Hsian-Rong Tseng - US grants

DESCRIPTION (provided by applicant): Positron emission tomography (PET) is a very sensitive non-invasive imaging technology for measuring biochemical processes at a whole body level. One of the major roadblocks which limits the widespread use of this powerful technology in both preclinical and clinical settings is the availability of PET probes. New approaches are needed to enable biologists and clinicians to synthesize a wide range of PET probes. Integrated microfluidic technology with intrinsic advantages of speed, chemical economy, flexibility, user- friendliness, safety, modularity and low cost is a prime technology platform for producing radiolabeled molecular probes. Over the past three years, our research groups have demonstrated that integrated microfluidic devices can be used for efficient production of PET probes. In this proposal, we will create an automated, user-friendly and cost efficient microfluidic platform to facilitate syntheses and labeling of [18F]- labeled PET probes, and several small molecule- and bimolecule-based [18F]-labeled PET probes with sizes ranging from 1 to 10 nm will be produced using these microfluidic platform. Initially, we will develop three separate microfluidic functional modules in parallel, including: (i) An off-chip module for concentration of [18F]fluoride, (ii) the core-a set of digitally controlled microfluidic circuits for reagent mixing, solvent exchange, deprotection and/or functional group transformations. (Here, polyperfluoropolyether (PFPE)-elastomer will be utilized to fabricate this core module to achieve improved chemical inertness and device robustness), and (iii) an in-line purification and characterization system. We will assemble the three functional modules into an integrated device, which will be hosted in a standalone, light- weight, self-shielded hot cell, equipped with a digitally controlled interface. Based on a breadboard concept, we will build two new types of integrated devices with relatively more complicated device configurations to meet the synthetic protocols of two major categories of PET probes, i.e., small molecules and radiolabeled biomolecules. We will simplify and generalize the device design and the module connections to allow "plug-in" device reconfiguration. In parallel, a user-friendly operation interface will be developed for broader implementation of the proposed technology. We will then test the feasibility to quickly build new devices for producing novel PET probes. The resulting [18F]-labeled compounds will be evaluated through our collaborative efforts in our research Institute. This proposal brings together the expertise of eight research groups covering the fields of radiochemistry, microfluidics, polymer materials, device prototyping, molecular imaging and antibody engineering. We envision the success of proposed of research will provide a powerful, universal technology to allow a convenient supply of a wide range of [18F]-labeled PET probes, accelerate the discovery and development processes o new PET probes, and facilitate a broader implementation of PET imaging. PUBLIC HEALTH RELEVANCE: Our idea is to create a modular, automated and user-friendly microfluidic platform capable of synthesizing and labeling known and novel [18F]-labeled positron emission tomography (PET) imaging probes on demand. The long term objective of this proposal is to make [18F]-labeled PET probes easily accessible so that researchers and clinicians can perform a wide range of PET studies targeting specific molecular lesions in cancer.

DESCRIPTION (provided by applicant): The long-term objective of this application is to develop an integrated technology platform for highly sensitive detection and molecular analysis of circulating tumor cells (CTCs) from whole blood. The unique working mechanism based on the high affinity nanopillar-grafted substrate confers the advantages of enhanced CTC capture efficiency/purity, low operation cost and ease of use to this new technology. The PI's research group has demonstrated that a silicon nanopillar (SiNP)-covered substrate, coated with anti-EpCAM, exhibits outstanding efficiency when employed to isolate viable CTCs from whole blood samples. With a simple stationary device setting and operation protocol, CTCs can be immobilized onto the SiNP substrates because of enhanced topographic interactions between the SiNPs and cell surface components. The clinical studies of this CTC capture technology have been initiated for side-by-side validation with the FDA-approved CellSearchTM assay. In parallel, a quantitative ICC approach for multiparametric molecular profile of individual cancer cells has been established and can be directly applied for molecular analysis of CTCs. These preliminary results constitute a solid foundation for our proposed research. CTCs are cancer cells that break away from either the primary tumor or metastatic site(s) and circulate in the peripheral blood. Enumeration and characterization of CTCs in patient blood provides valuable information for examining early-stage cancer metastases, predicting patient prognosis and monitoring therapeutic interventions and outcomes. Over the past decade, a variety of technologies capable of isolating and counting CTCs have been developed based on different working mechanisms. Some of these technologies have been demonstrated in the clinical setting and allow reproducible detection of CTCs in the patient blood. However, challenges remain in improving CTC capture efficiency, reducing measurement costs and conducting sequential molecular analysis of these cells. Herein, we propose to first perform a comprehensive optimization of the SiNP-based CTC capture technology by (i) exploring the use of polymer-based nanopillars, (ii) altering the dimension and packing density of nanopillars, (iii) enabling a capability to capture a broader diversity of CTCs, (iv) incorporating anti- biofouling function, and (v) integrating a microfluidic chaotic mixer. In parallel, we will carry out optimization of an operation protocol for ICC quantification of 4-protein molecules, including cytokeratin (CK), CD45, androgen receptor (AR) and CD44, in the isolated CTCs. Next, we will use optimal CTC capture conditions to detect CTCs from whole blood samples obtained from prostate cancer patients at different stages. Sequentially, single-cell multiparametric molecular analysis (i.e., CK, CD45, AR and CD44) of the substrate-immobilized CTCs will be carried out using the quantitative ICC approach to unveil the molecular properties and cellular heterogeneity of the CTCs. PUBLIC HEALTH RELEVANCE: The long term objective of this application is to develop a new technology platform for detection and characterization of circulating tumor cells (CTCs) from cancer patient blood. This new CTC-based diagnostic platform offers the advantages of high CTC capture sensitivity, low operation cost and user-friendliness, thus introducing a valuable point-of-care tool for patients with metastatic cancer.

DESCRIPTION (provided by applicant): Project Summary The long-term objective of this research proposal is to perform advanced development and analytical validation of a technology for enrichment of circulating tumor cells (CTCs). The goal is to further develop our highly efficient and specific CTC capture technology to pave the way not only for CTC enumeration to serve as a biomarker for PC to better predict clinical outcomes, but also as a source of clinical material (i.e., CTCs as a liquid biopsy) for sequential molecular analyses that can be used to direct appropriate therapies for individual patients (i.e., the right treatment for the right patient). Our joint team has demonstrated a unique, relatively inexpensive cell affinity assay, which is capable of identification, enumeration and capture of viable (preservative-free) CTCs in whole-blood samples collected from PC patients. Initially, we pioneered the concept of applying anti-EpCAM (epithelial cell adhesion molecule)-coated nanostructured surfaces as a high-affinity substrate for enrichment of CTCs. By integrating the high-affinity substrate with a microfluidic component capable of generating chaotic turbulence, further improved CTC capture efficiency (up to 99%) has recently been achieved as a result of the enhanced collisions between CTCs and the substrate. Side-by-side analytical validation was conducted to compare our nanostructure substrates with CellSearchTM assay using blood spiked with PC cell lines as well as 33 blood samples isolated from in PC patients at predefined stages. CTCs are cancer cells that break away from either the primary tumor or metastatic sites and circulate in the peripheral blood. Enumeration of CTCs has established clinical utility in patients with metastatic, castration-resistant (CR; i.e. hormone refractory) PC, in whom CTCs are an independent predictor for response to chemotherapy, disease free survival and overall survival. It is conceivable that the molecular and functional characterization of CTCs could provide much valuable information for predicting patient prognosis and monitoring therapeutic interventions and outcomes. Herein, we will first develop a new-generation integrated CTC chip capable of highly efficient and specific enrichment of CTCs with improved blood handling capacity, followed by comprehensive analytical validation using blood samples collected from PC patients at predefined stages (e.g., CRPC, PSA recurrence). We will then purify and isolate individual CTCs for quantification of 16 genes using a commercial real-time qPCR System. We propose to quantify expression of 16 genes, which we have chosen as markers of differentiation state, epithelial-mesenchymal transition, and the AR signaling axis. The molecular signatures imparted by these genes not only depict various cellular phenotypes but also offer the promise of predicting response/ resistance to anti-cancer therapeutics.

DESCRIPTION (provided by applicant): Stem cells have the potential to revolutionize medical practice by enabling regenerative medicine. This proposal aims to develop highly efficient generation of human induced pluripotent stem cells (hiPSCs) by utilizing a new class of nanoparticle (NP)-based vectors. These NPs are capable of delivering reprogramming transcription factors (TFs), namely OCT4, SOX2, KLF4 and c-MYC. Current reprogramming systems raise safety concerns because they utilize viral expression of the four key TFs, resulting in hiPSCs with multiple viral integrations. Safer strategies for generating hiPSCs have recently been demonstrated by introducing cell- penetrating peptide-fused reprogramming TFs into human somatic cells, averting any potential dangers of genetic manipulation. Still, effective delivery of TFs remains a key obstacle in creating hiPSCs. Three research groups at UCLA with expertise covering synthetic chemistry, nanoparticles, microfluidics (Tseng and Lu) and stem cell biology (Pyle) have collaborated and accomplished preliminary results consisting of the following fundamental proof-of-concept studies: (i) self-assembly production of supramolecular nanoparticles (SNPs) for delivery of TFs, (ii) (ii) a single protein nano-capsule technology, (iii) digital microreactors for large-scale screening, (iv) microfluidic image cytometry (MIC) technology for quantitative phenotyping of single hiPSCs, and (v) extensive experience in generating hiPSCs. The proposed research will leverage the multidisciplinary team to implement the following two specific aims: 1) We will synthesize a variety of polymer building blocks, cross linkers, functional ligands, as well as, nano- capsules containing the four reprogramming TFs for self-assembly of SNP-based delivery vectors. 2) We will generate a combinatorial library of reprogramming TF-encapsulated SNPs (i.e., OCT4/SOX2/ KLF4/c-MYC?SNPs) by performing ratiometric mixing of the four TF-containing nano-capsules, polymer building blocks, cross linkers and functional ligands. Human ESC-derived fibroblast cells with an OCT4-EGFP reporter will be employed as target cells. Subsequently, the MIC technology will be employed to quantify reprogramming performance by measuring pluripotent markers and colony formation in the SNPs-treated cells. If the efficiency is too low, we propose to co-deliver apoptotic inhibitors (e.g., siRNA_p53) with the four reprogramming TFs using siRNA/TFs?SNPs-based vectors. We anticipate that combination of apoptotic inhibitors and reprogramming TFs could dramatically increase the efficiency of reprogramming. PUBLIC HEALTH RELEVANCE: The long-term objective of this research proposal is to explore the use of supramolecular nanoparticles (SNPs) as a new category of artificial vector for simultaneous delivery of the four reprogramming transcription factors (i.e., OCT4, SOX2, KLF4 and c-MYC) into human somatic cells to induce reprogramming to the induced pluripotent cell (iPSC) state.

The objective of Project 3 in this PPG is to exploit a microfluidic diagnostics toolbox established by our research team for quantification of multiple signaling events and genomic lesions from fine needle aspirated (FNA) biopsies or circulating melanoma cells (CMCs). We will examine the feasibility of applying minimally invasive sampling techniques (i.e., FNA biopsy and peripheral blood draws for CMC enrichment) to repeatedly sample melanoma cells over the course of BRAF inhibitor (BRAFi) treatment. Tumor cells isolated from FNA biopsies and CMCs then will be subjected to single-cell signaling profiling technologies including microfluidic image cytometry (MIC) for quantitative proteomic analysis of multiple signaling molecules, and the Fluidigm BioMark^'^ system for reverse-transcriptase polymerase chain reaction (RTPCR) and targeted DNA sequencing. With bioinformatic analysis, our microfluidic diagnostics enable a systems pathology approach, capable of dissecting tumor heterogeneity and monitoring temporal disease evolution. Our long-term goal is eariy clinical detection of resistance mechanisms, and 'in patient-treatment' based prediction of tumor responsiveness to articular kinase inhibitors based on signaling responses. Activating BRAFV600E kinase mutations occur in 50% of human melanomas. Clinical experience with the novel mutant BRAF-selectlve inhibitor vemurafenib found an unprecedented 60-80% antitumor response rate among patients with BRAFV600E-positive melanomas. However, acquired drug resistance frequently develops after initial responses in almost all treated patients. Recent studies by our joint team found that mechanisms of acquired resistance to BRAF inhibition include reactivation of the MAPK pathway (e.g., via NRAS mutation) or activation of alternative signaling through the RTK/AKT pathway (e.g., via PDGFRp overexpression). To overcome BRAFi resistance, we need to better understand, monitor and study evolution of resistance mechanisms during BRAFi treatment. Project 3 aims to demonstrate microfluidic diagnostics for dynamic monitoring the clinical evolution of BRAFi resistance. As the joint research endeavor unfolds, our microfluldlcs-derived single-cell proteomic and genomic assays will be applied to detect the resistance-associated genomic and phospho-profile findings from Projects 1 and 2 in clinical patient samples to help guide therapy choices. We also envision that the proposed microfluidic diagnostics can be employed to assess that the Impact of BRAF inhibitors on immune therapies (Project 4). RELEVANCE (See instructions): A key issue In analyzing acquired resistance in melanoma is the limitation of repeated diagnostic measurements of tumors. This can be overcome by applying minimally invasive sampling techniques to characterize the progressive tumors over the course of treatment. The objective of Project 3 in this PPG is to exploit a microfluidic diagnostics toolbox for quantification of multiple signaling events and genomic lesions from fine needle aspirated (FNA) biopsies or circulating melanoma cells (CMCs).

DESCRIPTION (provided by applicant): The long-term objective of this research proposal is to i) develop a single-cell isolation technology by coupling a NanoVelcro Chip with Laser MicroDissection (LMD) techniques to enable highly efficient enumeration and specific isolation of viable/preservative-free circulating melanoma cells (CMCs) from blood, and ii) to demonstrate the feasibility of performing molecular and functional analyses of the isolated single CMCs. In collaboration with the UCLA melanoma team, we will validate the clinical utility of the proposed single-CMC molecular assays for dynamically monitoring disease progression, treatment outcomes and drug resistance in melanoma patients treated with BRAF inhibiters (BRAFi). Our team at UCLA has demonstrated a highly efficient, inexpensive circulating tumor cell (CTC) assay capable of enriching, identifying and isolating CTCs in whole-blood samples collected from patients with different solid tumors. First, we pioneered a unique concept of NanoVelcro cell-affinity substrates, by which capture agent (antibodies or aptamers) -coated nanostructured surfaces were utilized to immobilize CTCs in a stationary device setting. Second, by integrating the NanoVelcro substrate with an overlaid microfluidic component that can generate vertical flows, further improved CTC capture efficiency (>85%) has been achieved as a result of the enhanced collisions between CTCs and the substrate. Side-by-side analytical validation studies using both artificial and patient CTC samples suggested that the sensitivity of NanoVelcro CTC Assay outperformed that of CellSearchTM. CTCs and CMCs are cancer cells that break away from either the primary tumor or metastatic sites and circulate in the peripheral blood. Enumeration of CTCs/CMCs has established clinical utility in patients with metastatic solids tumors, in whom the CTC/CMCs number becomes an independent and accurate predictor for a patient's response to chemotherapy, disease free/overall survival. It is conceivable that a minimally invasive blood-based diagnostic technique could allow repeated characterization of CTCs/CMCs, providing insight into tumor biology during the critical window where intervention could actually make the difference. Currently, FDA- cleared CellSearchTM Assay is costly and inefficient in capturing CTCs/CMCs without contamination of surrounding white blood cells, thus the diagnostic values of CTCs/CMCs are not fully utilized. Herein, we will explore the combined use of new NanoVelcro Assay and LMD technique for isolating viable/preservative-free single CMCs from blood samples collected from melanoma patients over the course of BRAFi treatment. We will then subject the isolated CMCs for molecular and functional analysis. We envision the variation of CMC number and resulting CMC-based molecular signatures can be used to better investigate and monitor evolution of resistance mechanisms during BRAFi treatment, and to guide development of next- generation kinase inhibitor-based melanoma treatments.

DESCRIPTION (provided by applicant): The long-term objective of this R21 proposal is to develop a new class of nanoparticle (NP)-based positron emission tomography (PET) probes that enable high-performance tumor imaging. We propose to adopt a pretargeted imaging strategy to decouple the NP components from their corresponding radiolabeled reporters. First, a pair of tumor-targeting NP component and radiolabeled reporter with desired PKs will be synthesized separately via rational molecular designs. We will then modulate the interplay between other experimental variables such as injection times and dosage in order to achieve optimal PET imaging outcomes. A prerequisite to successful pretargeted imaging is to accomplish selective and irreversible coupling of the tumor- targeting NP and sequentially injected radiolabeled reporter in vivo. We thus exploit the use of a bioorthogonal conjugation chemistry based on a pair of reactive motifs, i.e., trans-cyclooctene (TCO) and tetrazine (Tz), which have fast reaction kinetics and biological stability. Future progress in PET imaging will involve designing molecular imaging probes that preferentially accumulate in tumors. Aside from small molecule and affinity ligand-based PET imaging probes, NPs exhibiting unique enhanced permeability and retention (EPR) effects represent a new category of PET probes capable of passively targeting leaky vasculature - a universal characteristic observed for most solid tumors. While a variety of NP PET probes have been examined in pre-clinical setting, challenges remain to further improve tumor uptake and reduce nonspecific distribution in other organs. In our molecular design, the TCO motif is covalently attached onto a polymer building block of supra-molecular nanoparticle (SNP). Self-assembly of the molecular building blocks leads to encapsulation of TCO to yield TCO-encapsulated SNP (TCO?SNP) as the tumor-targeting NP component. Further, the radiolabeled reporter is composed of the complementary Tz motif and 18F-tag. In the proposed PET imaging study, TCO?SNP is first administered to an animal. When the TCO?SNPs approach their optimal accumulation in tumor, the radiolabeled reporter is then injected. In vivo bio-orthogonal reaction occurs instantaneously, resulting in high-contras PET imaging. Our joint team has some preliminary data supporting the feasibility of this new class of NP PET imaging probes. We will implement the following two Specific Aims to accomplish our research endeavors, 1) Prepare and select TCO?SNPs and radiolabeled reporters with optimal PKs, and 2) In vivo demonstration of pretargeted PET imaging using pairs of TCO?SNPs and radiolabeled reporters. This proposal brings together the expertise of four research groups (PI and 3 co-investigators) covering the fields of supramolecular chemistry, nanoparticle, radiochemistry, molecular imaging and cancer biology. We envision that the successful demonstration of our proposed research could change current paradigm in oncologic PET imaging, and open up new opportunities for pretargeted drug delivery.

? DESCRIPTION (provided by applicant): The goal of this SBIR Phase II proposal is to conduct the advanced development of the 3rd-gen Thermoresponsive NanoVelcro assay in order to achieve rapid purification of circulating tumor cells (CTCs) from non-small cell lung cancer (NSCLC) patient blood samples, paving the way for CTC-derived molecular signatures and functional readouts. This project is led by Dr. Garcia (PI), who has extensive experience in early-stage development of the technology and has a background in surface chemistry, microfluidics, and in vitro diagnostic technologies. He is supported by an interdisciplinary team comprising business development, FDA expertise, QC/QA management, nanotechnology support, lung cancer, clinical utility, genetic analysis, biostatistics, industrial collaborators, nd downstream potential customers. NSCLC accounts for >70% of lung cancer cases. Since NSCLCs are usually not very sensitive to chemotherapy and/or radiation, the advent of targeted therapy by epidermal growth factor receptor (EGFR) inhibitors offer a great treatment options to a sub-population of NSCLC patients who carry oncogenic driver mutations in their EGFR genes. To guide the implementation of targeted therapy, invasive biopsy or surgery is employed to sample NSCLC tissues for determining the presence of these EGFR mutations. However, these invasive sampling procedures impose significant risk to the patients. As an alternative, CTCs can be captured repetitively and analyzed in a minimally invasive manner thus providing a systemic picture of the malignant clones that possess high metastatic capacity. The proposed Thermoresponsive NanoVelcro assay is composed of two individual components: i) a digital fluidic handler with an embedded temperature control module, and ii) a custom-designed chip holder, in which a clamp-down design allows instant assembly of a NanoVelcro substrate with an overlaid PDMS component, will be designed and fabricated at CytoLumina. To highlight the significance of our downstream studies, we will gather serial blood samples from lung cancer patients. We will collect the purified CTCs and subject them to mutational analysis for eight genes, including EGFR., Further, the purified CTCs will be introduced to a variety of in vitro cell culture systems (i.e., microfluidic and 3D cell-culture platforms) established by our joint team (UCLA and CytoLumina) to create viable CTC cell lines. The personalized cell lines will be used to study patterns in drug susceptibility, which is linked to the underlying genetic driver mutation.

? DESCRIPTION (provided by applicant): The long-term goal of this U01 proposal is to develop Thermoresponsive (TR)-NanoVelcro circulating tumor cell (CTC) purification system that can be digitally programmed to achieve optimal performance for recovering viable CTCs in prostate cancer (PC) patients' blood, allowing seamless coupling with various downstream functional and molecular assays. Dr. Tseng (PI/UCLA) and Dr. Posadas (co-PI/Cedars Sinai Medical Center) will bring together an interdisciplinary research team to implement the proposed research activities. CTCs are regarded as a liquid biopsy of tumors, allowing non-invasive, repetitive, and systemic sampling of the disease. Although detecting and enumerating CTCs is of prognostic significance in metastatic PC, it is conceivable that performing molecular and functional characterization on CTCs will reveal unprecedented insight into the pathogenic mechanisms driving lethal PC. In order to obtain CTC-derived molecular signatures and functional readouts, it is important to develop improved methodologies that can not only detect/enumerate CTCs with high sensitivity, but also recover CTCs with minimum contamination by white blood cells and negligible disruption to CTCs' viability. Our working hypothesis, based on preliminary data gathered of temperature-dependent purification of viable CTCs using polymer brush-grafted nanosubstrates, is that the performance of the proposed TR- NanoVelcro CTC purification system can be i) optimized by rationally modulating surface chemistry, cocktail capture agents, flow rates, and heating/cooling cycles, and ii) validated using both artificial and prostate cancer patient blood samples. PC CTCs purified by TR-NanoVelcro CTC purification system will be of sufficient viability and purity, paving the way for i) short-term in vitro culture, ii) long-term i vitro maintenance, and iii) in vivo tumorigenic models as patient-derived xenografts. The ex vivo expanded CTCs will provide sufficient high-quality gDNA and mRNA that can be characterized by next-generation sequencing (NGS) for de novo identification of key molecular events in PC. Using bioinformatic approaches, we will assemble PC-specific genomic/transcriptomic panels for cross-validation by NGS using CTCs freshly isolated from multiple PC patients. We envision that TR-NanoVelcro system will enable instant purification of viable CTCs from PC patients, paving the way for performing a variety of downstream molecular and functional assays that can significantly contribute to understanding PC progression, implementation of personalized treatment, and development of new therapeutics.

Project Summary The long-term goal of this R01 proposal is to develop a circulating tumor cell-based assay to identify prostate cancer (PCa) patients who are at risk for developing visceral metastasis (VM). Drs. Posadas (Cedars-Sinai) and Tseng (CytoLumina) have formed a unique and functional academic/industrial partnership geared toward this project. VM in metastatic, castration-resistant PCa (mCRPC) is an emerging and unaddressed problem. Patients with VM have significantly foreshortened cancer-specific survival and die from organ failure in a fashion distinct from patients with bone-predominant disease. VM are typically found on imaging requested only when organ function is already compromised-typically late in the clinical course but affect over 45% of patients with advanced PCa. Early treatment can improve outcome but this requires timely detection. Thus, there is an unmet need to identify patients at risk for VM to customize imaging surveillance and create an opportunity to alter disease trajectory. Circulating tumor cells (CTCs) are rare cancer cells that can be isolated from whole blood. The NanoVelcro assay is a novel cellular isolation technology introduced by CytoLumina that is capable of identifying CTCs in small volumes of blood (as little as 1 mL). Use of NanoVelcro assay has led to the identification of CTC subsets based on nuclear morphology including those with nuclei less than 8.5 µm in diameter called very small nuclear CTCs (vsnCTCs). We have found that the appearance of vsnCTCs is associated with the presence of VM in men with PCa. We hypothesize that vsnCTCs appear before the VM are detectable by conventional radiographic assessment in mCRPC. This hypothesis will be tested by (aim 1) an analysis of CTC samples that have been serially collected over the past 3 years in our annotated CTC/blood bank ? a unique and invaluable resource for this work and, (aim 2) a prospective CTC analysis of men with mCRPC. Our early work shows that vsnCTCs appear months before the VM are detectable by conventional imaging techniques. This investigative project will create an opportunity for early imaging and therapy which can change the clinical course for patients. As a byproduct, this work will create a new clinical space in PCa by identifying men at risk for VM. The NanoVelcro vsnCTC Assay will provide a simple, minimally-invasive, and cost-effective means of identifying mCRPC patients at risk for VM, thereby allowing physicians to personalize patient monitoring, treatment, and therapy.

PROJECT SUMMARY/ABSTRACT This R21 proposal specifically responds to RFA-CA-18-002 ? Innovative Molecular and Cellular Analysis Technologies for Basic and Clinical Cancer Research. The long-term goal is to develop and validate a novel click chemistry-mediated cell sorting method (i.e., Click Chips) for enumeration and quantitative molecular characterization of circulating tumor cells (CTCs) in hepatocellular carcinoma (HCC). We envision that Click Chips can be seamlessly coupled with a multi-marker sorting strategy to capture and purify HCC CTCs from blood samples to expedite the detection and characterization of HCC CTCs. CTCs are regarded as a liquid biopsy of tumors, allowing non-invasive and systemic sampling of the disease. CTCs can be recovered and analyzed repeatedly over the disease course, providing potential insights into the molecular mechanisms governing disease progression, while averting the need for numerous invasive biopsy. HCC, the 2nd most common cause of cancer-related deaths worldwide, is in dire need of prognostic biomarkers. Current clinicopathologic and radiographic staging systems, and serum biomarkers (e.g., AFP) poorly discriminate between early-stage patients amenable to surgical therapy and advanced-stage patients receiving chemotherapy. Our joint research team at UCLA has recently developed a multi-marker capture cocktail that allows for detection of HCC CTCs across all disease stages. Developing new liquid biopsy diagnostics, capable of conducting both HCC CTC enumeration and molecular analysis, holds great promise to significantly augment the ability of current staging criteria to realize longitudinal monitoring of disease progression and treatment responses. Recognizing the limitations associated with the conventional antibody-mediated CTC sorting, our team aims to develop a new class of CTC assays based on click chemistry-mediated cell capture. In contrast to antibody-mediated CTC sorting methods, a pair of highly reactive click chemistry motifs (i.e., tetrazine, Tz, and trans-cyclooctene, TCO) were grafted onto cell-capture substrates and CTCs, respectively. When TCO-grafted CTCs flow through the integrated device, a click reaction (between TCO on CTCs and Tz on the substrate) leads to irreversible immobilization of CTCs with dramatically improved sensitivity and specificity. Further, by incorporating a disulfide bond into the surface linker that tethers Tz onto the substrate, the CTCs captured on the substrate can be released/recovered upon exposure to a mild disulfide cleavage agent (i.e., dithiobutylamine), allowing for effective CTC purification. The innovation of Click Chips includes i) increased sensitivity and specificity of CTC enrichment by replacing antibody-mediated capture with click chemistry, and ii) highly effective CTC purification due to the disulfide-cleavage driven CTC release mechanism. The proposal will be implemented via Specific Aim 1: to conduct exploratory development of Click Chips for HCC CTCs, and Specific Aim 2: to conduct initial clinical validation of Click Chips using HCC blood samples.

PROJECT SUMMARY/ABSTRACT The long-term goal of this revised U01 proposal is to conduct advanced development and rigorous validation of an emerging circulating trophoblast (cTB)-based noninvasive prenatal diagnostic (NIPD) technology, capable of i) enriching/counting cTBs from maternal blood, and ii) isolating single cTBs for genome-wide detection of fetal genetic abnormalities during the first trimester of pregnancy. An alternative research plan is also presented to explore the use of the same workflow for isolating and characterizing trophoblasts (TBs) in cervix samples. Among potential circulating fetal nucleated cells (CFNCs) in maternal blood, cTBs are an ideal target considering their (i) short lifespan, which excludes the presence of cTBs from prior pregnancies or miscarriages, (ii) representation of fetal karyotype and genotype, and (iii) expression of a unique collection of biomarkers that can be used for both enrichment and identification. However, isolating pure cTBs has been technically challenging due to their extremely low abundance. Over the past decade, Dr. Tseng?s research team at UCLA has developed nanomaterial-embedded diagnostic platforms (a.k.a., NanoVelcro Chips). To exploit the NIPD utility of NanoVelcro Chips, the team first developed a nanoimprinting fabrication process to prepare the laser capture microdissection (LCM)-compatible nanosubstrates in a cost-efficient and scalable manner. These chips, in conjunction with the use of capture and immunocytochemistry (ICC) agents, exhibit superb cTB capture performance. In parallel, high-resolution microscopy imaging and analysis software has been developed to identify and register individual cTBs on the substrates, enabling highly accurate isolation of single cTBs by LCM. In collaboration with Dr. Pisarska, the joint team demonstrated a workflow starting with blood processing, single cTB isolation, and DNA amplification, all the way through whole genome profiling of cTBs by ArrayCGH and/or next generation sequencing. Our central hypothesis is that >10 cTBs can be harvested from 5-mL of maternal blood (>50 TBs from a cervix sample), collected from a pregnant woman during the first trimester of pregnancy (8-12 weeks of gestational age), and whole genome profiling of these cTBs/TBs can be used for diagnosing fetal genetic abnormalities. Over the 5-year funding period, the proposed research will be implemented via two Specific Aims: i) to develop, optimize and validate the proposed cTB-based NIPD technology, and ii) to conduct initial clinical validation in pregnant women recruited from UCLA and CSMC. The joint team envisions that the successful demonstration of the proposed cTBs-based NIPD technology will introduce a revolutionary NIPD solution with the sensitivity and specificity of the gold standard diagnostic tests without the associated risks to the fetus.

Hepatocellular carcinoma (HCC), the third most common cause of cancer-related deaths worldwide, most often develops in patients with underlying liver cirrhosis or chronic injury secondary to alcohol abuse, non- alcoholic fatty liver disease, or viral hepatitis infections. Cirrhosis from any cause is a well-established risk factor for HCC. The poor prognosis of HCC is due to the fact that diagnosis is often made at a late stage in disease development. The earlier detection of HCC is necessary towards reducing the high HCC mortality rates since those with early stage disease have multiple, potentially curative, treatment options available. However, current surveillance regimens with abdominal imaging and serum biomarkers (e.g., AFP) have poor sensitivity for diagnosing HCC at an early-stage. Therefore, biomarkers that sensitively distinguish early-stage HCC from liver cirrhosis are desperately needed. Extracellular vesicles (EVs) are a heterogeneous group of phospholipid bilayer-enclosed particles known to contain cell-type-specific ?cargo,? including RNA, DNA, and protein. Cargo profiling of tumor-derived EVs is an emerging liquid biopsy strategy for non-invasive cancer diagnosis and treatment monitoring. Our joint research team at UCLA has recently developed a new type of ?NanoVilli Chip? capable of highly efficient isolation and characterization of tumor-derived EVs from HCC patients. Exploring the use of NanoVilli Chips for cargo profiling of HCC-derived EVs holds great promise as a novel biomarker for detecting early-stage HCC noninvasively. Conventional methods for isolating total EVs, such as ultracentrifugation, filtration, and precipitation, are incapable of discriminating tumor-derived EVs from non-tumor-derived EVs. To address this unmet need, our project team will develop ?NanoVilli Chips? based on biomimetic nanostructures and specific immunoaffinity-mediated capturing for HCC-derived EVs. HCC-specific multi-marker capture cocktails (targeting ASGPR, GPC3, and EpCAM) will be grafted onto silicon nanowires (SiNWS) embedded in the chips. When plasma samples approach the SiNWS, specific interactions (between antigens located on the surfaces of tumor-derived EVs and corresponding antibodies grafted on the substrate) lead to selective immobilization of HCC-derived EVs, with dramatically improved sensitivity and specificity. Further, by incorporating Droplet Digital PCR (ddPCR) technology, the HCC-derived EVs captured on the NanoVilli Chips can be characterized by quantifying a panel of 10 well-validated HCC-specific mRNA markers. The proposed research will conduct an exploratory development of NanoVilli Chips for HCC-derived EVs, and an initial clinical validation of NanoVilli Chips using HCC and liver cirrhosis blood samples. Our long-term goal is to explore the use of NanoVilli Chips coated with HCC-associated multi-marker capture cocktails for capturing HCC-derived EVs, allowing for quantification of HCC-specific mRNA signature to augment current HCC early diagnostic algorithms.

PROJECT SUMMARY Extracellular vesicles (EVs) are a heterogeneous group of phospholipid bilayer-enclosed particles with the biomolecular contents mirroring those of their parental cells. Since EVs are present in circulation at a relatively early stage of disease and persist across all disease stages, purification and characterization of tumor-derived EVs are expected to offer an opportunity for early cancer diagnosis. Hepatocellular carcinoma (HCC), the fourth most common cause of cancer-related deaths worldwide, is in dire need of diagnostic and prognostic biomarkers. Current clinical radiographic system and serum biomarkers (e.g., alpha-fetoprotein (AFP)) poorly discriminate early-stage HCC (where potentially curative therapies are available) from at-risk liver cirrhosis (where HCC surveillance is indicated). Moreover, sensitive biomarkers for HCC postoperative recurrence (where timely salvage treatment interventions can suppress disease progression) after curative-intent liver resection and liver transplantation remain a significant challenge for early-stage HCC. Therefore, exploiting the diagnostic potential of HCC EVs and EV cargo profiling for HCC early detection and postoperative recurrence holds great promise to significantly augment the ability of current diagnostic modalities. Conventional methods for isolating EVs, such as ultracentrifugation, filtration, and precipitation, are incapable of discriminating tumor-derived EVs from non-tumor-derived EVs. To address this unmet need, our team developed ?EV Click Chips? for HCC EV purification. The innovation of our devices includes i) the covalent chemistry-mediated EV capture/release couples click chemistry-mediated EV capture and disulfide cleavage- driven EV release, ii) an optimized multi-marker cocktail targeting HCC-associated surface markers was adopted to overcome the heterogeneity of HCC EVs; iii) the incorporation of densely packed silicon nanowire substrates (SiNWS) dramatically increases the device surface areas for contacting/interacting with EVs; and iv) the microfluidic chaotic mixer facilitates repeated physical contact between SiNWS and the flow-through EVs, further enhancing the performance of EV purification. The purified HCC EVs can be characterized by quantifying a panel of 10 well-validated HCC-specific mRNA markers by incorporating Droplet Digital PCR (ddPCR) technology. The proposed research will conduct: i) an exploratory development and optimization of EV Click Chips for HCC EV purification, and ii) clinical validations of EV Click Chips for HCC early detection and postoperative recurrence using patient blood samples. Our long-term goal is to develop a new HCC EV purification system (i.e., EV Click Chips) by synergistically integrating four very powerful approaches, including covalent chemistry-mediated EV capture/release, multimarker antibody cocktails, nanostructured substrates, and microfluidic chaotic mixers. The purified HCC EVs will readily allow for quantitative cargo profiling to augment current HCC diagnostic algorithms.

PROJECT SUMMARY Hepatocellular carcinoma (HCC) is the 2nd most common cause of cancer-related deaths worldwide. Liver transplantation (LT) is the only curative therapy for HCC patients with unresectable, non-metastatic disease who meet strict radiologic tumor size and number criteria (Milan criteria). Eligible candidates undergo a finite observation period (>6 months) that allows for an assessment of tumor biology, but which inherently risks HCC progression and wait-list dropout in 15-20% of patients after 1 year. Despite these selection practices, post-LT HCC recurrence plagues up to 20% of patients, and is a major cause of allograft loss and patient mortality. There is a dire need for non-invasive biomarkers capable of dynamic monitoring of tumor biology to better balance the risk of wait-list dropout and post-LT recurrence, and allowing for improved prioritization of HCC patients to receive scarce liver allografts. This proposal aims to develop an integrated blood-based analysis (i.e., NanoVelcro vimCTC Assay for detecting vimentin+ circulating tumor cells [CTCs] and HCC CTC-RNA Assay for HCC- specific RNA signatures) for wait-listed HCC patients, to identify patients most suitable for LT. The integrated assay will provide a novel approach to study both phenotypic and molecular characteristics of HCC CTCs. Using an HCC-specific multi-marker capture cocktail and optimized immunocytochemistry (ICC) staining protocol, the proposed NanoVelcro vimCTC Assay is capable of identifying a subpopulation of HCC CTCs with vimentin expression (named vimCTC, DAPI+/CK+/CD45-/vimentin+). This subpopulation is associated with increased recurrence in the subset of clinically indistinguishable early-stage patients undergoing curative-intent treatment. The HCC CTC-RNA Assay was developed by combining CTC isolation with Click Chip, featuring click chemistry-mediated cell capture and disulfide-cleavage cell release, with downstream RNA expression profiling of the purified CTCs with NanoString's nCounter platform. This allows for accurate quantification of a panel of HCC CTC-derived mRNA markers in a non-invasive manner. The resulting vimCTC counts and mRNA profiles hold great promise to augment the ability of the current LT candidate selection algorithm. The proposed research will be implemented via Specific Aim 1a: Conducting a retrospective study in banked blood samples using NanoVelcro vimCTC Assay to refine the association between vimCTC counts and post- LT recurrence/wait-list dropout.; Specific Aim 1b: Conducting a prospective study on freshly collected blood samples to determine association between vimCTC counts and post-LT recurrence/wait-list dropout; and Specific Aim 2: Conducting a prospective study on freshly collected blood samples to determine the association between HCC CTC-RNA Assay and post-LT recurrence/wait-list dropout. The central hypothesis evaluated will be that baseline and longitudinal changes in vimCTCs and aggressive RNA signatures will significantly improve the ability of current clinicoradiologic LT selection criteria in predicting post-LT recurrence and wait-list dropout, paving the way for tumor-biology based HCC LT candidate selection practices.