Biology subjects

Rice, L.

Publications and source records attributed to Rice, L..

12 recordsLinked to original sources

bioRxiv2026

A Research-Integrated Curriculum on CAR-T Cell Therapy

Chimeric antigen receptor (CAR) T cells are patient-derived T cells engineered to recognize specific antigens on malignant cells, representing a major breakthrough in personalized cancer immunotherapy. While CAR-T cell therapy is an established treatment for relapsed or refractory hematologic malignancies, understanding the rationale and methodology behind its development is essential for training the next generation of oncology researchers. Here, we describe a novel, hands-on small-enrollment laboratory course designed to teach upper-level undergraduate and graduate students about immunotherapies and CAR-T cell technology by paralleling a typical bench-scale development process. Students isolated T cells from porcine peripheral blood mononuclear cells (PBMCs) via immunomagnetic selection, followed by flow cytometry to assess purity, viability, and yield. Students then used pre-engineered B7H3 CAR-T cells to perform co-culture assays with U87 glioblastoma cells to evaluate tumor cell killing efficacy. Cytotoxicity was qualitatively evaluated using immunofluorescence microscopy, while IFN-gamma release was quantified using Enzyme-linked Immunosorbent Assay (ELISA). Student performance was evaluated through electronic laboratory notebooks, discussion questions, a capstone project, and student-generated data. Our results demonstrate students high academic performance across assignments and the successful execution of complex laboratory workflows. Collectively, these findings establish the feasibility and implementation of a research-integrated curriculum providing foundational exposure to immuno-oncology research tools and CAR-T cell production techniques.

cancer biology↗

bioRxiv2025

Dimeric Cin8 motors have an inherent plus-end bias and weak inter-head coordination

Kinesin-5 motors are bipolar tetramers that crosslink and slide antiparallel microtubules during mitotic spindle assembly. Fungal kinesin-5 motors, such as Cin8, exhibit bidirectional motility, switching between minus- and plus-end-directed stepping in response to environmental conditions; however, the molecular basis of this directional switching remains unclear. To better understand the origin of this bidirectional behavior, we investigated the motility and ATPase kinetics of two Cin8 dimers, created by fusing the motor domains to a stable coiled-coil domain from kinesin-1. To investigate the role of the proximal neck coiled-coil region in coordinating motor activity, we compared Cin8 dimers that included or lacked the first four heptads of the Cin8 neck-coil domain. By analyzing the stepping kinetics, microtubule residence times, and directional switching dynamics, we found that these Cin8 dimers move processively with a net plus-end directionality along with undirected movements, behaviors that mimic the plus-ended motility state of wild-type Cin8. However, fast minus-ended motility seen in wild-type Cin8 tetramers was not observed in the dimers. The instantaneous velocity distributions and ATPase rates were inconsistent with the undirected movement being solely due to passive diffusion, suggesting that they reflect random bidirectional stepping. Fewer undirected movements were seen on yeast microtubules, their native physiological substrate, compared to on bovine microtubules. Replacing the Cin8 neck-coil domain with a stable coiled-coil led to faster plus-end stepping, fewer undirected movements, a reduction in the microtubule binding duration, and enhanced coupling between ATP hydrolysis and plus-end stepping. Our results suggest that the native Cin8 neck coil confers flexibility between the two motor domains that contributes to bidirectional stepping, and that sustained minus-end movement requires regions outside the motor domain. Statement of SignificanceThe kinesin-5 family of motors, which contain two pairs of heads located on either end of a long stalk domain, power mitotic spindle formation by sliding antiparallel microtubules. The yeast kinesin-5, Cin8 moves to microtubule minus-ends under specific conditions, breaking the dogma that N-terminal kinesins move to microtubule plus-ends. To gain insight into how Cin8 changes its walking direction, we analyzed engineered Cin8 dimers, models of one half of full-length Cin8. The dimers step erratically, consistent with stepping in both directions, but have a plus-end bias. We find evidence that the two heads poorly coordinate, which contrasts with other kinesins, and suggest that the stepping direction may be regulated by altering the degree of inter-head coordination.

biophysics↗

bioRxiv2025

Direct single-molecule visualization of Hsp90-mediated relief of a Hsp70-folding block

Hsp70 and Hsp90 are ubiquitous molecular chaperones that cooperate to promote the correct folding and maturation of client proteins. Despite their central role in proteostasis, the molecular mechanisms by which Hsp90 coordinates with Hsp70 to remodel clients remain poorly understood. In particular, how ATP hydrolysis by Hsp90 is coupled to client engagement and conformational change has been a long-standing question. This gap in understanding is largely due to the challenge of visualizing client conformations during the highly dynamic and heterogeneous interactions with the Hsp70/Hsp90 chaperone machinery. To address this, we used a combination of single-molecule fluorescence resonance energy transfer (smFRET) and total internal reflection fluorescence microscopy to observe individual firefly luciferase client proteins as they are sequentially engaged by Hsp70 and Hsp90. Here, we show that Hsp90 reduces rebinding of Hsp70 to folding intermediates while still allowing engagement to misfolded clients, thereby enabling productive refolding in the presence of typically inhibitory concentrations of Hsp70. Furthermore, Hsp90 uses ATP binding and hydrolysis to actively remodel the conformational landscape of the client, promoting controlled folding through localized compaction across multiple regions. These controlled folding events reduce misfolding and are essential for establishing native interdomain contacts. Using smFRET and kinetic simulations, we further demonstrate that heterogeneous Hsp70 binding generates region-specific folding kinetics and conformational dynamics, which are likely driven by variations in the number of available Hsp70-binding sites. This is then exploited during Hsp70/Hsp90-mediated folding to support localized folding of client subdomains, thereby reducing non-native interactions from distal regions to facilitate proper folding of multi-domain proteins.

biophysics↗

bioRxiv2024

Specific Bacterial Taxa and Their Metabolite, DHPS, Linked to Alzheimers Disease, Parkinsons Disease, and Amyotrophic Lateral Sclerosis.

Neurodegenerative diseases (NDDs) are multifactorial disorders frequently associated with gut dysbiosis, oxidative stress, and inflammation; however, the pathophysiological mechanisms remain poorly understood. We investigated bacterial and metabolic dyshomeostasis in the gut microbiome associated with early disease stages across three NDDs, amyotrophic lateral sclerosis (ALS), Alzheimers Disease (AD), Parkinsons Disease (PD), and healthy controls (HC) and discovered a previously unrecognized link between a microbial-derived metabolite with an unknown role in human physiology, 2,3-dihydroxypropane-1-sulfonate (DHPS), and NDDs. DHPS was downregulated in AD, ALS, and PD, while Eubacterium and Desulfovibrio, capable of metabolizing this metabolite,1-4 were increased in all disease cohorts. Additionally, select taxa within the Clostridia class had strong negative correlations to DHPS suggesting a potential role in DHPS metabolism. Hydrogen sulfide is a catabolic product of DHPS,1,5 and hydrogen sulfide promotes inflammation,6-8 oxidative stress,9 mitochondrial damage,10 and gut dysbiosis,2,11 known hallmarks of NDD. These findings suggest that cryptic sulfur metabolism via DHPS is a missing link in our current understanding of NDD onset and progression. To the best of our knowledge, we are the first to provide evidence of a conserved gut-brain axis linkage of specific bacterial taxa and their metabolism of DHPS shared by three neurodegenerative diseases.

neuroscience↗

bioRxiv2023

The incidence of movement disorders increases with age and contrasts with subtle and limited neuroimaging abnormalities in argininosuccinic aciduria.

Argininosuccinate lyase is integral to the urea cycle detoxifying neurotoxic ammonia and the nitric oxide biosynthesis cycle. Inherited argininosuccinate lyase deficiency causes argininosuccinic aciduria (ASA), a rare disease with hyperammonaemia and nitric oxide deficiency. Patients present with developmental delay, epilepsy and movement disorders, associated with nitric oxide-mediated downregulation of central catecholamine biosynthesis. A neurodegenerative phenotype has been proposed in ASA. To better characterise this neurodegenerative phenotype in ASA, we conducted a retrospective study in six paediatric and adult metabolic centres in the UK in 2022. We identified 60 patients and specifically looked for movement disorders-related symptoms: movement disorders such as ataxia, tremor and dystonia, hypotonia and abnormal behaviour. We analysed neuroimaging with diffusion tensor imaging (DTI) magnetic resonance imaging (MRI) in an ASA patient with movement disorders. We assessed conventional and DTI MRI alongside single photon emission computer tomography (SPECT) with dopamine analogue radionuclide 123I-ioflupane, in Asl-deficient mice treated by hASL mRNA with normalised ureagenesis. Movement disorders in ASA appears in the 2nd and 3rd decades of life, becoming more prevalent with ageing and independent from the age of onset of hyperammonaemia. Neuroimaging can show abnormal DTI features affecting both grey and white matter, preferentially basal ganglia. ASA mouse model with normalised ureagenesis did not recapitulate these DTI findings and showed normal 123I-ioflupane SPECT and cerebral dopamine metabolomics. Altogether these findings support the pathophysiology of a late-onset movement disorders with functional central catecholamine dysregulation but without or limited neurodegeneration of dopaminergic neurons, making these symptoms amenable to targeted therapy. SynopsisMovement disorders-related symptoms in ASA appear in the 2nd and 3rd decades of life, becoming more prevalent with age and shows abnormal neuroimaging features of basal ganglia in ASA patients, not recapitulated in ASA mice.

genetics↗

bioRxiv2023

Macrophage inhibitor clodronate enhances liver transduction of lentiviral but not AAV vectors or mRNA lipid nanoparticles in vivo.

Recently approved adeno-associated viral (AAV) vectors for liver monogenic diseases hemophilia A and B are exemplifying the success of liver-directed viral gene therapy. In parallel, additional strategies are rapidly emerging to overcome some inherent AAV limitations, such as non-persistence of episomal transgene in rapidly growing liver and immune response. Integrating lentiviral vectors and non-viral lipid nanoparticles encapsulating mRNA (LNP-mRNA) are rapidly being developed, currently at preclinical and clinical stages respectively. Macrophages are first effector cells of the innate immune response triggered by gene therapy vectors. Macrophage uptake and activation following administration of viral gene therapy and LNPs has been reported. In this study, we assessed the biodistribution of AAV, lentiviral and LNP-mRNA gene therapy following inhibition of tissue macrophages by clodronate liposomes in neonatal and juvenile mice. Juvenile clodronate-treated mice showed significant increase of lentiviral-transduced hepatocytes, and increasing trend of transduction was shown in neonatally-injected mice. In contrast, AAV- and LNP-mRNA-treated neonatal and juvenile animals did not show significant increase of liver biodistribution following clodronate administration. These findings will have translational application for liver-targeting gene therapy programmes.

molecular biology↗

bioRxiv2023

Ex vivo primary liver sections recapitulate disease phenotype and therapeutic rescue for liver monogenic diseases

In academic research and the pharmaceutical industry, in vitro single cell line cultures and in vivo animal models are considered as gold standards in modelling diseases and assessing therapeutic efficacy. However, both models have limitations, with incomplete reproduction of pathophysiological characteristics and absence of 3-dimensional architecture with cell lines or the use of live animals brings ethical considerations, limiting the experimental scale and design. The use of precision-cut tissue slices can bridge the gap between these mainstream models as this technique combines the advantages of studying all cell sub-types whilst preserving the tissue-matrix architecture, thereby closely mimicking a mini-organ. Here, we describe an optimised and easy-to-implement protocol for the culture of sections from mouse livers. We show that precision-cut liver sections can be a reliable model for recapitulating the biological phenotype of inherited metabolic diseases, exemplified by common urea cycle defects citrullinemia type 1 and argininosuccinic aciduria, caused by argininosuccinic synthase (ASS1) and argininosuccinic lyase (ASL) deficiencies respectively. Therapeutic response to gene therapy such as messenger RNA replacement delivered via lipid nanoparticles can be monitored, demonstrating that precision-cut liver sections can be used as a preclinical screening tool to assess therapeutic response and toxicity in monogenic liver diseases.

cell biology↗

bioRxiv2022

mRNA therapy restores ureagenesis and corrects glutathione metabolism in argininosuccinic aciduria

Argininosuccinate lyase (ASL) is a key enzyme integral to the hepatic urea cycle which is required for ammonia detoxification, and the citrulline-nitric oxide (NO) cycle for NO production. ASL deficient patients present with argininosuccinic aciduria (ASA), an inherited metabolic disease with hyperammonaemia and a chronic systemic phenotype with neurocognitive impairment and chronic liver disease. ASL deficiency as an inherited model of systemic NO deficiency, shows enhanced nitrosative and oxidative stress. Here, we describe the dysregulation of glutathione biosynthesis and upstream cysteine utilization in ASL-deficient patients and mice using targeted metabolomics and in vivo positron emission tomography (PET) imaging using (S)-4-(3-18F-fluoropropyl)-L-glutamate ([18F]FSPG). Upregulation of cysteine metabolism contrasted with glutathione depletion and down-regulated antioxidant pathways. hASL mRNA encapsulated in lipid nanoparticles corrected and rescued the neonatal and adult Asl-deficient mouse phenotypes, respectively, enhancing ureagenesis and glutathione metabolism and ameliorating chronic liver disease. We further present [18F]FSPG PET as a novel non-invasive diagnostic tool to assess liver disease and therapeutic efficacy in ASA. These findings support clinical translation of mRNA therapy for ASA.

genetics↗

bioRxiv2022

Stimulating microtubule growth is not the essential function of the microtubule polymerase Stu2

ch-TOG family proteins, including the budding yeast Stu2, are essential for spindle formation and chromosome segregation. Such functions depend on an array of activities ranging from microtubule nucleation, polymerization and depolymerization, to conferring tension sensitivity to kinetochores. This functional diversity makes it challenging to dissect these various functions and understand their relative importance. Here, we developed separation-of-function mutants and used artificial tethering tools to elucidate several important mechanistic insights into Stu2s essential role. We show that Stu2s microtubule polymerization activity depends on its basic linker region but is surprisingly dispensable for viability; that in fact, Stu2 carries out an essential kinetochore-associated function; and finally, that Stu2s precise location within the kinetochore is critical for its function, suggesting a spatial separation mode of action may underlie its ability to confer tension sensitivity. Our findings highlight the significance of Stu2s kinetochore role and provide insights into the molecular mechanisms by which it performs its various functions.

cell biology↗

bioRxiv2021

Naegleria's mitotic spindles are built from unique tubulins and highlight core spindle features

Naegleria gruberi is a unicellular eukaryote whose evolutionary distance from animals and fungi has made it useful for developing hypotheses about the last common eukaryotic ancestor. Naegleria amoebae lack a cytoplasmic microtubule cytoskeleton and assemble microtubules only during mitosis, and thus provides a unique system to study the evolution and functional specificity of mitotic tubulins and the resulting spindle. Previous studies showed that Naegleria amoebae express a divergent -tubulin during mitosis and we now show that Naegleria amoebae express a second mitotic - and two mitotic {beta}-tubulins. The mitotic tubulins are evolutionarily divergent relative to typical - and {beta}- tubulins, contain residues that suggest distinct microtubule properties, and may represent drug targets for the "brain-eating amoeba" Naegleria fowleri. Using quantitative light microscopy, we find that Naeglerias mitotic spindle is a distinctive barrel-like structure built from a ring of microtubule bundles. Similar to those of other species, Naeglerias spindle is twisted and its length increases during mitosis suggesting that these aspects of mitosis are ancestral features. Because bundle numbers change during metaphase, we hypothesize that the initial bundles represent kinetochore fibers, and secondary bundles function as bridging fibers.

cell biology↗

bioRxiv2019

Microtubules form by progressively faster tubulin accretion, not by nucleation-elongation

Microtubules are dynamic polymers that play fundamental roles in all eukaryotes. Despite their importance, how new microtubules form is poorly understood. Textbooks have focused on variations of a nucleation-elongation mechanism in which monomers rapidly equilibrate with an unstable oligomer (nucleus) that limits the rate of polymer formation; once formed, the polymer then elongates efficiently from this nucleus by monomer addition. Such models faithfully describe actin assembly, but they fail to account for how more complex polymers like hollow microtubules assemble. Here we articulate a new model for microtubule formation that has three key features: i) microtubules initiate via rectangular, sheet-like structures which grow faster the larger they become; ii) the dominant pathway proceeds via accretion, stepwise addition of longitudinal or lateral layers; iii) a straightening penalty to account for the energetic cost of tubulins curved-to-straight conformational transition. This model can quantitatively fit experimental assembly data, providing new insights into biochemical determinants and assembly pathways for microtubule nucleation.

cell biology↗

bioRxiv2018

A Stu2-mediated intrinsic tension-sensing pathway promotes chromosome biorientation in vivo

Accurate segregation of chromosomes to daughter cells is a critical aspect of cell division. It requires the kinetochores on duplicated chromosomes to biorient, attaching to microtubules from opposite poles of the cell. Bioriented attachments come under tension, while incorrect attachments lack tension and must be destabilized. A well-studied error correction pathway is mediated by the Aurora B kinase, which destabilizes low tension-bearing attachments. We recently discovered that in vitro, kinetochores display an additional intrinsic tension-sensing pathway that utilizes Stu2. This pathways contribution to error correction in cells, however, was unknown. Here, we identify a Stu2 mutant that abolishes its kinetochore function and show that it causes error correction defects in vivo. We also show that this intrinsic tension-sensing pathway functions in concert with the Aurora B-mediated pathway. Together, our work indicates that cells employ at least two pathways to ensure biorientation and the accuracy of chromosome segregation.

cell biology↗