Pub Date : 2024-09-08DOI: 10.1101/2024.09.04.611290
Pramod Shinde, Lisa Willemsen, Michael Anderson, Minori Aoki, Saonli Basu, Julie G Burel, Peng Cheng, Souradipto Ghosh Dastidar, Aidan Dunleavy, Tal Einav, Jamie Forschmiedt, Slim Fourati, Javier Garcia, William Gibson, Jason A Greenbaum, Leying Guan, Weikang Guan, Jeremy P Gygi, Brendan Ha, Joe Hou, Jason Hsiao, Yunda Huang, Rick Jansen, Bhargob Kakoty, Zhiyu Kang, James J Kobie, Mari Kojima, Anna Konstorum, Jiyeun Lee, Sloan A Lewis, Aixin Li, Eric F Lock, Jarjapu Mahita, Marcus Mendes, Hailong Meng, Aidan Neher, Somayeh Nili, Shelby Orfield, James Overton, Nidhi Pai, Cokie Parker, Brian Qian, Mikkel Rasmussen, Joaquin Reyna, Eve Richardson, Sandra Safo, Josey Sorenson, Aparna Srinivasan, Nicky Thrupp, Rashmi Tippalagama, Raphael Trevizani, Steffen Ventz, Jiuzhou Wang, Cheng-Chang Wu, Ferhat Ay, Barry Grant, Steven H Kleinstein, Bjoern Peters
Systems vaccinology studies have been used to build computational models that predict individual vaccine responses and identify the factors contributing to differences in outcome. Comparing such models is challenging due to variability in study designs. To address this, we established a community resource to compare models predicting B. pertussis booster responses and generate experimental data for the explicit purpose of model evaluation. We here describe our second computational prediction challenge using this resource, where we benchmarked 49 algorithms from 53 scientists. We found that the most successful models stood out in their handling of nonlinearities, reducing large feature sets to representative subsets, and advanced data preprocessing. In contrast, we found that models adopted from literature that were developed to predict vaccine antibody responses in other settings performed poorly, reinforcing the need for purpose-built models. Overall, this demonstrates the value of purpose-generated datasets for rigorous and open model evaluations to identify features that improve the reliability and applicability of computational models in vaccine response prediction.
{"title":"Putting computational models of immunity to the test - an invited challenge to predict B. pertussis vaccination outcomes","authors":"Pramod Shinde, Lisa Willemsen, Michael Anderson, Minori Aoki, Saonli Basu, Julie G Burel, Peng Cheng, Souradipto Ghosh Dastidar, Aidan Dunleavy, Tal Einav, Jamie Forschmiedt, Slim Fourati, Javier Garcia, William Gibson, Jason A Greenbaum, Leying Guan, Weikang Guan, Jeremy P Gygi, Brendan Ha, Joe Hou, Jason Hsiao, Yunda Huang, Rick Jansen, Bhargob Kakoty, Zhiyu Kang, James J Kobie, Mari Kojima, Anna Konstorum, Jiyeun Lee, Sloan A Lewis, Aixin Li, Eric F Lock, Jarjapu Mahita, Marcus Mendes, Hailong Meng, Aidan Neher, Somayeh Nili, Shelby Orfield, James Overton, Nidhi Pai, Cokie Parker, Brian Qian, Mikkel Rasmussen, Joaquin Reyna, Eve Richardson, Sandra Safo, Josey Sorenson, Aparna Srinivasan, Nicky Thrupp, Rashmi Tippalagama, Raphael Trevizani, Steffen Ventz, Jiuzhou Wang, Cheng-Chang Wu, Ferhat Ay, Barry Grant, Steven H Kleinstein, Bjoern Peters","doi":"10.1101/2024.09.04.611290","DOIUrl":"https://doi.org/10.1101/2024.09.04.611290","url":null,"abstract":"Systems vaccinology studies have been used to build computational models that predict individual vaccine responses and identify the factors contributing to differences in outcome. Comparing such models is challenging due to variability in study designs. To address this, we established a community resource to compare models predicting B. pertussis booster responses and generate experimental data for the explicit purpose of model evaluation. We here describe our second computational prediction challenge using this resource, where we benchmarked 49 algorithms from 53 scientists. We found that the most successful models stood out in their handling of nonlinearities, reducing large feature sets to representative subsets, and advanced data preprocessing. In contrast, we found that models adopted from literature that were developed to predict vaccine antibody responses in other settings performed poorly, reinforcing the need for purpose-built models. Overall, this demonstrates the value of purpose-generated datasets for rigorous and open model evaluations to identify features that improve the reliability and applicability of computational models in vaccine response prediction.","PeriodicalId":501182,"journal":{"name":"bioRxiv - Immunology","volume":"26 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142211265","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 : 2024-09-08DOI: 10.1101/2024.09.04.611226
Sean M Thomas, Laurisa M Ankley, Kayla N Conner, Alexander W Rapp, Abigail P McGee, Francois LeSage, Christopher D Tanner, Taryn E Vielma, Eleanor C Scheeres, Joshua J Obar, Andrew J Olive
Alveolar macrophages (AMs) are key mediators of lung function and are potential targets for therapies during respiratory infections. TGFβ is an important regulator of AM differentiation and maintenance, but how TGFβ directly modulates the innate immune responses of AMs remains unclear. This shortcoming prevents effective targeting of AMs to improve lung function in health and disease. Here we leveraged an optimized ex vivo AM model system, fetal-liver derived alveolar-like macrophages (FLAMs), to dissect the role of TGFβ in AMs. Using transcriptional analysis, we first globally defined how TGFβ regulates gene expression of resting FLAMs. We found that TGFβ maintains the baseline metabolic state of AMs by driving lipid metabolism through oxidative phosphorylation and restricting inflammation. To better understand inflammatory regulation in FLAMs, we next directly tested how TGFβ alters the response to TLR2 agonists. While both TGFβ (+) and TGFβ (-) FLAMs robustly responded to TLR2 agonists, we found an unexpected activation of type I interferon (IFN) responses in FLAMs and primary AMs in a TGFβ-dependent manner. Surprisingly, mitochondrial antiviral signaling protein and the interferon regulator factors 3 and 7 were required for IFN production by TLR2 agonists. Together, these data suggest that TGFβ modulates AM metabolic networks and innate immune signaling cascades to control inflammatory pathways in AMs.
{"title":"TGFβ primes alveolar-like macrophages to induce type I IFN following TLR2 activation","authors":"Sean M Thomas, Laurisa M Ankley, Kayla N Conner, Alexander W Rapp, Abigail P McGee, Francois LeSage, Christopher D Tanner, Taryn E Vielma, Eleanor C Scheeres, Joshua J Obar, Andrew J Olive","doi":"10.1101/2024.09.04.611226","DOIUrl":"https://doi.org/10.1101/2024.09.04.611226","url":null,"abstract":"Alveolar macrophages (AMs) are key mediators of lung function and are potential targets for therapies during respiratory infections. TGFβ is an important regulator of AM differentiation and maintenance, but how TGFβ directly modulates the innate immune responses of AMs remains unclear. This shortcoming prevents effective targeting of AMs to improve lung function in health and disease. Here we leveraged an optimized ex vivo AM model system, fetal-liver derived alveolar-like macrophages (FLAMs), to dissect the role of TGFβ in AMs. Using transcriptional analysis, we first globally defined how TGFβ regulates gene expression of resting FLAMs. We found that TGFβ maintains the baseline metabolic state of AMs by driving lipid metabolism through oxidative phosphorylation and restricting inflammation. To better understand inflammatory regulation in FLAMs, we next directly tested how TGFβ alters the response to TLR2 agonists. While both TGFβ (+) and TGFβ (-) FLAMs robustly responded to TLR2 agonists, we found an unexpected activation of type I interferon (IFN) responses in FLAMs and primary AMs in a TGFβ-dependent manner. Surprisingly, mitochondrial antiviral signaling protein and the interferon regulator factors 3 and 7 were required for IFN production by TLR2 agonists. Together, these data suggest that TGFβ modulates AM metabolic networks and innate immune signaling cascades to control inflammatory pathways in AMs.","PeriodicalId":501182,"journal":{"name":"bioRxiv - Immunology","volume":"24 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142211269","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 : 2024-09-08DOI: 10.1101/2024.09.03.611096
Getahun Abate, Krystal A Meza, Chase Colbert, Christopher S Eickhoff
The prevalence of pulmonary nontuberculous mycobacteria (NTM) is increasing in Europe and North America. Most pulmonary NTM are caused by Mycobacterium avium complex (MAC). The treatment of pulmonary MAC is suboptimal with failure rates ranging from 30% to 40% and there is a need to develop new vaccines. In this study, we tested the ability of two whole cell vaccines, DAR-901 (heat killed M. obuense) and BCG (live attenuated M. bovis), to induce MAC cross-reactive immunity by first immunizing BALB/c mice and then performing IFN-gamma ELISPOT assay after overnight stimulation of splenocytes with live MAC. To study the ability of these vaccines to protect against MAC infection, BALB/c mice were vaccinated with DAR-901 (intradermal) or BCG (subcutaneous or intranasal) and challenged with aerosolized MAC 4 weeks later. Some mice vaccinated with BCG were treated with clarithromycin via gavage. Lung CFU in immunized mice and unvaccinated controls were quantified 4 weeks after infection. Our results showed that i) DAR-901 induced cross-reactive immunity to MAC and the level of MAC cross-reactive immunity was similar to the level of immunity induced by BCG, ii) DAR-901 and BCG protect against aerosol MAC, iii) mucosal BCG vaccination provided the best protection against MAC challenge, and iv) BCG vaccination did not interfere with anti-MAC activities of clarithromycin.
在欧洲和北美，肺非结核分枝杆菌（NTM）的发病率正在上升。大多数肺非结核分枝杆菌由复合分枝杆菌（MAC）引起。肺部 MAC 的治疗效果并不理想，失败率在 30% 到 40% 之间，因此需要开发新的疫苗。在本研究中，我们测试了两种全细胞疫苗--DAR-901（热杀M. obuense）和卡介苗（减毒M. bovis活疫苗）--诱导MAC交叉反应免疫的能力，首先免疫BALB/c小鼠，然后用活MAC刺激脾细胞过夜后进行IFN-gamma ELISPOT检测。为了研究这些疫苗对 MAC 感染的保护能力，给 BALB/c 小鼠接种了 DAR-901（皮内）或卡介苗（皮下或鼻内），4 周后用气雾化 MAC 进行挑战。一些接种卡介苗的小鼠通过灌胃接受了克拉霉素治疗。感染 4 周后，对免疫小鼠和未接种对照组的肺部 CFU 进行量化。我们的研究结果表明：i）DAR-901 能诱导 MAC 交叉反应免疫，MAC 交叉反应免疫水平与卡介苗诱导的免疫水平相似；ii）DAR-901 和卡介苗都能抵御气溶胶 MAC；iii）卡介苗粘膜接种能为 MAC 挑战提供最佳保护；iv）卡介苗接种不会干扰克拉霉素的抗 MAC 活性。
{"title":"Immunity against Mycobacterium avium induced by DAR-901 and BCG","authors":"Getahun Abate, Krystal A Meza, Chase Colbert, Christopher S Eickhoff","doi":"10.1101/2024.09.03.611096","DOIUrl":"https://doi.org/10.1101/2024.09.03.611096","url":null,"abstract":"The prevalence of pulmonary nontuberculous mycobacteria (NTM) is increasing in Europe and North America. Most pulmonary NTM are caused by Mycobacterium avium complex (MAC). The treatment of pulmonary MAC is suboptimal with failure rates ranging from 30% to 40% and there is a need to develop new vaccines. In this study, we tested the ability of two whole cell vaccines, DAR-901 (heat killed M. obuense) and BCG (live attenuated M. bovis), to induce MAC cross-reactive immunity by first immunizing BALB/c mice and then performing IFN-gamma ELISPOT assay after overnight stimulation of splenocytes with live MAC. To study the ability of these vaccines to protect against MAC infection, BALB/c mice were vaccinated with DAR-901 (intradermal) or BCG (subcutaneous or intranasal) and challenged with aerosolized MAC 4 weeks later. Some mice vaccinated with BCG were treated with clarithromycin via gavage. Lung CFU in immunized mice and unvaccinated controls were quantified 4 weeks after infection. Our results showed that i) DAR-901 induced cross-reactive immunity to MAC and the level of MAC cross-reactive immunity was similar to the level of immunity induced by BCG, ii) DAR-901 and BCG protect against aerosol MAC, iii) mucosal BCG vaccination provided the best protection against MAC challenge, and iv) BCG vaccination did not interfere with anti-MAC activities of clarithromycin.","PeriodicalId":501182,"journal":{"name":"bioRxiv - Immunology","volume":"18 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142211315","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 : 2024-09-08DOI: 10.1101/2024.09.04.611277
Benjamin L Allsup, Supriya J Gharpure, Bryan D Bryson
Proteomic analyses of the phagosome has significantly improved our understanding of the proteins which contribute to critical phagosome functions such as apoptotic cell clearance and microbial killing. However, previous methods of isolating phagosomes for proteomic analysis have relied on cell fractionation with some intrinsic limitations. Here, we present an alternative and modular proximity-labeling based strategy for mass spectrometry proteomic analysis of the phagosome lumen, termed PhagoID. We optimize proximity labeling in the phagosome and apply PhagoID to immortalized murine macrophages as well as primary human macrophages. Analysis of proteins detected by PhagoID in murine macrophages demonstrate that PhagoID corroborates previous proteomic studies, but also nominates novel proteins with unexpected residence at the phagosome for further study. A direct comparison between the proteins detected by PhagoID between mouse and human macrophages further reveals that human macrophage phagosomes have an increased abundance of proteins involved in the oxidative burst and antigen presentation. Our study develops and benchmarks a new approach to measure the protein composition of the phagosome and validates a subset of these findings, ultimately using PhagoID to grant further insight into the core constituent proteins and species differences at the phagosome lumen.
{"title":"Proximity labeling defines the phagosome lumen proteome of murine and primary human macrophages","authors":"Benjamin L Allsup, Supriya J Gharpure, Bryan D Bryson","doi":"10.1101/2024.09.04.611277","DOIUrl":"https://doi.org/10.1101/2024.09.04.611277","url":null,"abstract":"Proteomic analyses of the phagosome has significantly improved our understanding of the proteins which contribute to critical phagosome functions such as apoptotic cell clearance and microbial killing. However, previous methods of isolating phagosomes for proteomic analysis have relied on cell fractionation with some intrinsic limitations. Here, we present an alternative and modular proximity-labeling based strategy for mass spectrometry proteomic analysis of the phagosome lumen, termed PhagoID. We optimize proximity labeling in the phagosome and apply PhagoID to immortalized murine macrophages as well as primary human macrophages. Analysis of proteins detected by PhagoID in murine macrophages demonstrate that PhagoID corroborates previous proteomic studies, but also nominates novel proteins with unexpected residence at the phagosome for further study. A direct comparison between the proteins detected by PhagoID between mouse and human macrophages further reveals that human macrophage phagosomes have an increased abundance of proteins involved in the oxidative burst and antigen presentation. Our study develops and benchmarks a new approach to measure the protein composition of the phagosome and validates a subset of these findings, ultimately using PhagoID to grant further insight into the core constituent proteins and species differences at the phagosome lumen.","PeriodicalId":501182,"journal":{"name":"bioRxiv - Immunology","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142211267","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}
Innate immune responses can be initiated through the detection of pathogen or damage-associated molecular patterns by host receptors that are often present on the surface of immune cells. While certain invertebrates like Caenorhabditis elegans lack professional immune cells, they still respond to infection in a pathogen-specific manner. It has been debated for years whether homologues of the canonical pathogen recognition receptors are also functioning in the nematode. Here we show that C-type lectin receptors mediate species-specific recognition of divergent oomycetes in C. elegans. A CLEC-27/CLEC-35 pair is essential for recognition of the oomycete Myzocytiopsis humicola, while a CLEC-26/CLEC-36 pair is required for detection of Haptoglossa zoospora. Both clec pairs are transcriptionally regulated through a shared promoter by the conserved PRD-like homeodomain transcription factor CEH-37/OTX2 and act in sensory neurons and the anterior intestine to trigger a protective immune response in the epidermis. This system enables redundant tissue sensing of oomycete threats through canonical CLEC receptors and host defense via cross-tissue communication.
{"title":"Paired C-type lectin receptors mediate specific recognition of divergent oomycete pathogens in C. elegans.","authors":"Kenneth Liu, Manish Grover, Franziska Trusch, Christina Vagena-Pantoula, Domenica Ippolito, Michalis Barkoulas","doi":"10.1101/2024.09.05.611528","DOIUrl":"https://doi.org/10.1101/2024.09.05.611528","url":null,"abstract":"Innate immune responses can be initiated through the detection of pathogen or damage-associated molecular patterns by host receptors that are often present on the surface of immune cells. While certain invertebrates like Caenorhabditis elegans lack professional immune cells, they still respond to infection in a pathogen-specific manner. It has been debated for years whether homologues of the canonical pathogen recognition receptors are also functioning in the nematode. Here we show that C-type lectin receptors mediate species-specific recognition of divergent oomycetes in C. elegans. A CLEC-27/CLEC-35 pair is essential for recognition of the oomycete Myzocytiopsis humicola, while a CLEC-26/CLEC-36 pair is required for detection of Haptoglossa zoospora. Both clec pairs are transcriptionally regulated through a shared promoter by the conserved PRD-like homeodomain transcription factor CEH-37/OTX2 and act in sensory neurons and the anterior intestine to trigger a protective immune response in the epidermis. This system enables redundant tissue sensing of oomycete threats through canonical CLEC receptors and host defense via cross-tissue communication.","PeriodicalId":501182,"journal":{"name":"bioRxiv - Immunology","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142211316","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 : 2024-09-08DOI: 10.1101/2024.09.04.611190
Susan Westfall, Maria E Gentile, Tayla M Olsen, Danielle Karo-Atar, Andrei Bogza, Franziska Roestel, Ryan Pardy, Giordano Mandato, Ghislaine Fontes, DeBroski Herbert, Heather J Melichar, Valerie Abadie, Martin Richer, Donald C Vinh, Joshua FE Koenig, Oliver J Harrison, Maziar J Divangahi, Sebastian Weis, Alex Gregorieff, Irah L King
Type 1 immunity mediates host defense through pathogen elimination, but whether this pathway also impacts tissue function is unknown. Here we demonstrate that rapid induction of IFNg signaling coordinates a multi-cellular response that is critical to limit tissue damage and maintain gut motility following infection of mice with a tissue-invasive helminth. IFNg production is initiated by antigen-independent activation of lamina propria CD8+ T cells following MyD88-dependent recognition of the microbiota during helminth-induced barrier invasion. IFNg acted directly on intestinal stromal cells to recruit neutrophils that limited parasite-induced tissue injury. IFNg sensing also limited the expansion of smooth muscle actin-expressing cells to prevent pathological gut dysmotility. Importantly, this tissue-protective response had limited impact on parasite burden, indicating that IFNg supports a disease tolerance defense strategy. Our results have important implications for managing the pathophysiological sequelae of post-infectious gut dysfunction and chronic inflammatory diseases associated with stromal remodelling.
{"title":"A type 1 immune-stromal cell network mediates disease tolerance and barrier protection against intestinal infection","authors":"Susan Westfall, Maria E Gentile, Tayla M Olsen, Danielle Karo-Atar, Andrei Bogza, Franziska Roestel, Ryan Pardy, Giordano Mandato, Ghislaine Fontes, DeBroski Herbert, Heather J Melichar, Valerie Abadie, Martin Richer, Donald C Vinh, Joshua FE Koenig, Oliver J Harrison, Maziar J Divangahi, Sebastian Weis, Alex Gregorieff, Irah L King","doi":"10.1101/2024.09.04.611190","DOIUrl":"https://doi.org/10.1101/2024.09.04.611190","url":null,"abstract":"Type 1 immunity mediates host defense through pathogen elimination, but whether this pathway also impacts tissue function is unknown. Here we demonstrate that rapid induction of IFNg signaling coordinates a multi-cellular response that is critical to limit tissue damage and maintain gut motility following infection of mice with a tissue-invasive helminth. IFNg production is initiated by antigen-independent activation of lamina propria CD8+ T cells following MyD88-dependent recognition of the microbiota during helminth-induced barrier invasion. IFNg acted directly on intestinal stromal cells to recruit neutrophils that limited parasite-induced tissue injury. IFNg sensing also limited the expansion of smooth muscle actin-expressing cells to prevent pathological gut dysmotility. Importantly, this tissue-protective response had limited impact on parasite burden, indicating that IFNg supports a disease tolerance defense strategy. Our results have important implications for managing the pathophysiological sequelae of post-infectious gut dysfunction and chronic inflammatory diseases associated with stromal remodelling.","PeriodicalId":501182,"journal":{"name":"bioRxiv - Immunology","volume":"20 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142211268","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 : 2024-09-08DOI: 10.1101/2024.09.04.611263
James T Gordy, Jean J Zheng, Amanda R Maxwell, Alannah D Taylor, Styliani Karanika, Rowan E Bates, Heemee Ton, Jacob Meza, Yangchen Li, Jiaqi Zhang, Petros C Karakousis, Richard B Markham
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), is the leading cause of mortality due to a single infectious organism. While generally curable, TB requires a lengthy and complex antibiotic regimen, due in large part to bacteria that can shift to a persistent state in the presence of antibiotic pressure. RelMtb is the primary enzyme regulating the stringent response, which contributes to the metabolic shift of Mtb to a persistent state. Targeting RelMtb with a vaccine to eliminate persistent bacteria through the induction of RelMtb-specific T-cell immunity in combination with antibiotics to kill dividing bacteria has shown promise in model systems. In a mouse model of Mtb infection, a vaccine created by genetically fusing relMtb to the chemokine macrophage inflammatory protein 3α (MIP3α), a ligand for the CC chemokine receptor type 6 (CCR6) present on immature dendritic cells, has been shown to enhance T-cell responses and accelerate eradication of infection in mouse models compared to a vaccine lacking the chemokine component. In this study, immunogenicity studies in the mouse and rhesus macaque models provide evidence that intranasal administrations of the DNA form of the MipRel vaccine led to enhanced lung infiltration of T cells after a series of immunizations. Furthermore, despite similar T-cell immunity seen in PBMCs between MipRel and Rel vaccinations, lung and bronchoalveolar lavage cell samples are more enriched for cytokine-secreting T cells in MipRel groups compared to Rel groups. We conclude that intranasal immunization with a MIP-3α fusion vaccine represents a novel strategy for use of a simple DNA vaccine formulation to elicit T-cell immune responses within the respiratory tract. That this formulation is immunogenic in a non-human primate model historically viewed as poorly responsive to DNA vaccines indicates the potential for clinical application in the treatment of Mtb infection, with possible application to other respiratory pathogens. Future studies will further characterize the protective effect of this vaccination platform.
结核分枝杆菌（Mtb）是肺结核（TB）的致病菌，也是单一传染性有机体导致死亡的主要原因。虽然结核病一般可以治愈，但需要长期和复杂的抗生素治疗，这在很大程度上是由于细菌在抗生素的压力下会转变为持久状态。RelMtb是调节严格反应的主要酶，它有助于Mtb的代谢转变为持久状态。在模型系统中，通过诱导 RelMtb 特异性 T 细胞免疫，并结合使用抗生素杀死分裂中的细菌，以 RelMtb 为靶标的疫苗有望消灭持续存在的细菌。在Mtb感染的小鼠模型中，通过将relMtb与趋化因子巨噬细胞炎症蛋白3α（MIP3α）（一种存在于未成熟树突状细胞上的CC趋化因子受体6型（CCR6）的配体）进行基因融合而制成的疫苗，与缺乏趋化因子成分的疫苗相比，能增强T细胞反应并加速小鼠模型中感染的根除。在这项研究中，对小鼠和猕猴模型进行的免疫原性研究证明，鼻内注射 DNA 形式的 MipRel 疫苗可在一系列免疫接种后增强肺部 T 细胞浸润。此外，尽管在接种 MipRel 和 Rel 疫苗的 PBMCs 中看到了相似的 T 细胞免疫，但与 Rel 组相比，MipRel 组的肺和支气管肺泡灌洗液细胞样本更富含分泌细胞因子的 T 细胞。我们的结论是，MIP-3α融合疫苗的鼻内免疫是使用简单的DNA疫苗制剂引起呼吸道T细胞免疫反应的一种新策略。这种制剂在历来被认为对 DNA 疫苗反应较差的非人灵长类动物模型中具有免疫原性，这表明它在治疗 Mtb 感染方面具有临床应用潜力，并有可能应用于其他呼吸道病原体。未来的研究将进一步确定这种疫苗接种平台的保护效果。
{"title":"MIP3α-RelMtb intranasal DNA vaccination induces reactive T-cell infiltration into the lungs in mice and macaques","authors":"James T Gordy, Jean J Zheng, Amanda R Maxwell, Alannah D Taylor, Styliani Karanika, Rowan E Bates, Heemee Ton, Jacob Meza, Yangchen Li, Jiaqi Zhang, Petros C Karakousis, Richard B Markham","doi":"10.1101/2024.09.04.611263","DOIUrl":"https://doi.org/10.1101/2024.09.04.611263","url":null,"abstract":"Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), is the leading cause of mortality due to a single infectious organism. While generally curable, TB requires a lengthy and complex antibiotic regimen, due in large part to bacteria that can shift to a persistent state in the presence of antibiotic pressure. RelMtb is the primary enzyme regulating the stringent response, which contributes to the metabolic shift of Mtb to a persistent state. Targeting RelMtb with a vaccine to eliminate persistent bacteria through the induction of RelMtb-specific T-cell immunity in combination with antibiotics to kill dividing bacteria has shown promise in model systems. In a mouse model of Mtb infection, a vaccine created by genetically fusing relMtb to the chemokine macrophage inflammatory protein 3α (MIP3α), a ligand for the CC chemokine receptor type 6 (CCR6) present on immature dendritic cells, has been shown to enhance T-cell responses and accelerate eradication of infection in mouse models compared to a vaccine lacking the chemokine component. In this study, immunogenicity studies in the mouse and rhesus macaque models provide evidence that intranasal administrations of the DNA form of the MipRel vaccine led to enhanced lung infiltration of T cells after a series of immunizations. Furthermore, despite similar T-cell immunity seen in PBMCs between MipRel and Rel vaccinations, lung and bronchoalveolar lavage cell samples are more enriched for cytokine-secreting T cells in MipRel groups compared to Rel groups. We conclude that intranasal immunization with a MIP-3α fusion vaccine represents a novel strategy for use of a simple DNA vaccine formulation to elicit T-cell immune responses within the respiratory tract. That this formulation is immunogenic in a non-human primate model historically viewed as poorly responsive to DNA vaccines indicates the potential for clinical application in the treatment of Mtb infection, with possible application to other respiratory pathogens. Future studies will further characterize the protective effect of this vaccination platform.","PeriodicalId":501182,"journal":{"name":"bioRxiv - Immunology","volume":"4 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142211317","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 : 2024-09-07DOI: 10.1101/2024.09.05.611513
Khyati Girdhar, Keiichiro Mine, Jeffrey M DaCosta, Mark A Atkinson, Johnny Ludvigsson, Emrah Altindis
While studies have reported altered levels of cytokines in type 1 diabetes (T1D) patients, the results are inconsistent, likely because of variable factors. This study tests the hypothesis that there are sex-based differences in cytokine levels in T1D, prior to and after disease onset. We analyzed 48 blood cytokine, chemokine, and growth factor levels using a multiplex assay. We found only two cytokines, M-CSF and IL-6, with significant differences between T1D patients (n=25) versus controls overall (n=25). However, we identified notable alterations when comparing sex-age-matched controls and T1D samples. Inflammatory cytokines (TNF-α, IL-6, IL-1a), Th2 cytokines (IL-4, IL-13), and chemokines (MIP-1α, RANTES, MIP-3) were lower in female T1D patients compared to female controls, but not in males. IL-22 was lower in female T1D patients compared to female controls, while it was higher in male T1D patients compared to male controls. In contrast, growth factors (EGF, PDGF-AB/BB) were higher in male T1D patients compared to male controls. In T1D progressors (children who developed the disease years after the sample collection, n=16-21), GROa was lower compared to controls in both sexes. Our findings underscore the importance of understanding sex-specific differences in T1D pathogenesis and their implications for developing personalized treatments.
{"title":"Sex-Specific Cytokine, Chemokine, and Growth Factor Signatures in T1D Patients and Progressors","authors":"Khyati Girdhar, Keiichiro Mine, Jeffrey M DaCosta, Mark A Atkinson, Johnny Ludvigsson, Emrah Altindis","doi":"10.1101/2024.09.05.611513","DOIUrl":"https://doi.org/10.1101/2024.09.05.611513","url":null,"abstract":"While studies have reported altered levels of cytokines in type 1 diabetes (T1D) patients, the results are inconsistent, likely because of variable factors. This study tests the hypothesis that there are sex-based differences in cytokine levels in T1D, prior to and after disease onset. We analyzed 48 blood cytokine, chemokine, and growth factor levels using a multiplex assay. We found only two cytokines, M-CSF and IL-6, with significant differences between T1D patients (n=25) versus controls overall (n=25). However, we identified notable alterations when comparing sex-age-matched controls and T1D samples. Inflammatory cytokines (TNF-α, IL-6, IL-1a), Th2 cytokines (IL-4, IL-13), and chemokines (MIP-1α, RANTES, MIP-3) were lower in female T1D patients compared to female controls, but not in males. IL-22 was lower in female T1D patients compared to female controls, while it was higher in male T1D patients compared to male controls. In contrast, growth factors (EGF, PDGF-AB/BB) were higher in male T1D patients compared to male controls. In T1D progressors (children who developed the disease years after the sample collection, n=16-21), GROa was lower compared to controls in both sexes. Our findings underscore the importance of understanding sex-specific differences in T1D pathogenesis and their implications for developing personalized treatments.","PeriodicalId":501182,"journal":{"name":"bioRxiv - Immunology","volume":"264 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142211324","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 : 2024-09-07DOI: 10.1101/2024.09.03.611042
Jacob Bridge, Matthew J Johnson, Jihyun Kim, Sophia Wenthe, Joshua Krueger, Bryce Wick, Mitchell Kluesner, Andrew T Crane, Jason Bell, Joseph G Skeate, Branden S Moriarity, Beau R Webber
Gamma delta (γδ) T cells are defined by their unique ability to recognize a limited repertoire of non-peptide, non-MHC-associated antigens on transformed and pathogen-infected cells. In addition to their lack of alloreactivity, γδ T cells exhibit properties distinct from other lymphocyte subsets, prompting significant interest in their development as an off-the-shelf cellular immunotherapeutic. However, their low abundance in circulation, heterogeneity, limited methods for ex vivo expansion, and under-developed methodologies for genetic modification have hindered basic study and clinical application of γδ T cells. Here, we implement a feeder-free, scalable approach for ex vivo manufacture of polyclonal, non-virally modified, gene edited chimeric antigen receptor (CAR)-γδ T cells in support of therapeutic application. Engineered CAR-γδ T cells demonstrate high function in vitro and and in vivo. Longitudinal in vivo pharmacokinetic profiling of adoptively transferred polyclonal CAR-γδ T cells uncover subset-specific responses to IL-15 cytokine armoring and multiplex base editing. Our results present a robust platform for genetic modification of polyclonal CAR-γδ T cells and present unique opportunities to further define synergy and the contribution of discrete, engineered CAR-γδ T cell subsets to therapeutic efficacy in vivo.
γδ（γδ）T 细胞具有独特的能力，能识别转化细胞和病原体感染细胞上有限的非肽、非 MHC 相关抗原。除了缺乏异源活性外，γδ T 细胞还表现出不同于其他淋巴细胞亚群的特性，这促使人们对将其开发为现成的细胞免疫疗法产生了浓厚的兴趣。然而，γδ T 细胞在血液循环中的丰度低、异质性强、体外扩增方法有限以及基因修饰方法不完善等因素阻碍了γδ T 细胞的基础研究和临床应用。在这里，我们采用了一种无喂养器、可扩展的方法，在体外制造多克隆、非病毒修饰、基因编辑的嵌合抗原受体（CAR）-γδ T 细胞，以支持治疗应用。改造的 CAR-γδ T 细胞在体外和体内都表现出很高的功能。多克隆CAR-γδ T细胞的纵向体内药代动力学分析发现了亚群对IL-15细胞因子铠装和多重碱基编辑的特异性反应。我们的研究结果为多克隆 CAR-γδ T 细胞的基因修饰提供了一个强大的平台，并为进一步确定协同作用以及离散、工程化 CAR-γδ T 细胞亚群对体内疗效的贡献提供了独特的机会。
{"title":"Efficient multiplex non-viral engineering and expansion of polyclonal γδ CAR-T cells for immunotherapy","authors":"Jacob Bridge, Matthew J Johnson, Jihyun Kim, Sophia Wenthe, Joshua Krueger, Bryce Wick, Mitchell Kluesner, Andrew T Crane, Jason Bell, Joseph G Skeate, Branden S Moriarity, Beau R Webber","doi":"10.1101/2024.09.03.611042","DOIUrl":"https://doi.org/10.1101/2024.09.03.611042","url":null,"abstract":"Gamma delta (γδ) T cells are defined by their unique ability to recognize a limited repertoire of non-peptide, non-MHC-associated antigens on transformed and pathogen-infected cells. In addition to their lack of alloreactivity, γδ T cells exhibit properties distinct from other lymphocyte subsets, prompting significant interest in their development as an off-the-shelf cellular immunotherapeutic. However, their low abundance in circulation, heterogeneity, limited methods for ex vivo expansion, and under-developed methodologies for genetic modification have hindered basic study and clinical application of γδ T cells. Here, we implement a feeder-free, scalable approach for ex vivo manufacture of polyclonal, non-virally modified, gene edited chimeric antigen receptor (CAR)-γδ T cells in support of therapeutic application. Engineered CAR-γδ T cells demonstrate high function in vitro and and in vivo. Longitudinal in vivo pharmacokinetic profiling of adoptively transferred polyclonal CAR-γδ T cells uncover subset-specific responses to IL-15 cytokine armoring and multiplex base editing. Our results present a robust platform for genetic modification of polyclonal CAR-γδ T cells and present unique opportunities to further define synergy and the contribution of discrete, engineered CAR-γδ T cell subsets to therapeutic efficacy in vivo.","PeriodicalId":501182,"journal":{"name":"bioRxiv - Immunology","volume":"75 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142211325","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 : 2024-09-07DOI: 10.1101/2024.09.03.611055
Styliani Karanika, Tianyin Wang, Addis Yilma, Jennie Ruelas Castillo, James T. Gordy, Hannah Bailey, Darla Quijada, Kaitlyn Fessler, Rokeya Tasneen, Elisa M. Rouse Salcido, Harley Harris, Rowan E. Bates, Heeme Ton, Jacob Meza, Yangchen Li, Alannah D. Taylor, Jean J. Zhenq, Jiaqi Zhang, J David Peske, Theodoros Karantanos, Amanda R. Maxwell, Eric Nuermberger, Richard B. Markham, Petros C. Karakousis
Mycobacterium tuberculosis (Mtb) is one of the leading infectious causes of death worldwide. There is no available licensed therapeutic vaccine that shortens active tuberculosis (TB) disease drug treatment and prevents relapse, despite the World Health Organization's calls. Here, we show that an intranasal DNA vaccine containing a fusion of the stringent response relMtb gene with the gene encoding the immature dendritic cell-targeting chemokine, MIP-3α/CCL20, shortens the duration of curative TB treatment in immunocompetent mice. Compared to the first-line regimen for drug-susceptible TB alone, our novel adjunctive vaccine induced greater RelMtb-specific T-cell responses associated with optimal TB control in spleen, blood, lungs, mediastinal lymph nodes, and bronchoalveolar lavage (BAL) fluid. These responses were sustained, if not augmented, over time. It also triggered more effective dendritic cell recruitment, activation, and colocalization with T cells, implying enhanced crosstalk between innate and adaptive immunity. Moreover, it potentiated a 6-month TB drug-resistant regimen, rendering it effective across treatment regimens, and also showed promising results in CD4+ knockout mice, perhaps due to enhanced Rel-specific CD8+ T-cell responses. Notably, our novel fusion vaccine was also immunogenic in nonhuman primates, the gold standard animal model for TB vaccine studies, eliciting antigen-specific T-cell responses in blood and BAL fluid analogous to those observed in protected mice. Our findings have critical implications for therapeutic TB vaccine clinical development in immunocompetent and immunocompromised populations and may serve as a model for defining immunological correlates of therapeutic vaccine-induced protection.
结核分枝杆菌（Mtb）是导致全球死亡的主要传染病因之一。尽管世界卫生组织发出了呼吁，但目前尚无可缩短活动性结核病（TB）药物治疗和预防复发的特许治疗疫苗。在这里，我们展示了一种含有严格反应 relMtb 基因与编码未成熟树突状细胞靶向趋化因子 MIP-3α/CCL20 基因融合的鼻内 DNA 疫苗，它能缩短免疫功能正常小鼠的结核病治愈治疗时间。与单用药物治疗易感肺结核的一线方案相比，我们的新型辅助疫苗能诱导更多的 RelMtb 特异性 T 细胞应答，从而在脾脏、血液、肺部、纵隔淋巴结和支气管肺泡灌洗液（BAL）中达到最佳肺结核控制效果。这些反应即使没有增强，也会随着时间的推移而持续。它还能更有效地引发树突状细胞的招募、活化以及与 T 细胞的共定位，这意味着先天性免疫和适应性免疫之间的串联得到了增强。此外，它还增强了为期 6 个月的结核病耐药治疗方案，使其在各种治疗方案中都有效，而且在 CD4+ 基因敲除小鼠中也显示出良好的效果，这可能是由于 Rel 特异性 CD8+ T 细胞反应增强的缘故。值得注意的是，我们的新型融合疫苗在非人灵长类动物（结核病疫苗研究的黄金标准动物模型）中也具有免疫原性，在血液和 BAL 液中引起的抗原特异性 T 细胞反应与在受保护小鼠中观察到的反应类似。我们的研究结果对免疫功能健全和免疫功能低下人群的治疗性结核病疫苗临床开发具有重要意义，并可作为确定治疗性疫苗诱导保护的免疫学相关因素的模型。
{"title":"Therapeutic DNA Vaccine Targeting Mycobacterium tuberculosis Persisters Shortens Curative Tuberculosis Treatment","authors":"Styliani Karanika, Tianyin Wang, Addis Yilma, Jennie Ruelas Castillo, James T. Gordy, Hannah Bailey, Darla Quijada, Kaitlyn Fessler, Rokeya Tasneen, Elisa M. Rouse Salcido, Harley Harris, Rowan E. Bates, Heeme Ton, Jacob Meza, Yangchen Li, Alannah D. Taylor, Jean J. Zhenq, Jiaqi Zhang, J David Peske, Theodoros Karantanos, Amanda R. Maxwell, Eric Nuermberger, Richard B. Markham, Petros C. Karakousis","doi":"10.1101/2024.09.03.611055","DOIUrl":"https://doi.org/10.1101/2024.09.03.611055","url":null,"abstract":"Mycobacterium tuberculosis (Mtb) is one of the leading infectious causes of death worldwide. There is no available licensed therapeutic vaccine that shortens active tuberculosis (TB) disease drug treatment and prevents relapse, despite the World Health Organization's calls. Here, we show that an intranasal DNA vaccine containing a fusion of the stringent response relMtb gene with the gene encoding the immature dendritic cell-targeting chemokine, MIP-3α/CCL20, shortens the duration of curative TB treatment in immunocompetent mice. Compared to the first-line regimen for drug-susceptible TB alone, our novel adjunctive vaccine induced greater RelMtb-specific T-cell responses associated with optimal TB control in spleen, blood, lungs, mediastinal lymph nodes, and bronchoalveolar lavage (BAL) fluid. These responses were sustained, if not augmented, over time. It also triggered more effective dendritic cell recruitment, activation, and colocalization with T cells, implying enhanced crosstalk between innate and adaptive immunity. Moreover, it potentiated a 6-month TB drug-resistant regimen, rendering it effective across treatment regimens, and also showed promising results in CD4+ knockout mice, perhaps due to enhanced Rel-specific CD8+ T-cell responses. Notably, our novel fusion vaccine was also immunogenic in nonhuman primates, the gold standard animal model for TB vaccine studies, eliciting antigen-specific T-cell responses in blood and BAL fluid analogous to those observed in protected mice. Our findings have critical implications for therapeutic TB vaccine clinical development in immunocompetent and immunocompromised populations and may serve as a model for defining immunological correlates of therapeutic vaccine-induced protection.","PeriodicalId":501182,"journal":{"name":"bioRxiv - Immunology","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142211319","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}
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