Integrative mapping of pre-existing influenza immune landscapes predicts vaccine response

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Abstract

BACKGROUND. Predicting individual vaccine responses is a substantial public health challenge. We developed immunaut, an open-source, data-driven framework for systems vaccinologists to analyze and predict immunological outcomes across diverse vaccination settings, beyond traditional assessments. METHODS. Using a comprehensive live attenuated influenza vaccine (LAIV) dataset from 244 Gambian children, immunaut integrated pre- and post-vaccination humoral, mucosal, cellular, and transcriptomic data. Through advanced modeling, our framework provided a holistic, systems-level view of LAIV-induced immunity. RESULTS. The analysis identified three distinct immunophenotypic profiles driven by baseline immunity: (1) CD8 T-cell responders with strong pre-existing immunity boosting memory T-cell responses; (2) Mucosal responders with prior influenza A virus immunity developing robust mucosal IgA and subsequent influenza B virus seroconversion; and (3) Systemic, broad influenza A virus responders starting from immune naivety who mounted broad systemic antibody responses. Pathway analysis revealed how pre-existing immune landscapes and baseline features, such as mucosal preparedness and cellular support, quantitatively dictate vaccine outcomes. CONCLUSION. Our findings emphasize the power of integrative, predictive frameworks for advancing precision vaccinology. The immunaut framework is a valuable resource for deciphering vaccine response heterogeneity and can be applied to optimize immunization strategies across diverse populations and vaccine platforms. FUNDING. Wellcome Trust (110058/Z/15/Z); Bill & Melinda Gates Foundation (INV-004222); HIC-Vac consortium; NIAID (R21 AI151917); NIAID CEIRR Network (75N93021C00045).

Authors

Stephanie Hao, Ivan Tomic, Benjamin B. Lindsey, Ya Jankey Jagne, Katja Hoschler, Adam Meijer, Juan Manuel Carreño Quiroz, Philip Meade, Kaori Sano, Chikondi Peno, André G. Costa-Martins, Debby Bogaert, Beate Kampmann, Helder Nakaya, Florian Krammer, Thushan I. de Silva, Adriana Tomic

cGAS activation converges with intracellular acidification to promote STING aggregation and pyroptosis in tumor models

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Abstract

The cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway is intimately associated with anti-tumoral immunity; however, the direct involvement of this pathway in tumor cell demise remains elusive. Here, we identified a compound dodecyl 6-hydroxy-2-naphthoate (DHN) that induces pyroptosis in melanoma cells through activating the non-canonical cGAS-STING signaling. DHN targets mitochondrial protein cyclophilin D (CypD) to induce the release of mitochondrial DNA, leading to cGAS activation and cyclic GMP-AMP (cGAMP) generation. Meanwhile, DHN-caused intracellular acidification induces PRKR-like endoplasmic reticulum kinase (PERK) activation, which promotes STING phosphorylation and polymerization in the presence of cGAMP, thereby facilitating the aggregation of STING in the endoplasmic reticulum, which serves as a platform to recruit Fas associated via death domain (FADD) and caspase-8, leading to caspase-8 activation and subsequent gasdermin E (GSDME) cleavage, which ultimately results in pyroptosis of tumor cells and tumor regression in mouse models. The occurrence of this non-canonical cGAS-STING pathway-associated pyroptosis is also observed when both cGAS is activated and intracellular pH declines. Collectively, our findings reveal a pathway that links non-canonical cGAS-STING signaling to GSDME-mediated pyroptosis, thereby offering valuable insights for tumor therapy.

Authors

Li Xiao, Yuan-li Ai, Xiang-yu Mi, Han Liang, Xiang Zhi, Liu-zheng Wu, Qi-tao Chen, Tong Gou, Chao Chen, Bo Zhou, Wen-bin Hong, Lu-ming Yao, Jun-jie Chen, Xianming Deng, Fu-nan Li, Qiao Wu, Hang-zi Chen

The GLYT1 inhibitor bitopertin mitigates erythroid PPIX production and liver disease in erythroid protoporphyria

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Abstract

Erythropoietic protoporphyria (EPP) is a genetic disorder typically resulting from decreased ferrochelatase (FECH) activity, the last enzyme in heme biosynthesis. Patients with X-linked protoporphyria (XLPP) have an overlapping phenotype caused by increased activity of 5-aminolevulinic acid synthase 2 (ALAS2), the first enzyme in erythroid heme synthesis. In both cases, protoporphyrin IX (PPIX) accumulates in erythrocytes and secondarily in plasma and tissues. Patients develop acute phototoxicity reactions upon brief exposure to sunlight. Some also suffer from chronic liver disease, and a small fraction develop acute cholestatic liver failure. Therapeutic options are limited, and none, save hematopoietic stem cell transplantation, directly targets erythroid PPIX accumulation. Bitopertin is an investigational orally available small molecule inhibitor of the erythroid cell surface glycine transporter GLYT1. We establish the bitopertin PPIX inhibitory half-maximal effective concentration in a human erythroblast EPP model and confirm a marked reduction of PPIX in erythroblasts derived from EPP patients. We demonstrate that bitopertin also reduces erythrocyte and plasma PPIX accumulation in vivo in mouse models of both EPP and XLPP. Finally, the reduction in erythroid PPIX ameliorates liver disease in the EPP mouse model. Altogether, these data support the development of bitopertin to treat patients with EPP or XLPP.

Authors

Sarah Ducamp, Min Wu, Juan Putra, Dean R. Campagna, Yi Xiang, Vu Hong, Matthew M. Heeney, Amy K. Dickey, Rebecca K. Leaf, Mark D. Fleming, Brian MacDonald, Paul J. Schmidt

Efficacy and safety of a therapeutic humanized FSH–blocking antibody in obesity and Alzheimer’s disease models

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Abstract

There is growing evidence for direct actions of follicle–stimulating hormone (FSH) on tissues other than the ovaries and testes. Blocking FSH action, either genetically or pharmacologically, protects against bone loss, fat gain, and memory loss in mice. We thus developed a humanized FSH–blocking antibody––MS-Hu6––as a lead therapeutic for three diseases of public health magnitude––osteoporosis, obesity and Alzheimer’s disease (AD) that track together in post–menopausal women. Here, we report the crystal structure of MS-Hu6 and its interaction with FSH in atomistic detail. Using our Good–Laboratory–Practice–Compliant platform (21CFR58), we formulated MS-Hu6 and the murine equivalent Hf2 at an ultra–high concentration; both formulated antibodies displayed enhanced thermal and colloidal stability. A single injection of 89Zr–labelled MS-Hu6 revealed a beta–phase t½ of 89 and 131 hours for female and male mice, respectively, with retention in regions of interest. Female mice injected subcutaneously with Hf2 displayed a dose–dependent reduction in body weight and body fat. Hf2 also rescued recognition memory and spatial learning loss in a context– and time–dependent manner in AD–prone 3xTg and APP/PS1 mice. MS-Hu6 injected into African green monkeys (8 mg/kg) intravenously, and then subcutaneously at monthly intervals, was safe, and without effects on vitals, blood chemistries or blood counts. There was a notable ~4% weight loss in all four monkeys after the first injection, which continued in two of four monkeys. We thus provide IND–enabling data towards an upcoming first–in–human study.

Authors

Anusha R. Pallapati, Funda Korkmaz, Satish Rojekar, Steven Sims, Anurag Misra, Judit Gimenez–Roig, Aishwarya Gangadhar, Victoria Laurencin, Anissa Gumerova, Uliana Cheliadinova, Farhath Sultana, Darya Vasilyeva, Liam Cullen, Jonathan Schuermann, Jazz Munitz, Hasni Kannangara, Surabhi Parte, Georgii Pevnev, Guzel Burganova, Zehra Tumoglu, Ronit Witztum, Soleil Wizman, Natan Kramskiy, Liah Igel, Fazilet Sen, Anna Ranzenigo, Anne Macdonald, Susan Hutchison, Abraham J.P. Teunissen, Heather Burkart, Mansi Saxena, Yelena Ginzburg, Ki Goosens, Weibin Zhou, Vitaly Ryu, Ofer Moldavski, Orly Barak, Michael Pazianas, John Caminis, Shalender Bhasin, Richard Fitzgerald, Se-Min Kim, Matthew Quinn, Shozeb Haider, Susan Appt, Tal Frolinger, Clifford J. Rosen, Daria Lizneva, Yogesh K. Gupta, Tony Yuen, Mone Zaidi

Organ-specific features of human kidney lymphatics are disrupted in chronic transplant rejection

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Abstract

Lymphatic vessels maintain tissue fluid homeostasis and modulate inflammation, yet their spatial organisation and molecular identity in the healthy human kidney, and how these change during chronic transplant rejection, remain poorly defined. Here, we show that lymphatic capillaries initiate adjacent to cortical kidney tubules and lack smooth muscle coverage. These vessels exhibit an organ-specific molecular signature, enriched for CCL14, DNASE1L3, and MDK, with limited expression of canonical immune-trafficking markers found in other organ lymphatics, such as LYVE1 and CXCL8. In allografts with chronic mixed rejection, lymphatics become disorganised and infiltrate the medulla, with their endothelial junctions remodelling from a button-like to a continuous, zipper-like architecture. Lymphatics in rejecting kidneys localise around and interconnect tertiary lymphoid structures at different maturation stages, with altered intra- and peri-lymphatic CD4⁺ T cell distribution. The infiltrating T cells express IFNγ, which upregulates co-inhibitory ligands in lymphatic endothelial cells, including PVR and LGALS9. Simultaneously, lymphatics acquire HLA class II expression and exhibit C4d deposition, consistent with alloantibody binding and complement activation. Together, these findings define the spatial and molecular features of human kidney lymphatics, revealing tolerogenic reprogramming, accompanied by structural perturbations, during chronic transplant rejection.

Authors

Daniyal J. Jafree, Benjamin J Stewart, Karen L. Price, Maria Kolatsi-Joannou, Camille Laroche, Barian Mohidin, Benjamin Davis, Hannah Mitchell, Lauren G. Russell, Lucía Marinas del Rey, Chun Jing Wang, William J. Mason, Byung Il Lee, Lauren Heptinstall, Ayshwarya Subramanian, Gideon Pomeranz, Dale Moulding, Laura Wilson, Tahmina Wickenden, Saif N. Malik, Natalie Holroyd, Claire L. Walsh, Jennifer C. Chandler, Kevin X. Cao, Paul J.D. Winyard, Adrian S. Woolf, Marc Aurel Busche, Simon Walker-Samuel, Lucy S.K. Walker, Tessa Crompton, Peter J. Scambler, Reza Motallebzadeh, Menna R. Clatworthy, David A. Long

Age-dependent brain responses to mechanical stress determine resilience in a chronic lymphatic drainage impairment model

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Abstract

The outflow of 'dirty' brain fluids from the glymphatic system drains via the meningeal lymphatic vessels to the lymph nodes in the neck, primarily the deep cervical lymph nodes (dcLN). However, it is unclear whether dcLN drainage is essential for normal cerebral homeostasis. Using dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) and computational fluid dynamics, we studied the impact of long-term mechanical stress from compromised dcLN drainage on brain solute and fluid outflow in anesthetized rats. We found that in young, but not middle-aged rats, impairment of dcLN drainage was linked to moderately increased intracranial pressure and the emergence of extracranial peri-venous drainage, with no evidence of hydrocephalus at any age. Surprisingly, both age groups showed enhanced brain solute clearance despite reduced glymphatic influx. CSF proteomic analysis revealed cellular stress in the form of low-grade inflammation, and up-regulation of pathways associated with neurodegeneration and blood brain barrier leakage in the rats with impaired lymphatic drainage. Our findings highlight that dcLN drainage is indeed a prerequisite for normal cerebral homeostasis in the rat and reveal the brain’s age-dependent compensatory responses to chronic impairment of its lymphatic drainage pathways.

Authors

Zachary H. Gursky, Zohaib Nisar Khan, Sunil Koundal, Ankita Bhardwaj, Joaquin Caceres Melgarejo, Kaiming Xu, Xinan Chen, Hung-Mo Lin, Xianfeng Gu, Hedok Lee, Jonathan Kipnis, Yoav Dori, Allen Tannenbaum, Laura Santambrogio, Helene Benveniste

NFAT5 dictates crosstalk between intestinal epithelial regenerative capacity and microbiota in murine colitis models

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Abstract

Hypertonic and hyperosmolar stimuli frequently pose challenges to the intestinal tract. Therefore, a resilient epithelial barrier is essential for maintaining gut homeostasis in the presence of osmotic perturbations. NFAT5, an osmosensitive transcription factor, primarily maintains cellular homeostasis under hypertonic conditions. However, the osmoprotective role of NFAT5 in enterocyte homeostasis is poorly understood. Here, we demonstrate that NFAT5 is critical for the survival and proliferation of intestinal epithelial cells (IECs) and that its deficiency accelerates chemically induced or spontaneous colitis in mice. Mechanistically, NFAT5 promotes the survival of IECs and the renewal of intestinal stem cells, thereby regulating the production of mucus and antimicrobial compounds, including RegIII and lysozyme, which consequently shape the gut microbial composition to prevent colitis. Transcriptome analysis identifies HSP70 as a key downstream target of NFAT5 in epithelial regeneration. Loss- and gain-of-function experiments of HSP70 revealed that NFAT5 mitigates experimental colitis through IEC Hsp70, which protected stem cells from inflammation-induced injury and maintained barrier function. In conclusion, our study demonstrates a previously unknown role for NFAT5 in dictating the crosstalk between intestinal stem cells and the microbiota, underscoring the importance of the NFAT5–HSP70 axis in maintaining epithelial regeneration related to gut barrier function, balancing microbial composition, and subsequently preventing colitis progression.

Authors

Se Hyeon Park, Dae Hee Cheon, Yu-Mi Kim, Yeji Choi, Yong-Joon Cho, Bong-Ki Hong, Sang-Hyun Cho, Mi‑Na Kweon, Hyug Moo Kwon, Eugene B. Chang, Donghyun Kim, Wan-Uk Kim

Treg activation during allograft tolerance induction requires mitochondrial-induced TGFβ1 in type 1 conventional dendritic cells

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Abstract

The role of type 1 conventional dendritic cells (cDC1) in tolerance induction to solid organ allografts is unknown and important for strategies that seek to prolong allograft viability. Using a murine model deficient in cDC1s, we report cDC1s are required for donor antigen and costimulation blockade (DST + CoB) tolerance induction and survival of cardiac allografts. cDC1 deficiency led to decreases in CD4+CD25+FoxP3+ T cells within both allograft and spleen tissue of transplant recipients and this was found to be antigen specific. Donor antigen stimulation induced TGF-β1 expression both in vivo cDC1 and in vitro Flt3L derived cDC1. Genetic deletion of Tgfβ1 in cDC1s prevented induction of antigen specific CD4+CD25+FoxP3+ T cells and was associated with cardiac allograft rejection. In parallel, single-cell RNA sequencing and metabolic analysis revealed upregulation of cDC1 mitochondrial metabolic signatures after in vivo exposure to DST + CoB. Genetic inactivation of cDC1 mitochondrial metabolism reduced expression of cDC1 TGF-β1, decreased antigen specific T regulatory cell populations, and impaired allograft tolerance. Taken together, our findings newly implicate cDC1s in strategies to preserve solid organ allografts and also implicate mitochondrial metabolism of cDC1s as a molecular mechanism to enhance the generation of antigen-specific CD4+CD25+FoxP3+ T cells through TGF-β1.

Authors

Samantha L Schroth, Lei Zhang, Rebecca T.L. Jones, Kristofor Glinton, Nikita L. Mani, Hiroyasu Inui, Jesse T. Davidson, Samuel E. Weinberg, Navdeep Chandel, Maria-Luisa Alegre, Edward B. Thorp

Gut-specific histamine 3 receptor signaling orchestrates microglia-dependent resolution of peripheral inflammation

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Abstract

Chronic inflammatory diseases, like rheumatoid arthritis (RA) have been described to cause central nervous system (CNS) activation. Less is known about environmental factors that enable the CNS to suppress peripheral inflammation in RA. Here, we identified gut microbiota-derived histamine as such factor. We show that low levels of histamine activate the enteric nervous system, increase inhibitory neurotransmitter concentrations in the spinal cord and restore homeostatic microglia, thereby reducing inflammation in the joints. Selective histamine 3 receptor (H3R) signaling in the intestine is critical for this effect, as systemic and intrathecal application did not show effects. Microglia depletion or pharmacological silencing of local nerve fibers impaired oral H3R agonist-induced pro-resolving effects on arthritis. Moreover, therapeutic supplementation of the short-chain fatty acid (SCFA) propionate identified one way to expand local intestinal histamine concentrations in mice and humans. Thus, we define a gut-CNS-joint axis pathway where microbiota-derived histamine initiates the resolution of arthritis via the CNS.

Authors

Kerstin Dürholz, Leona Ehnes, Mathias Linnerbauer, Eva Schmid, Heike Danzer, Michael Hinzpeter-Schmidt, Lena Lößlein, Lena Amend, Michael Frech, Vugar Azizov, Fabian Schälter, Arne Gessner, Sébastien Lucas, Till-Robin Lesker, R. Verena Taudte, Jörg Hofmann, Felix Beyer, Hadar Bootz-Maoz, Yasmin Reich, Hadar Romano, Daniele Mauro, Ruth Beckervordersandforth, Maja Skov Kragsnaes, Torkell Ellingsen, Wei Xiang, Aiden Haghikia, Cezmi A. Akdis, Francesco Ciccia, Tobias Bäuerle, Kerstin Sarter, Till Strowig, Nissan Yissachar, Georg Schett, Veit Rothhammer, Mario M. Zaiss

Combinatorial therapy regimens targeting preclinical models of melanoma resistant to immune checkpoint blockade

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Abstract

Few effective therapeutic options exist following progression on immune checkpoint blockade (ICB) for melanoma. Here we utilize a platform incorporating transcriptomic profiling, high-throughput drug screening (HTDS) and murine models to demonstrate the pre-clinical efficacy of several combinatorial regimens against ICB-resistant melanoma. Transcriptomic analysis of ICB-resistant melanomas demonstrated activation of several targetable pathways. HTDS targeting these pathways identified several effective combinations in ICB-resistant patient-derived xenograft models. The combination of cobimetinib and regorafenib (termed Cobi+Reg) emerged as a particularly promising regimen, with efficacy against distinct molecular melanoma subtypes and following progression on ICB in immunocompetent models. Transcriptomic and spatial analysis of Cobi+Reg-treated tumors demonstrated upregulation of antigen presentation machinery, with concomitantly increased activated T cell infiltration. Combining Cobi+Reg with ICB was superior to either modality in vivo. This analytical platform exploits the biology of ICB-resistant melanoma to identify therapeutic vulnerabilities, resulting in the identification of drug combinations that form the basis for rational clinical trial design in the setting of advanced melanoma resistant to ICB.

Authors

Imran Khan, Aida Rodriguez-Brotons, Anukana Bhattacharjee, Vladimir Bezrookove, Altaf Dar, David De Semir, Mehdi Nosrati, Ryan Ice, Liliana Soroceanu, Stanley P. Leong, Kevin B. Kim, Yihui Shi, James E. Cleaver, James R. Miller, Pierre-Yves Desprez, John M. Kirkwood, Marcus Bosenberg, Nathan Salomonis, Sean McAllister, Mohammed Kashani-Sabet