Single cell analysis: the new frontier in ‘Omics’ Daojing Wang 1 and Steven Bodovitz 2 1. Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 2. BioPerspectives, San Francisco, CA Corresponding author: Wang, D. (djwang@lbl.gov) Cellular heterogeneity arising from stochastic expression of genes, proteins, and metabolites is a fundamental principle of cell biology, but single cell analysis has been beyond the capabilities of ‘Omics’ technologies. This is rapidly changing with the recent examples of single cell genomics, transcriptomics, proteomics, and metabolomics. The rate of change is expected to accelerate owing to emerging technologies that range from micro/nanofluidics to microfabricated interfaces for mass spectrometry to third- and fourth-generation automated DNA sequencers. As described in this review, single cell analysis is the new frontier in Omics, and single cell Omics has the potential to transform systems biology through new discoveries derived from cellular heterogeneity. Single cell analysis: needs and applications Cellular heterogeneity Cellular heterogeneity within an isogenic cell population is a widespread event [1, 2]. Stochastic gene and protein expression at the single cell level has been clearly demonstrated in different systems using a variety of techniques [3-5]. Therefore, analyzing cell ensembles individually with high spatiotemporal resolutions will lead to a

Single cell analysis: the new frontier in 'Omics'

High-throughput metabolic analysis is of significance in diagnostics, while tedious sample pretreatment has largely hindered its clinic application. Herein, we designed FeOOH@ZIF-8 composites with enhanced ionization efficiency and size-exclusion effect for laser desorption/ionization mass spectrometry (LDI-MS)-based metabolic diagnosis of gynecological cancers. The FeOOH@ZIF-8-assisted LDI-MS achieved rapid, sensitive, and selective metabolic fingerprints of the native serum without any enrichment or purification. Further analysis of extracted serum metabolic fingerprints successfully discriminated patients with gynecological cancers (GCs) from healthy controls and also differentiated three major subtypes of GCs. Given the low cost, high-throughput, and easy operation, our approach brings a new dimension to disease analysis and classification.

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FeOOH@Metal–Organic Framework Core–Satellite Nanocomposites for the Serum Metabolic Fingerprinting of Gynecological Cancers

Schizophrenia (SZ) detection enables effective treatment to improve the clinical outcome, but objective and reliable SZ diagnostics are still limited. An ideal diagnosis of SZ suited for robust clinical screening must address detection throughput, low invasiveness, and diagnosis accuracy. Herein, we built a multi-shelled hollow Cr 2 O 3 spheres (MHCSs) assisted laser desorption/ionization mass spectrometry (LDI MS) platform for the direct metabolic profiling of biofluids towards SZ diagnostics. The MHCSs displayed strong light absorption for enhanced ionization and microscale surface roughness with stability for the effective LDI of metabolites. We profiled urine and serum metabolites (~ 1 μL) with the enhanced LDI efficacy in seconds. We discriminated SZ patients (SZs) from healthy controls (HCs) with the highest area under the curve (AUC) value of 1.000 for the blind test. We identified four compounds with optimal diagnostic power as a simplified metabolite panel for SZ and demonstrated the metabolite quantification for clinic use. Our approach accelerates the growth of new platforms toward a precision diagnosis in the near future.

Design of Multi-Shelled Hollow Cr2O3 Spheres for Metabolic Fingerprinting

The conventional microbial cell analyses are mostly population-averaged methods that conceal the characteristics of single-cell in the community. Single-cell analysis can provide information on the functional and structural variation of each cell, resulting in the elimination of long and tedious microbial cultivation techniques. Raman spectroscopy is a label-free, noninvasive, and in-vivo method ideal for single-cell measurement to obtain spatially resolved chemical information. In the current review, recent developments in Raman spectroscopic techniques for microbial characterization at the single-cell level are presented, focusing on Raman imaging of single cells to study the intracellular distribution of different components. The review also discusses the limitation and challenges of each technique and put forward some future outlook for improving Raman spectroscopy-based techniques for single-cell analysis. Raman spectroscopic methods at the single-cell level have potential in precision measurements, metabolic analysis, antibiotic susceptibility testing, resuscitation capability, and correlating phenotypic information to genomics for cells, the integration of Raman spectroscopy with other techniques such as microfluidics, stable isotope probing (SIP), and atomic force microscope can further improve the resolution and provide extensive information. Future focuses should be given to advance algorithms for data analysis, standardized reference libraries, and automated cell isolation techniques in future.

Recent developments in Raman spectral analysis of microbial single cells: Techniques and applications.

Low molecular weight compounds play an important role in encoding the current physiological state of an individual Laser desorption/ionization mass spectrometry (LDI MS) offers high sensitivity with low cost for molecular detection, but it is not able to cover small molecules due to the drawbacks of the conventional matrix Advanced materials are better alternatives, showing little background interference and high LDI efficiency Herein, we first classify the current materials with a summary of compositions and structures Matrix preparation protocols are then reviewed, to enhance the selectivity and reproducibility of MS data better Finally, we highlight the biomedical applications of material-assisted LDI MS, at the tissue, bio-fluid, and cellular levels We foresee that the advanced materials will bring far-reaching implications in LDI MS towards real-case applications, especially in clinical settings

Material-assisted mass spectrometric analysis of low molecular weight compounds for biomedical applications

Metal‐Organic Framework Hybrids Aid Metabolic Profiling for Colorectal Cancer

Given the existence of cell heterogeneity, single cell analysis is undergoing a rapid expansion for life science and precision medicine. Recent numerous innovations in analytical platforms and instruments have re-energized the field and led to the emergence of single cell omics with high sensitivity, throughput and multiplexity. The omics knowledge builds the bridge between underlying molecular changes and cell behavior, and facilitates a deeper understanding of disease development processes. Here, the authors highlight important achievements of single cell omics mainly including genomics, epigenomics, transcriptomics, proteomics, and metabolomics, and discuss the biomedical applications of single cell omics in stem cells differentiation, immune cells function, nerve cells development and activity, and circulating tumor cells based cancer research.

https://onlinelibrary.wiley.com/doi/epdf/10.1002/biot.201900262

Single Cell Omics: From Assay Design to Biomedical Application.

We designed a novel polymer-metal oxide nanoparticles matrix for the detection of the metabolites analyzed using laser desorption/ionization mass spectrometry (MALDI MS). These nanoparticles were sensitive towards the small molecules. Due to their unique surface morphology and physicochemical properties, these nanoparticles demonstrated superior multiplicity, salt and protein tolerance in the analysis of small molecules. Our research suggested the utility of conductive polymers as potential matrix in the LDI MS detection.

Polymer-metal Oxide Nanoparticles for Small Metabolite Detection

Novel plate-like metal oxide nanostructure was demonstrated for analysis of small metabolites by laser desorption/ionization mass spectrometry (LDI MS). We prepared the nanoplates using hydrothermal method. Owing to the unique nanostructure and physicochemical properties, our method displayed high sensitivity and high accuracy towards the analysis of standard molecules and metabolites of serum samples. The nanomaterials also indicated great salt tolerance and protein endurance in complex biosamples in LDI MS. This work provided an innovative matrix for metabolic analysis and clinical diagnose in LDI MS.

Anuja Shreeram Kulkarni

Papers

Metal‐Organic Framework Hybrids Aid Metabolic Profiling for Colorectal Cancer

Single Cell Omics: From Assay Design to Biomedical Application.

Material-assisted mass spectrometric analysis of low molecular weight compounds for biomedical applications

Polymer-metal Oxide Nanoparticles for Small Metabolite Detection

Plate-like Metal Oxide Nanostructure for Detection of Small Metabolites by Mass Spectrometry