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Abstract
Glioblastoma (GBM) is a lethal brain tumor with a 95% five-year mortality rate, and remains a major unmet clinical need. An innovative approach to target GBM is administration of chimeric antigen receptor (CAR) T cells. In this study we identified B7-H3 as a favorable target antigen for CAR T cell therapy of GBM and developed a B7-H3 targeting CAR T cell. This CAR demonstrates robust, antigen-specific cytolysis and cytokine production, low tonic signaling, and preservation of a stem/naïve cell phenotype. Using orthotopic xenograft models of GBM we show that a single intravenous administration of this B7-H3 targeted CAR confers tumor control, and long-term survival. We identified upregulation of T cell inhibitory ligands PD-L1 and PD-L2 as a mechanism of resistance, and modified our B7-H3 targeting CAR vector to include a secreted a PD-1 blocking scFv. We further demonstrate that concomitant PD-1 blockade by the secreted PD-1 blocking scFv augments the antitumor capabilities of B7-H3-targeting CAR T cells through increased intratumoral infiltration by the CAR T cells and improved effector function. These data demonstrate B7-H3 targeting CAR T cells with concomitant PD-1 blockade is a safe and efficient method for improving the antitumor capacity of CAR T cells for GBM.
Authors
Jonathan F. Khan, Parwiz Abrahimi, Winson Cai, Lauren Dong, Kenny Kwok-Hei Yu, Svena Verma, Yacine Marouf, Sadna Budhu, Tara Pal Chaudhuri, Valeria Estrada Navarro, Mamadou A. Bah, Kelsey Hopland, Yanhong Yang, Terence J. Purdon, Ileana C. Miranda, Viviane Tabar, Jedd D. Wolchok, Taha Merghoub, Renier J. Brentjens
Abstract
Authors
Rocio J. Jimenez-Valdes, Quoc Vo, Alison Morris, Chad Steele, Seyed Mehdi Nouraie, Jonathan K. Alder, Kambez H. Benam
Abstract
Although 95% of serotonin in the human body is produced in the gastrointestinal tract, most prior research work has focused on the brain. Despite its abundance in the gut, serotonin’s role in early intestinal development remains poorly understood. Here we show that serotonin is detected in both the small intestine and large intestine as early as 14 to 15 weeks gestational age. Using single-cell transcriptomics with histological validation, we generated a spatiotemporal atlas of serotonin and serotonin-related genes in the human gut from first trimester to late adulthood. The serotonin synthesis gene, TPH1, was exclusively expressed in enteroendocrine cells at all time points analyzed, with the highest expression in the second trimester. The serotonin reuptake gene, SLC6A4, was largely restricted to mature absorptive enterocytes and increased postnatally. Serotonin receptors also displayed distinct cellular and developmental expression patterns. HTR1E was confined to the first trimester during highly proliferative stage. HTR4 was enriched for in crypt regions, suggesting a role in proliferation for serotonin. Finally, HTR3E was associated with tuft cells throughout development. Together, these findings reveal the dynamic, cell-type-specific regulation of serotonin in the developing human gut, suggesting its importance in early intestinal development, and provide a framework to study its roles in intestinal development and diseases.
Authors
Long Phan, Lauren Smith, Kristin M. Milano, Weihong Gu, Madison S. Strine, Harvey J. Kliman, Liza Konnikova
Abstract
Testosterone is a key determinant of red blood cell (RBC) biology and susceptibility to hemolysis; however, its contribution to donor-dependent variation in RBC quality and transfusion effectiveness remains unclear. Using data from 2,357 male participants in the NHLBI REDS-III RBC-Omics study, we quantified plasma total testosterone, free testosterone (bioavailable form), and androstenedione and evaluated their associations with donor characteristics, RBC hemolysis, and recipient post-transfusion hemoglobin increments, a clinical measure of RBC transfusion effectiveness. Subphysiological testosterone concentrations were common (~35%) and independently associated with increased storage and osmotic hemolysis. Frequent blood donations were independently associated with lower circulating free testosterone concentrations, even after adjustment for demographic and hematologic factors. Genome-wide association analyses identified loci associated with circulating testosterone, including regions near SHBG, TNFSF12, and the long noncoding RNA BALR6. Several testosterone variants were associated with RBC transfusion effectiveness. Specifically, variants associated with lower testosterone (e.g., TNFSF12) corresponded to higher post-transfusion hemoglobin increments (+9%), whereas BALR6 variants associated with higher testosterone were linked to reduced hemoglobin increments (–40%). In contrast, androstenedione-associated variants were not related to hemolysis or transfusion outcomes. Together, these findings demonstrate that genetic and physiologic variation in testosterone contributes to inter-individual variability in RBC quality and transfusion effectiveness.
Authors
Fang Fang, Nareg Roubinian, Xutao Deng, Cassie Kemmler, Jost Klawitter, Jelena Klawitter, Touraj Shokati, Uwe Christians, Grier P. Page, Tamir Kanias
Abstract
The role of CD8+ T cells in filarial infections remains poorly understood. Given the chronic nature of these infections, individuals living in endemic regions are frequently exposed to other pathogens including viruses. Because CD8 cells are essential for antiviral immunity, understanding how filarial infections shape the cytotoxic compartment is essential to elucidate their impact on bystander immunity. We evaluated the phenotype and function of CD8+ T cells from Loa loa-infected (Fil+) and -uninfected (Fil–) individuals at baseline and following cytomegalovirus (CMV) re-stimulation. Filarial infection was associated with increased activation and proliferation of CD8+ T cells, characterized by elevated expression of Ki-67, CD107a, and production of type 1 and 17 cytokines. Upon CMV re-stimulation, Fil+ individuals showed markedly reduced expansion of antigen-experienced (CD137+) and polyfunctional (CD137+IFN-γ+TNF-α+, CD137+IFN-γ+TNF-α+IL-2+) CD8+ T cells, along with decreased cytotoxic activity. Unbiased clustering analysis revealed markedly reduced frequency of the CD8+CD45RA+CD57+ subset in Fil+ individuals- a population further defined through transcriptomic profiling that showed enrichment for cytolytic gene signatures (GZMB, GNLY, GZMH, CD244, CX3CR1). These results demonstrated that filarial infection is associated with an altered CD8+ T cell profile that is associated with failure to mount effective viral-specific effector responses, including impaired cytokine production and cytotoxic activity.
Authors
Camila Queiroz-Glauss, Justin Lack, Daniel E. Sturdevant, Thomas B. Nutman
Abstract
The hypothesized cellular and molecular mechanisms underlying dystonia are broad and include mutations that perturb Ca2+ signaling, including those affecting voltage gated calcium channels (VGCC). In mice, pharmacological activation of neuronal L-type VGCCs induces dystonia in a dose dependent manner. Here we demonstrate that mice expressing a gain-of-function mutation in the L-type VGCC CaV1.2, associated with Timothy syndrome (TS), exhibit motor dysfunction consistent with dystonia. Although CaV1.2 is broadly expressed throughout peripheral tissues and across the brain, we establish that the dystonia-like behavior is driven by neuronal expression of the mutant calcium channel and observe an associated potential excitatory/inhibitory (E/I) imbalance. Because patients with TS have profound metabolic dysregulation, which is associated with some dystonias, we measured changes in circulating metabolites. The dystonia-like events are sensitive to perturbations in pyruvate metabolism, reminiscent of a subset of dystonias associated with pyruvate dysregulation. Our study provides insight into the potential convergence of previously established causes of dystonia, calcium signaling and metabolic homeostasis.
Authors
Patrick Towers, Hong-Gang Wang, Maiko Matsui, Geoffrey S. Pitt
Abstract
Pneumocystis jirovecii pneumonia (PCP) remains a major cause of life-threatening respiratory failure in people with advanced HIV, yet the biological factors associated with mortality are incompletely understood. We performed integrated transcriptomic, proteomic, and metabolomic profiling of bronchoalveolar lavage fluid from 42 adults with HIV-associated PCP, relating molecular signatures to mortality. We found that fungal burden, measured by sputum immunofluorescence, Pneumocystis qPCR, and 1,3-β-D-glucan, did not differ between survivors and non-survivors or correlate with baseline gas exchange. Instead, non-survivors exhibited a bronchoalveolar immunometabolic failure signature characterised by marked depletion of immunoglobulins and complement, reduced pattern recognition receptors and fibroblast growth factor family proteins, and broad disruption of extracellular matrix organisation. Metabolomic profiling revealed enrichment of arginine-urea cycle and tricarboxylic acid pathways, with coordinated accumulation of arginine, citrulline, and TCA cycle intermediates consistent with nitrosative and mitochondrial stress. An integrated proteo-metabolomic score summarising this state was significantly higher in non-survivors and did not correlate with fungal burden or cytomegalovirus co-infection. In an immunodeficient precision-cut lung slice model, antigen-screened intravenous immunoglobulin restored macrophage-mediated Pneumocystis clearance, providing proof-of-concept for opsonic augmentation. Our findings indicate that mortality in HIV-PCP is defined by profound immunometabolic failure, highlighting humoral depletion and impaired alveolar repair as potential targets for host-directed adjunctive therapy.
Authors
Peter Rossi-Smith, Ayanda Trevor Mnguni, Dora Pungan, Robert J. Samuels, Vaishnavi R. Kumaran, Leena Syed, Trevor Ferris, Kamil Skirlo, Joseph N. Jarvis, Nelesh P. Govender, Graeme Meintjes, Sean Wasserman, Jay K. Kolls, Rachel P.J. Lai
Abstract
BACKGROUND. Body weight and insulin resistance in women increase in midlife. It is not known whether this is driven by the menopause transition or solely by chronological aging. We aimed to determine the role of the menopause transition and menopause-related BMI changes in the development of insulin resistance in midlife women. METHODS. Mixed effects, linear spline modeling of longitudinal data in 1315 women, 42- to 52-years-old, pre- or early perimenopausal in 1995 to 1996 with up to 16 follow up visits by 2018. Homeostatic-model-assessed-insulin-resistance (HOMA-IR) was measured up to 12 times. Date of final menstrual period (FMP) was prospectively determined. RESULTS. HOMA-IR increased faster over a 4-year interval extending from 1.5 years prior to 2.5 years after the FMP, than in the years before or after it; p value for both slope changes < 0.0001. In the referent woman (White, age 52 years at FMP, non-smoker, body mass index [BMI] 25.6 kg/m2 at baseline, and not on sex hormone therapy or statins), the average annualized rate of HOMA-IR increase, adjusted for covariates including changes in BMI, was 1.2%, 4.3%, and 0.9% respectively, before, during, and after the 4-year transition. CONCLUSION. Consistent with an independent effect of the menopause transition, insulin resistance increased significantly faster during the transition (from 1.5 years before the to 2.5 years after the FMP) than in the years preceding or following the transition. Future studies need to investigate mechanisms underpinning this observed association and determine the impact of lifestyle on dampening menopause-associated increases in insulin resistance. FUNDING. National Institutes of Health.
Authors
Arun S. Karlamangla, Wei Juan Han, Preethi Srikanthan, Albert Shieh, Duncan Thomas, Barbara Sternfeld, Monique M. Hedderson, Gail A. Greendale
Abstract
Chronic liver disease affects over a billion people worldwide. Despite diverse etiologies, a unifying feature of chronic liver disease is the liver’s impaired ability to regenerate during progression to cirrhosis, but no common molecular mechanism has been identified. Hepatocyte proliferation and liver regeneration depend on nucleoplasmic calcium (Ca2+) signals, and Ca2+ signals in hepatocytes depend on the type 2 inositol trisphosphate receptor (ITPR2) calcium release channel. Here, we found that ITPR2 was localized in part to the hepatocyte nucleus, and this localization depended on the presence of nucleoporin 62 (NUP62). Loss of either ITPR2 or NUP62 disrupted nuclear Ca2+ signaling, and impaired Ca2+ signals in the nucleus blunted nuclear entry of β-catenin. Remarkably, both ITPR2 and NUP62 are progressively lost from hepatocytes in patients with the four most common types of chronic liver disease. These findings identify a microdomain regulating Ca2+ signaling in the hepatocyte nucleus that becomes progressively disrupted as liver disease progresses. Preservation of this nuclear microdomain may be a novel approach to maintain liver regeneration and slow the progression to cirrhosis in chronic liver disease.
Authors
Jittima Weerachayaphorn, Mateus T. Guerra, Naotaka Kugiyama, Emma Kruglov, Dejian Zhao, Piyachat Chansela, Vitoon Saengsirisuwan, Marie E. Robert, Teruo Utsumi, Yasuko Iwakiri, Michael H. Nathanson
Abstract
Persistent production of type I interferons (IFN-Is) is a hallmark of cutaneous lupus erythematosus (CLE). Ultraviolet (UV) light stimulates IFN-I response in the skin and exacerbates CLE. Here, we identify V-type immunoglobulin domain-containing suppressor of T cell activation (VISTA) as a negative regulator of both basal and UV-induced IFN-I response in the skin and show that VISTA limits skin photosensitivity in an IFN-I-dependent manner, in part through Stimulator of Interferon Genes (STING). Furthermore, we demonstrate a novel role for VISTA in keratinocytes both at steady state and in response to UV light. Conditional deletion of VISTA in epidermal keratinocytes results in a ~10-fold increase in basal skin IFN-I scores and a heightened UV-induced skin injury score, both of which are dependent on IFN-I signaling. VISTA-targeting monoclonal antibodies suppress the UV-induced IFN-I response in human keratinocytes and in mice expressing human VISTA in vivo, thereby reducing UV-induced skin injury scores. Together, these findings identify VISTA as a keratinocyte-intrinsic checkpoint that restrains STING-associated IFN-I response in the skin and suggest VISTA agonism as a therapeutic strategy to limit photosensitivity in CLE.
Authors
Zachary T. Peters, Lindsay K. Mendyka, J'Voughnn A. Blake, Himanshu B. Goswami, Angelique N. Cortez, Grace E. Crossland, Sicong Shan, Elizabeth C. Nowak, Myana Keusch, Mrinal K. Sarkar, Johann E. Gudjonsson, Christopher M. Burns, Dorothea T. Barton, Bruce R. Blazar, Tyler J. Curiel, Rodwell Mabaera, Victoria P. Werth, Andrea Kalus, Keith B. Elkon, Randolph J. Noelle, Sladjana Skopelja-Gardner
Abstract
Missense mutations in the UMOD gene are a well-established genetic cause of autosomal dominant tubulointerstitial kidney disease (ADTKD). Here, we report two ADTKD pedigrees carrying de novo UMOD mutations, p.His36Tyr (H36Y) and p.Trp31Cys (W31C). To elucidate the underlying pathogenic mechanisms and explore targeted therapeutic strategies, we generated a UMODH36Y/+ knock-in mouse model using CRISPR/Cas9 technology, which recapitulated the major clinical manifestations observed in patients. Through single-cell RNA sequencing and experimental validation, we demonstrated that uromodulin mutations triggered endoplasmic reticulum (ER) stress and the unfolded protein response, with ferroptosis identified as the predominant mode of cell death in this disease. These findings were further confirmed in plasmid-transfected cell models expressing UMODH36Y and UMODW31C. Moreover, the molecular chaperone HSPA1A was identified as a potential therapeutic target. Geranylgeranylacetone, targeting HSPA1A as a chaperone drug, effectively mitigated endoplasmic reticulum stress, alleviated ferroptosis, and delayed the progression of renal dysfunction. Based on novel uromodulin mutations, our study reveals a pathogenic ER-ferroptosis axis in ADTKD-UMOD, deepens the insight into the pathogenesis of ADTKD-UMOD, and provides a promising strategy for developing chaperone therapy with drug repurposing in genetic kidney diseases.
Authors
Wen Shi, Yan Yang, Xianli Wen, Qianqian Wu, Jinxuan Wei, Xin-Lu Wang, Junyuan Shen, Siqi Peng, Xiaoliang Zhang, Bi-Cheng Liu, Bin Wang
Abstract
The hypothalamic-pituitary-adrenal (HPA) axis integrates central neural processing and responses to stress with endocrine and metabolic responses. We utilized a monoclonal antibody binding corticotrophin-releasing factor (anti-CRF) to achieve durable HPA axis modulation. In mice, anti-CRF treatment decreased plasma corticosterone, food-intake, body weight and fat mass, but preserved lean mass and improved metabolic parameters including insulin sensitization. These body composition effects were observed in middle aged mice on normal chow or high fat diet, aged mice, and Mc4r-/- and ob/ob mice. Single-dose studies demonstrated impacts on weight gain and body composition lasting beyond the period of pharmacological target engagement. Multi-organ transcriptomic and proteomic analyses revealed organ-specific effects of anti-CRF and are consistent with altered glucocorticoid receptor (GR) signaling as a mediator of the observed phenotypes. These studies support anti-CRF-mediated HPA-axis modulation as a metabolic and anti-obesity therapeutic approach distinct from incretins.
Authors
Zachary A. Krumm, Tariful Islam, Caroline M. Watson, Yong Ran, Yona Levites, Hunter S. Futch, Luming Yin, Edgardo Rodriguez-Lebron, Xuefei Liu, Kazi Farhana Afroz, Ariella Goloborodsky, Thomas B. Ladd, Kristy D. Dillon, Danny Ryu, Jennifer L. Bizon, Jada Lewis, Karen A. Scott, Annette de Kloet, Nicholas T. Seyfried, Eric G. Krause, Karen N. McFarland, Todd E. Golde
Anti-Notch plus endocrine therapy in ER+ breast cancer inhibits cancer stem cells by increasing DAXX
Abstract
Resistance to endocrine therapy (ET) in ER+ breast cancer is mediated by Notch signaling, but the clinical application of anti-Notch therapy has been limited by the lack of predictive biomarkers. To identify Notch-regulated biomarkers, we conducted a pre-surgical window study evaluating ET combined with the γ-secretase inhibitor (GSI) MK-0752. RNA expressions in tumors were measured using an Affymetrix array and by real-time PCR. ET plus GSI showed more genes were decreased than ET alone. Specifically, DAXX, NOXA, and LFNG RNAs were increased, while fifteen additional transcripts were decreased. Mechanistically, GSI reduced Notch1 occupancy at CSL-binding elements within HES1, HEY2, HEYL, CCND1, MKI67, and DAXX genes, and inhibited cancer stem cells (CSCs) by 90% to 100%. This anti-CSC effect required DAXX, while GSI treatment or Notch1/4 knockdown increased DAXX expression, suggesting transcriptional repression by Notch. Using mouse tumor xenograft studies, ET plus MK-0752 resulted in complete regression of MCF-7 tumors, with DAXX-high tumors showing greater treatment sensitivity. Clinically, high DAXX expression was associated with improved recurrence-free and overall survival. This study found that anti-Notch plus ET in ER+ breast cancer inhibits cancer stem cells by increasing DAXX, a promising predictive biomarker. These findings support clinical evaluation of therapies that increase DAXX expression.
Authors
Kathy S. Albain, Debra Wyatt, Andrei Zlobin, Susan G. Hilsenbeck, Cheryl M. Czerlanis, Daniel S. Peiffer, Kyle R. Convington, Constantine Godellas, Shelly S. Lo, Patricia A. Robinson, Kathy Czaplicki, Barbara Busby, Davide Bova, Ping Tang, Patrick J. Stiff, Suzanne A.W. Fuqua, Lucio Miele, Clodia Osipo
Serine palmitoyltransferase (SPT) inhibition in SPTSSA-related complex hereditary spastic paraplegia
Abstract
Defective feedback inhibition of serine palmitoyltransferase (SPT) caused by pathogenic SPTSSA variants underlies childhood-onset complex hereditary spastic paraplegia, yet the developmental timing and therapeutic reversibility of sphingolipid dysregulation remain unclear. We generated a knock-in mouse carrying the disease-associated SptssaT51I variant and show that heterozygous animals exhibit preserved intrinsic SPT activity but impaired ORMDL-mediated regulation, leading to sustained elevation of bioactive sphingolipid intermediates that peak during postnatal myelination. Although gross myelin formation was initially maintained, excess sphingolipid flux rendered oligodendrocytes and neurons selectively vulnerable. Dietary L-serine, which augments SPT substrate availability, amplified sphingolipid accumulation in mutant but not wild-type mice, unmasking progressive spasticity, axonal injury, myelin ultrastructural defects, and, when administered during early postnatal development, severe pulmonary pathology likely responsible for lethality. Pharmacologic SPT inhibition with myriocin normalized sphingolipid synthesis, prevented serine-induced lethality, and reversed neurological and metabolic abnormalities. Translating these findings, treatment of a child with SPTSSA-T51I–associated complex hereditary spastic paraplegia using the FDA approved SPT inhibitor D-Cycloserine resulted in sustained improvement in spasticity, reduced baclofen requirement, and decreased plasma levels of neurofilament light chain (NFL). These data define dysregulated sphingolipid biosynthesis as a developmentally and metabolically sensitive driver of neurodegeneration and suggest SPT inhibition as a mechanistically grounded therapeutic strategy.
Authors
Yi Gong, Robert Thompson, Ashley M. Glover, Kenneth Gable, Sita D. Gupta, Natalie Golovanov, Julie Tassinari, Nathan Casey, Brian D. Wishart, Elise L. Townsend, April Qian, Martin Selig, Armen Yerevanian, Teresa M. Dunn, Florian Eichler
Abstract
Premature infants often require supplemental oxygen therapy, a major risk factor for bronchopulmonary dysplasia and subsequent neurodevelopmental impairment. To determine how neonatal hyperoxia affects prefrontal cortex (PFC) development, we exposed neonatal mice to 85% oxygen (O₂) from postnatal day (P)1–P14 and performed integrated single-nucleus transcriptomic and chromatin accessibility profiling with in vivo and in vitro validation. Hyperoxia induced sex-dependent cellular remodeling, reducing L4/5 intratelencephalic projecting glutamatergic neurons in females and mature oligodendrocytes in males. Across both sexes, hyperoxia suppressed oligodendrocyte maturation, with decreased expression of the myelination genes proteolipid protein 1 (Plp1) and myelin basic protein (Mbp), altered chromatin accessibility, and increased oligodendrocyte transcription factor 2 (OLIG2) protein expression. Regulatory responses were sex specific, with tumor protein p53 (TP53)-regulated metabolic disruption and lysine demethylase 3A (Kdm3a) induction in females, and Netrin-1 signaling in males. Hyperoxia impaired oligodendrocyte progenitor cell (OPC) proliferation and differentiation. These abnormalities were recapitulated in postmortem PFC tissue from infants with BPD and human induced pluripotent stem cell (iPSC)-derived OPCs. These findings show that neonatal hyperoxia disrupts PFC development through sex-dependent effects on neuronal and oligodendrocyte lineages while converging on impaired myelination, highlighting oligodendrocyte dysfunction as a clinically relevant consequence of neonatal oxygen exposure.
Authors
Xingrao Ke, Wei Yu, Carl F. Schreck, Joseph M. Varberg, Melissa A. Gener, Daniel A. Louiselle, Sheng Xia, Sherry M. Mabry, Heather L. Menden, Venkatesh Sampath, Robert H. Lane, Kaela M. Varberg
Abstract
BACKGROUND. Long-COVID, or post-acute sequelae of COVID-19 (PASC), leads to debilitating physical and cognitive deficits. No PASC molecular signature present in patients with diverse symptoms has been described. While PASC engages pathways regulating pro-fibrotic programs, no comparison of PASC with fibrosis-associated epigenetic landscapes has been reported at the bulk or single-cell level. We hypothesize that a subset of DNA methylation changes are present in PASC patients from multiple cohorts, predominate in specific immune or inflammatory cell-types, and overlap with the epigenetic profile of patients at risk of pulmonary fibrosis. METHODS. Two distinct prospective cohorts, in 2021 and in 2022-24, involving 203 patients with PASC underwent bulk whole genome methylation sequencing (WGMS). Single-cell WGMS data was generated from an independent PASC cohort. Sixty-eight pre-pandemic patients with conditions elevating risk of pulmonary fibrosis development were compared with PASC. RESULTS. Sixteen differentially methylated regions distinguished PASC versus multiple independent, healthy controls. Single-cell analysis of these regions indicated trending relative hypermethylation at multiple cell types, with T4 lymphocytes eliciting hypermethylation at most of the sequences identified to be PASC-specific DMRs in the bulk analysis. Patients at risk of pulmonary fibrosis development elicited DNA methylation changes overlapping PASC. CONCLUSION. In two independent prospective cohorts, blood WGMS identifies differentially methylated regions associated with PASC. Hypermethylation of these regions is predominantly, although not exclusively, associated with T4 lymphocytes and overlap with changes present in pre-pandemic pulmonary fibrosis at-risk patients. FUNDING. National Institutes of Health award HL160661 (AJ); and AI173035 (AJ and RSA).
Authors
Andy Madrid, Joseph Balnis, Lisa A. Drake, Anupama Tiwari, Vraj J. Patel, Paul J. Feustel, Jihua Liu, Sündüz Keleş, Fangxiu Xu, Chris L. Wright, Alvaro G. Hernandez, Recai Yucel, Marc A. Judson, Harold A. Singer, Reid S. Alisch, Ariel Jaitovich
Abstract
BACKGROUND. Hepatocellular carcinoma (HCC) exhibits molecular heterogeneity that challenges histopathologic classification and biomarker discovery. We assessed whether spatially resolved N-glycan imaging with machine learning could classify tumor regions and infer glutamine synthetase (GS) status. METHODS. In this retrospective study, MALDI mass spectrometry imaging of N-glycans was performed on formalin-fixed, paraffin-embedded sections from two independent cohorts (discovery, n = 88; validation, n = 60) with pathologist annotation. An XGBoost classifier was trained on 90 discriminative N-glycan features using patient-grouped cross-validation. Performance was assessed by AUC for pixel- and biopsy-level discrimination of tumor from adjacent non-tumor tissue, and for GS status classification. RESULTS. Pixel-level AUCs were 0.95 (cross-validation) and 0.89 (external validation); biopsy-level AUCs were 1.0 and 0.97, correctly identifying 97% of tumor-containing biopsies. Probability maps recapitulated pathologist-defined boundaries; UMAP embeddings captured inter- and intratumoral heterogeneity. Discriminative species (m/z 2393.846, 1905.634, 1743.579, 1809.639) reflected complex, fucosylated, branched remodeling. N-glycans bearing six GlcNAc residues were enriched in GS+ (n = 45) versus GS− (n = 17) tumors (P = 0.001) and discriminated GS status (AUC = 0.75), consistent with GLUL and MGAT5 upregulation in TCGA-LIHC. CONCLUSION. MALDI N-glycan imaging with machine learning enables spatially resolved, objective classification of HCC and links glycan phenotypes to tumor-associated metabolic programs. TRIAL REGISTRATION. Not applicable; retrospective analysis of archival, de-identified tissue. FUNDING. NIH/NCI R01CA285370, 1R01CA289381, R33CA267226, R01CA282022, R21CA263464, R21CA286287, R01CA253460, S10OD030212, R01CA251155, R01CA250227, U01CA271887, P50CA295495, P30CA138313, P20GM130457, P30DK123704, P30DK120531,R24DK139775; NIH/NIA R01AG078702; Smart State Endowment, State of South Carolina; LeDucq Foundation.
Authors
Muhammed F. Bayram, Jade K. Macdonald, Andrew DelaCourt, Peggi M. Angel, Richard R. Drake, Aatur Singhi, David Geller, Satdarshan P. Monga, Amit Singal, Anand Mehta
Abstract
BACKGROUND. Neurological Long COVID (n-LC) includes persistent cognitive and autonomic symptoms after SARS-CoV-2 infection. Prior studies of post-COVID conditions have described diverse humoral autoreactivity. It remains unclear whether n-LC is associated with a consistent CNS-directed humoral signature. METHODS. We performed a cross-cohort case-control analysis to detect autoantibodies in cerebrospinal fluid (CSF) and serum from n-LC participants. In the Yale COVID Mind Study cohort, CSF from n-LC participants and pre-pandemic and recovered controls was assessed using mouse brain immunofluorescence and proteome-wide phage immunoprecipitation sequencing (PhIP-Seq), followed by supervised modeling and orthogonal validation assays. In the Epidemiology, Immunology, and Clinical Characteristics of Emerging Infectious Diseases with Pandemic Potential (IDCRP EPICC) cohort, post-COVID sera collected prior to iPhone- or iPad-based cognitive screening were profiled by PhIP-Seq and compared between participants with and without cognitive impairment. RESULTS. CSF immunoreactivity on mouse brain tissue was observed in both n-LC and controls, with similar overall frequencies. PhIP-Seq identified sparse, patient-specific peptide reactivities to nuclear and neuronal proteins in CSF and serum. Supervised models provided limited discrimination between cases and controls. Candidate autoantigens had limited disease specificity on orthogonal testing. EPICC serum autoantibody profiling similarly failed to distinguish individuals with and without cognitive impairment. CONCLUSIONS. Across cohorts and compartments, n-LC was not associated with a shared CNS-directed autoantibody signature using the approaches employed. Observed heterogeneity may reflect biological diversity, although limited statistical power to detect a shared response cannot be excluded. FUNDING. Grants HU00012020067, HU00012120103, HU00011920111, R01NS125693, R01MH125737, and R01AI157488 from the Defense Health Program and NIH.
Authors
Debanjana Chakravarty, Ravi Dandekar, Vishal D. Lashkari, Iris Tilton, Lindsay McAlpine, Jennifer Chiarella, Allison Nelson, Thomas Ngo, PeiXi Chen, Chung-Yu Wang, Aditi Saxena, Bryan Castillo-Rojas, Kelsey Zorn, David R. Tribble, Timothy H. Burgess, Leah H. Rubin, Stephanie A. Richard, Brian K. Agan, Simon D. Pollett, Shelli Farhadian, Serena Spudich, Samuel J. Pleasure, Michael R. Wilson
Abstract
Recent ACC/AHA guidelines recommend ≥5% weight loss over six months to reduce cardiovascular risk in obesity. However, some populations paradoxically exhibit increased cardiovascular disease (CVD) following weight loss. We investigated whether mild food restriction (MfR) accelerates atherogenesis through pro-atherogenic lipid remodelling. ApoE-deficient mice were fed Chow or a high-cholesterol/high-fat(HCHF) diet for six months, with MfR producing 5% lower body-weight gain. Atherosclerotic burden was quantified histologically, and hepatic lipidomes were analysed by ESI–MS/MS and compared with plasma lipidomic profiles from CVD patients. MfR improved insulin sensitivity by lowering blood glucose and triglycerides but increased circulating cholesterol and accelerated atherosclerosis. HCHF-fed mice developed larger, more numerous plaques with increased necrotic core formation, thinner fibrous caps, higher intima-to-media ratios, and inflammatory cell infiltration. Similar pro-atherogenic changes occurred in Chow-fed mice subjected to MfR. Mechanistically, MfR increased hepatic free cholesterol and enriched pro-atherogenic phosphatidylcholine, phosphatidylethanolamine, lysophosphatidylcholine, sphingomyelin, ceramide, and cholesterol ester species, yielding a CERT1 score of 8.1 indicative of cardiovascular risk. These lipid alterations mirrored plasma lipidomic signatures from CVD patients with diabetes. Collectively, our findings demonstrate that mild caloric restriction is not universally atheroprotective and can accelerate atherosclerosis in hypercholesterolaemic states by disrupting cholesterol homeostasis and promoting pro-atherogenic lipid remodelling.
Authors
Yun Zhu, Yanzhe Xu, Gerhard Liebisch, Juergen Borlak
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis (Mtb) is the leading infectious cause of death globally. Despite wide use of antiretroviral therapy (ART) by people living with HIV, the risk of TB remains increased. To understand immune interactions within lung granulomas, we compared spatial transcriptomics of Mtb and simian immunodeficiency virus (SIV) in co-infected macaques with or without ART as a model for HIV/Mtb co-infection. Spatially differentiated transcriptional profiles were observed in Mtb-only granulomas, with myeloid cells enriched in metabolic/antimicrobial pathways within the inner ring and T cell co-stimulatory/activation pathways enriched in the outer ring. These spatially distinct patterns were lost in SIV/Mtb granulomas with higher enrichment in type I IFN pathways compared to Mtb-only granulomas. SIV/ART/Mtb granulomas had an intermediate transcriptional pattern without restoration to Mtb-only granulomas, despite a lack of viral replication. Cell-cell communication was reduced among SIV/Mtb co-infected groups. These data suggest that HIV disrupts spatially organized immune functions of granulomas, which are not fully restored by ART.
Authors
Jessica M. Medrano, Persis Sunny, Collin R. Diedrich, Pauline Maiello, Christopher Kline, Tara Rutledge, Edwin Klein, Joshua T. Mattila, Jishnu Das, Zandrea Ambrose, Philana Ling Lin
