GPSAdb: a comprehensive web resource for interactive exploration of genetic perturbation RNA-seq datasets.

Gene knock-out/down methods are commonly used to explore the functions of genes of interest, but a database that systematically collects perturbed data is not available currently. Manual curation of all the available human cell line perturbed RNA-seq datasets enabled us to develop a comprehensive human perturbation database (GPSAdb, https://www.gpsadb.com/). The current version of GPSAdb collected 3048 RNA-seq datasets associated with 1458 genes, which were knocked out/down by siRNA, shRNA, CRISPR/Cas9, or CRISPRi. The database provides full exploration of these datasets and generated 6096 new perturbed gene sets (up and down separately). GPSAdb integrated the gene sets and developed an online tool, genetic perturbation similarity analysis (GPSA), to identify candidate causal perturbations from differential gene expression data. In summary, GPSAdb is a powerful platform that aims to assist life science researchers to easily access and analyze public perturbed data and explore differential gene expression data in depth.

Identification of an HLA-A*11:01-restricted neoepitope of mutant PIK3CA and its specific T cell receptors for cancer immunotherapy targeting hotspot driver mutations.

Hotspot driver mutations presented by human leukocyte antigens might be recognized by anti-tumor T cells. Based on their advantages of tumor-specificity and immunogenicity, neoantigens derived from hotspot mutations, such as PIK3CAH1047L, may serve as emerging targets for cancer immunotherapies. NetMHCpan V4.1 was utilized for predicting neoepitopes of PIK3CA hotspot mutation. Using in vitro stimulation, antigen-specific T cells targeting the HLA-A*11:01-restricted PIK3CA mutation were isolated from healthy donor-derived peripheral blood mononuclear cells. T cell receptors (TCRs) were cloned using single-cell PCR and sequencing. Their functionality was assessed through T cell activation markers, cytokine production and cytotoxic response to cancer cell lines pulsed with peptides or transduced genes of mutant PIK3CA. Immunogenic mutant antigens from PIK3CA and their corresponding CD8+ T cells were identified. These PIK3CA mutation-specific CD8+ T cells were subsequently enriched, and their TCRs were isolated. The TCR clones exhibited mutation-specific and HLA-restricted reactivity, demonstrating varying degrees of functional avidity. Identified TCR genes were transferred into CD8+ Jurkat cells and primary T cells deficient of endogenous TCRs. TCR-expressing cells demonstrated specific recognition and reactivity against the PIK3CAH1047L peptide presented by HLA-A*11:01-expressing K562 cells. Furthermore, mutation-specific TCR-T cells demonstrated an elevation in cytokine production and profound cytotoxic effects against HLA-A*11:01+ malignant cell lines harboring PIK3CAH1047L. Our data demonstrate the immunogenicity of an HLA-A*11:01-restricted PIK3CA hotspot mutation and its targeting therapeutic potential, together with promising candidates of TCR-T cell therapy.

Association of depressive symptoms and sleep disturbances with survival among US adult cancer survivors.

BACKGROUND: Depression and sleep disturbances are associated with increased risks of various diseases and mortality, but their impacts on mortality in cancer survivors remain unclear. The objective of this study was to characterize the independent and joint associations of depressive symptoms and sleep disturbances with mortality outcomes in cancer survivors. METHODS: This population-based prospective cohort study included cancer survivors aged ≥ 20 years (n = 2947; weighted population, 21,003,811) from the National Health and Nutrition Examination Survey (NHANES) 2007-2018 cycles. Depressive symptoms and sleep disturbances were self-reported. Depressive symptoms were assessed using the Patient Health Questionnaire 9 (PHQ-9). Death outcomes were determined by correlation with National Death Index records through December 31, 2019. Primary outcomes included all-cause, cancer-specific, and noncancer mortality. RESULTS: During the median follow-up of 69 months (interquartile range, 37-109 months), 686 deaths occurred: 240 participants died from cancer, 146 from heart disease, and 300 from other causes. Separate analyses revealed that compared with a PHQ-9 score (0-4), a PHQ-9 score (5-9) was associated with a greater risk of all-cause mortality (hazard ratio [HR], 1.28; 95% CI, 1.03-1.59), and a PHQ-9 score (≥ 10) was associated with greater risk of all-cause mortality (HR, 1.37; 95% CI, 1.04-1.80) and noncancer mortality (HR, 1.45; 95% CI, 1.01-2.10). Single sleep disturbances were not associated with mortality risk. In joint analyses, the combination of a PHQ-9 score ≥ 5 and no sleep disturbances, but not sleep disturbances, was associated with increased risks of all-cause mortality, cancer-specific mortality, and noncancer mortality. Specifically, compared with individuals with a PHQ-9 score of 0-4 and no sleep disturbances, HRs for all-cause mortality and noncancer mortality in individuals with a PHQ-9 score of 5-9 and no sleep disturbances were 1.72 (1.21-2.44) and 1.69 (1.10-2.61), respectively, and 2.61 (1.43-4.78) and 2.77 (1.27-6.07), respectively, in individuals with a PHQ-9 score ≥ 10 and no sleep disturbances; HRs for cancer-specific mortality in individuals with a PHQ-9 score ≥ 5 and no sleep disturbances were 1.95 (1.16-3.27). CONCLUSIONS: Depressive symptoms were linked to a high risk of mortality in cancer survivors. The combination of a PHQ-9 score (≥ 5) and an absence of self-perceived sleep disturbances was associated with greater all-cause mortality, cancer-specific mortality, and noncancer mortality risks, particularly in individuals with a PHQ-9 score (≥ 10).

Construction and significance of a breast cancer prognostic model based on cuproptosis-related genotyping and lncRNAs.

BACKGROUND: /Purpose: Cuproptosis may play a significant role in breast cancer (BC). We aimed to investigate the prognostic impact of cuproptosis-related lncRNAs in BC. METHODS: Consensus clustering analysis categorized TCGA-BRCA samples into 3 clusters, followed by survival and immune analyses of the 3 clusters. LASSO-COX analysis was performed on cuproptosis-related lncRNAs differentially expressed in BC to construct a BC prognostic model. Gene Ontology/Kyoto Encyclopedia of Genes and Genomes (GO/KEGG) enrichment, immune, and drug prediction analyses were performed on the high-risk and low-risk groups. Cell experiments were conducted to analyze the results of drug prediction and two cuproptosis-related lncRNAs (AC104211.1 and LINC01863). RESULTS: Significant differences were observed in survival outcomes and immune infiltration levels among the three clusters (p < 0.05). The validation of the model showed significant differences in survival outcomes between the high-risk and low-risk groups in both the training and validation sets (p < 0.05). Differential mRNAs between the two groups were significantly enriched in the Neuroactive ligand-receptor interaction and cAMP signaling pathway. Additionally, significant differences were found in immune infiltration levels, human leukocyte antigen (HLA) expression, Immunophenoscore (IPS) scores, and Tumor Immune Dysfunction and Exclusion (TIDE) scores between the two groups (p < 0.05). Drug prediction and corresponding cell experimental results showed that Trametinib, 5-fluorouracil, and AICAR significantly inhibited the viability of MCF-7 cells (p < 0.05). AC104211.1 and LINC01863 were found to impact the proliferation of BC cells. CONCLUSION: The risk-scoring model obtained in this study may serve as a robust prognostic biomarker, potentially aiding in clinical decision-making for BC patients.

Label-Free DNA Hybridization Detection Using a Highly Sensitive Fiber Microcavity Biosensor.

A novel label-free optical fiber biosensor, based on a microcavity fiber Mach-Zehnder interferometer, was developed and practically demonstrated for DNA detection. The biosensor was fabricated using offset splicing standard communication single-mode fibers (SMFs). The light path of the sensor was influenced by the liquid sample in the offset open cavity. In the experiment, a high sensitivity of -17,905 nm/RIU was achieved in the refractive index (RI) measurement. On this basis, the probe DNA (pDNA) was immobilized onto the sensor's surface using APTES, enabling real-time monitoring of captured complementary DNA (cDNA) samples. The experimental results demonstrate that the biosensor exhibited a high sensitivity of 0.32 nm/fM and a limit of detection of 48.9 aM. Meanwhile, the sensor has highly repeatable and specific performance. This work reports an easy-to-manufacture, ultrasensitive, and label-free DNA biosensor, which has significant potential applications in medical diagnostics, bioengineering, gene identification, environmental science, and other biological fields.

Characterization of starvation response-related genes for predicting prognosis in breast cancer.

Breast cancer (BRCA) cells typically exist in nutrient-deficient microenvironments and quickly adapt to states with fluctuating nutrient levels. The tumor microenvironment of starvation is intensely related to metabolism and the malignant progression of BRCA. However, the potential molecular mechanism has not been thoroughly scrutinized. As a result, this study aimed to dissect the prognostic implications of mRNAs involved in the starvation response and construct a signature for forecasting the outcomes of BRCA. In this research, we investigated how starvation could affect BRCA cells' propensities for invasion and migration. The effects of autophagy and glucose metabolism mediated by starved stimulation were examined through transwell assays, western blot, and the detection of glucose concentration. A starvation response-related gene (SRRG) signature was ultimately generated by integrated analysis. The risk score was recognized as an independent risk indicator. The nomogram and calibration curves revealed that the model had excellent prediction accuracy. Functional enrichment analysis indicated this signature was significantly enriched in metabolic-related pathways and energy stress-related biological processes. Furthermore, phosphorylated protein expression of the model core gene EIF2AK3 increased after the stimulus of starvation, and EIF2AK3 may play an essential role in the progression of BRCA in the starved microenvironment. To sum up, we constructed and validated a novel SRRG signature that could accurately predict outcomes and may be developed as a therapeutic target for the precise treatment of BRCA.

A dual-targeting near-infrared biomimetic drug delivery system for HBV treatment.

Hepatitis B virus (HBV) infection is a serious global public health threat. It remains elusive to achieve a functional HBV cure with currently available antivirals. Herein, a photo-responsive delivery vehicle composed of Nd3+ -sensitized core-shell upconversion nanoparticle (UCNP), mesoporous silica nanoparticle (MSN), antisense oligonucleotides (ASOs), and capsid-binding inhibitor C39 was established, which was named UMAC according to the initials of its components. Subsequently, the as-synthesized delivery vehicle was encapsulated by ß- D-galactopyranoside (Gal) modified red blood cell (RBC) membrane vesicles, which enabled precise targeting of the liver cells (UMAC-M-Gal). Both in vitro and in vivo experiments demonstrated that this biomimetic system could successfully achieve controlled drug release under light conditions at 808 nm, leading to effective suppression of HBV replication in this dual-targeted therapeutic approach. Together, these results substantiate the system has huge prospects for application to achieve functional HBV cure, and provides a promising novel strategy for drug delivery.

Tunable composite lattice structure for low-frequency and ultra-broadband underwater sound absorption.

The underwater sound absorption technique in low-frequency and broadband has far-reaching prospects since it is essential for noise reduction of deep-sea operation requirements and evading advanced underwater target detection. Here, we propose an underwater sound-absorbing composite lattice with low-frequency and ultra-broadband characteristics. The composite lattice is constructed by regular spatially stacking cells with different sizes of metallic core spheres. All the core spheres are coated with silicon rubbers, and cells are embedded in the rubber matrix. In the composite lattice stereostructure, the lattice cells convert incident longitudinal waves into transverse waves through multiple local resonance coupling and multiple scattering. The energy is localized and dissipated in the composite lattice. We analyze the relationship among the corresponding absorption spectrums, the displacement clouds, and the resonance modes of lattice cells. Then, we construct a composite lattice and realize low-frequency broadband absorption from 693 to 1106 Hz with absorptance above 0.8. Further, our investigation demonstrates that the absorption bandwidth can be extended to ultra-broadband from 1077 to 10 000 Hz, where the thickness of the composite lattice is λ/17.05. The proposed composite lattice provides a practical approach to designing ultrathin low-frequency and ultra-broadband acoustic absorption coating for underwater noise suppression.

Plasmonic fiber-optic sensing system for in situ monitoring the capacitance and temperature of supercapacitors.

Compared with ex situ measurement, the in situ measurement is more suitable for inspecting complex electrochemical reactions and improving the intelligent energy storage management. However, most of the in situ investigation instruments are bulky and expensive. Here we demonstrate a miniaturized, portable, and low-cost fiber-optic sensing system for in situ monitoring the capacitance and temperature. It can help evaluate the self-discharge rate in supercapacitors (SCs). The fiber-optic sensing system with two probes are implanted inside the SCs to monitor the capacitance and temperature, respectively. The dual fiber-optic probes can work independently and avoid cross-interference through structure design. The fiber-optic localized surface plasmon resonance (LSPR) probe near the electrode surface can detect the capacitance in real-time by monitoring ion aggregation on the opposite electrode. The fiber-optic surface plasmon resonance (SPR) probe encapsulated in the thermosensitive liquid can independently detect the temperature change. The measurement uncertainties of the two sensing probes are 5.6 mF and 0.08 ℃, respectively. The proposed tiny and flexible fiber-optic sensing system provides a promising method for in situ monitoring the critical parameters. It is also a powerful tool for investigating electrochemical reactions in various energy storage devices.

Real-time regulation of room temperature based on individual thermal sensation using an online brain-computer interface.

Regulation of indoor temperature based on neurophysiological and psychological signals is one of the most promising technologies for intelligent buildings. In this study, we developed a system for closed-loop control of indoor temperature based on brain-computer interface (BCI) technology for the first time. Electroencephalogram (EEG) signals were collected from subjects for two room temperature categories (cool comfortable and hot uncomfortable) and used to build a thermal-sensation discrimination model (TSDM) with an ensemble learning method. Then, an online BCI system was developed based on the TSDM. In the online room temperature control experiment, when the TSDM detected that the subjects felt hot and uncomfortable, BCI would automatically turn on the air conditioner, and when the TSDM detected that the subjects felt cool and comfortable, BCI would automatically turn off the air conditioner. The results of online experiments in a hot environment showed that a BCI could significantly improve the thermal comfort of subjects (the subjective thermal comfort score decreased from 2.45 (hot uncomfortable) to 0.55 (cool comfortable), p < 0.001). A parallel experiment further showed that if the subjects wore thicker clothes during the experiment, the BCI would turn on the air conditioner for a longer time to ensure the thermal comfort of the subjects. This has further confirmed the effectiveness of TSDM model in evaluating thermal sensation under the dynamic change of room temperature and showed the model's good robustness. This study proposed a new paradigm of human-building interaction, which is expected to play a promising role in the development of human-centered intelligent buildings.

Fabrication of avidin-stabilized gold nanoclusters with dual emissions and their application in biosensing.

Protein-stabilized gold nanoclusters (Prot-Au NCs) have been widely used in biosensing and cell imaging owing to their excellent optical properties and low biotoxicity. However, several Prot-Au NCs reported in the literature do not retain the biological role of the protein, which greatly limits their ability to directly detect biomarkers. This study demonstrated for the first time the successful synthesis of dual-function avidin-stabilized gold nanoclusters (Av-Au NCs) using a one-pot method. The resulting Av-Au NCs exhibited intense blue and red emissions under 374 nm excitation. Furthermore, the Av-Au NCs retained the native functionality of avidin to bind to biotin. When DNA strands modified with biotin at both ends (i.e., linker chains) were mixed with Av-Au NCs, large polymers were formed, indicating that Av-Au NCs could achieve fluorescence signal amplification by interacting with biotin. Taking advantage of the aforementioned properties, we constructed a novel enzyme-free fluorescent biosensor based on the Av-Au NCs-biotin system to detect DNA. The designed fluorescent biosensor could detect target DNA down to 0.043 nM, with a wide line range from 0.2 nM to 20 µM. Thus, these dual-functional Av-Au NCs were shown to be an excellent fluorescent material for biosensing.

Pre-treatment circulating reproductive hormones levels predict pathological and survival outcomes in breast cancer submitted to neoadjuvant chemotherapy.

PURPOSE: This study aimed to evaluate the correlation of pre-treatment circulating reproductive hormones levels with pathological and survival outcomes in breast cancer patients received neoadjuvant chemotherapy (NAC). METHODS: Information from 196 premenopausal and 137 postmenopausal breast cancer patients who received NAC were retrospectively analyzed. Treatment response to NAC, with odds ratios (OR) and 95% confidence intervals (95% CI) was estimated using logistic regression adjusted for key confounders. Survival outcomes with hazard ratios (HR) and 95% CI were estimated using Cox regression adjusted for key confounders. The Kaplan-Meier method was applied in the survival analysis. RESULTS: Premenopausal patients with lower testosterone levels (OR = 0.996, 95% CI 0.992-0.999, P = 0.026), and postmenopausal patients with higher follicle-stimulating hormone (FSH) levels (OR = 1.045, 95% CI 1.014-1.077, P = 0.005) were likely to achieve pathological complete response (pCR). In multivariate survival analysis, the lowest tertile (T) progesterone was associated with worse overall survival (OS) in premenopausal patients (T2 vs T1, HR = 0.113, 95% CI 0.013-0.953, P = 0.045; T3 vs T1, HR = 0.109, 95% CI 0.013-0.916, P = 0.041). Premenopausal patients with the lowest tertile progesterone exhibited worse 3-year OS compared with those with higher tertiles (72.9% vs 97.4%, log-rank, P = 0.007). CONCLUSION: Pre-treatment testosterone and FSH are significant independent predictors for pCR to NAC in premenopausal and postmenopausal patients, respectively. Low progesterone levels are correlated with worse OS in premenopausal patients. These findings may provide a theoretical basis for pre-operative endocrine therapy combined with NAC in breast cancer.

Plasma fibrinogen acts as a predictive factor for pathological complete response to neoadjuvant chemotherapy in breast cancer: a retrospective study of 1004 Chinese breast cancer patients.

BACKGROUND: The aim of this study was to evaluate the relationship between pre-treatment plasma fibrinogen (Fib) level and pathological complete response (pCR) to neoadjuvant chemotherapy (NAC) in breast cancer patients and to assess the role of plasma Fib as a predictive factor. METHODS: Data from 1004 consecutive patients with invasive breast cancer who received NAC and subsequent surgery were retrospectively analysed. Both univariate and multivariate analyses based on logistic regression model were performed to identify clinicopathological factors associated with pCR to NAC. Cox regression model was used to determine the correlation between clinical or pathological parameters and recurrence-free survival (RFS). The Kaplan-Meier method and the log-rank test were applied in the survival analysis. RESULTS: The median value of Fib, rather than other plasma coagulation parameters, was significantly increased in non-pCR patients compared with pCR patients (P = 0.002). Based on the cut-off value estimated by the receiver operating characteristic (ROC) curve analysis, patients were divided into low or high Fib groups (Fib < 3.435 g/L or ≥ 3.435 g/L). Low Fib levels were significantly associated with premenopausal or perimenopausal status (P <  0.001), tumour size ≤5 cm (P = 0.002), and positive hormone receptor status (P = 0.002). After adjusted for other clinicopathological factors in the multivariate logistic regression model, low Fib status was strongly associated with pCR to NAC (OR = 3.038, 95% CI 1.667-5.537, P <  0.001). Survival analysis showed that patients with low Fib levels exhibited better 3-year RFS compared with patients with high Fib levels in the tumour size>5 cm group (77.5% vs 58.4%, log-rank, P = 0.0168). CONCLUSIONS: This study demonstrates that low pre-treatment plasma Fib (Fib < 3.435 g/L) is an independent predictive factor for pCR to NAC in breast cancer patients. Moreover, T3-featured breast cancer patients with lower Fib level exhibit better RFS outcomes after NAC compared with high Fib status.

Low-frequency multi-order acoustic absorber based on spiral metasurface.

In this work, we propose a spiral metasurface for multi-order sound absorption in the low-frequency range (<1000 Hz). By dividing the long channel of the spiral metasurface into a series of tunable sub-cavities and employing recessed necks, the metasurface can quasi-perfectly (>0.95 in experiments) absorb airborne sound at multiple low-frequency orders without being limited by the number of equivalent cavities. Owing to the superior impedance manipulation provided by the spiral metasurface, each absorption order can be tuned flexibly with a constant external shape. By suitably modulating the sub-cavities and the recessed necks, we obtained multi-order high-absorption metasurfaces with dual-chamber, tri-chamber, and four-chamber designs. The ratio of the lowest resonant wavelength to the thickness is as high as 78. The samples, which are fabricated by three-dimensional printing technology, were measured to verify the theoretical results. We also investigate the relationship between the geometric parameters of the recessed necks and the sound absorption performance, which facilitates the more feasibly designed multi-order metasurfaces. The concept can be further applied to broadband absorption with ultra-thin thickness and has potential applications for noise reduction.

Development and validation of a novel 15-CpG-based signature for predicting prognosis in triple-negative breast cancer.

DNA methylation is an important biological regulatory mechanism that changes gene expression without altering the DNA sequence. Increasing studies have revealed that DNA methylation data play a vital role in the field of oncology. However, the methylation site signature in triple-negative breast cancer (TNBC) remains unknown. In our research, we analysed 158 TNBC samples and 98 noncancerous samples from The Cancer Genome Atlas (TCGA) in three phases. In the discovery phase, 86 CpGs were identified by univariate Cox proportional hazards regression (CPHR) analyses to be significantly correlated with overall survival (P < 0.01). In the training phase, these candidate CpGs were further narrowed down to a 15-CpG-based signature by conducting least absolute shrinkage and selector operator (LASSO) Cox regression in the training set. In the validation phase, the 15-CpG-based signature was verified using two different internal sets and one external validation set. Furthermore, a nomogram comprising the CpG-based signature and TNM stage was generated to predict the 1-, 3- and 5-year overall survival in the primary set, and it showed excellent performance in the three validation sets (concordance indexes: 0.924, 0.974 and 0.637). This study showed that our nomogram has a precise predictive effect on the prognosis of TNBC and can potentially be implemented for clinical treatment and diagnosis.

Exploring the systematic effect of N-substituted PxxP motifs on peptoid affinity to ARHGEF5/TIM SH3 domain and its relationship with ARHGEF5/TIM activation.

The TIM protein is a short isoform of full-length Rho guanine nucleotide exchange factor 5 (ARHGEF5), which acts as a functional regulator of Rho-dependent signaling pathways by activating the Rho family of GTPases. The activation is auto-inhibited by a putative helix N-terminal to the DH domain of TIM, which is stabilized by the intramolecular interaction of C-terminal SH3 domain with a proline-rich region 47 SSPRQPRKAL56 (termed as SSP peptide) between the putative helix and the DH domain. Previously, we demonstrate that the auto-inhibitory state of TIM protein can be relieved by targeting its SH3 domain with rationally designed peptide ligands. However, the designed natural peptides have only a moderately increased affinity (~2-fold) as compared to the cognate SH3-SSP interaction and are susceptible to protease degradation. Here, considering that proline is the only endogenous N-substituted amino acid that plays a critical role in SH3-peptide recognition, the two key proline residues Pro49 and Pro52 in the core 49 PxxP52 motif of SSP peptide are systematically replaced by 19 N-substituted amino acid types to derive a variety of nonnatural peptoid ligands for TIM SH3 domain. Dynamics and energetics analyses reveal that the replacement would impair the active polyproline II (PPII) helical conformation of SSP peptide due to lack of structural constraint introduced by the five-membered ring of native proline side-chains, thus increasing the peptide flexibility that could incur a large entropy penalty upon binding to the domain. However, the impairment is not very significant and the peptide affinity may also be restored and improved if the N-substituted motif of derived peptiod ligands can effectively interact with the PxxP-binding site of TIM SH3 domain. Consequently, a number of potent peptoids are successfully designed by fluorescence spectroscopy confirmation, in which three (ie, SSP[N-Ile49, N-Asn52], SSP[N-Phe49, N-Gln52], and SSP[N-Tyr49, N-Asn52]) exhibit considerably increased affinity (Kd = 0.09, 0.07, and 0.04 µM, respectively) relative to the native SSP peptide (Kd = 0.87 µM). In addition, guanine nucleotide exchange assays also substantiate that the designed SH3-targeted peptiods can effectively enhance TIM-catalyzed RhoA exchange activity (EA), which is observed to present an exponential relationship with the measured SH3-peptoid binding affinity (pKd ).

Analysis of genetic polymorphisms for age-related macular degeneration (AMD) in Chinese Tujia ethnic minority group.

BACKGROUND: Age-related macular degeneration (AMD) can cause vision loss or blindness in elderly. The associations between single nucleotide polymorphism (SNP) and AMD in Chinese Tujia ethnic minority group are still unclear. METHODS: A total of 2122 Tujia volunteers were recruited and 197 of them were diagnosed with AMD (either dry or wet type).Then the blood specimens of these 197 AMD patients and 404 controls from the remaining 1925 normal Tujia volunteers were collected to detect the frequencies of 39 chosen SNPs. The Bonferroni method was used to correct the P values from the Fisher's exact test. RESULTS: The mean age of the 197 AMD patients(113 males and 84 females) was 68.4197 years old. No significant differences in allelic and genotypic frequencies were found for all the 39 SNPs between the patients and controls. However, weak correlations between 10 SNPs (CFH rs1329428 TT genotype, CFH rs3753394 CC genotype and T allele, CFH rs1410996 AA genotype, CFH rs800292 AA genotype, CFH rs800292 A allele, VEGF rs833061 TT genotype and C allele, VEGF rs2010963 CG genotype, VEGFR2 rs1531289 TT genotype, ARMS2 rs10490924 TT genotype, KCTD10 rs238104 GC genotype, rs1531289 T allele and ARMS2 rs10490924 T allele) and AMD were shown. CONCLUSIONS: The effects of 39 SNPs have found no associations with the morbidity of AMD in Chinese Tujia ethnic minority group.

Rap1b enhances the invasion and migration of hepatocellular carcinoma cells by up-regulating Twist 1.

Rap1b was found be dysregulated in several types of cancers. Previously, we have demonstrated that Rap1b affects proliferation, migration and invasion of hepatocellular carcinoma (HCC) cells. However, the definite function of Rap1b in HCC remains unknown. Here, we reported that Rap1b was significantly up-regulated in HCC tissues compared with the non-tumoral liver tissues. Overexpression of Rap1b promoted tumor growth and migration in vitro and tumor formation in vivo. Oppositely, inhibition of Rap1b suppressed the proliferation and migration of HCC cells. Mechanism study revealed that Rap1b could up-regulate Twist 1 expression by enhancing its promoter activity. We concluded that Rap1b increased Twist 1 expression by targeting its promoter activity to induce proliferation and migration of HCC cells.

Amplified fluorescence imaging of HER2 dimerization on cancer cells by using a co-localization triggered DNA nanoassembly.

Convenient and sensitive detection of human epidermal growth factor receptor 2 (HER2) dimerization is highly desirable for molecule subtyping and guiding personalized HER2 targeted therapy of breast cancer. A colocalization-triggered DNA nanoassembly (CtDNA) strategy was developed for amplified imaging of HER2 dimerization. It exploits (a) the advantage of the specificity of aptamer proximity hybridization, and (b) the high sensitivity of hairpin-free nonlinear HCR. The mechanism of step-by-step hairpin-free nonlinear HCR for DNA dendritic nanoassembly was studied by native polyacrylamide gel electrophoresis, atomic force microscopy and fluorometry. The results revealed a high specificity, sensitivity, and excellent controllability of the DNA dendritic nanoassembly. The method was used to identify HER2 homodimers and HER2/HER3 heterodimers in various breast cancer cell lines using fluorescence microscopy. It was then extended to image and quantitatively evaluate HER2 homodimers in clinical formalin-fixed paraffin-embedded breast cancer tissue specimens. This revealed its remarkable accuracy and practicality for clinical diagnostics. Graphical abstract Schematic presentation of amplified imaging of human epidermal growth factor receptor 2 (HER2) dimerization on cancer cell surfaces by using a co-localization triggered DNA nanoassembly (CtDNA).

Assessment of the predictive role of pretreatment Ki-67 and Ki-67 changes in breast cancer patients receiving neoadjuvant chemotherapy according to the molecular classification: a retrospective study of 1010 patients.

PURPOSE: To assess the predictive role of pretreatment ki67 and Ki67 changes in breast cancer (BC) patients treated with neoadjuvant chemotherapy (NAC) in various molecular subtypes. METHODS: 1010 BC patients who had undergone anthracycline and taxane-based NAC from January 2012 to July 2017 were retrospectively analyzed. Clinical and pathological parameters of the patients were retrieved and the predictive factors for NAC response were evaluated. RESULTS: 705 patients showed clinical response (cRes), and 131 patients acquired pathologic complete response (pCR). Patients with higher pretreatment Ki67 (≥ 14%), tumor size ≥ 4 cm, and positive clinical nodal had better clinical therapy response, while patients with negative ER and PR, higher pretreatment Ki67 (≥ 14%), and tumor size < 4 cm were more probable to attain pCR. The pretreatment Ki67 could be used as a predictor of NAC only in luminal subtypes, and 25.5% were identified as an ideal cut-off point to differentiate the cRes from non-cRes cases. Although a decrease in Ki67 had been found in almost all molecular subtypes after NAC, no statistically significant differences were found in the decrease of Ki67 were validated between the cRes and non-cRes group in HER2-rich and triple-negative subtypes (P = 0.488 and P = 0.111, respectively). CONCLUSIONS: The best cut-off for pretreatment Ki67 in predicting the connection with the tumor size lessening was 25.5% in luminal subtype. Aggressive adjuvant systemic treatments should be considered for patients with HER2-rich and triple-negative subtype who exhibit tumor shrinkage in NAC but still have high levels of Ki67.