首页 > 最新文献

bioRxiv : the preprint server for biology最新文献

英文 中文
Kinase Plasticity in Response to Vandetanib Enhances Sensitivity to Tamoxifen in Estrogen Receptor Positive Breast Cancer.
Pub Date : 2025-03-03 DOI: 10.1101/2024.12.19.629395
Rasha T Kakati, Austin A Whitman, Santiago Haase, Attila T Szenasi, Christine Hnc Thai, Elizabeth Brunk, Denis O Okumu, Michael P East, Charles M Perou, Gary L Johnson, Philip M Spanheimer

Resistance to endocrine therapy (ET) is common in estrogen receptor (ER) positive breast cancer. Multiple studies have demonstrated that upregulation of MAPK signaling pathways contributes to ET resistance. Herein we show that vandetanib treatment enhances sensitivity to ET in ET-sensitive and -resistant ER+ breast cancer models. Vandetanib treatment alters the gene expression program of ER+ breast cancer cells resulting in a less proliferative and more estrogen responsive Luminal-A like character. Tyrosine kinase network reprogramming was assessed using multiplexed kinase inhibitor beads-mass spectrometry (MIB/MS) assay to identify adaptive resistance mechanisms to vandetanib treatment, including upregulation of HER2 activity. Co-treatment to inhibit HER2 with lapatinib enhanced sensitivity to vandetanib, demonstrating biologic activity of HER2 upregulation. Using a CRISPR knockout model, we demonstrate that vandetanib effects are partially mediated by RET receptor tyrosine kinase. Finally, we use our operating room-to-laboratory assay that measures drug response in individual primary tumor cells in short term cultures to demonstrate conserved gene expression changes, including increased HER2 activity signatures, in vandetanib treated cells, and identify features associated with vandetanib response. These results support future investigation of RET targeting strategies considering reprogrammed networks, such as activated HER2, in patients with ET resistant ER+ breast cancer.

Significance: Vandetanib enhances sensitivity to tamoxifen in ER+ breast cancer cells by reprograming kinase signaling networks, which can be used to select patients most likely to respond and develop more efficacious co-treatment strategies.

{"title":"Kinase Plasticity in Response to Vandetanib Enhances Sensitivity to Tamoxifen in Estrogen Receptor Positive Breast Cancer.","authors":"Rasha T Kakati, Austin A Whitman, Santiago Haase, Attila T Szenasi, Christine Hnc Thai, Elizabeth Brunk, Denis O Okumu, Michael P East, Charles M Perou, Gary L Johnson, Philip M Spanheimer","doi":"10.1101/2024.12.19.629395","DOIUrl":"10.1101/2024.12.19.629395","url":null,"abstract":"<p><p>Resistance to endocrine therapy (ET) is common in estrogen receptor (ER) positive breast cancer. Multiple studies have demonstrated that upregulation of MAPK signaling pathways contributes to ET resistance. Herein we show that vandetanib treatment enhances sensitivity to ET in ET-sensitive and -resistant ER+ breast cancer models. Vandetanib treatment alters the gene expression program of ER+ breast cancer cells resulting in a less proliferative and more estrogen responsive Luminal-A like character. Tyrosine kinase network reprogramming was assessed using multiplexed kinase inhibitor beads-mass spectrometry (MIB/MS) assay to identify adaptive resistance mechanisms to vandetanib treatment, including upregulation of HER2 activity. Co-treatment to inhibit HER2 with lapatinib enhanced sensitivity to vandetanib, demonstrating biologic activity of HER2 upregulation. Using a CRISPR knockout model, we demonstrate that vandetanib effects are partially mediated by RET receptor tyrosine kinase. Finally, we use our operating room-to-laboratory assay that measures drug response in individual primary tumor cells in short term cultures to demonstrate conserved gene expression changes, including increased HER2 activity signatures, in vandetanib treated cells, and identify features associated with vandetanib response. These results support future investigation of RET targeting strategies considering reprogrammed networks, such as activated HER2, in patients with ET resistant ER+ breast cancer.</p><p><strong>Significance: </strong>Vandetanib enhances sensitivity to tamoxifen in ER+ breast cancer cells by reprograming kinase signaling networks, which can be used to select patients most likely to respond and develop more efficacious co-treatment strategies.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11838206/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143461716","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Cell states and neighborhoods in distinct clinical stages of primary and metastatic esophageal adenocarcinoma. 原发性和转移性食管腺癌不同临床阶段的细胞状态和邻近区。
Pub Date : 2025-03-03 DOI: 10.1101/2024.08.17.608386
Josephine Yates, Camille Mathey-Andrews, Jihye Park, Amanda Garza, Andréanne Gagné, Samantha Hoffman, Kevin Bi, Breanna Titchen, Connor Hennessey, Joshua Remland, Erin Shannon, Sabrina Camp, Siddhi Balamurali, Shweta Kiran Cavale, Zhixin Li, Akhouri Kishore Raghawan, Agnieszka Kraft, Genevieve Boland, Andrew J Aguirre, Nilay S Sethi, Valentina Boeva, Eliezer Van Allen

Esophageal adenocarcinoma (EAC) is a highly lethal cancer of the upper gastrointestinal tract with rising incidence in western populations. To decipher EAC disease progression and therapeutic response, we performed multiomic analyses of a cohort of primary and metastatic EAC tumors, incorporating single-nuclei transcriptomic and chromatin accessibility sequencing, along with spatial profiling. We identified tumor microenvironmental features previously described to associate with therapy response. We identified five malignant cell programs, including undifferentiated, intermediate, differentiated, epithelial-to-mesenchymal transition, and cycling programs, which were associated with differential epigenetic plasticity and clinical outcomes, and for which we inferred candidate transcription factor regulons. Furthermore, we revealed diverse spatial localizations of malignant cells expressing their associated transcriptional programs and predicted their significant interactions with microenvironmental cell types. We validated our findings in three external single-cell RNA-seq and three bulk RNA-seq studies. Altogether, our findings advance the understanding of EAC heterogeneity, disease progression, and therapeutic response.

食管腺癌(EAC)是一种致死率极高的上消化道癌症,在西方人群中的发病率不断上升。为了解读食管腺癌的疾病进展和治疗反应,我们对一组原发性和转移性食管腺癌肿瘤进行了多组学分析,其中包括单核转录组和染色质可及性测序以及空间谱分析。我们确定了以前描述过的与治疗反应相关的肿瘤微环境特征。我们确定了五种恶性细胞程序,包括未分化程序、中间程序、分化程序、上皮向间质转化程序和循环程序,这些程序与不同的表观遗传可塑性和临床结果有关,我们还推断出了候选转录因子调控子。此外,我们还揭示了表达相关转录程序的恶性细胞的不同空间定位,并预测了它们与微环境细胞类型的重要相互作用。我们在三项外部单细胞RNA-seq研究和三项大体RNA-seq研究中验证了我们的发现。总之,我们的研究结果促进了对 EAC 异质性、疾病进展和治疗反应的理解。
{"title":"Cell states and neighborhoods in distinct clinical stages of primary and metastatic esophageal adenocarcinoma.","authors":"Josephine Yates, Camille Mathey-Andrews, Jihye Park, Amanda Garza, Andréanne Gagné, Samantha Hoffman, Kevin Bi, Breanna Titchen, Connor Hennessey, Joshua Remland, Erin Shannon, Sabrina Camp, Siddhi Balamurali, Shweta Kiran Cavale, Zhixin Li, Akhouri Kishore Raghawan, Agnieszka Kraft, Genevieve Boland, Andrew J Aguirre, Nilay S Sethi, Valentina Boeva, Eliezer Van Allen","doi":"10.1101/2024.08.17.608386","DOIUrl":"10.1101/2024.08.17.608386","url":null,"abstract":"<p><p>Esophageal adenocarcinoma (EAC) is a highly lethal cancer of the upper gastrointestinal tract with rising incidence in western populations. To decipher EAC disease progression and therapeutic response, we performed multiomic analyses of a cohort of primary and metastatic EAC tumors, incorporating single-nuclei transcriptomic and chromatin accessibility sequencing, along with spatial profiling. We identified tumor microenvironmental features previously described to associate with therapy response. We identified five malignant cell programs, including undifferentiated, intermediate, differentiated, epithelial-to-mesenchymal transition, and cycling programs, which were associated with differential epigenetic plasticity and clinical outcomes, and for which we inferred candidate transcription factor regulons. Furthermore, we revealed diverse spatial localizations of malignant cells expressing their associated transcriptional programs and predicted their significant interactions with microenvironmental cell types. We validated our findings in three external single-cell RNA-seq and three bulk RNA-seq studies. Altogether, our findings advance the understanding of EAC heterogeneity, disease progression, and therapeutic response.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11370330/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142127981","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Load-based divergence in the dynamic allostery of two TCRs recognizing the same pMHC. 两种识别相同 pMHC 的 TCR 在动态异构过程中基于负荷的差异。
Pub Date : 2025-03-03 DOI: 10.1101/2024.10.16.618634
Ana C Chang-Gonzalez, Aoi Akitsu, Robert J Mallis, Matthew J Lang, Ellis L Reinherz, Wonmuk Hwang

Increasing evidence suggests that mechanical load on the αβ T cell receptor (TCR) is crucial for recognizing the antigenic peptide-loaded major histocompatibility complex (pMHC) molecule. Our recent all-atom molecular dynamics (MD) simulations revealed that the inter-domain motion of the TCR is responsible for the load-induced catch bond behavior of the TCR-pMHC complex and peptide discrimination. To further examine the generality of the mechanism, we perform all-atom MD simulations of the B7 TCR under different conditions for comparison with our previous simulations of the A6 TCR. The two TCRs recognize the same pMHC and have similar interfaces with pMHC in crystal structures. We find that the B7 TCR-pMHC interface stabilizes under ∼15-pN load using a conserved dynamic allostery mechanism that involves the asymmetric motion of the TCR chassis. However, despite forming comparable contacts with pMHC as A6 in the crystal structure, B7 has fewer high-occupancy contacts with pMHC and exhibits higher mechanical compliance during the simulation. These results indicate that the dynamic allostery common to the TCR αβ chassis can amplify slight differences in interfacial contacts into distinctive mechanical responses and nuanced biological outcomes.

越来越多的证据表明,αβ T 细胞受体(TCR)上的机械负荷对于识别抗原肽负载的主要组织相容性复合体(pMHC)分子至关重要。我们最近进行的全原子分子动力学(MD)模拟发现,TCR的域间运动是TCR-pMHC复合物负载诱导的捕捉键行为和肽识别的原因。为了进一步检验该机制的普遍性,我们在不同条件下对 B7 TCR 进行了全原子 MD 模拟,并与之前对 A6 TCR 的模拟进行了比较。这两种 TCR 识别相同的 pMHC,并且在晶体结构中与 pMHC 有相似的界面。我们发现,B7 TCR-pMHC 界面在 15-pN 负荷下保持稳定,使用的是一种保守的动态异位机制,其中涉及 TCR 底盘的不对称运动。然而,尽管在晶体结构中 B7 与 pMHC 形成了与 A6 类似的接触,但在模拟过程中,B7 与 pMHC 的高占位接触较少。这些结果表明,TCR αβ 底盘常见的动态异位可将界面接触的细微差别放大为独特的机械反应和潜在的细微生物学结果。
{"title":"Load-based divergence in the dynamic allostery of two TCRs recognizing the same pMHC.","authors":"Ana C Chang-Gonzalez, Aoi Akitsu, Robert J Mallis, Matthew J Lang, Ellis L Reinherz, Wonmuk Hwang","doi":"10.1101/2024.10.16.618634","DOIUrl":"10.1101/2024.10.16.618634","url":null,"abstract":"<p><p>Increasing evidence suggests that mechanical load on the <i>αβ</i> T cell receptor (TCR) is crucial for recognizing the antigenic peptide-loaded major histocompatibility complex (pMHC) molecule. Our recent all-atom molecular dynamics (MD) simulations revealed that the inter-domain motion of the TCR is responsible for the load-induced catch bond behavior of the TCR-pMHC complex and peptide discrimination. To further examine the generality of the mechanism, we perform all-atom MD simulations of the B7 TCR under different conditions for comparison with our previous simulations of the A6 TCR. The two TCRs recognize the same pMHC and have similar interfaces with pMHC in crystal structures. We find that the B7 TCR-pMHC interface stabilizes under ∼15-pN load using a conserved dynamic allostery mechanism that involves the asymmetric motion of the TCR chassis. However, despite forming comparable contacts with pMHC as A6 in the crystal structure, B7 has fewer high-occupancy contacts with pMHC and exhibits higher mechanical compliance during the simulation. These results indicate that the dynamic allostery common to the TCR <i>αβ</i> chassis can amplify slight differences in interfacial contacts into distinctive mechanical responses and nuanced biological outcomes.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11507873/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142516071","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Developing ERAF-AI: An Early-Stage Biotechnology Research Assessment Framework Optimized For Artificial Intelligence Integration.
Pub Date : 2025-03-03 DOI: 10.1101/2025.01.08.631843
David Falvo, Lukas Weidener, Martin Karlsson

Today, most research evaluation frameworks are designed to assess mature projects with well-defined data and clearly articulated outcomes. Yet, few, if any, are equipped to evaluate the promise of early-stage biotechnology research, which is inherently characterized by limited evidence, high uncertainty, and evolving objectives. These early-stage projects require nuanced assessments that can adapt to incomplete information, project maturity, and shifting research questions. Furthermore, these challenges are compounded by the difficulty of systematically scaling evaluations with the increasing volume of research projects. As a step toward addressing this gap, we introduce the biotechnology-oriented Early-Stage Research Assessment Framework for Artificial Intelligence (ERAF-AI), a systematic approach to evaluate research at Technology Readiness Levels (TRLs) 1 to 3 - research maturity levels where ideas are more conceptual and only preliminary evidence exists to indicate potential viability. By leveraging AI-driven methodologies and platforms such as the Coordination.Network, ERAF-AI ensures transparent, scalable, and context-sensitive evaluations that integrate research maturity classification, adaptive scoring, and strategic decision-making. Importantly, ERAF-AI aligns criteria with the unique demands of early-stage research, guiding evaluation through the 4P framework (Promote, Pause, Pivot, Perish) to inform next steps. As an initial demonstration of its potential, we apply ERAF-AI to a high-impact early-stage project, providing actionable insights and measurable improvement over conventional practices. Although ERAF-AI shows significant promise in improving the prioritization of early-stage research, further refinement, and validation across a wider range of disciplines and datasets is required to refine its scalability and adaptability. Overall, we expect this framework to serve as a valuable tool for empowering researchers to make informed decisions and to prioritize high-potential initiatives in the face of uncertainty and limited data.

{"title":"Developing ERAF-AI: An Early-Stage Biotechnology Research Assessment Framework Optimized For Artificial Intelligence Integration.","authors":"David Falvo, Lukas Weidener, Martin Karlsson","doi":"10.1101/2025.01.08.631843","DOIUrl":"10.1101/2025.01.08.631843","url":null,"abstract":"<p><p>Today, most research evaluation frameworks are designed to assess mature projects with well-defined data and clearly articulated outcomes. Yet, few, if any, are equipped to evaluate the promise of early-stage biotechnology research, which is inherently characterized by limited evidence, high uncertainty, and evolving objectives. These early-stage projects require nuanced assessments that can adapt to incomplete information, project maturity, and shifting research questions. Furthermore, these challenges are compounded by the difficulty of systematically scaling evaluations with the increasing volume of research projects. As a step toward addressing this gap, we introduce the biotechnology-oriented Early-Stage Research Assessment Framework for Artificial Intelligence (ERAF-AI), a systematic approach to evaluate research at Technology Readiness Levels (TRLs) 1 to 3 - research maturity levels where ideas are more conceptual and only preliminary evidence exists to indicate potential viability. By leveraging AI-driven methodologies and platforms such as the Coordination.Network, ERAF-AI ensures transparent, scalable, and context-sensitive evaluations that integrate research maturity classification, adaptive scoring, and strategic decision-making. Importantly, ERAF-AI aligns criteria with the unique demands of early-stage research, guiding evaluation through the 4P framework (Promote, Pause, Pivot, Perish) to inform next steps. As an initial demonstration of its potential, we apply ERAF-AI to a high-impact early-stage project, providing actionable insights and measurable improvement over conventional practices. Although ERAF-AI shows significant promise in improving the prioritization of early-stage research, further refinement, and validation across a wider range of disciplines and datasets is required to refine its scalability and adaptability. Overall, we expect this framework to serve as a valuable tool for empowering researchers to make informed decisions and to prioritize high-potential initiatives in the face of uncertainty and limited data.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11760726/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143049465","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
CrisprBuildr: an open-source application for CRISPR-mediated genome engineering in Drosophila melanogaster.
Pub Date : 2025-03-02 DOI: 10.1101/2025.02.28.640916
Nicole Horsley, Adam von Barnau Sythoff, Mark Delgado, Selina Liu, Clemens Cabernard

CRISPR/Cas9 is a powerful tool for targeted genome engineering experiments. With CRISPR/Cas9, genes can be deleted or modified by inserting small peptides, fluorescent proteins or other tags for protein labelling experiments. Such experiments are important for detailed protein characterization in vivo . However, designing and cloning the corresponding constructs can be repetitive, time consuming and laborious. To aid users in CRISPR/Cas9-based genome engineering experiments, we built CrisprBuildr, a web-based application that allows users to delete genes or insert fluorescent proteins at the N- or C-terminus of their gene of choice. The application is built on the Drosophila melanogaster genome but can be used as a template for other available genomes. We have also generated new tagging vectors, using EGFP and mCherry combined with the small peptide SspB-Q73R for use in iLID-based optogenetic experiments. CrisprBuildr guides users through the process of designing guide RNAs and repair template vectors. CrisprBuildr is an open-source application and future releases could incorporate additional tagging or deletion vectors, genomes or CRISPR applications.

{"title":"CrisprBuildr: an open-source application for CRISPR-mediated genome engineering in <i>Drosophila melanogaster</i>.","authors":"Nicole Horsley, Adam von Barnau Sythoff, Mark Delgado, Selina Liu, Clemens Cabernard","doi":"10.1101/2025.02.28.640916","DOIUrl":"10.1101/2025.02.28.640916","url":null,"abstract":"<p><p>CRISPR/Cas9 is a powerful tool for targeted genome engineering experiments. With CRISPR/Cas9, genes can be deleted or modified by inserting small peptides, fluorescent proteins or other tags for protein labelling experiments. Such experiments are important for detailed protein characterization <i>in vivo</i> . However, designing and cloning the corresponding constructs can be repetitive, time consuming and laborious. To aid users in CRISPR/Cas9-based genome engineering experiments, we built CrisprBuildr, a web-based application that allows users to delete genes or insert fluorescent proteins at the N- or C-terminus of their gene of choice. The application is built on the <i>Drosophila melanogaster</i> genome but can be used as a template for other available genomes. We have also generated new tagging vectors, using EGFP and mCherry combined with the small peptide SspB-Q73R for use in iLID-based optogenetic experiments. CrisprBuildr guides users through the process of designing guide RNAs and repair template vectors. CrisprBuildr is an open-source application and future releases could incorporate additional tagging or deletion vectors, genomes or CRISPR applications.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11888379/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143589389","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A genome wide CRISPR screen reveals novel determinants of long-lived plasma cell secretory capacity.
Pub Date : 2025-03-02 DOI: 10.1101/2025.02.28.640639
Lucas J D'Souza, Jonathan N Young, Heather Coffman, Edward P Petrow, Deepta Bhattacharya

Plasma cell subsets vary in their lifespans and ability to sustain humoral immunity. We conducted a genome-wide CRISPR-Cas9 screen in a myeloma cell line for factors that promote surface expression of CD98, a marker of longevity in primary mouse plasma cells. A large fraction of genes found to promote CD98 expression in this screen are involved in secretory and other vesicles, including many subunits of the V-type ATPase complex. Chemical inhibition or genetic ablation of V-type ATPases in myeloma cells reduced antibody secretion. Primary mouse and human long-lived plasma cells had greater numbers of acidified vesicles than did their short-lived counterparts, and this correlated with increased secretory capacity of IgM, IgG, and IgA. The screen also identified PI4KB, which promoted acidified vesicle numbers and secretory capacity, and DDX3X, an ATP-dependent RNA helicase, the deletion of which reduced immunoglobulin secretion independently of vesicular acidification. Finally, we report a plasma-cell intrinsic function of the signaling adapter MYD88 in both antibody secretion and plasma cell survival in vivo. These data reveal novel regulators of plasma cell secretory capacity, including those that also promote lifespan.

{"title":"A genome wide CRISPR screen reveals novel determinants of long-lived plasma cell secretory capacity.","authors":"Lucas J D'Souza, Jonathan N Young, Heather Coffman, Edward P Petrow, Deepta Bhattacharya","doi":"10.1101/2025.02.28.640639","DOIUrl":"10.1101/2025.02.28.640639","url":null,"abstract":"<p><p>Plasma cell subsets vary in their lifespans and ability to sustain humoral immunity. We conducted a genome-wide CRISPR-Cas9 screen in a myeloma cell line for factors that promote surface expression of CD98, a marker of longevity in primary mouse plasma cells. A large fraction of genes found to promote CD98 expression in this screen are involved in secretory and other vesicles, including many subunits of the V-type ATPase complex. Chemical inhibition or genetic ablation of V-type ATPases in myeloma cells reduced antibody secretion. Primary mouse and human long-lived plasma cells had greater numbers of acidified vesicles than did their short-lived counterparts, and this correlated with increased secretory capacity of IgM, IgG, and IgA. The screen also identified PI4KB, which promoted acidified vesicle numbers and secretory capacity, and DDX3X, an ATP-dependent RNA helicase, the deletion of which reduced immunoglobulin secretion independently of vesicular acidification. Finally, we report a plasma-cell intrinsic function of the signaling adapter MYD88 in both antibody secretion and plasma cell survival <i>in vivo</i>. These data reveal novel regulators of plasma cell secretory capacity, including those that also promote lifespan.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11888458/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143589281","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
EasyEyes: Crowded Dynamic Fixation for Online Psychophysics.
Pub Date : 2025-03-02 DOI: 10.1101/2025.02.26.640403
Fengping Hu, Joyce Yi Xin Chen, Denis G Pelli, Jonathan Winawer

Online vision testing enables efficient data collection from diverse participants but requires accurate fixation. Fixation accuracy is traditionally ensured by using a camera to track gaze. That works well in the lab, but tracking during online testing with a built-in webcam is not yet sufficiently precise. Kurzawski, Pombo, et al. (2023) introduced a fixation task that improves fixation through hand-eye coordination, requiring participants to track a moving crosshair with a mouse-controlled cursor. This dynamic fixation task greatly reduces peeking at peripheral targets relative to a stationary fixation task, but does not eliminate it. Here, we enhance fixation further by leveraging "crowding," adding clutter around the fixation mark-a method we call crowded dynamic fixation. We assessed fixation accuracy during peripheral threshold measurement. Relative to the RMS gaze error during the stationary fixation task, dynamic fixation error was 61%, while crowded dynamic fixation error was only 47%. With a 1.5° tolerance, peeking occurred on 9% of trials with stationary fixation, 4% with dynamic fixation, and 0% with crowded dynamic fixation. This improvement eliminated implausibly low peripheral thresholds, likely by preventing peeking. We conclude that crowded dynamic fixation enables accurate gaze control for online testing.

{"title":"EasyEyes: Crowded Dynamic Fixation for Online Psychophysics.","authors":"Fengping Hu, Joyce Yi Xin Chen, Denis G Pelli, Jonathan Winawer","doi":"10.1101/2025.02.26.640403","DOIUrl":"10.1101/2025.02.26.640403","url":null,"abstract":"<p><p>Online vision testing enables efficient data collection from diverse participants but requires accurate fixation. Fixation accuracy is traditionally ensured by using a camera to track gaze. That works well in the lab, but tracking during online testing with a built-in webcam is not yet sufficiently precise. Kurzawski, Pombo, et al. (2023) introduced a fixation task that improves fixation through hand-eye coordination, requiring participants to track a moving crosshair with a mouse-controlled cursor. This <i>dynamic fixation</i> task greatly reduces peeking at peripheral targets relative to a stationary fixation task, but does not eliminate it. Here, we enhance fixation further by leveraging \"crowding,\" adding clutter around the fixation mark-a method we call <i>crowded dynamic fixation</i>. We assessed fixation accuracy during peripheral threshold measurement. Relative to the RMS gaze error during the stationary fixation task, dynamic fixation error was 61%, while crowded dynamic fixation error was only 47%. With a 1.5° tolerance, peeking occurred on 9% of trials with stationary fixation, 4% with dynamic fixation, and 0% with crowded dynamic fixation. This improvement eliminated implausibly low peripheral thresholds, likely by preventing peeking. We conclude that crowded dynamic fixation enables accurate gaze control for online testing.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11888485/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143589307","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Enhanced fluorescence lifetime imaging microscopy denoising via principal component analysis.
Pub Date : 2025-03-02 DOI: 10.1101/2025.02.26.640419
Soheil Soltani, Jack G Paulson, Emma J Fong, Shannon M Mumenthaler, Andrea M Armani

Fluorescence Lifetime Imaging Microscopy (FLIM) quantifies the autofluorescence lifetime to measure cellular metabolism, therapeutic efficacy, and disease progression. These dynamic processes are intrinsically heterogeneous, increasing the complexity of the signal analysis. Often noise reduction strategies that combine thresholding and non-selective data smoothing filters are applied. These can result in error introduction and data loss. To mitigate these issues, we develop noise-corrected principal component analysis (NC-PCA). This approach isolates the signal of interest by selectively identifying and removing the noise. To validate NC-PCA, a secondary analysis of FLIM images of patient-derived colorectal cancer organoids exposed to a range of therapeutics was performed. First, we demonstrate that NC-PCA decreases the uncertainty up to 4-fold in comparison to conventional analysis with no data loss. Then, using a merged data set, we show that NC-PCA, unlike conventional methods, identifies multiple metabolic states. Thus, NC-PCA provides an enabling tool to advance FLIM analysis across fields.

{"title":"Enhanced fluorescence lifetime imaging microscopy denoising via principal component analysis.","authors":"Soheil Soltani, Jack G Paulson, Emma J Fong, Shannon M Mumenthaler, Andrea M Armani","doi":"10.1101/2025.02.26.640419","DOIUrl":"10.1101/2025.02.26.640419","url":null,"abstract":"<p><p>Fluorescence Lifetime Imaging Microscopy (FLIM) quantifies the autofluorescence lifetime to measure cellular metabolism, therapeutic efficacy, and disease progression. These dynamic processes are intrinsically heterogeneous, increasing the complexity of the signal analysis. Often noise reduction strategies that combine thresholding and non-selective data smoothing filters are applied. These can result in error introduction and data loss. To mitigate these issues, we develop noise-corrected principal component analysis (NC-PCA). This approach isolates the signal of interest by selectively identifying and removing the noise. To validate NC-PCA, a secondary analysis of FLIM images of patient-derived colorectal cancer organoids exposed to a range of therapeutics was performed. First, we demonstrate that NC-PCA decreases the uncertainty up to 4-fold in comparison to conventional analysis with no data loss. Then, using a merged data set, we show that NC-PCA, unlike conventional methods, identifies multiple metabolic states. Thus, NC-PCA provides an enabling tool to advance FLIM analysis across fields.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11888454/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143589396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Identifying unmeasured heterogeneity in microbiome data via quantile thresholding (QuanT). 通过量子阈值法(QuanT)识别微生物组数据中未测量的异质性。
Pub Date : 2025-03-02 DOI: 10.1101/2024.08.16.608281
Jiuyao Lu, Glen A Satten, Katie A Meyer, Lenore J Launer, Wodan Ling, Ni Zhao

Microbiome data, like other high-throughput data, suffer from technical heterogeneity stemming from differential experimental designs and processing. In addition to measured artifacts such as batch effects, there is heterogeneity due to unknown or unmeasured factors, which lead to spurious conclusions if unaccounted for. With the advent of large-scale multi-center microbiome studies and the increasing availability of public datasets, this issue becomes more pronounced. Current approaches for addressing unmeasured heterogeneity in high-throughput data were developed for microarray and/or RNA sequencing data. They cannot accommodate the unique characteristics of microbiome data such as sparsity and over-dispersion. Here, we introduce Quantile Thresholding (QuanT), a novel non-parametric approach for identifying unmeasured heterogeneity tailored to microbiome data. QuanT applies quantile regression across multiple quantile levels to threshold the microbiome abundance data and uncovers latent heterogeneity using thresholded binary residual matrices. We validated QuanT using both synthetic and real microbiome datasets, demonstrating its superiority in capturing and mitigating heterogeneity and improving the accuracy of downstream analyses, such as prediction analysis, differential abundance tests, and community-level diversity evaluations.

由于处理和实验设计的不同,微生物组数据表现出技术和生物医学的异质性,如果不加以纠正,可能会导致虚假结果。在这里,我们介绍了量化阈值(QuanT)方法,这是一种全面的非参数隐藏变量推断方法,可适应微生物读数计数和相对丰度的复杂分布。我们将 QuanT 应用于合成数据集和真实数据集,并展示了它识别未测量异质性和改进下游分析的能力。
{"title":"Identifying unmeasured heterogeneity in microbiome data via quantile thresholding (QuanT).","authors":"Jiuyao Lu, Glen A Satten, Katie A Meyer, Lenore J Launer, Wodan Ling, Ni Zhao","doi":"10.1101/2024.08.16.608281","DOIUrl":"10.1101/2024.08.16.608281","url":null,"abstract":"<p><p>Microbiome data, like other high-throughput data, suffer from technical heterogeneity stemming from differential experimental designs and processing. In addition to measured artifacts such as batch effects, there is heterogeneity due to unknown or unmeasured factors, which lead to spurious conclusions if unaccounted for. With the advent of large-scale multi-center microbiome studies and the increasing availability of public datasets, this issue becomes more pronounced. Current approaches for addressing unmeasured heterogeneity in high-throughput data were developed for microarray and/or RNA sequencing data. They cannot accommodate the unique characteristics of microbiome data such as sparsity and over-dispersion. Here, we introduce Quantile Thresholding (QuanT), a novel non-parametric approach for identifying unmeasured heterogeneity tailored to microbiome data. QuanT applies quantile regression across multiple quantile levels to threshold the microbiome abundance data and uncovers latent heterogeneity using thresholded binary residual matrices. We validated QuanT using both synthetic and real microbiome datasets, demonstrating its superiority in capturing and mitigating heterogeneity and improving the accuracy of downstream analyses, such as prediction analysis, differential abundance tests, and community-level diversity evaluations.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11370469/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142128057","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Detection of Iron Protein Supercomplexes in Pseudomonas aeruginosa by Native Metalloproteomics.
Pub Date : 2025-03-02 DOI: 10.1101/2025.01.15.633287
Mak A Saito, Matthew R McIlvin

Pseudomonas aeruginosa is a major contributor to human infections and is widely distributed in the environment. Its ability for growth under aerobic and anaerobic conditions provides adaptability to environmental changes and to confront immune responses. We applied high-throughput native 2-dimensional metalloproteomics to P. aeruginosa to examine how use of iron within the metallome responds to oxic and anoxic conditions. Metalloproteomic analyses revealed four major iron peaks, each comprised of metalloproteins with synergistic functions, including: 1) respiratory and metabolic enzymes, 2) oxidative stress response enzymes, 3) DNA synthesis and nitrogen assimilation enzymes, and 4) denitrification enzymes and related copper enzymes. Three ferritins co-eluted with the first and third iron peaks, localizing iron storage with these functions. Several metalloenzymes were more abundant at low oxygen, including alkylhydroperoxide reductase C that deactivates organic radicals produced by denitrification, all three classes of ribonucleotide reductases, ferritin (increasing in ratio relative to bacterioferritin), and denitrification enzymes. Superoxide dismutase and homogentisate 1,2-dioxygenase were more abundant at high oxygen. The co-eluting Fe peaks contained multiple iron metalloproteins of varying size, implying the presence protein supercomplexes with related functionality and co-localized iron storage. This coordination with functionality implies cellular organization at the protein complex level optimized for metal trafficking that contributes to efficient iron use and prioritization, particularly for Pseudomonas with its large genome and flexible metabolism. This study provides insight into prokaryotic metallome dynamics in response to oxygen availability and demonstrates the capabilities of native metalloproteomic methods in understanding metal use and protein-protein interactions in biological systems.

{"title":"Detection of Iron Protein Supercomplexes in <i>Pseudomonas aeruginosa</i> by Native Metalloproteomics.","authors":"Mak A Saito, Matthew R McIlvin","doi":"10.1101/2025.01.15.633287","DOIUrl":"10.1101/2025.01.15.633287","url":null,"abstract":"<p><p><i>Pseudomonas aeruginosa</i> is a major contributor to human infections and is widely distributed in the environment. Its ability for growth under aerobic and anaerobic conditions provides adaptability to environmental changes and to confront immune responses. We applied high-throughput native 2-dimensional metalloproteomics to <i>P. aeruginosa</i> to examine how use of iron within the metallome responds to oxic and anoxic conditions. Metalloproteomic analyses revealed four major iron peaks, each comprised of metalloproteins with synergistic functions, including: 1) respiratory and metabolic enzymes, 2) oxidative stress response enzymes, 3) DNA synthesis and nitrogen assimilation enzymes, and 4) denitrification enzymes and related copper enzymes. Three ferritins co-eluted with the first and third iron peaks, localizing iron storage with these functions. Several metalloenzymes were more abundant at low oxygen, including alkylhydroperoxide reductase C that deactivates organic radicals produced by denitrification, all three classes of ribonucleotide reductases, ferritin (increasing in ratio relative to bacterioferritin), and denitrification enzymes. Superoxide dismutase and homogentisate 1,2-dioxygenase were more abundant at high oxygen. The co-eluting Fe peaks contained multiple iron metalloproteins of varying size, implying the presence protein supercomplexes with related functionality and co-localized iron storage. This coordination with functionality implies cellular organization at the protein complex level optimized for metal trafficking that contributes to efficient iron use and prioritization, particularly for <i>Pseudomonas</i> with its large genome and flexible metabolism. This study provides insight into prokaryotic metallome dynamics in response to oxygen availability and demonstrates the capabilities of native metalloproteomic methods in understanding metal use and protein-protein interactions in biological systems.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11760780/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143049429","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
期刊
bioRxiv : the preprint server for biology
全部 Acc. Chem. Res. ACS Applied Bio Materials ACS Appl. Electron. Mater. ACS Appl. Energy Mater. ACS Appl. Mater. Interfaces ACS Appl. Nano Mater. ACS Appl. Polym. Mater. ACS BIOMATER-SCI ENG ACS Catal. ACS Cent. Sci. ACS Chem. Biol. ACS Chemical Health & Safety ACS Chem. Neurosci. ACS Comb. Sci. ACS Earth Space Chem. ACS Energy Lett. ACS Infect. Dis. ACS Macro Lett. ACS Mater. Lett. ACS Med. Chem. Lett. ACS Nano ACS Omega ACS Photonics ACS Sens. ACS Sustainable Chem. Eng. ACS Synth. Biol. Anal. Chem. BIOCHEMISTRY-US Bioconjugate Chem. BIOMACROMOLECULES Chem. Res. Toxicol. Chem. Rev. Chem. Mater. CRYST GROWTH DES ENERG FUEL Environ. Sci. Technol. Environ. Sci. Technol. Lett. Eur. J. Inorg. Chem. IND ENG CHEM RES Inorg. Chem. J. Agric. Food. Chem. J. Chem. Eng. Data J. Chem. Educ. J. Chem. Inf. Model. J. Chem. Theory Comput. J. Med. Chem. J. Nat. Prod. J PROTEOME RES J. Am. Chem. Soc. LANGMUIR MACROMOLECULES Mol. Pharmaceutics Nano Lett. Org. Lett. ORG PROCESS RES DEV ORGANOMETALLICS J. Org. Chem. J. Phys. Chem. J. Phys. Chem. A J. Phys. Chem. B J. Phys. Chem. C J. Phys. Chem. Lett. Analyst Anal. Methods Biomater. Sci. Catal. Sci. Technol. Chem. Commun. Chem. Soc. Rev. CHEM EDUC RES PRACT CRYSTENGCOMM Dalton Trans. Energy Environ. Sci. ENVIRON SCI-NANO ENVIRON SCI-PROC IMP ENVIRON SCI-WAT RES Faraday Discuss. Food Funct. Green Chem. Inorg. Chem. Front. Integr. Biol. J. Anal. At. Spectrom. J. Mater. Chem. A J. Mater. Chem. B J. Mater. Chem. C Lab Chip Mater. Chem. Front. Mater. Horiz. MEDCHEMCOMM Metallomics Mol. Biosyst. Mol. Syst. Des. Eng. Nanoscale Nanoscale Horiz. Nat. Prod. Rep. New J. Chem. Org. Biomol. Chem. Org. Chem. Front. PHOTOCH PHOTOBIO SCI PCCP Polym. Chem.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1