Pub Date : 2024-05-31DOI: 10.1101/2024.05.29.596240
Nicholas P Krabbe, Ann M Mitzey, Saswati Bhattacharya, Elaina R Razo, Xiankun Zeng, Nell Bekiares, Amy Moy, Amy Kamholz, Julie A Karl, Gregory Daggett, Grace VanSleet, Terry Morgan, Saverio V Capuano, Heather A Simmons, Puja Basu, Andrea M Weiler, David H O'Connor, Thomas C Friedrich, Thaddeus G Golos, Emma L. Mohr
Infection with clade I Mpox virus (MPXV) results in adverse pregnancy outcomes, yet the potential for vertical transmission resulting in fetal harm with clade IIb MPXV, the clade that is currently circulating in the Western Hemisphere, remains unknown. We established a rhesus macaque model of vertical MPXV transmission with early gestation inoculation. Three pregnant rhesus macaques were inoculated intradermally with 1.5 x 10^5 plaque forming units (PFU) of clade IIb MPXV near gestational day (GD) 30 and animals were monitored for viremia and maternal and fetal well-being. Animals were euthanized to collect tissues at 5, 14, or 25 days post-inoculation (dpi). Tissues were evaluated for viral DNA (vDNA) loads, infectious virus titers, histopathology, MPXV mRNA and protein localization, as well as MPXV protein co-localization with placental cells including, Hofbauer cells, mesenchymal stromal cells, endothelial cells, and trophoblasts. vDNA was detected in maternal blood and skin lesions by 5 dpi. Lack of fetal heartbeat was observed at 14 or 25 dpi for two dams indicating fetal demise; the third dam developed significant vaginal bleeding at 5 dpi and was deemed an impending miscarriage. vDNA was detected in placental and fetal tissue in both fetal demise cases. MPXV localized to placental villi by ISH and IHC. Clade IIb MPXV infection in pregnant rhesus macaques results in vertical transmission to the fetus and adverse pregnancy outcomes, like clade I MPXV. Further studies are needed to determine whether antiviral therapy with tecovirimat will prevent vertical transmission and improve pregnancy outcomes.
{"title":"Mpox virus (MPXV) vertical transmission and fetal demise in a pregnant rhesus macaque model","authors":"Nicholas P Krabbe, Ann M Mitzey, Saswati Bhattacharya, Elaina R Razo, Xiankun Zeng, Nell Bekiares, Amy Moy, Amy Kamholz, Julie A Karl, Gregory Daggett, Grace VanSleet, Terry Morgan, Saverio V Capuano, Heather A Simmons, Puja Basu, Andrea M Weiler, David H O'Connor, Thomas C Friedrich, Thaddeus G Golos, Emma L. Mohr","doi":"10.1101/2024.05.29.596240","DOIUrl":"https://doi.org/10.1101/2024.05.29.596240","url":null,"abstract":"Infection with clade I Mpox virus (MPXV) results in adverse pregnancy outcomes, yet the potential for vertical transmission resulting in fetal harm with clade IIb MPXV, the clade that is currently circulating in the Western Hemisphere, remains unknown. We established a rhesus macaque model of vertical MPXV transmission with early gestation inoculation. Three pregnant rhesus macaques were inoculated intradermally with 1.5 x 10^5 plaque forming units (PFU) of clade IIb MPXV near gestational day (GD) 30 and animals were monitored for viremia and maternal and fetal well-being. Animals were euthanized to collect tissues at 5, 14, or 25 days post-inoculation (dpi). Tissues were evaluated for viral DNA (vDNA) loads, infectious virus titers, histopathology, MPXV mRNA and protein localization, as well as MPXV protein co-localization with placental cells including, Hofbauer cells, mesenchymal stromal cells, endothelial cells, and trophoblasts. vDNA was detected in maternal blood and skin lesions by 5 dpi. Lack of fetal heartbeat was observed at 14 or 25 dpi for two dams indicating fetal demise; the third dam developed significant vaginal bleeding at 5 dpi and was deemed an impending miscarriage. vDNA was detected in placental and fetal tissue in both fetal demise cases. MPXV localized to placental villi by ISH and IHC. Clade IIb MPXV infection in pregnant rhesus macaques results in vertical transmission to the fetus and adverse pregnancy outcomes, like clade I MPXV. Further studies are needed to determine whether antiviral therapy with tecovirimat will prevent vertical transmission and improve pregnancy outcomes.","PeriodicalId":501471,"journal":{"name":"bioRxiv - Pathology","volume":"36 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141198093","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 : 2024-05-30DOI: 10.1101/2024.05.29.596471
Philip Stavrides, Chris N. Goulbourne, James Peddy, Chunfeng Huo, Mala Rao, Vinod Khetarpal, Deanna M. Marchionini, Ralph A. Nixon, Dun-Sheng Yang
Huntington’s disease (HD) is caused by expansion of the polyglutamine stretch in huntingtin protein (HTT) resulting in hallmark aggresomes/inclusion bodies (IBs) composed of mutant huntingtin protein (mHTT) and its fragments. Stimulating autophagy to enhance mHTT clearance is considered a potential therapeutic strategy for HD. Our recent evaluation of the autophagic-lysosomal pathway (ALP) in human HD brain reveals upregulated lysosomal biogenesis and relatively normal autophagy flux in early Vonsattel grade brains, but impaired autolysosome clearance in late grade brains, suggesting that autophagy stimulation could have therapeutic benefits as an earlier clinical intervention. Here, we tested this hypothesis by crossing the Q175 HD knock-in model with our autophagy reporter mouse TRGL (Thy-1-RFP-GFP-LC3) to investigate in vivo neuronal ALP dynamics. In the Q175 and/or TRGL/Q175 mice, mHTT was detected in autophagic vacuoles and also exhibited high level colocalization with autophagy receptors p62/SQSTM1 and ubiquitin in the IBs. Compared to the robust lysosomal pathology in late-stage human HD striatum, ALP alterations in Q175 models are also late-onset but milder that included a lowered phospho-p70S6K level, lysosome depletion and autolysosome elevation including more poorly acidified autolysosomes and larger-sized lipofuscin granules, reflecting impaired autophagic flux. Administration of a mTOR inhibitor to 6-mo-old TRGL/Q175 normalized lysosome number, ameliorated aggresome pathology while reducing mHTT-, p62- and ubiquitin-immunoreactivities, suggesting beneficial potential of autophagy modulation at early stages of disease progression.
亨廷顿氏病（Huntington's disease，HD）是由亨廷丁蛋白（HTT）中的多聚谷氨酰胺伸展引起的，导致由突变亨廷丁蛋白（mHTT）及其片段组成的标志性侵染体/包涵体（IB）。刺激自噬以加强 mHTT 的清除被认为是一种潜在的 HD 治疗策略。我们最近对人类 HD 大脑中的自噬-溶酶体途径（ALP）进行了评估，结果显示，在早期 Vonsattel 等级的大脑中，溶酶体生物生成上调，自噬通量相对正常，但在晚期等级的大脑中，自溶酶体清除能力受损，这表明刺激自噬作为早期临床干预可能具有治疗效果。在这里，我们通过将 Q175 HD 基因敲入模型与我们的自噬报告小鼠 TRGL（Thy-1-RFP-GFP-LC3）进行杂交来研究体内神经元 ALP 动态，从而验证了这一假设。在Q175和/或TRGL/Q175小鼠中，mHTT在自噬空泡中被检测到，并且在IB中与自噬受体p62/SQSTM1和泛素高度共定位。与晚期人类 HD 纹状体中强大的溶酶体病理学相比，Q175 模型中的 ALP 改变也是晚期发生的，但较轻微，包括磷酸化-p70S6K 水平降低、溶酶体耗竭和自溶体升高，包括更多酸化不良的自溶体和更大尺寸的脂褐质颗粒，反映出自噬通量受损。给6个月大的TRGL/Q175注射mTOR抑制剂可使溶酶体数量恢复正常，改善侵袭体病理学，同时降低mHTT、p62和泛素免疫活性，这表明在疾病进展的早期阶段调节自噬是有益的。
{"title":"mTOR inhibition in Q175 Huntington’s disease model mice facilitates neuronal autophagy and mutant huntingtin clearance","authors":"Philip Stavrides, Chris N. Goulbourne, James Peddy, Chunfeng Huo, Mala Rao, Vinod Khetarpal, Deanna M. Marchionini, Ralph A. Nixon, Dun-Sheng Yang","doi":"10.1101/2024.05.29.596471","DOIUrl":"https://doi.org/10.1101/2024.05.29.596471","url":null,"abstract":"Huntington’s disease (HD) is caused by expansion of the polyglutamine stretch in huntingtin protein (HTT) resulting in hallmark aggresomes/inclusion bodies (IBs) composed of mutant huntingtin protein (mHTT) and its fragments. Stimulating autophagy to enhance mHTT clearance is considered a potential therapeutic strategy for HD. Our recent evaluation of the autophagic-lysosomal pathway (ALP) in human HD brain reveals upregulated lysosomal biogenesis and relatively normal autophagy flux in early Vonsattel grade brains, but impaired autolysosome clearance in late grade brains, suggesting that autophagy stimulation could have therapeutic benefits as an earlier clinical intervention. Here, we tested this hypothesis by crossing the Q175 HD knock-in model with our autophagy reporter mouse TRGL (<strong>T</strong>hy-1-<strong>R</strong>FP-<strong>G</strong>FP-<strong>L</strong>C3) to investigate <em>in vivo</em> neuronal ALP dynamics. In the Q175 and/or TRGL/Q175 mice, mHTT was detected in autophagic vacuoles and also exhibited high level colocalization with autophagy receptors p62/SQSTM1 and ubiquitin in the IBs. Compared to the robust lysosomal pathology in late-stage human HD striatum, ALP alterations in Q175 models are also late-onset but milder that included a lowered phospho-p70S6K level, lysosome depletion and autolysosome elevation including more poorly acidified autolysosomes and larger-sized lipofuscin granules, reflecting impaired autophagic flux. Administration of a mTOR inhibitor to 6-mo-old TRGL/Q175 normalized lysosome number, ameliorated aggresome pathology while reducing mHTT-, p62- and ubiquitin-immunoreactivities, suggesting beneficial potential of autophagy modulation at early stages of disease progression.","PeriodicalId":501471,"journal":{"name":"bioRxiv - Pathology","volume":"34 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141196843","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 : 2024-05-30DOI: 10.1101/2024.05.29.596470
Martin J Berg, Veeranna, Corrinne M Rosa, Asok Kumar, Panaiyur S Mohan, Philip Stavrides, Deanna M Marchionini, Dun-Sheng Yang, Ralph A Nixon
Accumulated levels of mutant huntingtin protein (mHTT) and its fragments are considered contributors to the pathogenesis of Huntington's disease (HD). Although lowering mHTT by stimulating autophagy has been considered a possible therapeutic strategy, the role and competence of autophagy-lysosomal pathway (ALP) during HD progression in the human disease remains largely unknown. Here, we used multiplex confocal and ultrastructural immunocytochemical analyses of ALP functional markers in relation to mHTT aggresome pathology in striatum and the less affected cortex of HD brains staged from HD2 to HD4 by Vonsattel neuropathological criteria compared to controls. Immunolabeling revealed the localization of HTT/mHTT in ALP vesicular compartments labeled by autophagy-related adaptor proteins p62/SQSTM1 and ubiquitin, and cathepsin D (CTSD) as well as HTT-positive inclusions. Although comparatively normal at HD2, neurons at later HD stages exhibited progressive enlargement and clustering of CTSD-immunoreactive autolysosomes/lysosomes and, ultrastructurally, autophagic vacuole/lipofuscin granules accumulated progressively, more prominently in striatum than cortex. These changes were accompanied by rises in levels of HTT/mHTT and p62/SQSTM1, particularly their fragments, in striatum but not in the cortex, and by increases of LAMP1 and LAMP2 RNA and LAMP1 protein. Importantly, no blockage in autophagosome formation and autophagosome-lysosome fusion was detected, thus pinpointing autophagy substrate clearance deficits as a basis for autophagic flux declines. The findings collectively suggest that upregulated lysosomal biogenesis and preserved proteolysis maintain autophagic clearance in early-stage HD, but failure at advanced stages contributes to progressive HTT build-up and potential neurotoxicity. These findings support the prospect that ALP stimulation applied at early disease stages, when clearance machinery is fully competent, may have therapeutic benefits in HD patients.
突变亨廷汀蛋白（mHTT）及其片段的累积水平被认为是亨廷顿氏病（HD）的发病机理之一。虽然通过刺激自噬来降低 mHTT 被认为是一种可能的治疗策略，但自噬-溶酶体途径（ALP）在人类 HD 疾病进展过程中的作用和能力在很大程度上仍不为人所知。在这里，我们利用多重共聚焦和超微结构免疫细胞化学分析了ALP功能标记物与mHTT侵袭体病理学的关系，并将Vonsattel神经病理学标准分期为HD2至HD4的HD大脑纹状体和受影响较小的皮层与对照组进行了比较。免疫标记显示，HTT/mHTT定位在ALP囊泡区块中，这些区块由自噬相关适配蛋白p62/SQSTM1和泛素以及cathepsin D (CTSD)标记，以及HTT阳性包涵体标记。虽然 HD2 阶段的神经元相对正常，但 HD 后期的神经元表现出 CTSD 免疫反应性自溶酶体/溶酶体的逐渐增大和聚集，超微结构上，自噬空泡/脂褐素颗粒逐渐累积，在纹状体中比在皮质中更为显著。伴随这些变化的是纹状体中 HTT/mHTT 和 p62/SQSTM1（尤其是它们的片段）水平的升高，而皮质中没有升高，LAMP1 和 LAMP2 RNA 以及 LAMP1 蛋白也有所增加。重要的是，没有检测到自噬体形成和自噬体-溶酶体融合受阻，从而确定自噬底物清除缺陷是自噬通量下降的基础。这些研究结果共同表明，溶酶体生物生成的上调和蛋白水解的保留可维持早期HD的自噬清除，但晚期的失败则会导致HTT的逐步积累和潜在的神经毒性。这些发现支持了在疾病早期阶段，当清除机制完全胜任时，应用ALP刺激可能对HD患者有治疗效果的前景。
{"title":"Pathobiology of the autophagy-lysosomal pathway in the Huntington's disease brain","authors":"Martin J Berg, Veeranna, Corrinne M Rosa, Asok Kumar, Panaiyur S Mohan, Philip Stavrides, Deanna M Marchionini, Dun-Sheng Yang, Ralph A Nixon","doi":"10.1101/2024.05.29.596470","DOIUrl":"https://doi.org/10.1101/2024.05.29.596470","url":null,"abstract":"Accumulated levels of mutant huntingtin protein (mHTT) and its fragments are considered contributors to the pathogenesis of Huntington's disease (HD). Although lowering mHTT by stimulating autophagy has been considered a possible therapeutic strategy, the role and competence of autophagy-lysosomal pathway (ALP) during HD progression in the human disease remains largely unknown. Here, we used multiplex confocal and ultrastructural immunocytochemical analyses of ALP functional markers in relation to mHTT aggresome pathology in striatum and the less affected cortex of HD brains staged from HD2 to HD4 by Vonsattel neuropathological criteria compared to controls. Immunolabeling revealed the localization of HTT/mHTT in ALP vesicular compartments labeled by autophagy-related adaptor proteins p62/SQSTM1 and ubiquitin, and cathepsin D (CTSD) as well as HTT-positive inclusions. Although comparatively normal at HD2, neurons at later HD stages exhibited progressive enlargement and clustering of CTSD-immunoreactive autolysosomes/lysosomes and, ultrastructurally, autophagic vacuole/lipofuscin granules accumulated progressively, more prominently in striatum than cortex. These changes were accompanied by rises in levels of HTT/mHTT and p62/SQSTM1, particularly their fragments, in striatum but not in the cortex, and by increases of LAMP1 and LAMP2 RNA and LAMP1 protein. Importantly, no blockage in autophagosome formation and autophagosome-lysosome fusion was detected, thus pinpointing autophagy substrate clearance deficits as a basis for autophagic flux declines. The findings collectively suggest that upregulated lysosomal biogenesis and preserved proteolysis maintain autophagic clearance in early-stage HD, but failure at advanced stages contributes to progressive HTT build-up and potential neurotoxicity. These findings support the prospect that ALP stimulation applied at early disease stages, when clearance machinery is fully competent, may have therapeutic benefits in HD patients.","PeriodicalId":501471,"journal":{"name":"bioRxiv - Pathology","volume":"43 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141196824","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 : 2024-05-29DOI: 10.1101/2024.05.29.596393
Agnes Carolin, David Frazer, Kexin Yan, Cameron R. Bishop, Bing Tang, Wilson Nguyen, Sheridan L. Helman, Jay Horvat, Thibaut Larcher, Daniel J. Rawle, Andreas Suhrbier
The severity of Coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is often dictated by a range of comorbidities. A considerable literature suggests iron deficiency and iron overload may contribute to increased infection, inflammation and disease severity, although direct causal relationships have been difficult to establish. Here we generate iron deficient and iron loaded C57BL/6J mice by feeding low and high iron diets, with mice on a normal iron diet representing controls. All mice were infected with a primary omicron XXB SARS-CoV-2 isolate and lung inflammatory responses were analyzed by histology, immunohistochemistry and RNA-Seq. Compared with controls, iron deficient mice showed no significant changes in lung viral loads or histopathology, whereas, iron loaded mice showed slightly, but significantly, reduced lung viral loads and histopathology. Transcriptional changes were modest, but illustrated widespread dysregulation of inflammation signatures for both iron deficient vs. controls, and iron loaded vs. controls. Some of these changes could be associated with detrimental outcomes, whereas others would be viewed as beneficial. Diet-associated iron deficiency or overload thus induced modest modulations of inflammatory signatures, but no significant histopathologically detectable disease exacerbations.
{"title":"The effects of iron deficient and high iron diets on SARS-CoV-2 lung infection and disease","authors":"Agnes Carolin, David Frazer, Kexin Yan, Cameron R. Bishop, Bing Tang, Wilson Nguyen, Sheridan L. Helman, Jay Horvat, Thibaut Larcher, Daniel J. Rawle, Andreas Suhrbier","doi":"10.1101/2024.05.29.596393","DOIUrl":"https://doi.org/10.1101/2024.05.29.596393","url":null,"abstract":"The severity of Coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is often dictated by a range of comorbidities. A considerable literature suggests iron deficiency and iron overload may contribute to increased infection, inflammation and disease severity, although direct causal relationships have been difficult to establish. Here we generate iron deficient and iron loaded C57BL/6J mice by feeding low and high iron diets, with mice on a normal iron diet representing controls. All mice were infected with a primary omicron XXB SARS-CoV-2 isolate and lung inflammatory responses were analyzed by histology, immunohistochemistry and RNA-Seq. Compared with controls, iron deficient mice showed no significant changes in lung viral loads or histopathology, whereas, iron loaded mice showed slightly, but significantly, reduced lung viral loads and histopathology. Transcriptional changes were modest, but illustrated widespread dysregulation of inflammation signatures for both iron deficient vs. controls, and iron loaded vs. controls. Some of these changes could be associated with detrimental outcomes, whereas others would be viewed as beneficial. Diet-associated iron deficiency or overload thus induced modest modulations of inflammatory signatures, but no significant histopathologically detectable disease exacerbations.","PeriodicalId":501471,"journal":{"name":"bioRxiv - Pathology","volume":"43 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141196845","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 : 2024-05-26DOI: 10.1101/2024.05.22.595389
Satoe Takahashi, Yingjie Zhou, Mary Ann Cheatham, Kazuaki Homma
Prestin,s voltage-driven motor activity confers sound-elicited somatic electromotility in auditory outer hair cells (OHCs) and is essential for the exquisite sensitivity and frequency selectivity of mammalian hearing. Lack of prestin results in hearing threshold shifts across frequency, supporting the causal association of variants in the prestin-coding gene, SLC26A5, with human hearing loss, DFNB61. However, cochlear function can tolerate reductions in prestin-mediated OHC electromotility. We found that two deafness-associated prestin variants, p.A100T and p.P119S, do not deprive prestin of its fast motor function but significantly reduce membrane expression, leading to large reductions in OHC electromotility that were only ~30% of wildtype (WT). Mice harboring these missense variants suffered congenital hearing loss that was worse at high frequencies; however, they retained WT-like auditory brainstem response thresholds at 8 kHz, which is processed at the apex of the mouse cochlea. This observation suggests the increasing importance of prestin-driven cochlear amplification at higher frequencies relevant to mammalian hearing. The observation also suggests the promising clinical possibility that small enhancements of OHC electromotility could significantly ameliorate DFNB61 hearing loss in human patients.
{"title":"The frequency dependence of prestin-mediated fast electromotility for mammalian cochlear amplification","authors":"Satoe Takahashi, Yingjie Zhou, Mary Ann Cheatham, Kazuaki Homma","doi":"10.1101/2024.05.22.595389","DOIUrl":"https://doi.org/10.1101/2024.05.22.595389","url":null,"abstract":"Prestin<sup>,</sup>s voltage-driven motor activity confers sound-elicited somatic electromotility in auditory outer hair cells (OHCs) and is essential for the exquisite sensitivity and frequency selectivity of mammalian hearing. Lack of prestin results in hearing threshold shifts across frequency, supporting the causal association of variants in the prestin-coding gene, SLC26A5, with human hearing loss, DFNB61. However, cochlear function can tolerate reductions in prestin-mediated OHC electromotility. We found that two deafness-associated prestin variants, p.A100T and p.P119S, do not deprive prestin of its fast motor function but significantly reduce membrane expression, leading to large reductions in OHC electromotility that were only ~30% of wildtype (WT). Mice harboring these missense variants suffered congenital hearing loss that was worse at high frequencies; however, they retained WT-like auditory brainstem response thresholds at 8 kHz, which is processed at the apex of the mouse cochlea. This observation suggests the increasing importance of prestin-driven cochlear amplification at higher frequencies relevant to mammalian hearing. The observation also suggests the promising clinical possibility that small enhancements of OHC electromotility could significantly ameliorate DFNB61 hearing loss in human patients.","PeriodicalId":501471,"journal":{"name":"bioRxiv - Pathology","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141165872","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 : 2024-05-26DOI: 10.1101/2024.05.22.595381
Kethmi Jayawardhane, Tharangani Somarathna, Victor P Manoli, Sheau-Fang Hwang, Stephen E Strelkov, Stacy D Singer, Guanqun Gavin Chen
Soilborne pathogens can be highly devastating, and clubroot, caused by Plasmodiophora brassicae, is particularly destructive to cruciferous plants. Although many AP2/ERF family transcription factors (TFs) have crucial physiological functions, very little is known regarding their functions in the context of soilborne diseases. Here we investigated the roles of AINTEGUMENTA-LIKE 7 (AIL7), an AIL sub-family TF in the AP2/ERF family, in plant immunity against clubroot. Unexpectedly, both AIL7 overexpression and mutant Arabidopsis lines exhibited increased tolerance to P. brassicae. Subsequent analysis revealed significant transcriptional alterations in genes linked to pathogen response, along with notable differences in genes associated with salicylic acid (SA) and jasmonic acid (JA) defense pathways, compared to wild-type plants. Interestingly, there was a tendency for up-regulation of SA- and JA-related genes in AIL7 overexpression and mutant lines in the absence, rather than presence, of P. brassicae. Subsequent phytohormone analyses confirmed these results. Taken together, AIL7 has an important role in maintaining constitutive systemic acquired resistance, involving phytohormone mediated defense, and this, rather than an accumulation of SA following P. brassicae challenge, primes the plants for improved clubroot resistance, which would shed light on exploring the functions of other AP2/ERF family TFs in plant immunity against soilborne pathogens.
土传病原体具有极大的破坏性，而由黄铜疫霉（Plasmodiophora brassicae）引起的棒根病对十字花科植物的破坏性尤为严重。虽然许多 AP2/ERF 家族转录因子（TFs）具有重要的生理功能，但人们对它们在土传病害中的功能知之甚少。在这里，我们研究了AP2/ERF家族中的AIL亚家族转录因子AINTEGUMENTA-LIKE 7（AIL7）在植物抗球根病免疫中的作用。意想不到的是，AIL7 过表达株系和突变株系都表现出了对拟南芥的更强的耐受性。随后的分析发现，与野生型植物相比，与病原体反应相关的基因发生了显著的转录变化，与水杨酸（SA）和茉莉酸（JA）防御途径相关的基因也有明显差异。有趣的是，AIL7 过表达株系和突变株系中与 SA 和 JA 相关的基因有上调的趋势，而不是在没有铜锈蝇的情况下。随后的植物激素分析证实了这些结果。综上所述，AIL7 在维持组成型系统获得性抗性方面具有重要作用，涉及植物激素介导的防御，而这一作用，而不是在黄刺苣苔受到挑战后 SA 的积累，为植物提高抗球根病能力奠定了基础，这将有助于探索其他 AP2/ERF 家族 TFs 在植物对土传病原体的免疫中的功能。
{"title":"Functions of the AP2/ERF family transcription factor AIL7 in immunity against soilborne clubroot pathogen in Arabidopsis","authors":"Kethmi Jayawardhane, Tharangani Somarathna, Victor P Manoli, Sheau-Fang Hwang, Stephen E Strelkov, Stacy D Singer, Guanqun Gavin Chen","doi":"10.1101/2024.05.22.595381","DOIUrl":"https://doi.org/10.1101/2024.05.22.595381","url":null,"abstract":"Soilborne pathogens can be highly devastating, and clubroot, caused by Plasmodiophora brassicae, is particularly destructive to cruciferous plants. Although many AP2/ERF family transcription factors (TFs) have crucial physiological functions, very little is known regarding their functions in the context of soilborne diseases. Here we investigated the roles of AINTEGUMENTA-LIKE 7 (AIL7), an AIL sub-family TF in the AP2/ERF family, in plant immunity against clubroot. Unexpectedly, both AIL7 overexpression and mutant Arabidopsis lines exhibited increased tolerance to P. brassicae. Subsequent analysis revealed significant transcriptional alterations in genes linked to pathogen response, along with notable differences in genes associated with salicylic acid (SA) and jasmonic acid (JA) defense pathways, compared to wild-type plants. Interestingly, there was a tendency for up-regulation of SA- and JA-related genes in AIL7 overexpression and mutant lines in the absence, rather than presence, of P. brassicae. Subsequent phytohormone analyses confirmed these results. Taken together, AIL7 has an important role in maintaining constitutive systemic acquired resistance, involving phytohormone mediated defense, and this, rather than an accumulation of SA following P. brassicae challenge, primes the plants for improved clubroot resistance, which would shed light on exploring the functions of other AP2/ERF family TFs in plant immunity against soilborne pathogens.","PeriodicalId":501471,"journal":{"name":"bioRxiv - Pathology","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141165659","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 : 2024-05-25DOI: 10.1101/2024.05.23.595398
Tobiasz Z Druciarek, Alejandro Rojas, Ioannis Tzanetakis
Understanding the interaction between rose rosette emaravirus (RRV) and its vectors is pivotal in addressing the epidemic outbreak of rose rosette disease. This study employed quantitative real-time RT-PCR to assess RRV genome copy numbers in Phyllocoptes fructiphilus and P. adalius, providing insights into the viral dynamics and vector competency. Our findings suggest active virus replication within P. fructiphilus, a confirmed vector species, unlike P. adalius, highlighting its non-vector status. Furthermore, the study highlights the variability in virus concentration in mites over time, underlining possible developmental stage-specific response and influence of mite lifestyle on RRV retention and replication. This research is the first step in understanding the virus-mite interactome, which is essential for developing effective management strategies against rose rosette disease.
了解玫瑰轮纹病病毒（RRV）及其载体之间的相互作用对于解决玫瑰轮纹病的爆发至关重要。本研究采用定量实时 RT-PCR 技术评估了 Phyllocoptes fructiphilus 和 P. adalius 中的 RRV 基因组拷贝数，为了解病毒动态和载体能力提供了线索。我们的研究结果表明，Phyllocoptes fructiphilus（一种已确认的病媒物种）体内病毒复制活跃，而 P. adalius 则不同，突出了其非病媒地位。此外，该研究还强调了螨虫体内病毒浓度随时间变化的差异性，强调了螨虫生活方式对 RRV 的保留和复制可能产生的发育阶段特异性反应和影响。这项研究是了解病毒与螨虫相互作用组的第一步，对于制定有效的玫瑰轮纹病管理策略至关重要。
{"title":"Quantification of rose rosette emaravirus (RRV) titers in eriophyoid mites: insights into viral dynamics and vector competency","authors":"Tobiasz Z Druciarek, Alejandro Rojas, Ioannis Tzanetakis","doi":"10.1101/2024.05.23.595398","DOIUrl":"https://doi.org/10.1101/2024.05.23.595398","url":null,"abstract":"Understanding the interaction between rose rosette emaravirus (RRV) and its vectors is pivotal in addressing the epidemic outbreak of rose rosette disease. This study employed quantitative real-time RT-PCR to assess RRV genome copy numbers in Phyllocoptes fructiphilus and P. adalius, providing insights into the viral dynamics and vector competency. Our findings suggest active virus replication within P. fructiphilus, a confirmed vector species, unlike P. adalius, highlighting its non-vector status. Furthermore, the study highlights the variability in virus concentration in mites over time, underlining possible developmental stage-specific response and influence of mite lifestyle on RRV retention and replication. This research is the first step in understanding the virus-mite interactome, which is essential for developing effective management strategies against rose rosette disease.","PeriodicalId":501471,"journal":{"name":"bioRxiv - Pathology","volume":"48 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141151972","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 : 2024-05-23DOI: 10.1101/2024.05.21.595074
Jessica Lawrence, Davis Seelig, Kimberly Demos-Davies, Clara Ferreira, Yanan Ren, Li Wang, Sk Kayum Alam, Rendong Yang, Alonso Guedes, Angela Craig, Luke H. Hoeppner
Over half of all people diagnosed with cancer receive radiation therapy. Moderate to severe radiation dermatitis occurs in most human radiation patients, causing pain, aesthetic distress, and a negative impact on tumor control. No effective prevention or treatment for radiation dermatitis exists. The lack of well-characterized, clinically relevant animal models of human radiation dermatitis contributes to the absence of strategies to mitigate radiation dermatitis. Here, we establish and characterize a hairless SKH-1 mouse model of human radiation dermatitis by correlating temporal stages of clinical and pathological skin injury. We demonstrate that a single ionizing radiation treatment of 30 Gy using 6 MeV electrons induces severe clinical grade 3 peak toxicity at 12 days, defined by marked erythema, desquamation and partial ulceration, with resolution occurring by 25 days. Histopathology reveals that radiation-induced skin injury features temporally unique inflammatory changes. Upregulation of epidermal and dermal TGF-β1 and COX-2 protein expression occurs at peak dermatitis, with sustained epidermal TGF-β1 expression beyond resolution. Specific histopathological variables that remain substantially high at peak toxicity and early clinical resolution, including epidermal thickening, hyperkeratosis and dermal fibroplasia/fibrosis, serve as specific measurable parameters for in vivo interventional preclinical studies that seek to mitigate radiation-induced skin injury.
{"title":"Radiation dermatitis in the hairless mouse model mimics human radiation dermatitis","authors":"Jessica Lawrence, Davis Seelig, Kimberly Demos-Davies, Clara Ferreira, Yanan Ren, Li Wang, Sk Kayum Alam, Rendong Yang, Alonso Guedes, Angela Craig, Luke H. Hoeppner","doi":"10.1101/2024.05.21.595074","DOIUrl":"https://doi.org/10.1101/2024.05.21.595074","url":null,"abstract":"Over half of all people diagnosed with cancer receive radiation therapy. Moderate to severe radiation dermatitis occurs in most human radiation patients, causing pain, aesthetic distress, and a negative impact on tumor control. No effective prevention or treatment for radiation dermatitis exists. The lack of well-characterized, clinically relevant animal models of human radiation dermatitis contributes to the absence of strategies to mitigate radiation dermatitis. Here, we establish and characterize a hairless SKH-1 mouse model of human radiation dermatitis by correlating temporal stages of clinical and pathological skin injury. We demonstrate that a single ionizing radiation treatment of 30 Gy using 6 MeV electrons induces severe clinical grade 3 peak toxicity at 12 days, defined by marked erythema, desquamation and partial ulceration, with resolution occurring by 25 days. Histopathology reveals that radiation-induced skin injury features temporally unique inflammatory changes. Upregulation of epidermal and dermal TGF-β1 and COX-2 protein expression occurs at peak dermatitis, with sustained epidermal TGF-β1 expression beyond resolution. Specific histopathological variables that remain substantially high at peak toxicity and early clinical resolution, including epidermal thickening, hyperkeratosis and dermal fibroplasia/fibrosis, serve as specific measurable parameters for in vivo interventional preclinical studies that seek to mitigate radiation-induced skin injury.","PeriodicalId":501471,"journal":{"name":"bioRxiv - Pathology","volume":"220 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141151945","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 : 2024-05-17DOI: 10.1101/2024.05.15.594372
Sina Ghandian, Liane Albarghouthi, Kiana Nava, Shivam R. Rai Sharma, Lise Minaud, Laurel Beckett, Naomi Saito, Charles DeCarli, Robert A. Rissman, Andrew F. Teich, Lee-Way Jin, Brittany N. Dugger, Michael J. Keiser
Accumulation of abnormal tau protein into neurofibrillary tangles (NFTs) is a pathologic hallmark of Alzheimer disease. Accurate and efficient detection and quantification of NFTs in tissue samples aids in deeper phenotyping of Alzheimer disease and may reveal relationships with clinical, demographic, and genetic features. However, expert manual analysis can be time-consuming, subject to observer variability, and limited in handling the large amounts of data generated by modern imaging techniques. We present a scalable, open access, deep learning-based approach to quantify the NFT burden in digital whole slide images (WSIs) of post-mortem human brain tissue. We trained a UNet model on 45 annotated 2400 μm by 1200 μm regions of interest (ROIs) selected from 15 unique WSIs of temporal cortex from Alzheimer disease cases from three institutes (University of California (UC)-Davis, UC-San Diego, and Columbia University). We developed a method to generate detailed segmentation ground truth masks at the pixel level directly from simple point annotations. The model achieved a precision of 0.53, recall of 0.60, and F1 score of 0.53 on a held-out test set of 7 WSIs, providing researchers with an efficient and reliable tool for NFT burden quantification. We compared this to an object detection model on the same dataset, which achieved comparable but more coarse-grained performance. Both models correlated with expert semi-quantitative scores at the whole-slide level. Our approach provides an open deep learning pipeline for detailed and scalable NFT spatial distribution and morphology analysis across large cohorts, which is not feasible through manual assessment.
异常 tau 蛋白聚集成神经纤维缠结（NFT）是阿尔茨海默病的病理特征。准确、高效地检测和量化组织样本中的 NFTs 有助于对阿尔茨海默病进行更深入的表型分析，并揭示其与临床、人口统计学和遗传学特征之间的关系。然而，专家的人工分析可能会耗费大量时间，受观察者变异性的影响，并且在处理现代成像技术产生的大量数据时受到限制。我们提出了一种可扩展、开放访问、基于深度学习的方法，用于量化死后人类脑组织数字全切片图像（WSI）中的NFT负担。我们从三个研究所（加州大学戴维斯分校、加州大学圣迭戈分校和哥伦比亚大学）的 15 个阿尔茨海默病病例的颞叶皮层 WSI 图像中挑选出 45 个注释为 2400 μm x 1200 μm 的感兴趣区（ROI），在这些感兴趣区上训练了一个 UNet 模型。我们开发了一种方法，可直接从简单的点注释生成像素级的详细分割基本真实掩码。该模型的精确度达到 0.53，召回率达到 0.60，在 7 个 WSI 的保留测试集上的 F1 得分为 0.53，为研究人员提供了一种高效可靠的 NFT 负担量化工具。我们将其与同一数据集上的物体检测模型进行了比较，后者的性能相当，但更粗粒度。这两个模型都与专家在整张幻灯片层面的半定量评分相关。我们的方法提供了一个开放的深度学习管道，可在大型队列中进行详细、可扩展的 NFT 空间分布和形态分析，这在人工评估中是不可行的。
{"title":"Learning precise segmentation of neurofibrillary tangles from rapid manual point annotations","authors":"Sina Ghandian, Liane Albarghouthi, Kiana Nava, Shivam R. Rai Sharma, Lise Minaud, Laurel Beckett, Naomi Saito, Charles DeCarli, Robert A. Rissman, Andrew F. Teich, Lee-Way Jin, Brittany N. Dugger, Michael J. Keiser","doi":"10.1101/2024.05.15.594372","DOIUrl":"https://doi.org/10.1101/2024.05.15.594372","url":null,"abstract":"Accumulation of abnormal tau protein into neurofibrillary tangles (NFTs) is a pathologic hallmark of Alzheimer disease. Accurate and efficient detection and quantification of NFTs in tissue samples aids in deeper phenotyping of Alzheimer disease and may reveal relationships with clinical, demographic, and genetic features. However, expert manual analysis can be time-consuming, subject to observer variability, and limited in handling the large amounts of data generated by modern imaging techniques. We present a scalable, open access, deep learning-based approach to quantify the NFT burden in digital whole slide images (WSIs) of post-mortem human brain tissue. We trained a UNet model on 45 annotated 2400 μm by 1200 μm regions of interest (ROIs) selected from 15 unique WSIs of temporal cortex from Alzheimer disease cases from three institutes (University of California (UC)-Davis, UC-San Diego, and Columbia University). We developed a method to generate detailed segmentation ground truth masks at the pixel level directly from simple point annotations. The model achieved a precision of 0.53, recall of 0.60, and F1 score of 0.53 on a held-out test set of 7 WSIs, providing researchers with an efficient and reliable tool for NFT burden quantification. We compared this to an object detection model on the same dataset, which achieved comparable but more coarse-grained performance. Both models correlated with expert semi-quantitative scores at the whole-slide level. Our approach provides an open deep learning pipeline for detailed and scalable NFT spatial distribution and morphology analysis across large cohorts, which is not feasible through manual assessment.","PeriodicalId":501471,"journal":{"name":"bioRxiv - Pathology","volume":"30 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141058733","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}
Computational pathology, utilizing whole slide image (WSI) for pathological diagnosis, has advanced the development of intelligent healthcare. However, the scarcity of annotated data and histological differences hinder the general application of existing methods. Extensive histopathological data and the robustness of self-supervised models in small-scale data demonstrate promising prospects for developing foundation pathology models. In this work, we propose the BEPH (BEiT-based model Pre-training on Histopathological image), a general method that leverages self-supervised learning to learn meaningful representations from 11 million unlabeled histopathological images. These representations are then efficiently adapted to various tasks, including patch-level cancer recognition, WSI-level cancer classification, and survival prediction for multiple cancer subtypes. Experimental results demonstrate that our model consistently outperformsseveral comparative models, even with limited training data reduced to 50%. Especially when the downstream structure is the same, the model can improve ResNet and DINO by up to a maximum increase of 8.8% and 7.2% (WSI level classification), and 6.44% and 3.28% on average (survival prediction), respectively. Therefore, BEPH offers a universal solution to enhance model performance, reduce the burden of expert annotations, and enable widespread clinical applications of artificial intelligence. The code and models can be obtained at https://github.com/Zhcyoung/BEPH. And currently, online fine-tuning of WSI classification tasks is available for use on http://yulab-sjtu.natapp1.cc/BEPH.
{"title":"A foundation model for generalizable cancer diagnosis and survival prediction from histopathological images","authors":"Zhangsheng Yu, Zhaochang Yang, Ting Wei, Ying Liang, Xin Yuan, Ruitian Gao, Yujia Xia, Jie Zhou, Yue Zhang","doi":"10.1101/2024.05.16.594499","DOIUrl":"https://doi.org/10.1101/2024.05.16.594499","url":null,"abstract":"Computational pathology, utilizing whole slide image (WSI) for pathological diagnosis, has advanced the development of intelligent healthcare. However, the scarcity of annotated data and histological differences hinder the general application of existing methods. Extensive\u0000histopathological data and the robustness of self-supervised models in small-scale data demonstrate promising prospects for developing foundation pathology models. In this work, we propose the BEPH (BEiT-based model Pre-training on Histopathological image), a general method that leverages self-supervised learning to learn meaningful representations from 11 million unlabeled\u0000histopathological images. These representations are then efficiently adapted to various tasks, including patch-level cancer recognition, WSI-level cancer classification, and survival prediction for multiple cancer subtypes. Experimental results demonstrate that our model consistently outperformsseveral comparative models, even with limited training data reduced to 50%. Especially\u0000when the downstream structure is the same, the model can improve ResNet and DINO by up to a maximum increase of 8.8% and 7.2% (WSI level classification), and 6.44% and 3.28% on average (survival prediction), respectively. Therefore, BEPH offers a universal solution to enhance model performance, reduce the burden of expert annotations, and enable widespread clinical applications of artificial intelligence. The code and models can be obtained at https://github.com/Zhcyoung/BEPH. And currently, online fine-tuning of WSI classification tasks\u0000is available for use on http://yulab-sjtu.natapp1.cc/BEPH.","PeriodicalId":501471,"journal":{"name":"bioRxiv - Pathology","volume":"66 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141058734","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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