Denoising OCT videos based on temporal redundancy.

The identification of eye diseases and their progression often relies on a clear visualization of the anatomy and on different metrics extracted from Optical Coherence Tomography (OCT) B-scans. However, speckle noise hinders the quality of rapid OCT imaging, hampering the extraction and reliability of biomarkers that require time series. By synchronizing the acquisition of OCT images with the timing of the cardiac pulse, we transform a low-quality OCT video into a clear version by phase-wrapping each frame to the heart pulsation and averaging frames that correspond to the same instant in the cardiac cycle. Here, we compare the performance of our one-cycle denoising strategy with a deep-learning architecture, Noise2Noise, as well as classical denoising methods such as BM3D and Non-Local Means (NLM). We systematically analyze different image quality descriptors as well as region-specific metrics to assess the denoising performance based on the anatomy of the eye. The one-cycle method achieves the highest denoising performance, increases image quality and preserves the high-resolution structures within the eye tissues. The proposed workflow can be readily implemented in a clinical setting.

Machine learning predictions of T cell antigen specificity from intracellular calcium dynamics.

Adoptive T cell therapies rely on the production of T cells with an antigen receptor that directs their specificity toward tumor-specific antigens. Methods for identifying relevant T cell receptor (TCR) sequences, predominantly achieved through the enrichment of antigen-specific T cells, represent a major bottleneck in the production of TCR-engineered cell therapies. Fluctuation of intracellular calcium is a proximal readout of TCR signaling and candidate marker for antigen-specific T cell identification that does not require T cell expansion; however, calcium fluctuations downstream of TCR engagement are highly variable. We propose that machine learning algorithms may allow for T cell classification from complex datasets such as polyclonal T cell signaling events. Using deep learning tools, we demonstrate accurate prediction of TCR-transgenic CD8+ T cell activation based on calcium fluctuations and test the algorithm against T cells bearing a distinct TCR as well as polyclonal T cells. This provides the foundation for an antigen-specific TCR sequence identification pipeline for adoptive T cell therapies.

Ocular rigidity and choroidal thickness changes in response to microgravity: A case study.

Purpose: To evaluate ocular rigidity and choroidal thickness changes in response to microgravity and the Valsalva maneuver in a private astronaut. Methods: Ophthalmological examination and Optical Coherence Tomography were performed before, during, and after space flight. Choroidal thickness was measured at all time points at rest and during the Valsalva maneuver. Ocular rigidity was obtained before and after flight using a non-invasive method enhanced with deep learning-based choroid segmentation. Results: Ocular rigidity decreased after space flight compared to baseline. There was an increase in average choroidal thickness during the Valsalva maneuver compared to the resting condition before, during, and after space flight, and such increase was greater when the Valsalva maneuver was performed during space flight. Conclusions and importance: The data indicates biomechanical changes to ocular tissues because of space flight and greater choroidal thickness increase. The findings could lead to a better understanding of space flight-associated neuro-ocular syndrome and may have repercussions for short duration missions in a nascent industry.

Migration speed of captured breast cancer subpopulations correlates with metastatic fitness.

The genetic alterations contributing to migration proficiency, a phenotypic hallmark of metastatic cells required for colonizing distant organs, remain poorly defined. Here, we used single-cell magneto-optical capture (scMOCa) to isolate fast cells from heterogeneous human breast cancer cell populations, based on their migratory ability alone. We show that captured fast cell subpopulations retain higher migration speed and focal adhesion dynamics over many generations as a result of a motility-related transcriptomic profile. Upregulated genes in isolated fast cells encoded integrin subunits, proto-cadherins and numerous other genes associated with cell migration. Dysregulation of several of these genes correlates with poor survival outcomes in people with breast cancer, and primary tumors established from fast cells generated a higher number of circulating tumor cells and soft tissue metastases in pre-clinical mouse models. Subpopulations of cells selected for a highly migratory phenotype demonstrated an increased fitness for metastasis.

Quantification of Hypotony Maculopathy Using Spectral-Domain Optical Coherence Tomography.

PRCIS: We provide a free-to-use, open-source algorithm to quantify macular hypotony based on optical coherence tomography (OCT) images. This numerical approach calculates a metric that measures the deviations of Bruch's membrane from a smooth ideal retinal layer. PURPOSE: Hypotony maculopathy is a recurrent complication of glaucoma surgical interventions in which extremely low intraocular pressure triggers changes in the shape of retinal layers. Abnormal folds can often be observed in the retina using standard fundoscopy, but OCT is particularly important to appreciate the severity of symptoms at different depths. Despite the need for metrics that could be used for the informed clinical decision to evaluate the progression and resolution of macular hypotony, algorithms that quantify the retinal folds are not available in the literature or included in clinical imaging equipment. The purpose of this work is to introduce a simple algorithm that can be used to assess hypotony maculopathy from OCT B-Scans and volumes and a free, open-source implementation. METHODS: The pipeline we present is based on a straightforward segmentation of Bruch's membrane complex. The principal idea of quantification is to compute a smoothed version of this complex and analyze the deviations from an ideal interface. Such deviations are then measured and added to create a metric that characterizes each OCT B-Scan. A full OCT volume reconstruction is thus characterized by the average metric obtained from all planes. RESULTS: We tested the metric we proposed against the assessment of 3 experts and obtained a very good correspondence, with Pearson correlation coefficients higher than 0.8. Furthermore, agreement with automatic analysis seemed better than between experts. We describe the pipeline in detail and illustrate the results with a group of patients, comparing baseline images, severe hypotony maculopathy, and a variety of outcomes. CONCLUSION: The tool we introduce and openly provide fills a clinical gap to quantitatively grade hypotony maculopathy. It offers a metric of relatively simple interpretation that can be used to help clinicians in cases where the regression of symptoms is not obvious to the naked eye. Our pilot study demonstrates reliable results, and an open-source implementation facilitates easy improvements to our algorithm.

Ocular rigidity and neuroretinal damage in patients with vasospasticity: a pilot study.

OBJECTIVE: Evidence suggests that ocular blood flow dysregulation in patients with vasospasticity could occur in response to biomechanical stimuli, contributing to optic nerve head susceptibility in glaucoma. We evaluate the role of vasospasticity in the association between ocular rigidity (OR) and neuroretinal damage, hypothesizing that low OR correlates with greater glaucoma damage in patients with vasospasticity. DESIGN: Cross-sectional study. PARTICIPANTS: Patients with open-angle glaucoma (OAG), suspect discs, or no glaucoma. METHODS: OR was measured using a noninvasive, validated method developed by our group. Retinal nerve fibre layer (RNFL) and ganglion cell complex thicknesses were acquired using spectral domain optical coherence tomography. Vasospasticity was assessed by a standardized questionnaire that was based on existing validated questionnaires and adapted to our requirements. Atherosclerosis was evaluated based on Broadway and Drance's (1998) cardiovascular disease score. Correlations between OR and structural parameters were assessed in patients with vasospasticity and those with atherosclerosis. RESULTS: Of 118 patients with either OAG (n = 67), suspect discs (n = 26), or no glaucoma (n = 25) who were recruited consecutively, 10 were classified as having vasospasticity, and 37 as having atherosclerosis. In the vasospastic group, significant correlations were found between OR and the minimum ganglion cell complex thickness (rs = 0.681, p = 0.030), the average RNFL thickness (rs = 0.745, p = 0.013), and the RNFL in the temporal quadrant (rs = 0.772, p = 0.009), indicating more damage with lower OR. Similar trends were maintained when applying multiple testing correction; however, only the eighth RNFL clock hour corresponding to the inferior-temporal peripapillary region remained significantly correlated with OR in the vasospastic group (p = 0.015). In contrast, no correlation was found in the atherosclerotic group (p > 0.05). CONCLUSIONS: The findings of the current pilot study indicate a trend for more neuronal structural damage in less-rigid eyes of patients with vasospasticity, meaning that OR may play a greater role in glaucoma in vasospastic patients than in patients with atherosclerosis. Although these results provide interesting insight into the pathophysiology of OAG, further investigation is needed to confirm our observations.

Laser-Assisted Single-Cell Labeling and Capture.

Single-cell technologies have become critical tools to understand and characterize the complex dynamics that govern biological systems, from embryonic development to cancer heterogeneity. In this context, identification and capture of live individual cells in heterogenous ensembles typically rely on genetic manipulations that encode fluorescent probes. However, a precise understanding of how several molecular components interact to yield the phenotype of interest is a prerequisite to distinguishing and isolating such target cells based on fluorescence alone. Indeed, cellular phenotypes associated with migration, shape, location, or intracellular protein distribution play critical and well-understood roles in cancer biology, but the technologies to tag and isolate cells based on information obtained from imaging are not readily available.Cell labeling via photobleaching (CLaP) and single-cell magneto-optical capture (scMOCa) represent convenient and cost-effective systems for labeling, capturing, and expanding single cells from a heterogenous population, without altering cellular physiology and therefore enabling not only transcriptomic profiling but also biological characterization of target cells. Both techniques allow capturing cells after observation and permit researchers to choose target cells based on information obtained from images. The implementation of these technologies only needs the lasers of a confocal microscope and low-cost, commercially available chemical reagents. Here, we describe a detailed protocol to set up and perform CLaP and scMOCa and highlight critical points for optimal performance.

Mapping Pulsatile Optic Nerve Head Deformation Using OCT.

Objective: To develop a noninvasive technique to quantitatively assess the pulsatile deformation due to cardiac contractions of the optic nerve head (ONH). Design: Evaluation of a diagnostic test or technology. Participants: Healthy subjects with no history of refractive surgery, divided into 2 cohorts on the basis of their axial length (AL). Methods: We present a noninvasive technique to quantitatively assess the pulsatile deformation of the ONH tissue by combining high-frequency OCT imaging and widely available image processing algorithms. We performed a thorough validation of the approach, numerically and experimentally, evaluating the sensitivity of the method to artificially induced deformation and its robustness to different noise levels. We performed deformation measurements in cohorts of healthy (n = 9) and myopic (n = 5) subjects in different physiological strain conditions by calculating the amplitude of tissue displacement in both the primary position and abduction. The head rotation was measured using a goniometer. During imaging in abduction, the head was rotated 40° ± 3°, and subjects were instructed to direct their gaze toward the OCT visual target. Main Outcome Measures: Pulsatile tissue displacement maps. Results: The robustness of the method was assessed using artificial deformations and increasing noise levels. The results show acceptable absolute errors before the noise simulations grossly exaggerate image degradation. For the group of subjects with AL of < 25 mm (n = 9), the median pulsatile displacement of the ONH was 7.8 ± 1.3 µm in the primary position and 8.9 ± 1.2 µm in abduction. The Wilcoxon test showed a significant difference (P ≤ 0.005) between the 2 paired measures. Reproducibility was tested in 2 different sessions in 5 different subjects with the same intraocular pressure, and an intraclass correlation coefficient of 0.99 was obtained (P < 0.005). Conclusions: The computational pipeline demonstrated good reproducibility and had the capacity to accurately map the pulsatile deformation of the optic nerve. In a clinical setting, we detected physiological changes in normal subjects supporting its translation potential as a novel biomarker for the diagnosis and progression of optic nerve diseases.

Spatially mapping the immune landscape of melanoma using imaging mass cytometry.

Melanoma is an immunogenic cancer with a high response rate to immune checkpoint inhibitors (ICIs). It harbors a high mutation burden compared with other cancers and, as a result, has abundant tumor-infiltrating lymphocytes (TILs) within its microenvironment. However, understanding the complex interplay between the stroma, tumor cells, and distinct TIL subsets remains a substantial challenge in immune oncology. To properly study this interplay, quantifying spatial relationships of multiple cell types within the tumor microenvironment is crucial. To address this, we used cytometry time-of-flight (CyTOF) imaging mass cytometry (IMC) to simultaneously quantify the expression of 35 protein markers, characterizing the microenvironment of 5 benign nevi and 67 melanomas. We profiled more than 220,000 individual cells to identify melanoma, lymphocyte subsets, macrophage/monocyte, and stromal cell populations, allowing for in-depth spatial quantification of the melanoma microenvironment. We found that within pretreatment melanomas, the abundance of proliferating antigen-experienced cytotoxic T cells (CD8+CD45RO+Ki67+) and the proximity of antigen-experienced cytotoxic T cells to melanoma cells were associated with positive response to ICIs. Our study highlights the potential of multiplexed single-cell technology to quantify spatial cell-cell interactions within the tumor microenvironment to understand immune therapy responses.

Nanophotonics Enable Targeted Photothermal Silencing of Nociceptor Neurons.

The sensory nervous and immune systems work in concert to preserve homeostasis. While this endogenous interplay protects from danger, it may drive chronic pathologies. Currently, genetic engineering of neurons remains the primary approach to interfere selectively with this potentially deleterious interplay. However, such manipulations are not feasible in a clinical setting. Here, this work reports a nanotechnology-enabled concept to silence subsets of unmodified nociceptor neurons that exploits their ability to respond to heat via the transient receptor potential vanilloid type 1 (TRPV1) channel. This strategy uses laser stimulation of antibody-coated gold nanoparticles to heat-activate TRPV1, turning this channel into a cell-specific drug-entry port. This delivery method allows transport of a charged cationic derivative of an N-type calcium channel blocker (CNCB-2) into targeted sensory fibers. CNCB-2 delivery blocks neuronal calcium currents and neuropeptides release, resulting in targeted silencing of nociceptors. Finally, this work demonstrates the ability of the approach to probe neuro-immune crosstalk by targeting cytokine-responsive nociceptors and by successfully preventing nociceptor-induced CD8+ T-cells polarization. Overall, this work constitutes the first demonstration of targeted silencing of nociceptor neuron subsets without requiring genetic modification, establishing a strategy for interfering with deleterious neuro-immune interplays.

Correlation of ocular rigidity with intraocular pressure spike after intravitreal injection of bevacizumab in exudative retinal disease.

BACKGROUND/AIMS: To evaluate the non-invasive measurement of ocular rigidity (OR), an important biomechanical property of the eye, as a predictor of intraocular pressure (IOP) elevation after anti-vascular endothelial growth factor (anti-VEGF) intravitreal injection (IVI). METHODS: Subjects requiring IVI of anti-VEGF for a pre-existing retinal condition were enrolled in this prospective cross-sectional study. OR was assessed in 18 eyes of 18 participants by measurement of pulsatile choroidal volume change using video-rate optical coherence tomography, and pulsatile IOP change using dynamic contour tonometry. IOP was measured using Tono-Pen XL before and immediately following the injection and was correlated with OR. RESULTS: The average increase in IOP following IVI was 19±9 mm Hg, with a range of 7-33 mm Hg. The Spearman correlation coefficient between OR and IOP elevation following IVI was 0.796 (p<0.001), showing higher IOP elevation in more rigid eyes. A regression line was also calculated to predict the IOP spike based on the OR coefficient, such that IOP spike=664.17 mm Hg·µL×OR + 4.59 mm Hg. CONCLUSION: This study shows a strong positive correlation between OR and acute IOP elevation following IVI. These findings indicate that the non-invasive measurement of OR could be an effective tool in identifying patients at risk of IOP spikes following IVI.

The Association Between Ocular Rigidity and Neuroretinal Damage in Glaucoma.

Purpose: Ocular rigidity (OR) is an important biomechanical property, thought to be relevant in the pathophysiology of open-angle glaucoma (OAG). This study aims to evaluate the relationship between OR and neuroretinal damage caused by glaucoma. Methods: One hundred eight subjects (22 with healthy eyes, 23 with suspect discs, and 63 with OAG) were included in this study. OR was measured using a noninvasive optical coherence tomography (OCT)-based method developed by our group. We also measured central corneal thickness (CCT), corneal hysteresis (CH), and corneal resistance factor (CRF). Pearson and partial correlations were performed to evaluate the relationship between OR and glaucomatous damage represented by ganglion cell complex (GCC), retinal nerve fiber layer (RNFL) thicknesses, and neuroretinal rim area. Results: Significant positive correlations were found between OR and minimum GCC thickness (r = 0.325, P = 0.001), average GCC thickness (r = 0.320, P = 0.002), rim area (r = 0.344, P < 0.001), and RNFL thickness in the superior (r = 0.225, P = 0.023), and inferior (r = 0.281, P = 0.004) quadrants. These correlations were generally greater than those found for CCT, CH, and CRF. Furthermore, no correlation was found between OR and corneal biomechanical parameters. After adjusting for age, sex, and ethnicity, significant correlations were found between OR and minimum and average GCC thickness (r = 0.357, P = 0.001 and r = 0.344, P = 0.001, respectively), rim area (r = 0.327, P = 0.001), average RNFL thickness (r = 0.331, P = 0.001), and RNFL thickness in the superior (r = 0.296, P = 0.003) and inferior (r = 0.317, P = 0.001) quadrants. Conclusions: In this study, we found a positive correlation between structural OCT-based parameters and OR, indicating more neuroretinal damage in eyes with lower OR. These findings could provide insight into the pathophysiology of OAG.

Novel Anti-Interleukin-1ß Therapy Preserves Retinal Integrity: A Longitudinal Investigation Using OCT Imaging and Automated Retinal Segmentation in Small Rodents.

Retinopathy of prematurity (ROP) is the leading cause of blindness in neonates. Inflammation, in particular interleukin-1ß (IL-1ß), is increased in early stages of the disorder, and contributes to inner and outer retinal vasoobliteration in the oxygen-induced retinopathy (OIR) model of ROP. A small peptide antagonist of IL-1 receptor, composed of the amino acid sequence, rytvela, has been shown to exert beneficial anti-inflammatory effects without compromising immunovigilance-related NF-κB in reproductive tissues. We conducted a longitudinal study to determine the efficacy of "rytvela" in preserving the integrity of the retina in OIR model, using optical coherence tomography (OCT) which provides high-resolution cross-sectional imaging of ocular structures in vivo. Sprague-Dawley rats subjected to OIR and treated or not with "rytvela" were compared to IL-1 receptor antagonist (Kineret). OCT imaging and custom automated segmentation algorithm used to measure retinal thickness (RT) were obtained at P14 and P30; gold-standard immunohistochemistry (IHC) was used to confirm retinal anatomical changes. OCT revealed significant retinal thinning in untreated animals by P30, confirmed by IHC; these changes were coherently associated with increased apoptosis. Both rytvela and Kineret subsided apoptosis and preserved RT. As anticipated, Kineret diminished both SAPK/JNK and NF-κB axes, whereas rytvela selectively abated the former which resulted in preserved monocyte phagocytic function. Altogether, OCT imaging with automated segmentation is a reliable non-invasive approach to study longitudinally retinal pathology in small animal models of retinopathy.

BMP9 signaling promotes the normalization of tumor blood vessels.

The presence of an immature tumor vascular network contributes to cancer dissemination and the development of resistance to therapies. Strategies to normalize the tumor vasculature are therefore of significant therapeutic interest for cancer treatments. VEGF inhibitors are used clinically to normalize tumor blood vessels. However, the time frame and dosage of these inhibitors required to achieve normalization is rather narrow, and there is a need to identify additional signaling targets to attain vascular normalization. In addition to VEGF, the endothelial-specific receptor Alk1 plays a critical role in vascular development and promotes vascular remodeling and maturation. Therefore, we sought to evaluate the effects of the Alk1 ligand BMP9 on tumor vascular formation. BMP9 overexpression in Lewis Lung Carcinoma (LLC) tumors significantly delayed tumor growth. Blood vessels in BMP9-overexpressing LLC tumors displayed markers of vascular maturation and were characterized by increased perivascular cell coverage. Tumor vasculature normalization was associated with decreased permeability and increased perfusion. These changes in vascular function in BMP9-overexpressing LLC tumors resulted in significant alterations of the tumor microenvironment, characterized by a decrease in hypoxia and an increase in immune infiltration. In conclusion, we show that BMP9 promotes vascular normalization in LLC tumors that leads to changes in the microenvironment.

C3a elicits unique migratory responses in immature low-density neutrophils.

Neutrophils represent the immune system's first line of defense and are rapidly recruited into inflamed tissue. In cancer associated inflammation, phenotypic heterogeneity has been ascribed to this cell type, whereby neutrophils can manifest anti- or pro-metastatic functions depending on the cellular/micro-environmental context. Here, we demonstrate that pro-metastatic immature low-density neutrophils (iLDNs) more efficiently accumulate in the livers of mice bearing metastatic lesions compared with anti-metastatic mature high-density neutrophils (HDNs). Transcriptomic analyses reveal enrichment of a migration signature in iLDNs relative to HDNs. We find that conditioned media derived from liver-metastatic breast cancer cells, but not lung-metastatic variants, specifically induces chemotaxis of iLDNs and not HDNs. Chemotactic responses are due to increased surface expression of C3aR in iLDNs relative to HDNs. In addition, we detect elevated secretion of cancer-cell derived C3a from liver-metastatic versus lung-metastatic breast cancer cells. Perturbation of C3a/C3aR signaling axis with either a small molecule inhibitor, SB290157, or reducing the levels of secreted C3a from liver-metastatic breast cancer cells by short hairpin RNAs, can abrogate the chemotactic response of iLDNs both in vitro and in vivo, respectively. Together, these data reveal novel mechanisms through which iLDNs prefentially accumulate in liver tissue harboring metastases in response to tumor-derived C3a secreted from the liver-aggressive 4T1 breast cancer cells.

A potent nuclear export mechanism imposes USP16 cytoplasmic localization during interphase.

USP16 (also known as UBP-M) has emerged as a histone H2AK119 deubiquitylase (DUB) implicated in the regulation of chromatin-associated processes and cell cycle progression. Despite this, available evidence suggests that this DUB is also present in the cytoplasm. How the nucleo-cytoplasmic transport of USP16, and hence its function, is regulated has remained elusive. Here, we show that USP16 is predominantly cytoplasmic in all cell cycle phases. We identified the nuclear export signal (NES) responsible for maintaining USP16 in the cytoplasm. We found that USP16 is only transiently retained in the nucleus following mitosis and then rapidly exported from this compartment. We also defined a non-canonical nuclear localization signal (NLS) sequence that plays a minimal role in directing USP16 into the nucleus. We further established that this DUB does not accumulate in the nucleus following DNA damage. Instead, only enforced nuclear localization of USP16 abolishes DNA double-strand break (DSB) repair, possibly due to unrestrained DUB activity. Thus, in contrast to the prevailing view, our data indicate that USP16 is actively excluded from the nucleus and that this DUB might indirectly regulate DSB repair.This article has an associated First Person interview with the first author of the paper.

Non-invasive in vivo measurement of ocular rigidity: Clinical validation, repeatability and method improvement.

Ocular rigidity (OR) is thought to play a role in the pathogenesis of glaucoma, but the lack of reliable non-invasive measurements has been a major technical challenge. We recently developed a clinical method using optical coherence tomography time-lapse imaging and automated choroidal segmentation to measure the pulsatile choroidal volume change (ΔV) and calculate OR using Friedenwald's equation. Here we assess the validity and repeatability of this non-invasive technique. We also propose an improved mathematical model of choroidal thickness to extrapolate ΔV from the pulsatile submacular choroidal thickness change more accurately. The new mathematical model uses anatomical data accounting for the choroid thickness near the equator. The validity of the technique was tested by comparing OR coefficients obtained using our non-invasive method (OROCT) and those obtained with an invasive procedure involving intravitreal injections of Bevacizumab (ORIVI) in 12 eyes. Intrasession and intersession repeatability was assessed for 72 and 8 eyes respectively with two consecutive measurements of OR. Using the new mathematical model, we obtained OR values which are closer to those obtained using the invasive procedure and previously reported techniques. A regression line was calculated to predict the ORIVI based on OROCT, such that ORIVI = 0.655 × OROCT. A strong correlation between OROCT and ORIVI was found, with a Spearman coefficient of 0.853 (p < 0.001). The intraclass correlation coefficient for intrasession and intersession repeatability was 0.925, 95% CI [0.881, 0.953] and 0.950, 95% CI [0.763, 0.990] respectively. This confirms the validity and good repeatability of OR measurements using our non-invasive clinical method.

Stalled developmental programs at the root of pediatric brain tumors.

Childhood brain tumors have suspected prenatal origins. To identify vulnerable developmental states, we generated a single-cell transcriptome atlas of >65,000 cells from embryonal pons and forebrain, two major tumor locations. We derived signatures for 191 distinct cell populations and defined the regional cellular diversity and differentiation dynamics. Projection of bulk tumor transcriptomes onto this dataset shows that WNT medulloblastomas match the rhombic lip-derived mossy fiber neuronal lineage and embryonal tumors with multilayered rosettes fully recapitulate a neuronal lineage, while group 2a/b atypical teratoid/rhabdoid tumors may originate outside the neuroectoderm. Importantly, single-cell tumor profiles reveal highly defined cell hierarchies that mirror transcriptional programs of the corresponding normal lineages. Our findings identify impaired differentiation of specific neural progenitors as a common mechanism underlying these pediatric cancers and provide a rational framework for future modeling and therapeutic interventions.

Opto-magnetic capture of individual cells based on visual phenotypes.

The ability to isolate rare live cells within a heterogeneous population based solely on visual criteria remains technically challenging, due largely to limitations imposed by existing sorting technologies. Here, we present a new method that permits labeling cells of interest by attaching streptavidin-coated magnetic beads to their membranes using the lasers of a confocal microscope. A simple magnet allows highly specific isolation of the labeled cells, which then remain viable and proliferate normally. As proof of principle, we tagged, isolated, and expanded individual cells based on three biologically relevant visual characteristics: i) presence of multiple nuclei, ii) accumulation of lipid vesicles, and iii) ability to resolve ionizing radiation-induced DNA damage foci. Our method constitutes a rapid, efficient, and cost-effective approach for isolation and subsequent characterization of rare cells based on observable traits such as movement, shape, or location, which in turn can generate novel mechanistic insights into important biological processes.

Exploiting Molecular Barcodes in High-Throughput Cellular Assays.

Multiplexing strategies, which greatly increase the number of simultaneously measured parameters in single experiments, are now being widely implemented by both the pharmaceutical industry and academic researchers. Color has long been used to identify biological signals and, when combined with molecular barcodes, has substantially enhanced the depth of multiplexed sample characterization. Moreover, the recent advent of DNA barcodes has led to an explosion of innovative cell sequencing approaches. Novel barcoding strategies also show great promise for encoding spatial information in transcriptomic studies, and for precise assessment of molecular abundance. Both color- and DNA-based barcodes can be conveniently analyzed with either a microscope or a cytometer, or via DNA sequencing. Here we review the basic principles of several technologies used to create barcodes and detail the type of samples that can be identified with such tags.