The folding and trafficking of transmembrane glycoproteins are essential for cellular homeostasis and compromised in many diseases. In Niemann-Pick type C disease, a lysosomal disorder characterized by impaired intracellular cholesterol trafficking, the transmembrane glycoprotein NPC1 misfolds due to disease-causing missense mutations. While mutant NPC1 has emerged as a robust target for proteostasis modulators, these drug development efforts have been unsuccessful in mouse models. Here, we demonstrate unexpected differences in trafficking through the medial Golgi between mouse and human I1061T-NPC1, a common disease-causing mutant. We establish that these distinctions are governed by differences in the NPC1 protein sequence rather than by variations in the ER folding environment. Moreover, we demonstrate direct effects of mutant protein trafficking on the response to small molecules that modulate the endoplasmic reticulum folding environment by affecting Ca++ concentration. Finally, we develop a panel of isogenic human NPC1 iNeurons expressing wild type, I1061T-, and R934L-NPC1 and demonstrate their utility in testing these candidate therapeutics. Our findings identify important rules governing mutant NPC1’s response to proteostatic modulators and highlight the importance of species- and mutation-specific responses for therapy development.
Mark L. Schultz, Kylie J. Schache, Ruth D. Azaria, Esmée Q. Kuiper, Steven Erwood, Evgueni A. Ivakine, Nicole Y. Farhat, Forbes D. Porter, Koralege C. Pathmasiri, Stephanie M. Cologna, Michael D. Uhler, Andrew P. Lieberman
Pancreatic neuroendocrine tumors (PNETs) are malignancies arising from the islets of Langerhans. Therapeutic options are limited for the over 50% of patients who present with metastatic disease. We aimed to identify mechanisms to remodel the PNET tumor microenvironment (TME) to ultimately enhance susceptibility to immunotherapy. The TMEs of localized and metastatic PNETs were investigated using an approach that combines RNA-sequencing, cancer and T cell profiling, and pharmacologic perturbations. RNA-sequencing analysis indicated that the primary tumors of metastatic PNETs showed significant activation of inflammatory and immune-related pathways. We determined that metastatic PNETs featured increased numbers of tumor-infiltrating T cells compared to localized tumors. T cells isolated from both localized and metastatic PNETs showed evidence of recruitment and antigen-dependent activation, suggestive of an immune-permissive microenvironment. A computational analysis suggested that vorinostat, a histone deacetylase inhibitor, may perturb the transcriptomic signature of metastatic PNETs. Treatment of PNET cell lines with vorinostat increased chemokine CCR5 expression by NF-κB activation. Vorinostat treatment of patient-derived metastatic PNET tissues augmented recruitment of autologous T cells, which was substantiated in a mouse model of PNET. Pharmacologic induction of chemokine expression may represent a promising approach for enhancing the immunogenicity of metastatic PNET TMEs.
Jacques Greenberg, Jessica Limberg, Akanksha Verma, David Kim, Xiang Chen, Yeon J. Lee, Maureen D. Moore, Timothy M. Ullmann, Jessica W. Thiesmeyer, Zachary Loewenstein, Kevin J. Chen, Caitlin E. Egan, Dessislava Stefanova, Rohan Bareja, Rasa Zarnegar, Brendan M. Finnerty, Theresa Scognamiglio, Yi-Chieh Nancy Du, Olivier Elemento, Thomas J. Fahey III, Irene M. Min
Vogt-Koyanagi-Harada (VKH) disease is an important refractory uveitis mediated by pathological T cells (TCs). Tofacitinib (TOFA) is a Janus kinases (JAKs) targeted therapy for several autoimmune diseases. However, the specific pathogenesis and targeted therapeutics for VKH remain largely unknown. Based on single-cell RNA sequencing and mass cytometry, we present the first multimodal high-dimensional analysis to determine a comprehensive human immune atlas of VKH patients undergoing TOFA therapy in the context of subset composition, gene signatures, enriched pathways, and intercellular interactions. VKH patients are characterized by TCs polarization from naive to effector and memory subsets, altogether with accrued monocytes, upregulated cytokines and JAK-STAT signaling pathways. In vitro, TOFA reversed Th17/ regulatory T-cell (Treg) imbalance and inhibited IL-2-induced STAT1/3 phosphorylation. TOFA alleviated VKH symptoms by restoring pathological TCs polarization and functional marker expression and downregulating cytokine signaling and lymphocyte function. Remarkably, inflammation-related responses and intercellular interactions decreased after TOFA treatment, particularly in monocytes. Notably, we identified two inflammation- and JAK-associated monocyte subpopulations that were strongly implicated in VKH pathogenesis and mechanisms involved in TOFA treatment. Here, we provide a novel JAK-targeted therapy for VKH and elaborate on the possible therapeutic mechanisms of TOFA, expanding our knowledge of VKH pathological patterns.
Xiuxing Liu, Qi Jiang, Jianjie Lv, Shizhao Yang, Zhaohao Huang, Runping Duan, Tianyu Tao, Zhaohuai Li, Rong Ju, Yingfeng Zheng, Wenru Su
Consecutive mRNA vaccinations against SARS-CoV-2 reinforced both innate and adaptive immune responses. However, it remains unclear whether the enhanced innate immune responses are mediated by epigenetic regulation and, if so, whether these effects persist. Using mass cytometry, RNA-seq, and ATAC-seq, we show that BNT162b2 mRNA vaccination upregulated antiviral and IFN-stimulated gene expression in monocytes with greater effects after the second vaccination than those after the first vaccination. Transcription factor-binding motif analysis also revealed enriched IFN regulatory factors and PU.1 motifs in accessible chromatin regions. Importantly, although consecutive BNT162b2 mRNA vaccinations boosted innate immune responses and caused epigenetic changes in isolated monocytes, we showed that these effects occur only transiently and disappear 4 weeks after the second vaccination. Furthermore, single-cell RNA sequencing analysis revealed that a similar gene signature was impaired in the monocytes of unvaccinated COVID-19 patients with acute respiratory distress syndrome. These results reinforce the importance of the innate immune response in the determination of COVID-19 severity but indicate that, unlike adaptive immunity, innate immunity is not unexpectedly sustained even after consecutive vaccination. This study, which focuses on innate immmune memory, may provide novel insights into the vaccine development against infectious diseases.
Yuta Yamaguchi, Yasuhiro Kato, Ryuya Edahiro, Jonas N. Søndergaard, Teruaki Murakami, Saori Amiya, Shinichiro Nameki, Yuko Yoshimine, Takayoshi Morita, Yusuke Takeshima, Shuhei Sakakibara, Yoko Naito, Daisuke Motooka, Yu-Chen Liu, Yuya Shirai, Yasutaka Okita, Jun Fujimoto, Haruhiko Hirata, Yoshito Takeda, James B. Wing, Daisuke Okuzaki, Yukinori Okada, Atsushi Kumanogoh
Oncogenic FOXO1 gene fusions drive a subset of rhabdomyosarcoma (RMS) with poor survival and to date these cancer drivers are therapeutically intractable. To identify new therapies for this disease, we undertook an isogenic CRISPR-interference screen to define PAX3-FOXO1 specific genetic dependencies and identified genes in the GATOR2 complex. GATOR2 loss in RMS abrogated amino acid-induced lysosomal localization of mTORC1 and consequent downstream signaling, slowing G1-S cell cycle transition. In vivo suppression of GATOR2 impaired the growth of tumor xenografts and favored the outgrowth of cells lacking PAX3-FOXO1. Loss of a subset of GATOR2 members can be compensated by direct genetic activation of mTORC1. RAS mutations are also sufficient to decouple mTORC1 activation from GATOR2, and indeed fusion negative RMS harboring such mutations exhibit amino acid-independent mTORC1 activity. A bi-steric, mTORC1-selective small molecule induced tumor regressions in fusion positive patient-derived tumor xenografts. These findings highlight a vulnerability in FOXO1 fusion positive RMS and provide rationale for the clinical evaluation of bi-steric mTORC1 inhibitors, currently in phase 1 testing, to treat this disease. Isogenic genetic screens can thus identify potentially exploitable vulnerabilities in fusion driven pediatric cancers which otherwise remain mostly undruggable.
Jacqueline Morales, David V. Allegakoen, José A. Garcia, Kristen Kwong, Pushpendra K. Sahu, Drew A. Fajardo, Yue Pan, Max A. Horlbeck, Jonathan S. Weissman, W. Clay Gustafson, Trever G. Bivona, Amit J. Sabnis
Therapeutics that inhibit IL-6 at different points in its signaling pathway are in clinical use yet whether the immunologic effects of these interventions differ based on their molecular target is unknown. We performed short-term interventions in individuals with type 1 diabetes using anti-IL-6 (siltuximab) or anti-IL-6 receptor (IL-6R; tocilizumab) and investigated the impact of this in vivo blockade on T cell fate and function. Immune outcomes were influenced by the target of the therapeutic intervention (IL-6 versus IL-6R) and by peak drug concentration. Tocilizumab reduced IL-6-driven STAT3 phosphorylation, ICOS expression on T follicular helper cell populations and TCR-driven STAT3 phosphorylation. Siltuximab reversed resistance to regulatory T cell-mediated suppression and increased TCR driven pSTAT3, and production of IL-10, IL-21 and IL-27 by T effectors. Together these findings indicate that the context of IL-6 blockade in vivo drives distinct T cell intrinsic changes that may influence therapeutic outcomes.
Cate Speake, Tania Habib, Katharina Lambert, Christian Hundhausen, Sandra Lord, Matthew J. Dufort, Samuel O. Skinner, Alex Hu, MacKenzie Kinsman, Britta E. Jones, Megan D. Maerz, Megan Tatum, Anne M. Hocking, Gerald T. Nepom, Carla J. Greenbaum, Jane H. Buckner
Docetaxel (DTX) combined with cisplatin and 5-FU has been used as induction chemotherapy for head and neck squamous cell carcinoma (HNSCC). However, the development of acquired resistance remains a major obstacle to treatment response. Tumor-associated macrophages are associated with chemotherapeutic resistance. In the present study, increased infiltration of macrophages into the tumor microenvironment was significantly associated with shorter overall survival and increased resistance to chemotherapeutic drugs, particularly DTX in HNSCC patients. Macrophage co-culture induced expression of intercellular adhesion molecule 1 (ICAM1), which promotes stemness and the formation of polyploid giant cancer cells, thereby reducing the efficacy of DTX. Both genetic silencing and pharmacological inhibition of ICAM1 sensitized HNSCC to DTX. Macrophage secretion of IL-1β was found to induce tumor expression of ICAM1. IL-1β neutralization and IL-1 receptor blockade reversed DTX resistance induced by macrophage co-culture. IL-1β activated superoxide dismutase 2 and inhibited catalase, thereby modulating intracellular levels of reactive oxygen species (ROS) and inducing ICAM1 expression. Arsenic trioxide (ATO) reduced macrophage infiltration into the TME and impaired IL-1β secretion by macrophages. The combinatorial use of ATO enhanced the in vivo efficacy of DTX in a mouse model, which may provide a revolutionary approach to overcoming acquired therapeutic resistance in HNSCC.
Ching-Yun Hsieh, Ching-Chan Lin, Yu-Wen Huang, Jong-Hang Chen, Yung-An Tsou, Ling-Chu Chang, Chi-Chen Fan, Chen-Yuan Lin, Wei-Chao Chang
Pathological angiogenesis is a major cause of irreversible blindness in individuals of all age groups with proliferative retinopathy (PR). Mononuclear phagocytes (MPs) within neovascular areas contribute to aberrant retinal angiogenesis. Due to their cellular heterogeneity, defining the roles of MP subsets in PR onset and progression has been challenging. Here, we aimed to investigate the heterogeneity of microglia associated with neovascularization and characterize the transcriptional profiles and metabolic pathways of pro-angiogenic microglia in a mouse model of oxygen-induced proliferative retinopathy (OIR). Using transcriptional single-cell sorting, we comprehensively map all microglia populations in retinas of room air (RA) and OIR mice. We unveil several unique types of PR-associated microglia (PRAM) and identify markers, signaling pathways, and regulons associated with these cells. Among these microglia subpopulations, we found a highly proliferative microglia subset with high self-renewal capacity and a hyper-metabolic microglia subset that expresses high levels of activating microglia markers, glycolytic enzymes and pro-angiogenic insulin-like growth factor 1. Immunohistochemical staining shows these PRAMs were spatially located within or around neovascular (NV) tufts. These unique microglia-types have the potential to promote retinal angiogenesis, which may have important implications for future treatment of PR and other pathological ocular angiogenesis-related diseases.
Zhiping Liu, Huidong Shi, Jiean Xu, Qiuhua Yang, Qian Ma, Xiaoxiao Mao, Zhimin Xu, Yaqi Zhou, Qingen Da, Yongfeng Cai, David J.R. Fulton, Zheng Dong, Akrit Sodhi, Ruth B. Caldwell, Yuqing Huo
We describe affected members of a two-generation family segregating a Stargardt disease-like phenotype caused by a two base pair deletion-insertion, c.1014_1015delGAinsCT;p(Trp338_Asn339delinsCysTyr), in BEST1. The variant was identified by whole exome sequencing and its pathogenicity was verified through chloride channel recording using wild-type (WT) and transfected mutant HEK293 cells. Clinical examination of both patients revealed a similar phenotype at two different disease stages that were attributable to difference in their age at presentation. Hyperautofluorescent flecks along the arcades were observed in the proband, while the affected mother exhibited more advanced retinal pigment epithelium (RPE) loss in the central macula. Full-field electroretinogram testing was unremarkable in the daughter, however, moderate attenuation of generalized cone function was detected in the mother. Electro-oculogram testing in the daughter was consistent with widespread dysfunction of the RPE characteristic of Best disease. Whole-cell patch clamp recordings revealed statistically significant decrease in chloride conductance of the mutant compared to WT cells. This report broadens the clinical spectrum of BEST1-associated retinopathy in the form of a mother and daughter with BEST1 genotype phenocopying Stargardt disease.
Masha Kolesnikova, Jin Kyun Oh, Jiali Wang, Winston Lee, Jana Zernant, Pei-Yin Su, Angela H. Kim, Laura A. Jenny, Tingting Yang, Rando Allikmets, Stephen H. Tsang
Deficiency of glycogen debranching enzyme in glycogen storage disease type III (GSD III) results in excessive glycogen accumulation in multiple tissues, primarily the liver, heart, and skeletal muscle. We recently reported that an adeno-associated virus (AAV) vector expressing a bacterial debranching enzyme (Pullulanase) driven by the ubiquitous CMV enhancer/chicken β-actin (CB) promoter cleared glycogen in major affected tissues of infant GSD IIIa mice. In this study, we developed a novel dual promoter consisting of a liver-specific promoter (LSP) and the CB promoter for gene therapy in adult GSD IIIa mice. Ten-week treatment with an AAV vector containing the LSP-CB dual promoter in adult GSD IIIa mice significantly increased Pullulanase expression and reduced glycogen contents in the liver (-60%), heart (-76%), and skeletal muscle (-63%), accompanied by the reversal of liver fibrosis, improved muscle function, and significant decrease in plasma biomarkers alanine aminotransferase, aspartate aminotransferase, and creatine kinase. Compared to the CB promoter, the dual promoter effectively decreased Pullulanase-induced cytotoxic T lymphocyte responses and enabled persistent therapeutic gene expression in adult GSD IIIa mice. Future studies are needed to determine the long-term durability of the dual promoter mediated expression of Pullulanase in adult GSD IIIa mice and in large animal models.
Jeong-A Lim, Priya S. Kishnani, Baodong Sun
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