bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tear cytokine profiling for ocular graft versus host disease utilizing a new multiplex assay
Authors: Li Andrew J , Martinez-Guasch Fernando , Sajjan Seema , Cao Xuefang , Atanackovic Djordje , Sunshine Sarah 
Published: August 2023

Abstract
Many patients who have undergone allogeneic hematopoietic stem cell transplantation (aHSCT) as part of cancer therapy achieve remission. However, nearly 50% of these patients develop Graft versus Host Disease (GVHD), a chronic autoimmune disease that can damage eyes. Quantifying specific cytokine changes in tears may reveal biomarkers and future treatment targets for ocular GVHD (oGVHD). Compared to other assays, the IsoLight Codeplex Secretome multiplex assay (Isoplexis) has advantages of high-throughput analyses and small sample requirements, but has yet to be validated for tears. This study evaluates the tears of a patient with oGVHD utilizing Isoplexis and correlates the cytokine profile with clinical disease severity.
As a pilot study, we collected normal and oGVHD patient tears which we analyzed on two backgrounds– standard Bovine Serum Albumin (BSA) or artificial tears (ATs). The controls were ATs (negative) and a concentrated cytokine solution (positive).
The cytokine levels of artificial tears alone were below the limit of detection (LOD) as expected. Out of a 22 cytokine panel, oGVHD patient tears had elevated TNF-α, TNF-β, perforin, MIP-1α, MIP-1β, MCP-1, IL-2, IL-4, IL-5, IL-7A, IL-9, IL-13, IL-15, IFN-γ, granzyme B, and GM-CSF with ATS background, but no cytokines above the LOD in the BSA background plate. The control tears had elevated IP-10. Elevated cytokines for the oGVHD patient corresponded to clinical symptom findings.
The results suggest that using ATs as the background improves sensitivity to detect tear cytokines on Isoplexis. Elevated IL-7A and GM-CSF in oGVHD tears parallel literature findings. Further sample evaluation will continue to validate Isoplexis for tear cytokine analyses.
Supported by Program for Research Initiated by Students and Mentors (PRISM), University of Maryland School of Medicine Office of Student Research and Eversight, Cigarette Restitution Fund, University of Maryland Greenebaum Comprehensive Cancer Center
Therapeutic improvement of Parkinson’s disease transplantation therapy through modulating the immune system
Authors: Park Tae Yoon , Kim Kwang-Soo 
Published: August 2023

Abstract
We report clinically the implantation of patient-derived midbrain dopaminergic progenitor cells (mDAPs), differentiated in vitro from autologous iPSCs, in a patient with idiopathic Parkinson’s disease (PD). The patient-specific mDAPs were produced under Good Manufacturing Practice conditions and characterized as having the phenotypic properties of substantia nigra pars compacta neurons; testing in a humanized mouse model indicated an absence of immunogenicity to these cells. The cells were implanted into the putamen (left hemisphere followed by right hemisphere, 6 months apart) of a patient with PD, without the need for immunosuppression. Clinical measures of symptoms of PD after surgery stabilized or improved at 18 to 24 months after implantation. Although our previous data (Schweitzer*, Park* et al., NEJM, 382(20) p1926–1932, 2020) showed that using autologous mDAPs can avoid graft rejection, cell survival and functional recovery in the first patient as assessed by 18F-DOPA PET scan analysis and clinical motor assessments was modest, suggesting that survival of mDA neurons may have been suboptimal even in autologous implantation. We have developed a safer and more effective treatment by not only increasing mDA neuron survival by simultaneously controlling the causative immune response, but also by modulating the problematic proliferative property, which is a characteristic of progenitor cells after implantation. In conclusion, our new study suggests that initial, specific mDA neuron survival in these grafts is strongly affected by the host innate immune response, while long-term graft survival is subject to the adaptive immune response, elucidating a two-phase involvement of the immune system for graft survival.
This work was supported by NIH grants (NS070577 and OD024622), the Parkinson’s Cell Therapy Research Fund at McLean Hospital and Massachusetts General Hospital, and the Masson Family Endowed Scholar in Neurosurgery, and the George A. Lopez, MD Endowed Chair in Neurosurgery.
Identification of Novel Immunosuppressive Drug Targets for Liver Transplantation Using Genome-Scale Metabolic Modeling
Authors: Aghamiri Sara Sadat , Puniya Bhanwar Lal , Amin Rada , Murry Daryl J , Helikar Tomáš 
Published: August 2023

Abstract
The global database on donation and transplantation reported 129,681 worldwide organ transplants in 2020, with kidneys and livers being the most commonly transplanted organs. Rejection of the transplanted organ by the host’s immune system is a common complication and a major reason for graft failure and patient mortality. To address these limitations, we developed genome-scale metabolic models of liver and CD4+ T cells using the pipeline for MetAbolic Drug Repurposing IDentification-MADRID and integrating our data analysis results from RNA-seq, proteomics, and microarray human sample datasets (step 1). Drug targets obtained from the ConnectivityMap database are mapped to metabolic genes in the model where systematic knockouts are performed on each gene which leads to identifying differential fluxes (step 2). Our human-cell-specific models identified novel immunosuppressive drug targets by integrating differentially expressed genes in post-liver transplanted non-tolerant versus healthy control individuals and differential fluxes (step 3). We identified 193, 217, and 196 potential metabolic gene targets for T-helper 1, 2, and 17, respectively, against patients with a non-tolerant phenotype after liver transplantation. This genome-scale metabolic modeling approach for liver transplantation can assist in personalized treatment by using any individual’s sample data at step 1 and 2. It can also save time and resources in preclinical drug development studies by predicting more precise drug targets and drug repurposing based on patients’ omics data. By using this approach, we aim to improve the success rates of liver transplantations and reduce the complications associated with organ rejection.
The work was supported by University of Nebraska collaboration initiatives.
Serum proteomic analysis of peripartum cardiomyopathy reveals a unique disease with distinctive dysregulation of inflammatory and cholesterol metabolism pathways
Authors: Lovell Jana , Bermea Kevin , Rousseau Sylvie , Cohen Charles D , Bhalodia Aashik , Zita Marcelle Dina , Yu Jinsheng , Head Richard D , Blumenthal Roger S , McNamara Dennis M , Sharma Garima , Adamo Luigi 
Published: August 2023

Abstract

Background
The pathophysiology of peripartum cardiomyopathy (PPCM) and its defining features when compared to other forms of cardiomyopathy remain unclear, thus limiting the development of targeted therapies.

Methods
To address this knowledge gap, we utilized a systems biology approach and performed high-throughput aptamer-based proteomic analysis (SOMAscan 7K) of serum samples from women with PPCM (n = 67) or non-peripartum cardiomyopathy (NPCM, n = 31), and age-matched peripartum and non-peripartum healthy women (n = 10 each). Samples were obtained from the Investigation in Pregnancy-Associated Cardiomyopathy and the Intervention in Myocarditis and Acute Cardiomyopathy studies. Comparative analyses were performed based on the presence of cardiomyopathy and peripartum status.

Results
Principal component analysis revealed distinct proteomic signatures of PPCM, NPCM, and each healthy control group (p&lt;0.00001 for all pairwise comparisons). Comparative analyses of PPCM and NPCM identified hundreds of differentially expressed serum proteins before and after normalization to healthy controls. Pathway enrichment analyses of proteins differentially expressed in PPCM highlighted dysregulation of several biological pathways related to inflammation and cholesterol metabolism, including upregulation of the anti-inflammatory liver-X receptor/retinoid X receptor (LXR/RXR) pathway.

Conclusions
Serum proteomic profiling of PPCM indicates that PPCM is a unique disease entity characterized by the dysregulation of pro-inflammatory and cholesterol metabolism-related anti-inflammatory pathways. These pathways may represent potential novel therapeutic targets in PPCM.
Complement activation as a biomarker and a pathogenic factor in rhabdomyolysis-induced acute kidney injury
Authors: Roumenina Lubka T , Boudhabhay Idris , Grunenwald Anne 
Published: August 2023

Abstract
Rhabdomyolysis is a life-threatening condition caused by skeletal muscle damage with acute kidney injury (AKI) being the main complication dramatically worsening the prognosis. Specific treatment for rhabdomyolysis-induced acute kidney injury (RIAKI) is lacking and the mechanisms of the injury are unclear.
We discovered intra-kidney complement activation in tubules and vessels of patients and mice with rhabdomyolysis-induced acute kidney injury. Moreover, elevation of complement proteins and activation fragments in the urine of RIAKI patients compared to rhabdomyolysis without RIAKI and healthy donors by complement multiplex assays supported a pathogenic role of the complement system. Urinary C5a distinguished AKI, while Ba was elevated even for the patients without AKI, suggesting infra-clinical manifestations. Complement deficient mice (C3−/−, FB−/−) were protected from RIAKI. The transcriptomic signature of RIAKI mice included a strong inflammatory and apoptotic component, which were C3/complement-dependent, as they were normalized in C3 knockout mice. The intra-kidney macrophage population expressed a complement-sensitive phenotype, overexpressing CD11b and C5aR1. A kinetic mouse model of RIAKI revealed that heme toxicity is the first pathogenic mechanism to injure the tubules, evidenced by kidney transcriptomic signature (QuantiGene RNA assay), followed by neutrophils and inflammatory monocytes, upregulating C5aR1 (flow cytometry). Thus, our results demonstrate a direct pathological role of heme and complement in rhabdomyolysis-induced acute kidney injury.
CSL Behring research grant
Circulating Antibodies Specific for Dietary Fiber Glycans
Authors: Patnode Michael , Vega Giovanni , Hernandez-Kaempf Nicolette , Deshpande Nikita 
Published: August 2023

Abstract
The mammalian gut lumen contains an extremely diverse collection of microbial species and dietary constituents. Protein and carbohydrate antigens on commensal bacterial surfaces stimulate the production of specific antibodies, which can be secreted and bind their epitopes in the lumen. Despite the high abundance of plant polysaccharides (dietary fiber) in the intestine, it remains unclear whether these foreign carbohydrates stimulate the production of secreted anti-fiber antibodies. Here, we characterize antibody specificity in mice using a panel of artificial food particles composed of microscopic magnetic beads, each simultaneously tagged with a fluorescent barcode and coated with one of 64 different dietary or host glycan preparations. Using this approach, we detected secreted antibodies in the cecum and circulating antibodies in serum that selectively bind subsets of dietary glycans. Alteration of the host diet to include supplemental dietary fiber led to a significant increase in anti-fiber antibodies in serum. In contrast, cecal fiber-specific antibody reactivity was not increased after fiber feeding. Analysis of the gut microbiota revealed that relative abundances of Akkermansia muciniphila were significantly higher in mice fed supplemental fiber relative to mice fed a control diet. This work raises the possibility that taxa such as A. muciniphila are involved in the production of antibodies specific for dietary components.
Supported by a grant from NIH (K01 DK124445)
Fates of Commensal Specific, Innate-like CD8+ T cells in the Gut
Authors: Farley Taylor K , Krishnamurthy Siddharth , Powrie Fiona , Belkaid Yasmine 
Published: August 2023

Abstract
Barrier tissues such as the skin and gut are host to a variety of microbes collectively termed the microbiota. To maintain host homeostasis, sufficient exposure to the microbiota is necessary, however, diseases such as Inflammatory Bowel Disease (IBD), have been described as occurring amidst breakdown in the normal communication between host and microbe. Fundamentally, IBD is a disease of aberrant immune activation to the microbiota and epithelial barrier dysfunction. At the skin barrier, we have previously described the H2-M3 restricted, CD8+ T cell response in mice after topical exposure to a commensal microbe that aids in barrier maintenance and epithelial repair. However, the residence of these H2-M3 restricted, commensal specific T cells in the gut, and potential contribution to barrier function in this tissue is unknown. We have now identified H2-M3 restricted CD8+ T cells populating the lamina propria and intraepithelial compartments of both the colon and small intestine following novel commensal exposure. Further, during inflammatory conditions these cells drastically expand and produce pro-inflammatory Type 1 cytokines. Following these discoveries, we have developed novel tetramer reagents to track and interrogate the function of H2-M3 restricted T cell responses to Helicobacter hepaticus, a common gut commensal with known roles in perpetuating colitis in immunocompromised animals. Utilizing these tools, we hope to uncover how these non-classically restricted immune responses to the same commensal under homeostatic or inflammatory conditions differ, to identify potential targets to correct aberrant reactivity to the microbiota during colitis.
NIH-Oxford Cambridge Scholars Program
Vaccination prior to SARS-CoV-2 infection reduces autoreactive antibody induction
Authors: Lin Chun-Yang , Castellaw Ashley , Brice David ,   SJTRC Study Team, Schultz-Cherry Stacey , Thomas Paul , Wolf Josh , McGargill Maureen 
Published: August 2023

Abstract
SARS-CoV-2 infection leads to diverse outcomes ranging from asymptomatic infection to death. Several studies reported elevated autoreactive antibodies in SARS-CoV-2-infected individuals compared to healthy controls, suggesting SARS-CoV-2 infection promotes autoantibodies, which could increase the risk of autoimmunity. However, it is not known whether autoreactive antibodies observed after infection were present in individuals prior to infection. Further, the prevalence, duration, and vaccine impact on autoreactive antibodies are unresolved. Since elevated autoreactive antibodies precede the onset of autoimmune disease, it is important to investigate the impact of SARS-CoV-2 infection on self-reactive antibodies. We established a longitudinal study to collect baseline PBMC and plasma samples from participants at enrollment, before SARS-CoV-2 infection or vaccination. Participants were screened weekly by nasal swab PCR to detect asymptomatic infection. Additional samples were collected after confirmed SARS-CoV-2 infection and assessed for autoreactive antibodies predictive of various autoimmune disorders. Preliminary analysis showed that a subset of individuals exhibited an increase in autoreactive antibodies following infection, while other individuals unexpectedly displayed decreased levels. Notably, individuals infected after vaccination displayed fewer changes in autoreactive antibodies compared to infection prior to vaccination. Our data suggest that SARS-CoV-2 infection increases specific autoreactive antibody levels but does not induce a widespread increase in all autoreactive antibodies. Moreover, SARS-CoV-2 vaccination prior to infection reduced autoantibody induction.
Supported by grants from NIH CEIRS HHSN272201400006C and Household Respiratory Virus SARS-CoV-2 Transmission and Immunity Sub-Study (HRTS) 3U01AI144616-02S1
Thymic innate lymphoid cells promote thymocyte differentiation of transplanted hematopoietic progenitors in immunodeficient mice
Authors: Houques Chloe , Machado Alice , Pouzolles Marie , Harly Christelle , Taylor Naomi , Zimmermann Valérie S 
Published: August 2023

Abstract
Patients with combined immunodeficiencies can be cured by intravenous transfer of allogeneic hematopoietic stem and progenitor cells (HSPC). However, complications such as an impaired and delayed T cell differentiation are unfortunately common, notably due to the defective thymic architecture in these patients and the requirement of HSPC homing to the thymus. To circumvent these problems, we have developed an innovative approach based on the direct targeting of HSPC into the thymus by intrathymic (IT) injection. Using ZAP70-deficient mice as a paradigm, we previously showed that IT injection of HSPC can support a long-term thymus-autonomous differentiation. Here, we show that the IT injection of WT HSPC results in a rapid engraftment and differentiation. Donor-derived thymocytes expand &gt;100-fold, accounting for &gt;13% of thymus cellularity by 3 weeks post IT transfer and importantly, engraftment occurs in the absence of cytoreductive conditioning. While mature CD4 thymocyte differentiation occurs in 3 weeks, the differentiation of mature Treg thymocytes requires 4 weeks. The kinetics of thymic Treg development parallels the generation of a thymic medulla, with the appearance of mature medullary thymic epithelial cells at 3–4 weeks post transplantation. Notably, the generation of the thymic medulla is associated with the differentiation of donor-derived RORγT+ innate lymphoid cells (ILC). While ILC are not required for physiological thymopoiesis, we find that they are critical for T cell differentiation in ZAP70-deficient mice presenting with an absence of the thymic medulla. These results may open new therapeutic avenues, promoting the differentiation of ILC via IT-mediated HSPC transfer, enhancing T cell differentiation.
Supported by grants from ANR (CHIC) and AFM-Telethon
Role of paracrine mTOR signaling in regulating thymus size and function
Authors: Wedemeyer Sarah A , Jones Nicholas , Wimberly Kymberly , Xiao Yangming , Griffith Ann V 
Published: August 2023

Abstract
The thymus is the primary site of T cell generation, where the unique thymic stromal microenvironment governs T cell differentiation. However, the size of the thymus declines precipitously relatively early in life, resulting in declining production of naïve T cells. Homeostatic mechanisms drive a shift toward an oligoclonal T cell memory, leaving the elderly less responsive to vaccines and new infections. Preventing or reversing age-associated thymic atrophy therefore holds potential for extending the health span. Mechanisms governing thymic atrophy have been difficult to identify because the primary targets of atrophy, cortical thymic epithelial cells (cTECs), are rare and difficult to isolate. Characterization of the transcriptional response of thymic stromal cells during age-related atrophy and experimental regeneration suggested that paracrine mTOR signaling in cTECs promoted by ligands expressed in medullary TECs (mTECs) may be required to maintain the cellular architecture of the cortical stroma and preserve thymus size. To test these hypotheses, we generated two new tissue-specific transgenic mouse lines overexpressing mTOR-activating growth factors (IGF1 and FGF21) in most mTECs. Ongoing flow cytometry and confocal microscopy experiments indicate faithful transgene expression in mTECs, and suggest that mTEC-derived growth factors promote temporally distinct patterns of mTORC1 and mTORC2 signaling in cTECs to promote thymus growth and maintenance with age. This work was supported by NIH R21AI154109 and T32 AI138944-05.
Supported by grants from NIH (R21 AI154109, T32 AI138944-05)
NDRG3 is a novel regulator of T and B cell development with phosphorylation-specific activity and phenotypes
Authors: Boone D Tyler , Abdullah Leena , Huang Yina H 
Published: August 2023

Abstract
Common lymphoid progenitors (CLPs) in the bone marrow give rise to both T and B cells, but the mechanisms underpinning downstream cell fate decisions have yet to be fully elucidated. We have identified N-Myc Downstream Regulated Gene 3 (NDRG3) - a highly conserved regulator of Wnt/B-catenin signaling - as a novel regulator of lymphocyte cell fate decisions and a substrate of Akt kinase. To determine the effect of NDRG3 phosphorylation, hematopoietic stem cells (HSCs) overexpressing a phospho-null (S331A) or phospho-mimetic (S331E) mutant of NDRG3 were transferred into lethally irradiated mice followed by analysis of the reconstituted immune populations. S331A-expressing cells developed a 3:1 preference for the T cell fate while those expressing S331E had a 9:1 preference for the B cell fate. To further probe the effects of NDRG3 phosphorylation, we developed a mouse model that utilizes IL-7Ra-driven Cre to express phospho-null NDRG3-S331A from the endogenous locus. NDRG3-S331A expressing thymocytes displayed a faster transition through the preTCR and TCR checkpoints. Given the importance of TCF1 in thymocyte development, NDRG3-S331A mice were crossed to TCF1-GFP and TCF1-RE-GFP reporter mice to examine effects on the Wnt/TCF1 signaling pathway. In the spleen, T cells were increase at the expense of B cells. Within the B cell population, NDRG3-S331A cells exhibited a 4:1 preference for the marginal zone to follicular B cell fate that was associated with increased levels of IRF4 and IRF8 transcription factors, which are necessary for proper B cell development. These data reveal that NDRG3 controls the developmental kinetics and pathways governing T and B cell development and maturation in a phosphorylation-dependent manner.
Supported by NIH grant R01 AI089805 and a training fellowship from the Burroughs Wellcome Fund.
Aire Drives Steroid Hormone Biosynthesis by Medullary Thymic Epithelial Cells
Authors: Donahue Kaitlynn , Taves Matthew , Ashwell Jonathan D 
Published: August 2023

Abstract
Thymocytes progress toward mature T cells through a series of antigen-specific selection steps facilitated by thymic epithelial cells (TECs) in the cortex, the site of positive selection, and medulla, the site of negative selection. TECs produce glucocorticoids (GCs), which enhance positive selection and increase the fitness of the T cell antigen-specific repertoire, but which TEC subpopultion does this, and how it is regulated, is unknown. We generated a reporter mouse that expresses a fusion protein containing Cyp11b1, the enzyme that mediates the last step in de novo GC production, and the fluorescent tag mScarlet knocked into the endogenous Cyp11b1 locus. We found that Cyp11b1 is exclusively expressed in medullary TECs (mTECs), consistent with the notion that GC antagonize negative selection. This is seemingly at odds with the fact that mTECs facilitate negative selection via the transcription factor Aire, which drives promiscuous expression of tissue-restricted antigens (TRAs) vital for establishing central immune tolerance. We found that Cyp11b1 is primarily expressed in Aire+ and post-Aire mTECs and is absent in mTECs of Aire-deficient mice. Transcriptomic analysis showed that most genes of the GC biosynthetic pathway are expressed in mTECs in an Aire-dependent manor. Moreover, we found that their actual steroid product was produced by WT but not Aire-deficient thymi. We propose that in addition to its well-established role of inducing TRAs that promote negative selection, Aire has an obverse function in inducing production of GC that antagonize negative selection, which together expand and enhance the TCR repertoire.