Biology subjects

Lee, S.

Publications and source records attributed to Lee, S..

At least 181 records · Page 10Linked to original sources

bioRxiv2025

Effective imaging and treatment of Acute Myeloid Leukemia with radiotheranostics targeting the activated conformation of integrin-Beta2

There remains an unmet clinical need for improved treatment strategies in Acute Myeloid Leukemia (AML). Although radiopharmaceutical therapies targeting non-cancer-selective antigens have shown promise in AML, their clinical utility is often limited by prolonged bone marrow suppression. Using a unique proteomics-based strategy, we recently identified the active conformation of integrin-{beta}2 (aITGB2) as a novel, tumor-selective target for AML. Importantly, this conformational epitope is expressed widely on AML cells but minimally on normal marrow progenitors/healthy tissues. Here we first confirmed widespread aITGB2 expression on AML tumors that was largely independent of tumor genotype or prior therapeutic regimen. We developed diagnostic and therapeutic radiopharmaceuticals targeting aITGB2 utilizing a conformation-specific antibody (clone 7065). PET/CT imaging with 89Zr and 134Ce-labeled 7065 in AML models revealed high target-mediated uptake, greater than that compared to standard of care [18F]-FDG. PET/CT imaging with [89Zr]DFO*-7065 showed reduced binding to normal bone marrow and immune cells in humanized immune system mice compared to [89Zr]DFO*-anti-CD33. For therapy, we developed [225Ac]Macropa-PEG4-7065 using an optimized chelator-linker combination. Treatment with [225Ac]Macropa-PEG4-7065 in Nomo-1 and PDX AML disseminated models delayed tumor growth and improved overall survival compared to controls, including [225Ac]DOTA-anti-CD33, a clinical stage-radioimmunotherapy under evaluation in AML. Relapsed tumors demonstrated persistent aITGB2 expression, supporting continued development of fractionated dosing schemes, and proteomics analysis indicated activation of TCA cycle and carbon metabolism pathways, consistent with therapy-induced stress responses. These findings highlight [89Zr]DFO*-7065 and [225Ac]Macropa-7065 as a promising aITGB2-targeted theranostic pair with potential for imaging and treatment in future clinical translation. One Sentence SummaryThis study demonstrates promising preclinical efficacy of aITGB2-targeted radiotheranostics for selective imaging and therapy in AML.

cancer biology↗

bioRxiv2025

NSF is required for diverse endocytic modes by promoting fusion and fission pore closure in secretory cells

The ATPase N-ethylmaleimide-sensitive factor (NSF), known for disassembling SNARE complexes, plays key roles in neurotransmitter release, neurotransmitter (AMPA, GABA, dopamine) receptor trafficking, and synaptic plasticity, and its dysfunction or mutation is linked to neurological disorders. These roles are largely attributed to SNARE-mediated exocytosis. Here, we reveal a previously unrecognized role for NSF: mediating diverse modes of endocytosis--including slow, fast, ultrafast, overshoot, and bulk--by driving closure of both fusion and fission pores. This function was consistently observed across large calyx nerve terminals, small hippocampal boutons, and chromaffin cells using capacitance recordings, synaptopHluorin imaging, electron microscopy, and multi-color pore-closure imaging. Results were robust across four NSF inhibitors, gene knockout, knockdown, and specific mutations. These findings establish NSF as a central regulator of membrane fission, kiss-and-run fusion, endocytosis, and exo-endocytosis coupling--offering new mechanistic insights into its diverse physiological and pathological roles in synaptic transmission, receptor trafficking, and neurological diseases.

neuroscience↗

bioRxiv2025

Trim47 inhibits murine norovirus replication in a strain-dependent manner

Human norovirus is the leading cause of gastroenteritis worldwide. Norovirus exhibits remarkable genetic diversity. Understanding the impact of genetic diversity on infection and immunity has been challenging due to the difficulties of in vitro cultivation and the current lack of a small animal model. Murine norovirus (MNV) has emerged as a premier model system to investigate norovirus biology. Here, we identify Trim47 as a host restriction factor that potently inhibits MNV infection in a strain dependent manner. We determine that Trim47 expression inhibits an early stage of the viral life cycle for the MNV strain CR6, while the replication of the closely related strain CW3 is not restricted by Trim47. Using a forward genetic screen we determine that genetic variation within the nonstructural gene NS1 accounts for this differential sensitivity to Trim47. While most TRIM containing proteins promote the ubiquitination and degradation of its targets, Trim47 does neither. Instead, Trim47 promotes the deubiquitination of the NS1/2 precursor protein. Our data provide new insight into a potential antiviral gene and mechanistic insight into norovirus evolution that may impact viral tropism. ImportanceViruses exist as genetically heterogeneous populations. Understanding the contribution of viral genetic variation on infection outcomes is critical in predicting emerging viruses and their variants. Noroviruses are genetically diverse but human norovirus has been technically challenging to study. In this study we use the model system murine norovirus to identify a viral strain specific restriction mechanism where a host gene can specifically restrict one strain of the virus but has no impact on a closely related strain. Dissecting the mechanism of this specificity provides insight into viral diversity and possible host restriction pathways.

microbiology↗

bioRxiv2025

Developing future resilience from signatures of adaptation across the sorghum pangenome

While the green revolution adapted a handful of crops to homogenous and high-input industrialized agriculture, much of the global population still relies on local food production from low-input smallholder farms that grow highly variable crop cultivars. The high diversity of the grain and bioenergy crop sorghum 1-4, and many other crops that were not homogenized during the green revolution 5, not only provides the raw materials for breeders to make substantial gains in cultivar improvement, but also constrains breeding efforts due to highly specialized locally adapted plant phenotypes 6. Here, we construct a 33-member pangenome and identify trait-associated variants in 1,988 cultivars and landraces. We then apply these resources to explore the complex interplay between historical contingency, ongoing adaptation, and the potential for future gains through climate-aware genome-enabled breeding. Specifically, our analyses conclusively demonstrate that multiple nested, deeply diverged, and previously uncharacterized structural variants in the domestication gene SHATTERING1 distinguish the previously established multicentric origin of sorghum. We then apply landscape genomics tests to reveal how gene flow, adaptation, and secondary contact created the complex genetic mosaic in current global breeding networks. Further analysis of climate-gene associations highlights candidate loci underlying adaptation, including the biosynthetic gene cluster for the cyanogenic glucoside dhurrin. Combined, the pangenome-informed variants developed here will enable both trait discovery and subsequent marker assays to accelerate breeding and provide a framework for similar applications in other diverse and non-model crops.

genomics↗

bioRxiv2025

Optogenetic activation of liver-innervating vagal sensory neurons increases anxiety-like behavior in mice.

The liver plays a central role in energy balance, glucose homeostasis, and lipid metabolism through neural and humoral pathways. Intriguingly, impaired hepatic lipid metabolism has been also associated with an increased risk of anxiety and depression in rodents and humans. However, the mechanisms by which it affects mood behaviors via neural pathways remain poorly understood. This study investigated whether activation of the liver-brain axis can modulate anxiety-like behavior in mice. Advillin (Avil)CreERT2; channelrhodopsin-tdTomato mice and wireless optogenetics were used to selectively stimulate Avil-positive vagal sensory neurons that innervate the liver in freely moving mice. Acute optogenetic stimulation of their nerves in the liver activated neurons in the nodose ganglia and the dorsal motor nucleus of the vagus, and to a lesser extent, those in the nucleus of the solitary tract (NTS). Behavioral assessments revealed that acute optogenetic stimulation of these liver-innervating vagal sensory nerves increased anxiety-like behavior in male and female mice during open field, elevated plus maze, and light/dark box tests. Retrograde viral tracing revealed that neurons in the NTS sent projections to the locus coeruleus (LC), and optogenetic stimulation of liver-innervating vagal sensory nerves resulted in significant activation of norepinephrine-expressing neurons in the LC. Chemogenetic inhibition of LC norepinephrine (NE) neurons completely abolished the anxiogenic effect of stimulating Slc6a2{square}positive vagal sensory neurons, demonstrating that LC NE neuron activity is essential for this behavioral response. Therefore, these findings reveal a novel liver - NTS - LC circuit that plays a role in the regulation of anxiety-like behavior through vagal sensory neurons. Unlike the traditional top-down neuronal circuits associated with the liver, this newly identified liver-brain axis is essential for regulating not only systemic energy homeostasis but also emotional behaviors.

animal behavior and cognition↗

bioRxiv2025

A molecular and spinal circuit basis for the functional segregation of itch and pain

Recent advances reveal an extensive cellular diversity within the dorsal horn. How this complexity processes distinct sensations, like itch and pain, remains a fundamental question. We discovered hidden within a population of neurons expressing the gastrin-releasing peptide receptor (Grpr+), thought to be itch-specific, are highly homologous yet functionally distinct subtypes distinguished by expression of Tachykinin-1 (Tac1). While the Tac1- subtype mediates itch, the Tac1+ subtype mediates mechanical allodynia across diverse pain states. Inhibitory populations and differential sensitivities to GRP serve as key modulators of the Grpr+ neuron subtypes, shaping modality specific output. Leveraging computationally designed genomic enhancers to silence the Tac1- population reverses itch while silencing the Tac1+ subtype reverses mechanical allodynia broadly. The work demonstrates the nuance of differential sensory modality coding within the dorsal horn and the power of genomic enhancer-based strategies for modality-specific targeting.

neuroscience↗

bioRxiv2025

Kinetic Plasticity of Nitrite-Oxidizing Bacteria Containing Cytoplasmic Nitrite Oxidoreductase

Nitrite oxidation, the second step of nitrification, is essential to the global nitrogen cycle. Nitrite-oxidizing bacteria (NOB) are classified into two groups based on the cellular localization of their key enzyme nitrite oxidoreductase (NXR): periplasmic (pNXR) and cytoplasmic (cNXR). The use of a cNXR by NOB has been reported to be linked to a lower nitrite affinity and energy efficiency of nitrite oxidation, indicating adaptation to nitrogen-rich environments. In this study, cNXR NOB model strains demonstrated nitrite concentration-dependent shifts in optimal growth pH, a behavior not observed in pNXR NOB. Nitrobacter winogradskyi Nb-255 (cNXR NOB), grown at 1 mM nitrite (pH 7.5), exhibited a high nitrite affinity in terms of apparent Km (25.9 M) and a high specific affinity a{degrees} (440.5 l g cells-1 h-1), both comparable to pNXR NOB in microrespirometry-based kinetic assays. Unexpectedly, cells pre-grown at 10 mM nitrite (pH 7.5) achieved a pNXR-like affinity at pH 5.5 without prior adaptation to acidic conditions. In contrast, pNXR NOB exhibited consistent kinetic behavior across different pH conditions. Kinetic inhibition in the presence of nitrate suggested that this plasticity is driven by a regulated interplay between nitrite uniport and nitrite/nitrate antiporter systems. Our findings indicate that Nitrobacter can dynamically modulate nitrite affinity in response to both nitrite concentration and pH, conferring a flexible adaptation strategy that features traits of both r-and K-strategists across a range of environmental conditions. This adaptive plasticity likely extends to other cNXR-containing NOB in response to fluctuating environmental conditions.

microbiology↗

bioRxiv2025

MeCP2 regulates cell type-specific functions of depressive-like symptoms in the nucleus accumbens

MeCP2 (methyl CpG binding protein 2) is a transcriptional regulator that modulates gene expression in response to environmental stimuli. Although recent studies have implicated MeCP2 in stress responses and depression, its precise role is not completely understood. In this study, we identify a cell type-specific function of MeCP2 in the regulation of depression-like symptoms within the nucleus accumbens (NAc), a key brain region for emotional and stress processing. We observed differential MeCP2 expression in distinct cell populations of the NAc following chronic restraint stress (CRS) and investigated the behavioral and electrophysiological consequences of cell type-specific MeCP2 manipulation. We also explored the molecular mechanisms by which MeCP2 alleviates depression-like symptoms in the NAc and associated neural circuit regions through cell type-specific profiling of the spatial transcriptome. Our findings demonstrate that MeCP2 contributes to synaptic and circuit-level regulation in a cell type-specific manner within the NAc and ultimately mitigates CRS-induced depression-like behaviors. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=147 SRC="FIGDIR/small/666523v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@1ae5875org.highwire.dtl.DTLVardef@1319231org.highwire.dtl.DTLVardef@174ef60org.highwire.dtl.DTLVardef@fb061_HPS_FORMAT_FIGEXP M_FIG Graphical abstract.Schematic Summary of the functional role of accumbal MeCP2 C_FIG

neuroscience↗

bioRxiv2025

An updated resource of 180K soybean SNP genotyping array based on the T2T reference genome

Single nucleotide polymorphism (SNP) genotyping has revolutionized crop improvement by enabling high-resolution genomic analyses and accelerating breeding programs. In soybean (Glycine max (L.) Merr.), a globally important legume crop, existing genotyping data for 180,961 SNP markers from the Korean soybean core collection were generated using the outdated Williams 82 reference genome version 1 (Wm82.v1), which contains numerous assembly gaps and misassemblies that limit genomic resolution. While high-quality reference genomes including Wm82.v4 and Wm82.v6 (telomere-to-telomere assembly) are now available, the valuable existing SNP array data have not been integrated with these improved genomic resources. Here we show successful remapping of the 180K SNP array data to both Wm82.v4 and Wm82.v6 reference genomes through sequence-based alignment of flanking regions. We extracted flanking sequences from SNP marker positions in Wm82.v1 and mapped them to the newer reference versions based on sequence similarity, excluding markers with mapping failures, allele mismatches, low-identity alignments, or multiple mappings, which resulted in successful mapping of 175,202 and 175,763 markers to Wm82.v4 and Wm82.v6, respectively. We also remapped genotype data from 927 soybean accessions (497 USDA-GRIN accessions and 430 Korean core collection accessions) to both reference versions. This updated SNP dataset provides the soybean research community with a comprehensive genomic resource that leverages both existing genotyping investments and state-of-the-art reference genome assemblies for enhanced crop improvement and genomic studies.

genomics↗

bioRxiv2025

LeGO-Teknik reveals that the neurogenesis pathway is a clone-specific hallmark of brain metastasis in breast cancer

Breast cancer exhibits substantial inter- and intra-patient heterogeneity. Yet the molecular features underlying this diversity and their roles in tumour progression are not yet fully elucidated. Within a primary tumour, certain clones possess a unique capacity to metastasize to distant organs, such as the brain, and this propensity may be associated with specific gene expression profiles. To investigate this phenomenon, we developed a new optical barcoding library, LeGO-Teknik, compatible with high resolution imaging, flow cytometry, single-cell RNA sequencing and machine learning computational methods. Using this new tool, we systematically assessed the fitness and organ tropism of multiple human breast cancer clones in spontaneous metastasis assays. Linking transcriptomic profiles of individual cancer cells to their clonal identities and metastatic behaviours, we identified that clones predisposed to forming brain metastases exhibit distinct molecular signatures. Notably, individual cells from these clones showed enriched expression of neurogenesis-related genes. Using SCENIC transcription factor analysis, we found that some of these features are driven by the transcription factor SOX4. This hallmark, likely due to a process of cellular reprogramming, is a remarkable example of organ mimicry during clonal selection. Together, this work provides critical insights into brain metastasis and highlights the potential for identifying predictive biomarkers and therapeutic targets for metastatic breast cancer.

cancer biology↗

bioRxiv2025

Growth Cost and Transport Efficiency Tradeoffs Define Root System Optimization Across Varying Developmental Stages and Environments in Arabidopsis

Root system architecture (RSA) is central to plant adaptation and fitness, yet the design principles and regulatory mechanisms connecting RSA to environmental adaptation are not well understood. We developed Ariadne, a semi-automated software for quantifying cost-efficiency tradeoffs of RSA by mapping root networks onto a Pareto-optimality framework, which describes the balance between resource transport efficiency and construction cost. Applying Ariadne to Arabidopsis thaliana, we found that root architectures consistently assume Pareto-optimal forms across developmental stages, genotypes, and environmental conditions. Using the Discovery Engine, an engine that combines machine learning together with interpretability techniques, we found developmental stage, the hy5/chl1-5 genotype, and manganese availability as important determinants of the cost-efficiency tradeoff, with manganese exerting a unique influence not observed for other nutrients. These results reveal that RSA plasticity is genetically constrained to cost-efficiency optimal configurations and that developmental and environmental factors shift RSA on the pareto front, with manganese acting as a strong modulator of the transport efficiency and construction cost balance.

plant biology↗

bioRxiv2025

Reduced Model-Based Control in Gambling Disorder Despite Intact Neural Value and Task Structure Representations

Disordered gambling has been linked to impairments in goal-directed (model-based) control and reinforcement learning. Here we investigated the potential neural basis of this impairment using a sequential reinforcement learning task (modified two-step-task), computational modeling, and functional magnetic resonance imaging (fMRI) in individuals exhibiting symptoms of disordered gambling (GD) and matched healthy controls (HC, n=30 per group). Model-agnostic analyses replicated the effects of reduced performance and reduced model-based control in the gambling group, both in terms of choice and response time effects. Computational modeling of choice behavior confirmed that this effect was due to reduced model-based control in the gambling group. Analyses of choices and response times using drift diffusion modeling revealed a more complex pattern, where behavioral impairments in the gambling group were linked to changes across several parameters reflecting drift rate modulation and asymptote, as well as non-decision time. Despite these pronounced behavioral differences, the gambling group exhibited largely intact neural effects related to the task transition structure, reward feedback and trial-to-trial behavioral adjustments. Results are discussed with respect to current neurocomputational models of behavioral dysregulation in disordered gambling.

neuroscience↗

bioRxiv2025

Antigen reactivity defines tissue-resident memory and exhausted T cells in tumours

CD8+ T cells are a key weapon in the therapeutic armamentarium against cancer. While CD8+CD103+ T cells with a tissue-resident memory T (TRM) cell phenotype have been favourably correlated with patient prognoses1-6, the tumour microenvironment also contains dysfunctional exhausted T (TEX) cells that exhibit a myriad of TRM-like features, leading to conflation of these two populations. Here, we deconvolute TRM and TEX cells within the intratumoural CD8+CD103+ T cell pool across human cancers, ascribing markers and gene signatures that distinguish these CD8+ populations and enable their functional distinction. We found that while TRM cells exhibit superior functionality and are associated with long-term survival post-tumour resection, they are not associated with responsiveness to immune checkpoint blockade. Deconvolution of the two populations showed that tumour-associated TEX and TRM cells are clonally distinct, with the latter comprising both tumour-independent bystanders and tumour-specific cells segregated from their cognate antigen. Intratumoural TRM cells can be forced towards an exhausted fate when chronic antigen stimulation occurs, arguing that the presence or absence of continuous antigen exposure within the microenvironment is the key distinction between respective tumour-associated TEX and TRM populations. These results suggest unique roles for TRM and TEX cells in tumour control, underscoring the need for distinct strategies to harness these T cell populations in novel cancer therapies.

immunology↗

bioRxiv2025

Male mice lacking Magel2 in hypothalamic POMC neurons that innervate the medial amygdala exhibit increased stress-induced anxiety-like behavior and display reduced spatial reward learning.

Prader-Willi syndrome (PWS) results from a lack of expression in several paternally inherited, imprinted contiguous genes. Among the genes inactivated in PWS, the Magel2 gene is considered a significant contributor to the etiology of the syndrome. The loss of the Magel2 gene causes abnormalities in growth and fertility and increased adiposity with altered metabolism in adulthood, which aligns with some of the pathologies observed in PWS. Given that anxiety is a prominent phenotypic behavior in PWS, we investigate the role of the Magel2 gene, particularly in hypothalamic POMC neurons innervating the medial amygdala (MeA), in the behavioral phenotypes associated with Prader-Willi Syndrome (PWS). Both male and female mice lacking the Magel2 gene in MeA-innervating ARCPomc neurons display no alterations in anxiety-like behavior during the open field test, light/dark test, and elevated plus maze test in the absence of exposure to acute stress. However, male mice with a Magel2 gene deletion in these particular neurons exhibit increased stress-induced anxiety-like behavior and reduce motivation/spatial learning, while female mice do not show these behavioral changes. Our results suggest that the Magel2 gene in ARCPomc neurons, especially in males, influences the impact of stress on anxiety-like behavior and spatial learning deficits associated with a food reward. With the recent approval of a novel treatment for hyperphagia in PWS by the FDA that seems to target the hypothalamic melanocortin system, understanding the cellular mechanisms by which MAGEL2 in ARCPomc neurons innervating the MeA regulates emotional behaviors might help the development of new therapeutic strategies for addressing mental illness in individuals with PWS.

animal behavior and cognition↗

bioRxiv2025

A Fibroblast State Choreographs an Epithelial YAP-dependent Regenerative Program Essential to (Pre)malignancy via ECM-mediated Mechanotransduction

Chronic lung injury generates metaplasia which occasionally, but ominously, progresses to squamous dysplasia and squamous lung cancer. To identify mechanisms through which disrupted tissue homeostasis contributes to malignant initiation and progression, we used in vivo and in vitro heterotypic recombinant models of human bronchial epithelial cells (hBECs) and fibroblasts. We demonstrate that injury-associated TGF-{beta} signaling creates a fibroblast state dependent upon HSP47 upregulation. These fibroblasts accumulated collagen, thus elevating tissue stiffness and activating mechanosignaling that sustained YAP-dependent embryonic-like, pro-malignant activities in adjacent hBECs. This Stress/Tension-Instructive Fibroblast (STIF) state, exhibited by stressed fibroblasts in premalignant and malignant lesions across multiple cancer types, was sufficient to reprogram disease-free hBECs to metaplasia and to drive hBECs with compromised tumor suppressor function to dysplasia, yet could be inhibited and reversed. STIFs suffice to activate epithelial phenotypes reminiscent of oncogene-mediated cell transformation and induce (pre)malignancy via increased force transmission, providing novel targets for prevention. Statement of significanceTissue injury creates a regenerative pro-tumorigenic Stress/Tension-Instructive Fibroblast (STIF) state which is sufficient to activate a YAP-dependent, pre-malignant program to induce or unmask pre-cancerous phenotypes in epithelial cells through mechanotransduction. Inhibition of STIF activity or mechanosignaling prevents metaplasia and progression to dysplasia. HighlightsO_LITissue injury creates a pro-tumorigenic Stress/Tension-Instructive Fibroblast (STIF) state in multiple organs that precedes and persists through cancer C_LIO_LISTIF signaling alone, working through fibroblasts and not epithelial cells, is sufficient to activate embryonic-like plasticity and induce epithelial pre-cancerous metaplastic lesions C_LIO_LISTIFs program (pre)malignant phenotypes in adjacent epithelial cells through mechanosignaling by activating YAP prior to tumor formation C_LIO_LIInhibiting STIFs or mechanosignaling prevents/reverts metaplasia and prevents progression to dysplasia C_LI

cancer biology↗

bioRxiv2025

A Novel FNDC1-NAMPT-NAD axis is Implicated in Small and Large-vessel Arterial Disease and Drives Vascular Calcification

Vascular calcification represents a convergent pathological feature of diverse cardiovascular diseases, yet the upstream molecular programs orchestrating this process remain poorly defined. Here, we uncover fibronectin type III domain-containing 1 (FNDC1) as a previously unrecognized regulator of vascular calcification across both microvascular and macrovascular beds. Integrative transcriptomic profiling of human calciphylaxis lesions and atherosclerotic coronaries identified FNDC1 as one of the most significantly upregulated genes. In primary human vascular smooth muscle cells, FNDC1 drove osteogenic phenotype switch and vascular calcification through activation of PI3K/AKT signaling and metabolic reprogramming. Mechanistically, FNDC1 directly binds to nicotinamide phosphoribosyltransferase (NAMPT) resulting in elevated intracellular NAD levels, thus coupling vascular signaling to control of NAD biosynthesis. In murine models, genetic deletion of Fndc1 or pharmacologic inhibition of NAMPT suppressed arterial calcification and prolonged survival. Clinically, circulating FNDC1 levels were elevated in patients with both calciphylaxis and coronary artery disease and independently predicted cardiovascular risk in 42,687 UK Biobank participants. Together, these findings establish FNDC1 as a central mediator of vascular pathology and highlight the FNDC1- NAMPT-NAD+ axis as a promising target for therapeutic intervention.

cell biology↗

bioRxiv2025

Endogenous Nitroalkene Exploits Dependence on Autophagy-Lysosome Pathway in PARPi-Resistant TNBC

Lack of DNA double-strand break repair efficiency exquisitely sensitizes cancers to poly-ADP ribose polymerase inhibitors (PARPi). Unfortunately, resistance to PARPi poses an insurmountable challenge for patients. Mechanisms that confer insensitivity to PARPi therapy include enhanced DNA damage repair and autophagy. Natural and non-natural unsaturated fatty acid nitroalkene derivatives (NFA) show anticancer actions that sensitize TNBC cells to PARPi and other DNA-damaging treatments. We reveal that nitro-oleic acid (OA-NO2) re-sensitizes PARPi-resistant TNBC cells to PARPi. RNA-seq analysis of clinically relevant mutBRCA1 PARPi-resistant TNBC cell lines exhibited upregulation in autophagy and lysosomal pathways. Bio-orthogonal analysis identified the autophagy regulator SQSTM1/p62 as a novel OA-NO2 target, alkylating two redox-sensitive Cys residues of p62 (Cys105 and Cys113). These Cys are essential for p62 regulation of autophagy and mimicked the effects of p62 Cys105 and Cys113Ala mutants and when alkylated by OA-NO2 showed impaired p62 oligomerization, degradation, and inhibition of autophagy. Combination treatment of PARPi-resistant TNBC with a PARPi and OA-NO2 synergistically inhibited p62-associated autophagy and lysosome function. These data emphasize the clinical potential of OA-NO2 for treating PARPi-resistant TNBC patients.

pharmacology and toxicology↗

bioRxiv2025

Using Time Dependent Rate Analysis to Evaluate the Quality of Machine Learned Reaction Coordinates for Biasing and Computing Kinetics

Having an accurate reaction coordinate (RC) is essential for reliable kinetic characterization of molecular processes, but there are few quantitative metrics to evaluate RC quality. In this study, we consider the dimensionless{gamma} metric from the Exponential Average Time-dependent Rate (EATR) method, which represents the fraction of a biasing potential along the RC that contributes to increasing the rate constant. We demonstrate that{gamma} can be used to test whether the utility of a reaction coordinate for predicting kinetics with a Meta-dynamics bias improves as the coordinate is iteratively updated to include new data. We evaluate reaction coordinates approximated via the iterative State Predictive Information Bottleneck (SPIB) approach, which was previously shown to be accurate across six protein-ligand dissociation systems. For these same systems, we compute{gamma} values and mean accelerated times [Formula]. After systematically scanning over fitting parameters, the results show that{gamma} increases closer to 1, while [Formula] decreases, revealing a consistent inverse correlation. These results demonstrate that{gamma} serves as a practical criterion for RC evaluation and offers guidance for selecting SPIB-derived coordinates yielding quantitative kinetic predictions.

biophysics↗