Proximity sequencing for the detection of mRNA, extracellular proteins and extracellular protein complexes in single cells.

Complex cellular functions occur via the coordinated formation and dissociation of protein complexes. Functions such as the response to a signaling ligand can incorporate dozens of proteins and hundreds of complexes. Until recently, it has been difficult to measure multiple protein complexes at the single-cell level. Here, we present a step-by-step procedure for proximity sequencing, which enables the simultaneous measurement of proteins, mRNA and hundreds of protein complexes located on the outer membrane of cells. We guide the user through probe creation, sample preparation, staining, sequencing and computational quantification of protein complexes. This protocol empowers researchers to study, for example, the interplay between transcriptional states and cellular functions by coupling measurements of transcription to measurements of linked effector molecules, yet could be generalizable to other paired events. The protocol requires roughly 16 h spread over several days to complete by users with expertise in basic molecular biology and single-cell sequencing.

Processing stimulus dynamics by the NF-κB network in single cells.

Cells at the site of an infection experience numerous biochemical signals that vary in amplitude, space, and time. Despite the diversity of dynamic signals produced by pathogens and sentinel cells, information-processing pathways converge on a limited number of central signaling nodes to ultimately control cellular responses. In particular, the NF-κB pathway responds to dozens of signals from pathogens and self, and plays a vital role in processing proinflammatory inputs. Studies addressing the influence of stimulus dynamics on NF-κB signaling are rare due to technical limitations with live-cell measurements. However, recent advances in microfluidics, automation, and image analysis have enabled investigations that yield high temporal resolution at the single-cell level. Here, we summarize the recent research which measures and models the NF-κB response to pulsatile and fluctuating stimulus concentrations, as well as different combinations and sequences of signaling molecules. Collectively, these studies show that the NF-κB network integrates external inflammatory signals and translates these into downstream transcriptional responses.

Quantification of extracellular proteins, protein complexes and mRNAs in single cells by proximity sequencing.

We present proximity sequencing (Prox-seq) for simultaneous measurement of proteins, protein complexes and mRNAs in thousands of single cells. Prox-seq combines proximity ligation assay with single-cell sequencing to measure proteins and their complexes from all pairwise combinations of targeted proteins, providing quadratically scaled multiplexing. We validate Prox-seq and analyze a mixture of T cells and B cells to show that it accurately identifies these cell types and detects well-known protein complexes. Next, by studying human peripheral blood mononuclear cells, we discover that naïve CD8+ T cells display the protein complex CD8-CD9. Finally, we study protein interactions during Toll-like receptor (TLR) signaling in human macrophages. We observe the formation of signal-specific protein complexes, find CD36 co-receptor activity and additive signal integration under lipopolysaccharide (TLR4) and Pam2CSK4 (TLR2) stimulation, and show that quantification of protein complexes identifies signaling inputs received by macrophages. Prox-seq provides access to an untapped measurement modality for single-cell phenotyping and can discover uncharacterized protein interactions in different cell types.

Graphene Wrinkles Enable Spatially Defined Chemistry.

This paper reports a scalable approach to achieve spatially selective graphene functionalization using multiscale wrinkles. Graphene wrinkles were formed by relieving the strain in thermoplastic polystyrene substrates conformally coated with fluoropolymer and graphene skin layers. Chemical reactivity of a fluorination process could be tuned by changing the local curvature of the graphene nanostructures. Patterned areas of graphene nanowrinkles and crumples followed by a single-process plasma reaction resulted in substrates with regions having different fluorination levels. Notably, conductivity of the functionalized graphene nanostructures could be locally tuned as a function of feature size without affecting the mechanical properties.

Quantum Capacitance Based Amplified Graphene Phononics for Studying Neurodegenerative Diseases.

Amyotrophic lateral sclerosis (ALS) is the most common adult-onset motor neuron disease (MND) characterized by a rapid loss of upper and lower motor neurons resulting in patient death from respiratory failure within 3-5 years of initial symptom onset. Although at least 30 genes of major effect have been reported, the pathobiology of ALS is not well understood. Compounding this is the lack of a reliable laboratory test which can accurately diagnose this rapidly deteriorating disease. Herein, we report on the phonon vibration energies of graphene as a sensitive measure of the composite dipole moment of the interfaced cerebrospinal fluid (CSF) that includes a signature-composition specific to the patients with ALS disease. The second-order overtone of in-plane phonon vibration energy (2D peak) of graphene shifts by 3.2 ± 0.5 cm-1 for all ALS patients studied in this work. Further, the amount of n-doping-induced shift in the phonon energy of graphene, interfaced with CSF, is specific to the investigated neurodegenerative disease (ALS, multiple sclerosis, and MND). By removing a severe roadblock in disease detection, this technology can be applied to study diagnostic biomarkers for researchers developing therapeutics and clinicians initiating treatments for neurodegenerative diseases.

Cancer Cell Hyperactivity and Membrane Dipolarity Monitoring via Raman Mapping of Interfaced Graphene: Toward Non-Invasive Cancer Diagnostics.

Ultrasensitive detection, mapping, and monitoring of the activity of cancer cells is critical for treatment evaluation and patient care. Here, we demonstrate that a cancer cell's glycolysis-induced hyperactivity and enhanced electronegative membrane (from sialic acid) can sensitively modify the second-order overtone of in-plane phonon vibration energies (2D) of interfaced graphene via a hole-doping mechanism. By leveraging ultrathin graphene's high quantum capacitance and responsive phononics, we sensitively differentiated the activity of interfaced Glioblastoma Multiforme (GBM) cells, a malignant brain tumor, from that of human astrocytes at a single-cell resolution. GBM cell's high surface electronegativity (potential ∼310 mV) and hyperacidic-release induces hole-doping in graphene with a 3-fold higher 2D vibration energy shift of approximately 6 ± 0.5 cm-1 than astrocytes. From molecular dipole-induced quantum coupling, we estimate that the sialic acid density on the cell membrane increases from one molecule per ∼17 nm2 to one molecule per ∼7 nm2. Furthermore, graphene phononic response also identified enhanced acidity of cancer cell's growth medium. Graphene's phonon-sensitive platform to determine interfaced cell's activity/chemistry will potentially open avenues for studying activity of other cancer cell types, including metastatic tumors, and characterizing different grades of their malignancy.