To define the cellular composition and architecture of cutaneous squamous cell carcinoma (cSCC), we combined single-cell RNA sequencing with spatial transcriptomics and multiplexed ion beam imaging ...from a series of human cSCCs and matched normal skin. cSCC exhibited four tumor subpopulations, three recapitulating normal epidermal states, and a tumor-specific keratinocyte (TSK) population unique to cancer, which localized to a fibrovascular niche. Integration of single-cell and spatial data mapped ligand-receptor networks to specific cell types, revealing TSK cells as a hub for intercellular communication. Multiple features of potential immunosuppression were observed, including T regulatory cell (Treg) co-localization with CD8 T cells in compartmentalized tumor stroma. Finally, single-cell characterization of human tumor xenografts and in vivo CRISPR screens identified essential roles for specific tumor subpopulation-enriched gene networks in tumorigenesis. These data define cSCC tumor and stromal cell subpopulations, the spatial niches where they interact, and the communicating gene networks that they engage in cancer.
Display omitted
•Profiling of 10 human skin SCCs and matched normals via scRNA-seq, ST, and MIBI•Tumor-specific keratinocytes (TSKs) reside within a fibrovascular niche at leading edges•Distinct ligand-receptor and spatial niche associations for tumor and stromal cells.•Subpopulation essential tumorigenic gene networks defined by in vivo CRISPR screening
Integration of high-dimensional multi-omics approaches to characterize human cutaneous squamous cell carcinoma identifies a tumor-specific keratinocyte population as well as the immune infiltrates and heterogeneity at tumor leading edges.
Abstract
Simultaneous visualization of the relationship between multiple biomolecules and their ligands or small molecules at the nanometer scale in cells will enable greater understanding of how ...biological processes operate. We present here high-definition multiplex ion beam imaging (HD-MIBI), a secondary ion mass spectrometry approach capable of high-parameter imaging in 3D of targeted biological entities and exogenously added structurally-unmodified small molecules. With this technology, the atomic constituents of the biomolecules themselves can be used in our system as the “tag” and we demonstrate measurements down to ~30 nm lateral resolution. We correlated the subcellular localization of the chemotherapy drug cisplatin simultaneously with five subnuclear structures. Cisplatin was preferentially enriched in nuclear speckles and excluded from closed-chromatin regions, indicative of a role for cisplatin in active regions of chromatin. Unexpectedly, cells surviving multi-drug treatment with cisplatin and the BET inhibitor JQ1 demonstrated near total cisplatin exclusion from the nucleus, suggesting that selective subcellular drug relocalization may modulate resistance to this important chemotherapeutic treatment. Multiplexed high-resolution imaging techniques, such as HD-MIBI, will enable studies of biomolecules and drug distributions in biologically relevant subcellular microenvironments by visualizing the processes themselves in concert, rather than inferring mechanism through surrogate analyses.
Nontraditional luminogens (NTLs) do not contain any conventional chromophores (large π-conjugated structures), but they do show intrinsic photoluminescence. To achieve photoluminescence from NTLs, it ...is necessary to increase the extent of through-space conjugation (TSC) and suppress nonradiative decay. Incorporating strong physical interactions such as hydrogen bonding is an effective strategy to achieve this. In this work, we carried out comparative studies on the photoluminescence behaviors of two β-enamino esters with similar chemical structures, namely methyl 3-aminocrotonate (MAC) and methyl (E)-3-(1-pyrrolidinyl)-2-butenoate (MPB). MAC crystal emits blue fluorescence under UV irradiation. The critical cluster concentration of MAC in ethanol solutions was determined by studying the relationship between the photoluminescence intensity (UV–visible absorbance) and concentration. Furthermore, MAC exhibits solvatochromism, and its emission wavelength redshifts as the solvent polarity increases. On the contrary, MPB is non-emissive in both solid state and solutions. Crystal structures and theoretical calculation prove that strong inter- and intramolecular hydrogen bonds lead to the formation of large amounts of TSC of MAC molecules in aggregated states. No hydrogen bonds and thus no effective TSC can be formed between or within MPB molecules, and this is the reason for its non-emissive nature. This work provides a deeper understanding of how hydrogen bonding contributes to the luminescence of NTLs.
A shift in reservoir stratification and mixing significantly affects the water column ecosystem, which in turn leads to changes in phytoplankton abundance and community structure. To explore the ...effects of stratification and mixing on the phytoplankton community structure of a diversion reservoir, a 1-year survey was divided into a stratification period in 2020, a mixing period in 2020, and a stratification period in 2021, and redundancy analysis (RDA), variance partitioning analysis (VPA) and Pearson correlation analysis were used to analyse the key drivers affecting the phytoplankton functional groups, using Xikeng Reservoir as a case study. During the study period, 8 phyla, 69 genera and 9 major functional groups were observed in this reservoir. The dominant functional groups varied significantly, being X1 in the stratified period in 2020; P and D in the mixing period in 2020; and D, X1, and M in the stratified period in 2021. The phytoplankton diversity index was greater in the mixing period than in the stratification period, in agreement with the results of the aquatic ecological status evaluation (Q index, higher in the mixing period than in the stratification period). However, phytoplankton diversity of Xikeng Reservoir was of limited value in assessing the degree of water pollution, so should be considered in combination with the Q index. Water temperature (WT), mixing depth (Zmix), nitrogen-phosphorus ratio (N/P), and total nitrogen (TN) were important drivers of phytoplankton functional group dynamics in different periods. The study provides a valuable reference for assessing the relationship between environmental factors and phytoplankton communities, as well as for the evaluation and conservation of aquatic ecosystems in southern China's water diversion reservoirs.
Multiplexed ion beam imaging (MIBI) has been previously used to profile multiple parameters in two dimensions in single cells within tissue slices. Here, a mathematical and technical framework for ...three-dimensional (3D) subcellular MIBI is presented. Ion-beam tomography (IBT) compiles ion beam images that are acquired iteratively across successive, multiple scans, and later assembled into a 3D format without loss of depth resolution. Algorithmic deconvolution, tailored for ion beams, is then applied to the transformed ion image series, yielding 4-fold enhanced ion beam data cubes. To further generate 3D sub-ion-beam-width precision visuals, isolated ion molecules are localized in the raw ion beam images, creating an approach coined as SILM, secondary ion beam localization microscopy, providing sub-25 nm accuracy in original ion images. Using deep learning, a parameter-free reconstruction method for ion beam tomograms with high accuracy is developed for low-density targets. In cultured cancer cells and tissues, IBT enables accessible visualization of 3D volumetric distributions of genomic regions, RNA transcripts, and protein factors with 5 nm axial resolution using isotope-enrichments and label-free elemental analyses. Multiparameter imaging of subcellular features at near macromolecular resolution is implemented by the IBT tools as a general biocomputation pipeline for imaging mass spectrometry.
In this paper, a polydopamine-graphene composite gel (PDA-GA) was prepared from graphene oxide by a facile in-situ reduction assembly method using ascorbic acid combined with dopamine (DA). The ...morphology and microstructure of PDA-GA were characterized by SEM, XRD, FTIR, BET-BJH, and MIP, and the adsorption behavior of PDA-GA for Cu
2+
was studied. Furthermore, the response ability of graphene composite gel-modified glassy carbon electrode (PDA-GH-GCE) to trace Cu
2+
was investigated by linear sweep anodic stripping voltammetry. Results showed that when the mass ratio of graphene oxide to DA was 1:3, the adsorption effect of PDA-GA for Cu
2+
was the best, and the adsorption capacity reached 316 mg/g. PDA-GA-GCE was sensitive to trace Cu
2+
, and the detection limit could reach 1.6 × 10
−7
mol/L.
Through-bond conjugation (TBC) and/or through-space conjugation (TSC) determine the photophysical properties of organic luminescent compounds. No systematic studies have been carried out to ...understand the transition from aromatic TBC to non-aromatic TSC on the photoluminescence of organic luminescent compounds. In this work, a series of small aromatic and aliphatic aldimines were synthesized. For the aromatic imines, surprisingly,
,1-diphenylmethanimine with the highest TBC is non-emissive, while
-benzyl-1-phenylmethanimine and
-cyclohexyl-1-phenylmethanimine emit bright fluorescence in aggregate states. The aliphatic imines are all emissive, and their maximum emission wavelength decreases while the quantum yield increases with a decrease in steric hindrance. The imines show concentration-dependent and excitation-dependent emissions. Theoretical calculations show that the TBC extents in the aromatic imines are not strong enough to induce photoluminescence in a single molecule state, while the intermolecular TSC becomes dominant for the fluorescence emissions of both aromatic and aliphatic imines in aggregate states, and the configurations and spatial conformations of the molecules in aggregate states play a key role in the formation of effective TSC. This study provides an understanding of how chemical and spatial structures affect the formation of TBC and TSC and their functions on the photoluminescence of organic luminescent materials.
Highly multiplexed protein imaging is emerging as a potent technique for analyzing protein distribution within cells and tissues in their native context. However, existing cell annotation methods ...utilizing high-plex spatial proteomics data are resource intensive and necessitate iterative expert input, thereby constraining their scalability and practicality for extensive datasets. We introduce MAPS (Machine learning for Analysis of Proteomics in Spatial biology), a machine learning approach facilitating rapid and precise cell type identification with human-level accuracy from spatial proteomics data. Validated on multiple in-house and publicly available MIBI and CODEX datasets, MAPS outperforms current annotation techniques in terms of speed and accuracy, achieving pathologist-level precision even for typically challenging cell types, including tumor cells of immune origin. By democratizing rapidly deployable and scalable machine learning annotation, MAPS holds significant potential to expedite advances in tissue biology and disease comprehension.
Photoluminescence (PL) mechanisms of nontraditional luminogens (NTLs) have attracted great interest, and they are generally explained with intra/intermolecular through‐space conjugation (TSC) of ...nonconventional chromophores. Here a new concept of nonaromatic through‐bond conjugation (TBC) is proposed and it is proved that it plays an important role in the PL of NTLs. The PL behaviors of the three respective isomers of cyclohexanedione and gemdimethyl‐1,3‐cyclohexanedione were studied and correlated with their chemical and aggregate structures. These compounds show different fluorescence emissions as well as different concentration, excitation and solvent‐dependent emissions. The compounds which undergo keto‐enol tautomerism and hence with a conjugated ketone‐enol structure (i.e., nonaromatic TBC) show more red‐shifted emissions. TBC effect reduces the energy gaps and facilitates the formation of stronger TSC in the aggregate state. The compounds in the ketone‐enol form are also prone to occur excited state intra/intermolecular proton transfer (ESIPT). The cooperative effect of nonaromatic TBC and TSC determines the PL behaviors of NTLs. This work provides a novel understanding of the PL mechanisms of NTLs and is of great importance for directing the design and synthesis of novel NTLs.
A novel concept of nonaromatic through‐bond conjugation (TBC) is proposed and it is proven to play an important role in the photoluminescence of nontraditional luminogens by studying the relationship between the photophysical properties of the isomers of cyclohexanedione and dimethyl‐1,3‐cyclohexanedione and their chemical structures, aggregate structures and interactions.
This work is aimed to report a new type of multiple stimuli-responsive supramolecular polymers by combining dynamic covalent bonds with cucurbit8uril (CB8)-based host–guest interaction. Supramonomer ...(DSN) containing a disulfide bond can bind with CB8 to fabricate supramolecular polymers by host-enhanced π–π interaction. Additionally, the dynamic nature of disulfide bonds and host–guest chemistry endow these supramolecular polymers with redox and guest competitive responsiveness, respectively.
PDF
