automated-sample-preparation-for-multiplexed-analysis-single-cell

Automated Sample Preparation for the Multiplexed Analysis of Single-Cell Histone Post-Translational Modifications (sc-hPTM2)

Histone post-translational modifications (hPTMs) are central regulators of chromatin organization and gene expression. Their dysregulation is implicated ...

SCIENION

Liquid cell transmission electron microscopy (LCTEM) provides a unique insight into the dynamics of nanomaterials in solution. Controlling the addition of multiple solutions to the liquid cell remains a key hurdle in our ability to increase throughput and to study processes dependent on solution mixing including chemical reactions. Here, we report that a piezo dispensing technique allows for mixing of multiple solutions directly within the viewing area. This technique permits deposition of 50 pL droplets of various aqueous solutions onto the liquid cell window, before assembly of the cell in a fully controlled manner. This proof-of-concept study highlights the great potential of picoliter dispensing in combination with LCTEM for observing nanoparticle mixing in the solution phase and the creation of chemical gradients.

Picoliter Drop-On-Demand Dispensing for Multiplex Liquid Cell Transmission Electron Microscopy.

Oral delivery of therapeutics is the preferred route for systemic drug administration due to ease of access and improved patient compliance. However, many therapeutics suffer from low oral bioavailability due to low pH and enzymatic conditions, poor cellular permeability, and low residence time. Microfabrication techniques have been used to create planar, asymmetric microdevices for oral drug delivery to address these limitations. The geometry of these microdevices facilitates prolonged drug exposure with unidirectional release of drug toward gastrointestinal epithelium. While these devices have significantly enhanced drug permeability  and , loading drug into the micron-scale reservoirs of the devices in a low-waste, high-capacity manner remains challenging. Here, we use picoliter-volume inkjet printing to load topotecan and insulin into planar microdevices efficiently. Following a simple surface functionalization step, drug solution can be spotted into the microdevice reservoir. We show that relatively high capacities of both topotecan and insulin can be loaded into microdevices in a rapid, automated process with little to no drug waste.

Picoliter-volume inkjet printing into planar microdevice reservoirs for low-waste, high-capacity drug loading.

In this paper, we describe the use of liquid cell transmission electron microscopy (LCTEM) for inducing and imaging the formation of spherical micelles from amphiphilic block copolymers. Within the irradiated region of the liquid cell, diblock copolymers were produced which self-assembled, yielding a targeted spherical micellar phase via polymerization-induced self-assembly (PISA). Critically, we demonstrate that nanoparticle formation can be visualized in situ and that in the presence of excess monomer, nanoparticle growth occurs to yield sizes and morphologies consistent with standard PISA conditions. Experiments were enabled by employing automated LCTEM sample preparation and by analyzing LCTEM data with multi-object tracking algorithms designed for the detection of low-contrast materials.

Polymerization-Induced Self-Assembly of Micelles Observed by Liquid Cell Transmission Electron Microscopy.

Single-cell RNA sequencing (scRNA-seq) of tissues has revealed remarkable heterogeneity of cell types and states but does not provide information on the spatial organization of cells. To better understand how individual cells function within an anatomical space, we developed XYZeq, a workflow that encodes spatial metadata into scRNA-seq libraries. We used XYZeq to profile mouse tumor models to capture spatially barcoded transcriptomes from tens of thousands of cells. Analyses of these data revealed the spatial distribution of distinct cell types and a cell migration-associated transcriptomic program in tumor-associated mesenchymal stem cells (MSCs). Furthermore, we identify localized expression of tumor suppressor genes by MSCs that vary with proximity to the tumor core. We demonstrate that XYZeq can be used to map the transcriptome and spatial localization of individual cells in situ to reveal how cell composition and cell states can be affected by location within complex pathological tissue.

XYZeq: Spatially resolved single-cell RNA sequencing reveals expression heterogeneity in the tumor microenvironment.

Automated, pulsed liquid-phase sample delivery has the potential to greatly improve the efficiency of both sample and photon use at pulsed X-ray facilities. In this work, an automated drop on demand (DOD) system that accelerates sample exchange for serial femtosecond crystallography (SFX) is demonstrated. Four different protein crystal slurries were tested, and this technique is further improved here with an automatic sample-cycling system whose effectiveness was verified by the indexing results. Here, high-throughput SFX screening is shown to be possible at free-electron laser facilities with very low risk of cross contamination and minimal downtime. The development of this technique will significantly reduce sample consumption and enable structure determination of proteins that are difficult to crystallize in large quantities. This work also lays the foundation for automating sample delivery.

Serial crystallography using automated drop dispensing.

Many biological processes, such as cell division cycle and drug resistance, are reflected in protein covariation across single cells. This covariation can be quantified and interpreted by single-cell mass spectrometry with sufficiently high throughput and accuracy.

Exploring functional protein covariation across single cells using nPOP.

Single-cell proteomics by mass spectrometry (MS) allows quantifying proteins with high specificity and sensitivity. To increase its throughput, we developed nPOP, a method for parallel preparation of thousands of single cells in nanoliter volume droplets deposited on glass slides. Here, we describe its protocol with emphasis on its flexibility to prepare samples for different multiplexed MS methods. An implementation with plexDIA demonstrates accurate quantification of about 3,000 - 3,700 proteins per human cell. The protocol is implemented on the CellenONE instrument and uses readily available consumables, which should facilitate broad adoption. nPOP can be applied to all samples that can be processed to a single-cell suspension. It takes 1 or 2 days to prepare over 3,000 single cells. We provide metrics and software for quality control that can support the robust scaling of nPOP to higher plex reagents for achieving reliable high-throughput single-cell protein analysis.

Massively parallel sample preparation for multiplexed single-cell proteomics using nPOP.

Single-cell proteomics by mass spectrometry (MS) allows the quantification of proteins with high specificity and sensitivity. To increase its throughput, we developed nano-proteomic sample preparation (nPOP), a method for parallel preparation of thousands of single cells in nanoliter-volume droplets deposited on glass slides. Here, we describe its protocol with emphasis on its flexibility to prepare samples for different multiplexed MS methods. An implementation using the plexDIA MS multiplexing method, which uses non-isobaric mass tags to barcode peptides from different samples for data-independent acquisition, demonstrates accurate quantification of ~3,000-3,700 proteins per human cell. A separate implementation with isobaric mass tags and prioritized data acquisition demonstrates analysis of 1,827 single cells at a rate of >1,000 single cells per day at a depth of 800-1,200 proteins per human cell. The protocol is implemented by using a cell-dispensing and liquid-handling robot-the CellenONE instrument-and uses readily available consumables, which should facilitate broad adoption. nPOP can be applied to all samples that can be processed to a single-cell suspension. It takes 1 or 2 d to prepare >3,000 single cells. We provide metrics and software (the QuantQC R package) for quality control and data exploration. QuantQC supports the robust scaling of nPOP to higher plex reagents for achieving reliable and scalable single-cell proteomics.

Single-cell proteomics confidently quantifies cellular heterogeneity, however quantification of post-translational modifications, such as those deposited on histone proteins, remains elusive. Here, we develop a robust mass spectrometry-based method for the unbiased analysis of single-cell histone post-translational modifications (sc-hPTM). sc-hPTM identifies both single- and combinatorial histone post-translational modifications (67 peptidoforms in total), which includes nearly all frequently studied histone post-translational modifications with comparable reproducibility to traditional bulk experiments. As a proof of concept, we treat cells with sodium butyrate, a histone deacetylase inhibitor, and demonstrate that our method can i) distinguish between treated and untreated cells, ii) identify sub-populations of cells with heterogeneous response to the treatment, and iii) reveal differential co-regulation of histone post-translational modifications in the context of drug treatment. The sc-hPTM method enables comprehensive investigation of chromatin heterogeneity at single-cell resolution and provides a further understanding of the histone code.

Article	Year
Picoliter Drop-On-Demand Dispensing for Multiplex Liquid Cell Transmission Electron Microscopy. Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada\| PubMed ID: 27135268	2016
Picoliter-volume inkjet printing into planar microdevice reservoirs for low-waste, high-capacity drug loading. Bioengineering & translational medicine\| PubMed ID: 28503662	2017
Polymerization-Induced Self-Assembly of Micelles Observed by Liquid Cell Transmission Electron Microscopy. ACS central science\| PubMed ID: 29806000	2018
XYZeq: Spatially resolved single-cell RNA sequencing reveals expression heterogeneity in the tumor microenvironment. Science advances\| PubMed ID: 33883145	2021
Serial crystallography using automated drop dispensing. Journal of synchrotron radiation\| PubMed ID: 34475287	2021
Exploring functional protein covariation across single cells using nPOP. Genome biology\| PubMed ID: 36527135	2022
Massively parallel sample preparation for multiplexed single-cell proteomics using nPOP. bioRxiv : the preprint server for biology\| PubMed ID: 38076795	2023
Massively parallel sample preparation for multiplexed single-cell proteomics using nPOP. Nature protocols\| PubMed ID: 39117766	2024
Mass spectrometry-based profiling of single-cell histone post-translational modifications to dissect chromatin heterogeneity. Nature communications\| PubMed ID: 41387402	2025

Joshua Cantlon

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