An atlas of cell-type-specific interactome networks across 44 human tumor types.

BACKGROUND: Biological processes are controlled by groups of genes acting in concert. Investigating gene-gene interactions within different cell types can help researchers understand the regulatory mechanisms behind human complex diseases, such as tumors. METHODS: We collected extensive single-cell RNA-seq data from tumors, involving 563 patients with 44 different tumor types. Through our analysis, we identified various cell types in tumors and created an atlas of different immune cell subsets across different tumor types. Using the SCINET method, we reconstructed interactome networks specific to different cell types. Diverse functional data was then integrated to gain biological insights into the networks, including somatic mutation patterns and gene functional annotation. Additionally, genes with prognostic relevance within the networks were also identified. We also examined cell-cell communications to investigate how gene interactions modulate cell-cell interactions. RESULTS: We developed a data portal called CellNetdb for researchers to study cell-type-specific interactome networks. Our findings indicate that these networks can be used to identify genes with topological specificity in different cell types. We also found that prognostic genes can deconvolved into cell types through analyzing network connectivity. Additionally, we identified commonalities and differences in cell-type-specific networks across different tumor types. Our results suggest that these networks can be used to prioritize risk genes. CONCLUSIONS: This study presented CellNetdb, a comprehensive repository featuring an atlas of cell-type-specific interactome networks across 44 human tumor types. The findings underscore the utility of these networks in delineating the intricacies of tumor microenvironments and advancing the understanding of molecular mechanisms underpinning human tumors.

Melatonin enhances osteoblastogenesis of senescent bone marrow stromal cells through NSD2-mediated chromatin remodelling.

BACKGROUND: Aging-associated osteoporosis is frequently seen in the elderly in clinic, but efficient managements are limited because of unclear nosogenesis. The current study aims to investigate the role of melatonin on senescent bone marrow stromal cells (BMSCs) and the underlying regulating mechanism. METHODS: Melatonin levels were tested by ELISA. Gene expression profiles were performed by RNA-sequencing, enrichment of H3K36me2 on gene promoters was analyzed by Chromatin Immunoprecipitation Sequencing (ChIP-seq), and chromatin accessibility was determined by Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq). Osteogenesis of BMSCs in vitro was measured by Alizarin Red and Alkaline Phosphatase staining, and in vivo effects of melatonin was assessed by histological staining and micro computed tomography (micro-CT) scan. Correlation of NSD2 expression and severity of senile osteoporosis patients were analyzed by Pearson correlation. RESULTS: Melatonin levels were decreased during aging in human bone marrow, accompanied by downregulation of the histone methyltransferase nuclear receptor binding SET domain protein 2 (NSD2) expression in the senescent BMSCs. Melatonin stimulated the expression of NSD2 through MT1/2-mediated signaling pathways, resulting in the rebalancing of H3K36me2 and H3K27me3 modifications to increase chromatin accessibility of the osteogenic genes, runt-related transcription factor 2 (RUNX2) and bone gamma-carboxyglutamate protein (BGLAP). Melatonin promoted osteogenesis of BMSCs in vitro, and alleviates osteoporosis progression in the aging mice. In clinic, severity of senile osteoporosis (SOP) was negatively correlated with melatonin level in bone marrow, as well as NSD2 expression in BMSCs. Similarly, melatonin remarkably enhanced osteogenic differentiation of BMSCs derived from SOP patients in vitro. CONCLUSIONS: Collectively, our study dissects previously unreported mechanistic insights into the epigenetic regulating machinery of melatonin in meliorating osteogenic differentiation of senescent BMSC, and provides evidence for application of melatonin in preventing aging-associated bone loss.

scAPAatlas: an atlas of alternative polyadenylation across cell types in human and mouse.

Alternative polyadenylation (APA) has been widely recognized as a crucial step during the post-transcriptional regulation of eukaryotic genes. Recent studies have demonstrated that APA exerts key regulatory roles in many biological processes and often occurs in a tissue- and cell-type-specific manner. However, to our knowledge, there is no database incorporating information about APA at the cell-type level. Single-cell RNA-seq is a rapidly evolving and powerful tool that enable APA analysis at the cell-type level. Here, we present a comprehensive resource, scAPAatlas (http://www.bioailab.com:3838/scAPAatlas), for exploring APA across different cell types, and interpreting potential biological functions. Based on the curated scRNA-seq data from 24 human and 25 mouse normal tissues, we systematically identified cell-type-specific APA events for different cell types and examined the correlations between APA and gene expression level. We also estimated the crosstalk between cell-type-specific APA events and microRNAs or RNA-binding proteins. A user-friendly web interface has been constructed to support browsing, searching and visualizing multi-layer information of cell-type-specific APA events. Overall, scAPAatlas, incorporating a rich resource for exploration of APA at the cell-type level, will greatly help researchers chart cell type with APA and elucidate the biological functions of APA.

Observation and Active Control of a Collective Polariton Mode and Polaritonic Band Gap in Few-Layer WS2 Strongly Coupled with Plasmonic Lattices.

Two-dimensional semiconductors host excitons with very large oscillator strengths and binding energies due to significantly reduced carrier screening. Two-dimensional semiconductors integrated with optical cavities are emerging as a promising platform for studying strong light-matter interactions as a route to explore a variety of exotic many-body effects. Here, in few-layered WS2 coupled with plasmonic nanoparticle lattices, we observe the formation of a collective polaritonic mode near the exciton energy and the formation of a complete polariton band gap with energy scale comparable to the exciton-plasmon coupling strength. A coupled oscillator model reveals that the collective mode arises from the cooperative coupling of the excitons to the plasmonic lattice diffraction orders via exciton-exciton interactions, leading to ultrastrong coupling. The emergence of the collective mode is accompanied by a superlinear increase of the polariton mode splitting as a function of the square root of the exciton oscillator strength. The presence of these many body effects, which are enhanced in systems which lack bulk polarization, not only allows the formation of a collective mode with periodically varying field profiles, but also further enhances the exciton-plasmon coupling. By integrating the hybrid WS2-plasmonic lattice device with a field-effect transistor, we demonstrate active tuning of the collective mode and the polariton band gap. We also report electrically tunable waveguiding in the polariton band gap region through a line defect, which can be turned off with gate bias that can extinguish the collective mode and the polariton band gap. These systems provide new opportunities for obtaining a deeper and systematic understanding of many body cooperative phenomena in two-dimensional materials coupled with periodic photonic systems and for designing more complex and actively controllable polaritonic devices including switchable polariton lasers, waveguides, and optical logical elements.

Spatially dispersive circular photogalvanic effect in a Weyl semimetal.

Weyl semimetals (WSMs) are gapless topological states of matter with broken inversion and/or time reversal symmetry. WSMs can support a circulating photocurrent when illuminated by circularly polarized light at normal incidence. Here, we report a spatially dispersive circular photogalvanic effect (s-CPGE) in a WSM that occurs with a spatially varying beam profile. Our analysis shows that the s-CPGE is controlled by a symmetry selection rule combined with asymmetric carrier excitation and relaxation dynamics. By evaluating the s-CPGE for a minimal model of a WSM, a frequency-dependent scaling behaviour of the photocurrent is obtained. Wavelength-dependent measurements from the visible to mid-infrared range show evidence of Berry curvature singularities and band inversion in the s-CPGE response. We present the s-CPGE as a promising spectroscopic probe for topological band properties, with the potential for controlling photoresponse by patterning optical fields on topological materials to store, manipulate and transmit information.

Strong modulation of second-harmonic generation with very large contrast in semiconducting CdS via high-field domain.

Dynamic control of nonlinear signals is critical for a wide variety of optoelectronic applications, such as signal processing for optical computing. However, controlling nonlinear optical signals with large modulation strengths and near-perfect contrast remains a challenging problem due to intrinsic second-order nonlinear coefficients via bulk or surface contributions. Here, via electrical control, we turn on and tune second-order nonlinear coefficients in semiconducting CdS nanobelts from zero to up to 151 pm V-1, a value higher than other intrinsic nonlinear coefficients in CdS. We also observe ultrahigh ON/OFF ratio of >104 and modulation strengths ~200% V-1 of the nonlinear signal. The unusual nonlinear behavior, including super-quadratic voltage and power dependence, is ascribed to the high-field domain, which can be further controlled by near-infrared optical excitation and electrical gating. The ability to electrically control nonlinear optical signals in nanostructures can enable optoelectronic devices such as optical transistors and modulators for on-chip integrated photonics.

Inverting polar domains via electrical pulsing in metallic germanium telluride.

Germanium telluride (GeTe) is both polar and metallic, an unusual combination of properties in any material system. The large concentration of free-carriers in GeTe precludes the coupling of external electric field with internal polarization, rendering it ineffective for conventional ferroelectric applications and polarization switching. Here we investigate alternate ways of coupling the polar domains in GeTe to external electrical stimuli through optical second harmonic generation polarimetry and in situ TEM electrical testing on single-crystalline GeTe nanowires. We show that anti-phase boundaries, created from current pulses (heat shocks), invert the polarization of selective domains resulting in reorganization of certain 71o domain boundaries into 109o boundaries. These boundaries subsequently interact and evolve with the partial dislocations, which migrate from domain to domain with the carrier-wind force (electrical current). This work suggests that current pulses and carrier-wind force could be external stimuli for domain engineering in ferroelectrics with significant current leakage.

Highly sensitive hot electron bolometer based on disordered graphene.

A bolometer is a device that makes an electrical resistive response to the electromagnetic radiation resulted from a raise of temperature due to heating. The combination of the extremely weak electron-phonon interactions along with its small electron heat capacity makes graphene an ideal material for applications in ultra-fast and sensitive hot electron bolometer. However, a major issue is that the resistance of pristine graphene weakly depends on the electronic temperature. We propose using disordered graphene to obtain a strongly temperature dependent resistance. The measured electrical responsivity of the disordered graphene bolometer reaches 6 × 10(6) V/W at 1.5 K, corresponding to an optical responsivity of 1.6 × 10(5) V/W. The deduced electrical noise equivalent power is 1.2 fW/√Hz, corresponding to the optical noise equivalent power of 44 fW/√Hz. The minimal device structure and no requirement for high mobility graphene make a step forward towards the applications of graphene hot electron bolometers.