Biology subjects

Sun, R.

Publications and source records attributed to Sun, R..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Design of solubly expressed miniaturized SMART MHCs

The precise recognition of specific peptide-MHC (pMHC) complexes by T-cell receptors (TCRs) plays a key role in infectious disease, cancer and autoimmunity. A critical step in many immunobiological studies is the identification of T-cells expressing TCRs specific to a given pMHC antigen. However, the intrinsic instability of empty class-I MHCs limits their soluble expression in Escherichia coli (E. coli) and makes it very difficult to characterize even a small fraction of possible pMHC/TCR interactions. To overcome this limitation, we designed small proteins which buttress the peptide binding groove of class I MHCs, replacing {beta}2-microglobulin ({beta}2m) and the heavy chain 3 domain, and enable soluble expression of both H-2Db and A*02:01 in E. coli. We demonstrate that these soluble, monomeric, antigen-receptive, truncated (SMART) MHCs retain both peptide- and TCR-binding specificity, and that peptide-bound structures of both allomorphs are similar to their full-length, native counterparts. With extension to the majority of HLA alleles, SMART MHCs should be broadly useful for probing the T-cell repertoire in approaches ranging from yeast display to T-cell staining. SignificanceDespite the critical role that TCR/pMHC interactions play in human health, it has remained difficult to produce reagents necessary to study them. Requirements for refolding or sequence optimization limit immunologists and biochemists ability to characterize diverse pMHC/TCR interactions. Here, we develop a de-novo designed protein domain that stabilizes the H-2Db and A*02:01 class I MHC allomorphs, allowing soluble expression in E. coli without the need for a stabilizing peptide, and improving display on the yeast surface, while maintaining peptide and TCR binding interactions. These features facilitate a wide range of experiments to more fully understand the nature of pMHC/TCR interactions, and pave the way for the development of stabilizing domains for all MHC allomorphs.

biochemistry↗

bioRxiv2025

Predicting PROTAC-targeted Degradation and Designing Androgen Receptor Degraders with AiPROTAC

Proteolysis-targeting chimeras (PROTACs), a pioneering class of heterobifunctional ligands, have emerged as transformative tools in combating cancer and immune-related diseases due to their ability to target previously undruggable proteins and overcome drug resistance. Accurate assessment of the degradation potential of PROTACs is essential for advancing their therapeutic applications. However, the development of robust predictive models is hindered by the scarcity of large-scale datasets and domain-specific tools, as well as the underutilization of existing unlabeled data. To address these challenges, we developed an innovative method called AiPROTAC to predict the degradation capacity of PROTACs. In particular, AiPROTAC integrates graph augmentation, message-passing enhanced encoders and cross-attention mechanisms within a contrastive learning framework. Moreover, AiPROTAC leverages a curated specialized dataset combined with the PROTAC-DB dataset to enhance prediction accuracy. Experimental results across two datasets and six evaluation metrics demonstrate that AiPROTAC consistently outperforms state-of-the-art models. Further case studies underline its superior sensitivity and reliability. Notably, AiPROTAC facilitated the design of a novel androgen receptor (AR) degrader, PROTAC GT19, which achieved enhanced in vitro degradation compared to Bavdegalutamide (ARV-110). This advancement highlights our AiPROTACs potential to accelerate PROTAC-based therapeutic development and optimization.

bioinformatics↗

bioRxiv2025

ProteoAutoNet: high-throughput co-eluted protein analysis with robotics and a multi-database search strategy

Co-fractionation mass spectrometry (CF-MS) enables large-scale profiling of endogenous protein-protein interactions. Protein complexes identified by CF-MS using different databases are typically integrated. However, this integration uses varying cutoffs, leading to inconsistencies in protein complex identification. Here, we present ProteoAutoNet, a robotic experimental platform integrating multi-database search strategy into machine learning models, for high-throughput CF-MS analysis. This workflow increases the throughput of sample processing from protein complex to peptide by about two times. We then applied this workflow to map protein interaction networks in thyroid cancer cell lines, identifying significantly upregulated proteasome and prefoldin complexes in lung metastatic follicular thyroid carcinoma cell line FTC238 compared to normal thyroid cell line Nthy-ori 3-1. Notably, we identified a novel protein interaction network comprising PFAS, TGM2, and HK1 that was significantly upregulated in the papillary thyroid carcinoma cell line TPC-1. ProteoAutoNet provides an improved approach for investigating protein-protein interactions and uncovering novel networks, driving advancements in high-throughput proteomics research.

biochemistry↗

bioRxiv2025

Rapid and wash-free anti-drug antibody assay enabled by the complementary nanoluciferase biosensor

Biotherapeutics have demonstrated remarkable therapeutic efficacy across a wide range of diseases; however, their clinical application is often hindered by the development of anti-drug antibodies (ADAs). Traditionally, ADA monitoring has relied on ligand-binding assays (LBAs) such as enzyme-linked immunosorbent assays (ELISA) or electrochemiluminescence assays (ECLIA). Although effective, these methods require multiple washing and incubation steps, extending data generation time to several hours or even days. In contrast, homogeneous immunoassays offer a promising alternative due to their "mix-and-read" feature, which significantly reduces operational complexity, time, and cost compared to conventional LBAs. In this study, we explored the feasibility of rapid ADA detection using a wash-free homogeneous assay based on the split nanoluciferase (SplitNluc) biosensor system. Through case studies involving diverse therapeutic modalities including antibody-drug conjugates (ADC), Fc-fusion protein, Fc-less multidomain biotherapeutics (MDB), and single-domain antibody (SdAb), we demonstrated that the SplitNluc platform is a versatile and efficient tool for robust and rapid ADA monitoring. This approach not only streamlines the detection process but also holds potential for broader applications in biotherapeutic development and clinical monitoring.

pharmacology and toxicology↗

bioRxiv2025

A perturbation proteomics-based foundation model for virtual cell construction

Building a virtual cell requires comprehensive understanding of protein network dynamics of a cell which necessitates large-scale perturbation proteome data and intelligent computational models learned from the proteome data corpus. Here, we generate a large-scale dataset of over 38 million perturbed protein measurements in breast cancer cell lines and develop a neural ordinary differential equation-based foundation model, namely ProteinTalks. During pretraining, ProteinTalks gains a fundamental understanding of cellular protein network dynamics. Our model encodes protein networks and exhibits consistently improved predictive accuracy across various downstream tasks, highlighting its generalization capabilities and adaptability. In cancer cells, ProteinTalks robustly predicts drug efficacy and synergy, identifies novel drug combinations, and, through its interpretability, uncovers resistance-associated proteins. When applied to more complex system, patient-derived tumor xenografts, ProteinTalks predicts potential responses to drugs. Its integration with clinical patient data enhances the prognosis prediction of breast cancer patients. Collectively, we present a foundational model based on proteome dynamics, offering potential for various downstream applications, including drug discovery, and providing a basis for developing virtual cells.

systems biology↗

bioRxiv2025

Permissive central tolerance plus defective peripheral checkpoints licence pathogenic memory B cells in CASPR2-antibody encephalitis

Autoimmunity affects 10% of the population. Within this umbrella, autoantibody-mediated diseases targeting one autoantigen provide a unique opportunity to comprehensively understand the developmental pathway of disease-causing B cells and autoantibodies. While such autoreactivities are believed to be generated during germinal centre reactions, the roles of earlier immune checkpoints in autoantigen-specific B cell tolerance are poorly understood. We address this concept in patients with CASPR2-autoantibody encephalitis and healthy controls. In both groups, comparable and high ([~]0.5%) frequencies of unmutated CASPR2-reactive naive B cells were identified. By contrast, CASPR2-reactive memory B cells were exclusive to patients, and their B cell receptors demonstrated affinity-enhancing somatic mutations with heterogenous binding kinetics. These effector molecules possessed epitope-dependent pathogenic effects in vitro neuronal cultures and in vivo. The unmutated common ancestors of these memory B cells showed a distinctive balance between strong CASPR2 reactivity and very limited binding across the remaining human proteome. Our results are the first to propose mechanisms underlying autoantigen-specific tolerance in humans. We identify permissive central tolerance, defective peripheral tolerance and heterogenous autoantibody binding properties as sequential pathogenic steps which licence CASPR2-directed pathology. By leveraging the basic immunobiology, we rationally direct tolerance-restoring approaches in CASPR2-antibody diseases. This paradigm is applicable across autoimmune conditions.

immunology↗

bioRxiv2025

Extreme high-diversity barcoded HIV library enables single cell multi-omics analysis of viral expression and fate determination

HIV-1 persists as a global health challenge due to its ability to establish latent reservoirs that evade eradication by antiretroviral therapy (ART). This study introduces a high-diversity barcoded HIV-1 library combined with a novel peptide barcode system to enable single-cell multi-dimensional analysis of viral integration, transcription, splicing, and translation of distinct viral mRNA isoform. Our method revealed over 80 distinct HIV-1 splicing isoforms and uncovered significant temporal variation in mRNA diversity, driven by integration site and chromatin context. By linking HIV-1 5UTR with peptide barcoding, we quantified the translation efficiency of alternative 5' UTRs and demonstrated correlations with abundance of each viral mRNA isoform. Additionally, we showed that latency reversal agents, such as SAHA and Bryostatin, selectively reactivate proviruses depending on their genomic and chromatin context and leads to distinct viral RNA splicing program. This platform revealed the diversity of HIV-infected cells at levels of transcripts as well as at proteins, and subsequently the fate determination. The detailed understanding of the stochastic diversity and dynamic nature of HIV-1 latency, inform the development of targeted therapies to eliminate latent reservoirs.

microbiology↗

bioRxiv2025

PROTAC molecule-mediated SpCas9 protein degradation for precise genome editing

CRISPR (clustered regularly interspaced short palindromic repeats) technology has revolutionized both fundamental research and genomic medicine. The need for precise control of SpCas9-based CRISPR genome editing has led to the development of various strategies to regulate Cas9 activity, aiming to minimize off-target effects. Proteolysis-targeting chimeras (PROTACs) use the ubiquitin-proteasome system to selectively degrade target proteins. Here, we developed CASPROTAC 6, a reversible and cell-permeable PROTAC degrader that directly targets SpCas9 proteins for degradation. The CASPROTAC 6 molecule was derived by linking a known SpCas9 binder BRD7087 with an S-substituted Lenalidomide cereblon (CRBN) ligand via a six-carbon alkyl linker. Our data show that CASPROTAC 6 is a broad-spectrum degrader of SpCas9 and variants such as dCas9 and Cas9 nickases. CASPROTAC 6 degrades SpCas9 and the SpCas9-guide RNA complex via the proteasome system by approximately 50%. As a result, CASPROTAC 6 effectively enhanced the precision of CRISPR/Cas9-mediated genome editing by increasing target specificity. CASPROTAC 6 may serve as modulators of CRISPR/SpCas9-associated nucleases, enabling precise genome editing while reducing off-target effects and enhancing biosafety.

biochemistry↗

bioRxiv2024

Marine medaka responds differently to dioxin compared with its close freshwater relative, the Japanese medaka: the AHR molecular mechanism

The global water pollution now calls for precise risk assessment of chemicals, e.g., dioxins and the emerging dioxin-like compounds (DLCs). The freshwater and marine medaka have been widely implemented in the toxicity testing, and perhaps give mechanistic information for comparative biology. The question that will they report equal results due to their close phylogenetic relation has been raised, therefore, we explored their physiological and molecular responses to dioxin. As the mediator of the dioxin toxicity, the aryl hydrocarbon receptor (AHR) of marine medaka (Oryzias melastigma) has not been functionally characterized and might be species-specific. In terms of sensitivity to dioxin--2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), the EC50 values of omeAHR1a (0.16{+/-}0.12 nM), omeAHR1b (2.96{+/-}2.96 nM), omeAHR2a (0.44{+/-}0.30 nM), and omeAHR2b (9.00{+/-}6.88 nM) exhibit marked variations. The omeAHR2a and omeAHR1a display heightened sensitivity compared to the freshwater Japanese medaka (Oryzias latipes) counterparts olaAHR2a and olaAHR1a, respectively. The results indicate the in vitro sensitivity of AHR among species can vary by one or two orders of magnitude. Physiologically, the marine medaka (LC50: 1.64 ng/L (95% CI: 1.05-2.55 ng/L)) also exhibits a pronounced sensitivity to TCDD than Japanese medaka (LC50: 3.42 ng/L (95% CI: 1.37-6.48 ng/L), aligning with the in vitro AHR sensitivity. Further mechanistic investigations using additional ligands and computational modeling reveal that: 1) most of omeAHR2a, olaAHR2a, dreAHR2, and hsaAHR interact with ligands in the affinity order of TCDD > PCB126 > BNF > indole, mirroring their AHR transactivation potency, but the docking poses and dynamics can vary; 2) one AHR subforms high sensitivity to dioxin--TCDD may extend to DLCs but not to other types of ligands. These insights underscore the difference of AHR biology among species even the close relative species, and finger out the necessity for meticulous consideration when evaluating the toxicity of compounds and when extending predictive toxicity assessments to more species.

ecology↗

bioRxiv2024

Nanoscale biodegradable printing for designed tuneability of vaccine delivery kinetics

Two photon polymerization (2PP) 3D printing enables top-down biomaterial synthesis with nanoscale spatial resolution for de novo design of monodisperse injectable drug delivery systems. To address the limitations of current 2PP resins, we developed Spatiotemporal Controlled Release Inks of Biocompatible polyEsters (SCRIBE), a novel poly(lactic-co-glycolic acid)-triacrylate resin family with sub-micron resolution and tuneable hydrolysis. SCRIBE enables direct printing of hollow microparticles with tuneable chemistry and complex geometries inaccessible to molding techniques, which we use to engineer controlled protein release in vitro and in vivo. We use SCRIBE microparticles to modulate antibody titers and class switching as a function of antigen release rate and extend these findings to enable a single-injection vaccine formulation with extended antibody induction kinetics. Demonstrating how the chemistry and CAD of 2PP-printed microparticles can be used to tune responses to biomacromolecule release in vivo opens significant opportunities for a new generation of drug delivery vehicles. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=117 SRC="FIGDIR/small/616252v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@a2e8c0org.highwire.dtl.DTLVardef@15ecbf1org.highwire.dtl.DTLVardef@9f734forg.highwire.dtl.DTLVardef@4b7e39_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2024

Integral-Omics: serial extraction and profiling of metabolome, lipidome, genome, transcriptome, whole proteome and phosphoproteome using biopsy tissue

The integrative multi-omics characterization of minute amount of clinical tissue specimens has become increasingly important. Here, we present an approach called Integral-Omics, which enables sequential extraction of metabolites, lipids, genomic DNA, total RNA, proteins, and phosphopeptides from a single biopsy-level tissue specimen. We benchmarked this method with various samples and applied the workflow to perform multi-omics profiling of tissues from six patients with colorectal cancer and found that tumor tissues exhibited suppressed ferroptosis pathway at multi-omics levels. Together, this study presents a methodology that enables sequential extraction and profiling of metabolomics, lipidomics, genomics, transcriptomics, proteomics and phosphoproteomics using biopsy tissue specimens.

biochemistry↗

bioRxiv2024

Repurposing the plant-derived compound apigenin for senomorphic effect in antiaging pipelines

Cellular senescence is a cell fate triggered by inherent or environmental stress and characterized by stable cell cycle arrest accompanied by a hypersecretory feature, termed as the senescence-associated secretory phenotype (SASP). Senescent cell burden increases with natural aging, functionally contributing to age-related organ dysfunction and multiple disorders. In this study, we performed a large scale screening of a natural product library for senotherapeutic candidates by assessing their effects on human senescent cells. Apigenin, a dietary flavonoid previously reported with antioxidant and anti-inflammatory activities, exhibited a prominent capacity in targeting senescent cells as a senomorphic agent. In senescent cells, apigenin blocks the interactions between ATM/p38 and HSPA8, thus preventing transition of the acute stress-associated phenotype (ASAP) towards the SASP. Mechanistically, apigenin targets peroxiredoxin 6 (PRDX6), an intracellular redox-active molecule, suppressing the iPLA2 activity of PRDX6 and disrupting downstream reactions underlying the SASP development. Without reversing cellular senescence, apigenin deprives cancer cells of malignancy acquired from senescent stromal cells in culture, while reducing chemoresistance upon combination with chemotherapy in anticancer regimens. In preclinical trials, apigenin administration improves physical function of animals prematurely aged after whole body irradiation, alleviating physical frailty and cognitive impairment. Overall, our study demonstrates the potential of exploiting a naturally derived compound with senomorphic capacity to achieve geroprotective effects by modulating the SASP, thus providing a research platform for future exploration of novel natural agents against age-related conditions.

cell biology↗

bioRxiv2024

Coordinate control of the RNA polymerase II transcription cycle by CDK9-dependent, tripartite phosphorylation of SPT5

The RNA polymerase II (RNAPII) transcription cycle is regulated throughout its duration by reversible protein phosphorylation. The elongation factor SPT5 contains two regions targeted by cyclin-dependent kinase 9 (CDK9) and previously implicated in promoter-proximal pausing and termination: the linker between KOWx-4 and KOW5 domains and carboxy-terminal repeat (CTR) 1, respectively. Here we show that phosphorylations in the KOWx-4/5 linker, CTR1 and a third region, CTR2, coordinately control pause release, elongation speed and RNA processing. Pausing was increased by mutations preventing CTR1 or CTR2 phosphorylation, but attenuated when both CTRs were mutated. Whereas mutating CTR1 alone slowed elongation and repressed nascent transcription, simultaneous mutation of CTR2 partially reversed both effects. Nevertheless, mutating both CTRs led to aberrant splicing, dysregulated termination and diminished steady-state mRNA levels, and impaired cell proliferation more severely than did either single-CTR mutation. Therefore, tripartite SPT5 phosphorylation times pause release and regulates RNAPII elongation rates positively and negatively to ensure productive transcription and cell viability.

molecular biology↗

bioRxiv2024

Temporal-spatially metabolic reprogramming rewires the H3K27ac landscape to enable the initiation of liver regeneration

The liver possesses extensive regenerative capacity. Nevertheless, the most proximal events driving the transition from quiescent to proliferative hepatocytes remain largely elusive. Using the combination of spatiotemporal metabolomics and transcriptomics, our study mapped out the temporal-spatial landscape of metabolic reprogramming, epigenetic remodeling, and transcriptomic rewiring from 3 to 12 hours post-partial hepatectomy. Specifically, we identified a profound metabolic shift towards hyperactive fatty acid oxidation (FAO) and suppressed phospholipid biosynthesis during the preparation phase of liver regeneration, which were surprisingly reversed afterwards. FAO-dependent accumulation of Acetyl-CoA particularly remodeled H3K27ac landscape. These metabolic reprograming and epigenetic regulation were spatially specific, aligning with the zonation of hepatocyte proliferation. Blocking FAO in etomoxir-treated or hepatocyte-specific Cpt1a knockout mice, suppressing Acetyl-CoA biosynthesis, and inhibiting histone acetyltransferase all resulted in lethal liver regeneration deficiency. CUT&Tag analysis further revealed that the reshaping of H3K27ac profiles favored the transcription of genes associated with cell cycle transition and mitosis, and rewired the metabolic gene network. Collectively, we highlight a previously underappreciated role of FAO in epigenetic remodeling that is essential for the initiation of liver regeneration, offering exciting opportunity for the rescue of regeneration-deficient livers. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=181 HEIGHT=200 SRC="FIGDIR/small/602368v1_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@8dd836org.highwire.dtl.DTLVardef@6ddb27org.highwire.dtl.DTLVardef@4f1e49org.highwire.dtl.DTLVardef@4d7afe_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2024

Structures of Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus virions reveal species-specific tegument and envelope features

Epstein-Barr virus (EBV) and Kaposis sarcoma-associated herpesvirus (KSHV) are classified into the gammaherpesvirus subfamily of Herpesviridae, which stands out from its alpha- and betaherpesvirus relatives due to the tumorigenicity of its members. Although structures of human alpha- and betaherpesviruses by cryogenic electron tomography (cryoET) have been reported, reconstructions of intact human gammaherpesvirus virions remain elusive. Here, we structurally characterize extracellular virions of EBV and KSHV by deep learning-enhanced cryoET, resolving both previously known monomorphic capsid structures and previously unknown pleomorphic features beyond the capsid. Through subtomogram averaging and subsequent tomogram-guided sub-particle reconstruction, we determined the orientation of KSHV nucleocapsids from mature virions with respect to the portal to provide spatial context for the tegument within the virion. Both EBV and KSHV have an eccentric capsid position and polarized distribution of tegument. Tegument species span from the capsid to the envelope and may serve as scaffolds for tegumentation and envelopment. The envelopes of EBV and KSHV are less densely populated with glycoproteins than those of herpes simplex virus 1 and human cytomegalovirus, representative members of alpha- and betaherpesviruses, respectively. This population density of glycoproteins correlates with their relative infectivity against HEK293T cells. Also, we observed fusion protein gB trimers exist within triplet arrangements in addition to standalone complexes, which is relevant to understanding dynamic processes such as fusion pore formation. Taken together, this study reveals nuanced yet important differences in the tegument and envelope architectures among human herpesviruses and provides insights into their varied cell tropism and infection. ImportanceDiscovered in 1964, Epstein-Barr virus (EBV) is the first identified human oncogenic virus and the founding member of the gammaherpesvirus subfamily. In 1994, another cancer-causing virus was discovered in lesions of AIDS patients and later named Kaposis sarcoma-associated herpesvirus (KSHV), the second human gammaherpesvirus. Despite the historical importance of EBV and KSHV, technical difficulties with isolating large quantities of these viruses and the pleiomorphic nature of their envelope and tegument layers have limited structural characterization of their virions. In this study, we employed the latest technologies in cryogenic electron microscopy (cryoEM) and tomography (cryoET) supplemented with an artificial intelligence-powered data processing software package to reconstruct 3D structures of the EBV and KSHV virions. We uncovered unique properties of the envelope glycoproteins and tegument layers of both EBV and KSHV. Comparison of these features with their non-tumorigenic counterparts provides insights into their relevance during infection.

microbiology↗

bioRxiv2024

The up-regulation of TGF-beta1 by miRNA-132-3p/WT1 is involved in inducing leukemia cells to differentiate into macrophages

Although it has been shown that abnormal expression of Wilms tumor gene 1 (WT1) is associated with the occurrence of leukemia, the specific mechanism via which it induces leukemia cells to differentiate into macrophages remains poorly understood. Based on the prediction that the microRNA miRNA-132-3p is the miRNA that possibly lies upstream of the WT1 gene, we hypothesized that miRNA-132-3p may participate in the polarization process of macrophages through regulating expression of the WT1 gene. The focus of the present study was therefore to investigate the role of the miRNA-132-3p/WT1 signaling axis in the differentiation of THP-1 leukemia cells into macrophages induced by PMA. The results obtained indicated that, compared with the control group, the proliferation of THP-1 cells was clearly inhibited by PMA, and the cell cycle was arrested at G0/G1 phase, associated with an upregulation of CD11b and CD14 expression. Induced by PMA, the expression level of miRNA-132-3p was increased, WT1 expression was decreased, and the expression level of TGF-{beta}1 was increased. Following transfection with miRNA-132-3p mimics, however, the expression of WT1 in the THP-1 cells was downregulated, with upregulation of the CD11b and CD14 antigens, whereas this downregulation of WT1 mediated by miRNA-132-3p mimics could be reversed by co-transfection with WT1 vector, which was accompanied by downregulation of the CD11b and CD14 antigens. The luciferase activity of the co-transfected miRNA-132-3p mimic + WT1-wild-type (WT) group was found to be statistically significantly lower compared with that of the co-transfected miRNA-132-3p mimic + WT1-mutated (MUT) group. Furthermore, chromatin immunoprecipitation experiments showed that WT1 was able to directly target the promoter of the downstream target gene TGF-{beta}1, which led to the negative modulation of TGF-{beta}1 expression, whereas downregulation of WT1 led to an upregulation of the expression of TGF-{beta}1, which thereby promoted the differentiation of THP-1 cells into macrophages. Taken together, the present study has provided evidence, to the best of the authors knowledge for the first time, that the miRNA-132-3p/WT1/TGF-{beta}1 axis is able to regulate the committed differentiation of leukemia cells into macrophages.

immunology↗

bioRxiv2024

GeoAB: Towards Realistic Antibody Design and Reliable Affinity Maturation

Increasing works for antibody design are emerging to generate sequences and structures in Complementarity Determining Regions (CDRs), but problems still exist. We focus on two of them: (i) authenticity of the generated structure and (ii) rationality of the affinity maturation, and propose GEOAB as a solution. In specific, GeoABDesigner generates CDR structures with realistic internal geometries, composed of a generative geometry initializer (Geo-Initializer) and a position refiner (Geo-Refiner); GeoAB-Optimizer achieves affinity maturation by accurately predicting both the mutation effects and structures of mutant antibodies with the same network architecture as Geo-Refiner. Experiments show that GEOAB achieves state-of-the-art performance in CDR co-design and mutation effect predictions, and fulfills the discussed tasks effectively.

bioinformatics↗

bioRxiv2024

Assessing drug uptake and response differences in 2D and 3D cellular environments using stimulated Raman scattering microscopy

The architecture of cell culture--two-dimensional (2D) versus three-dimensional (3D)--significantly impacts various cellular factors, including cell-cell interactions, nutrient and oxygen gradients, metabolic activity, and gene expression profiles. This can result in different cellular responses during cancer drug treatment, with 3D-cultured cells often exhibiting higher resistance to chemotherapeutic drugs. While various genetic and proteomic analyses have been employed to investigate the underlying mechanisms of this increased resistance, complementary techniques that provide experimental evidence of spatial molecular profiling data are limited. Stimulated Raman scattering (SRS) microscopy has demonstrated its capability to measure both intracellular drug uptake and growth inhibition. In this work, we applied three-band SRS imaging to 2D and 3D cell cultures and provided a comparative analysis of drug uptake and response with the goal of understanding whether the difference in drug uptake explains the drug resistance in 3D culture compared to 2D. Our investigations revealed that despite similar intracellular drug levels in 2D and 3D A549 cells during lapatinib treatment, the growth of 3D spheroids is less impacted, supporting an enhanced drug tolerance in the 3D microenvironment. We further elucidated drug penetration patterns and the resulting heterogeneous cellular responses across different spheroid layers. Additionally, we investigated the role of the extracellular matrix in modulating drug delivery and cell response, and we discovered that limited drug penetration in 3D could also contribute to lower drug response. Our study provides valuable insights into the intricate mechanisms of increased drug resistance in 3D tumor models during cancer drug treatments.

cell biology↗