Single Live Cells Research Articles

Decoding the interplay between m6A modification and stress granule stability by live-cell imaging.

N6-methyladenosine (m6A)-modified mRNAs and their cytoplasmic reader YTHDFs are colocalized with stress granules (SGs) under stress conditions, but the interplay between m6A modification and SG stability remains unclear. Here, we presented a spatiotemporal m6A imaging system (SMIS) that can monitor the m6A modification and the translation of mRNAs with high specificity and sensitivity in a single live cell. SMIS showed that m6A-modified reporter mRNAs dynamically enriched into SGs under arsenite stress and gradually partitioned into the cytosol as SG disassembled. SMIS revealed that knockdown of YTHDF2 contributed to SG disassembly, resulting in the fast redistribution of mRNAs from SGs and rapid recovery of stalled translation. The mechanism is that YTHDF2 can regulate SG stability through the interaction with G3BP1 in m6A-modified RNA-dependent manner. Our results suggest a mechanism for the interplay between m6A modification and SG through YTHDF2 regulation.

Lensless On-Chip Chemiluminescence Imaging for High-Throughput Single-Cell Heterogeneity Analysis.

High-throughput single-cell heterogeneity imaging and analysis is essential for understanding complex biological systems and for advancing personalized precision disease diagnosis and treatment. Here, we present a miniaturized lensless chemiluminescence chip for high-throughput single-cell functional imaging with subcellular resolution. With the sensitive chemiluminescence sensing and wide field of view of contact lensless imaging, we demonstrated the chemiluminescent imaging of over 1000 single cells, and their membrane glycoprotein and the high-throughput single-cell heterogeneity of membrane protein imaging were examined for precision analysis. Furthermore, the functional adhesion and heterogeneity of single live cells were imaged and explored. This miniaturized lensless on-chip CL-CMOS imaging platform enables high-throughput single-cell imaging and analysis with high sensitivity and subcellular resolution, providing new techniques for the cellular study of biological heterogeneity and has potential application in precision disease diagnosis and treatment at the point-of-care settings.

Repeated FRAP of the actin-binding protein CapG in the cell nucleus—a functional assay for EGF signaling in the single live breast cancer cell

Compartmentalization and differential distribution of proteins within a cell maintain cellular function and viability. CapG is a gelsolin-related actin-binding protein that distributes in steady state diffusively throughout cytoplasm and cell nucleus. To detect changes in CapG’s nucleocytoplasmic shuttling in response to external stimuli on the single cell level, we established repeated FRAP experiments of one and the same breast cancer cell. With this experimental set up, we found that ATP-depletion reversibly decreased CapG’s shuttling into the cell nucleus. The addition of epidermal growth factor (EGF) increased CapG’s nuclear shuttling within minutes. Serum-starvation doubled the number of breast cancer cells from 40 to 80% displaying increased CapG shuttling in response to EGF. Testing five different potential CapG phosphorylation sites, we found that serine 70 mediates the increase in CapG’s nuclear shuttling triggered by EGF. Thus, repeated FRAP of CapG in the cell nucleus can be used as functional readout of signaling cascades in the same single live breast cancer cell.

Enabling high-sensitivity live single-cell mass spectrometry using an integrated electrical lysis and nano electrospray ionization interface

BackgroundLive single-cell metabolomic studies encounter inherent difficulties attributed to the limited sample volume, minimal compound quantity, and insufficient sensitivity in the Mass Spectrometry (MS) method used to obtain single-cell data. However, understanding cellular heterogeneity, functional diversity, and metabolic processes within individual cells is essential. Exploring how individual cells respond to stimuli, including drugs, environmental changes, or signaling molecules, offers insights into biology, oncology, and drug discovery. Efficient release of cell contents (lysis) is vital for accurate metabolite detection at the single-cell level. Despite this, traditional approaches in live single cell metabolomics methods do not emphasize efficient lysis to prevent sample dilution. Instead, current live single cell metabolomics methods use direct infusion to introduce the cell into the mass spectrometry without prior chromatographic separation or a lysis step, which adversely affects sensitivity and metabolic coverage. ResultsTo address this, we developed an integrated single-cell electrical lysis and nano spray (SCEL-nS) platform coupled to an Orbitrap MS capable of efficiently lysing a single cell after being sampled with specially manufactured micropipettes. Lysis efficiency was validated by comparing live cell stain fluorescent intensities of intact and electrically lysed cells through microscopy imaging. The SCEL-nS platform successfully induced the breakdown of a single cell, significantly reducing the live cell stain's fluorescent intensity indicating cell membrane breakdown. Additionally, SCEL-nS was validated by measuring single cells spiked with the anti-cancer drug tamoxifen by MS. SCEL-nS use resulted in statistically significant increase in the peak measured by the method compared to the traditional non-lysis method. SignificanceOverall, our results demonstrate that the newly incorporated SCEL-nS platform achieved higher sensitivities compared to traditional live single cell analysis methods.

Comprehensive Characterization of Islet Remodeling in Development and in Diabetes Using Mass Cytometry.

The pancreatic islet is the functional and structural unit of the pancreatic endocrine portion. Islet remodeling occurs in both normal development and pathogenesis of type 1 (T1D) and type 2 diabetes (T2D). However, accurately quantifying changes in islet cellular makeup and hormone expressions poses significant challenges due to large intra- and inter-donor heterogeneity and the limited scalability of traditional methods such as immunostaining. The cytometry by time-of-flight (CyTOF) technology enables simultaneous quantification of more than 30 protein markers at single-cell resolution in a high-throughput fashion. Moreover, with distinct DNA and viability markers, single live cells can be explicitly selected in CyTOF. Here, leveraging the CyTOF data generated by the Human Pancreas Analysis Program, we characterized more than 12 million islet cells from 71 donors. Our data revealed continued age-related changes in islet endocrine cell compositions, but the maturity of endocrine cells is reached by 3 years of age. We also observed significant changes in beta cell numbers and key protein expressions, along with a significant increase in bihormonal cells in T1D donors. In contrast, T2D donors exhibited minimal islet remodeling events. Our data shine a light on the islet dynamics during development and diabetes pathogenesis and suggest divergent pathogenesis processes of T1D and T2D. Our comprehensive approach not only elucidates islet plasticity but also establishes a foundation for integrated CyTOF analysis in islet biology and beyond.

Quality and Quantity Control of Mitochondria Injection Into Single Cells With Robot-Aided Micro-Manipulation System

Mitochondrial dysfunction plays a significant role in the development of fatal diseases such as aging, cancer, and Alzheimer’s. Transferring mitochondria to cells is a new and potential treatment for mitochondrial DNA (mtDNA)-related illnesses. This article describes a novel technique to control the quality and quantity of mitochondria injected into single live cells using a robot-aided microneedle and optical tweezers (OTs)-based micromanipulation system. Isolated mitochondria and cells are patterned in a 1-dimensional (1-D) array in a microfluidic device, and a robot-aided microneedle collects the predefined number of functional mitochondria with the help of OTs. Then, the microneedle precisely and non-invasively injects these collected mitochondria into single live cells. Given that the two manipulation tools of OTs and microneedle were used, a switch controller strategy is developed to enable mitochondria trapping and injection with OTs and microneedle-based micromanipulator, respectively. The effectiveness of the developed robotic system is experimentally demonstrated with automated injections of isolated mitochondria into HeLa and mesenchymal stem cells (aMSCs). A precise and efficient quality and quantity control of mitochondria injection was possible by using Ots in conjunction with microneedle and microfluidics technologies. Quality-and quantity-controlled ability is analyzed and compared with the traditional mitochondria transfer method (co-culture). Biological tests are further conducted to assess the viability of mitochondria recipient cells. Experimental results demonstrate that the developed system can non-invasively transfer healthy mitochondria into single live cells while precisely controlling the quantity and quality of injected mitochondria. The proposed mitochondrial transfer method has the potential to advance precision medicine methods, particularly for cellular therapy of (mtDNA)-related diseases. <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Note to Practitioners</i> —This study was motivated by the problem of inefficient methods of mitochondria injection into single, small, living cells. Due to the issue of microneedle clogging, existing mitochondria injection methods can only inject mitochondria into cells with a 0.3 to 2% efficiency. To address this issue, we have developed an automated method of mitochondria injection into cells that can inject mitochondria into single cells non-invasively with an efficiency of up to 80 %. Existing methods of mitochondria injection also ignored the heterogeneity of mitochondria, such as functionality and the precise number of mitochondria prior to injection. Our methodology can efficiently and precisely control the quality and quantity of mitochondria injection into single cells, which can be useful for the discovery of new information concerning precision medicine, particularly in diseases associated with mtDNA.

Single Living Cell "Observation-Analysis" Integrated Platform Decodes Cell Migration Plasticity Orchestrated by Nucleocytoplasmic STAT3.

Cell migration requires the interplay among diverse migration patterns. The molecular basis of distinct migration programs is undoubtedly vital but not fully explored. Meanwhile, the lack of tools for investigating spontaneous migratory plasticity in a single living cell also adds to the hindrance. Here, we developed a micro/nanotechnology-enabled single-cell analytical platform to achieve coherent monitoring of spontaneous migratory pattern and signaling molecules. Via the platform, we unveiled a previously unappreciated STAT3 regionalization on the multifunctional regulations of migration. Specifically, nuclear STAT3 is associated with amoeboid migration, while cytoplasmic STAT3 promotes mesenchymal movement. Opposing effects of JAK2 multisite phosphorylation shape its response to STAT3 distribution in a dynamic and antagonistic manner, eventually triggering a reversible amoeboid-mesenchymal transition. Based on the above results, bioinformatics further revealed a possible downstream regulator of nucleocytoplasmic STAT3. Thus, our platform, as an exciting technological advance in single-cell migration research, can provide in-depth mechanism interpretations of tumor metastasis and progression.

A Bioorthogonal Dual Fluorogenic Probe for the Live‐Cell Monitoring of Nutrient Uptake by Mammalian Cells

AbstractCells rely heavily on the uptake of exogenous nutrients for survival, growth, and differentiation. Yet quantifying the uptake of small molecule nutrients at the single cell level is difficult. Here we present a new approach to studying the nutrient uptake in live single cells using Inverse Electron‐Demand Diels Alder (IEDDA) chemistry. We have modified carboxyfluorescein‐diacetate‐succinimidyl esters (CFSE)—a quenched fluorophore that can covalently react with proteins and is only turned on in the cytosol of a cell following esterase activity—with a tetrazine. This tetrazine serves as a second quencher for the pendant fluorophore. Upon reaction with nutrients modified with an electron‐rich or strained dienophile in an IEDDA reaction, this quenching group is destroyed, thereby enabling the probe to fluoresce. This has allowed us to monitor the uptake of a variety of dienophile‐containing nutrients in live primary immune cell populations using flow cytometry and live‐cell microscopy.

A Bioorthogonal Dual Fluorogenic Probe for the Live-Cell Monitoring of Nutrient Uptake by Mammalian Cells.

Cells rely heavily on the uptake of exogenous nutrients for survival, growth, and differentiation. Yet quantifying the uptake of small molecule nutrients at the single cell level is difficult. Here we present a new approach to studying the nutrient uptake in live single cells using Inverse Electron-Demand Diels Alder (IEDDA) chemistry. We have modified carboxyfluorescein-diacetate-succinimidyl esters (CFSE)-a quenched fluorophore that can covalently react with proteins and is only turned on in the cytosol of a cell following esterase activity-with a tetrazine. This tetrazine serves as a second quencher for the pendant fluorophore. Upon reaction with nutrients modified with an electron-rich or strained dienophile in an IEDDA reaction, this quenching group is destroyed, thereby enabling the probe to fluoresce. This has allowed us to monitor the uptake of a variety of dienophile-containing nutrients in live primary immune cell populations using flow cytometry and live-cell microscopy.

Lineage-specific CDK activity dynamics characterize early mammalian development.

Cyclin-dependent kinases (CDK) are key regulatory enzymes that regulate proliferation dynamics and cell fate in response to extracellular inputs. It remains largely unknown how CDK activity fluctuates and influences cell commitment in vivo during early mammalian development. Here, we generated a transgenic mouse model expressing a CDK kinase translocation reporter (KTR) that enabled quantification of CDK activity in live single cells. By examining pre- and post-implantation mouse embryos at different stages, we observed a progressive decrease in CDK activity in cells from the trophectoderm (TE) prior to implantation. This drop correlated with the establishment of an FGF4-dependent signaling gradient through the embryonic-abembryonic axis. Furthermore, we showed that CDK activity levels do not determine cell fate decisions during pre-implantation development. Finally, we uncovered the existence of conserved regulatory mechanisms in mammals by revealing lineage-specific regulation of CDK activity in TE-like human cells.

Bioprobe-RNA-seq-microRaman system for deep tracking of the live single-cell metabolic pathway chemometrics

The integration between RNA-sequencing and micro-spectroscopic techniques has recently profiled the advanced transcriptomic discoveries on the cellular level. In the current study, by combining the sensation approach (including bio-molecules structural evaluation, high throughput next-generation sequencing (HT-NGS), and confocal Raman microscopy) the functionality on the single live cancer cells’ ferroptosis and apoptosis signaling pathways is visualized. Our study reveals a hydrophobic tunnel by phycocyanin-isoprene molecule (PC-SIM) electrostatic charge within hepatoma cells (HepG2) that activates the ferritin light chain (FTL) and caspase-8 associate protein (CASP8AP2) ferroptosis responsible genes. Moreover, this research proves that PC-vanillin (VAN) stimulation induces the actin-binding factor profilin-1 (PFN1), subsequently in situ tracking its expression at 1139.75 cm−1 microRaman wavenumber. While PC-thymol (THY) induces the lysophospholipase-2 (LYPLA2) (p-value = 0.009) and acetylneuraminate-9-O-acetyltransferase (CASD1) (p-value = 0.022) at 1143.19 cm−1. Our findings establish a new concept to promote the cross-disciplinary use of instant cellular-based detection technology for intermediary evaluating the signaling cellular transcriptome.

Single-cell RNA sequencing analysis of the human fetal epicardium reveals several new genes involved in regulation of epicardial activation

Abstract Funding Acknowledgements Type of funding sources: Foundation. Main funding source(s): Dutch Heart Foundation Background The outside mesothelial layer of the heart, the epicardium, is essential for cardiac development. Cells from this layer undergo epithelial-to-mesenchymal transition (EMT), migrate into the tissue and partake in cardiogenesis by contributing cells and by secreting growth factors. In the adult heart, the epicardium is quiescent but upon ischemic injury it is activated and conveys a partial regenerative response. This activation step is important for repair, but suboptimal compared to the cardiogenic potential during development. Understanding the processes and cells that underlie developmental epicardial activation could contribute to enhancing the adult post-injury response, but little is known about the human developing epicardium. Purpose to determine the cellular composition of the human fetal epicardial layer and to identify the processes that regulate the activation of the epicardium. Methods An epicardial-cell enriched dataset was obtained by specifically dissecting the epicardial layers from 4 fetal human hearts (14-15 weeks gestation, obtained under informed consent and according to local ethical approval). Single live cells were sorted into 384-wells plates and sequenced. Data analysis was performed on 2073 cells using R-packages RaceID3 and StemID2. Findings were validated using qPCR and immunohistochemistry on tissue sections and cell culture models. Results Sequencing analysis revealed a distinct clustering of epicardial (epithelial, pre-EMT) and epicardial-derived mesenchymal (post-EMT) cell populations. Besides the identification of novel markers for epicardial cell states, the regulation of epicardial cell activation and EMT was investigated by applying pseudo-time analysis. We selected genes that were highly regulated (&amp;gt;2 fold change) in this trajectory for further analysis in vitro. We identified several genes including CRIP1, SULF1 and others that are expressed in epithelial cells in vitro and in vivo and are rapidly downregulated upon EMT. The expression profiles positively correlated with epithelial cell related genes and negatively with mesenchymal cell genes. Based on GO-terms, and protein expression within the epicardial layers in fetal and adult epicardium, we anticipated a role for these genes in maintaining the epithelial-state. Indeed, siRNA experiments in vitro with cultured primary human epicardial cells confirmed an essential role in EMT regulation. We continue to evaluate other genes identified in our sequencing dataset, resulting in several other potent and previously unknown pathways involved in regulation of epicardial activation. Conclusions We shed light on the composition of the human fetal epicardium using a highly enriched scRNA dataset. We identify specific markers for different cell-states, and reveal novel regulators of activation that in the future may be influenced to optimize the post-injury response.

Effects of nanoparticles on sensitivity to injury and role of autophagy in alveolar epithelial cells

Autophagy, a housekeeping mechanism, is crucial in the maintenance of normal cellular function. Although the involvement of autophagic processes is recognized in numerous diseases, it is unknown how cellular homeostasis might be affected by alterations in available autophagic activity and/or autophagic capacity. In this study, we measured autophagic flux and cellular damage in primary cultured monolayers of rat alveolar epithelial cells (AEC) exposed separately and sequentially to two different autophagy inducers. Rat AEC monolayers were exposed apically for 24 hrs to (1) polystyrene nanoparticles (PNP, 20 nm, carboxylated, near-infrared dye-labeled), (2) tunicamycin (TN, a disruptor of protein synthesis and inducer of the unfolded protein response, at 1-15 μg/mL), or (3) TN (1-15 μg/mL) after 12 hrs of PNP pre-incubation. Release of the cytoplasmic enzyme lactate dehydrogenase (LDH) was used as an indicator of cellular damage and quantified by an LDH assay from Dojindo (Rockville, MD). Autophagic flux was assessed by live cell imaging using confocal microscopy and 0.1 μM DAPRed (Dojindo; Rockville, MD) in the presence (for 1 hr) and absence of 40 μM chloroquine. Serial z sections were collected over the entire cell volume of live single cells to detect DAPRed (autophagosome) fluorescence. PNP were taken up into AEC, where their cytosolic presence induced a gradually increased autophagic flux, reaching a steady state at ~10-24 hrs. When AEC were exposed to TN alone for 24 hrs, autophagy was also activated. Cellular damage in the presence of TN, determined by increased LDH release, revealed dose-dependent injury with LD50 of 8.12 μg/mL over 24 hr TN exposure. When AEC were pre-exposed to PNP for 12 hrs and subsequently exposed to TN, increased LDH release was seen with LD50 of 3.95 μg/mL. In summary, the intracellular presence of PNP taken up from apical fluid of rat AEC monolayers activated autophagy. When cellular protein synthesis was disrupted with TN alone, autophagy was also activated. Furthermore, TN induced dose-dependent cellular damage in AEC. However, after pre-exposure to PNP, TN induced greater cellular damage observed as increased LDH release. These results suggest that autophagic capacity is limited and that pre-induction of autophagy by inhaled PNP makes AEC more susceptible to secondary injury by TN. These findings are consistent with the hypothesis that environmental stressors (e.g., ambient air nanoparticles) exert their harmful effects, at least in part, by reducing available autophagic activity/capacity, thereby causing nanoparticle-exposed AEC to be more susceptible to secondary injury. Funding: NIH; WRMPPF. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Abstract 145: Chronic Electronic Cigarette Exposure Accelerates SMC Phenotypic Modulation And Activates The NMDA-type Glutamate Receptor (NMDAR) Pathway In Mediating Vascular Calcification

Introduction: Electronic cigarettes pose a serious emerging threat to cardiovascular health. The use of electronic nicotine delivery systems (ENDS) such as electronic cigarettes (e-cigs) have increased exponentially, especially among adolescents. Emerging data suggest e-cig use has been implicated in promoting atherosclerosis. This work explores the mechanism of e-cig exposure accelerated the atherosclerotic lesion development and vascular remodeling. Methods: SMC-lineage tracing mice (n=16) on a ApoE null hyperlipidemic background were put on high fat diet for 12 weeks and exposed to pod-based e-cigs (Juul) three times a week for 12 weeks in a whole-body chamber (inExpose, Scireq) and compared to WT mice exposed to air (n=16). The aortic sinus was dissected and digested, FACS was performed to sort for live single cells, then single-cell RNA-Seq (sc-RNAseq) and ATAC-seq were performed on the 10X Genomics platform. Analyses were completed with Seurat and Signac tools. The osteogenic load was assessed by histology with alkaline phosphatase (AP) enzymatic assay using the Ferangi Blue Chromogen kit. Results: scRNA-Seq analysis revealed that e-cig accelerated the SMC transition to a chondrogenic phenotype (CMC). We found a significantly increased proportion of chondromyocytes (CMC) expressing specific markers such as Col2a1 and Acan in the e-cig exposed mice compared to control. The scATAC-seq profiles showed that e-cig exposed mice develop a cell cluster that enriched for markers related to nicotine, glutamatergic and dopaminergic pathways. The genes highly enriched for chromatin accessibility in this cluster included Grin2a , a gene that encodes a N-methyl-D-aspartate receptor (NMDAR) GluN2A, which was found to be expressed in the fibromyocyte and CMC population of the scRNA-seq. Consistent with our finding from the scRNA-Seq data showing a greater CMC proportion in the e-cig exposed mice, we found the relative AP-stained area to be larger in the exposed group than in the WT group. Conclusion: Overall, these data indicate that e-cig exposure can promote atherosclerosis through adverse SMC phenotypic modulation. Moreover, e-cig exposure induces NMDAR activation that may be implicated in SMC modulation to a chondrogenic phenotype.

Comparative single-cell multiplex immunophenotyping of therapy-naive patients with rheumatoid arthritis, systemic sclerosis, and systemic lupus erythematosus shed light on disease-specific composition of the peripheral immune system.

Systemic autoimmune diseases (SADs) are a significant burden on the healthcare system. Understanding the complexity of the peripheral immunophenotype in SADs may facilitate the differential diagnosis and identification of potential therapeutic targets. Single-cell mass cytometric immunophenotyping was performed on peripheral blood mononuclear cells (PBMCs) from healthy controls (HCs) and therapy-naive patients with rheumatoid arthritis (RA), progressive systemic sclerosis (SSc), and systemic lupus erythematosus (SLE). Immunophenotyping was performed on 15,387,165 CD45+ live single cells from 52 participants (13cases/group), using an antibody panel to detect 34 markers. Using the t-SNE (t-distributed stochastic neighbor embedding) algorithm, the following 17 main immune cell types were determined: CD4+/CD57- T cells, CD4+/CD57+ T cells, CD8+/CD161- T cells, CD8+/CD161+/CD28+ T cells, CD8dim T cells, CD3+/CD4-/CD8- T cells, TCRγ/δ T cells, CD4+ NKT cells, CD8+ NKT cells, classic NK cells, CD56dim/CD98dim cells, B cells, plasmablasts, monocytes, CD11cdim/CD172dim cells, myeloid dendritic cells (mDCs), and plasmacytoid dendritic cells (pDCs). Seven of the 17 main cell types exhibited statistically significant frequencies in the investigated groups. The expression levels of the 34 markers in the main populations were compared between HCs and SADs. In summary, 59 scatter plots showed significant differences in the expression intensities between at least two groups. Next, each immune cell population was divided into subpopulations (metaclusters) using the FlowSOM (self-organizing map) algorithm. Finally, 121 metaclusters (MCs) of the 10 main immune cell populations were found to have significant differences to classify diseases. The single-cell T-cell heterogeneity represented 64MCs based on the expression of 34 markers, and the frequency of 23 MCs differed significantly between at least twoconditions. The CD3- non-T-cell compartment contained 57 MCs with 17 MCs differentiating at least two investigated groups. In summary, we are the first to demonstrate the complexity of the immunophenotype of34markers over 15 million single cells in HCs vs. therapy-naive patients withRA, SSc, and SLE. Disease specific population frequencies or expression patterns of peripheral immune cells provide a single-cell data resource to the scientific community.

Surface‐enhanced Raman scattering spatial fingerprinting decodes the digestion behavior of lysosomes in live single cells

AbstractLysosome, the digestive organelle in eukaryotic cells, plays an important role in the degradation and recirculation of cellular products as well as in maintaining the stability of cellular metabolic microenvironment. Surface‐enhanced Raman scattering (SERS) is a molecular fingerprint technology with high detection sensitivity and photostability, suited for revealing various intracellular molecular information by inducing endocytosis of SERS‐active nanoparticles. However, it remains challenging to selectively extract the molecular information of specific organelles (e.g., lysosomes) from a high‐dimensional spectral set. Herein, we proposed a novel paradigm by combining label‐free SERS spectroscopy with confocal fluorescence imaging to investigate the digestion behavior of lysosomes in cells. The structural similarity algorithm was innovatively introduced and exhibited its effectiveness in screening out the wavenumbers in the SERS spectral set with high correlation with the metabolic behaviors of lysosomes. With comprehensive experiments on HeLa single cells, we captured the intracellular macromolecular digestion phenomenon and discovered the changing pattern of cellular SERS spectra after starvation‐induced autophagy, and analyzed the molecular information within the lysosomes in three‐dimensional space.

Unveiling the Spatiotemporal and Dose Responses within a Single Live Cancer Cell to Photoswitchable Upconversion Nanoparticle Therapeutics Using Hybrid Hyperspectral Stimulated Raman Scattering and Transient Absorption Microscopy.

Photodynamic therapy (PDT) provides an alternative approach to targeted cancer treatment, but the therapeutic mechanism of advanced nanodrugs applied to live cells and tissue is still not well understood. Herein, we employ the hybrid hyperspectral stimulated Raman scattering (SRS) and transient absorption (TA) microscopy developed for real-time in vivo visualization of the dynamic interplay between the unique photoswichable lanthanide-doped upconversion nanoparticle-conjugated rose bengal and triphenylphosphonium (LD-UCNP@CS-Rb-TPP) probe synthesized and live cancer cells. The Langmuir pharmacokinetic model associated with SRS/TA imaging is built to quantitatively track the uptakes and pharmacokinetics of LD-UCNP@CS-Rb-TPP within cancer cells. Rapid SRS/TA imaging quantifies the endocytic internalization rates of the LD-UCNP@CS-Rb-TPP probe in individual HeLa cells, and the translocation of LD-UCNP@CS-Rb-TPP from mitochondria to cell nuclei monitored during PDT can be associated with mitochondria fragmentations and the increased nuclear membrane permeability, cascading the dual organelle ablations in cancer cells. The real-time SRS spectral changes of cellular components (e.g., proteins, lipids, and DNA) observed reflect the PDT-induced oxidative damage and the dose-dependent death pattern within a single live cancer cell, thereby facilitating the real-time screening of optimal light dose and illumination duration controls in PDT. This study provides new insights into the further understanding of drug delivery and therapeutic mechanisms of photoswitchable LD-UCNP nanomedicine in live cancer cells, which are critical in the optimization of nanodrug formulations and development of precision cancer treatment in PDT.

On-chip Raman spectroscopy of live single cells for the staging of oesophageal adenocarcinoma progression.

The absence of early diagnosis contributes to oesophageal cancer being the sixth most common cause of global cancer-associated deaths, with a 5-year survival rate of < 20%. Barrett's oesophagus is the main pre-cancerous condition to adenocarcinoma development, characterised by the morphological transition of oesophageal squamous epithelium to metaplastic columnar epithelium. Early tracking and treatment of oesophageal adenocarcinoma could dramatically improve with diagnosis and monitoring of patients with Barrett's Oesophagus. Current diagnostic methods involve invasive techniques such as endoscopies and, with only a few identified biomarkers of disease progression, the detection of oesophageal adenocarcinoma is costly and challenging. In this work, single-cell Raman spectroscopy was combined with microfluidic techniques to characterise the development of oesophageal adenocarcinoma through the progression of healthy epithelial, Barrett's oesophagus and oesophageal adenocarcinoma cell lines. Principal component analysis and linear discriminant analysis were used to classify the different stages of cancer progression. with the ability to differentiate between healthy and cancerous cells with an accuracy of 97%. Whilst the approach could also separate the dysplastic stages from healthy or cancer with high accuracy-the intra-class separation was approximately 68%. Overall, these results highlight the potential for rapid and reliable diagnostic/prognostic screening of Barrett's Oesophagus patients.

Real-Time Autophagic Flux Measurements in Live Cells Using a Novel Fluorescent Marker DAPRed.

Autophagy is a conserved homeostatic mechanism involved in cellular homeostasis and many disease processes. Although it was first described in yeast cells undergoing starvation, we have learned over the years that autophagy gets activated in many stress conditions and during development and aging in mammalian cells. Understanding the fundamental mechanisms underlying autophagy effects can bring us closer to better insights into the pathogenesis of many disease conditions (e.g., cardiac muscle necrosis, Alzheimer's disease, and chronic lung injury). Due to the complex and dynamic nature of the autophagic processes, many different techniques (e.g., western blotting, fluorescent labeling, and genetic modifications of key autophagy proteins) have been developed to delineate autophagy effects. Although these methods are valid, they are not well suited for the assessment of time-dependent autophagy kinetics. Here, we describe a novel approach: the use of DAPRed for autophagic flux measurement via live cell imaging, utilizing A549 cells, that can visualize and quantify autophagic flux in real time in single live cells. This approach is relatively straightforward in comparison to other experimental procedures and should be applicable to any in vitro cell/tissue models. Key features • Allows real-time qualitative imaging of autophagic flux at single-cell level. • Primary cells and cell lines can also be utilized with this technique. • Use of confocal microscopy allows visualization of autophagy without disturbing cellular functions.

Single Cell Isolation from Human Diabetic Fibrovascular Membranes for Single-Cell RNA Sequencing.

Single-cell transcriptomic analyses have emerged as very powerful tools to query the gene expression changes at the single-cell level in physiological and pathological conditions. The quality of the analysis is heavily dependent on tissue digestion protocols, with the goal of preserving thousands of single live cells to submit to the subsequent processing steps and analysis. Multiple digestion protocols that use different enzymes to digest the tissues have been described. Harsh digestion can damage certain cell types, but this might be required to digest especially fibrotic tissue as in our experimental condition. In this paper, we summarize a collagenase type I digestion protocol for preparing the single-cell suspension from fibrovascular tissues surgically removed from patients with proliferative diabetic retinopathy (PDR) for single-cell RNA sequencing (scRNA-Seq) analyses. We also provide a detailed description of the data analysis that we implemented in a previously published study. Key features • Single-cell suspension from fibrovascular membranes isolated from PDR patients. • Single-cell RNA sequencing analyses performed using Seurat package in RStudio. • Trajectory analyses or pseudotime analyses to study the trajectory over (pseudo)time of specific cell types. • This protocol requires Illumina HiSEQ4000 instrument and knowledge of R and RStudio language for the analyses.