Construction and validation of somatic mutation-derived long non-coding RNAs signatures of genomic instability to predict prognosis of hepatocellular carcinoma.

BACKGROUND: Long non-coding RNAs (LncRNAs) have been found to be a potential prognostic factor for cancers, including hepatocellular carcinoma (HCC). Some LncRNAs have been confirmed as potential indicators to quantify genomic instability (GI). Nevertheless, GI-LncRNAs remain largely unexplored. This study established a GI-derived LncRNA signature (GILncSig) that can predict the prognosis of HCC patients. AIM: To establish a GILncSig that can predict the prognosis of HCC patients. METHODS: Identification of GI-LncRNAs was conducted by combining LncRNA expression and somatic mutation profiles. The GI-LncRNAs were then analyzed for functional enrichment. The GILncSig was established in the training set by Cox regression analysis, and its predictive ability was verified in the testing set and TCGA set. In addition, we explored the effects of the GILncSig and TP53 on prognosis. RESULTS: A total of 88 GI-LncRNAs were found, and functional enrichment analysis showed that their functions were mainly involved in small molecule metabolism and GI. The GILncSig was constructed by 5 LncRNAs (miR210HG, AC016735.1, AC116351.1, AC010643.1, LUCAT1). In the training set, the prognosis of high-risk patients was significantly worse than that of low-risk patients, and similar results were verified in the testing set and TCGA set. Multivariate Cox regression analysis and stratified analysis confirmed that the GILncSig could be used as an independent prognostic factor. Receiver operating characteristic curve analysis of the GILncSig showed that the area under the curve (0.773) was higher than the two LncRNA signatures published recently. Furthermore, the GILncSig may have a better predictive performance than TP53 mutation status alone. CONCLUSION: We established a GILncSig that can predict the prognosis of HCC patients, which will help to guide prognostic evaluation and treatment decisions.

Metformin reduces hepatocarcinogenesis by inducing downregulation of Cyp26a1 and CD8+ T cells.

BACKGROUND: Hepatocellular carcinoma (HCC) is a highly heterogeneous cancer with major challenges in both prevention and therapy. Metformin, adenosine monophosphate-activated protein kinase (AMPK) activator, has been suggested to reduce the incidence of HCC when used for patients with diabetes in preclinical and clinical studies. However, the possible effects of metformin and their mechanisms of action in non-diabetic HCC have not been adequately investigated. METHODS: Fah-/-  mice were used to construct a liver-injury-induced non-diabetic HCC model for exploring hepatocarcinogenesis and therapeutic potential of metformin. Changes in relevant tumour and biochemical indicators were measured. Bulk and single-cell RNA-sequencing analyses were performed to validate the crucial role of proinflammatory/pro-tumour CD8+ T cells. In vitro and in vivo experiments were performed to confirm Cyp26a1-related antitumour mechanisms of metformin. RESULTS: RNA-sequencing analysis showed that chronic liver injury led to significant changes in AMPK-, glucose- and retinol metabolism-related pathways in Fah-/- mice. Metformin prevented the formation of non-diabetic HCC in Fah-/- mice with chronic liver injury. Cyp26a1 ddexpression in hepatocytes was significantly suppressed after metformin treatment. Moreover, downregulation of Cyp26a1 occurred in conjunction with increased levels of all-trans-retinoic acid (atRA), which is involved in the activation of metformin-suppressed hepatocarcinogenesis in Fah-/- mice. In contrast, both CD8+  T-cell infiltration and proinflammatory/pro-tumour cytokines in the liver were significantly upregulated in Fah-/- mice during chronic liver injury, which was notably reversed by either metformin or atRA treatment. Regarding mechanisms, metformin regulated the decrease in Cyp26a1 enzyme expression and increased atRA expression via the AMPK/STAT3/Gadd45ß/JNK/c-Jun pathway. CONCLUSIONS: Metformin inhibits non-diabetic HCC by upregulating atRA levels and downregulating CD8+ T cells. This is the first reporting that the traditional drug metformin regulates the metabolite atRA via the Cyp26a1-involved pathway. The present study provides a potential application of metformin and atRA in non-diabetic HCC.

Crosstalk between autophagy inhibitor and salidroside-induced apoptosis: A novel strategy for autophagy-based treatment of hepatocellular cancer.

Autophagy regulates many cell function related to cancer, including cell proliferation, invasion and apoptosis. Therefore, we investigated the potential value of crosstalk between autophagy and apoptosis. The present study demonstrated that seven autophagy related genes were screened from the biological network of salidroside (Sal) acting on liver cancer. The GO analysis showed that these genes were mainly involved in apoptosis and autophagy. The KEGG analysis showed that these genes regulated the process of liver cancer through Th17 cell differentiation, PI3K-Akt signaling pathway and other pathways. Moreover, seven genes were positively correlated with tumor purity, number of B cells, number of CD4+ T cells, number of CD8+ T cells, number of macrophages, number of dendritic cells and number of neutrophils. The overall survival time of liver cancer patients in the high expression group of BIRC5, HSP90AB1 and MTOR was lower than that in the low expression group (P < 0.05), while the overall survival time of the liver cancer patients in the high expression group of DLC1 and FOXO1 was higher than that in the low expression group (P < 0.05). In the pan-cancer analysis, we also found that BIRC5, HSP90AB1, MTOR, and ITGA6 were highly expressed in various cancers, while DLC1, FOXO1, and FOS were low expressed in various cancers. In the molecule docking analysis, we found that FOS, HSP90AB1, and MTOR had the best binding ability. Notably, in the vitro validation experiments, Sal was confirmed to induce autophagy and apoptosis, inhibite invasion and metastasis of liver cancer cells through the PI3K/Akt/mTOR signaling pathway. Meanwhile, inhibition of autophagy by chloroquine diphosphate (CQ) promoted Sal-induced mitochondrial apoptosis via corresponding cell and animal experiments. We speculated that Sal-induced autophagy might be a protective mechanism, inhibition of autophagy could further promote the progression of liver cancer. It may provide important insight into the molecular mechanism of crosstalk between autophagy and apoptosis, and provide a new theoretical basis of Sal combined with autophagy inhibitors as a adjuvant chemotherapeutic strategy for human liver cancer.

Liver cell therapies: cellular sources and grafting strategies.

The liver has a complex cellular composition and a remarkable regenerative capacity. The primary cell types in the liver are two parenchymal cell populations, hepatocytes and cholangiocytes, that perform most of the functions of the liver and that are helped through interactions with non-parenchymal cell types comprising stellate cells, endothelia and various hemopoietic cell populations. The regulation of the cells in the liver is mediated by an insoluble complex of proteins and carbohydrates, the extracellular matrix, working synergistically with soluble paracrine and systemic signals. In recent years, with the rapid development of genetic sequencing technologies, research on the liver's cellular composition and its regulatory mechanisms during various conditions has been extensively explored. Meanwhile breakthroughs in strategies for cell transplantation are enabling a future in which there can be a rescue of patients with end-stage liver diseases, offering potential solutions to the chronic shortage of livers and alternatives to liver transplantation. This review will focus on the cellular mechanisms of liver homeostasis and how to select ideal sources of cells to be transplanted to achieve liver regeneration and repair. Recent advances are summarized for promoting the treatment of end-stage liver diseases by forms of cell transplantation that now include grafting strategies.

Case report: Autosomal recessive bestrophinopathy with macular cysts and MNV over 13-year follow-up.

Purpose: To describe the phenotype and genotype of a patient with autosomal recessive bestrophinopathy (ARB) over a 13-year follow-up period. Methods: The phenotype of the subject was described after a complete ophthalmological examination, which included fundus photography, optical coherence tomography (OCT), fundus autofluorescence, fluorescein angiography (FA), indocyanine green angiography (ICGA), electroretinogram (EOG), electroretinography (ERG), and multifocal electroretinogram (mfERG). Genetic analyses were carried out by screening the variations via whole-exome sequencing. Results: This patient presented with retinoschisis and cystic changes when he was 7 years old and was diagnosed with X-linked retinoschisis. In the 13th year after the first presentation, enlarged macular cysts with retinoschisis, macular neovascularization (MNV), and subretinal fluid were displayed on OCT. Autofluorescence showed hyperfluorescence corresponding to the area of retinal pigment epithelium (RPE) change. EOG showed no light peak, and the Arden ratio was less than 2.0. Whole-exome sequencing revealed compound heterozygous sequence variations (p. [Arg47Leu; Trp287*]) in the coding sequence of the BEST1 allele inherited from his parents. Thus, a diagnosis of ARB combined with secondary MNV was made. Conclusion: Patients with compound heterozygous BEST1 mutations developed ARB, which could show significant retinoschisis at a young age. Genetic analyses, autofluorescence, and EOG are essential to diagnose ARB correctly in consequence of considerable phenotypic variations.

Gastrointestinal Langerhans cell histiocytosis with unifocal, single-system involvement in adults: Cases report and literature review.

BACKGROUND: Langerhans cell histiocytosis (LCH) is characterized by unifocal, multifocal single-system, or multi-system disease that occurs in all age groups, while it primarily attacks pediatric patients. Solitary gastrointestinal (GI) LCH in adults is exceedingly rare, so we aimed to investigate GI LCH in adults with unifocal single-system involvement and clarified the clinicopathologic characteristics of this disease. METHODS: Two cases of solitary GI LCH in adults were presented, and the clinicopathologic features of this diagnosis in the literature were reviewed. RESULTS: The main diagnostic feature of LCH is the morphologic identification of the characteristic Langerhans cells with prominent nuclear grooves and abundant eosinophilic cytoplasm, accompanied by a variable number of lymphocytes, eosinophils, and plasma cells. The distinctive cells expressed S100, CD1a, and langerin (CD207) on immunohistochemistry. BRAF V600E mutations were detected in the two patients. CONCLUSIONS: Gastrointestinal Langerhans cell histiocytosis in adults with unifocal, single-system involvement is extremely rare. Most patients were asymptomatic and usually a small solitary polyp in GI tract can be observed under routine endoscopy. Although the overall prognosis of unifocal single-system LCH is favorable, long-term follow-up is still necessary to rule out systemic disease.

Biomechanical Evaluation of Transforaminal Lumbar Interbody Fusion with Coflex-F and Pedicle Screw Fixation: Finite Element Analysis of Static and Vibration Conditions.

OBJECTIVE: To investigate the biomechanics of transforaminal lumbar interbody fusion (TLIF) with interspinous process device (IPD) or pedicle screw fixation under both static and vibration conditions by the finite element (FE) method. METHOD: A validated FE model of the L1-5 lumbar spine was used in this study. This FE model derived from computed tomography images of a healthy female adult volunteer of appropriate age. Then the model was modified to simulate L3-4 TLIF. Four conditions were compared: (i) intact; (ii) TLIF combined with bilateral pedicle screw fixation (BPSF); (iii) TLIF combined with U-shaped IPD Coflex-F (CF); and (iv) TLIF combined with unilateral pedicle screw fixation (UPSF). The intact and surgical FE models were analyzed under static and vibration loading conditions respectively. For static loading conditions, four motion modes (flexion, extension, lateral bending, and axial rotation) were simulated. For vibration loading conditions, the dynamic responses of lumbar spine under sinusoidal vertical load were simulated. RESULT: Under static loading conditions, compared with intact case, BPSF decreased range of motion (ROM) by 92%, 95%, 89% and 92% in flexion, extension, lateral bending and axial rotation, respectively. While CF decreased ROM by 87%, 90%, 69% and 80%, and UPSF decreased ROM by 84%, 89%, 66% and 82%, respectively. Compared with CF, UPSF increased the endplate stress by 5%-8% in flexion, 7%-10% in extension, 2%-4% in lateral bending, and decreased the endplate stress by 16%-19% in axial rotation. Compared with CF, UPSF increased the cage stress by 9% in flexion, 10% in extension, and decreased the cage stress by 3% in lateral bending, and 13% in axial rotation. BPSF decreased the stress responses of endplates and cage compared with CF and UPSF. Compared BPSF, CF decreased the facet joint force (FJF) by 6%-13%, and UPSF decreased the FJF by 4%-12%. During vibration loading conditions, compared with BPSF, CF reduced maximum values of the FJF by 16%-32%, and vibration amplitudes by 22%-35%, while UPSF reduced maximum values by 20%-40%, and vibration amplitudes by 31%-45%. CONCLUSION: Compared with other surgical models, BPSF increased the stability of lumbar spine, and also showed advantages in cage stress and endplate stress. CF showed advantages in IDP and FJF especially during vertical vibration, which may lead to lower risk of adjacent segment degeneration. CF may be an effective alternative to pedicle screw fixation in TLIF procedures.

Optimal Selection of Imaging Examination for Lymph Node Detection of Breast Cancer With Different Molecular Subtypes.

Objective: Axillary lymph node management is an important part of breast cancer surgery and the accuracy of preoperative imaging evaluation can provide adequate information to guide operation. Different molecular subtypes of breast cancer have distinct imaging characteristics. This article was aimed to evaluate the predictive ability of imaging methods in accessing the status of axillary lymph node in different molecular subtypes. Methods: A total of 2,340 patients diagnosed with primary invasive breast cancer after breast surgery from 2013 to 2018 in Jiangsu Breast Disease Center, the First Affiliated Hospital with Nanjing Medical University were included in the study. We collected lymph node assessment results from mammography, ultrasounds, and MRIs, performed receiver operating characteristic (ROC) analysis, and calculated the sensitivity and specificity of each test. The C-statistic among different imaging models were compared in different molecular subtypes to access the predictive abilities of these imaging models in evaluating the lymph node metastasis. Results: In Her-2 + patients, the C-statistic of ultrasound was better than that of MRI (0.6883 vs. 0.5935, p=0.0003). The combination of ultrasound and MRI did not raise the predictability compared to ultrasound alone (p=0.492). In ER/PR+HER2- patients, the C-statistic of ultrasound was similar with that of MRI (0.7489 vs. 0.7650, p=0.5619). Ultrasound+MRI raised the prediction accuracy compared to ultrasound alone (p=0.0001). In ER/PR-HER2- patients, the C-statistics of ultrasound was similar with MRI (0.7432 vs. 0.7194, p=0.5579). Combining ultrasound and MRI showed no improvement in the prediction accuracy compared to ultrasound alone (p=0.0532). Conclusion: From a clinical perspective, for Her-2+ patients, ultrasound was the most recommended examination to assess the status of axillary lymph node metastasis. For ER/PR+HER2- patients, we suggested that the lymph node should be evaluated by ultrasound plus MRI. For ER/PR-Her2- patients, ultrasound or MRI were both optional examinations in lymph node assessment. Furthermore, more new technologies should be explored, especially for Her2+ patients, to further raise the prediction accuracy of lymph node assessment.

Comparative analysis of transient receptor potential channel 5 opposite strand-induced gene expression patterns and protein-protein interactions in triple-negative breast cancer.

In patients with triple-negative breast cancer (TNBC), high tumour mutation burden and aberrant oncogene expression profiles are some of the causes of poor prognosis. Therefore, it is necessary to identify aberrantly expressed oncogenes, since they have the potential to serve as therapeutic targets. Transient receptor potential channel 5 opposite strand (TRPC5OS) has been previously shown to function as a novel tumour inducer. However, the underlying mechanism of TRPC5OS function in TNBC remain to be elucidated. Therefore, in the present study TRPC5OS expression was first measured in tissue samples of patients with TNBC and a panel of breast cancer cell lines (ZR-75-1, MDA-MB-453, SK-BR-3, JIMT-1, BT474 and HCC1937) by using qRT-PCR and Western blotting. Subsequently, the possible effects of TRPC5OS on MDA-MB-231 cells proliferation were determined using Cell Counting Kit-8 and 5-Ethynyl-2'-deoxyuridine assays after Lentiviral transfection of MDA-MB-231. In addition, potential interaction partners of TRPC5OS were explored using liquid chromatography-mass spectrometry (LC-MS)/MS. Gene expression patterns following TRPC5OS overexpression were also detected in MDA-MB-231 cells by using High-throughput sequencing. Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) analysis were then used to systematically verify the potential interactions among the TRPC5OS-regulated genes. The potential relationship between TRPC5OS-interacting proteins and gene expression patterns were studied using Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) analysis. TRPC5OS expression was found to be significantly higher in TNBC tumour tissues and breast cancer cell lines compared with luminal tumour tissues and ZR-75-1. In addition, the overexpression of TRPC5OS significantly increased cell proliferation. High-throughput sequencing results revealed that 5,256 genes exhibited differential expression following TRPC5OS overexpression, including 3,269 upregulated genes and 1,987 downregulated genes. GO analysis results indicated that the functions of these differentially expressed genes were enriched in the categories of 'cell division' and 'cell proliferation' regulation. KEGG analysis showed that the TRPC5OS-regulated genes were associated with processes of 'homologous recombination' and 'TNF signalling pathways'. Subsequently, 17 TRPC5OS-interacting proteins were found using LC-MS/MS and STRING analysis. The most important protein among interacting proteins was ENO1 which was associated with glycolysis and regulated proliferation of cancer. In summary, data from the present study suggest that TRPC5OS overexpression can increase TNBC cell proliferation and ENO1 may be a potential target protein mediated by TRPC5OS. Therefore, TRPC5OS may serve as a novel therapeutic target for TNBC.

TRPC5OS induces tumorigenesis by increasing ENO1-mediated glucose uptake in breast cancer.

Breast cancer is the most common malignant tumor worldwide and the leading cause of cancer-related deaths in female. Metabolic reprogramming plays critical roles in breast tumorigenesis and induces enhanced glucose uptake and glycolysis. TRPC5OS is encoded by short transient receptor potential channel 5 opposite strand, and predicted to correlate with tumor metabolic reprogramming. Here we aim to elucidate the function of TRPC5OS in aberrant metabolism mediated tumorigenesis. We detected TRPC5OS expression levels in cell lines and tissues by quantitative real-time polymerase chain reaction and immunohistochemistry. Then we assessed the effects of TRPC5OS on proliferation and cell cycle progression in breast cancer cells by cell counting kit-8, colony-formation, EdU-incorporation assays and flow cytometry. Tumor growth in vivo was observed in a mouse xenograft model. Mass spectrum analyses were performed to identify potential interactors of TRPC5OS in tumor cells, and the interaction between TRPC5OS and interactors was validated by co-immunoprecipitation (CO-IP), western blots, and immunofluorescent staining. Glucose uptake was measured by liquid scintillation spectrometry. TRPC5OS highly expresses both in breast tumors and cell lines, and might be an independent prognostic marker for breast cancer patients. Overexpressed TRPC5OS promotes breast cancer cell proliferation, cell cycle progression, and enhances tumor xenograft growth. Mass spectral and CO-IP data showed that TRPC5OS interacts with ENO1. We also demonstrate that TRPC5OS could enhance ENO1/PI3K/Akt-mediated glucose uptake in breast cancer cells. Our study demonstrated that TRPC5OS promotes breast tumorigenesis by ENO1/PI3K/Akt-mediated glucose uptake. TRPC5OS might be an independent prognostic marker and potential therapeutic target for breast cancer patients.

Altered glycolysis results in drug-resistant in clinical tumor therapy.

Cancer cells undergo metabolic reprogramming, including increased glucose metabolism, fatty acid synthesis and glutamine metabolic rates. These enhancements to three major metabolic pathways are closely associated with glycolysis, which is considered the central component of cancer cell metabolism. Increasing evidence suggests that dysfunctional glycolysis is commonly associated with drug resistance in cancer treatment, and aberrant glycolysis plays a significant role in drug-resistant cancer cells. Studies on the development of drugs targeting these abnormalities have led to improvements in the efficacy of tumor treatment. The present review discusses the changes in glycolysis targets that cause drug resistance in cancer cells, including hexokinase, pyruvate kinase, pyruvate dehydrogenase complex, glucose transporters, and lactate, as well the underlying molecular mechanisms and corresponding novel therapeutic strategies. In addition, the association between increased oxidative phosphorylation and drug resistance is introduced, which is caused by metabolic plasticity. Given that aberrant glycolysis has been identified as a common metabolic feature of drug-resistant tumor cells, targeting glycolysis may be a novel strategy to develop new drugs to benefit patients with drug-resistance.

Changes of lymphatic flow caused by core needle biopsy of axillary sentinel lymph node in a rabbit model.

BACKGROUND: Core needle biopsy (CNB) plays an important role in the preoperative axillary lymph node (ALN) assessment in breast cancer (BC) patients with the development of treatment, but little is known about the axillary lymph flow after CNB of ALNs. This study aimed to investigate the changes of lymphatic flow after CNB of sentinel lymph node (SLN) in a rabbit model. METHODS: The axillary SLN was biopsied in a rabbit model, and the changes of sentinel lymph flow were observed by methylthioninium chloride imaging at 1 and 12 days after the biopsy. Furthermore, the afferent lymphatic vessel was ligated and imaged once every 3 days to assess the changes of lymphatic flow. RESULTS: The SLN biopsied was characterized by disorganized medullary sinus containing erythrocytes, whereas clean medullary sinus containing a normal population of circulating lymphoid cells was observed in the contralateral normal SLN. At 1 day after biopsy, the sentinel lymphatic drainage was blocked. At 12 days after biopsy, the sentinel lymphatic flow was reconstructed or repaired. Ligation of afferent lymphatic vessel further confirmed the reconstruction of lymphatic flow. CONCLUSIONS: The sentinel lymphatic flow changes after CNB in a rabbit model, but it can be reconstructed or repaired.

Comparison of indocyanine green fluorescence and methylene blue dye in the detection of sentinel lymph nodes in breast cancer.

BACKGROUND: Previous studies have shown that sentinel lymph node biopsy (SLNB) can be successfully performed using methylene blue (MB); however, this method still has some drawbacks. Indocyanine green (ICG) fluorescence imaging, as a selective method, has the potential for guiding SLNB. This study aimed to compare the clinical sensitivity and efficacy between ICG and MB in SLNB in breast cancer. METHODS: A prospective study of 70 patients with biopsy-proven invasive breast cancer was conducted. Under the guidance of ICG and MB, administered by injection, SLNs were examined and removed. The detection rates, total number of SLNs detected, mean number of SLNs detected, and number of positive SLNs were compared between ICG and MB. RESULTS: The SLN detection rate was 100% and 93% (65/70) for ICG and MB, respectively. More SLNs were detected in the ICG group (243) than in the MB group (169). The mean number of SLNs detected with ICG and MB was 3.5±1.73 and 2.4±1.49, respectively. Moreover, there was a statistically significant difference between the number of SLNs detected using the two methods (t=6.648, P<0.05). Additionally, SLN metastasis was detected in 18 patients using ICG and 14 patients using MB; these patients immediately underwent axillary lymph node dissection (ALND). No postoperative complications were reported. CONCLUSIONS: ICG demonstrated a higher detection rate and better accuracy, as well as a lower false negative rate, than MB in detecting SLNs in breast cancer. ICG has potential as an alternative tool that could be clinically applied to detect SLNs in breast cancer patients.

Serum tRNA-derived fragments (tRFs) as potential candidates for diagnosis of nontriple negative breast cancer.

Breast cancer has become the most common cancer in women, and nontriple negative breast cancer (non-TNBC) accounts for 80-90% of all invasive breast cancers. Early detection, diagnosis, and treatment are considered key to a successful cure. Conventionally, breast imaging and needle core biopsy are used for detection and monitoring. However, small variations in volume might be ignored in imaging, and traditional biopsies are spatially and temporally limited, leading to a significant delay in cancer detection and thus prompting renewed focus on early and accurate diagnosis. In this article, we investigated whether there is an accurate molecule in peripheral blood that can help diagnose breast cancer. Similar to microRNAs, tRNA-derived fragments (tRFs) have been reported to be involved in many pathological processes in breast cancer, but whether they can serve as candidate biomarkers for breast cancer remains unclear. Using high-throughput sequencing technology, we identified 4,021 differentially expressed tRFs in normal and breast cancer cell lines, and eight tRFs were selected to establish a signature as a predictive biomarker of non-TNBC. Furthermore, quantitative reverse-transcriptase polymerase chain reaction was performed to verify the expression of the signature and analyze the correlation between dysregulated tRFs and breast cancer. The results indicated that tDR-7816, tDR-5334, and tDR-4733 might be promising biomarkers. Through further bioinformatics analysis, we predicted that tDR-7816 influences the xenobiotic metabolic processes that support the oncogenesis of breast cancer. In summary, our results provide a rationale for using circulating tDR-7816 expression as a novel potential biomarker for the diagnosis of patients with early non-TNBC.

ZFP57 suppress proliferation of breast cancer cells through down-regulation of MEST-mediated Wnt/ß-catenin signalling pathway.

Activation of oncogenes by promoter hypomethylation plays an important role in tumorigenesis. Zinc finger protein 57 (ZFP57), a member of KRAB-ZFPs, could maintain DNA methylation in embryonic stem cells (ESCs), although its role and underlying mechanisms in breast cancer are not well understood. In this study, we found that ZFP57 had low expression in breast cancer, and overexpression of ZFP57 could inhibit the proliferation of breast cancer cells by inhibiting the Wnt/ß-catenin pathway. MEST was validated as the direct target gene of ZFP57 and MEST may be down-regulated by ZFP57 through conserving DNA methylation. Furthermore, overexpression of MEST could restore the tumour-suppressed and the Wnt/ß-catenin pathway inactivated effects of ZFP57. ZFP57-MEST and the Wnt/ß-catenin pathway axis are involved in breast tumorigenesis, which may represent a potential diagnostic biomarker, and provide a new insight into a novel therapeutic strategy for breast cancer patients.

Hypoxia-induced tRNA-derived fragments, novel regulatory factor for doxorubicin resistance in triple-negative breast cancer.

Triple-negative breast cancer (TNBC) is an aggressive subtype of epithelial breast malignancy, and chemoresistance is the major obstacle for cancer therapy. TNBC is associated with a hypoxic phenotype, and hypoxia contributes to the chemoresistance in breast cancer. Transfer RNA-derived fragments (tDRs) represent a new class of small noncoding RNAs that can be induced specifically by hypoxia. Here, we conducted a comparative analysis of the aberrant expression of tDRs in hypoxia-treated TNBC cell lines through the use of high-throughput sequencing technique. Quantitative real-time polymerase chain reaction was used to validate the differently expressed tDRs between two samples. The results showed that tDR-0009 [derived from transfer RNA (tRNA)Gly-GCC-1-1 ] and tDR-7336 (derived from tRNA Gly-GCC-1-2 ) were significantly upregulated when the SUM-1315 cell lines were stimulated by hypoxia. Gene ontology (GO) and pathway analysis indicated that these two upregulated tDRs were mainly involved in maintenance of stem cell population and cellular response to interleukin (IL)-6, which may be the underlying mechanism of hypoxia-induced tDRs that facilitate the doxorubicin resistance in TNBC. The protein-protein interaction network for predicted target genes established by the STRING database manifested that tDR-0009 (tDR-7336) might be involved in the chemoresistance of TNBC via regulation of the activation of phosphorylation of STAT3. In summary, our study provided a comprehensive analysis of the deviant expression profiling of tDRs in hypoxia-treated TNBC cell lines. Specific tDRs may be a new class of regulatory factors involved in the hypoxia-induced chemoresistance in TNBC, and they could serve as potential biomarkers and intervention targets.

Target-induced self-assembly of DNA nanomachine on magnetic particle for multi-amplified biosensing of nucleic acid, protein, and cancer cell.

A biosensing system is established for the multi-amplified detection of DNA or specific substrates of aptamers under isothermal conditions, which combines nicked rolling circle amplification (N-RCA) and beacon assisted amplification (BAA) with sensitive colorimetric technique by using DNAzymes as reporter units. According to the configuration, the analysis of DNA is accomplished by recognizing the target to capture nucleic acid-functionalized magnetic particles, followed by the self-assembly of the other two nucleic acids into multicomponent DNA supramolecular structure on magnetic particles. After magnetic separation, the circularization with ligase and the fragmentation with polymerase activate N-RCA and BAA in the presence of polymerase, dNTPs, and the nicking endonuclease, successively producing horseradish peroxidase (HRP)-mimicking DNAzymes that act as colorimetric reporter to catalyze the oxidation of ABTS(2-) by H2O2 in the presence of hemin. Under the optimized conditions, we obtain a wide dynamic range for DNA analysis over 6 orders of magnitude from 1.0 × 10(-14) to 1.0 × 10(-9)M with a low limit of detection of 6.8 × 10(-15)M. In the absence of a target, neither self-assembly of nucleic acids nor amplification process can be initiated, indicating an excellent selectivity of the proposed strategy. Similarly, an analogous system is activated by cancer cells or lysozyme through cooperative self-assembly of nucleic acids on magnetic particles in the presence of respective substrates of aptamers to synthesize HRP-mimicking DNAzymes that give the readout signal for the recognition events, achieving LODs of 81 Ramos cells and 7.2 × 10(-15)M lysozyme, respectively.

Ultrasensitive detection of mRNA extracted from cancerous cells achieved by DNA rotaxane-based cross-rolling circle amplification.

An ultrasensitive and highly selective method for polymerase chain reaction-free (PCR-free) messenger RNA (mRNA) expression profiling is developed through a novel cross-rolling circle amplification (C-RCA) process based on DNA-rotaxane nanostructures. Two species of DNA pseudorotaxane (DPR) superstructures (DPR-I and DPR-II) are assembled by threading a linear DNA rod through a double-stranded DNA (dsDNA) ring containing two single-stranded gaps. In this assay, cDNA that is specific for ß-actin (ACTB) mRNA is taken as a model analyte. Upon the introduction of the target cDNA, the cDNA and the biotin-modified primer are hybridized to the single-stranded regions of the DNA rod and the gap-ring, respectively. As a result, the DPR-I dethreads into free DNA macrocycle and a dumbbell-shaped DNA nanostructure. In the presence of DNA polymerase/dNTPs, two release-DNA on the DPR-I are replaced by polymerase with strand-displacement activity, which can act as the input of the DPR-II to trigger the dethreading of DPR-II and the RCA reaction, releasing another two specified release-DNA strands those in turn serve as the "mimic cDNA" for DPR-I. The C-RCA reaction then proceeds autonomously. To overcome the high background induced by hemin itself, the biotinylated rolling circle products are captured by streptavidin-coated MNPs, achieving a detection limit as low as 0.1 zmol cDNA. The assay also exhibits an excellent selectivity due to its unique DNA nanostructure fabricated through base pairing hybridization. The ACTB mRNA expression in mammary cancer cells (MCF-7) is successfully detected.

Dumbbell probe-mediated cascade isothermal amplification: a novel strategy for label-free detection of microRNAs and its application to real sample assay.

Considering the great significance of microRNAs (miRNAs) in cancer detection and typing, the development of sensitive, specific, quantitative, and low-cost methods for the assay of expression levels of miRNAs is desirable. We describe a highly efficient amplification platform for ultrasensitive analysis of miRNA (taking let-7a miRNA as a model analyte) based on a dumbbell probe-mediated cascade isothermal amplification (DP-CIA) strategy. The method relies on the circularization of dumbbell probe by binding target miRNA, followed by rolling circle amplification (RCA) reaction and an autonomous DNA machine performed by nicking/polymerization/displacement cycles that continuously produces single-stranded G-quadruplex to assemble with hemin to generate a color signal. In terms of the high sensitivity (as low as 1 zmol), wide dynamic range (covering 9 orders of magnitude), good specificity (even single-base difference) and easy operation (one probe and three enzymes), the proposed label-free assay is successfully applied to direct detection of let-7a miRNA in real sample (total RNA extracted from human lung tissue), demonstrating an attractive alternative for miRNA analysis for gene expression profiling and molecular diagnostics, particularly for early cancer diagnosis.