Three-dimensional chromatin landscapes in hepatocellular carcinoma associated with hepatitis B virus.

BACKGROUND: Three-dimensional (3D) chromatin architecture frequently altered in cancer. However, its changes during the pathogenesis of hepatocellular carcinoma (HCC) remained elusive. METHODS: Hi-C and RNA-seq were applied to study the 3D chromatin landscapes and gene expression of HCC and ANHT. Hi-C Pro was used to generate genome-wide raw interaction matrices, which were normalized via iterative correction (ICE). Moreover, the chromosomes were divided into different compartments according to the first principal component (E1). Furthermore, topologically associated domains (TADs) were visualized via WashU Epigenome Browser. Furthermore, differential expression analysis of ANHT and HCC was performed using the DESeq2 R package. Additionally, dysregulated genes associated with 3D genome architecture altered were confirmed using TCGA, qRT-PCR, immunohistochemistry (IHC), etc. RESULTS: First, the intrachromosomal interactions of chr1, chr2, chr5, and chr11 were significantly different, and the interchromosomal interactions of chr4-chr10, chr13-chr21, chr15-chr22, and chr16-chr19 are remarkably different between ANHT and HCC, which resulted in the up-regulation of TP53I3 and ZNF738 and the down-regulation of APOC3 and APOA5 in HCC. Second, 49 compartment regions on 18 chromosomes have significantly switched (A-B or B-A) during HCC tumorigenesis, contributing to up-regulation of RAP2A. Finally, a tumor-specific TAD boundary located on chr5: 6271000-6478000 and enhancer hijacking were identified in HCC tissues, potentially associated with the elevated expression of MED10, whose expression were associated with poor prognosis of HCC patients. CONCLUSION: This study demonstrates the crucial role of chromosomal structure variation in HCC oncogenesis and potential novel biomarkers of HCC, laying a foundation for cancer precision medicine development.

Effect of dapagliflozin on liver and pancreatic fat in patients with type 2 diabetes and non-alcoholic fatty liver disease.

AIMS: To evaluate the effect of dapagliflozin on liver fat content (LFC) and pancreatic fat content (PFC). MATERIALS AND METHODS: 84 patients with type 2 diabetes (T2D) and non-alcoholic fatty liver disease (NAFLD) were randomly assigned to receive either dapagliflozin (n = 42) or serve as controls (n = 42). The primary endpoint is changes in LFC and PFC using magnetic resonance imaging estimated proton density fat fraction. Secondary outcomes include liver fibrosis index, inflammatory cytokine levels, and liver enzyme levels. RESULTS: At week 24, the dapagliflozin group significantly reduced LFC (P < 0.001) and PFC (P = 0.033) compared to the control group. Differences were also observed in serum levels of tumor necrosis factor-α (TNF-α) (P = 0.004), interleukin-6 (IL-6) (P = 0.001), and alanine aminotransferase (ALT) (P < 0.001) between the two groups. CONCLUSIONS: Dapagliflozin can significantly decrease LFC and PFC in patients with T2D and NAFLD. It also improves serum ALT, TNF-α, and IL-6 levels, making it a promising treatment option for NAFLD. The trial is registered on Chinese Clinical Trial Registry (Registration No. ChiCTR2100054612).

Immune escape mechanisms and immunotherapy of urothelial bladder cancer.

BACKGROUND AND AIM: Urothelial bladder cancer (UBC) is a common malignant tumor of the urogenital system with a high rate of recurrence. Due to the sophisticated and largely unexplored mechanisms of tumorigenesis of UBC, the classical therapeutic approaches including transurethral resection and radical cystectomy combined with chemotherapy have remained unchanged for decades. However, with increasingly in-depth understanding of the microenvironment and the composition of tumor-infiltrating lymphocytes of UBC, novel immunotherapeutic strategies have been developed. Bacillus Calmette-Guerin (BCG) therapy, immune checkpoint blockades, adoptive T cell immunotherapy, dendritic cell (DC) vaccines, etc., have all been intensively investigated as immunotherapies for UBC. This review will discuss the recent progress in immune escape mechanisms and immunotherapy of UBC. METHODS: Based on a comprehensive search of the PubMed and ClinicalTrials.gov database, this review included the literature reporting the immune escape mechanisms of UBC and clinical trials assessing the effect of immunotherapeutic strategies on tumor or immune cells in UBC patients published in English between 1999 and 2020. RESULTS: Immune surveillance, immune balance, and immune escape are the three major processes that occur during UBC tumorigenesis. First, the role of immunosuppressive cells, immunosuppressive molecules, immunosuppressive signaling molecules, and DCs in tumor microenvironment is introduced elaborately in the immune escape mechanisms of UBC section. In addition, recent progress of immunotherapies including BCG, checkpoint inhibitors, cytokines, adoptive T cell immunotherapy, DCs, and macrophages on UBC patients are summarized in detail. Finally, the need to explore the mechanisms, molecular characteristics and immune landscape during UBC tumorigenesis and development of novel and robust immunotherapies for UBC are also proposed and discussed. CONCLUSION: At present, BCG and immune checkpoint blockades have been approved by the US Food and Drug Administration for the treatment of UBC patients and have achieved encouraging therapeutic results, expanding the traditional chemotherapy and surgery-based treatment for UBC. RELEVANCE FOR PATIENTS: Immunotherapy has achieved desirable results in the treatment of UBC, which not only improve the overall survival but also reduce the recurrence rate and the occurrence of treatment-related adverse events of UBC patients. In addition, the indicators to predict the effectiveness and novel therapy strategies, such as combination regimen of checkpoint inhibitor with checkpoint inhibitor or chemotherapy, should be further studied.

[Molecular markers and mechanisms for stemness maintenance of liver cancer stem cells: a review].

Primary liver cancer (PLC) is an aggressive tumor and prone to metastasize and recur. According to pathological features, PLC are mainly categorized into hepatocellular carcinoma, intrahepatic cholangiocarcinoma, mixed hepatocellular cholangiocarcinoma, and fibrolamelic hepatocellular carcinoma, etc. At present, surgical resection, radiotherapy and chemotherapy are still the main treatments for PLC, but the specificities are poor and the clinical effects are limited with a 5-year overall survival rate of 18%. Liver cancer stem cells (LCSCs) are a specific cell subset existing in liver cancer tissues. They harbor the capabilities of self-renewal and strong tumorigenicity, driving tumor initiation, metastasis, drug resistance and recurrence of PLC. Therefore, the identification of molecular markers and the illustration of mechanisms for stemness maintenance of LCSCs can not only reveal the molecular mechanisms of PLC tumorigenesis, but also lay a theoretical foundation for the molecular classification, prognosis evaluation and targeted therapy of PLC. The latest research showed that the combination of 5-fluorouracil and CD13 inhibitors could inhibit the proliferation of CD13+ LCSCs, thereby reducing overall tumor burden. Taken together, LCSCs could be the promising therapeutic targets of PLC in the future. This review summarizes the latest progress in molecular markers, mechanisms for stemness maintenance and targeted therapies of LCSCs.

[CRISPR/Cas9 technology in disease research and therapy: a review].

Genome editing is a genetic manipulation technique that can modify DNA sequences at the genome level, including insertion, knockout, replacement and point mutation of specific DNA fragments. The ultimate principle of genome editing technology relying on engineered nucleases is to generate double-stranded DNA breaks at specific locations in genome and then repair them through non-homologous end joining or homologous recombination. With the intensive study of these nucleases, genome editing technology develops rapidly. The most used nucleases include meganucleases, zinc finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeats associated Cas proteins. Based on introducing the development and principles of above mentioned genome editing technologies, we review the research progress of CRISPR/Cas9 system in the application fields of identification of gene function, establishment of disease model, gene therapy, immunotherapy and its prospect.

Cancer stem cells: a major culprit of intra-tumor heterogeneity.

Cancer is recognized as a preeminent factor of the world's mortality. Although various modalities have been designed to cure this life-threatening ailment, a significant impediment in the effective output of cancer treatment is heterogeneity. Cancer is characterized as a heterogeneous health disorder that comprises a distinct group of transformed cells to assist anomalous proliferation of affected cells. Cancer stem cells (CSCs) are a leading cause of cancer heterogeneity that is continually transformed by cellular extrinsic and intrinsic factors. They intensify neoplastic cells aggressiveness by strengthening their dissemination, relapse and therapy resistance. Considering this viewpoint, in this review article we have discussed some intrinsic (transcription factors, cell signaling pathways, genetic alterations, epigenetic modifications, non-coding RNAs (ncRNAs) and epitranscriptomics) and extrinsic factors (tumor microenvironment (TME)) that contribute to CSC heterogeneity and plasticity, which may help scientists to meddle these processes and eventually improve cancer research and management. Besides, the potential role of CSCs heterogeneity in establishing metastasis and therapy resistance has been articulated which signifies the importance of developing novel anticancer therapies to target CSCs along with targeting bulk tumor mass to achieve an effective output.

Characteristics and Kinetic Analysis of AQS Transformation and Microbial Goethite Reduction:Insight into "Redox mediator-Microbe-Iron oxide" Interaction Process.

The characteristics and kinetics of redox transformation of a redox mediator, anthraquinone-2-sulfonate (AQS), during microbial goethite reduction by Shewanella decolorationis S12, a dissimilatory iron reduction bacterium (DIRB), were investigated to provide insights into "redox mediator-iron oxide" interaction in the presence of DIRB. Two pre-incubation reaction systems of the "strain S12- goethite" and the "strain S12-AQS" were used to investigate the dynamics of goethite reduction and AQS redox transformation. Results show that the concentrations of goethite and redox mediator, and the inoculation cell density all affect the characteristics of microbial goethite reduction, kinetic transformation between oxidized and reduced species of the redox mediator. Both abiotic and biotic reactions and their coupling regulate the kinetic process for "Quinone-Iron" interaction in the presence of DIRB. Our results provide some new insights into the characteristics and mechanisms of interaction among "quinone-DIRB- goethite" under biotic/abiotic driven.

Multifunctional nanoparticles of Fe(3)O(4)@SiO(2)(FITC)/PAH conjugated the recombinant plasmid of pIRSE2-EGFP/VEGF(165) with dual functions for gene delivery and cellular imaging.

OBJECTIVES: Technologies to increase tissue vascularity are critically important to the fields of tissue engineering and cardiovascular medicine. Angiogenic factors, like VEGF, have been widely investigated to induce vascular endothelial cell proliferation and angiogenesis for establishing a vascular network. However, effective transport of VEGF gene to target cells with minimal side effects remains a challenge despite the use of unique viral and non-viral delivery approaches. METHODS: This study presents a novel gene delivery system of fluorescein isothiocyanate (FITC) doped and poly(allylamine hydrochloride) (PAH) grafted Fe(3)O(4)@SiO(2) nanoparticles, which allows efficient loading of pVEGF to form Fe(3)O(4)@SiO(2)(FITC)/PAH/pVEGF nanocomplexes for VEGF gene delivery and cellular imaging. RESULTS: The nanocomplexes maintain their superparamagnetic property in the silica composites at room temperature, reaching a saturation magnetization value of 5.19 emu/g of material, and no appreciable change in magnetism even after PAH modification. The quantitative analysis of cellular internalization into the living human umbilical vein endothelial cells (HUVECs) demonstrated that the Fe(3)O(4)@SiO(2)(FITC)/PAH/pVEGF nanocomplexes could be entirely internalized by HUVECs, and exhibit high VEGF gene expression and an innocuous toxic profile. The magnetic resonance (MR) images showed that the superparamagnetic iron oxide core of Fe(3)O(4)@SiO(2)(FITC)/PAH/pVEGF nanocomplexes could also act as a contrast agent for MR imaging. This property provides a benefit for monitoring gene delivery. CONCLUSION: These data highlight multifunctional Fe(3)O(4)@SiO(2)(FITC)/PAH/pVEGF nanocomplexes as an attractive platform for gene delivery of angiogenesis, and also making it a potential candidate of nanoprobes for cellular fluorescent imaging or MR imaging.

Core/shell Fe3O4 @SiO2 nanoparticles modified with PAH as a vector for EGFP plasmid DNA delivery into HeLa cells.

Novel stable core/shell Fe(3)O(4)@SiO(2)/PAH nanoparticles are synthesized using 15 nm Fe(3)O(4) as the template that is modified with PAH. The resulting nanoparticles can absorb plasmid DNA to mediate gene transfer in cultured HeLa cells. An electrophoretic assay suggests that the Fe(3)O(4)@SiO(2)/PAH nanoparticles protect the plasmid DNA from serum and DNase I degradation. A cell viability assay shows that the Fe(3)O(4)@SiO(2)/PAH nanoparticles exhibit a low cytotoxicity toward endothelial cells. Qualitative analysis of transfection in HeLa cells by nanoparticles carrying a plasmid DNA encoding EGFP demonstrates a fairly high expression level, even in the presence of serum. Thus, Fe(3)O(4)@SiO(2)/PAH nanoparticles are biocompatible and suitable for nonviral delivery, and may find applications in cancer therapy.

Silica nanoparticles as promising drug/gene delivery carriers and fluorescent nano-probes: recent advances.

The application of nanotechnology to biomedical research is expected to have a major impact leading to the development of new types of diagnostic and therapeutic tools. One focus in nanobiotechnology is to develop safe and efficient drug/gene delivery vehicles. Research into the rational delivery and targeting of pharmaceutical, therapeutic and diagnostic agents is at the forefront of projects in nanomedicine. Silica, as a major and natural component of sand and glass, is a versatile material due to the variety of available chemical and physical modifications that are available, and recently have been widely applied in nanobiotechnology as drug/gene carriers or fluorescent nano-probes. The goal of this brief review is to illustrate selected examples of various functionalized silica nanoparticles as drug/gene delivery systems that have been applied to the arenas of human disease therapy or detection (molecular and cellular imaging).

Polymeric microbubbles for ultrasonic molecular imaging and targeted therapeutics.

Gas-filled microbubbles ultrasound agent have received wide attention, not only because they can improve ultrasound signals, but also they can be used as drug/gene carriers. Among all types of microbubbles fabricated by different membrane materials and core gases, polymer-shell microbubbles are highly promising. Polymeric microbubbles are more stable than other soft shell microbubbles in vivo. Under destructive ultrasound, polymer-stabilized microbubbles disintegrate and emit a strong non-linear signal, which enables ultrasound imaging with superior sensitivity. Except for ultrasound imaging, polymeric microbubbles could also be applied as drug/gene-delivery system. The thick polymeric shells allow loading a large amount of drugs. Meanwhile, site-specific targeting and controlled drug release in the area of interest can be realized through chemical and physical modification. In this review, we highlight some of the recent examples on polymeric microbubbles and their applications in ultrasound molecular imaging and drug delivery.