Single-cell Imaging Analysis Research Articles

High-multiplex single-cell imaging analysis reveals tumor immune contexture associated with clinical outcomes after CAR T cell therapy

Chimeric antigen receptor (CAR) T-cell therapy has made great progress in treating lymphoma, yet patient outcomes still vary greatly. The lymphoma microenvironment may be an important factor in the efficacy of CAR T therapy. In this study, we designed a highly multiplexed imaging mass cytometry (IMC) panel to simultaneously quantify 31 biomarkers from 13 patients with relapsed/refractory DLBCL who received CAR19/22 T-cell therapy. A total of twenty sections were sampled before CAR T-cell infusion or after infusion when relapse occurred. 35 cell clusters were identified, annotated and subsequently redefined into 10 metaclusters. The CD4+ T-cell fraction was positively associated with remission duration. Significantly higher Ki67, CD57, and TIM3 levels and lower CD69 levels on T cells, especially the CD8+/CD4+ Tem and Te cell subsets, were seen in patients with poor outcomes. Cellular neighborhood containing more immune cells was associated with longer remission. Fibroblasts and vascular endothelial cells resided much closer to tumor cells in patients with poor response and short remission after CAR T therapy. Our work comprehensively and systematically dissects the relationship between cell composition, state, and spatial arrangement in the DLBCL microenvironment and the outcomes of CAR T-cell therapy, which is beneficial to predict CAR T therapy efficacy.

A fast-acting lipid checkpoint in G1 prevents mitotic defects

Lipid synthesis increases during the cell cycle to ensure sufficient membrane mass, but how insufficient synthesis restricts cell-cycle entry is not understood. Here, we identify a lipid checkpoint in G1 phase of the mammalian cell cycle by using live single-cell imaging, lipidome, and transcriptome analysis of a non-transformed cell. We show that synthesis of fatty acids in G1 not only increases lipid mass but extensively shifts the lipid composition to unsaturated phospholipids and neutral lipids. Strikingly, acute lowering of lipid synthesis rapidly activates the PERK/ATF4 endoplasmic reticulum (ER) stress pathway that blocks cell-cycle entry by increasing p21 levels, decreasing Cyclin D levels, and suppressing Retinoblastoma protein phosphorylation. Together, our study identifies a rapid anticipatory ER lipid checkpoint in G1 that prevents cells from starting the cell cycle as long as lipid synthesis is low, thereby preventing mitotic defects, which are triggered by low lipid synthesis much later in mitosis.

Deep Learning-Based 3D Single-Cell Imaging Analysis Pipeline Enables Quantification of Cell-Cell Interaction Dynamics in the Tumor Microenvironment.

A 3D single-cell imaging pipeline that quantifies cancer cell interaction dynamics with other TME cell types using primary patient-derived samples can elucidate how cell-cell interactions impact tumor behavior and treatment responses.

Abstract 1844: Development of a high content screening (HCS) platform for novel cancer immunotherapeutics

Abstract There has been dramatic progress in the understanding of fundamental causes of cancer, giving rise to novel treatments which harness the power of the immune system to combat cancer progression. Despite this, no two cancers have the same pathogenesis and there is significant variation in patient response rates. Understanding mechanisms of carcinogenesis in model cell culture systems, such as aberrant signaling, as well as how tumor immunity can be initiated, retargeted or reinvigorated upon incorporation of the immune system will fuel drug discovery. High-Content Screening (HCS) platforms allow single-cell imaging analysis and are used to interrogate these models to enable drug development and understand mechanisms of action. They provide an opportunity to test novel cancer therapeutics in a translationally relevant setting that integrates primary immune effector function. Here we outline several macrophage-based HCS assays which allow assessment of therapeutics targeting;1) early aspects of immune cell activation 2) macrophage mitochondrial health 3) macrophage activation and re-polarization 4) immune cell infiltration and tumor killing. To test efficacy of drugs targeting immune signaling or activation, macrophages were treated with a canonical NF-ƙB activator +/- TCPA-1, a known inhibitor for benchmarking as a model therapeutic. Robust NF-ƙB translocation was observed and reduced in the presence of TCPA-1 rendering this an appropriate assay to screen therapeutic cytokines or TLR agonists activating NF-ƙB signaling. A macrophage inflammasome activation assay was developed to analyze levels of ASC and speck formation. CRID3i, an established inflammasome inhibitor was validated as a robust control therapeutic that prevented NLRP3 activation suggesting this is a relevant platform to assess cancer drug efficacy. Interrogating mitochondrial health and dynamics in primary macrophages is vital to understanding the impact of accumulating ROS species or metabolites in the tumor microenvironment. Assays modelling the effects of these molecules on macrophage polarization and activation as well as mitochondrial integrity were used to test macrophage repolarizing therapeutics, a key approach in immuno-oncology. Finally, a complex multi-cellular 3D spheroid tumor killing assay was optimized to model immune cell infiltration following exposure to IO-targeted therapeutics and robust enhancement of tumor killing was directly observed. Overall, these assays demonstrate the power of imaging in performing HCS to assess the efficacy and mechanisms of action of a range of IO-targeted therapeutics. This suite of assays is applicable to IO drug screens targeting macrophage function, immune cell activation and immune cell infiltration. Citation Format: Rebecca Roberts, Henry Leonard, Ilona Aylott, Douglas Best, Dan Rocca, Ben Thompson, Nunan Robert, Louise Brackenbury. Development of a high content screening (HCS) platform for novel cancer immunotherapeutics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1844.

In Vivo ETosis of Human Eosinophils: The Ultrastructural Signature Captured by TEM in Eosinophilic Diseases.

Eosinophilic diseases, also termed eosinophil-associated diseases (EADs), are characterized by eosinophil-rich inflammatory infiltrates and extensive eosinophil degranulation with clinically relevant organ pathology. Recent evidence shows that eosinophil cytolytic degranulation, that is, the release of intact, membrane-delimited granules that arises from the eosinophil cytolysis, occurs mainly through ETosis, meaning death with a cytolytic profile and extrusion of nucleus-originated DNA extracellular traps (ETs). The ultrastructural features of eosinophil ETosis (EETosis) have been studied mostly in vitro after stimulation, but are still poorly understood in vivo. Here, we investigated in detail, by transmission electron microscopy (TEM), the ultrastructure of EETosis in selected human EADs affecting several tissues and organ systems. Biopsies of patients diagnosed with eosinophilic chronic rhinosinusitis/ECRS (frontal sinus), ulcerative colitis/UC (intestine), and hypereosinophilic syndrome/HES (skin) were processed for conventional TEM. First, we found that a large proportion of tissue-infiltrated eosinophils in all diseases (~45-65% of all eosinophils) were undergoing cytolysis with release of free extracellular granules (FEGs). Second, we compared the morphology of tissue inflammatory eosinophils with that shown by in vitro ETosis-stimulated eosinophils. By applying single-cell imaging analysis, we sought typical early and late EETosis events: chromatin decondensation; nuclear delobulation and rounding; expanded nuclear area; nuclear envelope alterations and disruption; and extracellular decondensed chromatin spread as ETs. We detected that 53% (ECRS), 37% (UC), and 82% (HES) of all tissue cytolytic eosinophils had ultrastructural features of ETosis in different degrees. Eosinophils in early ETosis significantly increased their nuclear area compared to non-cytolytic eosinophils due to excessive chromatin decondensation and expansion observed before nuclear envelope disruption. ETosis led not only to the deposition of intact granules, but also to the release of eosinophil sombrero vesicles (EoSVs) and Charcot-Leyden crystals (CLCs). Free intact EoSVs and CLCs were associated with FEGs and extracellular DNA nets. Interestingly, not all cytolytic eosinophils in the same microenvironment exhibited ultrastructure of ETosis, thus indicating that different populations of eosinophils might be selectively activated into this pathway. Altogether, our findings captured an ultrastructural signature of EETosis in vivo in prototypic EADs highlighting the importance of this event as a form of eosinophil degranulation and release of inflammatory markers (EoSVs and CLCs).

Förster Resonance Energy Transfer-Based Single-Cell Imaging Reveals Piezo1-Induced Ca2+ Flux Mediates Membrane Ruffling and Cell Survival.

A mechanosensitive ion channel, Piezo1 induces non-selective cation flux in response to various mechanical stresses. However, the biological interpretation and underlying mechanisms of cells resulting from Piezo1 activation remain elusive. This study elucidates Piezo1-mediated Ca2+ influx driven by channel activation and cellular behavior using novel Förster Resonance Energy Transfer (FRET)-based biosensors and single-cell imaging analysis. Results reveal that extracellular Ca2+ influx via Piezo1 requires intact caveolin, cholesterol, and cytoskeletal support. Increased cytoplasmic Ca2+ levels enhance PKA, ERK, Rac1, and ROCK activity, which have the potential to promote cancer cell survival and migration. Furthermore, we demonstrate that Piezo1-mediated Ca2+ influx upregulates membrane ruffling, a characteristic feature of cancer cell metastasis, using spatiotemporal image correlation spectroscopy. Thus, our findings provide new insights into the function of Piezo1, suggesting that Piezo1 plays a significant role in the behavior of cancer cells.

Mitochondrial Population in Mouse Eosinophils: Ultrastructural Dynamics in Cell Differentiation and Inflammatory Diseases.

Mitochondria are multifunctional organelles of which ultrastructure is tightly linked to cell physiology. Accumulating evidence shows that mitochondrial remodeling has an impact on immune responses, but our current understanding of the mitochondrial architecture, interactions, and morphological changes in immune cells, mainly in eosinophils, is still poorly known. Here, we applied transmission electron microscopy (TEM), single-cell imaging analysis, and electron tomography, a technique that provides three-dimensional (3D) views at high resolution, to investigate mitochondrial dynamics in mouse eosinophils developing in cultures as well as in the context of inflammatory diseases characterized by recruitment and activation of these cells (mouse models of asthma, H1N1 influenza A virus (IAV) infection, and schistosomiasis mansoni). First, quantitative analyses showed that the mitochondrial area decrease 70% during eosinophil development (from undifferentiated precursor cells to mature eosinophils). Mitophagy, a consistent process revealed by TEM in immature but not in mature eosinophils, is likely operating in mitochondrial clearance during eosinophilopoiesis. Events of mitochondria interaction (inter-organelle membrane contacts) were also detected and quantitated within developing eosinophils and included mitochondria-endoplasmic reticulum, mitochondria-mitochondria, and mitochondria-secretory granules, all of them significantly higher in numbers in immature compared to mature cells. Moreover, single-mitochondrion analyses revealed that as the eosinophil matures, mitochondria cristae significantly increase in number and reshape to lamellar morphology. Eosinophils did not change (asthma) or reduced (IAV and Schistosoma infections) their mitochondrial mass in response to inflammatory diseases. However, asthma and schistosomiasis, but not IAV infection, induced amplification of both cristae numbers and volume in individual mitochondria. Mitochondrial cristae remodeling occurred in all inflammatory conditions with the proportions of mitochondria containing only lamellar or tubular, or mixed cristae (an ultrastructural aspect seen just in tissue eosinophils) depending on the tissue/disease microenvironment. The ability of mitochondria to interact with granules, mainly mobilized ones, was remarkably captured by TEM in eosinophils participating in all inflammatory diseases. Altogether, we demonstrate that the processes of eosinophilopoiesis and inflammation-induced activation interfere with the mitochondrial dynamics within mouse eosinophils leading to cristae remodeling and inter-organelle contacts. The understanding of how mitochondrial dynamics contribute to eosinophil immune functions is an open interesting field to be explored.

PKCλ/ι inhibition activates an ULK2-mediated interferon response to repress tumorigenesis

The interferon (IFN) pathway is critical for cytotoxic Tcell activation, which is central to tumor immunosurveillance and successful immunotherapy. We demonstrate here that PKCλ/ι inactivation results in the hyper-stimulation of the IFN cascade and the enhanced recruitment of CD8+ Tcells that impaired the growth of intestinal tumors. PKCλ/ι directly phosphorylates and represses the activity of ULK2, promoting its degradation through an endosomal microautophagy-driven ubiquitin-dependent mechanism. Loss of PKCλ/ι results in increased levels of enzymatically active ULK2, which, by direct phosphorylation, activates TBK1 to foster the activation of the STING-mediated IFN response. PKCλ/ι inactivation also triggers autophagy, which prevents STING degradation by chaperone-mediated autophagy. Thus, PKCλ/ι is a hub regulating the IFN pathway and three autophagic mechanisms that serve to maintain its homeostatic control. Importantly, single-cell multiplex imaging and bioinformatics analysis demonstrated that low PKCλ/ι levels correlate with enhanced IFN signaling and good prognosis in colorectal cancer patients.

Abstract 2742: Integrated multiregional transcriptomic and multi-parameter single-cell imaging analysis of clear cell renal cell carcinoma elucidates diverse cellular communities present within the tumor microenvironment

Abstract Although genomic analyses of clear cell renal cell carcinoma (ccRCC) patients have revealed targetable pathways that have led to FDA-approved therapies, the responses to these therapies remain limited. The significant success of immune checkpoint inhibitors and anti-angiogenic agents suggest that ccRCC has a unique tumor microenvironment composition and tumor behavior that influences therapeutic response. Here, we describe an integrated proteogenomic method to study intratumoral heterogeneity (ITH), microenvironment composition, tumor spatial behavior, and cellular communities in ccRCC. A unique AI-based segmentation platform for multiplex immunofluorescence (MxIF) was developed to analyze an entire tissue slide at single-cell resolution, including 70 regions of interest per slide, providing significant information regarding spatial architecture. Primary ccRCC tumors collected from patients were biopsied at multiple locations and subjected to MxIF (20 markers, n = 10 sites, 4 pts, ~1,000,000 cells), RNA-seq (n = 8 sites, 3 pts) and CyTOF (n = 21 sites, 6 pts), allowing integrated multi-omics analysis at the single-cell level. Integrated analysis showed that genomic intratumor heterogeneity (ITH) was remarkably similar across all regions biopsied from the same patient, and the cellular populations present within each region of the same patient were alike. However, some cell types such as TCM CD4 T cells and Tem CD38 and Tem PD1+CD69+CD38- CD8 T cells, and CD163+PDL1+LAMP+ showed great inter-patient differences in the proportion of these cell populations. Notably, 14 CD4 T cell, 13 CD8 T cell, and 10 macrophage subpopulations were identified across the ccRCC tumors. Moreover, 14 microenvironment proximity communities based on MxIF imaging analysis of ~1 million cells were identified. The presence of B cell- and T cell-enriched communities (e.g., CD8 T cell enrichment and T-cell enrichment at the tumor border) correlated with the expression of interferon-gamma, PD1, IL-6, IL-10, PD-L1, CXCL13, and others. Macrophage-enriched communities correlated with the expression of CXCL12 and PDGFRB. Finally, tertiary lymphoid structures within the “B cell-enriched” communities correlating with the expression of CXCL13 were found in two tumors collected from one patient, with subsequent validation via H&E staining. Further, B cell repertoire (BCR) analysis of RNA-seq of the tumors from this patient showed the presence of a large B cell clone in the tumors. In conclusion, via MxIF, 14 distinct spatial microenvironment communities with unique cytokine expression patterns were identified in ccRCC. Uncovering the spatial behavior of tumors can lead to the development of effective therapies personalized for each patient based on microenvironment composition and architecture. Citation Format: Natalia Miheecheva, Akshaya Ramachandran, Yang Lyu, Ekaterina Postovalova, Viktor Svekolkin, Ilia Galkin, Pavel Ovcharov, Diana Shamsutdinova, Vladimir Zyrin, Alexander Bagaev, Krystle Nomie, Felix Frenkel, Ravshan Ataullakhanov, James J. Hsieh. Integrated multiregional transcriptomic and multi-parameter single-cell imaging analysis of clear cell renal cell carcinoma elucidates diverse cellular communities present within the tumor microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2742.

\u03b2-Pix-dependent cellular protrusions propel collective mesoderm migration in the mouse embryo

Coordinated directional migration of cells in the mesoderm layer of the early embryo is essential for organization of the body plan. Here we show that mesoderm organization in mouse embryos depends on β-Pix (Arhgef7), a guanine nucleotide exchange factor for Rac1 and Cdc42. As early as E7.5, β-Pix mutants have an abnormally thick mesoderm layer; later, paraxial mesoderm fails to organize into somites. To define the mechanism of action of β-Pix in vivo, we optimize single-cell live-embryo imaging, cell tracking, and volumetric analysis of individual and groups of mesoderm cells. Use of these methods shows that wild-type cells move in the same direction as their neighbors, whereas adjacent β-Pix mutant cells move in random directions. Wild-type mesoderm cells have long polarized filopodia-like protrusions, which are absent in β-Pix mutants. The data indicate that β-Pix-dependent cellular protrusions drive and coordinate collective migration of the mesoderm in vivo.

Comparative Profiling of N-Respirasomes Predicts Aberrant Mitochondrial Bioenergetics at Single-Cell Resolution

Mitochondria sustain the energy demand of the cell. The composition and functional state of the mitochondrial oxidative phosphorylation system are informative indicators of organelle homeostasis and bioenergetic capacity. Here we describe a highly sensitive and reproducible method for single-cell visualization and quantification of mitochondrial respiratory supercomplexes as a novel means of measuring mitochondrial respiratory chain integrity. We apply a proximity ligation assay (PLA) and perform comparative studies of mitochondrial CI, CIII, CIV-containing supercomplexes (or N-respirasomes) in fixed human and mouse brain tissues, tumorigenic cells, iPSCs and iPSC-derived NPCs and neurons. Our optimized approach enables quantitative in-situ assessments of even subtle mitochondrial lesions associated with aberrant respiration. By combining quantitative proteomics with single cell imaging analysis, we also report the mechanistic contribution of the MICOS complex subunit CHCHD3 in regulating N-respirasomes. Overall, our PLA-based profiling of N-respirasomes establishes a sensitive and complementary technique for detecting cell-type specific mitochondrial perturbations in fixed materials.

Multiomics profiling of longitudinal melanoma specimens unravels molecular mechanisms of resistance to sequential targeted and cancer immunotherapies.

e22015 Background: We evaluated spatially-resolved protein profiling of longitudinal tumor specimens derived from two patients with metastatic melanoma who progressed on sequential therapies including targeted therapy (TT) and immune checkpoint blockade (ICB) therapy targeting T cell-surface antigens (CTLA-4 and PD-1). The purpose of this study was to identify molecular determinants of resistance to sequential TT and ICB therapies. Methods: We performed multiplexed and multidimensional spatial protein profiling using NanoString’s GeoMx Digital Spatial Profiling (DSP) platform and single-cell level imaging analysis with Cyclic Immunofluorescence (CycIF) to simultaneously determine dynamic changes in tumor intrinsic signaling pathways and immune response in the tumor microenvironment (TME). Results: The first patient presented with a BRAFV600E-positive brain metastasis. This patient was sequentially treated with ipilimumab (Ipi), the combination of dabrafenib and trametinib, and pembrolizumab (Pembro) and progressed despite of high expression of CD56 NK cell after all treatments. In addition, CycIF analysis revealed drug resistance in a subpopulation of cells that had continued activation of mTOR (pS6) and EGFR pathways. The second patient presented with dermal metastases on the flank with NRASQ61K mutation. This patient was sequentially treated with Pembo, Talimogene Laherparepvec, the combination of Ipi plus nivolumab, and two different investigational agents combined with Pembro. This patient displayed stable disease (SD) on Pembro but eventually progressed on the subsequent therapies. DSP analysis demonstrated CD68/CD40 myeloid cell infiltrates as well as HLA-DR and CD44 in the TME after the last treatment. CycIF analysis revealed dynamic changes in tumoral characteristics including DNA damage and proliferation during treatment. Furthermore, the analysis suggested that there might be a resistant subpopulation in the last tumor biopsy, which is in line with progression of the disease. Conclusions: In this study, we conducted detailed analyses on serial specimens from two patients to precisely define the spatial distribution of immune responses and cancer signaling pathways. The findings propose that concurrent proteomics analysis and immune monitoring of longitudinal tumor biopsies can be informative in clinical evaluation in order to identify salvage therapies to overcome drug resistance.

Subcellular Mass Spectrometry Imaging and Absolute Quantitative Analysis across Organelles.

Mass spectrometry imaging is a field that promises to become a mainstream bioanalysis technology by allowing the combination of single-cell imaging and subcellular quantitative analysis. The frontier of single-cell imaging has advanced to the point where it is now possible to compare the chemical contents of individual organelles in terms of raw or normalized ion signal. However, to realize the full potential of this technology, it is necessary to move beyond this concept of relative quantification. Here we present a nanoSIMS imaging method that directly measures the absolute concentration of an organelle-associated, isotopically labeled, pro-drug directly from a mass spectrometry image. This is validated with a recently developed nanoelectrochemistry method for single organelles. We establish a limit of detection based on the number of isotopic labels used and the volume of the organelle of interest, also offering this calculation as a web application. This approach allows subcellular quantification of drugs and metabolites, an overarching and previously unmet goal in cell science and pharmaceutical development.

Abstract 156: Endogenous Cardiomyocyte Dedifferentiation and Cycling Revealed by Single-Cell Imaging and Single-Nucleus Transcriptomic Analysis

Although the mammalian heart had been recognized as a post-mitotic non-regenerative organ, recent evidence demonstrated a measurable cardiomyocyte (CM) renewal at low rates in normal hearts and augmented in post-injury myocardium. However, the resources and cellular processes of such a new CM formation, and the underlying molecular programs remained largely undetermined. While CMs in neonatal hearts or adult CMs in tissue culture can undergo (partial) dedifferentiation and proliferation, the roles of in vivo CM dedifferentiation and cycling were unclear. Here, we report a multi-reporter transgenic mouse models featuring efficient adult CM (ACM) genetic cell fate mapping and real-time CM dedifferentiation reporting. In this triple-transgenic model, upon tamoxifen-induced gene recombination, only ACMs switched from expressing red fluorescent protein (RFP) to green fluorescent protein (GFP), and non-CMs remained expressing RFP. The nuclear blue fluorescent protein (BFP) signal was expressed in normal mature ACMs but reduced in neonatal or cultured dedifferentiated ACMs. Hence, all 4 plausible modes of new CM formation can be visualized using this model. Using ImageStream for single-cell imaging analysis, we demonstrated that non-myocytes (including putative cardiac progenitor cells) contributed negligibly to new ACM formation at baseline or after myocardial infarction (MI). In contrast, there was a significant increase in dedifferentiated (e.g. GFP + BFP - ) CMs in post-MI hearts compared to the sham. Cell cycling activity was enhanced within the dedifferentiated CM population compared to normal ACMs (GFP + BFP + ). Furthermore, we applied massive whole-heart single-nucleus RNA-seq to dissect the transcriptomes of dedifferentiated CMs. We found that CMs in post-MI hearts identified with dedifferentiation reporter had significant down-regulations of genes in networks for hypertrophic growth, cardiac contractile functions and metabolism, but up-regulation in signaling pathways for cell survival, active cell cycle and proliferation. Therefore, cellular dedifferentiation may be an important prerequisite for endogenous CM cell cycling and proliferation and explain the measurable cardiac myogenesis seen after MI.

High-Throughput Automated Single-Cell Imaging Analysis Reveals Dynamics of Glioblastoma Stem Cell Population During State Transition.

Cancer stem cells (CSCs) are a heterogeneous and dynamic self-renewing population that stands at the top of tumor cellular hierarchy and contribute to tumor recurrence and therapeutic resistance. As methods of CSC isolation and functional interrogation advance, there is a need for a reliable and accessible quantitative approach to assess heterogeneity and state transition dynamics in CSCs. We developed a high-throughput automated single cell imaging analysis (HASCIA) approach for the quantitative assessment of protein expression with single-cell resolution and applied the method to investigate spatiotemporal factors that influence CSC state transition using glioblastoma (GBM) CSCs (GSCs) as a model system. We were able to validate the quantitative nature of this approach through comparison of the protein expression levels determined by HASCIA to those determined by immunoblotting. A virtue of HASCIA was exemplified by detection of a subpopulation of SOX2-low cells, which expanded in fraction size during state transition. HASCIA also revealed that GSCs were committed to loose stem cell state at an earlier time point than the average SOX2 level decreased. Functional assessment of stem cell frequency in combination with the quantification of SOX2 expression by HASCIA defined a stable cutoff of SOX2 expression level for stem cell state. We also developed an approach to assess local cell density and found that denser monolayer areas possess higher average levels of SOX2, higher cell diversity, and a presence of a sub-population of slowly proliferating SOX2-low GSCs. HASCIA is an open source software that facilitates understanding the dynamics of heterogeneous cell population such as that of GSCs and their progeny. It is a powerful and easy-to-use image analysis and statistical analysis tool available at https://hascia.lerner.ccf.org. © 2019 International Society for Advancement of Cytometry.

The clock components Period2, Cryptochrome1a, and Cryptochrome2a function in establishing light-dependent behavioral rhythms and/or total activity levels in zebrafish

The circadian clock generates behavioral rhythms to maximize an organism’s physiological efficiency. Light induces the formation of these rhythms by synchronizing cellular clocks. In zebrafish, the circadian clock components Period2 (zPER2) and Cryptochrome1a (zCRY1a) are light-inducible, however their physiological functions are unclear. Here, we investigated the roles of zPER2 and zCRY1a in regulating locomotor activity and behavioral rhythms. zPer2/zCry1a double knockout (DKO) zebrafish displayed defects in total locomotor activity and in forming behavioral rhythms when briefly exposed to light for 3-h. Exposing DKO zebrafish to 12-h light improved behavioral rhythm formation, but not total activity. Our data suggest that the light-inducible circadian clock regulator zCRY2a supports rhythmicity in DKO animals exposed to 12-h light. Single cell imaging analysis revealed that zPER2, zCRY1a, and zCRY2a function in synchronizing cellular clocks. Furthermore, microarray analysis of DKO zebrafish showed aberrant expression of genes involved regulating cellular metabolism, including ATP production. Overall, our results suggest that zPER2, zCRY1a and zCRY2a help to synchronize cellular clocks in a light-dependent manner, thus contributing to behavioral rhythm formation in zebrafish. Further, zPER2 and zCRY1a regulate total physical activity, likely via regulating cellular energy metabolism. Therefore, these circadian clock components regulate the rhythmicity and amount of locomotor behavior.

Prevention of hepatocellular carcinoma by targeting MYCN-positive liver cancer stem cells with acyclic retinoid

Hepatocellular carcinoma (HCC) is a highly lethal cancer that has a high rate of recurrence, in part because of cancer stem cell (CSC)-dependent field cancerization. Acyclic retinoid (ACR) is a synthetic vitamin A-like compound capable of preventing the recurrence of HCC. Here, we performed a genome-wide transcriptome screen and showed that ACR selectively suppressed the expression of MYCN, a member of the MYC family of basic helix-loop-helix-zipper transcription factors, in HCC cell cultures, animal models, and liver biopsies obtained from HCC patients. MYCN expression in human HCC was correlated positively with both CSC and Wnt/β-catenin signaling markers but negatively with mature hepatocyte markers. Functional analysis showed repressed cell-cycle progression, proliferation, and colony formation, activated caspase-8, and induced cell death in HCC cells following silencing of MYCN expression. High-content single-cell imaging analysis and flow cytometric analysis identified a MYCN+ CSC subpopulation in the heterogeneous HCC cell cultures and showed that these cells were selectively killed by ACR. Particularly, EpCAM+ cells isolated using a cell-sorting system showed increased MYCN expression and sensitivity to ACR compared with EpCAM- cells. In a long-term (>10 y) follow-up study of 102 patients with HCC, MYCN was expressed at higher levels in the HCC tumor region than in nontumor regions, and there was a positive correlation between MYCN expression and recurrence of de novo HCC but not metastatic HCC after curative treatment. In summary, these results suggest that MYCN serves as a prognostic biomarker and therapeutic target of ACR for liver CSCs in de novo HCC.

TBP-like Protein (TLP) Disrupts the p53-MDM2 Interaction and Induces Long-lasting p53 Activation

Stress-induced activation of p53 is an essential cellular response to prevent aberrant cell proliferation and cancer development. The ubiquitin ligase MDM2 promotes p53 degradation and limits the duration of p53 activation. It remains unclear, however, how p53 persistently escapes MDM2-mediated negative control for making appropriate cell fate decisions. Here we report that TBP-like protein (TLP), a member of the TBP family, is a new regulatory factor for the p53-MDM2 interplay and thus for p53 activation. We found that TLP acts to stabilize p53 protein to ensure long-lasting p53 activation, leading to potentiation of p53-induced apoptosis and senescence after genotoxic stress. Mechanistically, TLP interferes with MDM2 binding and ubiquitination of p53. Moreover, single cell imaging analysis shows that TLP depletion accelerates MDM2-mediated nuclear export of p53. We further show that a cervical cancer-derived TLP mutant has less p53 binding ability and lacks a proliferation-repressive function. Our findings uncover a role of TLP as a competitive MDM2 blocker, proposing a novel mechanism by which p53 escapes the p53-MDM2 negative feedback loop to modulate cell fate decisions.

Symmetry breaking in the early mammalian embryo: the case for quantitative single-cell imaging analysis

In recent years, advances in imaging probes, cutting-edge microscopy techniques and powerful bioinformatics image analysis have markedly expanded the imaging toolbox available to developmental biologists. Apart from traditional qualitative studies, embryonic development can now be investigated in vivo with improved spatiotemporal resolution, with more detailed quantitative analyses down to the single-cell level of the developing embryo. Such imaging tools can provide many benefits to investigate the emergence of the asymmetry in the early mammalian embryo. Quantitative single-cell imaging has provided a deeper knowledge of the dynamic processes of how and why apparently indistinguishable cells adopt separate fates that ensure proper lineage allocation and segregation. To advance our understanding of the mechanisms governing such cell fate decisions, we will need to address current limitations of fluorescent probes, while at the same time take on challenges in image processing and analysis. New discoveries and developments in quantitative, single-cell imaging analysis will ultimately enable a truly comprehensive, multi-dimensional and multi-scale investigation of the dynamic morphogenetic processes that work in concert to shape the embryo.

Single Nuclei Raman Spectroscopy for Drug Evaluation

Detection of cellular changes at single-cell level has a great potential for biomedical and biopharmaceutical applications. Raman spectroscopy is an important tool for single-cell molecular imaging analysis. Raman spectroscopy can provide time-resolved information of the selected biomolecular distributions inside a single cell without the need of chemical labeling. In this study, we monitored the cellular responses to antineoplastic drug at a single cell basis with Raman spectroscopy. We demonstrated that single nuclei Raman spectroscopy has the ability to detect and identify nuclear changes related to cytotoxicity at lower concentrations and in shorter time span than conventional cell based assays. Thus, this strategy of using Raman spectroscopy of single, isolated nuclei may be very valuable for rapid and sensitive detection of cellular changes in response to chemotherapeutic agents.