Biology subjects

Yang, A.

Publications and source records attributed to Yang, A..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Somatic evolution of prostate cancer: mutation, selection, and epistasis across disease stages

BackgroundSomatic mutations involved in prostate cancer tumorigenesis and disease progression have been identified, but their evolutionary dynamics--including differential selective pressures across oncogenesis and metastatic spread--remain poorly understood. No prior study has systematically quantified the adaptive landscape from prostate organogenesis through tumor initiation and progression to metastatic castrate-resistant prostate cancer (mCRPC), nor characterized the selective epistatic interactions that structure this evolutionary trajectory. Methods and FindingsTo address this gap, we analyzed 2,704 low- and high-risk primary tumors and metastatic castration-resistant prostate cancers to quantify the mutation rates, mutational processes, and scaled selection coefficients of somatic mutations across disease stages. Trinucleotide mutational patterns were stable, but both mutation load and mutation rates increased with progression. In parallel, selective pressures on specific somatic mutations changed substantially, revealing a dynamic adaptive landscape. Stage-specific selective effects were associated with significant synergistic and antagonistic selective epistasis among key driver genes. Early selection on SPOP mutations in the BRD3 binding domain were under strong positive selection, and they increased selection for subsequent RHOA mutations while decreasing selection for TP53 mutations. Antagonistic selective epistasis was evident between mutations of CUL3 and both SPOP and PIK3CA. Mutations in KMT2C increased the selection for mutations in TP53, consistent with their frequent co-occurrence. Synergistic epistatic interactions between mutations of PTEN and both PIK3CA and AR support a strong therapeutic rationale for combined inhibition of PI3K/AR pathway in PTEN-deficient prostate cancers. ConclusionsThese findings provide a comprehensive map of the evolving selective and epistatic forces that shape prostate cancer progression across clinical stages. By distinguishing shifts in selection from changes in mutation rate and revealing the extents of cooperative and conflicting relationships among driver mutations, our work identifies critical points of vulnerability and informs that design of therapeutic strategies that anticipate and intercept the somatic evolutionary trajectory of prostate cancer.

cancer biology↗

bioRxiv2025

Harnessing the CD2 axis to broaden and enhance the efficacy of CAR T cell therapies

Patients with T-cell lymphomas and leukemias have overall poor outcomes due to the lack of targeted and effective treatments, particularly in the relapsed and refractory settings. Development of chimeric antigen receptor (CAR) T-cells against T-cell neoplasms is limited by a lack of discriminating T-cell antigens that allow for effective anti-tumor responses while preventing CAR T-cell fratricide. We hypothesized that targeting CD2, a pan-T-cell antigen, using anti-CD2 CAR T-cells engineered without CD2 expression (CART2), would support CAR T-cell manufacturability and preclinical efficacy. Optimized CD2-knockout CART2, generated using CRISPR-Cas9, eradicated primary patient-derived CD2+ hematological neoplasms in vitro and in vivo, secreted effector cytokines, and exhibited adequate proliferative capacity. Nevertheless, CD2 has a key costimulatory function, and its deletion could lead to CAR T-cell dysfunction. Therefore, we tested the role of the CD2:CD58 axis in CAR T-cells, using the anti-CD19 CART models. We demonstrate that CD2 loss attenuates CART19 efficacy by reducing avidity for tumor antigen, co-stimulation, and ultimately in vivo activity. Analogously, we show that tumor CD58 loss reduces CART19 efficacy. To overcome this issue, we developed a novel PD-1:CD2 switch receptor that rescues intracellular CD2 signaling, particularly when PD-L1 is engaged, resulting in improved in vivo outcomes. Collectively, we studied the role of CD2 both as a target for CAR T cell therapy and as a critical costimulatory protein, whose signaling can be rescued using the PD-1:CD2 switch receptor. This receptor can be incorporated into CAR T-cells and provides an effective strategy to overcome CD2-signaling deficiencies.

cancer biology↗

bioRxiv2025

Angiopoietin signalling is a central axis of amyloid-driven vascular dysfunction in Alzheimer's disease

The neurovascular unit is critical for brain health, and its dysfunction has been linked to Alzheimers disease (AD). However, a cell-type-resolved understanding of how diverse vascular cells become dysfunctional and contribute to disease has been missing. Here, we applied Vessel Isolation and Nuclei Extraction for Sequencing (VINE-seq) to build a comprehensive transcriptomic atlas from 101 individuals along AD progression. Our analysis of over 842,646 parenchymal and vascular nuclei reveals that vascular dysfunction in AD is driven by transcriptional changes rather than shifts in cell proportions, with brain endothelial cells (BECs) and smooth muscle cells (SMCs) most affected. Strikingly, these molecular signatures emerge early at the mild cognitive impairment (MCI) stage, implicating vascular dysfunction early in AD pathogenesis. Stratifying by pathology reveals distinct vascular responses to {beta}-amyloid and tau: {beta}-amyloid burden primarily perturbs BECs and SMCs, while tau pathology predominantly impacts glial cells. We identify dysregulated angiopoietin signaling across multiple vascular cell types as a key axis, with antagonistic ANGPT2 in vascular cells and ANGPT1 in astrocytes becoming progressively dysregulated with AD. Together, this work provides a foundational resource that reveals early and pathology-specific pathways of vascular dysfunction in AD. Key MessagesO_LIVINE-seq analysis from 101 individuals creates a comprehensive human brain vascular atlas across Alzheimers disease (AD) progression. C_LIO_LIAD vascular dysfunction is driven by transcriptional changes rather than shifts in cell proportions, with BECs and SMCs most affected. C_LIO_LITranscriptional signatures of vascular dysfunction emerge early at the mild cognitive impairment (MCI) stage, preceding severe cognitive symptoms and aligning more closely with AD than cognitively normal individuals. C_LIO_LIA{beta} and tau associate with distinct vascular changes: A{beta} mainly perturbs endothelial and smooth muscle cells, while tau impacts microglia and astrocytes. C_LIO_LIAngiopoietin signaling (antagonistic ANGPT2 in vascular cells vs. ANGPT1 in astrocytes) becomes progressively dysregulated during AD progression. C_LI

neuroscience↗

bioRxiv2025

Screening channelrhodopsins using robotic intracellularelectrophysiology and single cell sequencing

BackgroundOur ability to engineer opsins is limited by an incomplete understanding of how sequence variations influence function. The vastness of opsin sequence space makes systematic exploration difficult. New methodIn recognition of the need for datasets linking opsin genetic sequence to function, we pursued a novel method for screening channel-rhodopsins to obtain these datasets. In this method, we integrate advances in robotic intracellular electrophysiology (Patch) to measure optogenetic properties (Excite), harvest individual cells of interest (Pick) and subsequently sequence them (Sequence), thus tying sequence to function. ResultsWe used this method to sequence more than 50 cells with associated functional characterization. We further demonstrate the utility of this method with experiments on heterogeneous populations of known opsins and single point mutations of a known opsin. Of these point mutations, we found C160W ablates ChrimsonRs response to light. Conclusion and comparison to existing methodsCompared to traditional manual patch clamp screening, which is labor-intensive and low-throughput, this approach enables more efficient, standardized, and scalable characterization of large opsin libraries. This method can enable opsin engineering with large datasets to increase our understanding of opsin sequence-function relationships.

neuroscience↗

bioRxiv2025

Construction, Phenotypic Characterization, and Immunomodulatory Function Study of BMSC-Macrophagy Hybrid in vitro

ObjectiveThe aim of our study was to integrate bone marrow-derived stem cells (BMSCs) with macrophages and to investigate the performance of this hybrid in IgG clearance, immunosuppression, and the mitigation of inflammatory injury. MethodsBMSCs and RAW264.7 cells were fused through transient transfection using the COVID-19 spike glycoprotein and human angiotensin-converting enzyme 2 (hACE2), respectively. The resulting hybrids were purified using magnetic sorting, and their characteristics were evaluated by examining morphology, glucose uptake rates, phagocytic capacity, cytoskeletal morphology, and the levels of Fc{gamma} receptors, as well as anti-inflammatory, antioxidant, adhesion, and complement inhibitory factors. The IgG clearance capability of the hybrids was assessed by measuring internalization efficiency and infiltration into renal organoids. Additionally, the reparative effects of the hybrids were evaluated using doxorubicin-treated MPC5 damage models. Live cell imaging techniques were employed to investigate the interactions between the hybrids and immature dendritic cells (iDCs). Hybrid-derived nanovesicles were isolated, and their abilities to target IgG and clear IL-6 were evaluated using immunofluorescence and ELISA. Furthermore, chloroplasts and C-dots were co-incubated with the hybrids, and their benefits were assessed by measuring cell viability, oxygen content, ROS levels, mitochondrial function, and the levels of anti-inflammatory, antioxidant, and pro-repair factors. A scratch assay was conducted to determine the impact of chloroplast transplantation on the migration ability of 3T3 cells. ResultsHigh-purity hybrids were successfully produced that cleared IgG while maintaining their anti-inflammatory and antioxidant effects. They promoted the recovery of podocyte injury through vesicular and mitochondrial delivery, as well as efferocytosis. Furthermore, the hybrids inhibited iDCs primarily through migrasomes, intercellular nanomicrotubule connections, and phagocytosis. The derived nanovesicles were capable of residing in IgG-enriched regions and adsorbing IL-6. Interestingly, the transplanted chloroplasts enabled the hybrids to utilize light energy to enhance their antioxidant capacity and promote the migration of 3T3 cells, which contributes to wound repair. Subsequently, the loading of C-dots was beneficial for enhancing resistance to oxidative damage. ConclusionsOur results suggest that hybrids-mediated therapy is a new and creative therapeutic approach for managing immune-mediated nephropathies.Hybrids demonstrated effective immunomodulatory and promoted injury recovery. The derived nanovesicles have the potential to alleviate the inflammatory burden at sites of antibody immune complex deposition. Additionally, the incorporation of chloroplasts and C-dots enhanced the hybrids adaptability to ischemic-hypoxic microenvironments.

cell biology↗

bioRxiv2025

Longitudinal impacts of habitat fragmentation on Bartonella and hemotropic Mycoplasma dynamics in vampire bats

Habitat fragmentation can have negative impacts on wildlife including increased risk of infectious disease. To assess spatiotemporal changes in pathogen dynamics in vampire bats (Desmodus rotundus) in response to habitat fragmentation, we used general linear mixed models to investigate the influence of site, year, and tree cover on the prevalence of Bartonella and hemotropic Mycoplasma (hemoplasma) in bats in one large and one small forest fragment in northern Belize across seven years. Bartonella was marginally more prevalent in later years, while year and site differences in hemoplasma infections were driven by a peak in prevalence in the third year of the study in the small fragment. Bartonella prevalence increased with forest loss, but only in the large fragment, whereas hemoplasma prevalence showed a marginal negative response to forest loss. The effects of site, year, and forest loss on infection likelihood varied by pathogen genotype. Neither site nor year affected Bartonella genotypes, but one genotype was positively associated with tree cover. Two hemoplasma genotypes were influenced by year, but with differing trends. One genotype increased with tree cover regardless of site while another increased with forest loss at the small fragment only. Our work demonstrates that the effects of habitat fragmentation on infection prevalence depended on both the pathogen and specific genotype. Our findings complicate expectations of how habitat fragmentation affects infectious disease dynamics in bats. As such, management practices aimed at mitigating the impacts of infectious diseases in fragmented systems should be tailored to specific pathogens of concern.

ecology↗

bioRxiv2025

Neuroligin-3 interaction with CSPG4 regulates normal and malignant glial precursors through PIEZO1

Glioma pathophysiology is robustly regulated by interactions with neurons. Key to these interactions is the role of neuroligin-3 (NLGN3), a synaptic adhesion molecule shed in response to neuronal activity1-5 that functions as a paracrine factor crucial for glioma growth. Here, we elucidate the mechanistic pathway whereby shed NLGN3 interacts with glioma and their normal glial counterpart. NLGN3 interacts with Chondroitin Sulfate Proteoglycan 4 (CSPG4) on both glioma and healthy oligodendrocyte precursor cells (OPCs)6-9, facilitating CSPG4 shedding by ADAM10. NLGN3-CSPG4 interactions and consequent shedding alter membrane tension, thereby activating PIEZO1 mechanosensitive channels and causing membrane depolarization. The NLGN3-CSPG4-PIEZO1 axis maintains OPCs in an undifferentiated, stem-like state and promotes glioma proliferation, underscoring important functional roles for the NLGN3-CSPG4-PIEZO1 axis in both healthy and malignant glial precursors.

neuroscience↗

bioRxiv2025

Decoupled Information Theoretic Feature Selection for Rapid Protein Key Tuning Residue Identification

Rational protein engineering requires identifying residues that modulate function without disrupting functionality, a key challenge in protein engineering. Existing computational methods struggle to distinguish genuine functional sites from positions coevolving due to structural constraints, leading to high false-discovery rates. Here we present an information-theoretic decoupling framework that, without machine learning, isolates key tuning residues by computationally "denoising" sequence data, iteratively removing confounding evolutionary signals to reveal underlying functional sites. We validated this framework across 10 datasets spanning enzymes, fluorescent proteins, and antibodies. In a nanobody-antigen binding case study, our method identified > 25% (6/20) of verified binding-critical residues (p = 0.031), while the best of five benchmarked tools found zero. Performance was consistent across all datasets, with supervised variants achieving large effect sizes (Hedges g > 0.7, p < 0.01) and unsupervised variants also showing gains (g > 0.2, p < 0.05) over benchmarks. This interpretable framework provides a generalizable method to accelerate protein design, from focusing antibody maturation to optimizing biocatalysts.

bioinformatics↗

bioRxiv2025

Spatially Organized IGF1 mTOR Signaling Controls Human Forebrain Progenitor Fate Through Coordinated Transcriptional and Translational Programs

The specification and maintenance of human forebrain neural progenitor cells (NPCs) depend on both intrinsic gene networks and spatially localized niche signals, but the interplay between these cues remains incompletely understood. Here, we identify a spatially organized, paracrine IGF1 signaling architecture that regulates human FOXG1 NPCs through multilayered transcriptional and translational control. Using a pluripotent stem cell-derived forebrain model, we show that FOXG1 NPCs express IGF1 receptors but lack endogenous IGF1, instead depending on neighboring epithelial-like domains that secrete IGF1. IGF1 promotes progenitor proliferation, clonal expansion, and vertical tissue growth by activating PI3K-AKT-mTOR and MEK-ERK pathways. Ribosome profiling and 5'UTR reporter assays reveal that mTOR signaling selectively enhances translation of neurodevelopmental and biosynthetic transcripts-- including GSX1, a ventral fate determinant implicated in interneuron specification and autism. These findings uncover a human-specific regulatory mechanism in which spatially restricted IGF1-mTOR signaling integrates niche signals with translational output to support progenitor identity, biosynthetic capacity, and developmental resilience.

neuroscience↗

bioRxiv2025

APOE genotype confers context dependent neurovascular vulnerability in immune-vascularized human forebrain organoids

The APOE gene is a major genetic determinant of neurovascular and immune function, yet the mechanisms by which its isoforms modulate brain vulnerability to pathogenic stress remain incompletely understood. Here, we employ isogenic human iPSC-derived immune-vascularized--Forebrain Organoid-based Multicellular Assembled Cerebral Organoids (FORMA-COs)--to dissect isoform-specific responses to a clinically relevant viral challenge. We find that APOE2/2 and APOE4/4 FORMA-COs exhibit heightened viral RNA burden and distinct neuroinflammatory profiles compared to APOE3/3. Specifically, APOE4/4 promotes IL-1 and VEGFA induction, whereas APOE2/2 leads to elevated TNF-{beta} and VEGFA protein accumulation, indicating divergent pathways of injury. Integrated transcriptomic analyses, combined with known and predicted APOE protein-protein interaction networks, reveal genotype-dependent enrichment of cytokine signaling, angiogenic remodeling, and immune dysregulation. In vivo validation using humanized mouse models corroborates APOE genotype- specific vascular remodeling, microglial activation, and oligodendrocyte perturbation. These findings demonstrate that APOE genotype confers context-specific susceptibility to neuroimmune and vascular injury, providing insight into genetic risk mechanisms underlying infection-related and neurodegenerative brain disorders.

neuroscience↗

bioRxiv2025

Designed NGF mimetics with reduced nociceptive signatures in neurons

The clinical use of Nerve Growth Factor (NGF) for neuronal regeneration has been hampered by pain sensitization side effects. NGF signals through the receptor tyrosine kinase TrkA and the co-receptor p75NTR; pain sensitization is thought to involve p75NTR. We sought to overcome this limitation by de novo design of a TrkA agonist that does not bind p75NTR. We designed homodimeric TrkA engaging constructs that dimerize TrkA subunits in a variety of geometries, and identified those eliciting the strongest signaling. The resulting designed agonists are able to stimulate transdifferentiated neurons and neuroblastoma cell lines, leading to neurite outgrowth and neuronal differentiation, with considerably reduced transcription of inflammation and pain related genes. These agonists are promising candidates for promoting neuronal regeneration without adverse side effects. HighlightsO_LIDe novo designed TrkA agonists activate MAPK and PI3K-AKT signaling C_LIO_LIRigid fusions allow for highly tunable signaling signatures C_LIO_LITrkA agonists lead to neurite outgrowth in neuroblastoma cells comparable to retinoic acid C_LIO_LIModulation of the TrkA pathway without co-stimulating p75NTR leads to a downregulation of inflammatory and nociceptive signature in neurons. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/648806v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@c48066org.highwire.dtl.DTLVardef@c9c5a7org.highwire.dtl.DTLVardef@cf8ebdorg.highwire.dtl.DTLVardef@a4345a_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Indigenous gut microbes modulate neural cell state and neurodegenerative disease susceptibility

The native microbiome influences a plethora of host processes, including neurological function. However, its impacts on diverse brain cell types remains poorly understood. Here, we performed single nucleus RNA sequencing on hippocampi from wildtype, germ-free mice and reveal the microbiome-dependent transcriptional landscape across all major neural cell types. We found conserved impacts on key adaptive immune and neurodegenerative transcriptional pathways, underscoring the microbiomes contributions to disease-relevant processes. Mono-colonization with select indigenous microbes identified species-specific effects on the transcriptional state of brain myeloid cells. Colonization by Escherichia coli induced a distinct adaptive immune and neurogenerative disease-associated cell state, suggesting increased disease susceptibility. Indeed, E. coli exposure in the 5xFAD mouse model resulted in exacerbated cognitive decline and amyloid pathology, demonstrating its sufficiency to worsen Alzheimers disease-relevant outcomes. Together, these results emphasize the broad, species-specific, microbiome-dependent consequences on neurological transcriptional state and highlight the capacity of specific microbes to modulate disease susceptibility. HighlightsO_LIThe microbiome impacts the transcriptional landscape of all major brain cell types. C_LIO_LIDiscrete microbes specifically modulate resident myeloid cell status. C_LIO_LIGut E. coli triggers dynamic transcriptional responses across neural cell types. C_LIO_LIExposure to E. coli exacerbates behavioral and cellular pathologies in 5xFAD mice. C_LI

neuroscience↗

bioRxiv2024

Structural insights into cholesterol sensing by the LYCHOS-mTORC1 pathway

The mechanistic target of rapamycin complex 1 (mTORC1) pathway regulates cellular metabolism and growth by coordinating nutrient resources, including cholesterol, and its aberrant activation is linked to various age-related diseases. LYCHOS is a cholesterol sensor on the lysosome and bound to the GATOR1 complex, a GTPase-activating protein for the Rag GTPase, at high cholesterol concentrations, thereby activating the protein kinase mTORC1. However, how LYCHOS senses cholesterol and transduces signal to GATOR1 remain largely unknown. Here we report six cryo-electron microscopy structures of human LYCHOS, depicting five distinct states. These are categorized into a contracted state when complexed with a sufficient amount of the cholesterol analogue cholesteryl hemisuccinate (CHS), and an expanded state when CHS is deficient. The structure forms a homodimer, within each monomer the transmembrane region is divided into a permease-like domain (PLD) and a GPCR-like domain (GLD) with two clearly defined adjacent cholesterol binding sites between them. The PLD shares a conserved Na+/H+ antiporter (NhaA) fold, which much resembles plant auxin transporter PINs. Cholesterol locates between PLD and GLD and cholesterol binding induces a translation of GLD towards PLD and exposes the cytosolic extension of transmembrane 15, which mediates the interaction between LYCHOS and GATOR1. Strikingly, structure-guided mutations of Gly702 in GLD of LYCHOS increase its affinity for cholesterol, leading to sustained mTORC1 activation in cells. This indicates that LYCHOSs moderate affinity for cholesterol is crucial as a cholesterol sensor. Our results not only showed a solute carrier mechanistically coordinates a GPCR domain, elucidating the structural mechanism of cholesterol sensing by the mTORC1 pathway on the lysosome; but also provides a structural basis for developing inhibitors that selectively target to mTORC1 pathway to treat age-related diseases by blocking LYCHOS in its expanded state.

biochemistry↗

bioRxiv2024

Deep learning-based prediction of enzyme optimal pH and design of point mutations to improve acid resistance

An accurate deep learning predictor of enzyme optimal pH is essential to quantitatively describe how pH influences the enzyme catalytic activity. CatOpt, developed in this study, outperformed existing predictors of enzyme optimal pH (RMSE=0.833 and R2=0.479), and could provide good interpretability with informative residue attention weights. The classification of acidic and alkaline enzymes and prediction of enzyme optimal pH shifts caused by point mutations showcased the capability of CatOpt as an effective computational tool for identifying enzyme pH preferences. Furthermore, a single point mutation designed with the guidance of CatOpt successfully enhanced the activity of Pyrococcus horikoshii diacetylchitobiose deacetylase at low pH (pH=4.5/5.5) by approximately 7%, suggesting that CatOpt is a promising in-silico enzyme design tool for pH-dependent enzyme activities. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=166 HEIGHT=200 SRC="FIGDIR/small/623957v2_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@ff8b46org.highwire.dtl.DTLVardef@110c721org.highwire.dtl.DTLVardef@817014org.highwire.dtl.DTLVardef@1e55d6a_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2024

Epigenetic and 3D genome reprogramming during the aging of human hippocampus

Age-related cognitive decline is associated with altered physiology of the hippocampus. While changes in gene expression have been observed in aging brain, the regulatory mechanisms underlying these changes remain underexplored. We generated single-nucleus gene expression, chromatin accessibility, DNA methylation, and 3D genome data from 40 human hippocampal tissues spanning adult lifespan. We observed a striking loss of astrocytes, OPC, and endothelial cells during aging, including astrocytes that play a role in regulating synapses. Microglia undergo a dramatic switch from a homeostatic state to a primed inflammatory state through DNA methylome and 3D genome reprogramming. Aged cells experience erosion of their 3D genome architecture. Our study identifies age-associated changes in cell types/states and gene regulatory features that provide insight into cognitive decline during human aging.

genomics↗

bioRxiv2024

AMPK agonism optimizes the in vivo persistence and anti-leukemia efficacy of chimeric antigen receptor T cells

BACKGROUNDChimeric antigen receptor T cell (CART) therapy has seen great clinical success. However, up to 50% of leukemia patients relapse and long-term survivor data indicate that CART cell persistence is key to enforcing relapse-free survival. Unfortunately, ex vivo expansion protocols often drive metabolic and functional exhaustion, reducing in vivo efficacy. Preclinical models have demonstrated that redirecting metabolism ex vivo can improve in vivo T cell function and we hypothesized that exposure to an agonist targeting the metabolic regulator AMP-activated protein kinase (AMPK), would create CARTs capable of both efficient leukemia clearance and increased in vivo persistence. METHODSCART cells were generated from healthy human via lentiviral transduction. Following activation, cells were exposed to either Compound 991 or DMSO for 96 hours, followed by a 48-hour washout. During and after agonist treatment, T cells were harvested for metabolic and functional assessments. To test in vivo efficacy, immunodeficient mice were injected with luciferase+ NALM6 leukemia cells, followed one week later by either 991- or DMSO-expanded CARTs. Leukemia burden and anti-leukemia efficacy was assessed via radiance imaging and overall survival. RESULTSHuman T cells expanded in Compound 991 activated AMPK without limiting cellular expansion and gained both mitochondrial density and improved handling of reactive oxygen species (ROS). Importantly, receipt of 991-exposed CARTs significantly improved in vivo leukemia clearance, prolonged recipient survival, and increased CD4+ T cell yields at early times post-injection. Ex vivo, 991 agonist treatment mimicked nutrient starvation, increased autophagic flux, and promoted generation of mitochondrially-protective metabolites. DISCUSSIONEx vivo expansion processes are necessary to generate sufficient cell numbers, but often promote sustained activation and differentiation, negatively impacting in vivo persistence and function. Here, we demonstrate that promoting AMPK activity during CART expansion metabolically reprograms cells without limiting T cell yield, enhances in vivo anti-leukemia efficacy, and improves CD4+ in vivo persistence. Importantly, AMPK agonism achieves these results without further modifying the expansion media, changing the CART construct, or genetically altering the cells. Altogether, these data highlight AMPK agonism as a potent and readily translatable approach to improve the metabolic profile and overall efficacy of cancer-targeting T cells.

immunology↗

bioRxiv2024

Seq2Topt: a sequence-based deep learning predictor of enzyme optimal temperature

An accurate deep learning predictor is needed for enzyme optimal temperature (Topt), which quantitatively describes how temperature affects the enzyme catalytic activity. Seq2Topt, developed in this study, reached a superior accuracy on Topt prediction just using protein sequences (RMSE = 13.3 and R2=0.48) in comparison with existing models, and could capture key protein regions for enzyme Topt with multi-head attention on residues. Through case studies on thermophilic enzyme selection and predicting enzyme Topt shifts caused by point mutations, Seq2Topt was demonstrated as a promising computational tool for enzyme mining and in-silico enzyme design. Additionally, accurate deep learning predictors of enzyme optimal pH (Seq2pHopt, RMSE=0.92 and R2=0.37) and melting temperature (Seq2Tm, RMSE=7.57 and R2=0.64) were developed based on the model architecture of Seq2Topt, suggesting that the development of Seq2Topt could potentially give rise to a useful prediction platform of enzymes.

bioinformatics↗

bioRxiv2024

Reproductive state controls transcription in the murine liver, with implications for breast cancer liver metastasis

Liver biology is functionally linked to lactation, as liver size and metabolic output increase during lactation to support synthesis of breast milk. Upon weaning, the rodent liver returns to baseline homeostasis via hepatocyte cell death, in a process considered liver involution. To explore liver biology changes across a lactation-wean cycle, we employed transcriptomic profiling. We identified elevated hepatocyte proliferation and anabolic metabolism gene signatures during lactation, consistent with the liver being a major producer of substrates needed for milk production. Rapid loss of these capacities upon weaning correlated with catabolic metabolism, lysosomal-mediated cell death, and an influx of immune suppressive cells. Furthermore, we identified that the transcriptional profiles associated with liver involution share similarities with the gene expression patterns of liver pre-metastatic niches. This work identifies features of reproductive control of liver biology that sets a foundation for better understanding the potential role of the liver in maternal health.

cancer biology↗