Development of dynamical network biomarkers for regulation in Epstein-Barr virus positive peripheral T cell lymphoma unspecified type

Background: This study was performed to identify key regulatory network biomarkers including transcription factors (TFs), miRNAs and lncRNAs that may affect the oncogenesis of EBV positive PTCL-U.Methods: GSE34143 dataset was downloaded and analyzed to identify differentially expressed genes (DEGs) between EBV positive PTCL-U and normal samples. Gene ontology and pathway enrichment analyses were performed to illustrate the potential function of the DEGs. Then, key regulators including TFs, miRNAs and lncRNAs involved in EBV positive PTCL-U were identified by constructing TF–mRNA, lncRNA–miRNA–mRNA, and EBV encoded miRNA–mRNA regulatory networks.Results: A total of 96 DEGs were identified between EBV positive PTCL-U and normal tissues, which were related to immune responses, B cell receptor signaling pathway, chemokine activity. Pathway analysis indicated that the DEGs were mainly enriched in cytokine-cytokine receptor interaction and chemokine signaling pathway. Based on the TF network, hub TFs were identified regulate the target DEGs. Afterwards, a ceRNA network was constructed, in which miR-181(a/b/c/d) and lncRNA LINC01744 were found. According to the EBV-related miRNA regulatory network, CXCL10 and CXCL11 were found to be regulated by EBV-miR-BART1-3p and EBV-miR-BHRF1-3, respectively. By integrating the three networks, some key regulators were found and may serve as potential network biomarkers in the regulation of EBV positive PTCL-U.Conclusion: The network-based approach of the present study identified potential biomarkers including transcription factors, miRNAs, lncRNAs and EBV-related miRNAs involved in EBV positive PTCL-U, assisting us in understanding the molecular mechanisms that underlie the carcinogenesis and progression of EBV positive PTCL-U

Designing Artificial Two-Dimensional Landscapes via Room-Temperature Atomic-Layer Substitution

Manipulating materials with atomic-scale precision is essential for the development of next-generation material design toolbox. Tremendous efforts have been made to advance the compositional, structural, and spatial accuracy of material deposition and patterning. The family of 2D materials provides an ideal platform to realize atomic-level material architectures. The wide and rich physics of these materials have led to fabrication of heterostructures, superlattices, and twisted structures with breakthrough discoveries and applications. Here, we report a novel atomic-scale material design tool that selectively breaks and forms chemical bonds of 2D materials at room temperature, called atomic-layer substitution (ALS), through which we can substitute the top layer chalcogen atoms within the 3-atom-thick transition-metal dichalcogenides using arbitrary patterns. Flipping the layer via transfer allows us to perform the same procedure on the other side, yielding programmable in-plane multi-heterostructures with different out-of-plane crystal symmetry and electric polarization. First-principle calculations elucidate how the ALS process is overall exothermic in energy and only has a small reaction barrier, facilitating the reaction to occur at room temperature. Optical characterizations confirm the fidelity of this design approach, while TEM shows the direct evidence of Janus structure and suggests the atomic transition at the interface of designed heterostructure. Finally, transport and Kelvin probe measurements on MoXY (X,Y=S,Se; X and Y corresponding to the bottom and top layers) lateral multi-heterostructures reveal the surface potential and dipole orientation of each region, and the barrier height between them. Our approach for designing artificial 2D landscape down to a single layer of atoms can lead to unique electronic, photonic and mechanical properties previously not found in nature