Biology subjects

Harris, C. A.

Publications and source records attributed to Harris, C. A..

9 recordsLinked to original sources

bioRxiv2026

Double-bond geometry determines fatty acid metabolic fate and ferroptosis sensitivity

Ferroptosis is driven by the accumulation of oxidatively damaged membrane phospholipids, making membrane lipid composition a central determinant of cell death sensitivity. While fatty acid chain length and degree of unsaturation are well-established regulators of ferroptosis, whether fatty acid stereochemistry contributes to ferroptosis susceptibility is mostly unexplored. Here, we systematically screened structurally diverse fatty acids for their ability to modulate ferroptosis and unexpectedly identified trans-unsaturated fatty acids as potent sensitizers. Compared with its cis counterpart linoleic acid, the trans polyunsaturated fatty acid (PUFA) linoelaidic acid more strongly enhanced lipid peroxidation and promoted the accumulation of ferroptosis-susceptible phospholipid species. Unexpectedly, the trans monounsaturated fatty acid petroselaidic acid also sensitized cells to ferroptosis, whereas its cis stereoisomer petroselinic acid suppressed ferroptosis. Mechanistically, petroselaidic acid required stearoyl-CoA desaturase-dependent conversion to a PUFA, directly demonstrating that double-bond geometry can redirect fatty acid metabolic fate through altered recognition by lipid metabolic enzymes. Although linoelaidic acid and petroselaidic acid followed distinct metabolic pathways, both converged on phospholipid remodeling that expanded pools of ferroptosis-susceptible membrane lipids. Together, our findings demonstrate that fatty acid double-bond geometry determines their metabolic fate and the membrane phospholipid composition, establishing lipid stereochemistry as a previously unrecognized structural determinant of ferroptosis sensitivity.

cell biology↗

bioRxiv2025

Induced ubiquitination bypasses canonical ERAD to drive ER protein degradation

Heterobifunctional proteolysis-targeting chimeras (PROTACs) have emerged as a powerful strategy to degrade disease-relevant proteins, enabling targeting of previously "undruggable" proteins. Current degrader molecules primarily target cytosolic substrates, yet nearly one-third of the proteome resides in or transits the endoplasmic reticulum (ER), including receptors, secreted factors, and biosynthetic enzymes with high therapeutic relevance. Whether ER-localized proteins can be broadly targeted for induced degradation remains an open question. To address this gap, we employed a panel of fluorescent reporter cell lines and used the dTAG chemical-genetic system to recruit cytosolic E3 ligases. While lumenal substrates segregated from the cytosol were resistant to degradation, recruitment of cytosolic ligases effectively degraded ER membrane proteins across multiple topologies and with post-translational modifications. CRISPR genetic screens revealed that the induced degradation required the expected cullin RING ligase complexes but surprisingly bypassed ER-associated degradation (ERAD) machinery, with the exception of the AAA ATPase VCP. Mechanistic studies demonstrated that substrate ubiquitination was essential for VCP binding, and cleavage of ubiquitin chains released VCP, suggesting a model in which VCP directly extracts substrates independent of a dislocation apparatus. Extending this strategy to an endogenous substrate, we synthesized an HMGCR ERAD-TAC by linking atorvastatin to a cereblon E3 ligase recruiter and found that HMGCR degradation was likewise VCP-dependent. Together, these findings demonstrate that ER membrane proteins are generally susceptible to induced degradation via cytosolic ligase recruitment, uncovering a VCP-centered mechanism that operates independently of membrane-embedded ERAD machinery. This work establishes foundational principles for extending targeted protein degradation to the early secretory pathway. SIGNIFICANCE STATEMENTTargeted protein degradation has transformed drug discovery. Nearly one-third of the proteome reside in or transit the endoplasmic reticulum (ER), a compartment rich in therapeutically relevant but structurally complex targets. Whether these ER proteins can be broadly degraded using PROTACs has remained unknown. Here, we define the minimal requirements for degrading ER membrane proteins by recruiting cytosolic E3 ligases. Using chemical-genetic tools, genetic screens, and a statin-based degrader, we show that ubiquitination engages the VCP extraction machinery, enabling degradation of diverse ER membrane proteins independent of canonical ER-associated degradation components. These findings reveal a ubiquitin-driven route for membrane protein turnover, expand the landscape of druggable ER proteins, and establish principles for designing degraders operating in the early secretory pathway.

cell biology↗

bioRxiv2025

Vitamin B2 metabolism promotes FSP1 stability to prevent ferroptosis

Ferroptosis, a regulated form of cell death driven by excessive lipid peroxidation, has emerged as a promising therapeutic target in cancer. Ferroptosis suppressor protein 1 (FSP1) is a critical regulator of ferroptosis resistance, yet the mechanisms controlling its expression and stability remain mostly unexplored. To uncover regulators of FSP1 abundance, we conducted CRISPR-Cas9 screens utilizing a genome-edited, dual-fluorescent FSP1 reporter cell line, identifying both transcriptional and post-translational mechanisms that determine FSP1 levels. Notably, we identified riboflavin kinase (RFK) and FAD synthase (FLAD1), enzymes which are essential for synthesizing flavin adenine dinucleotide (FAD) from vitamin B2, as key contributors to FSP1 stability. Biochemical and cellular analyses revealed that FAD binding is critical for FSP1 activity. FAD deficiency, and mutations blocking FSP1-FAD binding, triggered FSP1 degradation via a ubiquitin-proteasome pathway that involves the E3 ligase RNF8. Unlike other vitamins that inhibit ferroptosis by scavenging radicals, vitamin B2 supports ferroptosis resistance through FAD cofactor binding, ensuring proper FSP1 stability and function. This study provides a rich resource detailing mechanisms that regulate FSP1 abundance and highlights a novel connection between vitamin B2 metabolism and ferroptosis resistance with implications for therapeutic strategies targeting FSP1 in cancer.

cell biology↗

bioRxiv2024

Building Brains for Robots: A Hands-On Approach to Learning Neuroscience in the Classroom

As the relevance of neuroscience in education grows, effective methods for teaching this complex subject in high school classrooms remain elusive. Integrating classroom experiments with brain-based robots offers a promising solution. This paper presents a structured curriculum designed around the use of camera-equipped mobile robots which enables students to construct and explore artificial neural networks. Through this hands-on approach, students engage directly with core concepts in neuroscience, learning to model spiking neural networks, decision-making processes in the basal ganglia, and principles of learning and memory. The curriculum not only makes challenging neuroscience concepts accessible and engaging but also demonstrates significant improvements in students understanding and self-efficacy. By detailing the curriculums development, implementation, and educational outcomes, this study outlines a scalable model for incorporating advanced scientific topics into secondary education, paving the way for a deeper student understanding of both theoretical neuroscience and its practical applications.

scientific communication and education↗

bioRxiv2021

Teacher Perceptions of Using Robots to Teach Neuroscience in Secondary School

The use of robots to help teachers to engage students in STEM subjects has been increasing in recent years, and much progress has been made in K12 schools to incorporate robots in the pedagogy. Recent studies indicate that robots can play a significant role to engage students in neuroscience subjects, but little is known about teachers perceptions of using robots to teach neuroscience. In this paper, we present a study based on a survey questionnaire conducted with 84 teachers across multiple high schools in the United States to understand their perceptions about the usefulness of using robots to teach neuroscience. To situate teachers with an example of how robots can be used in neuroscience classrooms, we describe an educational tool called the SpikerBot. Our preliminary results indicate that there is an opportunity for neuroscience-oriented robots in secondary education, provided sufficient on-boarding and training videos.

scientific communication and education↗

bioRxiv2021

A novel skeletal-specific adipogenesis pathway defines key origins and adaptations of bone marrow adipocytes with age and disease

Bone marrow adipocytes (BMAs) accumulate with age and in diverse disease states. However, their age- and disease-specific origins and adaptations remain unclear, impairing our understanding of their context-specific endocrine functions and relationship with surrounding tissues. In this study, we identified a novel, bone marrow-specific adipogenesis pathway using the AdipoqCre+/DTA+ fat free mouse (FF), a model in which Adipoq-Cre drives diphtheria toxin-induced cell death in all adiponectin-expressing cells. Adiponectin is highly expressed by BMAs, peripheral adipocytes, and a subset of bone marrow stromal progenitor cells with preadipocyte-like characteristics. Consistent with this, FF mice presented with uniform depletion of peripheral white and brown adipose tissues, in addition to loss of BMAs in canonical locations such as the tail vertebrae. However, unexpectedly, a distinctly localized subset of BMAs accumulated with age in FF mice in regions such as the femoral and tibial diaphysis that are generally devoid of bone marrow adipose tissue (BMAT). Ectopic BMAs in FF mice were defined by increased lipid storage and decreased expression of cytokines including hematopoietic support factor Cxcl12 and adipokines adiponectin, resistin, and adipsin. FF BMAs also displayed resistance to lipolytic stimuli including cold stress and {beta}3-adrenergic agonist CL316,243. This was associated with reduced expression of adrenergic receptors and monoacylglycerol lipase. Global ablation of adiponectin-expressing cells regulated bone accrual in an age- and sex-dependent manner. High bone mass was present early in life and this was more pronounced in females. However, with age, both male and female FF mice had decreased cortical thickness and mineral content. In addition, unlike BMAs in healthy mice, expansion of ectopic BMAs in FF mice was inversely correlated with cortical bone volume fraction. Subcutaneous fat transplant and normalization of systemic metabolic parameters was sufficient to prevent ectopic BMA expansion in FF mice but did not prevent the initial onset of the high bone mass phenotype. Altogether, this defines a novel, secondary adipogenesis pathway that relies on recruitment of adiponectin-negative stromal progenitors. This pathway is unique to the bone marrow and is activated with age and in states of metabolic stress, resulting in expansion of BMAs specialized for lipid storage with compromised lipid mobilization and endocrine function within regions traditionally devoted to hematopoiesis. Our findings further distinguish BMAT from peripheral adipose tissues and contribute to our understanding of BMA origins and adaptation with age and disease.

cell biology↗

bioRxiv2020

Adipose Tissue is a Critical Regulator of Osteoarthritis

Osteoarthritis (OA), the leading cause of pain and disability worldwide, disproportionally affects obese individuals. The mechanisms by which adipose tissue leads to the onset and progression of OA are unclear due to the complex interactions between the metabolic, biomechanical, and inflammatory factors that accompany obesity. We used a murine model of lipodystrophy (LD) to examine the direct contribution of adipose tissue to OA. Knee joints of LD mice were protected from spontaneous or post-traumatic OA, on either a chow and high fat diet, despite similar body weight and the presence of systemic inflammation. These findings indicate that adipose tissue itself plays a critical role in the pathophysiology of OA. Susceptibility to post-traumatic OA was reintroduced into LD mice using implantation of adipose tissue derived from wildtype animals or mouse embryonic fibroblasts that undergo spontaneous adipogenesis, implicating paracrine signaling from fat, rather than body weight, as a critical mediator of joint degeneration.Competing Interest StatementThe authors have declared no competing interest.View Full Text

physiology↗

bioRxiv2020

Open-source 3D printed Ventilation Device

COVID-19 is an acute respiratory tract infection caused by a coronavirus known as SARS-CoV-2. The common signs of infection include respiratory symptoms such as shortness of breath, breathing difficulties, dry cough, fever, and in some patients, severe acute respiratory syndrome, kidney failure, and death. 312,009 deaths from COVID-19 has been reported as of today. While respiratory symptoms are commonly caused by the infection, the use of mechanical ventilation is required for some patients. The following is intended to review the development and testing of a 3D printed and open-source mechanical ventilation device that is capable of adjusting breathing rate, volume, and pressure simultaneously and was designed according to the latest clinical observations of the current pandemic. The intuitive design of this device along with the use of primarily 3D printed or readily available components allow the rapid manufacturing and transportation of this ventilation device to the impacted regions.

bioengineering↗

bioRxiv2019

Short Neurorobotics Workshop for High School Students Promotes Competence and Confidence in Computational Neuroscience

Understanding the brain is a fascinating challenge, captivating the scientific community and the public alike. The lack of effective treatment for most brain disorders makes the training of the next generation of neuroscientists, engineers and physicians a key concern. Over the past decade there has been a growing effort to introduce neuroscience in primary and secondary schools, however hands-on laboratories have been limited to anatomical or electrophysiological activities. Modern neuroscience research labs are increasingly using computational tools to model circuits of the brain to understand information processing. Here we introduce the use of neurorobots - robots controlled by computer models of biological brains - as an introduction to computational neuroscience in the K-12 classroom. Neurorobotics has enormous potential as an education technology because it combines multiple activities with clear educational benefits including neuroscience, active learning, and robotics. We describe an introductory neurorobot workshop that teaches high school students how to use neurorobots to investigate key concepts in neuroscience, including spiking neural networks, synaptic plasticity, and adaptive action selection. Our do-it-yourself (DIY) neurorobot uses wheels, a camera, a speaker, and a distance sensor to interact with its environment, and can be built from generic parts costing about $150 in under 4 hrs. Our Neurorobot App visualizes the neurorobot's visual input and brain activity in real-time, and enables students to design new brains and deliver dopamine-like reward signals to reinforce chosen behaviors. We have tested the Neurorobot Workshop with high school students (n = 3 workshops, 9 students total) and have found that students were able to complete all exercises in under 3 hrs. In a post-workshop survey, students reported having gained the ability to develop neural networks that perform specific functions, including goal-directed behavior and memory. Here we provide DIY hardware assembly instructions, discuss our open-source Neurorobot App and demonstrate how to teach the Neurorobot Workshop. By doing this we hope to accelerate research in educational neurorobotics and promote the use of neurorobots to teach computational neuroscience in high school.

scientific communication and education↗