ZBTB40 is a telomere-associated protein and protects telomeres in human ALT cells.

Alternative lengthening of telomeres (ALTs) mechanism is activated in some somatic, germ cells, and human cancer cells. However, the key regulators and mechanisms of the ALT pathway remain elusive. Here we demonstrated that ZBTB40 is a novel telomere-associated protein and binds to telomeric dsDNA through its N-terminal BTB (BR-C, ttk and bab) or POZ (Pox virus and Zinc finger) domain in ALT cells. Notably, the knockout or knockdown of ZBTB40 resulted in the telomere dysfunction-induced foci and telomere lengthening in the ALT cells. The results also show that ZBTB40 is associated with ALT-associated promyelocytic leukemia nuclear bodies, and the loss of ZBTB40 induces the accumulation of the ALT-associated promyelocytic leukemia nuclear bodies in U2OS cells. Taken together, our results implicate that ZBTB40 is a key player of telomere protection and telomere lengthening regulation in human ALT cells.

Physical confinement and cell proximity increase cell migration rates and invasiveness: A mathematical model of cancer cell invasion through flexible channels.

Cancer cell migration between different body parts is the driving force behind cancer metastasis, which is the main cause of mortality of patients. Migration of cancer cells often proceeds by penetration through narrow cavities in locally stiff, yet flexible tissues. In our previous work, we developed a model for cell geometry evolution during invasion, which we extend here to investigate whether leader and follower (cancer) cells that only interact mechanically can benefit from sequential transmigration through narrow micro-channels and cavities. We consider two cases of cells sequentially migrating through a flexible channel: leader and follower cells being closely adjacent or distant. Using Wilcoxon's signed-rank test on the data collected from Monte Carlo simulations, we conclude that the modelled transmigration speed for the follower cell is significantly larger than for the leader cell when cells are distant, i.e. follower cells transmigrate after the leader has completed the crossing. Furthermore, it appears that there exists an optimum with respect to the width of the channel such that cell moves fastest. On the other hand, in the case of closely adjacent cells, effectively performing collective migration, the leader cell moves 12% faster since the follower cell pushes it. This work shows that mechanical interactions between cells can increase the net transmigration speed of cancer cells, resulting in increased invasiveness. In other words, interaction between cancer cells can accelerate metastatic invasion.

Deep convolutional neural networks using an active learning strategy for cervical cancer screening and diagnosis.

Cervical cancer (CC) is the fourth most common malignant tumor among women worldwide. Constructing a high-accuracy deep convolutional neural network (DCNN) for cervical cancer screening and diagnosis is important for the successful prevention of cervical cancer. In this work, we proposed a robust DCNN for cervical cancer screening using whole-slide images (WSI) of ThinPrep cytologic test (TCT) slides from 211 cervical cancer and 189 normal patients. We used an active learning strategy to improve the efficiency and accuracy of image labeling. The sensitivity, specificity, and accuracy of the best model were 96.21%, 98.95%, and 97.5% for CC patient identification respectively. Our results also demonstrated that the active learning strategy was superior to the traditional supervised learning strategy in cost reduction and improvement of image labeling quality. The related data and source code are freely available at https://github.com/hqyone/cancer_rcnn.

The biological function of metazoan-specific subunit nuclear factor related to kappaB binding protein of INO80 complex.

The INO80 chromatin remodeling complex plays an essential role in the regulation of gene transcription, which participate in a variety of important biological processes in cells including DNA repair and DNA replication. Difference from the yeast INO80 complex, metazoan INO80 complex have the specific subunit G, which is known as nuclear factor related to kappaB binding protein (NFRKB). Recently, NFRKB has been received much attention in many aspects, such as DNA repair, cell pluripotency, telomere protection, and protein activity regulation. To dig the new function of metazoan INO80 complex, a better understanding of the role of NFRKB is required. In this review, we provide an overview of the structure and function of NFRKB and discuss its potential role in cancer treatment and telomere regulation. Overall, this review provides an important reference for further research of the INO80 complex and NFRKB.

Effect of Fushengong Decoction on PTEN/PI3K/AKT/NF-κB Pathway in Rats With Chronic Renal Failure via Dual-Dimension Network Pharmacology Strategy.

Overview: The treatment of chronic renal failure (CRF) with traditional Chinese medicine has attracted much attention, but its mechanism is not clear. Network pharmacology is an effective strategy for exploring the interaction mechanisms between Chinese herbs and diseases, however, it still needs to be validated in cell and/or animal experiments due to its virtual screening characteristics. Herein, the anti-CRF mechanism of the Fushengong decoction (FSGD) was investigated using a dual-dimension network pharmacological strategy combined with in vivo experiment. Methods: The traditional Chinese medicine systems pharmacology (TCMSP) database (https://tcmspw.com) and UHPLC-MS/MS technology were used to identify the effective compounds of FSGD in theory and practice, such as quercetin, formononetin, and pachymic acid. The putative targets of FSGD and CRF were obtained from the Swisstarget prediction platform and the Genecards database, respectively. The common target pathways between FSGD and CRF were got from the dual-dimension network pharmacology analysis, which integrated the cross-common targets from the TCMSP components-Swisstarget-Genecards-Venn platform analysis in theory, and the UHPLC-MS/MS identified effective ingredients-Swisstarget screening, such as TNF and PI3K/AKT. Furthermore, system molecular determinations were used to prove the dual-dimension network pharmacology study through CRF rat models, which were constructed using adenine and treated with FSGD for 4 weeks. Results: A total of 121 and 9 effective compounds were obtained from the TCMSP database and UHPLC-MS/MS, respectively. After dual-dimension network pharmacology analysis, the possible mechanism of PTEN/PI3K/AKT/NF-κB pathway was found for FSGD in CRF. In vivo experiments indicated that FSGD can play a role in protecting renal function and reducing fibrosis by regulating the PTEN/PI3K/AKT/NF-κB pathway. These findings provide a reference for FSGD in CRF. Conclusion: Based on the theoretical and practical dual-dimension network pharmacology analysis for FSGD in CRF, the possible molecular mechanism of PTEN/PI3K/AKT/NF-κB was successfully predicted, and these results were verified by in vivo experiments. In this study, the dual-dimension network pharmacology was used to interpret the key signal pathway for FSGD in CRF, which also proved to be a smart strategy for the study of effective substances and pharmacology in FSGD.

A FRET-based ratiometric fluorescent probe for hydrogen polysulfide detection in living cells and zebrafish.

Hydrogen polysulfide (H2Sn, n > 1) is an important active sulfur molecule (RSS) in organisms, which have been considered to be involved in redox signaling and cytoprotective processes. In this work, in order to quickly and accurately detect H2Sn in biosystems, 2-fluoro-5-nitrobenzoic ester was used as the response moiety for H2Sn, and the FRET strategy was adopted to effectively connect the donor (6-hydroxy-2-naphthoic acid) and acceptor (4-substituted-1,8-naphthalimide) to construct a new ratiometric H2Sn fluorescent probe NPNA-H2Sn. NPNA-H2Sn exhibited a more than âˆ¼ 8.0-fold ratio enhancement towards H2Sn at I450/I526 and a very high sensitivity with a very low detection limit of 40.3 nM. Impressive, NPNA-H2Sn was further used for fluorescence imaging of H2Sn in living cells and zebrafish, which showed high-clear ratiometric images. Therefore, we have demonstrated that NPNA-H2Sn could be applied for ratiometric images of endogenous H2Sn in living biosystems and provide a powerful molecular tool for evaluating the physiological and pathological functions of H2Sn.

Nuclear Factor Related to KappaB Binding Protein (NFRKB) Is a Telomere-Associated Protein and Involved in Liver Cancer Development.

Alternative lengthening of telomeres (ALT) is a homologous recombination-based telomere maintenance mechanism activated in 10-15% of human cancers. Although significant progress has been made, the key regulators of the ALT pathway and its role in cancer development remain elusive. Bioinformatics methods were used to predict novel telomere-associated proteins (TAPs) by analysis of large-scale ChIP-Seq data. Immunostaining and fluorescence in situ hybridization experiments were applied to detect the subcellular location of target genes and telomeres. Western blot and reverse transcription-polymerase chain reaction (RT-PCR) were used to examine the expression of targeting genes. Overall survival (OS) analyses were used to evaluate the relationship between gene expression and survival time; immunohistochemistry was used to detect the distribution of target genes in liver cancer tissues. We found that nuclear factor related to kappaB binding protein (NFRKB), a metazoan-specific subunit of the INO80 complex, can associate with telomeres in human ALT cells. Loss of NFRKB induces dysfunction of telomeres and less PML bodies in U2OS cells. In addition, NFRKB is low/moderately expressed in cytoplasm of normal hepatocytes but heavily accumulating in the nucleus of liver cancer cells. Finally, the high expression of NFRKB is associated with short OS time and poor prognosis. NFRKB is a TAP and protects telomeres from DNA damage in ALT cells. It is highly expressed in hepatocellular carcinoma (HCC) cells and predicts a poor prognosis. NFRKB may be a promising prognostic biomarker for the treatment of HCC in the future.

Extrachromosomal Circular DNA (eccDNA): From Chaos to Function.

Extrachromosomal circular DNA (eccDNA) is a type of double-stranded circular DNA that is derived and free from chromosomes. It has a strong heterogeneity in sequence, length, and origin and has been identified in both normal and cancer cells. Although many studies suggested its potential roles in various physiological and pathological procedures including aging, telomere and rDNA maintenance, drug resistance, and tumorigenesis, the functional relevance of eccDNA remains to be elucidated. Recently, due to technological advancements, accumulated evidence highlighted that eccDNA plays an important role in cancers by regulating the expression of oncogenes, chromosome accessibility, genome replication, immune response, and cellular communications. Here, we review the features, biogenesis, physiological functions, potential functions in cancer, and research methods of eccDNAs with a focus on some open problems in the field and provide a perspective on how eccDNAs evolve specific functions out of the chaos in cells.

Integrated genomic analysis reveals regulatory pathways and dynamic landscapes of the tRNA transcriptome.

tRNAs and tRNA-derived RNA fragments (tRFs) play various roles in many cellular processes outside of protein synthesis. However, comprehensive investigations of tRNA/tRF regulation are rare. In this study, we used new algorithms to extensively analyze the publicly available data from 1332 ChIP-Seq and 42 small-RNA-Seq experiments in human cell lines and tissues to investigate the transcriptional and posttranscriptional regulatory mechanisms of tRNAs. We found that histone acetylation, cAMP, and pluripotency pathways play important roles in the regulation of the tRNA gene transcription in a cell-specific manner. Analysis of RNA-Seq data identified 950 high-confidence tRFs, and the results suggested that tRNA pools are dramatically distinct across the samples in terms of expression profiles and tRF composition. The mismatch analysis identified new potential modification sites and specific modification patterns in tRNA families. The results also show that RNA library preparation technologies have a considerable impact on tRNA profiling and need to be optimized in the future.

Construction of a lysosome-targetable ratiometric fluorescent probe for H2O2 tracing and imaging in living cells and an inflamed model.

Hydrogen peroxide (H2O2), an important reactive oxygen species (ROS) with unique destructive oxidation properties, can be produced in lysosomes to fight off pathogens. Although many fluorescent probes have been developed for the detection and imaging of H2O2, the development of a ratiometric fluorescent probe for H2O2 detection and imaging in lysosomes and an inflammation model remains rather scarce. Therefore, it is important to develop an efficient tool for monitoring H2O2 in inflamed tissues to evaluate the physiological and pathological relationship between inflammation and lysosomal H2O2. In this work, a new naphthalimide-based lysosome-targeting fluorescent probe (NPT-H2O2) for ratiometric detection and imaging was developed in vitro and in vivo. The probe exhibited two well-resolved emission peaks separated by 125 nm, rapid response (<40 s), and high selectivity and sensitivity toward H2O2, as well as low cytotoxicity in vitro. Inspired by prominent features of these results, we further successfully applied NPT-H2O2 for H2O2 imaging with a dual-channel in living cells, demonstrating that our probe NPT-H2O2 was targeted in the lysosomes. Finally, NPT-H2O2 was used for H2O2 detection in inflamed tissues and achieved satisfactory results. We predict that our probe can be used as a powerful tool to reveal the relationship between physiology and pathology of inflammation and lysosomal H2O2.

Agent-based modelling and parameter sensitivity analysis with a finite-element method for skin contraction.

In this paper, we extend the model of wound healing by Boon et al. (J Biomech 49(8):1388-1401, 2016). In addition to explaining the model explicitly regarding every component, namely cells, signalling molecules and tissue bundles, we categorized fibroblasts as regular fibroblasts and myofibroblasts. We do so since it is widely documented that myofibroblasts play a significant role during wound healing and skin contraction and that they are the main phenotype of cells that is responsible for the permanent deformations. Furthermore, we carried out some sensitivity tests of the model by modifying certain parameter values, and we observe that the model shows some consistency with several biological phenomena. Using Monte Carlo simulations, we found that there is a significant strong positive correlation between the final wound area and the minimal wound area. The high correlation between the wound area after 4 days and the final/minimal wound area makes it possible for physicians to predict the most probable time evolution of the wound of the patient. However, the collagen density ratio at the time when the wound area reaches its equilibrium and minimum, cannot indicate the degree of wound contractions, whereas at the 4th day post-wounding, when the collagen is accumulating from null, there is a strong negative correlation between the area and the collagen density ratio. Further, under the circumstances that we modelled, the probability that patients will end up with 5% contraction is about 0.627.