwhile, to verify the results of the analytical method, and the finite element method, four categories of finite element codes were introduced to calculate the push force, including CAESARII, ANSYS, AutoPIPE and ALGOR. The results show that the analytical results agree well with the numerical results, and the maximum relative error is only 4.1%. Therefore, the results obtained with the analytical method can satisfy engineering requirements.

Sublingual administration of a helper-dependent adenoviral vector expressing the codon-optimized soluble fusion glycoprotein of human respiratory syncytial virus elicits protective immunity in mice.

Sublingual (s.l.) immunization has been described as a convenient and safe way to induce mucosal immune responses in the respiratory and genital tracts. We constructed a helper-dependent adenoviral (HDAd) vector expressing a condon-optimized soluble fusion glycoprotein (sFsyn) of respiratory syncytial virus (HDAd-sFsyn) and explored the potential of s.l. immunization with HDAd-sFsyn to stimulate immune responses in the respiratory mucosa. The RSV specific systemic and mucosal immune responses were generated in BALB/c mice, and the serum IgG with neutralizing activity was significantly elevated after homologous boost with s.l. application of HDAd-sFsyn. Humoral immune responses could be measured even 14weeks after a single immunization. Upon challenge, s.l. immunization with HDAd-sFsyn displayed an effective protection against RSV infection. These findings suggest that s.l. administration of HDAd-sFsyn acts as an effective and safe mucosal vaccine against RSV infection, and may be a useful tool in the prevention of RSV infection.

Repurposing CRISPR/Cas9 for in situ functional assays.

RNAi combined with next-generation sequencing has proven to be a powerful and cost-effective genetic screening platform in mammalian cells. Still, this technology has its limitations and is incompatible with in situ mutagenesis screens on a genome-wide scale. Using p53 as a proof-of-principle target, we readapted the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR associated 9) genome-editing system to demonstrate the feasibility of this methodology for targeted gene disruption positive selection assays. By using novel "all-in-one" lentiviral and retroviral delivery vectors heterologously expressing both a codon-optimized Cas9 and its synthetic guide RNA (sgRNA), we show robust selection for the CRISPR-modified Trp53 locus following drug treatment. Furthermore, by linking Cas9 expression to GFP fluorescence, we use an "all-in-one" system to track disrupted Trp53 in chemoresistant lymphomas in the Eµ-myc mouse model. Deep sequencing analysis of the tumor-derived endogenous Cas9-modified Trp53 locus revealed a wide spectrum of mutants that were enriched with seemingly limited off-target effects. Taken together, these results establish Cas9 genome editing as a powerful and practical approach for positive in situ genetic screens.

Effects of allogeneic blood transfusion in patients with stage II colon cancer.

The aim of the present study was to determine whether allogeneic red blood cell transfusions showed a deleterious effect and what might be preoperative risk factors for blood transfusion in patients with TNM stage II colon cancer. Total 470 patients who fulfilled inclusion criteria were selected for a further 10-year follow-up study. We found that there were statistical significance between non-transfused and transfused group in mortality (P=0.018), local recurrence (P=0.000) and distant metastasis (P=0.040). Local recurrence and distant metastasis between 1 to 3 units and more than 3 units group did not show any significant differences. There was no difference in survival rate between non-transfused and 1 to 3 units group (log rank =0.031, P=0.860). The difference between different blood transfusion volume in transfused patients was found (78.77% vs 63.83%, P=0.006). Meanwhile, the significant difference of survival rate was existed between non-transfused group and more than 3 units group (84.83% vs 63.83%, P=0.002 ). Univariate analysis showed the following 3 variables to be associated with an increased risk of allogeneic blood transfusions: preoperative CEA level (P<0.05), location of tumor (P<0.01) and diameter of tumor (P<0.01). Multivariate analysis revealed that location of tumor and diameter of tumor are two independent factors for requirement of perioperative transfusions. Therefore, allogeneic transfusion increase the postoperative tumor mortality, local recurrence and distant metastasis in patients with stage II colon cancer. The postoperative tumor mortality, local recurrence and distant metastasis were not associated with the blood transfusion volume. The blood transfusion volume was associated with the survival rate. Location of tumor and diameter of tumor were the independent preoperative risk factors for blood transfusion.

Regulation of cisplatin resistance and homologous recombinational repair by the TFIIH subunit XPD.

We have recently completed screening of the National Cancer Institute human tumor cell line panel and demonstrated that among four nucleotide excision repair proteins (XPA, XPB, XPD, and ERCC1), only the TFIIH subunit XPD endogenous protein levels correlate with alkylating agent drug resistance. In the present study, we extended this work by investigating the biological consequences of XPD overexpression in the human glioma cell line SK-MG-4. Our results indicate that XPD overexpression in SK-MG-4 cells leads to cisplatin resistance without affecting the nucleotide excision repair activity or UV light sensitivity of the cell. In contrast, in SK-MG-4 cells treated with cisplatin, XPD overexpression leads to increased Rad51-related homologous recombinational repair, increased sister chromatid exchanges, and accelerated interstrand cross-link removal. Moreover, we present biochemical evidence of an XPD-Rad51 protein interaction, which is modulated by DNA damage. To our knowledge, this is the first description of functional cross-talk between XPD and Rad51, which leads to bifunctional alkylating agent drug resistance and accelerated removal of interstrand cross-links.