Biology subjects

Chen, Z.

Publications and source records attributed to Chen, Z..

At least 343 records · Page 19Linked to original sources

bioRxiv2024

The Autonomic Nervous System (ANS)-Immune Network in People Living With HIV

PurposePre-clinical studies have demonstrated direct influences of the autonomic nervous system (ANS) on the immune system. However, it remains unclear if ANS-immune connections delineated in pre-clinical studies underlie the relationship between autonomic dysregulation and chronic inflammatory diseases in patients with HIV. This study had three aims: 1.) Examine the relationship between IL-6 and the parasympathetic/vagal component of baroreflex sensitivity (BRS-V) in people with HIV; 2.) Determine if the subtype and severity of HIV-autonomic neuropathy (AN) would predict distinct immunotypes; 3.) Compare the burden of non-AIDS-related co-morbidities between immunotypes. Methods79 adults with well-controlled HIV underwent a standard battery of autonomic function tests summarized as the Composite Autonomic Severity Score and vagal and adrenergic baroreflex sensitivity (BRS-V and BRS-A).1 Levels of immune biomarkers were measured in all participants using the Target 96 Inflammation Panel on the Olink proteomics platform and immunotypes were identified using unbiased, non-negative matrix factorization. Mass cytometry (CyTOF) was completed on a subset of participants with and without autonomic neuropathy (N = 10). ResultsReduced BRS-V predicted higher levels of IL-6 (p=0.002). A pro-inflammatory immunotype defined by elevations in type 1 cytokines (IL-6, IL-17) and increased numbers of CD8+ T-cells was associated with autonomic neuropathy characterized by deficits in sympathetic nervous system activity (aOR=4.7, p=0.017). This pro-inflammatory immunotype was older with a greater burden of co-morbidities. ConclusionDeficits in the parasympathetic/cardiovagal and the sympathetic nervous system are associated with inflammation and disease burden in people living with HIV. Future longitudinal research is needed to examine causality.

immunology↗

bioRxiv2024

Genome of the enigmatic watering-pot shell reveals adaptations of a living suction anchor

The watering pot shells have been rightly called "the weirdest bivalves" for their highly modified body plan and fused tubular shell that resemble the spout of a watering can. This adventitious tube has defied rational explanation as an adaptive pathway and yet arose twice convergently. We present the first genome for the clade Anomalodesmata: an annotated chromosome-scale genome of Verpa penis (Linnaeus, 1758). The first watering pot shell ever described ranges across southeast Asia but is nonetheless extremely rare and has never previously been sequenced. The assembly length of 507 Mb, with a contig N50 of 5.33 Mb, has 96.5% of sequences anchored onto 19 pseudochromosomes. Contrary to expectations from such a highly modified body plan, there is no evidence of chromosome reduction compared to the ancestral condition of heterodont bivalves (1N=19). A new hypothesis based on analysis of the living animals and literature explains the adaptive significance of this body form: it is structurally optimised for vertical stability in soft sediments, with parallels to engineering principles of a suction anchor. Our study offers new insights to a long-standing mystery in molluscan body forms, and provides genomic resources that are relevant to understanding molluscan evolution, biomineralisation, and biomimetic design.

evolutionary biology↗

bioRxiv2024

In vivo two-photon FLIM resolves photosynthetic properties of maize bundle sheath cells

Maize (Zea mays L.) performs highly efficient C4 photosynthesis by dividing photosynthetic metabolism between mesophyll and bundle sheath cells. In vivo physiological measurements are indispensable for C4 photosynthesis research as any isolated cells or sectioned leaf often show interrupted and abnormal photosynthetic activities. Yet, direct in vivo observation regarding bundle sheath cells in the delicate anatomy of the C4 leaf is still challenging. In the current work, we used two-photon fluorescence-lifetime imaging microscopy (two-photon-FLIM) to access the photosynthetic properties of bundle sheath cells on intact maize leaves. The results provide spectroscopic evidence for the diminished total PSII activity in bundle sheath cells at its physiological level and show that the single PSIIs could undergo charge separation as causal. We also report an acetic acid-induced chlorophyll fluorescence quenching on intact maize leaves, which might be a physiological state related to the nonphotochemical quenching mechanism.

physiology↗

bioRxiv2024

Neural correlates differ between crystallized and fluid intelligence in adolescents

Fluid and crystallized intelligence are acknowledged as distinct facets of cognitive ability during brain development, but the specific neural substrates and molecular mechanisms underlying them remain unclear. This study used a sample comprising 7471 young adolescents (mean age 9.87 {+/-} 0.62 years) from the ABCD cohort to elucidate the differential neural correlates of fluid and crystallized intelligence. Our findings indicated that micro-level brain MRI phenotypes such as water diffusivity were closely associated with fluid intelligence, whereas macro-level brain MRI phenotypes such as gray matter cortical thickness were indicative of crystallized intelligence. We further investigated the molecular mechanisms underlying fluid and crystallized intelligence by correlating the characteristic MRI markers with spatial transcriptome profiles and PET imaging. Results showed that fluid intelligence had significant associations with serotonin and glutamate system, while crystallized intelligence was related to serotonin, dopamine and acetylcholine system. Furthermore, we examined the impacts of lifestyle factors on these two forms of intelligence and how the molecular pathways mediated these impacts. Our investigation suggested that physical activities, screen use and sleep duration influenced fluid intelligence mainly through mGlu5 receptors and crystallized intelligence through 5HT1a and D2 receptors. In conclusion, these findings illustrated a distinct neural basis between fluid and crystallized intelligence from the perspectives of neuroimaging, neurotransmitters, and lifestyles in young adolescents.

neuroscience↗

bioRxiv2024

Disruption of the Novel Nested Gene Aff3ir Mediates Disturbed Flow-Induced Atherosclerosis in Mice

Disturbed shear stress-induced endothelial atherogenic responses are pivotal in the initiation and progression of atherosclerosis, contributing to the uneven distribution of atherosclerotic lesions. This study investigates the role of Aff3ir-ORF2, a novel nested gene variant, in disturbed flow-induced endothelial cell activation and atherosclerosis. We demonstrate that disturbed shear stress significantly reduces Aff3ir-ORF2 expression in athero-prone regions. Using three distinct mouse models with manipulated AFF3ir-ORF2 expression, we demonstrate that AFF3ir-ORF2 exerts potent anti-inflammatory and anti-atherosclerotic effects in ApoE-/- mice. RNA sequencing revealed that interferon regulatory factor 5 (IRF5), a key regulator of inflammatory processes, mediates inflammatory responses associated with AFF3ir-ORF2 deficiency. AFF3ir-ORF2 interacts with IRF5, promoting its retention in the cytoplasm, thereby inhibiting the IRF5-dependent inflammatory pathways. Notably, IRF5 knockdown in AFF3ir-ORF2 deficient mice almost completely rescues the aggravated atherosclerotic phenotype. Moreover, endothelial-specific AFF3ir-ORF2 supplementation using the CRISPR/Cas9 system significantly ameliorated endothelial activation and atherosclerosis. These findings elucidate a novel role for AFF3ir-ORF2 in mitigating endothelial inflammation and atherosclerosis by acting as an inhibitor of IRF5, highlighting its potential as a valuable therapeutic approach for treating atherosclerosis.

cell biology↗

bioRxiv2024

Structural basis for saxitoxin congener binding and neutralization by anuran saxiphilins

Dinoflagellates and cyanobacteria in harmful red tide algal blooms produce saxitoxin (STX) and [~]50 congeners that block voltage-gated sodium channel (NaV) function and disrupt bioelectrical signals1-4. Consuming seafood carrying these lethal toxins causes paralytic shellfish poisoning (PSP), a growing public health hazard due to climate change5-7 that motivates efforts to detect these toxins and counteract their noxious effects. Although structural studies of NaVs8,9 and anuran soluble STX binding proteins known as saxiphilins (Sxphs)10,11 revealed convergent binding modes for the bis-guanidinium STX core10,11, the structural basis for STX congener recognition is unknown. Here, we show that American bullfrog (Rana catesbeiana) RcSxph10,11 and High Himalaya frog (Nanorana parkeri) NpSxph10 use a pre-organized pocket to sequester STX congeners through a binding mode shared with STX. This lock and key recognition yields a tradeoff between a relatively rigid high-affinity toxin binding site in which bound waters are crucial and the ability of Sxphs to accommodate STX congener modifications. Importantly, functional studies show that Sxphs act as toxin sponges that reverse NaV block by multiple STX congeners and can detect these bis-guanidinium toxins in a radioligand receptor binding assay (RBA) for PSP toxin environmental testing12,13. Our findings establish how Sxphs sequester diverse neurotoxins and reveal structural factors underlying STX congener binding differences between Sxphs and NaVs that are rooted in the distinct toxin binding orientations on these two targets. These insights expand the molecular foundation required for understanding toxin sponge action and for guiding development of new means to monitor PSTs and mitigate their harmful effects.

biophysics↗

bioRxiv2024

Effector T Cells under Hypoxia have an Altered Transcriptome Similar to Tumor-Stressed T Cells Found in Non-Responsive Melanoma Patients

BackgroundIn the Tumor Microenvironment (TME), hypoxia stands as a significant factor that modulates immune responses, especially those driven by T cells. As T cell-based therapies often fail to work in solid tumors, this study aims to investigate the effects of hypoxia on T cell topo-distribution in the TME, gene expression association with T cell states, and clinical responses in melanoma. MethodsTo generate detailed information on tumor oxygenation and T cell accessibility, we utilized mathematical modeling of human melanoma tissue microarrays (TMAs) that incorporate oxygen supply from vessels, intratumoral diffusion, and cellular uptake. We created tumor maps and derived plots showing the fraction of CD4 and CD8 T cells against the distance to the nearest vessel and oxygen pressure. To assess their function and transcriptional changes caused by hypoxia, effector T cells were generated and cultured under hypoxia (0.5% oxygen) or normoxia (21% oxygen). The T cell hypoxia-transcriptional signature was compared against datasets from msigDB, iATLAS (clinical trials of melanoma patients treated with immune checkpoint inhibitors), ORIEN AVATAR (real-world melanoma patients treated with immune checkpoint inhibitors, ICIs), and a single-cell atlas of tumor-infiltrating lymphocytes (TILs). ResultsWe made three specific observations: 1) in melanoma T cells preferentially accumulated in oxygenated areas close to blood vessels (50-100 micrometers from the vasculature in the regions of high oxygen availability) but not in hypoxic areas far from blood vessels. 2) Our analysis confirmed that under hypoxia, T cell functions were significantly reduced compared to normoxic conditions and accompanied by a unique gene signature. Furthermore, this hypoxic gene signature was prevalent in resting and non-activated T cells. Notably and clinically relevant, the hypoxic T cell gene set was found to correlate with reduced Overall Survival (OS) and reduced progression-free survival (PFS) in melanoma patients, which was more pronounced in non-responder patients undergoing ICI therapy. 3) Finally, compared with a single-cell atlas of tumor-infiltrating T cells, our hypoxia signature aligned with a population of cells at a state termed stress response state (TSTR). ConclusionOur study highlights the critical role of hypoxia in shaping T cell distribution and its correlation with clinical outcomes in melanoma. We revealed a preferential accumulation of T cells in oxygenated areas. Moreover, hypoxic T cells develop a distinct hypoxic gene signature prevalent in resting, non-activated T cells and TSTR that was also associated with poorer outcomes, particularly pronounced among non-responders to ICIs. Key MessagesWhat is already known on this topic: Hypoxia significantly impairs T cell functions, including reduced proliferation and cytokine production. This impairment may contribute to immune evasion and resistance to immune therapies, such as ICIs, adoptive transfer of TILs, and Chimeric Antigen Receptor (CAR) T cells. Despite the established impact of hypoxia on T cell function, the precise spatial distribution of T cells in relation to oxygen availability within the TME and how this affects clinical outcomes in melanoma patients remains unclear. Additionally, the specific transcriptional changes in T cells induced by hypoxia and their prevalence in different T cell states, as well as the implications for resistance to ICIs, have not been thoroughly investigated. Understanding these aspects is crucial for developing targeted therapies to overcome hypoxia-induced resistance and improve immunotherapy efficacy. What this study adds: This study elucidates the profound impact of hypoxia on T cells in melanoma. Our findings reveal that T cells accumulate in well-oxygenated regions near blood vessels, whereas hypoxic conditions significantly impair their proliferation and cytokine production. By addressing the transcriptional changes induced by hypoxia, we demonstrated its prevalence in resting and non-activated T cells and TSTR. Moreover, we found that hypoxia is associated with shorter OS and PFS in melanoma patients, particularly in non-responders to ICIs. This research highlights the critical role of hypoxia in modulating T cell spatial behavior, contributing to immune evasion and poor clinical outcomes in melanoma. How this study might affect research, practice, or policy: The findings emphasizes hypoxias critical role in modulating T cell behavior and its potential as a biomarker for treatment outcomes. These insights could inform the development of therapeutic strategies aimed at improving T cell function in hypoxic TMEs, thereby enhancing the efficacy of immunotherapies for melanoma and other solid tumors. Additionally, the studys results may influence policies regarding the evaluation and implementation of combination therapies that target hypoxia to improve patient outcomes.

immunology↗

bioRxiv2024

The dynamics of wild Vitis species in response to climate change facilitate the breeding of grapevine and its rootstocks with climate resilience

Climate change poses significant challenges to agricultural suitability and food security due to the limited adaptability of domesticated crops, however, our understanding of their climate adaptability is still limited. In this study, we compare the potential distributional dynamics in response to future climate change between grapevine and its wild relatives (Vitis L.) based on ecological niche models (ENMs). We reveal that the annual mean temperature is the primary factor influencing the potential distribution of cultivated grapes (V. vinifera L.). By 2080, under RCP 8.5, suitable areas for wine and table grapes from V. vinifera are predicted to reduced by 15.04x105 km{superscript 2} and 13.26x105 km{superscript 2}, respectively. The results suggest that grape cultivation, particularly for table grapes, will face serious threats from future climate change. In contrast, seventy percent of wild grapes are well able to withstand future climate conditions. For example, under RCP 8.5, North American wild grapes like V. rotundifolia and V. labrusca, as well as East Asian wild grapes such as V. heyneana and V. davidii, are projected to demonstrate significant adaptability. These wild grapes have the potential to provide rootstocks that could enhance the adaptability of cultivated grapes and serve as invaluable resources for breeding programs aimed at developing new cultivars better suited to withstand the environmental pressures of climate change. Our results not only predict potential suitable distribution areas of wild grapes in the future, but also emphasize the essential impact of these wild genetic resources on grape breeding for promoting adaptation to future climate change.

plant biology↗

bioRxiv2024

An all-in-one AAV vector for cardiac-specific gene silencing by an adenine base editor

ABE editing outcomes are highly variable and unpredictable, depending on various factors. Therefore, the success rate of creating targeted A*T-to-G*C conversions using ABE is not high. But utilizing ABE to target RNA splicing sites for gene silencing has a higher success rate. Another challenge for base editing in the heart is that traditional ABE is too large in size, necessitating dual AAV delivery. Whether single AAV delivery can be achieved remains to be explored. In this study, we demonstrated how the diversity of Cas9 homologs and screening of sgRNAs can facilitate cardiac base editing. Single-AAV base editing outperformed dual-AAV systems in the heart, potentially benefiting from chromatin accessibility-guided sgRNA selection. These findings have important implications for the development of more effective and predictable base editing tools for cardiac gene therapy.

molecular biology↗

bioRxiv2024

Interpreting Sleep Activity Through Neural Contrastive Learning

Memories are spontaneously replayed during sleep, a process thought to support memory consolidation. However, capturing this replay in humans has been challenging because unlike wakefulness, sleep EEG is dominated by slow, rhythmic background activity. Moreover, each sleep stage (e.g., NREM, REM) has distinct rhythms, hindering generalisation of models trained on wake-state data. To overcome these challenges, we developed the Sleep Interpreter (SI), a neural network model that decodes memory replay from sleep EEG. In a large dataset comprising 135 participants ([~]1,000 h of overnight sleep; [~]400 h of wake), we employed a TMR-like paradigm with 15 semantically congruent cue-image pairs to tag specific memories. SI was trained separately for NREM and REM using contrastive learning to align neural patterns across wake and sleep, filtering out stage-specific background rhythms. We also examined how slow oscillations and spindle coupling influence decoding in NREM sleep. In a 15-way classification, SI achieved up to 40.02% Top-1 accuracy on unseen subjects. To test generalisability, we followed up with two independent nap experiments in separate samples and applied the trained SI model off-the-shelf. The first probed spontaneous reactivation without auditory cues, while the second used semantic-free sounds with new images. In both, SI successfully decoded reactivation during sleep that correlated with post-nap memory performance. By openly sharing our dataset and SI system, we provide a unique resource for advancing research on memory and learning during sleep, and related disorders.

neuroscience↗

bioRxiv2024

NMI induces chemokine release and recruits neutrophils through the activation of NF-kappaB pathway

Neutrophils are essential components of the innate immune system, playing a pivotal role in immune responses. These cells rapidly migrate to sites of inflammation or tissue injury, facilitating pathogen clearance and tissue repair. The chemotactic signaling network regulating neutrophil recruitment is complex and not fully understood, particularly regarding damage-associated molecular patterns (DAMPs). In our previous research, we identified NMI as a DAMP that activates dendritic cells and macrophages, amplifying inflammatory responses and contributing to both acute and chronic inflammation. In this study, we investigated the role of NMI in neutrophil recruitment. We purified and characterized a recombinant murine NMI protein, ensuring endotoxin removal while preserving biological activity. In vivo experiments demonstrated that NMI enhances neutrophil recruitment in both a murine air pouch model and an acute peritonitis model, mediated by macrophage-derived chemokines. In vitro assays revealed a concentration-dependent increase in neutrophil migration induced by NMI, facilitated by chemokine secretion and subsequent migration through the CXCR2 receptor. Importantly, we established that NMI activates chemokine expression via the NF-{kappa}B signaling pathway. These findings provide insights into the mechanisms of NMI-induced neutrophil migration, enhancing our understanding of neutrophil recruitment during inflammation.

immunology↗

bioRxiv2024

Interpretable high-resolution dimension reduction of spatial transcriptomics data by DeepFuseNMF

Spatial transcriptomics (ST) technologies have revolutionized tissue architecture studies by capturing gene expression with spatial context. However, high-dimensional ST data often have limited spatial resolution and exhibit considerable noise and sparsity, posing significant challenges in deciphering subtle spatial structures and underlying biological activities. Here, we introduce SpaHDmap, an interpretable dimension reduction framework that enhances spatial resolution by integrating ST gene expression with high-resolution histology images. SpaHDmap incorporates non-negative matrix factorization into a multimodal fusion encoder-decoder architecture, enabling the identification of interpretable, high-resolution embeddings. Furthermore, SpaHDmap can simultaneously analyze multiple samples and is compatible with various types of histology images. Extensive evaluations on synthetic and real ST datasets from various technologies and tissue types demonstrate that SpaHDmap can effectively produce highly interpretable, high-resolution embeddings, and detects refined spatial structures. SpaHDmap represents a powerful approach for integrating ST data and histology images, offering deeper insights into complex tissue structures and functions.

bioinformatics↗

bioRxiv2024

A benchmarking study of copy number variation inference methods using single-cell RNA-sequencing data

Single-cell RNA-sequencing (scRNA-seq) has emerged as a powerful tool for cancer research, enabling in-depth characterization of tumor heterogeneity at the single-cell level. Recently, scRNA-seq copy number variation (scCNV) inference methods have been developed, expanding the application of scRNA-seq to study genetic heterogeneity in cancer using transcriptomic data. However, the fidelity of these methods has not been investigated systematically. In this study, we benchmarked five commonly used scCNV inference methods, HoneyBADGER, CopyKAT, CaSpER, inferCNV, and sciCNV. We evaluated their performance across four different scRNA-seq platforms derived data from a multicenter study. We further evaluated the scCNV performance using scRNA-seq datasets derived from mixed samples consisting of five human lung adenocarcinoma cell lines and generated a clinical scRNA-seq dataset from a human small cell lung cancer patient to validate our findings. Our evaluation criteria included sensitivity and specificity of CNV detection, and subclone identification from mixed cancer samples. We found that the sensitivity and specificity of the five scCNV inference methods varied, depending on the selection of reference data, sequencing depths, and read lengths. Overall, CopyKAT and CaSpER exhibited superior performance to other methods, while inferCNV, sciCNV, and CopyKAT outperformed other methods in subclone identification accuracy. Remarkably, inferCNV achieved high accuracy in subclone identification when using data from a "single scRNA-seq protocol", however, when applying these methods to a dataset derived from multiple scRNA-seq platforms from the mixed samples, we found that batch effects significantly affected the performance of subclone identification for most methods, except for HoneyBADGER. Our benchmarking study revealed the strengths and weaknesses of each of the five scCNV inference methods and provided guidance for selecting the optimal CNV inference method using scRNA-seq data.

bioinformatics↗

bioRxiv2024

Informing biologically relevant signal from spatial transcriptomic data

Visium is a spatial sequencing technology that utilizes messenger RNA (mRNA) to spatially map gene expression within tissues. Despite its potential, research utilizing deconvolution tools and exploring microenvironment dynamics remains challenging. We address this gap by benchmarking deconvolution tools across diverse biological contexts, identifying optimal methodologies. Subsequently, we introduce a novel pipeline integrating advanced deconvolution techniques and novel tools for reproducible tissue microenvironment analysis. Through this approach, we uncover intricate immune aggregate biology, highlighting the power of our methodology in unraveling complex biological phenomena.

bioinformatics↗

bioRxiv2024

Epigenomic, transcriptomic and proteomic characterizations of reference samples

A variety of newly developed next-generation sequencing technologies are making their way rapidly into the research and clinical applications, for which accuracy and cross-lab reproducibility are critical, and reference standards are much needed. Our previous multicenter studies under the SEQC-2 umbrella using a breast cancer cell line with paired B-cell line have produced a large amount of different genomic data including whole genome sequencing (Illumina, PacBio, Nanopore), HiC, and scRNA-seq with detailed analyses on somatic mutations, single-nucleotide variations (SNVs), and structural variations (SVs). However, there is still a lack of well-characterized reference materials which include epigenomic and proteomic data. Here we further performed ATAC-seq, Methyl-seq, RNA-seq, and proteomic analyses and provided a comprehensive catalog of the epigenomic landscape, which overlapped with the transcriptomes and proteomes for the two cell lines. We identified >7,700 peptide isoforms, where the majority (95%) of the genes had a single peptide isoform. Protein expression of the transcripts overlapping CGIs were much higher than the protein expression of the non-CGI transcripts in both cell lines. We further demonstrated the evidence that certain SNVs were incorporated into mutated peptides. We observed that open chromatin regions had low methylation which were largely regulated by CG density, where CG-rich regions had more accessible chromatin, low methylation, and higher gene and protein expression. The CG-poor regions had higher repressive epigenetic regulations (higher DNA methylation) and less open chromatin, resulting in a cell line specific methylation and gene expression patterns. Our studies provide well-defined reference materials consisting of two cell lines with genomic, epigenomic, transcriptomic, scRNA-seq and proteomic characterizations which can serve as standards for validating and benchmarking not only on various omics assays, but also on bioinformatics methods. It will be a valuable resource for both research and clinical communities.

genomics↗

bioRxiv2024

Structural mimicry of UM171 and neomorphic cancer mutants co-opts E3 ligase KBTBD4 for HDAC1/2 recruitment

Neomorphic mutations and drugs can elicit unanticipated effects that hinder mechanistic understanding for clinical practice. Recurrent indel mutations in the Kelch domain of the KBTBD4 E3 ligase rewire epigenetic programs for stemness in medulloblastoma by recruiting LSD1-CoREST-HDAC1/2 complexes as neo-substrates for ubiquitination and degradation. Remarkably, UM171, an investigational drug for haematopoietic stem cell transplantation, was found to degrade LSD1-CoREST-HDAC1/2 complexes in a wild-type KBTBD4-dependent manner, suggesting a potential common mode of action. We identified that these neomorphic interactions were mediated by the HDAC deacetylase domain. Cryo-EM studies of both wild-type and mutant KBTBD4 captured 2:1 and 2:2 KBTBD4-HDAC2 complexes at resolutions spanning 2.7 [A] to 3.1 [A]. The mutant and drug-induced complexes adopted similar structural assemblies requiring both Kelch domains in the KBTBD4 dimer for each HDAC2 interaction. UM171 was identified as a bona fide molecular glue binding across the ternary interface. Most strikingly, the indel mutation reshaped the same surface of KBTBD4 providing the first example of a natural mimic of a molecular glue. Together, the structures provide mechanistic understanding of neomorphic KBTBD4 and help to explain the structure-activity relationships of UM171 derivatives for future drug design.

molecular biology↗

bioRxiv2024

An antibiotic that mediates immune destruction of senescent cancer cells

Drugs that eliminate senescent cells, senolytics, can be powerful when combined with pro-senescence cancer therapies. Using a CRISPR/Cas9-based genetic screen, we identify here SLC25A23 as a vulnerability of senescent cancer cells. Suppressing SLC25A23 disrupts cellular calcium homeostasis, impairs oxidative phosphorylation and interferes with redox signaling, leading to death of senescent cells. These effects can be replicated by salinomycin, a cation ionophore antibiotic. Salinomycin prompts a PANoptosis-like cell death in senescent cells, including apoptosis and two forms of immunogenic cell death: necroptosis and pyroptosis. Notably, we observed that salinomycin treatment or SLC25A23 suppression elevates reactive oxygen species, upregulating death receptor 5 via JNK pathway activation. We show that a combination of a DR5 agonistic antibody and salinomycin is a robust senolytic cocktail. We provide evidence that this drug combination provokes a potent NK and CD8+ T cell mediated immune destruction of senescent cancer cells, mediated by the pyroptotic cytokine IL18. SignificanceThe efficacy of multiple cancer drugs is limited by the induction of senescence, which enables cancer cells to evade cell death. We uncover here a new selective vulnerability of senescent cancer cells and we show that this vulnerability can be targeted with a commonly-used antibiotic. We show that a combination of senescence-inducing therapy, combined with this antibiotic causes a highly immunogenic cell death phenotype that further stimulates potent immune destruction of senescent cancer cells.

cancer biology↗

bioRxiv2024

METTL3 inhibition-activated cGAS/STING axis enhances immunotherapy and PARP inhibitor sensitivity of lung carcinoma

The cGAS/STING-mediated type I interferon response can augment antitumor activity, while the regulatory factors within this innate immune response remain elusive. Herein we found that the RNA m6A methyltransferase METTL3 was upregulated in lung carcinoma tissues. Elevated METTL3 level was correlated with diminished CD8+ T cell infiltration and cancer progression in lung carcinoma patients. METTL3 deficiency exacerbated nuclear DNA leakage into the cytoplasm, activating the cGAS pathway and thereby enhancing anti-tumor immunity. Mechanistically, METTL3 deficiency reduced the homologous recombination repair efficacy via downregulation of MSH5, a mutS family protein involved in DNA mismatch repair, leading to increased cytosolic DNA levels. m6A methylation of A2521 of MSH5 stabilized its mRNA via binding with IGF2BP2. On the other hand, m6A methylation of A1545 at the CDS of cGAS decreased mRNA stability and regulates its protein expression. Functionally, knockdown of METTL3 sensitized lung carcinoma cells to the PARP inhibitors. In vivo and clinical data confirmed the positive roles of METTL3 inhibition-activated cGAS/STING axis in tumor growth and lung adenocarcinoma progression. Collectively, METTL3 inhibition activates the cGAS/STING-mediated anti-tumor immunity via induction of cytosolic DNA and cGAS expression, which in turn regulate PARP inhibitor response and cancer progression in lung carcinoma.

cancer biology↗