Pub Date : 2024-08-08DOI: 10.1101/2024.08.07.606971
Samarjit Jana, Abhishek Chowdhury, K. Somasundaram
H19, a lnc-pri-miRNA that encodes miR-675, is dysregulated in numerous cancers. However, the specific mechanisms underlying H19 processing, particularly miR-675 formation, remain unclear. Our study reveals that H19 is highly expressed and m6A modified in a METTL3-dependent manner in glioblastoma (GBM) and glioma stem cells (GSCs). Silencing METTL3 reduced both H19 and miR-675 levels, whereas overexpressing METTL3 promoted miR-675 processing without affecting H19 levels. Further, miR-675 derived from exogenously expressed H19 was affected considerably more in METTL3 silenced glioma cells compared to H19 levels, suggesting differential requirements in the processing of m6A modified H19 transcript. We demonstrate that H19 interacts with m6A reader proteins, IGF2BP2 and HNRNPA2B1, and silencing either reduced H19 and miR-675 levels. However, a high level of miR-675 seen in METTL3 overexpressing cells is severely affected in HNRNPA2B1-silenced compared to IGF2BP2-silenced glioma cells. Interestingly, IGF2BP2 silencing more significantly affected H19 stability from exogenous H19 construct, while HNRNPA2B1 silencing severely impacted miR-675 processing. Site-directed mutagenesis confirmed the presence of two m6A sites in the first exon of H19, with site #1 facilitating HNRNPA2B1 interaction to promote miR-675 processing. In contrast, the IGF2BP2 interaction is promoted by site #2, resulting in enhanced H19 stability. H19-METTL3-HNRNPA2B1-miR675 axis inhibited Calneuron 1 (CALN1), a known target of miR-675, to promote glioma cell migration. Notably, a low CALN1/high H19 predicted a poor prognosis in GBM patients and was further exacerbated by a high METTL3 or HNRNPA2B1 but not IGF2BP2 transcript levels. Thus, we found that the H19 transcript is highly expressed in GBM and m6A modified, and the m6A reader proteins, IGF2BP2 and HNRNPA2B1, regulate the H19 processing differently to promote glioma cell migration.
{"title":"Differential requirement of m6A reader proteins, IGF2BP2 and HNRNPA2B1 for the processing of N6-methyladenosine modified H19 lncRNA: Stability versus miR-675 biogenesis","authors":"Samarjit Jana, Abhishek Chowdhury, K. Somasundaram","doi":"10.1101/2024.08.07.606971","DOIUrl":"https://doi.org/10.1101/2024.08.07.606971","url":null,"abstract":"H19, a lnc-pri-miRNA that encodes miR-675, is dysregulated in numerous cancers. However, the specific mechanisms underlying H19 processing, particularly miR-675 formation, remain unclear. Our study reveals that H19 is highly expressed and m6A modified in a METTL3-dependent manner in glioblastoma (GBM) and glioma stem cells (GSCs). Silencing METTL3 reduced both H19 and miR-675 levels, whereas overexpressing METTL3 promoted miR-675 processing without affecting H19 levels. Further, miR-675 derived from exogenously expressed H19 was affected considerably more in METTL3 silenced glioma cells compared to H19 levels, suggesting differential requirements in the processing of m6A modified H19 transcript. We demonstrate that H19 interacts with m6A reader proteins, IGF2BP2 and HNRNPA2B1, and silencing either reduced H19 and miR-675 levels. However, a high level of miR-675 seen in METTL3 overexpressing cells is severely affected in HNRNPA2B1-silenced compared to IGF2BP2-silenced glioma cells. Interestingly, IGF2BP2 silencing more significantly affected H19 stability from exogenous H19 construct, while HNRNPA2B1 silencing severely impacted miR-675 processing. Site-directed mutagenesis confirmed the presence of two m6A sites in the first exon of H19, with site #1 facilitating HNRNPA2B1 interaction to promote miR-675 processing. In contrast, the IGF2BP2 interaction is promoted by site #2, resulting in enhanced H19 stability. H19-METTL3-HNRNPA2B1-miR675 axis inhibited Calneuron 1 (CALN1), a known target of miR-675, to promote glioma cell migration. Notably, a low CALN1/high H19 predicted a poor prognosis in GBM patients and was further exacerbated by a high METTL3 or HNRNPA2B1 but not IGF2BP2 transcript levels. Thus, we found that the H19 transcript is highly expressed in GBM and m6A modified, and the m6A reader proteins, IGF2BP2 and HNRNPA2B1, regulate the H19 processing differently to promote glioma cell migration.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141927821","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-08DOI: 10.1101/2024.08.06.606751
Naqiya Ambareen, Kusumika Gharami, S. Biswas
Dysfunctional autophagy is a primary characteristic of Alzheimer’s disease (AD) pathogenesis. How autophagic impairment leads to cellular changes that contributes to AD pathogenesis remains unclear. To study this further, we assessed levels of autophagy related proteins in 5xFAD mice brain at different ages and found their robust upregulation in cortex and hippocampus suggesting increased induction of autophagy with disease progression but failed clearance. We have identified a transcriptional coregulator Sertad1, as a key mediator of dysfunctional autophagy in AD mice. We found a progressive elevation in Sertad1 levels in 5xFAD mice with age compared to wild-type (WT) mice. Sertad1 knockdown in 5xFAD mice brain lowered levels of autophagy related proteins and lysosome marker, LAMP1 suggesting its role in autophagy flux modulation. FoxO3a is an important transcriptional regulator of the autophagy network and lies at the nexus of autophagy-apoptosis cross-talk. We found that Sertad1 knockdown blocked nuclear translocation of FoxO3a along with a restoration in Akt activity. Further, we showed that knockdown of Sertad1 in 5xFAD mice brain improved cognitive functions along with a remarkable restoration in synaptic health and dendritic spine density. Taken together, our results demonstrated that autophagy is robustly induced with disease progression but it is impaired; Sertad1 knockdown restored autophagy defects, synaptic loss and improved learning and memory in AD models. Thus, we propose that Sertad1 acts in a multimodal manner regulating crucial cell death pathways including apoptosis and autophagy and could be an excellent target for therapeutic intervention to combat a multifactorial disorder such as AD.
自噬功能障碍是阿尔茨海默病（AD）发病机制的一个主要特征。自噬功能受损如何导致细胞变化，从而导致阿尔茨海默病发病机制，目前仍不清楚。为了进一步研究这个问题，我们评估了不同年龄段 5xFAD 小鼠大脑中自噬相关蛋白的水平，发现它们在大脑皮层和海马中显著上调，这表明随着疾病的进展，自噬诱导增加，但清除失败。我们发现转录核心调节因子 Sertad1 是导致 AD 小鼠自噬功能障碍的关键介质。我们发现，与野生型（WT）小鼠相比，5xFAD 小鼠体内的 Sertad1 水平随着年龄的增长而逐渐升高。在5xFAD小鼠脑中敲除Sertad1会降低自噬相关蛋白和溶酶体标记物LAMP1的水平，这表明Sertad1在自噬通量调节中的作用。FoxO3a 是自噬网络的一个重要转录调节因子，位于自噬-凋亡交叉对话的中心。我们发现，敲除 Sertad1 阻断了 FoxO3a 的核转位，同时恢复了 Akt 的活性。此外，我们还发现，在 5xFAD 小鼠大脑中敲除 Sertad1 能改善认知功能，并显著恢复突触健康和树突棘密度。总之，我们的研究结果表明，自噬会随着疾病的进展而被强力诱导，但自噬会受损；Sertad1 的敲除可恢复 AD 模型的自噬缺陷、突触损失并改善学习和记忆。因此，我们认为 Sertad1 以多模式的方式调节包括细胞凋亡和自噬在内的关键细胞死亡途径，可以成为治疗干预的绝佳靶点，以对抗像 AD 这样的多因素疾病。
{"title":"Sertad1 is elevated and plays a necessary role in synaptic loss, neuron death and cognitive impairment in a model of Alzheimer’s disease","authors":"Naqiya Ambareen, Kusumika Gharami, S. Biswas","doi":"10.1101/2024.08.06.606751","DOIUrl":"https://doi.org/10.1101/2024.08.06.606751","url":null,"abstract":"Dysfunctional autophagy is a primary characteristic of Alzheimer’s disease (AD) pathogenesis. How autophagic impairment leads to cellular changes that contributes to AD pathogenesis remains unclear. To study this further, we assessed levels of autophagy related proteins in 5xFAD mice brain at different ages and found their robust upregulation in cortex and hippocampus suggesting increased induction of autophagy with disease progression but failed clearance. We have identified a transcriptional coregulator Sertad1, as a key mediator of dysfunctional autophagy in AD mice. We found a progressive elevation in Sertad1 levels in 5xFAD mice with age compared to wild-type (WT) mice. Sertad1 knockdown in 5xFAD mice brain lowered levels of autophagy related proteins and lysosome marker, LAMP1 suggesting its role in autophagy flux modulation. FoxO3a is an important transcriptional regulator of the autophagy network and lies at the nexus of autophagy-apoptosis cross-talk. We found that Sertad1 knockdown blocked nuclear translocation of FoxO3a along with a restoration in Akt activity. Further, we showed that knockdown of Sertad1 in 5xFAD mice brain improved cognitive functions along with a remarkable restoration in synaptic health and dendritic spine density. Taken together, our results demonstrated that autophagy is robustly induced with disease progression but it is impaired; Sertad1 knockdown restored autophagy defects, synaptic loss and improved learning and memory in AD models. Thus, we propose that Sertad1 acts in a multimodal manner regulating crucial cell death pathways including apoptosis and autophagy and could be an excellent target for therapeutic intervention to combat a multifactorial disorder such as AD.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141929396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-08DOI: 10.1101/2024.08.06.606833
Miguel Vivar-Lazo, Christopher R. Fetsch
Decision confidence plays a key role in flexible behavior, but exactly how and when it arises in the brain remains unclear. Theoretical accounts suggest that confidence can be inferred from the same evidence accumulation process that governs choice and response time (RT), implying that a provisional confidence assessment could be updated in parallel with decision formation. We tested this using a novel RT task in nonhuman primates that measures choice and confidence with a single eye movement on every trial. Monkey behavior was well fit by a 2D bounded accumulator model instantiating parallel processing of evidence, rejecting a serial model in which choice is resolved first followed by post-decision accumulation for confidence. Neural activity in area LIP reflected concurrent accumulation, exhibiting within-trial dynamics consistent with parallel updating at near zero time lag, and significant covariation in choice and confidence signals across the population. The results demonstrate that monkeys concurrently process a single stream of evidence to arrive at a choice and level of confidence, and illuminate a candidate neural mechanism for this ability.
{"title":"Neural basis of concurrent deliberation toward a choice and degree of confidence","authors":"Miguel Vivar-Lazo, Christopher R. Fetsch","doi":"10.1101/2024.08.06.606833","DOIUrl":"https://doi.org/10.1101/2024.08.06.606833","url":null,"abstract":"Decision confidence plays a key role in flexible behavior, but exactly how and when it arises in the brain remains unclear. Theoretical accounts suggest that confidence can be inferred from the same evidence accumulation process that governs choice and response time (RT), implying that a provisional confidence assessment could be updated in parallel with decision formation. We tested this using a novel RT task in nonhuman primates that measures choice and confidence with a single eye movement on every trial. Monkey behavior was well fit by a 2D bounded accumulator model instantiating parallel processing of evidence, rejecting a serial model in which choice is resolved first followed by post-decision accumulation for confidence. Neural activity in area LIP reflected concurrent accumulation, exhibiting within-trial dynamics consistent with parallel updating at near zero time lag, and significant covariation in choice and confidence signals across the population. The results demonstrate that monkeys concurrently process a single stream of evidence to arrive at a choice and level of confidence, and illuminate a candidate neural mechanism for this ability.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141929241","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-08DOI: 10.1101/2024.08.06.606489
R. Leahey, Martin Weber, Chang Hoon Cho, Seong Hur, Amber Cramer, Karla Manzanares, Brett Babin, Gladys Boenig, Taylor Kring, Liling Liu, Yusi Cui, Anjani Ganti, John P. Evans, Marika Nespi, Justin Ly, Alicia A Nugent, Samantha A. Green, Bryan Chan, Casper C. Hoogenraad, Anton Delwig, Flora I. Hinz
SARM1, an octameric NADase, is a key regulator of axon degeneration and an emerging target in small molecule drug discovery to treat a wide range of neurodegenerative diseases. Recently, a structurally diverse series of adduct-forming, orthosteric SARM1 inhibitors have been discovered. Here, we show that subinhibitory concentrations of these orthosteric inhibitors, under mildly SARM1 activating conditions, cause sustained SARM1 activation. This synergistic adverse effect leads to increased nicotinamide adenine dinucleotide (NAD) consumption, neurodegeneration and release of the biomarker neurofilament-light (NfL) in cultured cortical neurons. In two distinct animal models, we found that low-dose treatment with these orthosteric SARM1 inhibitors results in increased plasma NfL and adverse events when combined with cellular stress or injury conditions. This may present a critical liability for orthosteric SARM1 inhibitors in certain patient populations.
{"title":"SARM1 orthosteric base exchange inhibitors cause subinhibitory SARM1 activation","authors":"R. Leahey, Martin Weber, Chang Hoon Cho, Seong Hur, Amber Cramer, Karla Manzanares, Brett Babin, Gladys Boenig, Taylor Kring, Liling Liu, Yusi Cui, Anjani Ganti, John P. Evans, Marika Nespi, Justin Ly, Alicia A Nugent, Samantha A. Green, Bryan Chan, Casper C. Hoogenraad, Anton Delwig, Flora I. Hinz","doi":"10.1101/2024.08.06.606489","DOIUrl":"https://doi.org/10.1101/2024.08.06.606489","url":null,"abstract":"SARM1, an octameric NADase, is a key regulator of axon degeneration and an emerging target in small molecule drug discovery to treat a wide range of neurodegenerative diseases. Recently, a structurally diverse series of adduct-forming, orthosteric SARM1 inhibitors have been discovered. Here, we show that subinhibitory concentrations of these orthosteric inhibitors, under mildly SARM1 activating conditions, cause sustained SARM1 activation. This synergistic adverse effect leads to increased nicotinamide adenine dinucleotide (NAD) consumption, neurodegeneration and release of the biomarker neurofilament-light (NfL) in cultured cortical neurons. In two distinct animal models, we found that low-dose treatment with these orthosteric SARM1 inhibitors results in increased plasma NfL and adverse events when combined with cellular stress or injury conditions. This may present a critical liability for orthosteric SARM1 inhibitors in certain patient populations.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141928521","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-08DOI: 10.1101/2024.08.06.606883
Yixun Su, Hui Li, Wenjie Zhang, Shi Tao, Qi Wang, Mi Zhou, Yong Tang, Hui Chen, A. Verkhratsky, Zhengbao Zha, Jianqin Niu, Chenju Yi
Alzheimer’s disease (AD) is the major cause of senile dementia without effective therapeutic strategies. The fundamental role of microglia in AD pathology, particularly in the early stages, is well acknowledged, although cell-specific therapeutic targets were not identified. Here we show that microglial connexin 43 (Cx43) hemichannels controls microglial reactivity in AD, thus being a promising therapeutic target. We discovered a marked increase in Cx43 protein in the periplaque microglia in the post-mortem tissue from AD patients. Subsequently, using the APPswe/PS1dE9 mouse model of AD, we demonstrated that microglial Cx43 operating as hemichannels influences microglial function, which in turn affects β-amyloid pathology. Ablation of microglial Cx43 hemichannels by genetic knockout shifted microglia to neuroprotective phenotype, which promoted the microglia-plaque interaction while suppressing the neurotoxic microglial signature, thereby mitigating the progression of AD. Following this lead, we developed a novel formulation of a small molecule peptide, lipid nanoparticle-delivered molecule TAT-Cx43266-283 (TAT-CX43@LNPs), which selectively blocks Cx43 hemichannels. Our preclinical trial demonstrated its efficacy in delaying and rescuing β-amyloid-related neuropathology and cognitive impairment in AD mice. This study provides strong evidence to progress our novel drug into clinical trials and translate it to disease-preventing (when administered in the early disease stages) and disease-modifying agents.
阿尔茨海默病（AD）是老年痴呆症的主要病因，但却没有有效的治疗策略。小胶质细胞在阿尔茨海默病病理学中，尤其是在早期阶段的基本作用已得到公认，但细胞特异性治疗靶点尚未确定。在这里，我们发现小胶质细胞连接蛋白 43（Cx43）半通道控制着 AD 中小胶质细胞的反应性，因此是一个很有希望的治疗靶点。我们发现，在 AD 患者的尸检组织中，骨膜周围小胶质细胞中的 Cx43 蛋白明显增加。随后，我们利用APPswe/PS1dE9小鼠AD模型证明，小胶质细胞Cx43作为半通道影响小胶质细胞功能，进而影响β-淀粉样蛋白病理学。通过基因敲除消减小胶质细胞Cx43半通道可使小胶质细胞转为神经保护表型，从而促进小胶质细胞与斑块的相互作用，同时抑制小胶质细胞的神经毒性特征，从而缓解AD的进展。根据这一线索，我们开发了一种新型的小分子肽制剂--脂质纳米颗粒递送分子 TAT-Cx43266-283（TAT-CX43@LNPs），它能选择性地阻断 Cx43 半通道。我们的临床前试验证明了它在延缓和挽救β-淀粉样蛋白相关神经病理学和AD小鼠认知障碍方面的疗效。这项研究为我们的新药进入临床试验并转化为疾病预防（在疾病早期阶段给药）和疾病改变药物提供了强有力的证据。
{"title":"Turning microglia neuroprotective: Towards connexin43-specific therapy of Alzheimer’s disease","authors":"Yixun Su, Hui Li, Wenjie Zhang, Shi Tao, Qi Wang, Mi Zhou, Yong Tang, Hui Chen, A. Verkhratsky, Zhengbao Zha, Jianqin Niu, Chenju Yi","doi":"10.1101/2024.08.06.606883","DOIUrl":"https://doi.org/10.1101/2024.08.06.606883","url":null,"abstract":"Alzheimer’s disease (AD) is the major cause of senile dementia without effective therapeutic strategies. The fundamental role of microglia in AD pathology, particularly in the early stages, is well acknowledged, although cell-specific therapeutic targets were not identified. Here we show that microglial connexin 43 (Cx43) hemichannels controls microglial reactivity in AD, thus being a promising therapeutic target. We discovered a marked increase in Cx43 protein in the periplaque microglia in the post-mortem tissue from AD patients. Subsequently, using the APPswe/PS1dE9 mouse model of AD, we demonstrated that microglial Cx43 operating as hemichannels influences microglial function, which in turn affects β-amyloid pathology. Ablation of microglial Cx43 hemichannels by genetic knockout shifted microglia to neuroprotective phenotype, which promoted the microglia-plaque interaction while suppressing the neurotoxic microglial signature, thereby mitigating the progression of AD. Following this lead, we developed a novel formulation of a small molecule peptide, lipid nanoparticle-delivered molecule TAT-Cx43266-283 (TAT-CX43@LNPs), which selectively blocks Cx43 hemichannels. Our preclinical trial demonstrated its efficacy in delaying and rescuing β-amyloid-related neuropathology and cognitive impairment in AD mice. This study provides strong evidence to progress our novel drug into clinical trials and translate it to disease-preventing (when administered in the early disease stages) and disease-modifying agents.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141929570","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-08DOI: 10.1101/2024.08.05.606553
Xin Sui, Jennifer A. Lo, Shuchen Luo, Yichun He, Zefang Tang, Zuwan Lin, Yiming Zhou, Wendy Xueyi Wang, Jia Liu, Xiao Wang
Characterizing the transcriptional and translational gene expression patterns at the single-cell level within their three-dimensional (3D) tissue context is essential for revealing how genes shape tissue structure and function in health and disease. However, most existing spatial profiling techniques are limited to 5-20 µm thin tissue sections. Here, we developed Deep-STARmap and Deep-RIBOmap, which enable 3D in situ quantification of thousands of gene transcripts and their corresponding translation activities, respectively, within 200-µm thick tissue blocks. This is achieved through scalable probe synthesis, hydrogel embedding with efficient probe anchoring, and robust cDNA crosslinking. We first utilized Deep-STARmap in combination with multicolor fluorescent protein imaging for simultaneous molecular cell typing and 3D neuron morphology tracing in the mouse brain. We also demonstrate that 3D spatial profiling facilitates comprehensive and quantitative analysis of tumor-immune interactions in human skin cancer.
{"title":"Scalable spatial single-cell transcriptomics and translatomics in 3D thick tissue blocks","authors":"Xin Sui, Jennifer A. Lo, Shuchen Luo, Yichun He, Zefang Tang, Zuwan Lin, Yiming Zhou, Wendy Xueyi Wang, Jia Liu, Xiao Wang","doi":"10.1101/2024.08.05.606553","DOIUrl":"https://doi.org/10.1101/2024.08.05.606553","url":null,"abstract":"Characterizing the transcriptional and translational gene expression patterns at the single-cell level within their three-dimensional (3D) tissue context is essential for revealing how genes shape tissue structure and function in health and disease. However, most existing spatial profiling techniques are limited to 5-20 µm thin tissue sections. Here, we developed Deep-STARmap and Deep-RIBOmap, which enable 3D in situ quantification of thousands of gene transcripts and their corresponding translation activities, respectively, within 200-µm thick tissue blocks. This is achieved through scalable probe synthesis, hydrogel embedding with efficient probe anchoring, and robust cDNA crosslinking. We first utilized Deep-STARmap in combination with multicolor fluorescent protein imaging for simultaneous molecular cell typing and 3D neuron morphology tracing in the mouse brain. We also demonstrate that 3D spatial profiling facilitates comprehensive and quantitative analysis of tumor-immune interactions in human skin cancer.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141925555","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-08DOI: 10.1101/2024.08.06.606796
Lucas Stoffl, Andy Bonnetto, Stéphane d’Ascoli, Alexander Mathis
Natural behavior is hierarchical. Yet, there is a paucity of benchmarks addressing this aspect. Recognizing the scarcity of large-scale hierarchical behavioral benchmarks, we create a novel synthetic basketball playing benchmark (Shot7M2). Beyond synthetic data, we extend BABEL into a hierarchical action segmentation benchmark (hBABEL). Then, we develop a masked autoencoder framework (hBehaveMAE) to elucidate the hierarchical nature of motion capture data in an unsupervised fashion. We find that hBehaveMAE learns interpretable latents on Shot7M2 and hBABEL, where lower encoder levels show a superior ability to represent fine-grained movements, while higher encoder levels capture complex actions and activities. Additionally, we evaluate hBehaveMAE on MABe22, a representation learning benchmark with short and long-term behavioral states. hBehaveMAE achieves state-of-the-art performance without domain-specific feature extraction. Together, these components synergistically contribute towards unveiling the hierarchical organization of natural behavior. Models and benchmarks are available at https://github.com/amathislab/BehaveMAE.
{"title":"Elucidating the Hierarchical Nature of Behavior with Masked Autoencoders","authors":"Lucas Stoffl, Andy Bonnetto, Stéphane d’Ascoli, Alexander Mathis","doi":"10.1101/2024.08.06.606796","DOIUrl":"https://doi.org/10.1101/2024.08.06.606796","url":null,"abstract":"Natural behavior is hierarchical. Yet, there is a paucity of benchmarks addressing this aspect. Recognizing the scarcity of large-scale hierarchical behavioral benchmarks, we create a novel synthetic basketball playing benchmark (Shot7M2). Beyond synthetic data, we extend BABEL into a hierarchical action segmentation benchmark (hBABEL). Then, we develop a masked autoencoder framework (hBehaveMAE) to elucidate the hierarchical nature of motion capture data in an unsupervised fashion. We find that hBehaveMAE learns interpretable latents on Shot7M2 and hBABEL, where lower encoder levels show a superior ability to represent fine-grained movements, while higher encoder levels capture complex actions and activities. Additionally, we evaluate hBehaveMAE on MABe22, a representation learning benchmark with short and long-term behavioral states. hBehaveMAE achieves state-of-the-art performance without domain-specific feature extraction. Together, these components synergistically contribute towards unveiling the hierarchical organization of natural behavior. Models and benchmarks are available at https://github.com/amathislab/BehaveMAE.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141925991","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-08DOI: 10.1101/2024.08.06.606653
Ivan Ezquerra-Romano, Maansib Chowdhury, Patrick Haggard
Skin stimuli reach the brain via multiple neural channels specific for different stimulus types. These channels interact in the spinal cord, typically through inhibition. Interchannel interactions can be investigated by selectively stimulating one channel and comparing the sensations that result when another sensory channel is or is not concurrently stimulated. Applying this logic to thermal-mechanical interactions proves difficult, because most existing thermal stimulators involve skin contact. We used a novel non-tactile stimulator for focal cooling (9mm2) by using thermal imaging of skin temperature as a feedback signal to regulate exposure to a dry ice source. We could then investigate how touch modulates cold sensation by delivering cooling to the human hand dorsum in either the presence or absence of light touch. Across three signal detection experiments, we found that sensitivity to cooling was significantly reduced by touch. This reduction was specific to touch, since it did not occur when presenting auditory signals instead of the tactile input, making explanations based on distraction or attention unlikely. Our findings suggest that touch inhibits cold perception, recalling interactions of touch and pain previously described by Pain Gate Theory. We show, for the first time, a thermotactile gating mechanism between mechanical and cooling signals.
{"title":"Touch inhibits cold: non-contact cooling reveals a novel thermotactile gating mechanism","authors":"Ivan Ezquerra-Romano, Maansib Chowdhury, Patrick Haggard","doi":"10.1101/2024.08.06.606653","DOIUrl":"https://doi.org/10.1101/2024.08.06.606653","url":null,"abstract":"Skin stimuli reach the brain via multiple neural channels specific for different stimulus types. These channels interact in the spinal cord, typically through inhibition. Interchannel interactions can be investigated by selectively stimulating one channel and comparing the sensations that result when another sensory channel is or is not concurrently stimulated. Applying this logic to thermal-mechanical interactions proves difficult, because most existing thermal stimulators involve skin contact. We used a novel non-tactile stimulator for focal cooling (9mm2) by using thermal imaging of skin temperature as a feedback signal to regulate exposure to a dry ice source. We could then investigate how touch modulates cold sensation by delivering cooling to the human hand dorsum in either the presence or absence of light touch. Across three signal detection experiments, we found that sensitivity to cooling was significantly reduced by touch. This reduction was specific to touch, since it did not occur when presenting auditory signals instead of the tactile input, making explanations based on distraction or attention unlikely. Our findings suggest that touch inhibits cold perception, recalling interactions of touch and pain previously described by Pain Gate Theory. We show, for the first time, a thermotactile gating mechanism between mechanical and cooling signals.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141927276","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-08DOI: 10.1101/2024.08.06.606836
Fujue Ji, Haesung Lee, Haesung Lee, Jong-Hee Kim
Background Aging-induced frailty syndrome leads to significant functional decline in skeletal muscle. The specific histological changes in skeletal muscle due to frailty syndrome are not well-defined. While the positive effects of exercise on skeletal muscle histology are documented, its preventive impact on frailty syndrome requires further exploration. This study investigates the impact of frailty syndrome on skeletal muscle histology and evaluates the preventive effects of exercise. Method Mice were divided into five groups: young, adult, old, frailty syndrome, and exercise. The exercise group underwent endurance exercise for 60 minutes, three times a week, for 16 weeks. Body weight and lean mass ratio were measured. Muscle fiber cross-sectional area (CSA), myofiber number, extracellular matrix (ECM) content,and myosin heavy chain (MHC) isoforms of the plantaris, tibialis anterior, and quadriceps muscles were evaluated. Results Compared to the old group, the frailty syndrome group showed increased body weight and ECM content, with reductions in CSA and fiber number (P < 0.05). The proportion of MHC isoforms in skeletal muscles remained unchanged. Exercise significantly reduced body weight and ECM content, while increasing CSA, fiber number, and lean mass ratio (P < 0.05). Conclusion Frailty syndrome induces histological changes in skeletal muscle, contributing to functional decline. Exercise can mitigate these changes, highlighting its potential in preventing skeletal muscle muscle dysfunction associated with frailty syndrome. These findings provide valuable insights for the prevention, diagnosis, and treatment of frailty syndrome.
{"title":"The Impact of Frailty Syndrome on Skeletal Muscle Histology and the Preventive Effects of Exercise","authors":"Fujue Ji, Haesung Lee, Haesung Lee, Jong-Hee Kim","doi":"10.1101/2024.08.06.606836","DOIUrl":"https://doi.org/10.1101/2024.08.06.606836","url":null,"abstract":"Background Aging-induced frailty syndrome leads to significant functional decline in skeletal muscle. The specific histological changes in skeletal muscle due to frailty syndrome are not well-defined. While the positive effects of exercise on skeletal muscle histology are documented, its preventive impact on frailty syndrome requires further exploration. This study investigates the impact of frailty syndrome on skeletal muscle histology and evaluates the preventive effects of exercise. Method Mice were divided into five groups: young, adult, old, frailty syndrome, and exercise. The exercise group underwent endurance exercise for 60 minutes, three times a week, for 16 weeks. Body weight and lean mass ratio were measured. Muscle fiber cross-sectional area (CSA), myofiber number, extracellular matrix (ECM) content,and myosin heavy chain (MHC) isoforms of the plantaris, tibialis anterior, and quadriceps muscles were evaluated. Results Compared to the old group, the frailty syndrome group showed increased body weight and ECM content, with reductions in CSA and fiber number (P < 0.05). The proportion of MHC isoforms in skeletal muscles remained unchanged. Exercise significantly reduced body weight and ECM content, while increasing CSA, fiber number, and lean mass ratio (P < 0.05). Conclusion Frailty syndrome induces histological changes in skeletal muscle, contributing to functional decline. Exercise can mitigate these changes, highlighting its potential in preventing skeletal muscle muscle dysfunction associated with frailty syndrome. These findings provide valuable insights for the prevention, diagnosis, and treatment of frailty syndrome.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141928107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-08DOI: 10.1101/2024.08.06.606818
Nisha A. Viswan, Alexandre Tribut, Manvel Gasparyan, Ovidiu Radulescu, U. Bhalla
Biological signalling systems are complex, and efforts to build mechanistic models must confront a huge parameter space, indirect and incomplete data, and frequently encounter multiscale and multiphysics phenomena. We present HOSS, a framework for Hierarchical Optimization of Systems Simulations, to address such problems. HOSS operates by breaking down extensive systems models into individual pathway blocks organized in a nested hierarchy. At the first level, dependencies are solely on signalling inputs, and subsequent levels rely only on the preceding ones. We demonstrate that each independent pathway in every level can be efficiently optimized. Once optimized, its parameters are held constant while the pathway serves as input for succeeding levels. We develop an algorithmic approach to identify the necessary nested hierarchies for the application of HOSS in any given biochemical network. Furthermore, we devise two parallelizable variants that generate numerous model instances using stochastic scrambling of parameters during initial and intermediate stages of optimization. Our results indicate that these variants produce superior models and offer an estimate of solution degeneracy. Additionally, we showcase the effectiveness of the optimization methods for both abstracted, event-based simulations and ODE-based models. Author summary Biochemical pathway models integrate quantitative and qualitative data to understand cell functioning, disease effects, and to test treatments in silico. Constructing and optimizing these models is challenging due to the complexity and multitude of variables and parameters involved. Although hundreds of biochemical models have been developed and are available in repositories, they are rarely reused. To enhance the utilization of these models in biomedicine, we propose HOSS, an innovative hierarchical model optimization method. HOSS takes advantage of the modular structure of pathway models by breaking down large mechanistic computational models into smaller modules. These modules are then optimized progressively, starting with input modules and following causality paths. This method significantly reduces the computational burden as each step involves solving a simpler problem. By making the optimization process more manageable, HOSS accelerates the lifecycle of biochemical models and promotes their broader use in biomedical research and applications.
{"title":"Hierarchical optimization of biochemical networks","authors":"Nisha A. Viswan, Alexandre Tribut, Manvel Gasparyan, Ovidiu Radulescu, U. Bhalla","doi":"10.1101/2024.08.06.606818","DOIUrl":"https://doi.org/10.1101/2024.08.06.606818","url":null,"abstract":"Biological signalling systems are complex, and efforts to build mechanistic models must confront a huge parameter space, indirect and incomplete data, and frequently encounter multiscale and multiphysics phenomena. We present HOSS, a framework for Hierarchical Optimization of Systems Simulations, to address such problems. HOSS operates by breaking down extensive systems models into individual pathway blocks organized in a nested hierarchy. At the first level, dependencies are solely on signalling inputs, and subsequent levels rely only on the preceding ones. We demonstrate that each independent pathway in every level can be efficiently optimized. Once optimized, its parameters are held constant while the pathway serves as input for succeeding levels. We develop an algorithmic approach to identify the necessary nested hierarchies for the application of HOSS in any given biochemical network. Furthermore, we devise two parallelizable variants that generate numerous model instances using stochastic scrambling of parameters during initial and intermediate stages of optimization. Our results indicate that these variants produce superior models and offer an estimate of solution degeneracy. Additionally, we showcase the effectiveness of the optimization methods for both abstracted, event-based simulations and ODE-based models. Author summary Biochemical pathway models integrate quantitative and qualitative data to understand cell functioning, disease effects, and to test treatments in silico. Constructing and optimizing these models is challenging due to the complexity and multitude of variables and parameters involved. Although hundreds of biochemical models have been developed and are available in repositories, they are rarely reused. To enhance the utilization of these models in biomedicine, we propose HOSS, an innovative hierarchical model optimization method. HOSS takes advantage of the modular structure of pathway models by breaking down large mechanistic computational models into smaller modules. These modules are then optimized progressively, starting with input modules and following causality paths. This method significantly reduces the computational burden as each step involves solving a simpler problem. By making the optimization process more manageable, HOSS accelerates the lifecycle of biochemical models and promotes their broader use in biomedical research and applications.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141927769","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：