A distinct subset of urothelial cells with enhanced EMT features promotes chemotherapy resistance and cancer recurrence by increasing COL4A1-ITGB1 mediated angiogenesis.

Drug resistance and tumor recurrence remain clinical challenges in the treatment of urothelial carcinoma (UC). However, the underlying mechanism is not fully understood. Here, we performed single-cell RNA sequencing and identified a subset of urothelial cells with epithelial-mesenchymal transition (EMT) features (EMT-UC), which is significantly correlated with chemotherapy resistance and cancer recurrence. To validate the clinical significance of EMT-UC, we constructed EMT-UC like cells by introducing overexpression of two markers, Zinc Finger E-Box Binding Homeobox 1 (ZEB1) and Desmin (DES), and examined their histological distribution characteristics and malignant phenotypes. EMT-UC like cells were mainly enriched in UC tissues from patients with adverse prognosis and exhibited significantly elevated EMT, migration and gemcitabine tolerance in vitro. However, EMT-UC was not specifically identified from tumorous tissues, certain proportion of them were also identified in adjacent normal tissues. Tumorous EMT-UC highly expressed genes involved in malignant behaviors and exhibited adverse prognosis. Additionally, tumorous EMT-UC was associated with remodeled tumor microenvironment (TME), which exhibited high angiogenic and immunosuppressive potentials compared with the normal counterparts. Furthermore, a specific interaction of COL4A1 and ITGB1 was identified to be highly enriched in tumorous EMT-UC, and in the endothelial component. Targeting the interaction of COL4A1 and ITGB1 with specific antibodies significantly suppressed tumorous angiogenesis and alleviated gemcitabine resistance of UC. Overall, our findings demonstrated that the driven force of chemotherapy resistance and recurrence of UC was EMT-UC mediated COL4A1-ITGB1 interaction, providing a potential target for future UC treatment.

Quantum coherent energy transport in the Fenna-Matthews-Olson complex at low temperature.

In the primary step of natural light harvesting, the solar photon energy is captured in a photoexcited electron-hole pair, or an exciton, in chlorophyll. Its conversion to chemical potential occurs in the special pair reaction center, which is reached by downhill ultrafast excited-state energy transport through a network of chromophores. Being inherently quantum, transport could in principle occur via a matter wave, with vast implications for efficiency. How long a matter wave remains coherent is determined by the intensity by which the exciton is disturbed by the noisy biological environment. The stronger this is, the stronger the electronic coupling between chromophores must be to overcome the fluctuations and phase shifts. The current consensus is that under physiological conditions, quantum coherence vanishes on the 10-fs time scale, rendering it irrelevant for the observed picosecond transfer. Yet, at low-enough temperature, quantum coherence should in principle be present. Here, we reveal the onset of longer-lived electronic coherence at extremely low temperatures of ∼20 K. Using two-dimensional electronic spectroscopy, we determine the exciton coherence times in the Fenna-Matthew-Olson complex over an extensive temperature range. At 20 K, coherence persists out to 200 fs (close to the antenna) and marginally up to 500 fs at the reaction center. It decays markedly faster with modest increases in temperature to become irrelevant above 150 K. At low temperature, the fragile electronic coherence can be separated from the robust vibrational coherence, using a rigorous theoretical analysis. We believe that by this generic principle, light harvesting becomes robust against otherwise fragile quantum effects.

Equation-of-Motion Methods for the Calculation of Femtosecond Time-Resolved 4-Wave-Mixing and N-Wave-Mixing Signals.

Femtosecond nonlinear spectroscopy is the main tool for the time-resolved detection of photophysical and photochemical processes. Since most systems of chemical interest are rather complex, theoretical support is indispensable for the extraction of the intrinsic system dynamics from the detected spectroscopic responses. There exist two alternative theoretical formalisms for the calculation of spectroscopic signals, the nonlinear response-function (NRF) approach and the spectroscopic equation-of-motion (EOM) approach. In the NRF formalism, the system-field interaction is assumed to be sufficiently weak and is treated in lowest-order perturbation theory for each laser pulse interacting with the sample. The conceptual alternative to the NRF method is the extraction of the spectroscopic signals from the solutions of quantum mechanical, semiclassical, or quasiclassical EOMs which govern the time evolution of the material system interacting with the radiation field of the laser pulses. The NRF formalism and its applications to a broad range of material systems and spectroscopic signals have been comprehensively reviewed in the literature. This article provides a detailed review of the suite of EOM methods, including applications to 4-wave-mixing and N-wave-mixing signals detected with weak or strong fields. Under certain circumstances, the spectroscopic EOM methods may be more efficient than the NRF method for the computation of various nonlinear spectroscopic signals.

Finite temperature dynamics in a polarized sub-Ohmic heat bath: A hierarchical equations of motion-tensor train study.

The dynamics of the sub-Ohmic spin-boson model under polarized initial conditions at finite temperatures is investigated by employing both analytical tools and the numerically accurate hierarchical equations of motion-tensor train method. By analyzing the features of nonequilibrium dynamics, we discovered a bifurcation phenomenon, which separates two regimes of the dynamics. It is found that before the bifurcation time, increasing temperature slows down the population dynamics, while the opposite effect occurs after the bifurcation time. The dynamics is highly sensitive to both initial preparation of the bath and thermal effects.

Gut microbiome in men with chronic prostatitis/chronic pelvic pain syndrome: profiling and its predictive significance.

PURPOSE: To investigate the difference in gut microbiome composition between patients with chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) and healthy controls, and to assess the potential of gut microbiota as predictive markers for CP/CPPS risk. METHODS: The present study included 41 CP/CPPS patients and 43 healthy controls in China. Fecal specimen data were obtained and analysed using 16S rRNA gene sequencing. Alpha and beta-diversity indices, relative microbiome abundances, cluster analysis, and linear discriminant analysis effect size (LEfSe) were employed. Microbial biomarkers were selected for the development of a diagnostic classification model, and the functional prediction was conducted using PICRUSt2. RESULTS: Alpha-diversity measures revealed no statistically significant difference in bacterial community structure between CP/CPPS patients and controls. However, significant differences were observed in the relative abundances of several bacterial genera. Beta-diversity analysis revealed a distinct separation between the two groups. Significant inter-group differences were noted at various taxonomic levels, with specific bacterial genera being significantly different in abundance. The LEfSe analysis indicated that three bacterial species were highly representative and seven bacterial species were low in CP/CPPS patients as compared to the control group. A diagnostic model for CP/CPPS based on microbial biomarkers exhibited good performance. PICRUSt2 functional profiling indicated significant differences in the development and regeneration pathway. CONCLUSION: Significant differences in the gut microbiome composition were found between groups. The study provided a novel diagnostic model for CP/CPPS based on microbiota, presenting promising potential for future therapeutic targets and non-invasive diagnostic biomarkers for CP/CPPS patients.

Two-dimensional fluorescence excitation spectroscopy: A novel technique for monitoring excited-state photophysics of molecular species with high time and frequency resolution.

We propose a novel UV/Vis femtosecond spectroscopic technique, two-dimensional fluorescence-excitation (2D-FLEX) spectroscopy, which combines spectral resolution during the excitation process with exclusive monitoring of the excited-state system dynamics at high time and frequency resolution. We discuss the experimental feasibility and realizability of 2D-FLEX, develop the necessary theoretical framework, and demonstrate the high information content of this technique by simulating the 2D-FLEX spectra of a model four-level system and the Fenna-Matthews-Olson antenna complex. We show that the evolution of 2D-FLEX spectra with population time directly monitors energy transfer dynamics and can thus yield direct qualitative insight into the investigated system. This makes 2D-FLEX a highly efficient instrument for real-time monitoring of photophysical processes in polyatomic molecules and molecular aggregates.

Dynamics of the spin-boson model: The effect of bath initial conditions.

The dynamics of the (sub-)Ohmic spin-boson model under various bath initial conditions is investigated by employing the Dirac-Frenkel time-dependent variational approach with the multiple Davydov D1 Ansatz in the interaction picture. The validity of our approach is carefully checked by comparing the results with those of the hierarchy equations of motion method. By analyzing the features of nonequilibrium dynamics, we identify the phase diagrams for different bath initial conditions. We find that for the spectral exponent s < sc, there exists a transition from coherent to quasicoherent dynamics with increasing coupling strengths. For sc < s ≤ 1, the coherent to incoherent crossover occurs at a certain coupling strength and the quasicoherent dynamics emerges at much larger couplings. The initial preparation of the bath has a considerable influence on the dynamics.

Simulating optical linear absorption for mesoscale molecular aggregates: An adaptive hierarchy of pure states approach.

In this paper, we present dyadic adaptive HOPS (DadHOPS), a new method for calculating linear absorption spectra for large molecular aggregates. This method combines the adaptive HOPS (adHOPS) framework, which uses locality to improve computational scaling, with the dyadic HOPS method previously developed to calculate linear and nonlinear spectroscopic signals. To construct a local representation of dyadic HOPS, we introduce an initial state decomposition that reconstructs the linear absorption spectra from a sum over locally excited initial conditions. We demonstrate the sum over initial conditions can be efficiently Monte Carlo sampled and that the corresponding calculations achieve size-invariant [i.e., O(1)] scaling for sufficiently large aggregates while trivially incorporating static disorder in the Hamiltonian. We present calculations on the photosystem I core complex to explore the behavior of the initial state decomposition in complex molecular aggregates as well as proof-of-concept DadHOPS calculations on an artificial molecular aggregate inspired by perylene bis-imide to demonstrate the size-invariance of the method.

Future self-continuity and depression among college students: The role of presence of meaning and perceived social support.

INTRODUCTION: Future self-continuity has been shown to have a protective effect against depression. This study aims to investigate the longitudinal relationship between future self-continuity and depression among college students, and to explore the mediating role of the presence of meaning and the moderating role of perceived social support. METHODS: We conducted two studies in China in 2022 and 2023. Study 1 was a longitudinal cross-lagged study that examined the relationship between future self-continuity and depression among 173 participants (49.13% females, Mage = 19.39, SD = 1.63). Study 2 was a cross-sectional study that explored the mediating role of the presence of meaning and the moderating role of perceived social support among 426 participants (48.59% females, Mage = 19.30, SD = 1.60). RESULTS: Study 1 showed that future self-continuity (T1) could significantly predict depression (T2), but depression (T1) could not predict future self-continuity (T2). Study 2 showed that after controlling for gender, the presence of meaning mediated the relationship between future self-continuity and depression, whereas perceived social support moderated the first half of the mediated model's pathway and the direct pathway. CONCLUSIONS: These findings suggest that enhancing the future self-continuity of college students and increasing the level of presence of meaning are effective measures for alleviating depression. Meanwhile, educators and families are called upon to provide more social support to college students.

Excitations of Quantum Many-Body Systems via Purified Ensembles: A Unitary-Coupled-Cluster-Based Approach.

State-average calculations based on a mixture of states are increasingly being exploited across chemistry and physics as versatile procedures for addressing excitations of quantum many-body systems. If not too many states should need to be addressed, calculations performed on individual states are also a common option. Here we show how the two approaches can be merged into one method, dealing with a generalized yet single pure state. Implications in electronic structure calculations are discussed and for quantum computations are pointed out.

Pathogenic variants identified using whole-exome sequencing in Chinese patients with primary ciliary dyskinesia.

The genetic factors contributing to primary ciliary dyskinesia (PCD), a rare autosomal recessive disorder, remain elusive for ~20%-35% of patients with complex and abnormal clinical phenotypes. Our study aimed to identify causative variants of PCD-associated pathogenic candidate genes using whole-exome sequencing (WES). All patients were diagnosed with PCD based on clinical phenotype or transmission electron microscopy images of cilia. WES and bioinformatic analysis were then conducted on patients with PCD. Identified candidate variants were validated by Sanger sequencing. Pathogenicity of candidate variants was then evaluated using in silico software and the American College of Medical Genetics and Genomics (ACMG) database. In total, 13 rare variants were identified in patients with PCD, among which were three homozygous causative variants (including one splicing variant) in the PCD-associated genes CCDC40 and DNAI1. Moreover, two stop-gain heterozygous variants of DNAAF3 and DNAH1 were classified as pathogenic variants based on the ACMG criteria. This study identified novel potential pathogenic genetic factors associated with PCD. Noteworthy, the patients with PCD carried multiple rare causative gene variants, thereby suggesting that known causative genes along with other functional genes should be considered for such heterogeneous genetic disorders.

Endogenous hydrogen sulfide promotes human preimplantation embryonic development by regulating metabolism-related gene expression.

Hydrogen sulfide (H2S) as an endogenous gaseous signaling molecule had been proved to play a vital role in gametes physiology, covering meiosis, maturation and aging. However, little is known about H2S involvement in embryonic development. The present study explored the positive effect of H2S on human early embryonic development. Results validated that the two H2S producing enzymes, CBS and CSE mRNA and proteins were identified in donated human cleavage and blastocyst-stage embryos. The l-cysteine incubation produced endogenous H2S in human blastocysts. NaHS positively affected in vitro blastulation. Single-cell RNA-seq analysis identified 228 differentially expressed genes (DEGs) after NaHS treatment versus the control. The Gene Ontology (GO) enrichment analysis of DEGs showed that genes for protein modification and metabolism were significantly enriched in the NaHS treatment group. For the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, 2-oxocarboxylic acid metabolism, glycosaminoglycan biosynthesis-keratan sulfate, steroid biosynthesis, carbon metabolism, and biosynthesis of amino acids were significantly enriched. Six DEGs, including Neural EGFL like 1 (NELL1), aconitase 1 (ACO1), phosphoglycerate mutase 1 (PGAM1), TP53 induced glycolysis regulatory phosphatase (TIGAR), UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2 (B3GNT2), and carbohydrate Sulfotransferase 4 (CHST4) were validate by real-time RT-PCR. These findings suggest that H2S is a positive regulator of early embryonic development and may alter the transcription of embryonic genes for protein modification and metabolism in human embryos.

Calculating nonlinear response functions for multidimensional electronic spectroscopy using dyadic non-Markovian quantum state diffusion.

We present a methodology for simulating multidimensional electronic spectra of molecular aggregates with coupling of electronic excitation to a structured environment using the stochastic non-Markovian quantum state diffusion (NMQSD) method in combination with perturbation theory for the response functions. A crucial aspect of our approach is that we propagate the NMQSD equation in a doubled system Hilbert space but with the same noise. We demonstrate that our approach shows fast convergence with respect to the number of stochastic trajectories, providing a promising technique for numerical calculation of two-dimensional electronic spectra of large molecular aggregates.

Simulation of absorption spectra of molecular aggregates: A hierarchy of stochastic pure state approach.

Simulation of spectroscopic observables for molecular aggregates with strong and structured coupling of electronic excitation to vibrational degrees of freedom is an important but challenging task. The Hierarchy of Pure States (HOPS) provides a formally exact solution based on local, stochastic trajectories. Exploiting the localization of HOPS for the simulation of absorption spectra in large aggregates requires a formulation in terms of normalized trajectories. Here, we provide a normalized dyadic equation where the ket- and bra-states are propagated in different electronic Hilbert spaces. This work opens the door to applying adaptive HOPS methods for the simulation of absorption spectra.

Emission spectral non-Markovianity in qubit-cavity systems in the ultrastrong coupling regime.

We study the emission spectra of the dissipative Rabi and Jaynes-Cummings models in the non-Markovian and ultrastrong coupling regimes. We have derived a polaron-transformed Nakajima-Zwanzig master equation (PTNZE) to calculate the emission spectra, which eliminates the well-known limitations of the Markovian approximation and the standard second-order perturbation. Using the time-dependent variational approach with the multiple Davydov ansatz as a benchmark, the PTNZE is found to yield accurate emission spectra in certain ultrastrong coupling regimes where the standard second-order Nakajima-Zwanzig master equation breaks down. It is shown that the emission spectra of the dissipative Rabi and Jaynes-Cummings models are, in general, asymmetric under various initial conditions. Direct comparisons of spectra for the two models illustrate the essential role of the qubit-cavity counter-rotating term and the spectral features under different qubit-cavity coupling strengths and system initial conditions.

Metformin ameliorates bladder dysfunction in a rat model of partial bladder outlet obstruction.

Alteration of bladder morphology and function was the most important consequence of bladder outlet obstruction (BOO). Using a rat model of partial BOO (pBOO), we found that rats treated with metformin showed lower baseline pressures with a reduced inflammatory reaction in the early phase (2 wk) after pBOO. The NLR family pyrin domain containing 3 inflammasome pathway was inhibited in pBOO rat bladders with treatment of metformin in the early phase. Metformin reduced the activity of NLR family pyrin domain containing 3 in primary urothelial cells. In the chronic phase (9 wk after pBOO), metformin treatment ameliorated bladder fibrosis and improved the reduced compliance. Treatment with metformin suppressed the activation of Smad3 and compensated the diminished autophagy in 9-wk pBOO rat bladders. Autophagy was inhibited with upregulation of profibrotic proteins in primary fibroblasts from chronic pBOO bladders, which could be restored by administration of metformin. The antifibrotic effects of metformin on fibroblasts were diminished after silencing of AMP-activated protein kinase or light chain 3B. In summary, this study elucidates that oral administration of metformin relieves inflammation in the bladder during the early phase of pBOO. Long-term oral administration of metformin can prevent functional and histological changes in the pBOO rat bladder. The current study suggests that metformin might be used to prevent the development of bladder dysfunction secondary to BOO.NEW & NOTEWORTHY The present study in a rat model showed that oral administration of metformin alleviated inflammation following partial bladder outlet obstruction in the early phase and ameliorated bladder fibrosis as well as bladder dysfunction by long-term treatment. Our study indicated that metformin is a potential drug to inhibit bladder remodeling and alleviate bladder dysfunction. Clinical trials are needed to validate the effect of metformin on the bladder dysfunction and bladder fibrosis in the future.

KDM6A-ARHGDIB axis blocks metastasis of bladder cancer by inhibiting Rac1.

BACKGROUND: KDM6A, a histone demethylase, is frequently mutated in bladder cancer (BCa). However, the role and detailed molecular mechanism of KDM6A involved in bladder cancer progression remains unknown. METHODS: Tissue specimens were used to determine the expression levels and prognostic values of KDM6A and ARHGDIB. The MTT, colony formation, wound healing and Transwell migration and invasion assays were employed to detect the BCa cell proliferation, migration and invasion, respectively. Chemotaxis of macrophages was used to evaluate the ability of KDM6A to recruit macrophages. A subcutaneous tumour model and tail vein tumour injection in nude mice were used to assess the role of KDM6A in vivo. RNA sequencing, qPCR, Western blot, ChIP and phalloidin staining assay were performed to investigate the molecular functions of KDM6A. Dual-luciferase reporter assay was used to determine the effects of KDM6A and FOXA1 on the promoters of the ARHGDIB and KDM6A. RESULTS: We showed that the KDM6A inhibited the motility and invasiveness of the BCa cells. Mechanistically, KDM6A promotes the transcription of ARHGDIB by demethylating histone H3 lysine di/trimethylation (H3K27me2/3) and consequently leads to inhibition of Rac1. EZH2, which catalyses the methylation of H3K27, functions to silence ARHGDIB expression, and an EZH2 inhibitor can neutralize the metastatic effect caused by KDM6A deficiency. Furthermore, we demonstrated that FOXA1 directly binds to the KDM6A promoter and thus transactivates KDM6A, leading to diminished metastatic potential. CONCLUSION: Our findings establish the critical role of the FOXA1-KDM6A-ARHGDIB axis in restraining the malignancy of BCa and identify KDM6A and EZH2 as potential therapeutic targets in the management of BCa.

Methyltransferase-like protein 11A promotes migration of cervical cancer cells via up-regulating ELK3.

Cervical cancer is one of the common malignancies in women, which is characterized with high invasion and metastatic tendency in its advanced stage. Increasing evidence indicates that methyltransferase-like (METTL) gene family is involved in the progression of various cancers. However, the functional role of methyltransferase-like gene family in cervical cancer remains unclear. In the present study, we found that METTL11A, a member of the methyltransferase-like gene family, was significantly over-expressed in cervical carcinoma by analyzing TCGA database. This finding was further validated in clinical tissue samples. Moreover, ectopic expression of METTL11A in cervical cancer cell lines promoted cell proliferation and migration both in vitro and in vivo. Differential gene expression analysis in the transcriptomic sequencing data indicated that ELK3 was down-regulated in METTL11A-silenced cervical cancer cells, which was further verified at both protein and mRNA levels. Functional experiments identified that METTL11A promoted migration of cervical cancer cells in an ELK3-dependent manner. This study will promote understanding the mechanism of cervical cancer progression and the functional role of methyltransferase-like gene families in cancers.

Efficient simulation of time- and frequency-resolved four-wave-mixing signals with a multiconfigurational Ehrenfest approach.

We have extended the multiconfigurational Ehrenfest approach to the simulation of four-wave-mixing signals of systems involving multiple electronic and vibrational degrees of freedom. As an illustration, we calculate signals of three widely used spectroscopic techniques, time- and frequency-resolved fluorescence spectroscopy, transient absorption spectroscopy, and two-dimensional (2D) electronic spectroscopy, for a two-electronic-state, twenty-four vibrational-mode conical intersection model. It has been shown that all these three spectroscopic signals characterize fast population transfer from the higher excited electronic state to the lower excited electronic state. While the time- and frequency-resolved spectrum maps the wave packet propagation exclusively on the electronically excited states, the transient absorption and 2D electronic spectra reflect the wave packet dynamics on both electronically excited states and the electronic ground state. Combining trajectory-guided Gaussian basis functions and the nonlinear response function formalism, the present approach provides a promising general technique for the applications of various Gaussian basis methods to the calculations of four-wave-mixing spectra of polyatomic molecules.

Identification of a distinct luminal subgroup diagnosing and stratifying early stage prostate cancer by tissue-based single-cell RNA sequencing.

BACKGROUND: The highly intra-tumoral heterogeneity and complex cell origination of prostate cancer greatly limits the utility of traditional bulk RNA sequencing in finding better biomarker for disease diagnosis and stratification. Tissue specimens based single-cell RNA sequencing holds great promise for identification of novel biomarkers. However, this technique has yet been used in the study of prostate cancer heterogeneity. METHODS: Cell types and the corresponding marker genes were identified by single-cell RNA sequencing. Malignant states of different clusters were evaluated by copy number variation analysis and differentially expressed genes of pseudo-bulks sequencing. Diagnosis and stratification of prostate cancer was estimated by receiver operating characteristic curves of marker genes. Expression characteristics of marker genes were verified by immunostaining. RESULTS: Fifteen cell groups including three luminal clusters with different expression profiles were identified in prostate cancer tissues. The luminal cluster with the highest copy number variation level and marker genes enriched in prostate cancer-related metabolic processes was considered the malignant cluster. This cluster contained a distinct subgroup with high expression level of prostate cancer biomarkers and a strong distinguishing ability of normal and cancerous prostates across different pathology grading. In addition, we identified another marker gene, Hepsin (HPN), with a 0.930 area under the curve score distinguishing normal tissue from prostate cancer lesion. This finding was further validated by immunostaining of HPN in prostate cancer tissue array. CONCLUSION: Our findings provide a valuable resource for interpreting tumor heterogeneity in prostate cancer, and a novel candidate marker for prostate cancer management.