Skip to main content
eScholarship
Open Access Publications from the University of California

Open Access Policy Deposits

This series is automatically populated with publications deposited by UCLA Henry Samueli School of Engineering and Applied Science Department of Chemical and Biomolecular Engineering researchers in accordance with the University of California’s open access policies. For more information see Open Access Policy Deposits and the UC Publication Management System.

Cover page of Unraveling the role of the mitochondrial one-carbon pathway in undifferentiated thyroid cancer by multi-omics analyses.

Unraveling the role of the mitochondrial one-carbon pathway in undifferentiated thyroid cancer by multi-omics analyses.

(2024)

The role of the serine/glycine metabolic pathway (SGP) has recently been demonstrated in tumors; however, the pathological relevance of the SGP in thyroid cancer remains unexplored. Here, we perform metabolomic profiling of 17 tumor-normal pairs; bulk transcriptomics of 263 normal thyroid, 348 papillary, and 21 undifferentiated thyroid cancer samples; and single-cell transcriptomes from 15 cases, showing the impact of mitochondrial one-carbon metabolism in thyroid tumors. High expression of serine hydroxymethyltransferase-2 (SHMT2) and methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) is associated with low thyroid differentiation scores and poor clinical features. A subpopulation of tumor cells with high mitochondrial one-carbon pathway activity is observed in the single-cell dataset. SHMT2 inhibition significantly compromises mitochondrial respiration and decreases cell proliferation and tumor size in vitro and in vivo. Collectively, our results highlight the importance of the mitochondrial one-carbon pathway in undifferentiated thyroid cancer and suggest that SHMT2 is a potent therapeutic target.

Cover page of CAR-T cell manufacturing: Major process parameters and next-generation strategies.

CAR-T cell manufacturing: Major process parameters and next-generation strategies.

(2024)

Chimeric antigen receptor (CAR)-T cell therapies have demonstrated strong curative potential and become a critical component in the array of B-cell malignancy treatments. Successful deployment of CAR-T cell therapies to treat hematologic and solid cancers, as well as other indications such as autoimmune diseases, is dependent on effective CAR-T cell manufacturing that impacts not only product safety and efficacy but also overall accessibility to patients in need. In this review, we discuss the major process parameters of autologous CAR-T cell manufacturing, as well as regulatory considerations and ongoing developments that will enable the next generation of CAR-T cell therapies.

Cover page of Toward Systems-Level Metabolic Analysis in Endocrine Disorders and Cancer.

Toward Systems-Level Metabolic Analysis in Endocrine Disorders and Cancer.

(2023)

Metabolism is a dynamic network of biochemical reactions that support systemic homeostasis amidst changing nutritional, environmental, and physical activity factors. The circulatory system facilitates metabolite exchange among organs, while the endocrine system finely tunes metabolism through hormone release. Endocrine disorders like obesity, diabetes, and Cushings syndrome disrupt this balance, contributing to systemic inflammation and global health burdens. They accompany metabolic changes on multiple levels from molecular interactions to individual organs to the whole body. Understanding how metabolic fluxes relate to endocrine disorders illuminates the underlying dysregulation. Cancer is increasingly considered a systemic disorder because it not only affects cells in localized tumors but also the whole body, especially in metastasis. In tumorigenesis, cancer-specific mutations and nutrient availability in the tumor microenvironment reprogram cellular metabolism to meet increased energy and biosynthesis needs. Cancer cachexia results in metabolic changes to other organs like muscle, adipose tissue, and liver. This review explores the interplay between the endocrine system and systems-level metabolism in health and disease. We highlight metabolic fluxes in conditions like obesity, diabetes, Cushings syndrome, and cancers. Recent advances in metabolomics, fluxomics, and systems biology promise new insights into dynamic metabolism, offering potential biomarkers, therapeutic targets, and personalized medicine.

Cover page of Advances, Applications, and Emerging Opportunities in Electrostatic Hydrogels.

Advances, Applications, and Emerging Opportunities in Electrostatic Hydrogels.

(2023)

Polyelectrolyte complex (PEC) hydrogels, which self-assemble via complexation of oppositely charged block polymers, have recently risen to prominence owing to their unique characteristics such as hierarchical microstructure, tunable bulk properties, and the ability to precisely assimilate charged cargos (i.e., proteins and nucleic acids). Significant foundational research has delineated the structure-property relationship of PEC hydrogels for use in a wide range of applications. In this Perspective, we summarize key findings on the microstructure and bulk properties of PEC hydrogels and discuss how intrinsic and extrinsic factors can be tuned to create specifically tailored PEC hydrogels with desired properties. We highlight successful applications of PEC hydrogels while offering insight into strategies to overcome their shortcomings and elaborate on emerging opportunities in the field of electrostatic self-assemblies.

Cover page of M2 isoform of pyruvate kinase rewires glucose metabolism during radiation therapy to promote an antioxidant response and glioblastoma radioresistance

M2 isoform of pyruvate kinase rewires glucose metabolism during radiation therapy to promote an antioxidant response and glioblastoma radioresistance

(2023)

Background

Resistance to existing therapies is a significant challenge in improving outcomes for glioblastoma (GBM) patients. Metabolic plasticity has emerged as an important contributor to therapy resistance, including radiation therapy (RT). Here, we investigated how GBM cells reprogram their glucose metabolism in response to RT to promote radiation resistance.

Methods

Effects of radiation on glucose metabolism of human GBM specimens were examined in vitro and in vivo with the use of metabolic and enzymatic assays, targeted metabolomics, and FDG-PET. Radiosensitization potential of interfering with M2 isoform of pyruvate kinase (PKM2) activity was tested via gliomasphere formation assays and in vivo human GBM models.

Results

Here, we show that RT induces increased glucose utilization by GBM cells, and this is accompanied with translocation of GLUT3 transporters to the cell membrane. Irradiated GBM cells route glucose carbons through the pentose phosphate pathway (PPP) to harness the antioxidant power of the PPP and support survival after radiation. This response is regulated in part by the PKM2. Activators of PKM2 can antagonize the radiation-induced rewiring of glucose metabolism and radiosensitize GBM cells in vitro and in vivo.

Conclusions

These findings open the possibility that interventions designed to target cancer-specific regulators of metabolic plasticity, such as PKM2, rather than specific metabolic pathways, have the potential to improve the radiotherapeutic outcomes in GBM patients.

Cover page of Discovering pathways through ribozyme fitness landscapes using information theoretic quantification of epistasis.

Discovering pathways through ribozyme fitness landscapes using information theoretic quantification of epistasis.

(2023)

The identification of catalytic RNAs is typically achieved through primarily experimental means. However, only a small fraction of sequence space can be analyzed even with high-throughput techniques. Methods to extrapolate from a limited data set to predict additional ribozyme sequences, particularly in a human-interpretable fashion, could be useful both for designing new functional RNAs and for generating greater understanding about a ribozyme fitness landscape. Using information theory, we express the effects of epistasis (i.e., deviations from additivity) on a ribozyme. This representation was incorporated into a simple model of the epistatic fitness landscape, which identified potentially exploitable combinations of mutations. We used this model to theoretically predict mutants of high activity for a self-aminoacylating ribozyme, identifying potentially active triple and quadruple mutants beyond the experimental data set of single and double mutants. The predictions were validated experimentally, with nine out of nine sequences being accurately predicted to have high activity. This set of sequences included mutants that form a previously unknown evolutionary bridge between two ribozyme families that share a common motif. Individual steps in the method could be examined, understood, and guided by a human, combining interpretability and performance in a simple model to predict ribozyme sequences by extrapolation.

Cover page of Molecular design of an ultra-strong tissue adhesive hydrogel with tunable multifunctionality.

Molecular design of an ultra-strong tissue adhesive hydrogel with tunable multifunctionality.

(2023)

Designing adhesive hydrogels with optimal properties for the treatment of injured tissues is challenging due to the tradeoff between material stiffness and toughness while maintaining adherence to wet tissue surfaces. In most cases, bioadhesives with improved mechanical strength often lack an appropriate elastic compliance, hindering their application for sealing soft, elastic, and dynamic tissues. Here, we present a novel strategy for engineering tissue adhesives in which molecular building blocks are manipulated to allow for precise control and optimization of the various aforementioned properties without any tradeoffs. To introduce tunable mechanical properties and robust tissue adhesion, the hydrogel network presents different modes of covalent and noncovalent interactions using N-hydroxysuccinimide ester (NHS) conjugated alginate (Alg-NHS), poly (ethylene glycol) diacrylate (PEGDA), tannic acid (TA), and Fe3+ ions. Through combining and tuning different molecular interactions and a variety of crosslinking mechanisms, we were able to design an extremely elastic (924%) and tough (4697 kJ/m3) multifunctional hydrogel that could quickly adhere to wet tissue surfaces within 5 s of gentle pressing and deform to support physiological tissue function over time under wet conditions. While Alg-NHS provides covalent bonding with the tissue surfaces, the catechol moieties of TA molecules synergistically adopt a mussel-inspired adhesive mechanism to establish robust adherence to the wet tissue. The strong adhesion of the engineered bioadhesive patch is showcased by its application to rabbit conjunctiva and porcine cornea. Meanwhile, the engineered bioadhesive demonstrated painless detachable characteristics and in vitro biocompatibility. Additionally, due to the molecular interactions between TA and Fe3+, antioxidant and antibacterial properties required to support the wound healing pathways were also highlighted. Overall, by tuning various molecular interactions, we were able to develop a single-hydrogel platform with an all-in-one multifunctionality that can address current challenges of engineering hydrogel-based bioadhesives for tissue repair and sealing.

Cover page of Elucidating the active phases of CoOx films on Au(111) in the CO oxidation reaction.

Elucidating the active phases of CoOx films on Au(111) in the CO oxidation reaction.

(2023)

Noble metals supported on reducible oxides, like CoOx and TiOx, exhibit superior activity in many chemical reactions, but the origin of the increased activity is not well understood. To answer this question we studied thin films of CoOx supported on an Au(111) single crystal surface as a model for the CO oxidation reaction. We show that three reaction regimes exist in response to chemical and topographic restructuring of the CoOx catalyst as a function of reactant gas phase CO/O2 stoichiometry and temperature. Under oxygen-lean conditions and moderate temperatures (≤150 °C), partially oxidized films (CoOx<1) containing Co0 were found to be efficient catalysts. In contrast, stoichiometric CoO films containing only Co2+ form carbonates in the presence of CO that poison the reaction below 300 °C. Under oxygen-rich conditions a more oxidized catalyst phase (CoOx>1) forms containing Co3+ species that are effective in a wide temperature range. Resonant photoemission spectroscopy (ResPES) revealed the unique role of Co3+ sites in catalyzing the CO oxidation. Density function theory (DFT) calculations provided deeper insights into the pathway and free energy barriers for the reactions on these oxide phases. These findings in this work highlight the versatility of catalysts and their evolution to form different active phases, both topological and chemically, in response to reaction conditions exposing a new paradigm in the catalyst structure during operation.

Cover page of Accessing complex reconstructed material structures with hybrid global optimization accelerated via on-the-fly machine learning.

Accessing complex reconstructed material structures with hybrid global optimization accelerated via on-the-fly machine learning.

(2023)

The complex reconstructed structure of materials can be revealed by global optimization. This paper describes a hybrid evolutionary algorithm (HEA) that combines differential evolution and genetic algorithms with a multi-tribe framework. An on-the-fly machine learning calculator is adopted to expedite the identification of low-lying structures. With a superior performance to other well-established methods, we further demonstrate its efficacy by optimizing the complex oxidized surface of Pt/Pd/Cu with different facets under (4 × 4) periodicity. The obtained structures are consistent with experimental results and are energetically lower than the previously presented model.