Single cell proteomics microchip to profile immune function, with applications in stem cell biology, translational disease mechanism study and clinical therapeutics monitoring

In response to infection or tissue dysfunction, immune cells develop into highly heterogeneous repertoires with diverse functions. Capturing the full spectrum of these functions requires analysis of large numbers of effector molecules from single cells. However, currently only 3-5 functional proteins can be measured from single cells. We developed a single cell functional proteomics approach that integrates a microchip platform with multiplex cell purification. This approach can quantitate 20 proteins from >5,000 phenotypically pure single cells simultaneously. With a 1-million fold miniaturization, the system can detect down to ~100 molecules and requires only ~104 cells. Single cell functional proteomic analysis finds broad applications in basic, translational and clinical studies. In the three studies conducted, it yielded critical insights for understanding clinical cancer immunotherapy, inflammatory bowel disease (IBD) mechanism and hematopoietic stem cell (HSC) biology.

To study phenotypically defined cell populations, single cell barcode microchips were coupled with upstream multiplex cell purification based on up to 11 parameters. Statistical algorithms were developed to process and model the high dimensional readouts. This analysis evaluates rare cells and is versatile for various cells and proteins. (1) We conducted an immune monitoring study of a phase 2 cancer cellular immunotherapy clinical trial that used T-cell receptor (TCR) transgenic T cells as major therapeutics to treat metastatic melanoma. We evaluated the functional proteome of 4 antigen-specific, phenotypically defined T cell populations from peripheral blood of 3 patients across 8 time points. (2) Natural killer (NK) cells can play a protective role in chronic inflammation and their surface receptor – killer immunoglobulin-like receptor (KIR) – has been identified as a risk factor of IBD. We compared the functional behavior of NK cells that had differential KIR expressions. These NK cells were retrieved from the blood of 12 patients with different genetic backgrounds. (3) HSCs are the progenitors of immune cells and are thought to have no immediate functional capacity against pathogen. However, recent studies identified expression of Toll-like receptors (TLRs) on HSCs. We studied the functional capacity of HSCs upon TLR activation. The comparison of HSCs from wild-type mice against those from genetics knock-out mouse models elucidates the responding signaling pathway.

In all three cases, we observed profound functional heterogeneity within phenotypically defined cells. Polyfunctional cells that conduct multiple functions also produce those proteins in large amounts. They dominate the immune response. In the cancer immunotherapy, the strong cytotoxic and antitumor functions from transgenic TCR T cells contributed to a ~30% tumor reduction immediately after the therapy. However, this infused immune response disappeared within 2-3 weeks. Later on, some patients gained a second antitumor response, consisted of the emergence of endogenous antitumor cytotoxic T cells and their production of multiple antitumor functions. These patients showed more effective long-term tumor control. In the IBD mechanism study, we noticed that, compared with others, NK cells expressing KIR2DL3 receptor secreted a large array of effector proteins, such as TNF-α, CCLs and CXCLs. The functions from these cells regulated disease-contributing cells and protected host tissues. Their existence correlated with IBD disease susceptibility. In the HSC study, the HSCs exhibited functional capacity by producing TNF-α, IL-6 and GM-CSF. TLR stimulation activated the NF-κB signaling in HSCs. Single cell functional proteome contains rich information that is independent from the genome and transcriptome. In all three cases, functional proteomic evaluation uncovered critical biological insights that would not be resolved otherwise. The integrated single cell functional proteomic analysis constructed a detail kinetic picture of the immune response that took place during the clinical cancer immunotherapy. It revealed concrete functional evidence that connected genetics to IBD disease susceptibility. Further, it provided predictors that correlated with clinical responses and pathogenic outcomes.

Strength of tantalum at high pressures through Richtmyer-Meshkov laser compression experiments and simulations

Strength at extreme pressures (>1 Mbar or 100 GPa) and high strain rates (106-108 s-1) of materials is not well characterized. The goal of the research outlined in this thesis is to study the strength of tantalum (Ta) at these conditions. The Omega Laser in the Laboratory for Laser Energetics in Rochester, New York is used to create such extreme conditions. Targets are designed with ripples or waves on the surface, and these samples are subjected to high pressures using Omega’s high energy laser beams. In these experiments, the observational parameter is the Richtmyer-Meshkov (RM) instability in the form of ripple growth on single-mode ripples. The experimental platform used for these experiments is the “ride-along” laser compression recovery experiments, which provide a way to recover the specimens having been subjected to high pressures. Six different experiments are performed on the Omega laser using single-mode tantalum targets at different laser energies. The energy indicates the amount of laser energy that impinges the target. For each target, values for growth factor are obtained by comparing the profile of ripples before and after the experiment. With increasing energy, the growth factor increased.

Engineering simulations are used to interpret and correlate the measurements of growth factor to a measure of strength. In order to validate the engineering constitutive model for tantalum, a series of simulations are performed using the code Eureka, based on the Optimal Transportation Meshfree (OTM) method. Two different configurations are studied in the simulations: RM instabilities in single and multimode ripples. Six different simulations are performed for the single ripple configuration of the RM instability experiment, with drives corresponding to laser energies used in the experiments. Each successive simulation is performed at higher drive energy, and it is observed that with increasing energy, the growth factor increases. Overall, there is favorable agreement between the data from the simulations and the experiments. The peak growth factors from the simulations and the experiments are within 10% agreement. For the multimode simulations, the goal is to assist in the design of the laser driven experiments using the Omega laser. A series of three-mode and four-mode patterns are simulated at various energies and the resulting growth of the RM instability is computed. Based on the results of the simulations, a configuration is selected for the multimode experiments. These simulations also serve as validation for the constitutive model and the material parameters for tantalum that are used in the simulations.

By designing samples with initial perturbations in the form of single-mode and multimode ripples and subjecting these samples to high pressures, the Richtmyer-Meshkov instability is investigated in both laser compression experiments and simulations. By correlating the growth of these ripples to measures of strength, a better understanding of the strength of tantalum at high pressures is achieved.

Imaging the earth with ambient noise and earthquakes

In this thesis, I develop the velocity and structure models for the Los Angeles Basin and Southern Peru. The ultimate goal is to better understand the geological processes involved in the basin and subduction zone dynamics. The results are obtained from seismic interferometry using ambient noise and receiver functions using earthquake- generated waves. Some unusual signals specific to the local structures are also studied. The main findings are summarized as follows:

(1) Los Angeles Basin

The shear wave velocities range from 0.5 to 3.0 km/s in the sediments, with lateral gradients at the Newport-Inglewood, Compton-Los Alamitos, and Whittier Faults. The basin is a maximum of 8 km deep along the profile, and the Moho rises to a depth of 17 km under the basin. The basin has a stretch factor of 2.6 in the center decreasing to 1.3 at the edges, and is in approximate isostatic equilibrium. This "high-density" (~1 km spacing) "short-duration" (~1.5 month) experiment may serve as a prototype experiment that will allow basins to be covered by this type of low-cost survey.

(2) Peruvian subduction zone

Two prominent mid-crust structures are revealed in the 70 km thick crust under the Central Andes: a low-velocity zone interpreted as partially molten rocks beneath the Western Cordillera – Altiplano Plateau, and the underthrusting Brazilian Shield beneath the Eastern Cordillera. The low-velocity zone is oblique to the present trench, and possibly indicates the location of the volcanic arcs formed during the steepening of the Oligocene flat slab beneath the Altiplano Plateau.

The Nazca slab changes from normal dipping (~25 degrees) subduction in the southeast to flat subduction in the northwest of the study area. In the flat subduction regime, the slab subducts to ~100 km depth and then remains flat for ~300 km distance before it resumes a normal dipping geometry. The flat part closely follows the topography of the continental Moho above, indicating a strong suction force between the slab and the overriding plate. A high-velocity mantle wedge exists above the western half of the flat slab, which indicates the lack of melting and thus explains the cessation of the volcanism above. The velocity turns to normal values before the slab steepens again, indicating possible resumption of dehydration and ecologitization.

(3) Some unusual signals

Strong higher-mode Rayleigh waves due to the basin structure are observed in the periods less than 5 s. The particle motions provide a good test for distinguishing between the fundamental and higher mode. The precursor and coda waves relative to the interstation Rayleigh waves are observed, and modeled with a strong scatterer located in the active volcanic area in Southern Peru. In contrast with the usual receiver function analysis, multiples are extensively involved in this thesis. In the LA Basin, a good image is only from PpPs multiples, while in Peru, PpPp multiples contribute significantly to the final results.