Pub Date : 2024-09-16DOI: 10.1101/2024.09.12.612587
Brandon H. Schlomann, Ting-Wei Pai, Jazmin Sandhu, Genesis Ferrer Imbert, Thomas G.W. Graham, Hernan G Garcia
Immune responses in tissues display intricate patterns of gene expression that vary across space and time. While such patterns have been increasingly linked to disease outcomes, the mechanisms that generate them and the logic behind them remain poorly understood. As a tractable model of spatial immune responses, we investigated heterogeneous expression of antimicrobial peptides in the larval fly fat body, an organ functionally analogous to the liver. To capture the dynamics of immune response across the full tissue at single-cell resolution, we established live light sheet fluorescence microscopy of whole larvae. We discovered that expression of antimicrobial peptides occurs in a reproducible spatial pattern, with enhanced expression in the anterior and posterior lobes of the fat body. This pattern correlates with microbial localization via blood flow but is not caused by it: loss of heartbeat suppresses microbial transport but leaves the expression pattern unchanged. This result suggests that regions of the tissue most likely to encounter microbes via blood flow are primed to produce antimicrobials. Spatial transcriptomics revealed that these immune microenvironments are defined by genes spanning multiple biological processes, including lipid-binding proteins that regulate host cell death by the immune system. In sum, the larval fly fat body exhibits spatial compartmentalization of immune activity that resembles the strategic positioning of immune cells in mammals, such as in the liver, gut, and lymph nodes. This finding suggests that tissues may share a conserved spatial organization that optimizes immune responses for antimicrobial efficacy while preventing excessive self-damage.
{"title":"Spatial microenvironments tune immune response dynamics in the Drosophila larval fat body","authors":"Brandon H. Schlomann, Ting-Wei Pai, Jazmin Sandhu, Genesis Ferrer Imbert, Thomas G.W. Graham, Hernan G Garcia","doi":"10.1101/2024.09.12.612587","DOIUrl":"https://doi.org/10.1101/2024.09.12.612587","url":null,"abstract":"Immune responses in tissues display intricate patterns of gene expression that vary across space and time. While such patterns have been increasingly linked to disease outcomes, the mechanisms that generate them and the logic behind them remain poorly understood. As a tractable model of spatial immune responses, we investigated heterogeneous expression of antimicrobial peptides in the larval fly fat body, an organ functionally analogous to the liver. To capture the dynamics of immune response across the full tissue at single-cell resolution, we established live light sheet fluorescence microscopy of whole larvae. We discovered that expression of antimicrobial peptides occurs in a reproducible spatial pattern, with enhanced expression in the anterior and posterior lobes of the fat body. This pattern correlates with microbial localization via blood flow but is not caused by it: loss of heartbeat suppresses microbial transport but leaves the expression pattern unchanged. This result suggests that regions of the tissue most likely to encounter microbes via blood flow are primed to produce antimicrobials. Spatial transcriptomics revealed that these immune microenvironments are defined by genes spanning multiple biological processes, including lipid-binding proteins that regulate host cell death by the immune system. In sum, the larval fly fat body exhibits spatial compartmentalization of immune activity that resembles the strategic positioning of immune cells in mammals, such as in the liver, gut, and lymph nodes. This finding suggests that tissues may share a conserved spatial organization that optimizes immune responses for antimicrobial efficacy while preventing excessive self-damage.","PeriodicalId":501182,"journal":{"name":"bioRxiv - Immunology","volume":"26 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142268770","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 : 2024-09-16DOI: 10.1101/2024.09.13.613000
Tin Phan, Ruy Ribeiro, Gregory E Edelstein, Julie Boucau, Rockib Uddin, Caitlin Marino, May Y Liew, Mamadou Barry, Manish C Choudhary, Dessie Tien, Karry Su, Zahra Reynolds, Yijia Li, Shruti Sagar, Tammy D Vyas, Yumeko Kawano, Jeffrey A Sparks, Sarah P Hammond, Zachary Wallace, Jatin M Vyas, Jonathan Z. Li, Mark J Siedner, Amy K. Barczak, Jacob E Lemieux, Alan S. Perelson
In a subset of SARS-CoV-2 infected individuals treated with the oral antiviral nirmatrelvir-ritonavir, the virus rebounds following treatment. The mechanisms driving this rebound are not well understood. We used a mathematical model to describe the longitudinal viral load dynamics of 51 individuals treated with nirmatrelvir-ritonavir, 20 of whom rebounded. Target cell preservation, either by a robust innate immune response or initiation of nirmatrelvir-ritonavir near the time of symptom onset, coupled with incomplete viral clearance, appear to be the main factors leading to viral rebound. Moreover, the occurrence of viral rebound is likely influenced by time of treatment initiation relative to the progression of the infection, with earlier treatments leading to a higher chance of rebound. Finally, our model demonstrates that extending the course of nirmatrelvir-ritonavir treatment, in particular to a 10-day regimen, may greatly diminish the risk for rebound in people with mild-to-moderate COVID-19 and who are at high risk of progression to severe disease. Altogether, our results suggest that in some individuals, a standard 5-day course of nirmatrelvir-ritonavir starting around the time of symptom onset may not completely eliminate the virus. Thus, after treatment ends, the virus can rebound if an effective adaptive immune response has not fully developed. These findings on the role of target cell preservation and incomplete viral clearance also offer a possible explanation for viral rebounds following other antiviral treatments for SARS-CoV-2.
{"title":"Modeling suggests SARS-CoV-2 rebound after nirmatrelvir-ritonavir treatment is driven by target cell preservation coupled with incomplete viral clearance","authors":"Tin Phan, Ruy Ribeiro, Gregory E Edelstein, Julie Boucau, Rockib Uddin, Caitlin Marino, May Y Liew, Mamadou Barry, Manish C Choudhary, Dessie Tien, Karry Su, Zahra Reynolds, Yijia Li, Shruti Sagar, Tammy D Vyas, Yumeko Kawano, Jeffrey A Sparks, Sarah P Hammond, Zachary Wallace, Jatin M Vyas, Jonathan Z. Li, Mark J Siedner, Amy K. Barczak, Jacob E Lemieux, Alan S. Perelson","doi":"10.1101/2024.09.13.613000","DOIUrl":"https://doi.org/10.1101/2024.09.13.613000","url":null,"abstract":"In a subset of SARS-CoV-2 infected individuals treated with the oral antiviral nirmatrelvir-ritonavir, the virus rebounds following treatment. The mechanisms driving this rebound are not well understood. We used a mathematical model to describe the longitudinal viral load dynamics of 51 individuals treated with nirmatrelvir-ritonavir, 20 of whom rebounded. Target cell preservation, either by a robust innate immune response or initiation of nirmatrelvir-ritonavir near the time of symptom onset, coupled with incomplete viral clearance, appear to be the main factors leading to viral rebound. Moreover, the occurrence of viral rebound is likely influenced by time of treatment initiation relative to the progression of the infection, with earlier treatments leading to a higher chance of rebound. Finally, our model demonstrates that extending the course of nirmatrelvir-ritonavir treatment, in particular to a 10-day regimen, may greatly diminish the risk for rebound in people with mild-to-moderate COVID-19 and who are at high risk of progression to severe disease. Altogether, our results suggest that in some individuals, a standard 5-day course of nirmatrelvir-ritonavir starting around the time of symptom onset may not completely eliminate the virus. Thus, after treatment ends, the virus can rebound if an effective adaptive immune response has not fully developed. These findings on the role of target cell preservation and incomplete viral clearance also offer a possible explanation for viral rebounds following other antiviral treatments for SARS-CoV-2.","PeriodicalId":501182,"journal":{"name":"bioRxiv - Immunology","volume":"39 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142252117","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 : 2024-09-16DOI: 10.1101/2024.09.13.612733
Chloe Pasin, Peter Rusert, Daniel Schmidt, Merle Schanz, Nikolas Friedrich, Irene A. Abela, Katharina Kusejko, Cyrille Niklaus, Michèle Sickmann, Jacqueline Weber, Michael Huber, Amapola Manrique, Andri Rauch, Alexandra Calmy, Matthias Cavassini, Marcel Stöckle, Julia Notter, Enos Bernasconi, Dominique L. Braun, Huldrych F. Günthard, Roger D. Kouyos, Alexandra Trkola, the Swiss HIV Cohort Study
Broadly neutralizing antibodies (bnAbs) recognizing a diversity of HIV-1 strains are widely thought to be essential for an HIV-1 vaccine. Extensive knowledge on bnAbs has been gained from studying natural HIV infection by following bnAb evolution in individual people with HIV (PWH). However, it remains essential to increase knowledge of bnAb responses in large PWH cohorts to assess the feasibility of inducing bnAb activity by vaccination. To allow a systematic analysis, we created the XbnAb cohort, a large bnAb-inducer cohort selected by screening plasma of PWH enrolled in the Swiss HIV Cohort Study (SHCS) and the Zurich Primary HIV Infection Study (ZPHI). The XbnAb cohort represents a retrospective, biobank-based cohort comprising data of 304 PWH who developed bnAb activity during HIV-1 infection. Here, we report on the characteristics of the XbnAb cohort and its potential for HIV vaccine research.
{"title":"The XbnAb Cohort: 304 people with broadly neutralizing antibody activity to HIV-1","authors":"Chloe Pasin, Peter Rusert, Daniel Schmidt, Merle Schanz, Nikolas Friedrich, Irene A. Abela, Katharina Kusejko, Cyrille Niklaus, Michèle Sickmann, Jacqueline Weber, Michael Huber, Amapola Manrique, Andri Rauch, Alexandra Calmy, Matthias Cavassini, Marcel Stöckle, Julia Notter, Enos Bernasconi, Dominique L. Braun, Huldrych F. Günthard, Roger D. Kouyos, Alexandra Trkola, the Swiss HIV Cohort Study","doi":"10.1101/2024.09.13.612733","DOIUrl":"https://doi.org/10.1101/2024.09.13.612733","url":null,"abstract":"Broadly neutralizing antibodies (bnAbs) recognizing a diversity of HIV-1 strains are widely thought to be essential for an HIV-1 vaccine. Extensive knowledge on bnAbs has been gained from studying natural HIV infection by following bnAb evolution in individual people with HIV (PWH). However, it remains essential to increase knowledge of bnAb responses in large PWH cohorts to assess the feasibility of inducing bnAb activity by vaccination. To allow a systematic analysis, we created the XbnAb cohort, a large bnAb-inducer cohort selected by screening plasma of PWH enrolled in the Swiss HIV Cohort Study (SHCS) and the Zurich Primary HIV Infection Study (ZPHI). The XbnAb cohort represents a retrospective, biobank-based cohort comprising data of 304 PWH who developed bnAb activity during HIV-1 infection. Here, we report on the characteristics of the XbnAb cohort and its potential for HIV vaccine research.","PeriodicalId":501182,"journal":{"name":"bioRxiv - Immunology","volume":"65 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142252120","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 : 2024-09-16DOI: 10.1101/2024.09.09.612148
Anne Cao Le, Poh-Yi Gan, Daniel Koo Yuk Cheong, Virginie Oudin, Jonathan Dick, Maliha Alikhan, Mawj Mandwie, Ian Alexander, A. Richard Kitching, Grant J Logan, Kim Maree O'Sullivan
Extracellular DNA (ecDNA) released from injured and dying cells powerfully induces injurious inflammation. In this study we show ecDNA renal presence in patients and experimental mice with myeloperoxidase anti-neutrophil cytoplasmic antibody-associated glomerulonephritis (MPO-ANCA GN). Twice daily administration of intravenous DNase I (ivDNase I) in two models of anti-MPO GN was effective at reducing glomerular deposition of ecDNA, histological injury, leukocyte infiltration and NETosis. Comprehensive investigation into DNase I modes of action revealed the enzyme reduced lymph node DC numbers and their activation status, resulting in decreased frequency of MPO-specific CD4 effector T cells (IFN-gamma and IL17A producing), reductions in dermal anti-MPO delayed type hypersensitivity responses and increased frequency of MPO-specific T regulatory cells. Renal expression of inflammatory chemokines were also decreased. To overcome the translational obstacle of the short half-life of DNase I (<5 hours), we tested an adeno-associated viral vector encoding DNase I in one of the models. Along with the endpoint changes described above, a single vector treatment also enhanced therapeutic benefit as seen by reductions in MPO-ANCA and albuminuria. These results indicate ecDNA is a potent driver of anti-MPO GN and that DNase I is a potential therapeutic that can be delivered using gene technology.
受伤和死亡细胞释放的细胞外 DNA（ecDNA）可强力诱发损伤性炎症。在这项研究中，我们发现在髓过氧化物酶抗中性粒细胞胞浆抗体相关性肾小球肾炎（MPO-ANCA GN）患者和实验小鼠肾脏中存在 ecDNA。在两种抗 MPO GN 模型中，每天两次静脉注射 DNase I（ivDNase I）可有效减少肾小球的 ecDNA 沉积、组织学损伤、白细胞浸润和 NETosis。对 DNase I 作用模式的全面研究表明，该酶能减少淋巴结 DC 的数量及其活化状态，从而降低 MPO 特异性 CD4 效应 T 细胞（产生 IFN-gamma 和 IL17A）的频率，减少真皮抗 MPO 迟发型超敏反应，增加 MPO 特异性 T 调节细胞的频率。肾脏中炎症趋化因子的表达也有所减少。为了克服 DNase I 半衰期短（5 小时）这一转化障碍，我们在其中一个模型中测试了编码 DNase I 的腺相关病毒载体。除了上述终点变化外，单一载体治疗还能提高治疗效果，这体现在 MPO-ANCA 和白蛋白尿的减少上。这些结果表明，ecDNA 是抗 MPO GN 的强大驱动力，而且 DNase I 是一种可利用基因技术提供的潜在疗法。
{"title":"Treatment of anti-myeloperoxidase glomerulonephritis using recombinant deoxyribonuclease I is enhanced by adeno-associated virus gene therapy","authors":"Anne Cao Le, Poh-Yi Gan, Daniel Koo Yuk Cheong, Virginie Oudin, Jonathan Dick, Maliha Alikhan, Mawj Mandwie, Ian Alexander, A. Richard Kitching, Grant J Logan, Kim Maree O'Sullivan","doi":"10.1101/2024.09.09.612148","DOIUrl":"https://doi.org/10.1101/2024.09.09.612148","url":null,"abstract":"Extracellular DNA (ecDNA) released from injured and dying cells powerfully induces injurious inflammation. In this study we show ecDNA renal presence in patients and experimental mice with myeloperoxidase anti-neutrophil cytoplasmic antibody-associated glomerulonephritis (MPO-ANCA GN). Twice daily administration of intravenous DNase I (ivDNase I) in two models of anti-MPO GN was effective at reducing glomerular deposition of ecDNA, histological injury, leukocyte infiltration and NETosis. Comprehensive investigation into DNase I modes of action revealed the enzyme reduced lymph node DC numbers and their activation status, resulting in decreased frequency of MPO-specific CD4 effector T cells (IFN-gamma and IL17A producing), reductions in dermal anti-MPO delayed type hypersensitivity responses and increased frequency of MPO-specific T regulatory cells. Renal expression of inflammatory chemokines were also decreased. To overcome the translational obstacle of the short half-life of DNase I (<5 hours), we tested an adeno-associated viral vector encoding DNase I in one of the models. Along with the endpoint changes described above, a single vector treatment also enhanced therapeutic benefit as seen by reductions in MPO-ANCA and albuminuria. These results indicate ecDNA is a potent driver of anti-MPO GN and that DNase I is a potential therapeutic that can be delivered using gene technology.","PeriodicalId":501182,"journal":{"name":"bioRxiv - Immunology","volume":"207 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142268662","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 : 2024-09-16DOI: 10.1101/2024.09.16.613252
Alba Díaz Herrero, Hector Fernando Pelaez-Prestel, Lucile Massenet-Regad, Maëva Veyssiere, Julien Calvani, Caterina Cristinelli, Jacqueline Lehmann-Che, Véronique Meignin, Catherine Thieblemont, Véronique Blanc, Vassili Soumelis, Pierre Tonnerre
Diffuse Large B-cell Lymphoma (DLBCL) is the most prevalent subtype of non-Hodgkin lymphoma for which current therapeutic strategies remain insufficient. The diffuse nature of DLBCL, lacking distinct tissue structures, represents a challenge to elucidate the cellular organization and interactions within the tumor microenvironment (TME). In this study, we applied spatial transcriptomics to identify spatially-resolved gene expression profiles in 10 DLBCL tissue samples, identifying distinct immune cell infiltration and colocalization patterns. These profiles were classified into six cellular ecosystems (Cell-Eco) that differ in cellular composition, functional patterns, and neighborhood characteristics. The spatially-resolved Cell-Eco signatures provided prognostic scores that stratified patients with different overall survival rates. We also found that C1q+ tumor-associated macrophages are the primary cells interacting with malignant B cells and influencing the spatial architecture of the TME. This study provides novel biological insights into the complexity of the TME in DLBCL and highlights the potential prognostic value of its spatial organization.
{"title":"Spatial transcriptomics unveils immune cellular ecosystems associated with patient survival in diffuse large B-cell lymphoma","authors":"Alba Díaz Herrero, Hector Fernando Pelaez-Prestel, Lucile Massenet-Regad, Maëva Veyssiere, Julien Calvani, Caterina Cristinelli, Jacqueline Lehmann-Che, Véronique Meignin, Catherine Thieblemont, Véronique Blanc, Vassili Soumelis, Pierre Tonnerre","doi":"10.1101/2024.09.16.613252","DOIUrl":"https://doi.org/10.1101/2024.09.16.613252","url":null,"abstract":"Diffuse Large B-cell Lymphoma (DLBCL) is the most prevalent subtype of non-Hodgkin lymphoma for which current therapeutic strategies remain insufficient. The diffuse nature of DLBCL, lacking distinct tissue structures, represents a challenge to elucidate the cellular organization and interactions within the tumor microenvironment (TME). In this study, we applied spatial transcriptomics to identify spatially-resolved gene expression profiles in 10 DLBCL tissue samples, identifying distinct immune cell infiltration and colocalization patterns. These profiles were classified into six cellular ecosystems (Cell-Eco) that differ in cellular composition, functional patterns, and neighborhood characteristics. The spatially-resolved Cell-Eco signatures provided prognostic scores that stratified patients with different overall survival rates. We also found that C1q+ tumor-associated macrophages are the primary cells interacting with malignant B cells and influencing the spatial architecture of the TME. This study provides novel biological insights into the complexity of the TME in DLBCL and highlights the potential prognostic value of its spatial organization.","PeriodicalId":501182,"journal":{"name":"bioRxiv - Immunology","volume":"348 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142252118","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 : 2024-09-15DOI: 10.1101/2024.09.11.612410
Anna T Andrusaite, Olivia J Ridgewell, Anna AM Ahlback, Holly C Webster, Hiroki Yamaguchi, Molly Peel, Annika Frede, Sarwah K Al-Khalidi, Andrew Farthing, Anna LL Heawood, Annabelle Smith, Edward W Roberts, Allan Mcl Mowat, Rick M M Maizels, Georgia Perona-Wright, Simon WF Milling
The intestinal immune system maintains a balance between active immunity needed for protection and tolerance towards harmless antigens. Dendritic cells (DCs) found in the intestinal mucosa are key to the adaptive arm of these immunoregulatory events. DCs sample antigens in the tissue and then migrate to the draining lymph nodes, where they prime the T cells that then migrate back to the tissue as effector or regulatory cells. Intestinal DC are highly heterogeneous, and it remains unclear exactly which subsets induces the different kinds of immune response, or what signalling molecules and cellular mechanisms are involved. Here, we have studied these issues using Heligmosomoides polygyrus bakeri (Hpb) infection in mice, a model which is uniquely suited to dissecting this regulatory circuit in the gut, where it drives type 2 protective immunity at the same time as inhibiting other aspects of the immune response. Here, we characterise intestinal DC during Hpb infection for the first time. We observed a dynamical change of intestinal DC populations throughout the course of infection that correlated with altered phenotype and function. In particular, Hpb infection saw a rise in a population of CD103+ DC2 that retained a potent ability to drive Tregs during the infection and unlike CD103- DC2, had a reduced ability to induce pro-inflammatory immune response. Furthermore, transcriptional analysis revealed that TGFb signalling may be responsible for some of the changes observed. This was confirmed in vitro, where supplementation TGFb or Hpb-produced TGFb; mimic (TGM) replicated the immunomodulatory effects seen in DCs in vivo. Together, these results present a mechanistic explanation of how helminths such as Hpb may modulate host immune responses by altering the differentiation and function of local DCs. Furthermore, our work provides the basis for understanding immune homeostasis in the intestine at the molecular and cellular levels. Thus, this work fills out a crucial gap in our knowledge of basic biology underlining the DC decision between pro- and anti-inflammatory immune response in the central circuit of adaptive immune response.
肠道免疫系统在保护所需的主动免疫和对无害抗原的耐受之间保持平衡。肠粘膜中的树突状细胞（DC）是这些免疫调节事件中适应性臂的关键。树突状细胞对组织中的抗原进行采样，然后迁移到引流淋巴结，为 T 细胞提供能量，T 细胞再作为效应细胞或调节细胞迁移回组织。肠道 DC 具有高度异质性，目前仍不清楚究竟是哪个亚群诱导了不同类型的免疫反应，也不清楚其中涉及哪些信号分子和细胞机制。在这里，我们利用小鼠感染多角体螺旋体（Hpb）对这些问题进行了研究，Hpb 是一种独特的适合剖析肠道调节回路的模型，它在驱动 2 型保护性免疫的同时抑制免疫反应的其他方面。在这里，我们首次描述了 Hpb 感染期间肠道 DC 的特征。在整个感染过程中，我们观察到肠道直流电种群的动态变化，这种变化与表型和功能的改变有关。特别是，感染 Hpb 后，CD103+ DC2 的数量增加，它们在感染过程中保持了驱动 Tregs 的强大能力，与 CD103- DC2 不同的是，它们诱导促炎免疫反应的能力降低了。此外，转录分析表明，TGFb 信号可能是导致所观察到的某些变化的原因。这一点在体外得到了证实，补充 TGFb 或 Hpb 产生的 TGFb；模拟物（TGM）复制了体内 DCs 的免疫调节效应。总之，这些结果从机理上解释了 Hpb 等蠕虫如何通过改变当地 DC 的分化和功能来调节宿主的免疫反应。此外，我们的研究还为从分子和细胞水平理解肠道免疫平衡提供了基础。因此，这项工作填补了我们在基础生物学知识方面的一个重要空白，强调了适应性免疫反应中心回路中DC在促炎和抗炎免疫反应之间的决定作用。
{"title":"Intestinal helminth skews DC2 development towards regulatory phenotype to counter the anti-helminth immune response.","authors":"Anna T Andrusaite, Olivia J Ridgewell, Anna AM Ahlback, Holly C Webster, Hiroki Yamaguchi, Molly Peel, Annika Frede, Sarwah K Al-Khalidi, Andrew Farthing, Anna LL Heawood, Annabelle Smith, Edward W Roberts, Allan Mcl Mowat, Rick M M Maizels, Georgia Perona-Wright, Simon WF Milling","doi":"10.1101/2024.09.11.612410","DOIUrl":"https://doi.org/10.1101/2024.09.11.612410","url":null,"abstract":"The intestinal immune system maintains a balance between active immunity needed for protection and tolerance towards harmless antigens. Dendritic cells (DCs) found in the intestinal mucosa are key to the adaptive arm of these immunoregulatory events. DCs sample antigens in the tissue and then migrate to the draining lymph nodes, where they prime the T cells that then migrate back to the tissue as effector or regulatory cells. Intestinal DC are highly heterogeneous, and it remains unclear exactly which subsets induces the different kinds of immune response, or what signalling molecules and cellular mechanisms are involved. Here, we have studied these issues using Heligmosomoides polygyrus bakeri (Hpb) infection in mice, a model which is uniquely suited to dissecting this regulatory circuit in the gut, where it drives type 2 protective immunity at the same time as inhibiting other aspects of the immune response. Here, we characterise intestinal DC during Hpb infection for the first time. We observed a dynamical change of intestinal DC populations throughout the course of infection that correlated with altered phenotype and function. In particular, Hpb infection saw a rise in a population of CD103+ DC2 that retained a potent ability to drive Tregs during the infection and unlike CD103- DC2, had a reduced ability to induce pro-inflammatory immune response. Furthermore, transcriptional analysis revealed that TGFb signalling may be responsible for some of the changes observed. This was confirmed in vitro, where supplementation TGFb or Hpb-produced TGFb; mimic (TGM) replicated the immunomodulatory effects seen in DCs in vivo. Together, these results present a mechanistic explanation of how helminths such as Hpb may modulate host immune responses by altering the differentiation and function of local DCs. Furthermore, our work provides the basis for understanding immune homeostasis in the intestine at the molecular and cellular levels. Thus, this work fills out a crucial gap in our knowledge of basic biology underlining the DC decision between pro- and anti-inflammatory immune response in the central circuit of adaptive immune response.","PeriodicalId":501182,"journal":{"name":"bioRxiv - Immunology","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142252135","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 : 2024-09-15DOI: 10.1101/2024.09.09.612147
Alfred T Harding, Arianne J Crossen, Jennifer L Reedy, Kyle J Basham, Olivia W Hepworth, Yangting Zhang, Viral S Shah, Hannah Brown Harding, Manalee V Surve, Patricia Simaku, Geneva N Kwaku, Kirstine Nolling Jensen, Yohana Otto, Rebecca A. Ward, George R Thompson, Bruce S Klein, Jayaraj Rajagopal, Pritha Sen, Adam L Haber, Jatin M Vyas
Respiratory fungal infections pose a significant threat to human health. Animal models do not fully recapitulate human disease, necessitating advanced models to study human-fungal pathogen interactions. In this study, we utilized primary human airway epithelial cells (hAECs) to recapitulate the lung environment in vitro and investigate cellular responses to two diverse, clinically significant fungal pathogens, Aspergillus fumigatus and Coccidioides posadasii. To understand the mechanisms of early pathogenesis for both fungi, we performed single-cell RNA sequencing of infected hAECs. Analysis revealed that both fungi induced cellular stress and cytokine production. However, the cell subtypes affected and specific pathways differed between fungi, with A. fumigatus and C. posadasii triggering protein-folding-related stress in ciliated cells and hypoxia responses in secretory cells, respectively. This study represents one of the first reports of single-cell transcriptional analysis of hAECs infected with either A. fumigatus or C. posadasii, providing a vital dataset to dissect the mechanism of disease and potentially identify targetable pathways.
{"title":"Single-cell analysis of human airway epithelium identifies cell type-specific responses to Aspergillus and Coccidioides","authors":"Alfred T Harding, Arianne J Crossen, Jennifer L Reedy, Kyle J Basham, Olivia W Hepworth, Yangting Zhang, Viral S Shah, Hannah Brown Harding, Manalee V Surve, Patricia Simaku, Geneva N Kwaku, Kirstine Nolling Jensen, Yohana Otto, Rebecca A. Ward, George R Thompson, Bruce S Klein, Jayaraj Rajagopal, Pritha Sen, Adam L Haber, Jatin M Vyas","doi":"10.1101/2024.09.09.612147","DOIUrl":"https://doi.org/10.1101/2024.09.09.612147","url":null,"abstract":"Respiratory fungal infections pose a significant threat to human health. Animal models do not fully recapitulate human disease, necessitating advanced models to study human-fungal pathogen interactions. In this study, we utilized primary human airway epithelial cells (hAECs) to recapitulate the lung environment in vitro and investigate cellular responses to two diverse, clinically significant fungal pathogens, <em>Aspergillus fumigatus</em> and <em>Coccidioides posadasii</em>. To understand the mechanisms of early pathogenesis for both fungi, we performed single-cell RNA sequencing of infected hAECs. Analysis revealed that both fungi induced cellular stress and cytokine production. However, the cell subtypes affected and specific pathways differed between fungi, with <em>A. fumigatus</em> and <em>C. posadasi</em>i triggering protein-folding-related stress in ciliated cells and hypoxia responses in secretory cells, respectively. This study represents one of the first reports of single-cell transcriptional analysis of hAECs infected with either <em>A. fumigatus</em> or <em>C. posadasii</em>, providing a vital dataset to dissect the mechanism of disease and potentially identify targetable pathways.","PeriodicalId":501182,"journal":{"name":"bioRxiv - Immunology","volume":"17 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142268664","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 : 2024-09-15DOI: 10.1101/2024.09.12.612739
Jue Wang, Man Wu, Venkat Magupalli, Peter Dahlberg, Hao Wu, Grant Jensen
The NLRP3 inflammasome is a multi-protein molecular machine that mediates inflammatory responses in innate immunity. Its dysregulation has been linked to a large number of human diseases. Using cryogenic fluorescence-guided focused-ion-beam (cryo-FIB) milling and electron cryo-tomography (cryo-ET), we obtained 3-D images of the NLRP3 inflammasome in situ at various stages of its activation at macromolecular resolution. The cryo-tomograms unexpectedly reveal dense condensates of the human macrophage NLRP3 inflammasome that form within and around the microtubule organizing center (MTOC). We also find that following activation, the trans-Golgi network disperses and 50-nm NLRP3-associated vesicles appear which likely ferry NLRP3 to the MTOC. At later time points after activation, the electron-dense condensates progressively solidify and the cells undergo pyroptosis with widespread damaged mitochondria and autophagasomal structures.
{"title":"Human NLRP3 inflammasome activation leads to formation of condensate at the microtubule organizing center","authors":"Jue Wang, Man Wu, Venkat Magupalli, Peter Dahlberg, Hao Wu, Grant Jensen","doi":"10.1101/2024.09.12.612739","DOIUrl":"https://doi.org/10.1101/2024.09.12.612739","url":null,"abstract":"The NLRP3 inflammasome is a multi-protein molecular machine that mediates inflammatory responses in innate immunity. Its dysregulation has been linked to a large number of human diseases. Using cryogenic fluorescence-guided focused-ion-beam (cryo-FIB) milling and electron cryo-tomography (cryo-ET), we obtained 3-D images of the NLRP3 inflammasome in situ at various stages of its activation at macromolecular resolution. The cryo-tomograms unexpectedly reveal dense condensates of the human macrophage NLRP3 inflammasome that form within and around the microtubule organizing center (MTOC). We also find that following activation, the trans-Golgi network disperses and 50-nm NLRP3-associated vesicles appear which likely ferry NLRP3 to the MTOC. At later time points after activation, the electron-dense condensates progressively solidify and the cells undergo pyroptosis with widespread damaged mitochondria and autophagasomal structures.","PeriodicalId":501182,"journal":{"name":"bioRxiv - Immunology","volume":"56 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142268767","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 : 2024-09-14DOI: 10.1101/2024.09.12.612602
Margarita Rangel, Aimy Sebastian, Nicole Leon, Ashlee Phillips, Bria Gorman, Nicholas Hum, Dina R. Weilhammer
Neurotropic alphaviruses such as Venezuelan equine encephalitis virus (VEEV) are critical human pathogens that continually expand to naïve populations and for which there are no licensed vaccines or therapeutics. VEEV is highly infectious via the aerosol route and is a recognized weaponizable biothreat that causes neurological disease in humans. The neuropathology of VEEV has been attributed to an inflammatory immune response in the brain yet the underlying mechanisms and specific immune cell populations involved are not fully elucidated. This study uses single-cell RNA sequencing to produce a comprehensive transcriptional profile of immune cells isolated from the brain over a time course of infection in a mouse model of VEEV. Analyses reveal differentially activated subpopulations of microglia, including a distinct type I interferon-expressing subpopulation. This is followed by the sequential infiltration of myeloid cells and cytotoxic lymphocytes, also comprising subpopulations with unique transcriptional signatures. We identify a subpopulation of myeloid cells that form a distinct localization pattern in the hippocampal region whereas lymphocytes are widely distributed, indicating differential modes of recruitment, including that to specific regions of the brain. Altogether, this study provides a high-resolution analysis of the immune response to VEEV in the brain and highlights potential avenues of investigation for therapeutics that target neuroinflammation in the brain.
{"title":"Single-cell and spatiotemporal transcriptomic profiling of brain immune infiltration following Venezuelan equine encephalitis virus infection","authors":"Margarita Rangel, Aimy Sebastian, Nicole Leon, Ashlee Phillips, Bria Gorman, Nicholas Hum, Dina R. Weilhammer","doi":"10.1101/2024.09.12.612602","DOIUrl":"https://doi.org/10.1101/2024.09.12.612602","url":null,"abstract":"Neurotropic alphaviruses such as Venezuelan equine encephalitis virus (VEEV) are critical human pathogens that continually expand to naïve populations and for which there are no licensed vaccines or therapeutics. VEEV is highly infectious via the aerosol route and is a recognized weaponizable biothreat that causes neurological disease in humans. The neuropathology of VEEV has been attributed to an inflammatory immune response in the brain yet the underlying mechanisms and specific immune cell populations involved are not fully elucidated. This study uses single-cell RNA sequencing to produce a comprehensive transcriptional profile of immune cells isolated from the brain over a time course of infection in a mouse model of VEEV. Analyses reveal differentially activated subpopulations of microglia, including a distinct type I interferon-expressing subpopulation. This is followed by the sequential infiltration of myeloid cells and cytotoxic lymphocytes, also comprising subpopulations with unique transcriptional signatures. We identify a subpopulation of myeloid cells that form a distinct localization pattern in the hippocampal region whereas lymphocytes are widely distributed, indicating differential modes of recruitment, including that to specific regions of the brain. Altogether, this study provides a high-resolution analysis of the immune response to VEEV in the brain and highlights potential avenues of investigation for therapeutics that target neuroinflammation in the brain.","PeriodicalId":501182,"journal":{"name":"bioRxiv - Immunology","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142252137","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 : 2024-09-14DOI: 10.1101/2024.09.12.612764
Kimberly Kajihara, Donghong Yan, Gretchen Seim, Hannah Little-Hooy, Jing Kang, Cynthia Chen, Marco De Simone, Tim Delemarre, Spyros Darmanis, Haridha Shivram, Rebecca Bauer, Carrie M Rosenberger, Sharookh Kapadia, Min Xu, Miguel Reyes
Dysregulated myeloid states are associated with disease severity in both sepsis and COVID-19. However, their relevance in non-COVID-19 viral infection, the factors driving their induction, and their role in tissue injury remain poorly understood. We performed a meta-analysis of 1,622,180 myeloid cells from 890 COVID-19 or sepsis patients and controls across 19 published blood scRNA-seq datasets, which revealed severity-associated gene programs in both neutrophils and monocytes pointing to emergency myelopoiesis (EM). Using published bulk transcriptional data from 562 individuals with non-COVID-19 viral disease, we show that these signatures are similarly upregulated during severe influenza and RSV infection. Analysis of transcriptional and proteomic responses in tocilizumab-treated COVID-19 patients show that IL-6 signaling blockade results in a partial reduction of EM signatures and a compensatory increase in the growth factor G-CSF. Using a cellular model of human myelopoiesis, we show that both IL-6 and G-CSF stimulate the production of myeloid cells that express EM signatures in vitro. Using a mouse model of severe influenza infection, we demonstrate the effect of IL-6 and G-CSF signaling blockade on EM-associated myeloid cells, and highlight the opposing effects of EM-induced neutrophils and monocytes on tissue injury. Our study demonstrates the link between systemic cytokines and myeloid dysregulation during severe infection in humans, and highlights the cooperative role of IL-6 and G-CSF signaling in driving infection-induced myelopoiesis.
{"title":"G-CSF and IL-6 drive myeloid dysregulation during severe viral infection","authors":"Kimberly Kajihara, Donghong Yan, Gretchen Seim, Hannah Little-Hooy, Jing Kang, Cynthia Chen, Marco De Simone, Tim Delemarre, Spyros Darmanis, Haridha Shivram, Rebecca Bauer, Carrie M Rosenberger, Sharookh Kapadia, Min Xu, Miguel Reyes","doi":"10.1101/2024.09.12.612764","DOIUrl":"https://doi.org/10.1101/2024.09.12.612764","url":null,"abstract":"Dysregulated myeloid states are associated with disease severity in both sepsis and COVID-19. However, their relevance in non-COVID-19 viral infection, the factors driving their induction, and their role in tissue injury remain poorly understood. We performed a meta-analysis of 1,622,180 myeloid cells from 890 COVID-19 or sepsis patients and controls across 19 published blood scRNA-seq datasets, which revealed severity-associated gene programs in both neutrophils and monocytes pointing to emergency myelopoiesis (EM). Using published bulk transcriptional data from 562 individuals with non-COVID-19 viral disease, we show that these signatures are similarly upregulated during severe influenza and RSV infection. Analysis of transcriptional and proteomic responses in tocilizumab-treated COVID-19 patients show that IL-6 signaling blockade results in a partial reduction of EM signatures and a compensatory increase in the growth factor G-CSF. Using a cellular model of human myelopoiesis, we show that both IL-6 and G-CSF stimulate the production of myeloid cells that express EM signatures in vitro. Using a mouse model of severe influenza infection, we demonstrate the effect of IL-6 and G-CSF signaling blockade on EM-associated myeloid cells, and highlight the opposing effects of EM-induced neutrophils and monocytes on tissue injury. Our study demonstrates the link between systemic cytokines and myeloid dysregulation during severe infection in humans, and highlights the cooperative role of IL-6 and G-CSF signaling in driving infection-induced myelopoiesis.","PeriodicalId":501182,"journal":{"name":"bioRxiv - Immunology","volume":"192 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142252138","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：