ABSTRACT
High-risk human papillomavirus (hrHPV) infection is associated with cervical cancer; imbalanced vaginal microecology may contribute to HPV progression. Currently used methods for clinical vaginal-microecology (CVM) testing are associated with several disadvantages, such as low accuracy and complicated operation. This retrospective study presents a novel testing method to examine vaginal microecology via double-fluorescence staining and explores the relationship between hrHPV and CVM. We analyzed 1242 patients who underwent hrHPV testing at our hospital over a two-month period; of these, 695 also underwent clinical vaginal-microecology testing (CVMT). Patients underwent routine leukorrhea detection (n=322), functional testing (n=277), and our novel double-fluorescence staining-based CVMT approach (n=376). Patients with hrHPV exhibited more epithelial cells, miscellaneous bacteria, and hyphae than those without hrHPV on double-fluorescence staining-based CVMT approach. Double-fluorescence staining was effective in identifying indicators of hrHPV infection and may serve as an auxiliary tool for clinical hrHPV screening.
Subject(s)
Papillomaviridae , Papillomavirus Infections , Vagina , Humans , Female , Papillomavirus Infections/diagnosis , Papillomavirus Infections/virology , Retrospective Studies , Vagina/virology , Adult , Papillomaviridae/isolation & purification , Papillomaviridae/genetics , Middle Aged , Staining and Labeling/methods , Uterine Cervical Neoplasms/diagnosis , Uterine Cervical Neoplasms/virology , Uterine Cervical Neoplasms/pathology , Young Adult , FluorescenceABSTRACT
Ultrasensitive and accurate monitoring of carboxylesterase (CE) activity is extremely crucial for the early diagnosis of hepatocellular carcinoma (HCC), which is still a considerable challenge. Herein, using a co-reactive ligand engineering strategy, ultra-bright near-infrared (λmax = 830 nm) and self-enhanced electrochemiluminescence (ECL) Au nanoclusters (NCs) were in situ prepared with 2-(diethylamino) ethanethiol (DEAET) as a co-reactive ligand. Remarkably, the co-reactive ligand not only acts as a stabilizer like traditional ligands but also plays a crucial role as a co-reactant to ensure a confinement effect to shorten the charge transfer distance and increase the local concentration, significantly improving the collision efficiency between the electrogenerated free radicals. Consequently, the DEAET Au NCs exhibited a record and stable anodal ECL without the addition of an exogenous co-reactant, dramatically superior to classical Au NCs and Ru(bpy)32+ with a certain amount of the co-reactant. As a proof of concept, a convenient and label-free CE biosensor was innovatively constructed using 1-naphthyl acetate as a selective substrate, achieving ultrasensitive detection for CE activity with a low limit of detection of 9.1 × 10-7 U/L. Therefore, this work not only paves a co-reactive ligand engineering strategy for in situ preparation of high-efficiency metal NCs but also provides an ultrasensitive and convenient platform for the early diagnosis of HCC.
Subject(s)
Biosensing Techniques , Carcinoma, Hepatocellular , Liver Neoplasms , Metal Nanoparticles , Humans , Luminescent Measurements , Gold , Ligands , Electrochemical Techniques , Liver Neoplasms/diagnosis , Carboxylic Ester Hydrolases , Limit of DetectionABSTRACT
Designing artificial viral vectors (AVVs) programmed with biomolecules that can enter human cells and carry out molecular repairs will have broad applications. Here, we describe an assembly-line approach to build AVVs by engineering the well-characterized structural components of bacteriophage T4. Starting with a 120 × 86 nm capsid shell that can accommodate 171-Kbp DNA and thousands of protein copies, various combinations of biomolecules, including DNAs, proteins, RNAs, and ribonucleoproteins, are externally and internally incorporated. The nanoparticles are then coated with cationic lipid to enable efficient entry into human cells. As proof of concept, we assemble a series of AVVs designed to deliver full-length dystrophin gene or perform various molecular operations to remodel human genome, including genome editing, gene recombination, gene replacement, gene expression, and gene silencing. These large capacity, customizable, multiplex, and all-in-one phage-based AVVs represent an additional category of nanomaterial that could potentially transform gene therapies and personalized medicine.
Subject(s)
Bacteriophage T4 , Genome, Human , Humans , Bacteriophage T4/genetics , Bacteriophage T4/metabolism , Genetic Vectors/genetics , Capsid Proteins/metabolism , Capsid/metabolism , DNA, Viral/geneticsABSTRACT
Background: With the emergence of mutant versions that lead to continual spreading and recurrent infections of SARS-CoV-2, the COVID-19 vaccines can assist protection for high risk groups, particularly health workers. Even while booster shots have been widely used, longitude studies on immune responses in healthy subjects are uncommon. Methods: Eighty-five healthcare workers who received the BBIBP-CorV vaccine were prospectively enrolled and monitored for up to ten months. Automated Pylon immunoassays were used to quantify total anti-SARS-CoV2 antibody levels (TAb), surrogate neutralization antibody levels (NAb), and antibody avidities over the course of the follow-up. Additionally, hematology analyses were performed. Results: Pylon antibody testing revealed that every participant tested negative at the beginning, and 88.2% of them tested positive about 14 days after receiving their second dosage. The TAb levels and NAb levels peaked in 76.5% and 88.2% of the subjects, respectively, at the same time. Age was connected with the peak antibody levels, but not with gender, BMI, or baseline hematological factors. The positive rates and the antibody levels had already started to decline three months following the second injection. The antibody levels and avidities quickly increased following the booster doses to levels that were considerably greater than the peak antibody responses before to the booster shots. Hematology testing revealed no safety concerns with immunizations. Conclusion: In healthy workers, the two doses of BBIBP-CorV were able to induce humoral immunity; however, 3 months following vaccination, the antibody levels started to decline. The BBIBP-CorV booster injections increase both the quantity and quality of antibodies, which gave support for utilizing booster doses to prolong the duration of the vaccine's protective effects.
Subject(s)
Antibody Formation , COVID-19 , Humans , COVID-19 Vaccines , SARS-CoV-2 , COVID-19/prevention & control , Vaccination , Health Personnel , Antibodies, ViralABSTRACT
Chronic inflammation is associated with lung tumorigenesis, in which NF-κB-mediated epigenetic regulation plays a critical role. Lung tumor suppressor G protein-coupled receptor, family C, member 5A (GPRC5A), is repressed in most non-small cell lung cancer (NSCLC); however, the mechanisms remain unclear. Here, we show that NF-κB acts as a transcriptional repressor in suppression of GPRC5A. NF-κB induced GPRC5A repression both in vitro and in vivo. Intriguingly, transactivation of NF-κB downstream targets was not required, but the transactivation domain of RelA/p65 was required for GPRC5A repression. NF-κB did not bind to any potential cis-element in the GPRC5A promoter. Instead, p65 was complexed with retinoic acid receptor α/ß (RARα/ß) and recruited to the RA response element site at the GPRC5A promoter, resulting in disrupted RNA polymerase II complexing and suppressed transcription. Notably, phosphorylation on serine 276 of p65 was required for interaction with RARα/ß and repression of GPRC5A. Moreover, NF-κB-mediated epigenetic repression was through suppression of acetylated histone H3K9 (H3K9ac), but not DNA methylation of the CpG islands, at the GPRC5A promoter. Consistently, a histone deacetylase inhibitor, but not DNA methylation inhibitor, restored GPRC5A expression in NSCLC cells. Thus, NF-κB induces transcriptional repression of GPRC5A via a complex with RARα/ß and mediates epigenetic repression via suppression of H3K9ac.
Subject(s)
Carcinoma, Non-Small-Cell Lung , Lung Neoplasms , Humans , NF-kappa B/metabolism , Carcinoma, Non-Small-Cell Lung/genetics , Transcriptional Activation , Epigenesis, Genetic , Lung Neoplasms/genetics , Lung Neoplasms/metabolism , Lung/metabolism , Receptors, G-Protein-Coupled/genetics , Receptors, G-Protein-Coupled/metabolism , Receptors, Retinoic Acid/genetics , Receptors, Retinoic Acid/metabolism , Epithelial Cells/metabolismABSTRACT
Nucleus accumbens-associated 1 (NAC1) is a member of pox virus and zinc finger/bric-a-brac tramtrack broad complex (BTB/POZ) gene family. Overexpression of NAC1 is implicated in cancer development, recurrence and chemotherapy resistance. In our previous study, we found NAC1 was a potential small ubiquitin-like modifier (SUMO) substrate in prostate cancer cells. However, there was still lack of evidences to further support and validate the result. In this work, we found that NAC1 is a multi-SUMO-sites acceptor. The SUMO acceptor lysines were K167, K318, K368, K483 and K498. SUMOylation didn't alter the localization of NAC1, but facilitated the formation of NAC1 nuclear bodies. Compared with NAC1 wild type (NAC1 WT), the SUMO-sites mutant of NAC1 (NAC1 SM) suppressed cell proliferation and tumor growth in cellular and animal levels. This work uncovered the function of SUMOylation of NAC1 in prostate cancer cells.
Subject(s)
Prostatic Neoplasms , Repressor Proteins , Humans , Male , Animals , Repressor Proteins/genetics , Repressor Proteins/metabolism , Sumoylation , Prostatic Neoplasms/genetics , Cell Line, Tumor , Zinc FingersABSTRACT
Bacteriophages (phages), as natural antibacterial agents, are being rediscovered because of the growing threat of multi- and pan-drug-resistant bacterial pathogens globally. However, with an estimated 1031 phages on the planet, finding the right phage to recognize a specific bacterial host is like looking for a needle in a trillion haystacks. The host range of a phage is primarily determined by phage tail fibers (or spikes), which initially mediate reversible and specific recognition and adsorption by susceptible bacteria. Recent significant advances at single-molecule and atomic levels have begun to unravel the structural organization of tail fibers and underlying mechanisms of phage-host interactions. Here, we discuss the molecular mechanisms and models of the tail fibers of the well-characterized T4 phage's interaction with host surface receptors. Structure-function knowledge of tail fibers will pave the way for reprogramming phage host range and will bring future benefits through more-effective phage therapy in medicine. Furthermore, the design strategies of tail fiber engineering are briefly summarized, including machine-learning-assisted engineering inspired by the increasingly enormous amount of phage genetic information.
Subject(s)
Bacteriophages , Bacteriophages/physiology , Host Specificity , Virion , Carrier Proteins , Anti-Bacterial AgentsABSTRACT
In chronic myeloid leukemia (CML) patients, the involvement of the BCR/ABL1 isoform in tyrosine kinase inhibitors (TKIs) resistance has attracted lots of attention. In this work, a novel isoform that encoded truncated protein due to the deletion of ABL1 exon7, 8, and 9 was reported and named BCR/ABL1ΔE7-8-9 here. This isoform was detected only in 10.2% of CML patients with inadequate responses to TKIs. BCR/ABL1Δexon7-8-9 isoform promoted S phase cell proliferation and reduced the expression of fusion gene and ABL1 phosphorylation level more slowly than that of control cells after TKIs treatment. The novel isoform has the qualities of a functional tyrosine kinase, localized in the cytoplasm, and could not be imported into the nucleus by TKIs. These results indicated that BCR/ABL1Δexon7-8-9 showed poorer sensitivity to imatinib and nilotinib than wild-type BCR/ABL1. According to molecular docking studies, nilotinib and imatinib present different binding sites and have a lower binding capacity with BCR/ABL1ΔE7-8-9 protein than the wild type. Our findings suggested that the novel isoform BCR/ABL1ΔE7-8-9 may contribute to TKIs resistance in CML due to its weakened TKIs binding ability. It enriched the mechanism of spliceosome involved in TKIs resistance. Monitoring the expression of BCR/ABL1ΔE7-8-9 helps guide the treatment of CML patients in the clinic.
Subject(s)
Leukemia, Myelogenous, Chronic, BCR-ABL Positive , Humans , Molecular Docking Simulation , Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy , Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics , Protein IsoformsABSTRACT
While initiation is established as a critical step in tumorigenesis, the identity of the cell of origin for lung adenocarcinoma and the mechanism controlling susceptibility to initiation remain elusive. Here we show that lung tumor suppressor Gprc5a-knockout (KO) mice are susceptible to initiation of lung tumorigenesis. Bronchioalveolar stem cells (BASC) and alveolar type 2 (AT2) cells were aberrantly expanded in Gprc5a-KO mouse lungs compared with those in wild-type (WT) mice, suggesting that Gprc5a-KO might confer susceptibility to initiation by increasing the cell of origin in mouse lungs. BASCs from Gprc5a-KO mice (KO-BASC) exhibited significantly increased stemness and self-renewal potential and reduced differentiation capacity compared with BASCs from WT mice (WT-BASC). AT2 cells did not possess self-renewal potential regardless of Gprc5a status. KO-BASCs expressed a stem-like gene profile with upregulated Abcg2, EGFR, and NF-κB signaling compared with WT-BASCs. Blockade of EGFR and NF-κB signaling inhibited both expansion of BASC and AT2 cells and lung tumorigenesis. Abcg2 was expressed in active KO-BASCs as well as in lung tumor cells but not in quiescent WT-BASCs or AT2 cells, supporting that lung adenocarcinoma cells are derived from Abcg2-positive KO-BASCs (active). Taken together, Gprc5a deletion leads to expansion of active BASCs via dysregulated EGFR and NF-κB signaling that confers susceptibility to initiation of lung tumorigenesis, marking Abcg2-positive BASCs as candidate cell of origin for lung adenocarcinoma. SIGNIFICANCE: Identification of active bronchioalveolar stem cells as lung adenocarcinoma cells of origin provides insights into mechanisms of lung tumorigenesis and could facilitate development of effective strategies for cancer prevention and therapy. See related commentary by Osborne and Minna, p. 972.
Subject(s)
Adenocarcinoma of Lung , Lung Neoplasms , Stem Cells , Adenocarcinoma of Lung/genetics , Adenocarcinoma of Lung/metabolism , Animals , Carcinogenesis , Cell Transformation, Neoplastic , ErbB Receptors/genetics , ErbB Receptors/metabolism , Humans , Lung/metabolism , Lung Neoplasms/genetics , Lung Neoplasms/metabolism , Mice , Mice, Knockout , NF-kappa B/metabolism , Receptors, G-Protein-Coupled/genetics , Receptors, G-Protein-Coupled/metabolismABSTRACT
OBJECTIVE: To the clinical characteristics and prognostic value of the patients with complete deletion of TET_JBP domain (ΔJBP) in TET2 acute myeloid leukemia (AML). METHODS: Next Generation Sequencing technology was used to determine the mutations of 34 AML-related genes (including TET2 gene). The I-TASSER tool was used to predict the tertiary structure of the full-length TET2 protein and TET_JBP structure deletion. RESULTS: Among 38 AML patients with TET2 mutations, 22(57.9%) showed truncation mutations, of which 16 (72.7%) produced TET2ΔJBP truncation mutants. Protein structure prediction showed that the deletion of TET_JBP domain lead to the significant changes of tertiary structure in TET2 protein. Compared with the patients in non-ΔJBP group, the age of patients in ΔJBP group were older (63 vs 54 years old, P=0.047), and the occurrence rate of CEBPA double mutation (CEBPAdm) were more frequency (31.3% vs 0, P=0.009), the complete remission (CR) rate after induction chemotherapy(37.5% vs 81.8%, P=0.008) were lower, the median EFS (5 vs 19 months, P=0.000) and median OS (16 vs 22 months, P=0.041) were shorter. Univariate analysis showed that platelets <50×109/L (P=0.004) and CEBPAdm (P=0.001) were related to the shorter OS of the patients. Further COX multivariate analysis showed that CEBPAdm is an independent prognostic factors of OS in TET2ΔJBP patients (P=0.010). In addition, ΔJBP patients with CEBPAdm showed lower hemoglobin levels (62 vs 75g/L, P=0.030) and lower median OS (9 months vs 18 months, P=0.000) than the patients without CEBPAdm. CONCLUSION: AML patients with TET2ΔJBP truncation mutant shows lower CR rate, shorter EFS and OS after induction chemotherapy, which may be related to the poor prognosis, and co-mutation with CEBPAdm, which is the independent prognostic factors of OS in AML patients with TET2ΔJBP.
Subject(s)
Leukemia, Myeloid, Acute , DNA-Binding Proteins/genetics , Dioxygenases , Humans , Induction Chemotherapy , Leukemia, Myeloid, Acute/drug therapy , Leukemia, Myeloid, Acute/genetics , Middle Aged , Mutation , Prognosis , Proto-Oncogene Proteins/genetics , Remission InductionABSTRACT
INTRODUCTION: CEBPA mutation is a common mutation in normal karyotype AML. CEBPAdm AML has been recognized as a separate entity, but there is still controversy to the prognosis of CEBPAsm patients. METHODS: A total of 151 newly diagnosed cytogenetically normal AML patients treated at the Second Hospital Center of Shanxi Medical University from February 2017 to December 2019 were the subjects of the study. According to the number of mutations in the CEBPA gene, the patients were divided into three groups, CEBPAsm, CEBPAdm, and CEBPAwt patients. The clinical characteristics, gene mutations, response, and prognosis were retrospectively compared among the three groups. RESULTS: CEBPAsm patients had lower hemoglobin values compared to CEBPAdm (P = .049). There was no statistical difference between the CEBPAsm cases and the CEBPAdm cases in the mutation types and the distribution of mutation regions (P > .050). Compared with CEBPAdm, cases with CEBPAsm were more likely associated with multiple other gene mutations (P = .023). Patients with CEBPAdm had a higher CR, ORR, and OS than those CEBPAwt (P < .050). CEBPAsm patients had a similar OS with CEBPAdm and CEBPAwt patients (P = .281). These CEBPAsm patients with VAF<30% had lower OS than the patients with VAF≥30%. FLT3-ITD mutations could reduce CEBPAsm patients' OS (P = .019). CONCLUSION: Our data first highlighted the impact of CEBPAsm VAF on OS, and the results showed the lower the VAF was, the shorter the OS tended to. The VAF of CEBPAsm could provide specific significance in some extent for the prognosis of patients.
Subject(s)
CCAAT-Enhancer-Binding Proteins/genetics , Leukemia, Myeloid, Acute/genetics , Adolescent , Adult , Aged , Female , Humans , Leukemia, Myeloid, Acute/diagnosis , Male , Middle Aged , Mutation , Prognosis , Retrospective Studies , Young AdultABSTRACT
Sepsis is a common life-threatening disease in the intensive care unit (ICU) that is usually treated empirically without pathogen identification. As a non-invasive and high-throughput technology, plasma microbial cell-free DNA (mcfDNA) sequencing can detect unknown pathogens independent of previous clinical or laboratory information. In this study, a total of 199 cases suspected of bloodstream infection (BSI) from January 2020 to June 2020 were collected, and potential pathogens were detected by simultaneous blood culture and plasma mcfDNA sequencing. Other clinical microbiological assays were performed within 7 days of plasma mcfDNA sequencing, including smear, culture of samples taken from relevant infected sites, and ß-D-glucan/galactomannan (BDG/GM) tests, among others. The diagnoses were classified as sepsis [94 (47.2%)], non-sepsis [87 (43.7%)], and non-infectious disease [18 (9.0%)]. The sensitivity and specificity of plasma mcfDNA sequencing for diagnosing sepsis were 68.1 and 63.2%, respectively, which were significantly better than those of blood culture, especially for the common bacteria that cause hospital-acquired infection, namely, Acinetobacter baumannii (p < 0.01) and Klebsiella pneumoniae (p < 0.01), and DNA viruses (plasma mcfDNA sequencing only, p < 0.01). However, there was no significant difference in the rate of positivity between plasma mcfDNA sequencing and blood culture for antibiotic-non-exposed cases (43.6 vs. 30.9%, p = 0.17). In the non-sepsis group, 44.8% of cases (13/29) detected only by plasma mcfDNA sequencing showed infections in other parts of the body, such as lower respiratory infection (LRI), intra-abdominal infection (IAI) and central nervous system infection (CNSI). For some common pathogens (not including anaerobes), turnaround time (TAT) 3 (TAT from the initiation of blood sample processing by nucleic acid extraction to the completion of sequencing analysis) was longer than TAT1 (TAT from blood culture bottles in Virtuo to off Virtuo). With disease progression, significant dynamic changes in microbial species were clearly detected by plasma mcfDNA sequencing.
ABSTRACT
Recently, Cryptococcus and non-albicans Candida (NAC) have emerged as health-threatening pathogens for clinical fungal infections. Due to their increased resistance to existing antifungal drugs, novel antifungals are urgently needed. In this study, we evaluated the antifungal effect of VT-1161 and its comparators itraconazole and fluconazole against common fluconazole-sensitive or -resistant Cryptococcus and NAC strains. The tested strains were obtained from Chinese patients by the Invasive Fungal Infection Group within the past 2 years. The minimum inhibitory concentrations (MICs) of VT-1161 and other triazoles were measured according to the Clinical and Laboratory Standards Institute (CLSI) M27-Ed4 guidelines. We found that VT-1161 exhibited strong in vitro activity against Cryptococcus spp.. VT-1161 (geometric mean MIC = 0.024 µg/mL) was 21.7-fold and 104.5-fold more potent than itraconazole and fluconazole, respectively. Against the seven Cryptococcus neoformans isolates with higher fluconazole MICs (≥8 µg/mL based on the MIC90 value of this azole), VT-1161 maintained potent activities, with MICs ranging between 0.031 and 0.5 µg/mL. For NAC spp., VT-1161 (geometric mean MIC = 0.099 µg/mL) was 6.0-fold and 11.4-fold more effective than itraconazole and fluconazole, respectively. There is a positive correlation of the MICs between VT-1161 and itraconazole/fluconazole. The MIC values of VT-1161 against Candida glabrata and Candida tropicalis were significantly lower than those of fluconazole, whereas for Candida parapsilosis the differences in the MIC values between VT-1161 and fluconazole were not statistically significant. The results showed that tetrazole VT-1161 might be a promising candidate for treating Cryptococcus and NAC infections.
Subject(s)
Cryptococcus , Fluconazole , Candida , Fluconazole/pharmacology , Humans , Itraconazole/pharmacology , Microbial Sensitivity Tests , Pyridines , Tetrazoles/pharmacologyABSTRACT
In vitro cultured plant cells, in particular the tobacco BY-2 cell, have demonstrated their potential to provide a promising bioproduction platform for therapeutic proteins by integrating the merits of whole-plant cultivation systems with those of microbial and mammalian cell cultures. Over the past three decades, substantial progress has been made in improving the plant cell culture system, resulting in a few commercial success cases, such as taliglucerase alfa (Elelyso®), the first FDA-approved recombinant pharmaceutical protein derived from plant cells. However, compared to the major expression hosts (bacteria, yeast, and mammalian cells), plant cells are still largely underutilized, mainly due to low productivity and non-human glycosylation. Modern molecular biology tools, in particular RNAi and the latest genome editing technology CRISPR/Cas9, have been used to modulate the genome of plant cells to create new cell lines that exhibit desired "traits" for producing therapeutic proteins. This review highlights the recent advances in cellular engineering of plant cells towards improved recombinant protein production, including creating cell lines with deficient protease levels or humanized glycosylation, and considers potential development in the future.
Subject(s)
Molecular Biology/methods , Plant Cells/physiology , Recombinant Proteins/genetics , Cell Line , Cells, Cultured , Gene Editing , Glycosylation , Humans , Plants, Genetically Modified , Protein Engineering/methods , RNA Interference , Recombinant Proteins/metabolism , Recombinant Proteins/pharmacologyABSTRACT
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is spreading all over the world and has caused millions of deaths. Several sample-to-answer platforms, including Cepheid Xpert Xpress SARS-CoV-2 (Xpert Xpress), have received emergency use authorization for SARS-CoV-2 nucleic acid detection as a point of care test in the United States. However, their application niche is unclear when compared with real-time RT-PCR assays cleared by the National Medical Products Administration in China. In this study, the clinical performance, sensitivity, and workflow of Xpert Xpress and two real-time RT-PCR kits (BioGerm kit and Sansure kit) were evaluated by the specimens from 86 symptomatic patients. The positive percent agreement of Xpert Xpress was 100% compared with 96.15% for the BioGerm kit and 90% for the Sansure kit. The negative percent agreement was 100% for all three assays. The limit of detection is 100 copies/mL for Xpert Xpress and 500 copies/mL for the BioGerm kit and Sansure kit. By serially diluting five positive specimens, the Xpert Xpress had better detection capability. In the workflow and throughput analysis, the turnaround time was 51 minutes for Xpert Xpress, 150 minutes for the BioGerm kit, and 210 minutes for the Sansure kit. This study provides some indication for diagnosis methods selection.
Subject(s)
COVID-19 Nucleic Acid Testing/standards , COVID-19/diagnosis , RNA, Viral/genetics , Reagent Kits, Diagnostic/standards , Real-Time Polymerase Chain Reaction/standards , SARS-CoV-2/genetics , Benchmarking , COVID-19/epidemiology , COVID-19 Nucleic Acid Testing/instrumentation , COVID-19 Nucleic Acid Testing/methods , China/epidemiology , Humans , Limit of Detection , Point-of-Care Testing , United States/epidemiologyABSTRACT
Increasing evidences revealed that microRNAs (miRNAs) play critical roles in important biological processes. The identification of disease-related miRNAs is critical to understand the molecular mechanisms of human diseases. Most existing computational methods require diverse features to predict miRNA-disease associations. However, diverse features are not available for all miRNAs or diseases. In addition, most methods can't predict links for miRNAs or diseases without association information. In this paper, we propose a fast linear neighborhood similarity-based network link inference method, named FLNSNLI, to predict miRNA-disease associations. First, known miRNA-disease associations are formulated as a bipartite network, and miRNAs (or diseases) are expressed as association profiles. Second, miRNA-miRNA similarity and disease-disease similarity are calculated by fast linear neighborhood similarity measure and association profiles. Third, the label propagation algorithm is respectively implemented on two sides to score candidate miRNA-disease associations. Finally, FLNSNLI adopts the weighted average strategy and makes predictions. Moreover, we develop a link complementing approach, and extend FLNSNLI to predict links for miRNAs (or diseases) without known associations. In computational experiments, FLNSNLI produces high-accuracy performances, and outperforms other state-of-the-art methods. More importantly, FLNSNLI requires less information but performs well. Case studies on three popular diseases show that FLNSNLI is useful for the microRNA-disease association prediction.
Subject(s)
Computational Biology/methods , Genetic Predisposition to Disease/genetics , Machine Learning , MicroRNAs/genetics , Humans , Linear Models , Models, GeneticABSTRACT
Cancer cells need to generate large amounts of glutathione (GSH) to buffer oxidative stress during tumor development. A rate-limiting step for GSH biosynthesis is cystine uptake via a cystine/glutamate antiporter Xc-. Xc- is a sodium-independent antiporter passively driven by concentration gradients from extracellular cystine and intracellular glutamate across the cell membrane. Increased uptake of cystine via Xc- in cancer cells increases the level of extracellular glutamate, which would subsequently restrain cystine uptake via Xc-. Cancer cells must therefore evolve a mechanism to overcome this negative feedback regulation. In this study, we report that glutamate transporters, in particular SLC1A1, are tightly intertwined with cystine uptake and GSH biosynthesis in lung cancer cells. Dysregulated SLC1A1, a sodium-dependent glutamate carrier, actively recycled extracellular glutamate into cells, which enhanced the efficiency of cystine uptake via Xc- and GSH biosynthesis as measured by stable isotope-assisted metabolomics. Conversely, depletion of glutamate transporter SLC1A1 increased extracellular glutamate, which inhibited cystine uptake, blocked GSH synthesis, and induced oxidative stress-mediated cell death or growth inhibition. Moreover, glutamate transporters were frequently upregulated in tissue samples of patients with non-small cell lung cancer. Taken together, active uptake of glutamate via SLC1A1 propels cystine uptake via Xc- for GSH biosynthesis in lung tumorigenesis. SIGNIFICANCE: Cellular GSH in cancer cells is not only determined by upregulated Xc- but also by dysregulated glutamate transporters, which provide additional targets for therapeutic intervention.
Subject(s)
Cystine/metabolism , Excitatory Amino Acid Transporter 3/metabolism , Glutamic Acid/metabolism , Glutathione/biosynthesis , Lung Neoplasms/metabolism , Animals , Antiporters/metabolism , Cell Death , Cell Line, Tumor , Glutamine/deficiency , Lung Neoplasms/etiology , Lung Neoplasms/pathology , Mice , Mice, Nude , Oxidative Stress , Receptors, G-Protein-Coupled , Stress, Physiological , Up-RegulationABSTRACT
Treatment-free remission (TFR) is emerging as a new therapy goal for chronic myeloid leukemia (CML) patients in the tyrosine kinase inhibitors (TKI) era. Data indicates the unfavorable success rate of TFR. This study aimed to compare and evaluate the clinical value of dd-PCR in predicting relapse in CML patients entering TFR. Using dd-PCR and RT-qPCR technology, dynamic BCR/ABL transcripts were detected in 13 CML patients who discontinued TKI treatment after sustaining undetectable BCR-ABL levels for a median time of 25 months. The results showed that in 13 patients, only 2 cases (22.2%) of 9 patients who executed planned discontinuation achieved TFR within 12 months. In the first 6 months, the detection rate of BCR/ABL transcripts by dd-PCR was higher than that by RT-qPCR and the two methods kept a positive correlation (r=0.9651, P=0.0349). Meanwhile, the time of detectable BCR/ABL by dd-PCR were significantly shorter (P<0.05), which was an average of 2.98 months earlier than RT-qPCR. The total TKI therapy and MR4.5 duration time related with TFR were longer in patients with intermediate or high Sokal risk scores (p<0.05). The dd-PCR could be more sensitive than RT-qPCR for monitoring BCR/ABL transcripts of CML patients with deep molecular response to TKI. The technique can be used as a preferred method to detect the transcripts in the first 6 months after TKI cessation.
Subject(s)
Fusion Proteins, bcr-abl/genetics , Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy , Polymerase Chain Reaction/methods , Adult , Aged , Biomarkers, Pharmacological/analysis , Biomarkers, Pharmacological/blood , China , Disease-Free Survival , Female , Fusion Proteins, bcr-abl/analysis , Humans , Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics , Male , Middle Aged , Molecular Targeted Therapy/methods , Protein Kinase Inhibitors/pharmacology , Protein-Tyrosine Kinases/antagonists & inhibitors , Protein-Tyrosine Kinases/metabolism , Recurrence , Remission Induction/methodsABSTRACT
Lung squamous cell carcinomas (SCCs) are highly aggressive tumors, and there is currently no effective targeted therapy owing to the lack of specific mutation targets. Compared with lung adenocarcinoma (ADCs), lung SCCs reportedly utilized higher levels of glucose metabolism to meet the anabolic and catabolic needs required to sustain rapid tumor growth. Hexokinase 2 (HK2) is an enzyme that catalyzes the rate-limit and first committed step in glucose metabolism. Here, we investigated the expression and effect of HK2 in lung SCCs. We found a significantly higher HK2 expression in lung SCCs, but not lung ADC or normal tissues. HK2 depletion or inhibition decreased the glycolysis and tumor growth via activating AMPK signaling pathway, which downregulated mTORC1 activity. Furthermore, we found an increased oxygen respiration rate compensating for HK2 depletion. Thus, metformin treatment showed combinatorial therapeutic value, which resulted in greater induction of lung SCC apoptosis in vitro and in vivo. Our study suggests that HK2 depletion in combination with metformin might be a novel effective strategy for lung SCCs therapy.