An AS-qPCR-based method for the detection of Alzheimer's disease-related SNPs.

Alzheimer's disease (AD) is one of the most serious neurodegenerative diseases in the world and has a strong genetic predisposition. At present, there is still no effective method for the early diagnosis and prevention of AD. Accumulating evidence shows the association of several loci with AD risk, such as apolipoprotein E (APOE) and translocase of outer mitochondrial membrane 40 (TOMM40). However, for routine disease diagnosis in clinics, genotype detection methods based on gene sequencing technology are time-consuming and excessively costly. Thus, in this study, we developed a high-sensitivity, low-cost, and convenient single nucleotide polymorphism (SNP) detection assay method based on allele-specific quantitative polymerase chain reaction (AS-qPCR) technology, which can be used to determine the SNP genotype in APOE and TOMM40. A total of 40 patients were recruited from the outpatient department of the memory clinic of Dongzhimen Hospital, Beijing University of Chinese Medicine. The SNP detection assay method includes three steps. First, positive plasmids with different genotypes (TT/CC/TC) in APOE rs429358, rs7412, and TOMM40 rs11556505 were prepared. Second, 3'-T/3'-C primers were designed to amplify these positive plasmids for each SNP site. Finally, we calculated the log10 of the copy number ratio for each positive plasmid, and the genotype interpretation interval was established. Based on this method, we investigated whether the SNPs in 40 patients could be accurately calculated using AS-qPCR technology. The accuracy of SNP detection was verified by PCR-Pooling sequencing. The results showed that SNP genotypes assessed by AS-qPCR technology corresponded perfectly to the results obtained by conventional DNA sequencing. We have developed a genotype detection method for AD based on AS-qPCR, which can be performed easily, rapidly, accurately, and at low cost. The method will contribute to the early diagnosis of patients with late-onset Alzheimer's and the detection of large clinical samples in the future.

The Guiding Significance of Ocular Biometry in Evaluating the Refractive Status of Preschool Children.

INTRODUCTIONS: This study aimed to analyze the correlation between refractive status and ocular biological parameters in preschool-age children (3-6 years old), establish a regression curve, guide the clinical judgment of children's refractive status, and improve the accuracy of refractive screening for this age group. METHODS: A total of 508 children, aged 3-6 years, were admitted to the hospital, exhibiting symptoms of ametropia and a need for dilation optometry. Among these, 326 children were included in the statistics group, having been examined between August 2021 and October 2022, and 182 children were included in the validation group, having been examined between November 2022 and March 2023. Using IOL Master700, ocular biometry parameters were measured for all participants, including axial length (AL), keratometry readings (K1 and K2), anterior chamber depth (ACD), lens thickness (LT), and central corneal thickness (CCT). One percent atropine sulfate eye gel was administered, and then the spherical equivalent (SE) was calculated by Bennett's formula. The correlation between SE and other ocular biometrics was analyzed, followed by the establishment of an SE prediction equation. The SE prediction equation was used to calculate the spherical equivalent (SE#) using ocular biometry data from the validation group, and the consistency between SE and SE# was evaluated. RESULTS: SE showed a negative correlation with AL/CR (r = -0.936), AL (r = -0.811), ACD (r = -0.500), age (r = -0.396), and Km (r = -0.213) (p < 0.001), and positive correlation with LT (r = 0.301), LP (r = 0.176) (p < 0.001). A multiple linear regression equation was established for SE using the stepwise selection method, SE = 49.232 - 23.583 × AL/CR + 1.703 × ACD + 0.589 × Km - 0.609 × LP + 1.103 × LT (R2 = 0.997). Based on the regression equation, the predicted SE# highly correlated with SE after cycloplegia in the validation group (r = 0.998, p < 0.001). CONCLUSION: The main ocular biological factors of ocular diopter in children aged 3-6 years are AL/CR, ACD, Km, LP, and LT, which are jointly influenced by multiple factors. Ocular biometry is a reliable predictor of real refraction among children aged 3-6.

Chromatic visual evoked potentials identify optic nerve dysfunction in patients with Graves' orbitopathy.

PURPOSE: To explore visual dysfunction in Graves' orbitopathy (GO) objectively by analyzing chromatic visual evoked potentials (cVEP) and evaluate its diagnostic efficiency for dysthyroid optic neuropathy (DON). METHODS: In this cross-sectional study, we analyzed pattern-reversal VEP (pVEP), red-green (R-G) and blue-yellow (B-Y) cVEP in 93 subjects (21 with DON, Group A, 30 with GO, Group B, and 42 healthy controls, Group C) at Wuhan Union Hospital, China. RESULTS: Compared with Group C, the amplitudes of B-Y cVEP were significantly lower in Group B, whereas all amplitudes of cVEP, latencies and amplitudes of pVEP in Group A were significantly impaired. In addition, the pVEP latency at 60 arcmin (60'), pVEP amplitudes and R-G cVEP amplitudes were significantly different between Group A and B. Moreover, 60'cVEP R-G negative-positive (N-P) amplitude was correlated with crowding index (P = 0.001), the average thickness of ganglion cell layer and inner plexiform layer (P = 0.004). Furthermore, combination of 60'cVEP R-G amplitude and 60'pVEP P100 latency had better diagnostic efficiency than each single parameter, with optimal cut-off values of 14.20 µV and 110.65 ms, respectively. CONCLUSION: GO may induce electrophysiological changes. The presence of B-Y cVEP anomalies in moderate to severe GO patients may be an early sign of preclinical DON. A decline in 60'cVEP R-G amplitude is associated with apical crowding and thinner inner intra-retinal layers. The combination of 60'cVEP R-G N-P amplitude and 60'pVEP latency can be a useful diagnostic index for DON.

Iron Isotope Fractionations Reveal a Finite Bioavailable Fe Pool for Structural Fe(III) Reduction in Nontronite.

We report on stable Fe isotope fractionation during microbial and chemical reduction of structural Fe(III) in nontronite NAu-1. (56)Fe/(54)Fe fractionation factors between aqueous Fe(II) and structural Fe(III) ranged from -1.2 to +0.8‰. Microbial (Shewanella oneidensis and Geobacter sulfurreducens) and chemical (dithionite) reduction experiments revealed a two-stage process. Stage 1 was characterized by rapid reduction of a finite Fe(III) pool along the edges of the clay particles, accompanied by a limited release to solution of Fe(II), which partially adsorbed onto basal planes. Stable Fe isotope compositions revealed that electron transfer and atom exchange (ETAE) occurred between edge-bound Fe(II) and octahedral (structural) Fe(III) within the clay lattice, as well as between aqueous Fe(II) and structural Fe(III) via a transient sorbed phase. The isotopic fractionation factors decreased with increasing extent of reduction as a result of the depletion of the finite bioavailable Fe(III) pool. During stage 2, microbial reduction was inhibited while chemical reduction continued. However, further ETAE between aqueous Fe(II) and structural Fe(III) was not observed. Our results imply that the pool of bioavailable Fe(III) is restricted to structural Fe sites located near the edges of the clay particles. Blockage of ETAE distinguishes Fe(III) reduction of layered clay minerals from that of Fe oxyhydroxides, where accumulation of structural Fe(II) is much more limited.

Engineered Multivalent Nanobodies Efficiently Neutralize SARS-CoV-2 Omicron Subvariants BA.1, BA.4/5, XBB.1 and BQ.1.1.

Most available neutralizing antibodies are ineffective against highly mutated SARS-CoV-2 Omicron subvariants. Therefore, it is crucial to develop potent and broad-spectrum alternatives to effectively manage Omicron subvariants. Here, we constructed a high-diversity nanobody phage display library and identified nine nanobodies specific to the SARS-CoV-2 receptor-binding domain (RBD). Five of them exhibited cross-neutralization activity against the SARS-CoV-2 wild-type (WT) strain and the Omicron subvariants BA.1 and BA.4/5, and one nanobody demonstrated marked efficacy even against the Omicron subvariants BQ.1.1 and XBB.1. To enhance the therapeutic potential, we engineered a panel of multivalent nanobodies with increased neutralizing potency and breadth. The most potent multivalent nanobody, B13-B13-B13, cross-neutralized all tested pseudoviruses, with a geometric mean of the 50% inhibitory concentration (GM IC50) value of 20.83 ng/mL. An analysis of the mechanism underlying the enhancement of neutralization breadth by representative multivalent nanobodies demonstrated that the strategic engineering approach of combining two or three nanobodies into a multivalent molecule could improve the affinity between a single nanobody and spike, and could enhance tolerance toward escape mutations such as R346T and N460K. Our engineered multivalent nanobodies may be promising drug candidates for treating and preventing infection with Omicron subvariants and even future variants.

Development and applications of the heterostructures synthesis based on CdS nanowires.

Semiconducting nanowire heterostructures are of particular interest because of their fascinating properties and potential applications in the field of nanoscale science. CdS, with a direct bandgap of 2.42 eV, is considered to be an excellent material for various optoelectronic applications in the visible range of the electromagnetic spectrum. On account of this, the diverse heterostructures based on CdS nanowires have drawn great attention owing to their novel properties. Here, we focus on recent routes used to synthesize diverse heterostructures based on CdS nanowires and the emergent properties of the one-dimensional nanowires heterostructures, and discuss their potential applicability in different fields. In particular, the mechanisms of various synthetic methods for the heterostructure based on the CdS nanowires are discussed detailedly.

A Competitive Panning Method Reveals an Anti-SARS-CoV-2 Nanobody Specific for an RBD-ACE2 Binding Site.

Most neutralizing antibodies neutralize the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by directly blocking the interactions between the spike glycoprotein receptor-binding domain (RBD) and its receptor, human angiotensin-converting enzyme 2 (ACE2). Here, we report a novel nanobody (Nb) identified by an RBD-ACE2 competitive panning method that could specifically bind to the RBD of SARS-CoV-2 with a high affinity (EC50 = 0.03 nM) and successfully block the binding between the RBD and ACE2 recombinant protein. A structural simulation of the RBD-VHH complex also supports a mechanism of the Nb to block the interaction between the RBD and ACE2. A pseudovirus assay of the Nb showed it could neutralize the WT pseudovirus with high potency (IC50 = 0.026 µg/mL). Furthermore, we measured its binding to phages displaying RBDs of different SARS-CoV-2 variants and found that it could bind to recombinant phages displaying the RBD of beta and delta variants. This study also provides a method of phage library competitive panning, which could be useful for directly screening high-affinity antibodies targeting important functional regions.

Effects of various extraocular muscle enlargement patterns on muscle diameter index in graves ophthalmopathy patients: a retrospective cohort study.

Graves ophthalmopathy (GO) patients often undergo retrobulbar injection of glucocorticoids (GCs) as a common therapeutic approach. This study aimed to explore the impact of various patterns of extraocular muscle (EOM) enlargement on EOM changes following retrobulbar GCs injection in patients with GO. A retrospective analysis was conducted on GO patients who underwent retrobulbar GCs injections. Data pertaining to EOM diameter (EMD) and muscle diameter index (MDI) were collected from orbital computed tomography (CT) scans. The MDI change (ΔMDI) was calculated by comparing pre- and post-injection MDI values. The relationship between each pre EMD/MDI and ΔMDI was assessed using univariate and multivariate logistic regression analysis. A total of 68 patients with GO were included in this study, accounting for 118 eyes. After retrobulbar injections of GCs, 84 eyes showed a decrease in the MDI, while 34 eyes exhibited an increase in MDI. A threshold effect was observed in the relationship between medial pre EMD/MDI and ΔMDI. When the medial pre EMD/MDI was less than 0.28, a higher medial pre EMD/MDI was associated with a smaller ΔMDI (ß = - 25.21, p = 0.0175). However, when the medial pre EMD/MDI was greater than 0.28, no significant association was found between pre EMD/MDI and ΔMDI. There was a negative correlation between medial + lateral pre EMD/MDI and ΔMDI (ß = - 11.76, p < 0.0189). A higher medial + lateral pre EMD/MDI was associated with a greater decrease in MDI. Additionally, there was a positive correlation between superior rectus muscle-levator complex (SRLC) pre EMD/MDI and ΔMDI (ß = 11.92, p = 0.040). The higher the value of SRLC pre EMD/MDI, the greater the ΔMDI. There was an association between pre EMD/MDI and changes in EOMs after retrobulbar injection of GCs in GO patients. In patients with predominantly enlarged medial rectus muscles and severe degrees of enlargement, retrobulbar injection of GCs should be assessed for its benefit; a combination of medial and lateral rectus muscle enlargement is beneficial for the shrinkage of EOMs following retrobulbar injections; the involvement of the SRLC rectus muscle may be a disadvantageous pattern of shrinkage of EOMs following retrobulbar injections.Trial registration This study is retrospectively registered. We have registered this study with the Chinese Clinical Trials Registry ( www.chictr.org.cn , registration number: ChiCTR2200063429).

Insights into orbital morphological features and fracture patterns in medial and inferior wall fracture: a retrospective cohort study.

This study investigated the orbital morphological features that lead to fractures at different sites by comparing patients with isolated inferior wall fracture (IWF) to patients with isolated medial wall fracture (MWF). This study analyzed the orbital morphologic characteristics of all orbital fracture patients who underwent orbital computed tomography (CT) scans between January 2017 and October 2022. On CT scans, the bony structures of the orbit were measured. We investigated the bilateral symmetry of orbital. In addition, orbital morphological differences were compared between patients with fractures of the medial wall and those with fractures of the inferior wall. A total of 135 patients with orbital fractures were included in the study. Of these, 91 were isolated MWFs and 44 were isolated IWF. We confirmed the symmetry of bilateral orbits and measured the orbit of the uninjured side. No differences were found between the MWF group and the IWF group in terms of ocular prominence, horizontal orbital diameter, orbital rim angle, sagittal orbital depth, sagittal orbital depth, and angle of inferior wall inclination. The distance between the infraorbital nerve (ION) entry point and the orbital rim was significantly smaller in the inferior lateral wall fracture group than in the MWF group (11.87 ± 2.54 vs 14.90 ± 4.64, P < 0.001), and the percentage of type 1 ION was significantly lower in the IWF group than in the MWF group (40.9% vs 65.9%, P = 0.012). We demonstrated the symmetry of bilateral orbits and found that when the point where the ION enters the infraorbital canal is near the orbital rim, patients are more prone to suffering a fracture of the inferior wall after orbital trauma. It is less likely for patients with type 1 ION to suffer an IWF following an orbital fracture.

DMs-MAFM+EfficientNet: a hybrid model for predicting dysthyroid optic neuropathy.

Thyroid-associated ophthalmopathy (TAO) is a very common autoimmune orbital disease. Approximately 4%-8% of TAO patients will deteriorate and develop the most severe dysthyroid optic neuropathy (DON). According to the current data provided by clinical experts, there is still a certain proportion of suspected DON patients who cannot be diagnosed, and the clinical evaluation has low sensitivity and specificity. There is an urgent need for an efficient and accurate method to assist physicians in identifying DON. This study proposes a hybrid deep learning model to accurately identify suspected DON patients using computed tomography (CT). The hybrid model is mainly composed of the double multiscale and multi attention fusion module (DMs-MAFM) and a deep convolutional neural network. The DMs-MAFM is the feature extraction module proposed in this study, and it contains a multiscale feature fusion algorithm and improved channel attention and spatial attention, which can capture the features of tiny objects in the images. Multiscale feature fusion is combined with an attention mechanism to form a multilevel feature extraction module. The multiscale fusion algorithm can aggregate different receptive field features, and then fully obtain the channel and spatial correlation of the feature map through the multiscale channel attention aggregation module and spatial attention module, respectively. According to the experimental results, the hybrid model proposed in this study can accurately identify suspected DON patients, with Accuracy reaching 96%, Specificity reaching 99.5%, Sensitivity reaching 94%, Precision reaching 98.9% and F1-score reaching 96.4%. According to the evaluation by experts, the hybrid model proposed in this study has some enlightening significance for the diagnosis and prediction of clinically suspect DON.

Topical Chemotherapy for Treating Ocular Surface Squamous Neoplasia with a Combination of Interferon α-2b and 5-Fluorouracil.

INTRODUCTION: This study evaluated the efficacy of combined interferon α-2b (IFNα2b) and 5-fluorouracil (5-FU) as primary treatment for ocular surface squamous neoplasia (OSSN). METHODS: In this retrospective study, 27 eyes with OSSN followed by topical application of combined IFNα2b and 5-FU were examined. Reported outcome measures were tumor response, visual acuity, time to complete resolution, recurrence and treatment complications. RESULTS: Twenty-six patients (17 male, 9 female) had a mean age of 63.9 (median, 67; range 22-83) years. Complete tumor response was observed in 24 eyes (88.9%). Three eyes (11.1%) showed partial response to the chemotherapy agents and later underwent surgical tumor removal. The median time to complete resolution was 6 (mean, 6.1; range, 3-11) weeks. Of these, the patients received between one to three cycles of 5-FU therapy (median, 2; mean, 1.8). Complications noted were transient irritation at 5-FU cycle (11 eyes, 40.7%). There was no tumor recurrence at mean follow-up of 16.1 (median, 12; range 6-38) months. CONCLUSIONS: Combination therapy of IFNα2b and 5-FU was a safe and effective treatment, inducing a short duration of administration and low recurrence rate for OSSN. TRIAL REGISTRATION: Retrospectively registered, UHCT22048.

Intraorbital wooden foreign bodies: case series and literature review.

Intraorbital wooden foreign bodies (IOWFBs) constitute a relatively rare ocular trauma, which occupy a special type of intraorbital foreign bodies (IOFBs). Data regarding IOWFBs must be obtained from case reports or small case series due to their rarity. Here, we reported 5 cases of IOWFBs and reviewed the related literatures, which could provide comprehensive information regarding the clinical manifestations, diagnosis, and surgical treatment of IOWFBs. Combined with the published literature, a total of 51 independent cases were counted after we added 5 cases. Among them, the number of male and female patients was 35 and 16 respectively; the mean age was 27.3±18.2 (range 1-66)y. Obviously, the disorder seemed to occur mainly in young and middle-aged people. Because of the diversity in the clinical manifestations and imaging characteristics of IOWFBs, misdiagnosis and missed diagnosis often occur during the initial visit. Delayed diagnosis may lead to a high risk of orbital infection caused by IOWFBs. Surgery is the treatment of choice for most patients; however, the missed diagnosis and residue of foreign bodies after previous surgery cannot be ignored. Therefore, an accurate diagnosis is governed by the detailed trauma history, careful ocular examination, close observation of clinical manifestations, correct imaging diagnosis [e.g., magnetic resonance imaging (MRI) or computerized tomography (CT)], and timely and completely elimination of IOWFBs.

Changes in Meibum Lipid Composition With Ocular Demodex Infestation.

Purpose: The purpose of this study was to understand the impact of Demodex infection in the lipid component of meibum in patients. Methods: The meibum samples were collected from four groups of subjects: (1) Demodex-negative with non-MGD (D-M-; n = 10); (2) Demodex-positive with non-MGD (D+M-; n = 10); (3) Demodex-negative with MGD (D-M+; n = 10); and (4) Demodex-positive with MGD (D+M+; n = 10). A liquid chromatography-mass spectrometry (LC-MS) system consisting of ultra-performance liquid chromatography and a Q Exactive high-resolution mass spectrometer was used for lipids separation and detection. Results: Compared with the D-M- group, the D+M- group had lower levels of phosphatidylcholines (PCs) and lysophosphatidylcholines (LPCs) and higher levels of phosphatidylethanolamines (PEs). Compared with the D-M+ group, the levels of sphingomyelins (SMs) and PCs in the D+M+ group were decreased, whereas the levels of (O-acyl)-ω-hydroxy fatty acids (OAHFAs), ceramides (CERs), LPCs, and diacylglycerols (DGs) were significantly increased. Triacylglycerols (TGs), DGs, CERs, and OAHFAs were decreased in D-M+ group, whereas levels of PEs, phosphatidylinositols, and phosphatidylglycerols were increased in meibum obtained from the D-M+ group compared with those in the D-M- group. TGs, SMs, CERs, and PEs were decreased in the D+M+ group, whereas levels of LPCs, LPEs, PCs, and PEs were increased in meibum from the D-M+ group compared with those in the D+M- group. Conclusions: To the best of our knowledge, this is the first study to assess the changes in meibum from patients with ocular Demodex infestation. The significant increase of OAHFAs in the Demodex-positive group suggest that OAHFAs may be associated with the progress of ocular Demodex infections. Translational Relevance: OAHFAs could be a potential new therapeutic target for ocular Demodex infestation.

Novel BCMA-OR-CD38 tandem-dual chimeric antigen receptor T cells robustly control multiple myeloma.

BCMA-targeting chimeric antigen receptor (CAR)-T cell therapy has shown remarkable clinical efficacy against multiple myeloma, yet antigen escape and tumor relapse still occur after the use of these therapies. Designing CAR-T therapies that targets multiple antigens simultaneously seems a feasible way to avoid antigen escape, and it has been extensively studied elsewhere. Here, we report novel BCMA-OR-CD38 Tan CAR T cells that can trigger robust cytotoxicity against target cells expressing either BCMA or CD38. We demonstrate that, in in vitro studies, these BCMA-OR-CD38 Tan CAR T cells exhibit similar CAR expression, superior cytotoxicity and antigen-stimulated T cell proliferation as compared to single-targeted CAR T cells or CD38-OR-BCMA Tan CAR T cells. Importantly, these BCMA-OR-CD38 Tan CAR-T cells can achieve complete tumor clearance in myeloma-bearing mice with no relapse observed through the course of these experiments. Finally, this BCMA-OR-CD38 Tan CAR was fully compatible with existing clinical grade T cell manufacturing procedures and can be implemented using current clinical protocols. Taken together, our results present an effective solution to the challenge of antigen escape in BCMA CAR T-cell therapies.

Characterization of the Therapeutic Effects of Novel Chimeric Antigen Receptor T Cells Targeting CD38 on Multiple Myeloma.

Multiple myeloma (MM) is a tumor type characterized by the unregulated proliferation of clonal plasma cells in the bone marrow. Immunotherapy based on chimeric antigen receptor T cell (CAR-T) therapy has achieved exciting success in the treatment of hematological malignant tumors. CD38 is highly and evenly expressed in MM and is an attractive target for MM treatment. Here, we successfully constructed two novel second-generation CAR-T cells targeting CD38 by retroviral vector transduction. CD38 CAR-T cells could be activated effectively after stimulation with CD38-positive tumor cells and secrete cytokines such as IFN-γ and TNF-α to promote tumor cell apoptosis in in vitro experiments. Real-time fluorescence monitoring experiments, luciferase detection experiments and flow cytometry experiments revealed the efficient and specific killing abilities of CD38 CAR-T cells against CD38-positive tumor cells. The proliferation ability of CD38 CAR-T cells in vitro was higher than that of untransduced T cells. Further antitumor experiments in vivo showed that CD38 CAR-T cells could be quickly activated to secrete IFN-γ and eliminate tumors. Thus, novel CD38-targeted second-generation CAR-T cells have efficient and specific antitumor activity and may become a novel therapy for the clinical treatment of MM.

Co-Expression of miR155 or LSD1 shRNA Increases the Anti-Tumor Functions of CD19 CAR-T Cells.

Chimeric antigen receptor (CAR) T cells targeting CD19 antigen have produced remarkable clinical outcomes for cancer patients. However, identifying measures to enhance effector function remains one of the most challenging issues in CD19-targeted immunotherapy. Here, we report a novel approach in which a microRNA (miRNA) or short-hairpin RNA (shRNA) cassette was integrated into CAR-expressing retroviral vectors. Using this system, we generated anti-CD19 CAR-T cells co-expressing miR155 or LSD1 shRNA and found that anti-CD19 CAR-T cells with miR155 upregulation or LSD1 downregulation exhibited increased anti-tumor functions in vitro and in vivo. Transcriptional profiling analysis by RNA sequencing revealed the targets of miR155 and LSD1 in anti-CD19 CAR-T cells. Our experiments indicated that introduction of miRNA or shRNA expression into anti-CD19 CAR T-cells might be an effective strategy to improve the anti-tumor effects of CAR-T cell therapy.

Colorimetric and fluorescent detection of hydrazine with high sensitivity and excellent selectivity.

It is critical to develop probes for rapid, selective, and sensitive detection of the highly toxic hydrazine in both environmental and biological science. In this work, under mild condition, a novel colorimetric and off-on fluorescent probe was synthesized for rapid recognition of hydrazine with excellent selectivity over other various species including some biological species, metal ions and anions. The limit of quantification (LOQ) value was 1.5×10-4M-3.2×10-3M (colorimetric method) and 1.5×10-4M-3.2×10-3M (fluorescent method) with as low as detection limit of 46.2µM.

Genes directly regulated by NF-κB in human hepatocellular carcinoma HepG2.

It has been well-known that over activation of NF-κB has close relationship with hepatitis and hepatocellular carcinoma (HCC). However, the complete and exact underlying molecular pathways and mechanisms still remain not fully understood. By manipulating NF-κB activity with its recognized activator TNFα and using ChIP-seq and RNA-seq techniques, this study identified 699 NF-κB direct target genes (DTGs) in a widely used HCC cell line, HepG2, including 399 activated and 300 repressed genes. In these NF-κB DTGs, 216 genes (126 activated and 90 repressed genes) are among the current HCC gene signature. In comparison with NF-κB target genes identified in LPS-induced THP-1 and TNFα-induced HeLa cells, only limited numbers (24-46) of genes were shared by the two cell lines, indicating the HCC specificity of identified genes. Functional annotation revealed that NF-κB DTGs in HepG2 cell are mainly related with many typical NF-κB-related biological processes including immune system process, response to stress, response to stimulus, defense response, and cell death, and signaling pathways of MAPK, TNF, TGF-beta, Chemokine, NF-kappa B, and Toll-like receptor. Some NF-κB DTGs are also involved in Hepatitis C and B pathways. It was found that 82 NF-κB DTGs code secretory proteins, which include CCL2 and DKK1 that have already been used as HCC markers. Finally, the NF-κB DTGs were further confirmed by detecting the NF-κB binding and expression of 14 genes with ChIP-PCR and RT-PCR. This study thus provides a useful NF-κB DTG list for future studies of NF-κB-related molecular mechanisms and theranostic biomarkers of HCC.

TALEN-Mediated Knockout of CCR5 Confers Protection Against Infection of Human Immunodeficiency Virus.

Transcription activator-like effector nuclease (TALEN) represents a valuable tool for genomic engineering due to its single-nucleotide precision, high nuclease activity, and low cytotoxicity. We report here systematic design and characterization of 28 novel TALENs targeting multiple regions of CCR5 gene (CCR5-TALEN) which encodes the co-receptor critical for entry of human immunodeficiency virus type I (HIV-1). By systemic characterization of these CCR5-TALENs, we have identified one (CCR5-TALEN-515) with higher nuclease activity, specificity, and lower cytotoxicity compared with zinc-finger nuclease (CCR5-ZFN) currently undergoing clinical trials. Sequence analysis of target cell line GHOST-CCR5-CXCR4 and human primary CD4 T cells showed that the double-strand breaks at the TALEN targeted sites resulted in truncated or nonfunctional CCR5 proteins thereby conferring protection against HIV-1 infection in vitro. None of the CCR5-TALENs had detectable levels of off-target nuclease activity against the homologous region in CCR2 although substantial level was identified for CCR5-ZFN in the primary CD4 T cells. Our results suggest that the CCR5-TALENs identified here are highly functional nucleases that produce protective genetic alterations to human CCR5. Application of these TALENs directly to the primary CD4 T cells and CD34 hematopoietic stem cells (HSCs) of infected individuals could help to create an immune system resistant to HIV-1 infection, recapitulating the success of "Berlin patient" and serving as an essential first step towards a "functional" cure of AIDS.