MEMS-based two-photon microscopy with Lissajous scanning and image reconstruction under a feed-forward control strategy.

Two-photon microscopy (TPM) based on two-dimensional micro-electro-mechanical (MEMS) system mirrors shows promising applications in biomedicine and the life sciences. To improve the imaging quality and real-time performance of TPM, this paper proposes Lissajous scanning control and image reconstruction under a feed-forward control strategy, a dual-parameter alternating drive control algorithm and segmented phase synchronization mechanism, and pipe-lined fusion-mean filtering and median filtering to suppress image noise. A 10 fps frame rate (512 × 512 pixels), a 140 µm × 140 µm field of view, and a 0.62 µm lateral resolution were achieved. The imaging capability of MEMS-based Lissajous scanning TPM was verified by ex vivo and in vivo biological tissue imaging.

[Genetic analysis of a pedigree with atypical partial 4q trisomy].

OBJECTIVE: To explore the genetic basis for a Chinese pedigree affected with mental retardation. METHODS: G-banded karyotyping analysis and single nucleotide polymorphism microarray (SNP array) were used to detect the genetic variants within the family, and the origin of the variants was analyzed using UPDtool Statistics software. RESULTS: The patient, a 26-year-old female, was found to have a chromosomal karyotype of 46,XX,dup(4)(q28.2q31.3),and SNP array revealed a 25.71 Mb duplication at 4q28.2-q31.3. The duplication was inherited from her father, and her fetus was found to carry the same duplication. CONCLUSION: The duplication of the patient probably underlay the mental retardation. The gender of the carrier and parental origin of the duplication might have led to the variation in their clinical phenotype.

ACADSB regulates ferroptosis and affects the migration, invasion, and proliferation of colorectal cancer cells.

Colorectal cancer (CRC) is one of the most pressing health issues in today's society. As such, it is imperative that the scientific community devise effective methods to inhibit the proliferation and metastasis of CRC cells. Ferroptosis is a recently discovered regulatory cell death mode mainly manifested by dysregulation of cellular iron metabolism and mitochondrial lipid peroxidation. ACADSB is a member of the acyl-CoA dehydrogenase. This study finds that ACADSB is lowly expressed in CRC tissues. Its expression is negatively correlated with N- and M-stage CRC but positively correlated with the overall survival rate of CRC patients. In addition, it finds that ACADSB is found in the mitochondria of cells. Overexpression of ACADSB inhibits CRC cell migration, invasion, and proliferation, while ACADSB knockdown has the opposite effect. More importantly, the study finds that ACADSB negatively regulates expression of glutathione reductase and glutathione peroxidase 4, the two main enzymes responsible for clearing glutathione (GSH) in CRC cells. ACADSB overexpression enhances the concentration of malondialdehyde, Fe+ , superoxide dismutase, and lipid peroxidation in CRC cells, but reduces the concentration of GSH. This is significant, as all of these are important indicators of ferroptosis. Evaluating the data as a whole, this paper speculates that ACADSB affects CRC cell migration, invasion, and proliferation by regulating CRC cell ferroptosis.

Hyper-acetylation contributes to the sensitivity of chemo-resistant prostate cancer cells to histone deacetylase inhibitor Trichostatin A.

Therapeutic agents are urgently needed for treating metastatic castration-refractory prostate cancer (mCRPC) that is unresponsive to androgen deprivation and chemotherapy. Our screening assays demonstrated that chemotherapy-resistant prostate cancer (PCa) cells are more sensitive to HDAC inhibitors than paired sensitive PCa cells, as demonstrated by cell proliferation and apoptosis in vitro and in vivo. Kinetic study revealed that TSA-induced apoptosis was significantly dependent on enhanced transcription and protein synthesis in an early stage, which subsequently caused ER stress and apoptosis. ChIP analysis indicated that TSA increased H4K16 acetylation, promoting ER stress gene transcription. The changes in Ac-H4K16, ATF3 and ATF4 were also validated in TSA-treated animals. Further study revealed the higher enzyme activity of HDACs and an increase in acetylated proteins in resistant cells. The higher nucleocytoplasmic acetyl-CoA in resistant cells was responsible for elevated acetylation status of protein and a more vigorous growth state. These results strongly support the pre-clinical application of HDAC inhibitors for treating chemotherapy-resistant mCRPC.

Downregulation of reticulocalbin-1 differentially facilitates apoptosis and necroptosis in human prostate cancer cells.

Reticulocalbin 1 (RCN1), an endoplasmic reticulum (ER)-resident Ca2+ -binding protein, is dysregulated in cancers, but its pathophysiological roles are largely unclear. Here, we demonstrate that RCN1 is overexpressed in clinical prostate cancer (PCa) samples, associated with cyclin B, not cyclin D1 expression, compared to that of benign tissues in a Chinese Han population. Downregulation of endogenous RCN1 significantly suppresses PCa cell viability and arrests the cell cycles of DU145 and LNCaP cells at the S and G2/M phases, respectively. RCN1 depletion causes ER stress, which is evidenced by induction of GRP78, activation of PERK and phosphorylation of eIF2α in PCa cells. Remarkably, RCN1 loss triggers DU145 cell apoptosis in a caspase-dependent manner but mainly causes necroptosis in LNCaP cells. An animal-based analysis confirms that RCN1 depletion suppresses cell proliferation and promotes cell death. Further investigations reveal that RCN1 depletion leads to elevation of phosphatase and tensin homolog (PTEN) and inactivation of AKT in DU145 cells. Silencing of PTEN partially restores apoptotic cells upon RCN1 loss. In LNCaP cells, predominant activation of CaMKII is important for necroptosis in response to RCN1 depletion. Thus, RCN1 may promote cell survival and serve as a useful target for cancer therapy.

Pro-metastatic activity of AGR2 interrupts angiogenesis target bevacizumab efficiency via direct interaction with VEGFA and activation of NF-κB pathway.

Anterior gradient 2 (AGR2), an endoplasmic reticulum (ER)-resident protein-disulfide isomerase (PDI), is associated with cancer development and malignant progression. Here, we show that high level of AGR2 promotes the aggressive phenotype of prostate cancer (PCa) mouse models developed by either patient-derived xenografts or surgical intra-prostate implantation of PCa cells, associated with enrichment of the blood vessel network in tumor tissues. Angiogenesis markers VEGFR2 and CD34, accompanied with the invasive marker Vimentin, were predominantly stained in metastatic liver tissues. Secreted AGR2 was defined to enhance VEGFR2 activity as evidenced by physical interaction of purified recombinant human AGR2 (rhAGR2) with rhVEGFA through the formation of a disulfide bond. Mutant or deleted thioredoxin motif in rhAGR2 was also unable to bind to rhVEGFA that led to the significant abolishment in the vessel formation, but partially affecting the aggressive process, implicating alternative mechanisms are required for AGR2-conferring metastasis. Cytosolic AGR2 contributed to cell metastasis ascribed to its stabilizing effect on p65 protein, which subsequently activated the NF-κB and facilitated epithelial to mesenchymal transition (EMT). Importantly, GSH and cabozantinib, but not bevacizumab, effectively blocked the pro-angiogenic effect of rhAGR2 in vitro and in vivo, providing evidence that secreted AGR2 acts as a predictive biomarker for selection of angiogenesis-targeting therapeutic drugs based on its levels in the circular system.

Downregulation of LINC00894-002 Contributes to Tamoxifen Resistance by Enhancing the TGF-ß Signaling Pathway.

Tamoxifen is a widely used personalized medicine for estrogen receptor (ER)-positive breast cancer, but approximately 30% of patients receiving the treatment relapse due to tamoxifen resistance (TamR). Recently, several reports have linked lncRNAs to cancer drug resistance. However, the role of lncRNAs in TamR is unclear. To identify TamR-related lncRNAs, we first used a bioinformatic approach to predict whether they have connection with known TamR-associated genes by starBase v2.0 and divided them into two groups. Group A contains lncRNAs that connect with known TamR genes and group B contains lncRNAs that show no predicted interaction. Among the 12 lncRNAs in group A, 58.3% of them are either up- or downregulated in MCF-7/TamR cells compared to the sensitive cells. In contrast, the expression levels of all group B lncRNAs are not changed in MCF-7/TamR cells. LINC00894-002 exhibits the most sophisticated network pattern and is the most downregulated lncRNA in MCF-7/TamR cells. Moreover, we find that LINC00894-002 is directly upregulated by ERα. Knocking down LINC00894-002 downregulates expression of miR-200a-3p and miR-200b-3p, upregulates the expression of TGF-ß2 and ZEB1, and finally contributes to TamR. Herein, we report the first case of an inhibitory lncRNA against TamR through the miR-200-TGF-ß2-ZEB1 signaling pathway.

Development of an LC-MS/MS-based assay to determine artemitin in rat plasma and its application in a pharmacokinetic study.

Artemitin, a significant flavonol compound existing in Laggera pterodonta (DC.) Benth., Artemisia rupestris L, etc., is the subject of attention by researchers owing to its pharmacological activities (such as antioxidative, anti-inflammatory and antiviral). In this work, a highly sensitive and specific high-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (HPLC-ESI-MS/MS) assay combined with protein precipitation has been established and validated for determining artemitin concentration in rat plasma. Both artemitin and warfarin sodium (internal standard, IS) were separated on an Agela Venusil XBP Phenyl column through the isocratic elution mode of methanol-water containing 0.1% formic acid (80:20, v/v), at a flow rate of 0.4 mL/min. The MS/MS system was operated in a positive ion and ESI multiple reaction monitoring mode, and the multiple reaction monitoring transition was optimized as m/z 389.0 → 373.0 for artemitin and 309.2 → 163.0 for IS. The method showed good linearity in the range of 2.5-2000 ng/mL (R2 = 1.0000) and high sensitivity for artemitin with the lower limit of quantification of 2.5 ng/mL. The intra- and inter-day accuracies were 97.4-100.9 and 93.4-100.3%, respectively. The intra- and inter-day precisions were <4.8 and 6.5%, respectively. The extraction efficiency and absolute recovery were >66.5 and 71.3%, respectively. In addition, a good matrix effect of <9.5% was obtained. As a result, the method developed herein was successfully applied for the pharmacokinetic study of artemitin after an intravenous administration in rats.

CD44-Targeted Hyaluronic Acid-Coated Redox-Responsive Hyperbranched Poly(amido amine)/Plasmid DNA Ternary Nanoassemblies for Efficient Gene Delivery.

Hyaluronic acid (HA), which can specifically bind to CD44 receptor, is a specific ligand for targeting to CD44-overexpressing cancer cells. The current study aimed to develop ternary nanoassemblies based on HA-coating for targeted gene delivery to CD44-positive tumors. A novel reducible hyperbranched poly(amido amine) (RHB) was assembled with plasmid DNA (pDNA) to form RHB/pDNA nanoassemblies. HA/RHB/pDNA nanoassemblies were fabricated by coating HA on the surface of the RHB/pDNA nanoassembly core through electrostatic interaction. After optimization, HA/RHB/pDNA nanoassemblies were spherical, core-shell nanoparticles with nanosize (187.6 ± 11.4 nm) and negative charge (-9.1 ± 0.3 mV). The ternary nanoassemblies could efficiently protect the condensed pDNA from enzymatic degradation by DNase I, and HA could significantly improve the stability of nanoassemblies in the sodium heparin solution or serum in vitro. As expected, HA significantly decreased the cytotoxicity of RHB/pDNA nanoassemblies due to the negative surface charges. Moreover, it revealed that HA/RHB/pDNA nanoassemblies showed higher transfection activity than RHB/pDNA nanoassemblies in B16F10 cells, especially in the presence of serum in vitro. Because of the active recognition between HA and CD44 receptor, there was significantly different transfection efficiency between B16F10 (CD44+) and NIH3T3 (CD44-) cells after treatment with HA/RHB/pDNA nanoassemblies. In addition, the cellular targeting and transfection activity of HA/RHB/pDNA nanoassemblies were further evaluated in vivo. The results indicated that the interaction between HA and CD44 receptor dramatically improved the accumulation of HA/RHB/pDNA nanoassemblies in CD44-positive tumor, leading to higher gene expression than RHB/pDNA nanoassemblies. Therefore, HA/RHB/pDNA ternary nanoassemblies may be a potential gene vector for delivery of therapeutic genes to treat CD44-overexpressing tumors in vivo.

Diagnostic and treatment delays of multidrug-resistant tuberculosis before initiating treatment: a cross-sectional study.

OBJECTIVE: Shandong Province has implemented the standardised treatment of multidrug-resistant tuberculosis (MDR-TB) supported by the Global Fund. The study aimed to understand the managements and delays of patients with MDR-TB before initiating their treatments. METHODS: All patients with MDR-TB who had completed intensive phase treatment from January 2010 to May 2012 were interviewed using a structured questionnaire. Delays and treatments were analysed. Diagnosis delay is defined as the period between having sputum smear results and drug susceptibility test (DST) results. Treatment delay was defined as starting MDR-TB treatment more than 2 days after receiving the diagnosis of MDR-TB. Total delay is the sum of diagnosis delay and treatment delay. RESULTS: In total, 110 patients with MDR-TB participated in the study. Median delay for diagnosis was 102 days. Over 80% of patients had a diagnosis delay longer than 90 days. MDR-TB treatments commenced after a median of 9 days after DST results, and over 37% of the patients with MDR-TB experienced treatment delays. Chronic cases or patients with indifferent attitude had significantly longer treatment delay than other groups (P = 0.03 and 0.03, respectively). During their delays, of 44 patients with retreatment failures, 12 (27.3%) were treated through adding single second line drugs (SLDs) to first-line regimens, and 25 (56.8%) were treated with first-line drugs. A high proportion of initial treatment failure/relapsed/returned cases (37%) and new cases (43%) were administered with SLDs. CONCLUSIONS: Most of the patients with MDR-TB experienced prolonged diagnosis delay, which was the most important factor contributing to the total delay. Misuse of SLDs during the days was common, so necessary training should be given to prevent irrational prescription of medications.

Changes in pulmonary tuberculosis prevalence: evidence from the 2010 population survey in a populous province of China.

BACKGROUND: This paper reports findings from the prevalence survey conducted in Shandong China in 2010, a province with a population of 94 million. This study aimed to estimate TB prevalence of the province in 2010 in comparison with the 2000 survey; and to compare yields of TB cases from different case finding approaches. METHODS: A population based, cross-sectional survey was conducted using multi-stage random cluster sampling. 54,279 adults participated in the survey with a response rate of 96%. Doctors interviewed and classified participants as suspected TB cases if they presented with persistent cough, abnormal chest X-ray (CXRAY), or both. Three sputum specimens of all suspected cases were collected and sent for smear microscopy and culture. RESULTS: Adjusted prevalence rate of bacteriologically confirmed cases was 34 per 100,000 for adults in Shandong in 2010. Compared to the 2000 survey, TB prevalence has declined by 80%. 53% of bacteriologically confirmed cases did not present persistent cough. The yield of bacteriologically confirmed cases was 47% by symptom screening and 95% by CXRAY. Over 50% of TB cases were among over 65's. CONCLUSIONS: The prevalence rate of bacteriologically confirmed cases was significantly reduced compared with 2000. The survey raised challenges to identify TB cases without clear symptoms.

Explore variations of DOM components in different landcover areas of riparian zone by EEM-PARAFAC and partial least squares structural equation model.

Dissolved organic matter (DOM) plays key roles in species-distribution of contaminants and the biogeochemical cycle of carbon in ecosystems. Riparian zone is the representative of water-land ecotone and controls the DOM exchange between water and land. However, the variance of DOM in different landcover areas of an urban river riparian zone is unknown. In this study, fluorescence excitation-emission matrix (EEM) spectroscopy coupled with parallel factor analysis (PARAFAC) and partial least squares structural equation model (PLS-SEM) was applied to character dissolved organic matter (DOM) fractions in four types of landcover riparian areas (natural forest, artificial forest, semi-natural grassland, and cropland) of Puhe River and trace latent factors. Soil samples were collected at 0-20 cm, 20-40 cm, 40-60 cm, and 60-80 cm. The results showed that soil DOM components and humification varied between forests with grassland and cropland samples, and soil humification was obviously higher in the forest samples than that in the grassland and cropland samples. In the natural and artificial forest soils, the humic/fulvic-like were the dominant fractions of DOM, whose variations were smaller than the protein-like with soil depths. However, the tyrosine-like was the representative component in the grassland and cropland soils, whose variation was smaller than the humus substances. According to the PLS-SEM, the DOM components and humification were affected by soil physiochemical properties and DOM sources. The humification in the forest soils had a positive correlation with tryptophan-like, which derived from blended source of the autochthonous and terrigenous. Nevertheless, a positive correlation was observed between humification and humus substances, which could derive from microbial degradation of tyrosine-like, in the grassland and cropland soils. Moreover, the soil physiochemical properties were negatively related to DOM components in all soil samples, which could affect indirectly soil humification. Therefore, EEM combined with PARAFAC and PLS-SEM might be an effective method to investigate DOM fractions and trace the latent factors in different landcover areas of the riparian zone.

Integrating TCGA and single-cell sequencing data for colorectal cancer: a 10-gene prognostic risk assessment model.

Colorectal cancer represents a significant health threat, yet a standardized method for early clinical assessment and prognosis remains elusive. This study sought to address this gap by using the Seurat package to analyze a single-cell sequencing dataset (GSE178318) of colorectal cancer, thereby identifying distinctive marker genes characterizing various cell subpopulations. Through CIBERSORT analysis of colorectal cancer data within The Cancer Genome Atlas (TCGA) database, significant differences existed in both cell subpopulations and prognostic values. Employing WGCNA, we pinpointed modules exhibiting strong correlations with these subpopulations, subsequently utilizing the survival package coxph to isolate genes within these modules. Further stratification of TCGA dataset based on these selected genes brought to light notable variations between subtypes. The prognostic relevance of these differentially expressed genes was rigorously assessed through survival analysis, with LASSO regression employed for modeling prognostic factors. Our resulting model, anchored by a 10-gene signature originating from these differentially expressed genes and LASSO regression, proved adept at accurately predicting clinical prognoses, even when tested against external datasets. Specifically, natural killer cells from the C7 subpopulation were found to bear significant associations with colorectal cancer survival and prognosis, as observed within the TCGA database. These findings underscore the promise of an integrated 10-gene signature prognostic risk assessment model, harmonizing single-cell sequencing insights with TCGA data, for effectively estimating the risk associated with colorectal cancer.

Genome-wide analysis of the FOXA1 transcriptional regulatory network identifies super enhancer associated LncRNAs in tamoxifen resistance.

Breast cancer is the leading cause of death in female cancers, and what's worse, tamoxifen resistance occurs in almost 30% breast cancer patients and has seriously attenuated the therapeutic effect. It is widely studied that epigenetic regulation has played important role in the development of tamoxifen resistance. FOXA1 is a pioneer transcription factor that can translate epigenetic signature into transcription regulation and also drive genome-wide enhancer reprogramming in breast cancer. However, the chromatin super enhancer landscape orchestrated by FOXA1 and the key downstream targets of the FOXA1 oncogenic network in tamoxifen resistance remain elusive. Through analyzing the FOXA1 ChIP-seq data in tamoxifen sensitive MCF7 and tamoxifen resistant MCF7/TamR cells, we show that the FOXA1 chromatin occupancy is enhanced in both the promoter and enhancer regions, and the recruitment events may be E2 dependent in both MCF7 and MCF7/TamR cells. By integratively analyzing the FOXA1 ChIP-seq data and RNA-seq data of MCF7 and MCF7/TamR cells, we find that the enhanced or reduced FOXA1 chromatin binding densities may synchronize the transcriptional activity in tamoxifen resistance. Besides, we identify 1003 super enhancer associated protein coding genes and five super enhancer associated lncRNAs (ATP1A1-AS1, CASC11, CASC15, KCTD21-AS1, LINC00885) in tamoxifen resistance. By KM survival analysis, we find that high expression level of ATP1A1-AS1 and its sense transcript ATP1A1 indicates favorable clinical outcome among the luminal endocrine treated breast cancer patients. Further coexpression analysis indicates that ATP1A1-AS1 is significantly correlated with ATP1A1, and RT-qPCR results show that they both are downregulated in MCF7/TamR cells. Our study shows that the FOXA1 transcriptional regulatory network may promote the development of tamoxifen resistance, and identifies one super enhancer associated lncRNA ATP1A1-AS1 that may work as promising biomarker or drug target in tamoxifen resistance.

B-Cell Translocation Gene 2 Upregulation Is Associated with Favorable Prognosis in Lung Adenocarcinoma and Prolonged Patient Survival.

The tumor suppressor protein B-cell translocation gene 2 (BTG2) is downexpressed in lung adenocarcinoma (LUAD); however, its role in LUAD survival remains unknown. This investigation is aimed at exploring the activity of BTG2 in LUAD. We analyzed BTG2 expression in LUAD datasets of the TCGA database and examined that BTG2 was markedly downregulated in comparison with adjacent normal tissues. The prognostic analysis suggested that higher expression of BTG2 protein correlates with prolonged survival in patients. Vectors expressing BTG2 were stably transduced into lung adenocarcinoma A549 cells. The overexpression of BTG2 in A549 cells causes cellular G1 phase arrest but did not affect cell proliferation, accompanied by increased activation of NF-κB. Our data indicate that BTG2 overexpression may trigger an autoregulatory prosurvival NF-κB pathway, which is resistant to environmental intervention owing to an increased level of BTG2.

Metagenomic Next-Generation Sequencing Reveals the Profile of Viral Infections in Kidney Transplant Recipients During the COVID-19 Pandemic.

Background: To study the clinical application of metagenomic next-generation sequencing (mNGS) in the detection of viral infections in kidney transplant recipients (KTRs) during the COVID-19 pandemic. Methods: Using mNGS technology, 50 human fluid samples of KTRs were detected, including 20 bronchoalveolar lavage fluid (BALF) samples, 21 urine samples and 9 blood samples. The detected nucleic acid sequences were compared and analyzed with the existing viral nucleic acid sequences in the database, and the virus infection spectrum of KTRs was drawn. Results: The viral nucleic acids of 15 types of viruses were detected in 96.00% (48/50) of the samples, of which 11 types of viruses were in BALF (95.00%, 19/20), and the dominant viruses were torque teno virus (TTV) (65.00%; 13/20), cytomegalovirus (CMV) (45.00%; 9/20) and human alphaherpesvirus 1 (25.00%; 5/20). 12 viruses (95.24%, 20/21) were detected in the urine, and the dominant viruses were TTV (52.38%; 11/21), JC polyomavirus (52.38%; 11/21), BK polyomavirus (42.86%; 9/21), CMV (33.33%; 7/21) and human betaherpesvirus 6B (28.57%; 6/21). 7 viruses were detected in the blood (100.00%, 9/9), and the dominant virus was TTV (100.00%; 9/9). Four rare viruses were detected in BALF and urine, including WU polyomavirus, primate bocaparvovirus 1, simian virus 12, and volepox virus. Further analysis showed that TTV infection with high reads indicated a higher risk of acute rejection (P < 0.05). Conclusions: mNGS detection reveals the rich virus spectrum of infected KTRs, and improves the detection rate of rare viruses. TTV may be a new biomarker for predicting rejection.

Evaluation of active tuberculosis case finding through symptom screening and sputum microscopy of close contacts in Shandong, China.

OBJECTIVES: To evaluate the effect of active case finding through symptom screening and sputum microscopy of close contacts in a Fidelis (Fund for Innovative DOTS Expansion through Local Initiatives to Stop TB) project. METHODS: Secondary data from all 35 counties were collected during implementation and used. They comprised new cases identified, number of close contacts screened and their relationships. Fifty-four in-depth interviews were conducted with staff from key stakeholders. RESULTS: A total of 13 310 symptomatic contacts of 5255 index cases were screened, and 90 new smear-positive cases were detected with a yield rate of 0.7%. The yield rate of close contacts was positively associated with smear grades of the index cases (P<0.01). Close contacts of cases, such as classmates and workmates, who lived in a closed contained setting, had a higher yield rate than family members (P<0.001). Gaps in project implementation such as training, incentives and sputum collection were identified through in-depth interviews. CONCLUSIONS: The yield rate of close-contact screening of 0.7% was similar to other findings in China. There was a higher yield from screening of close contacts in congregated settings like schools and workshops. Future active case finding projects should provide clear operational guidelines and adequate training.

TP53 Mutation Related and Directly Regulated lncRNA Prognosis Markers in Hepatocellular Carcinoma.

PURPOSE: TP53 mutation is the most common genetic variation type in Hepatocellular carcinoma (HCC). We aim to illustrate the landscape of genomic alterations and TP53 mutation related and directly regulated lncRNA prognosis markers. MATERIALS AND METHODS: Utilizing the clinical and transcriptome data from The Cancer Genome Atlas (TCGA) website, we present the landscape of genomic alterations and RNA differential expression profiles. By analyzing the ENCODE TP53 ChIP-seq data, we get the TP53 chromatin binding profiles. By Kaplan-Meier (KM) survival analysis and ROC analysis, we identify lncRNA prognosis markers. RESULTS: TP53 ranks the highest mutation frequency gene and the maximum mutation type of TP53 is Missense Mutation (> 2.5×104). TP53 mutation showed poor clinical outcome among the pathological Stage II and Stage III HCC patients. By differential expression analysis of the TP53 wild type and mutation HCC, we find thousands of misregulated genes, including 699 differential expression lncRNAs (p <0.05, |log2FC| ≥1). Functional enrichment analysis of the misregulated genes shows that TP53 mutation events mainly alter DNA replication, cell cycle and immune response signaling pathways. By estimation of tumor-infiltrating immune cells through CIBERSORT, we find that the TP53 mutation events are significantly correlated with the different proportions of nine immune cells. We then integratively analyze the differential expression lncRNAs in TP53 wild type and mutation groups and the TP53 ChIP-seq binding lncRNAs, and get 112 overlap lncRNAs. By Kaplan-Meier survival analysis and ROC analysis, we identify two lncRNAs (RP4-736L20.3 and SNRK-AS1) that show significant prognosis value. Using the collected HCC samples, we validate the misregulated expression of RP4-736L20.3 and SNRK-AS1. CONCLUSION: The work presents the landscape of genomic variations and two TP53 mutation related and directly regulated lncRNA prognosis markers of HCC.

Mesenchymal stem cell exosomal tsRNA-21109 alleviate systemic lupus erythematosus by inhibiting macrophage M1 polarization.

Systemic lupus erythematosus (SLE) is a chronic autoimmune disease with M1-type macrophage activation. Mesenchymal stem cells (MSCs) therapies have shown promise in models of pathologies relevant to SLE, while the function and mechanism of MSC-derived exosomes (MSC-exo) were still unclear. We aimed to interrogate the effect of MSC-exo on M1-type polarization of macrophage and investigate mechanisms underlying MSC-exo. Exosomes were isolated from MSC and the effect of MSC-exo on macrophage polarization was evaluated. The key tRNA-derived fragments (tRFs) carried by exosomes were identified by small RNA sequencing and verified in clinical samples. The effect of exosomal-tRFs on macrophage polarization was examined. In this study, MSC-exo dramatically suppressed expression of M1 markers, and reduced the levels of TNF-α and IL-1ß, while increased M2 markers in macrophages. A total of 243 differently expressed tRFs (DEtRFs) were identified between MSC-exo treated and untreated macrophage, among which 103 DEtRFs were up-regulated in response to MSC-exo treatment, including tsRNA-21109. The target genes of tsRNA-21109 were mainly enriched in DNA transcription-related GO function, and mainly involved in inflammatory-related pathways, including Rap1, Ras, Hippo, Wnt, MAPK, TGF-beta signaling pathway. The tsRNA-21109 was lowly expressed in clinical samples and was associated with the patient data in SLE. Compared to the normal MSC-exo, the tsRNA-21109-privative MSC-exo up-regulated M1 marker (CD80, NOS2, MCP1) and down-regulated M2 marker (CD206, ARG1, MRC2), also increased the levels of TNF-α and IL-1ß in macrophages. Western blot and immunofluorescence confirmed that the proportion of CD80/ARG-1 was increased in macrophages treated with tsRNA-21109-privatived MSC-exo compared to that with control MSC-exo. In conclusion, MSC-exo inhibited the M1-type polarization of macrophages, possibly through transferring tsRNA-21109, which may develop as a novel therapeutic target for SLE.