SLFN5-mediated chromatin dynamics sculpt higher-order DNA repair topology.

Repair of DNA double-strand breaks (DSBs) elicits three-dimensional (3D) chromatin topological changes. A recent finding reveals that 53BP1 assembles into a 3D chromatin topology pattern around DSBs. How this formation of a higher-order structure is configured and regulated remains enigmatic. Here, we report that SLFN5 is a critical factor for 53BP1 topological arrangement at DSBs. Using super-resolution imaging, we find that SLFN5 binds to 53BP1 chromatin domains to assemble a higher-order microdomain architecture by driving damaged chromatin dynamics at both DSBs and deprotected telomeres. Mechanistically, we propose that 53BP1 topology is shaped by two processes: (1) chromatin mobility driven by the SLFN5-LINC-microtubule axis and (2) the assembly of 53BP1 oligomers mediated by SLFN5. In mammals, SLFN5 deficiency disrupts the DSB repair topology and impairs non-homologous end joining, telomere fusions, class switch recombination, and sensitivity to poly (ADP-ribose) polymerase inhibitor. We establish a molecular mechanism that shapes higher-order chromatin topologies to safeguard genomic stability.

A phosphorylation-deubiquitination cascade regulates the BRCA2-RAD51 axis in homologous recombination.

Homologous recombination (HR) is one of the major DNA double-strand break (DSB) repair pathways in mammalian cells. Defects in HR trigger genomic instability and result in cancer predisposition. The defining step of HR is homologous strand exchange directed by the protein RAD51, which is recruited to DSBs by BRCA2. However, the regulation of the BRCA2-RAD51 axis remains unclear. Here we report that ubiquitination of RAD51 hinders RAD51-BRCA2 interaction, while deubiquitination of RAD51 facilitates RAD51-BRCA2 binding and RAD51 recruitment and thus is critical for proper HR. Mechanistically, in response to DNA damage, the deubiquitinase UCHL3 is phosphorylated and activated by ATM. UCHL3, in turn, deubiquitinates RAD51 and promotes the binding between RAD51 and BRCA2. Overexpression of UCHL3 renders breast cancer cells resistant to radiation and chemotherapy, while depletion of UCHL3 sensitizes cells to these treatments, suggesting a determinant role of UCHL3 in cancer therapy. Overall, we identify UCHL3 as a novel regulator of DNA repair and reveal a model in which a phosphorylation-deubiquitination cascade dynamically regulates the BRCA2-RAD51 pathway.

USP37 regulates DNA damage response through stabilizing and deubiquitinating BLM.

The human RecQ helicase BLM is involved in the DNA damage response, DNA metabolism, and genetic stability. Loss of function mutations in BLM cause the genetic instability/cancer predisposition syndrome Bloom syndrome. However, the molecular mechanism underlying the regulation of BLM in cancers remains largely elusive. Here, we demonstrate that the deubiquitinating enzyme USP37 interacts with BLM and that USP37 deubiquitinates and stabilizes BLM, thereby sustaining the DNA damage response (DDR). Mechanistically, DNA double-strand breaks (DSB) promotes ATM phosphorylation of USP37 and enhances the binding between USP37 and BLM. Moreover, knockdown of USP37 increases BLM polyubiquitination, accelerates its proteolysis, and impairs its function in DNA damage response. This leads to enhanced DNA damage and sensitizes breast cancer cells to DNA-damaging agents in both cell culture and in vivo mouse models. Collectively, our results establish a novel molecular mechanism for the USP37-BLM axis in regulating DSB repair with an important role in chemotherapy and radiotherapy response in human cancers.

USP17L2-SIRT7 axis regulates DNA damage repair and chemoresistance in breast cancer cells.

PURPOSE: Sirtuin7 (SIRT7), as a member of the sirtuin and NAD+-dependent protein-modifying enzyme family, plays an important role in regulating cellular metabolism, stress responses, tumorigenesis, and aging. Ubiquitination and deubiquitination are reversible post-translational modifications that regulate protein stability, enzyme activity, protein-protein interactions, and cellular signaling transduction. However, whether SIRT7 is regulated by deubiquitination signaling is unclear. This study aims to elucidate the molecular mechanism of SIRT7 via deubiquitination signaling. METHODS: USP17L2 or SIRT7-targeting shRNAs were used to deplete USP17L2 or SIRT7. Western blot was applied to assess the effects of USP17L2 or SIRT7 depletion. A co-immunoprecipitation assay was used to detect the interaction relationship. Cell Counting Kit-8 assays were applied to assess the viability of breast cancer cells. An immunohistochemistry assay was employed to detect the protein level in samples from breast cancer patients, and the TCGA database was applied to analyze the survival rate of breast cancer patients. Statistical analyses were performed with the Student's t test (two-tailed unpaired) and χ2 test. RESULTS: We find that the deubiquitinase USP17L2 interacts with and deubiquitinates SIRT7, thereby increasing SIRT7 protein stability. In addition, USP17L2 regulates DNA damage repair through SIRT7. Furthermore, SIRT7 polyubiquitination is increased by knocking down of USP17L2, which leads to cancer cells sensitizing to chemotherapy. In breast cancer patient samples, high expression of USP17L2 is correlated with increased levels of SIRT7 protein. In conclusion, our study demonstrates that the USP17L2-SIRT7 axis is the new regulator in DNA damage response and chemo-response, suggesting that USP17L2 may be a prognostic factor and a potential therapeutic target in breast cancer. CONCLUSION: Our results highlighted that USP17L2 regulates the chemoresistance of breast cancer cells in a SIRT7-dependent manner. Moreover, the role of USP17L2 as a potential therapeutic target in breast cancer and a prognostic factor for patients was elucidated.

USP49 negatively regulates tumorigenesis and chemoresistance through FKBP51-AKT signaling.

The AKT pathway is a fundamental signaling pathway that mediates multiple cellular processes, such as cell proliferation and survival, angiogenesis, and glucose metabolism. We recently reported that the immunophilin FKBP51 is a scaffolding protein that can enhance PHLPP-AKT interaction and facilitate PHLPP-mediated dephosphorylation of AKT at Ser473, negatively regulating AKT activation. However, the regulation of FKBP51-PHLPP-AKT pathway remains unclear. Here we report that a deubiquitinase, USP49, is a new regulator of the AKT pathway. Mechanistically, USP49 deubiquitinates and stabilizes FKBP51, which in turn enhances PHLPP's capability to dephosphorylate AKT Furthermore, USP49 inhibited pancreatic cancer cell proliferation and enhanced cellular response to gemcitabine in a FKBP51-AKT-dependent manner. Clinically, decreased expression of USP49 in patients with pancreatic cancer was associated with decreased FKBP51 expression and increased AKT phosphorylation. Overall, our findings establish USP49 as a novel regulator of AKT pathway with a critical role in tumorigenesis and chemo-response in pancreatic cancer.

A Pair of CoII Supramolecular Isomers Based on Flexible Bis-Pyridyl-Bis-Amide and Angular Dicarboxylate Ligands.

Thermal reactions of cobalt(II) salts with flexible N,N'-bis(pyrid-3-ylmethyl)adipoamide (L) and angular 4,4'-sulfonyldibenzoic acid (H2SDA) in H2O and CH3OH afforded a pair of supramolecular isomers: [Co2(L)(SDA)2], 1, and [Co2(L)(SDA)2]⋅CH3OH⋅H2O, 2. The structure of complex 1 can be simplified as a one-dimensional (1D) looped chain with L ligands penetrating into the middles of squares, forming a new type of self-catenated net with the (42⋅54)(4)2(5)2 topology, whereas complex 2 displays a 2-fold interpenetrated 2D net with the rare (42⋅68⋅8⋅104)(4)2-2,6L1 topology. While both complexes 1 and 2 display antiferromagnetism with strong spin-orbital coupling, the antiferromagnetism of 2 is accompanied by a cross-over behavior and probably a spin canting phenomenon.

Histone deacetylase 2 is essential for LPS-induced inflammatory responses in macrophages.

The role of specific histone deacetylase (HDAC) proteins in regulating the lipopolysaccharide (LPS)-induced inflammatory response and its underlying mechanisms are unclear. Here, HDAC2, a class I HDAC family protein, is essential for the LPS-triggered inflammatory response in macrophages. LPS stimulation increases HDAC2 expression in macrophages. Knockdown of HDAC2 decreases the expression of proinflammatory genes, such as IL-12, TNF-α and iNOS following stimulation with LPS. The adoptive transfer of HDAC2 knockdown macrophages attenuates the LPS-triggered innate inflammatory response in vivo, and these mice are less sensitive to endotoxin shock and Escherichia coli-induced sepsis. Mechanistically, the c-Jun protein is the main target of HDAC2-mediated LPS-induced production of proinflammatory cytokines. Moreover, HDAC2 knockdown increases the expression of c-Jun, which directly binds the promoters of proinflammatory genes and forms nuclear receptor corepressor complexes to inhibit the transcription of proinflammatory genes in macrophages. These effects are rescued by c-Jun expression. According to the chromatin immunoprecipitation analysis, HDAC2 also selectively suppresses c-Jun expression by directly binding to its promoter and modifying histone acetylation after LPS stimulation. Our findings define a new function and mechanism of the HDAC2/c-Jun signaling network that regulates the LPS-induced immune response in macrophages.

CDK-mediated RNF4 phosphorylation regulates homologous recombination in S-phase.

There are the two major pathways responsible for the repair of DNA double-strand breaks (DSBs): non-homologous end-joining (NHEJ) and homologous recombination (HR). NHEJ operates throughout the cell-cycle, while HR is primarily active in the S/G2 phases suggesting that there are cell cycle-specific mechanisms that regulate the balance between NHEJ and HR. Here we reported that CDK2 could phosphorylate RNF4 on T26 and T112 and enhance RNF4 E3 ligase activity, which is important for MDC1 degradation and proper HR repair during S phase. Mutation of the RNF4 phosphorylation sites results in MDC1 stabilization, which in turn compromised HR during S-phase. These results suggest that in addition to drive cell cycle progression, CDK also targets RNF4, which is involved in the regulatory network of DSBs repair.

Wnt5a Promotes Cytokines Production and Cell Proliferation in Human Hepatic Stellate Cells Independent of Canonical Wnt Pathway.

BACKGROUND: Wnt5a is involved in the activation of human hepatic stellate cells (HSC) and related with the occurrence of liver fibrosis. As the function and mechanism that Wnt5a mediates HSC activation remains unclear, we sought to investigate them. METHODS: Wnt5a levels were determined in the HSC cell line LX-2 after lipopolysaccharide (LPS) and TNF-α stimulation. HSC cells showing stable and efficient overexpression or featuring knockdown of Wnt5a were constructed by a lentivirus system. Regulation of cytokine and collagen expressions were confirmed by quantitative PCR or ELISA in stable LX-2 cell lines showing Wnt5a overexpression or knockdown. Proliferation was determined by 5-ethynyl-2'-deoxyuridine labeling. Relevant signaling pathways were identified using specific protein antibodies. RESULTS: LPS and TNF-α induced Wnt5a expression in LX-2 cells. Compared with control cells, an increase in IL-10, IL-6, COL1, and COL3 secretion in a stable LX-2 cell line showing Wnt5a overexpression was observed. Knockdown of Wnt5a obviously reduced the production of IL-1ß, IL-6, COL1, and COL3. Wnt5a overexpression promoted LX-2 proliferation, while Wnt5a knockdown dramatically inhibited cell proliferation. Compared with the effects of Wnt5a knockdown cells, Wnt5a-overexpressing cells triggered the phosphorylation of c-Jun N-terminal kinase (JNK) and ß-catenin, which leads to ß-catenin degradation and inactivates the canonical Wnt/ß-catenin pathway. CONCLUSIONS: Wnt5a regulates inflammatory cytokine and collagen production and cell proliferation, which is independent of the canonical Wnt signaling pathway. The results reveal a new signaling mechanism in HSC activation and could provide a new strategy for hepatic fibrosis treatment.

Large area single crystal gold of single nanometer thickness for nanophotonics.

Two-dimensional single crystal metals, in which the behavior of highly confined optical modes is intertwined with quantum phenomena, are highly sought after for next-generation technologies. Here, we report large area (>104 µm2), single crystal two-dimensional gold flakes (2DGFs) with thicknesses down to a single nanometer level, employing an atomic-level precision chemical etching approach. The decrease of the thickness down to such scales leads to the quantization of the electronic states, endowing 2DGFs with quantum-confinement-augmented optical nonlinearity, particularly leading to more than two orders of magnitude enhancement in harmonic generation compared with their thick polycrystalline counterparts. The nanometer-scale thickness and single crystal quality makes 2DGFs a promising platform for realizing plasmonic nanostructures with nanoscale optical confinement. This is demonstrated by patterning 2DGFs into nanoribbon arrays, exhibiting strongly confined near infrared plasmonic resonances with high quality factors. The developed 2DGFs provide an emerging platform for nanophotonic research and open up opportunities for applications in ultrathin plasmonic, optoelectronic and quantum devices.

USP25 Elevates SHLD2-Mediated DNA Double-Strand Break Repair and Regulates Chemoresponse in Cancer.

DNA damage plays a significant role in the tumorigenesis and progression of the disease. Abnormal DNA repair affects the therapy and prognosis of cancer. In this study, it is demonstrated that the deubiquitinase USP25 promotes non-homologous end joining (NHEJ), which in turn contributes to chemoresistance in cancer. It is shown that USP25 deubiquitinates SHLD2 at the K64 site, which enhances its binding with REV7 and promotes NHEJ. Furthermore, USP25 deficiency impairs NHEJ-mediated DNA repair and reduces class switch recombination (CSR) in USP25-deficient mice. USP25 is overexpressed in a subset of colon cancers. Depletion of USP25 sensitizes colon cancer cells to IR, 5-Fu, and cisplatin. TRIM25 is also identified, an E3 ligase, as the enzyme responsible for degrading USP25. Downregulation of TRIM25 leads to an increase in USP25 levels, which in turn induces chemoresistance in colon cancer cells. Finally, a peptide that disrupts the USP25-SHLD2 interaction is successfully identified, impairing NHEJ and increasing sensitivity to chemotherapy in PDX model. Overall, these findings reveal USP25 as a critical effector of SHLD2 in regulating the NHEJ repair pathway and suggest its potential as a therapeutic target for cancer therapy.

Phonon-induced relaxation mechanisms are changed by a chelating effect in a CoII single-ion magnet.

It is well known that phonon-induced relaxation processes play a significant role in accelerating magnetization relaxation in the low-temperature regime. Unfortunately, many SIMs (single-ion magnets) suffer from being quenched by these mechanisms such that neither out-of-phase signals nor magnetization hysteresis can be readily observed. Nevertheless, because it involves molecular motions at low-frequency (low-energy) levels, methods for synthetically controlling this factor have not yet been addressed by chemists. In this study, we prepared a series of three compounds in which one contains a rigid chelating ligand, and the other two contain analogous ligands that can coordinate more liberally. To our surprise, compound 1, with a rigid chelating ligand, displayed promising SIM behavior with out-of-phase signals up to 11 K in a zero d.c. magnetic field at an a.c. frequency of 1000 Hz. The other two (2 and 3) with dangling ligands failed to show significant out-of-phase signals until an extra d.c. field was applied. The results of magnetization relaxation studies suggest that the phonon-induced relaxation processes play an essential role in 2 and 3, even at very low temperatures. Nevertheless, the rigid chelating ligand in 1 prevents the molecule from being involved in phonon-induced relaxation processes that seriously interfere with the magnetization relaxation up to 5.6 K. Therefore, we concluded that the presence of a rigid chelating ligand can efficiently change the phonon-induced relaxation processes at low temperatures.

Construction of a DNA damage repair gene signature for predicting prognosis and immune response in breast cancer.

DNA damage repair (DDR) genes are involved in developing breast cancer. Recently, a targeted therapeutic strategy through DNA repair machinery, including PARPi, has initially shown broad development and application prospects in breast cancer therapy. However, few studies that focused on the correlation between the expression level of DNA repair genes, prognosis, and immune response in breast cancer patients have been recently conducted. Herein, we focused on identifying differentially expressed DNA repair genes (DEGs) in breast cancer specimens and normal samples using the Wilcoxon rank-sum test. Biofunction enrichment analysis was performed with DEGs using the R software "cluster Profiler" package. DNA repair genes were involved in multivariate and univariate Cox regression analyses. After the optimization by AIC value, 11 DNA repair genes were sorted as prognostic DNA repair genes for breast cancer patients to calculate risk scores. Simultaneously, a nomogram was used to represent the prognostic model, which was validated using a calibration curve and C-index. Single-sample gene set enrichment analysis (ssGSEA), CIBERSORT algorithms, and ESTIMATE scores were applied to evaluate the immune filtration of tumor samples. Subsequently, anticarcinogen sensitivity analysis was performed using the R software "pRRophetic" package. Unsupervised clustering was used to excavate the correlation between the expression level of prognostic-significant DNA repair genes and clinical features. In summary, 56 DEGs were sorted, and their potential enriched biofunction pathways were revealed. In total, 11 DNA repair genes (UBE2A, RBBP8, RAD50 , FAAP20, RPA3, ENDOV, DDB2, UBE2V2, MRE11 , RRM2B, and PARP3 ) were preserved as prognostic genes to estimate risk score, which was applied to establish the prognostic model and stratified breast cancer patients into two groups with high or low risk. The calibration curve and C-index indicated that they reliably predicted the survival of breast cancer patients. Immune filtration analysis, anticarcinogen sensitivity analysis, and unsupervised clustering were applied to reveal the character of DNA repair genes between low- and high-risk groups. We identified 11 prognosis-significant DNA repair genes to establish prediction models and immune responses in breast cancer patients.

DUB3/KLF4 combats tumor growth and chemoresistance in hepatocellular carcinoma.

This study aimed to investigate the role of deubiquitinating enzyme 3 (DUB3) in the regulation of Krüppel-like factor 4 (KLF4) expression in hepatocellular carcinoma (HCC). Gain- and loss-of-function assay, luciferase reporter assay, co-immunoprecipitation, and intracellular and extracellular deubiquitination assays were conducted in vitro. A tumor xenograft mouse model was established. The expression of DUB3 and KLF4 was examined in HCC patient specimens. The results showed that DUB3 upregulated KLF4 expression by deubiquitinating and stabilizing KLF4 protein in HCC cells through binding with KLF4. DUB3 inhibited HCC cell proliferation in vitro and tumor growth in vivo while enhancing the chemosensitivity of HCC cells in a KLF4-dependent manner. Furthermore, KLF4 promoted DUB3 transcription by binding to the DUB3 promoter. In HCC patients, DUB3 expression positively correlated with KLF4 expression in HCC tissues. Low DUB3 expression predicted worse overall survival and recurrence in HCC patients. In conclusion, this study revealed a positive DUB3/KLF4 feedback loop that inhibits tumor growth and chemoresistance in HCC. These results suggest that DUB3/KLF4 activation might be a potential therapeutic approach for HCC treatment.

A multi-axis robot-based bioprinting system supporting natural cell function preservation and cardiac tissue fabrication.

Despite the recent advances in artificial tissue and organ engineering, how to generate large size viable and functional complex organs still remains as a grand challenge for regenerative medicine. Three-dimensional bioprinting has demonstrated its advantages as one of the major methods in fabricating simple tissues, yet it still faces difficulties to generate vasculatures and preserve cell functions in complex organ production. Here, we overcome the limitations of conventional bioprinting systems by converting a six degree-of-freedom robotic arm into a bioprinter, therefore enables cell printing on 3D complex-shaped vascular scaffolds from all directions. We also developed an oil bath-based cell printing method to better preserve cell natural functions after printing. Together with a self-designed bioreactor and a repeated print-and-culture strategy, our bioprinting system is capable to generate vascularized, contractible, and long-term survived cardiac tissues. Such bioprinting strategy mimics the in vivo organ development process and presents a promising solution for in vitro fabrication of complex organs.

Slow magnetization relaxation in a tetrahedrally coordinated mononuclear Co(II) complex exclusively ligated with phenanthroline ligands.

This paper describes a tetrahedral mononuclear Co(ii) complex [CoL2](ClO4)2 (1) in which L = 2,9-diphenyl-1,10-phenanthroline. The structure of 1, which was determined by single crystal X-ray diffraction, indicates that it exists in the triclinic space group P1[combining macron]. Magnetic property studies were conducted by reduced magnetization measurements, ab initio calculations and X-band EPR experiments, the results of which revealed a large zero-field splitting, with D ∼ -45.9 cm-1. The Arrhenius equation indicates that the kinetic energy barrier of 1 is Ueff = 46.9 cm-1. This study describes a very rare case of a Co(ii) single ion magnet (SIM) that is purely tetrahedrally coordinated by pyridine like ligands.

Interactive Partitioning of 3D Models into Printable Parts.

In this paper, we present an easy, flexible and interactive tool for partitioning a 3D model, which is larger than 3D-printers working volume, into printable parts in an intuitive way. Our presented tool is based on the elegant partitioning optimization framework Chopper. Our tool aims at improving Chopper by providing users three easy-to-use interactive operations: no-go region painting, cutting plane specification and components re-union. With these operations, we show that (1) exhaustive search in the BSP tree --- the most time-consuming step in Chopper --- can be avoided, (2) more flexible geometric configurations can be provided, (3) users design intention is considered naturally and efficiently, and customized 3D partitioning results can be obtained. We test our tool on a wide range of 3D models and observe promising results. A preliminary user study also demonstrates its effectiveness and efficiency.

USP39 regulates DNA damage response and chemo-radiation resistance by deubiquitinating and stabilizing CHK2.

The serine/threonine kinase, CHK2 (checkpoint kinase 2), is a key mediator in DNA damage response and a tumor suppressor, which is implicated in promoting cell cycle arrest, apoptosis and DNA repair. Accumulating evidence suggests that these functions are primarily exerted through phosphorylation downstream factors such as p53 and BRCA1. Recent studies have shown that ubiquitination is an important mode of regulation of CHK2. However, it remains largely unclear whether deubiquitinases participate in regulation of CHK2. Here, we report that a deubiquitinase, USP39, is a new regulator of CHK2. Mechanistically, USP39 deubiquitinates and stabilizes CHK2, which in turn enhances CHK2 stability. Short hairpin RNA (shRNA) mediated knockdown of USP39 led to deregulate CHK2, which resulted in compromising the DNA damage-induced G2/M checkpoint, decreasing apoptosis, and conferring cancer cells resistance to chemotherapy drugs and radiation treatment. Collectively, we identify USP39 as a novel regulator of CHK2 in the DNA damage response.

Minimally invasive and open gastrectomy for gastric cancer: A protocol for systematic review and network meta-analysis.

BACKGROUND: The aim of this study is to find the better treatment for gastric cancer by comparing robotic gastrectomy, laparoscopic gastrectomy, and open gastrectomy using Bayesian network meta-analysis. METHODS: We will search PubMed, Embase, and the Cochrane Library for eligible studies published before 1 September 2018. There will be no language restrictions. Randomized clinical trials that compare robotic gastrectomy, laparoscopic gastrectomy, or open gastrectomy for patients with gastric cancer will be included. The risk of bias of included studies will be assessed by the Cochrane Collaboration's tool for assessing risk of bias in randomized trial. The outcomes of the study include operation time, estimated blood loss, time of ambulation, times to first flatus, time of oral intake, hospitalization, and the occurrence of complication. If sufficient data is collected and adequate clinical homogeneity is established among studies, we will conduct pairwise meta-analyses and Bayesian network meta-analyses for all related outcome measures. ETHICS AND DISSEMINATION: The study does not involve human subjects and does not need ethical approval and patient consent. The results of the network meta-analysis will be disseminated in a peer-reviewed journal for publication.

Interactive Partitioning of 3D Models into Printable Parts.

This article presents an easy, flexible and interactive tool for partitioning a 3D model, which is larger than a 3D printers working volume, into printable parts in an intuitive way. Our tool is based on the elegant partitioning optimization framework Chopper. Our tool aims at improving Chopper by providing users three easy-to-use interactive operations: no-go region painting, cutting plane specification and components reunion. With these operations, we show that (1) exhaustive search in the BSP tree-the most time-consuming step in Chopper-can be avoided, (2) more flexible geometric configurations can be provided, (3) users design intention is considered naturally and efficiently, and customized 3D partitioning results can be obtained. We test our tool on a wide range of 3D models and observe promising results. A preliminary user study also demonstrates its effectiveness and efficiency.