bluuebunny/crossref_metadata_2025_split huggingface dataset:
A tumor-restricted glycoepitope of podocalyxin correlates with immune evasion in high-grade serous ovarian carcinoma.
Authors: Brassard Julyanne , Hernaez Diana Canals , Hughes Michael R , Milne Katy , Dean Pamela , Warren Mary , Zhang Kevin , Banville Allyson C , Smazynski Julian , Bond David , Nelson Brad H , Roskelley Calvin D , McNagny Kelly M 
Published: January 2023

Abstract
High-grade serous ovarian carcinoma (HGSOC) is an aggressive tumor with a 5-year disease-free survival of roughly 15%, partly because it is usually diagnosed at an advanced stage. Podocalyxin (Podxl) is a highly glycosylated sialomucin normally expressed by vascular endothelia and kidney podocytes. Strikingly, Podxl expression is frequently upregulated by a variety of tumors (including HGSOC) and is consistently associated with poor prognosis. We capitalized on the fact that glycosylation pathways are frequently dysregulated in cancer to develop an antibody, PODO447, that recognizes a tumor-restricted glycoform of Podxl not expressed on normal tissue. While the exact epitope remains to be identified, our results suggest that PODO447 binds an epitope comprising a peptide domain of Podxl in combination with the core 1 O-GalNAc glycan (T-antigen). When coupled to a cytotoxin, a PODO447-antibody-drug conjugate (ADC) effectively kills human tumor cells in vitro and in xenografted mice. While the vast majority of ovarian tumors highly express the Podxl core protein, only a subset of these express the PODO447 epitope. Strikingly, tumors that express a high level of PODO447 epitope tend to be those that lack infiltrating CD8+ T cells and CD20+ B cells: a phenotype that has previously been linked to immune evasion and poorest disease-free survival. Furthermore, we find that PODO447 is a more consistent marker of these immunologically “cold” tumors than a number of other markers, including CA125, mesothelin and folate receptor α. These results highlight the PODO447-epitope as a highly selective diagnostic marker of poor outcome tumors and the PODO447-ADC as a novel strategy for therapeutic intervention.
This research was supported by the Canadian Institutes of Health Research (Grant Number: PJT-166180), the School of Biomedical Engineering (The University of British Columbia) postdoctoral fellowship and the Michael Smith Foundation for Health Research (MSFHR) research trainee award.
Role of the extracellular ATP/adenosine pathway in neutrophil-mediated T cell suppression in ovarian cancer microenvironment
Authors: Giridharan Thejaswini , Suzuki Sora , Emmons Tiffany R , Khan A N M Nazmul , Yaffe Michael B , Zsiros Emese , Odunsi Kunle , Bhalla Manmeet , Ghanem Elsa Bou , Segal Brahm H 
Published: January 2023

Abstract
The extracellular ATP (eATP)/adenosine (ADO) pathway is a key modulator of innate and adaptive immunity and is a target for immunotherapy for cancer. In the tumor microenvironment (TME) and conditions of chronic injury, ATP is released by dying cells and is hydrolyzed by the ecto-nucleotidase CD39 to AMP, and further to ADO by CD73. We previously observed that normal neutrophils (PMN) acquire a T cell suppressor phenotype mimicking PMN-MDSCs when exposed to the TME. Using a coculture system consisting of ascites supernatants (ASC) from patients with ovarian cancer (OC) as an authentic component of the TME and concentrations of healthy donor PMN and T cells that mimic those in OC ascites, we found that ASC-primed PMNs inhibit stimulated T cell proliferation, activation and metabolic responses. This suppressor activity was dependent on several PMN pathways, including complement signaling and NADPH oxidase. Since PMNs regulate and respond to signaling from the eATP/ADO pathway, we asked whether eATP/ADO mediates PMN suppressor function. PMNs had high constitutive expression of CD39 that was unaffected by ASC exposure, and inhibition of CD39 by POM-1 abrogated PMN suppressor function. CD73 inhibitor Adenosine 5′-(α,β-methylene) diphosphate also abrogated PMN suppressor function while using a different inhibitor (AB-680) had no effect. Neither ADO receptor inhibitors nor the addition of adenosine deaminase to deplete ADO affected PMN suppressor function. Together, these studies point to eATP as a modulator of PMN suppressor function in the TME and the potential to abrogate suppression by targeting CD39. Future studies will address the specific signaling functions of eATP on PMN in the TME that drive suppressor function.
Supported by grant from NIH (5R01CA188900)
“X”ploring the multifaceted functions of NLRX1 in triple-negative breast cancer
Authors: Nagai Margaret A , Woolls Mackenzie , Imran Khan M , Tupik Juselyn , Allen Irving C 
Published: January 2023

Abstract
Breast cancer is a devastatingly common and deadly malignancy, and despite improved survival resulting from improved detection and treatment, triple-negative breast cancer (TNBC) remains difficult to treat. While historically studied in the context of infectious diseases, a multifaceted anti-inflammatory pattern recognition receptor called NLRX1 has recently been investigated in several types of cancers due to its involvement in several pathways significant to tumorigenesis and disease progression. This project seeks to define the role of NLRX1 in TNBC. To achieve this, we generated novel Nlrx1−/−(KO) mice compatible with the widely-used 4T1 murine model of TNBC. We also generated 4T1 cells that either overexpress or knockdown NLRX1, as well as their respective controls (4T1OE, 4T1OE-CTL, 4T1KD, 4T1KD-CTL). KO and wild-type (WT) mice were then injected with unaltered 4T1 cells or one of the four altered 4T1 cell lines. We then quantified tumor growth, final tumor volume, and lung metastasis as a measure of disease burden. This in vivo work demonstrated that NLRX1 is protective against disease burden when expressed in healthy host tissues but is problematic when overexpressed by 4T1 cells. Ex vivo and in vitro experiments then revealed a pro-migratory phenotype in 4T1OE cells, likely as the result of altered TGF-β signaling and/or the PI3K-Akt-mTOR pathway as a means to impact epithelial-mesenchymal transition. Combined, we believe the function of NLRX1 in TNBC depends on the cell in which it is expressed (i.e. healthy vs cancerous), and that this function may ultimately be a result of altered epithelial-mesenchymal transition pathways.
Leveraging the Treg-intrinsic CTLA4-PKCη signaling pathway for cancer immunotherapy
Authors: Liu Hsin Yu , Pedros Christophe , Kong Kok-Fai , Canonigo-Balancio Ann J , Xue Wen , Altman Amnon 
Published: January 2023

Abstract
Our previous studies revealed a critical role of a novel CTLA4-PKCη signaling in mediating the suppressive activity of Tregs in antitumor immunity. Here, we extended these findings into a biologically and clinically more relevant context. We have analyzed the role of PKCη in antitumor immunity in intact tumor-bearing mice with Treg− or CD8+ T cell-specific Prkch deletion, including in a therapeutic model of combinatorial treatment. Using two models of mouse transplantable cancer and a genetically engineered autochthonous hepatocellular carcinoma (HCC) model, we found that mice with Treg-specific Prkch deletion displayed a significantly reduced growth of B16-F10 melanoma and TRAMP-C1 adenocarcinoma tumors. Tumor growth reduction was associated with a less immunosuppressive tumor microenvironment, indicated by increased numbers and function of tumor-infiltrating CD8+ T cells and elevated expression of the costimulatory ligand CD86 on CD103+ DCs. In contrast, CD8+ T cell-specific Prkch deletion had no effect on tumor growth and the abundance or functionality of CD8+ T cells. Similar beneficial antitumor effects were found in mice with germline or Treg-specific Prkch deletion that were induced to develop an autochthonous HCC. Lastly, using a therapeutic model, we found that monotherapies consisting of Treg-specific Prkch deletion or vaccination with irradiated Flt3L-expressing B16-F10 tumor cells post-tumor implantation significantly delayed tumor growth. This effect was more pronounced in mice receiving a combination of the two immunotherapies. These findings demonstrate the potential utility of PKCη inhibition as a viable clinical approach to treat cancer patients, especially when combined with adjuvant therapies.
Funded by the NIH grant 5R01CA233862
Identification of CPAF as the immunoprevalent antigen of Chlamydia trachomatis
Authors: Li Yanli , Warren Joanna , Poston Taylor , Shaw Fiona , Conrad Shayla , Xu Yinyan , Zheng Xiaojing , O’Connell Catherine M , Hillier Sharon L , Wiesenfeld Harold C , Darville Toni , Goonetilleke Nilu 
Published: January 2023

Abstract
Chlamydia trachomatis (CT) is a common sexually transmitted bacterial infection, that in women can cause pelvic inflammatory disease and infertility. No preventative vaccine has been developed against CT. Immunity to CT is primarily mediated by Th1 CD4+ T cells. We are defining immunoprevalent CT proteins in a well-defined cohort of CT seropositive women with the goal of defining novel vaccine immunogens. We screened 30 women one month after a CT-positive test by cultured IFN-γ ELISpot. Ten-day short-term cell lines (STCL) were generated against overlapping peptides spanning 21 CT antigens. The threshold for a positive CT-specific T cell response (≥ 300 spot-forming cells, SFU, per 106 cells) was defined following a screening of 12 CT seronegative donors. CT− specific T cell responses were detected in 27/30 CT-seropositive women. On average, women harbored T cell responses to two CT proteins (range 0–6). Strikingly, CT858 (CPAF) elicited a T cell response in 16/30 women with an average of 966 IFN-g SFU/106 cells (range 300–3,633 SFU/106 cells). Data to date suggest CPAF-specific T cell responses are predominantly CD4-restricted. In preliminary studies, we have also detected CT-specific T cell responses in men with documented CT infection, including a T cell response to CPAF. We are currently mapping CPAF T cell epitopes and expanding our screen to other CT secreted proteins. In summary, CT858 (CPAF) is an immunoprevalent antigen in women and a promising vaccine immunogen.
Supported by UNC Chlamydia Vaccine Initiative (U19AI144181)
Establishment of influenza-specific lung tissue-resident helper memory CD4+ T cells relies on expression the eATP sensor P2RX7
Authors: da Silva Henrique Borges , Santiago-Carvalho Igor , de Gois Macedo Bruna , Vardam-Kaur Trupti , van Dijk Sarah 
Published: January 2023

Abstract
Influenza remains an infection of high medical relevance. Development of universal anti-influenza vaccines will require a better knowledge of lung immune responses. That includes influenza-specific CD4+ T cells, which establish long-term lung residency and induce a diversified local protective response to subsequent infection. Lung-resident memory CD4+ T cells are heterogeneous, including Th1-like cells, and a subset that shares phenotypic and functional features with follicular helper (Tfh) cells – called tissue-resident helper (Trh). Notably, both Tfh and lung Trh cells express the extracellular ATP (eATP) sensor P2RX7 at high levels. Given its known deleterious role in Tfh cells, we investigated if P2RX7 could also limit the Trh pool in influenza-infected lungs. Contrary to our hypothesis, T cell-specific P2RX7 ablation led to a significant decrease in the Trh cell subset. Consequently, lungs of T cell-P2RX7 knockout mice harbor reduced B cell and CD8+ T cell responses. Initial Trh cell establishment is not affected by P2RX7 knockout; rather, P2RX7-deficient Trh cells gradually decay over time. This is associated with increased apoptosis and decreased in situ proliferation of P2RX7-knockout Trh cells. Our bulk RNA-seq analysis of lung CD4+ T cells revealed many cell cycle-associated genes poorly expressed in P2RX7-knockout cells. Some (but not all) Trh-fate genes are also decreased in P2RX7 deficiency. We are currently performing single-cell RNA-seq to define whether P2RX7 promotes the Trh fate in a particular subset of lung precursor cells. Our data shows that, in response to influenza, P2RX7 promotes lung-resident Trh cells, suggesting this eATP sensor has opposite roles in Tfh-like CD4+ T cells in a tissue-specific manner.
Supported by grant from NIH (R00 AI139381)
Induction of Autophagy reduces IFN-I mediated Inflammation and restores anti-HIV-1 T Cell response in vivo
Authors: Zhen Anjie , Mu Wenli , Rezek Valerie , Martin Heather , Carrillo Mayra , Hamid Philip , Lizarraga Miguel , Yang Otto , Jamieson Beth , Kitchen Scott 
Published: January 2023

Abstract
A hallmark of HIV-1 infection is chronic inflammation. Chronic immune activation drives the pathogenesis of HIV-1 infection, leading to loss of CD4+ T cells and immune exhaustion. Previously, we demonstrated that persistent type I interferon (IFN-I) signaling drives T cell exhaustion during chronic HIV infection and combined anti-retroviral therapy (ART) and IFN-I receptor blockade could lead to reduced inflammation, accelerated viral suppression and HIV reservoir. However, as IFN-Is are key regulators for antiviral immunity, more specific interventions to fine-tune IFN-I signaling and chronic inflammation are needed. Autophagy is a homeostatic mechanism for disposal of damaged cellular organelles and elimination of intracellular pathogens, which is pivotal for cellular homeostasis, T cell development and function. Autophagy is also impaired during HIV-1 infection. Here we demonstrate that autophagy is directly linked to IFN-I signaling. Impairment of autophagy leads to accumulation of damaged mitochondria and spontaneous IFN-I signaling. Autophagy inducers reduce IFN-I signaling in activated macrophages and restore functions of exhausted anti-HIV-1 T cells in vitro. Importantly, autophagy inducer treatment in HIV-1 infected humanized bone marrow/liver/thymus (BLT) mice significantly reduced persistent IFN-I signaling and immune activation, restored exhausted antiviral T cell responses, and accelerated viral suppression by ART. Autophagy inducer treatment also led to reduced viral rebound after ART withdrawal. Taken together, our data suggest that therapeutically targeting autophagy is a promising approach for treating persistent immune activation and improve immune control of HIV replication.
This work was funded by NIAID 1R21AI140866 (to Zhen), NIDA R01DA-52841 (to Zhen), NIAID R2120200174 (PIs: Xie&Zhen), NCI 1R01CA239261-01 (to Kitchen), NIH Grants NIH Grants P30AI28697 (the UCLA CFAR Virology Core, Gene and Cell Therapy Core, and Humanized Mouse Core), U19AI149504(PIs: Kitchen & Chen), CIRM DISC2-10748, UPLIFT: UCLA Postdocs’ Longitudinal Investment in Faculty (Award # K12 GM106996) (to Carrillo), R01 AG052340 (to Jamieson). This work was also supported by the UCLA AIDS Institute, the James B. Pendleton Charitable Trust, and the McCarthy Family Foundation. We would also like to thank Drs. Romas Geleziunas and Jeff Murry and the people at Gilead for providing the antiretroviral drugs used in this study.
Characterization of cytokine measurement in human serum, plasma, urine, tears, milk, CSF, and saliva with a MILLIPLEX® multiplex immunoassay
Authors: Steiner Harold L , Luo Hong , Ahmed Tanzir , Gilliam Brooke , Saporita Anthony J , Qiang Xiao 
Published: January 2023

Abstract
Multiplex immunoassays are valuable research tools for studying circulating cytokines. Here we evaluate the ability of the MILLIPLEX® Human Cytokine/Chemokine/Growth Factor Panel A (Cat. No. HCYTA-60K) 48-plex immunoassay to reproducibly measure cytokines in matched human serum and plasma samples from healthy donors. For comparison, three other bead-based cytokine multiplex kits, featuring many of the same analytes, were analyzed in parallel. Two different lots from each kit were tested with the same matched sample cohort and data were analyzed with Belysa® software. The HCYTA-60K kit was unique in its use of a fixed standard curve, resulting in superior consistency in curve performance between lots. Sample value ratios and correlation demonstrated remarkable consistency of serum and plasma measurement between lots of the HCYTA-60K kit.
Further, detectability of additional sample types (urine, tears, milk, CSF, and saliva) was determined with the HCYTA-60K kit. Samples from healthy donors for each biofluid were tested to determine detectability. All analytes could be measured in at least one of the additional sample types. To characterize neuroinflammation during progressive stages of neurological disease, CSF cytokines were measured in samples from mild cognitive impairment, Alzheimer’s Disease, and healthy controls.
Our study illustrates the reliability of the MILLIPLEX® HCYTA-60K kit for reproducible measurement of cytokines in serum and plasma between different kit lots. Additionally, we characterize its ability to measure cytokines in urine, tears, milk, CSF, and saliva. These results highlight the utility and robustness of the HCYTA-60K multiplex panel for the quantification of cytokines in diverse biofluids.
Ablation of cDC2 lineage specification by mutations within the −165 kb Zeb2 enhancer
Authors: Liu Tiantian , Kim Sunkyung , Desai Pritesh , Kim Do-Hyun , Huang Xiao , Ferris Stephen T , Wu Renee , Ou Feiya , Egawa Takeshi , Van Dyken Steven J , Diamond Michael S , Kubo Masato , Murphy Theresa L , Murphy Kenneth M 
Published: January 2023

Abstract
Efforts to determine the unique functions of the two types of classical dendritic cells, cDC1 and cDC2, are hindered by limited understanding of the divergence of the common dendritic cell progenitor (CDP). Some transcription factors act in commitment of already specified progenitors, such as Batf3 which stabilizes Irf8 autoactivation at the +32 kb Irf8 enhancer, but how other factors control CDP divergence remains unknown. Here, we report the transcriptional mechanism of CDP divergence and describe the first requirements for pre-cDC2 specification. Genetic epistasis analysis suggested that Nfil3 acts upstream of Id2, Batf3, and Zeb2 in cDC1 development but has not revealed its mechanism or targets. Analysis of newly generated NFIL3 reporter mice showed extremely transient NFIL3 expression during cDC1 specification. CUT&RUN and ChIP-seq analysis identified NFIL3 binding in the −165 kb Zeb2 enhancer at sites that also bind CCAAT-enhancer-binding proteins (C/EBPs). Mutation of these NFIL3/C/EBP sites by in vivo CRISPR/Cas9 targeting revealed functional redundancy, with C/EBPs and NFIL3 competing in binding these sites to support or repress Zeb2 expression, respectively. Mutation of these three NFIL3/C/EBP sites eliminated Zeb2 expression in myeloid, but not lymphoid progenitors, producing mice that completely lacked pre-cDC2 specification and mature cDC2 in vivo. These mice failed to make an appropriate TH2 response against H. polygyrus infection, consistent with cDC2 supporting TH2 responses to helminths. Notably, Zeb2 expression is not required to maintain cDC2 identity, but acts only to block cDC1 specification. Thus, the competition between C/EBPs and NFIL3 binding at the −165 kb Zeb2 enhancer determines CDP divergence.
Pathological metabolic adaptation of neutrophils recruited to cystic fibrosis airway microenvironment can not be reversed by modulator therapy
Authors: Cammarata-Mouchtouris Alexandre , Collins Genoah L , Kim Susan O , Moncada Diego , Tirouvanziam Rabindra , Chandler Joshua D 
Published: January 2023

Abstract

Background
Neutrophilic inflammation is a hallmark of cystic fibrosis (CF) lung disease. Prior studies from our group show that blood neutrophils undergo metabolic and functional adaptations upon entry into the CF lung lumen that causes them to become anabolic, while repressing bacterial killing function and enhancing degranulation. The recent advent of highly effective modulator therapy (HEMT) for the CFTR channel (mutated in CF) has improved patient outcomes, but it is unclear how HEMT impact CF lung neutrophilic inflammation.

Method
We used an organotypic model in which blood neutrophils are transmigrated through differentiated airway epithelial cells towards a chemoattractant control (leukotriene B4, LTB4), or airway supernatant from CF patients not on HEMT (CFASN) or on HEMT (CFMOD). We conducted phenotypic (FACS, CFU-assay) and metabolomic (metabolomics,13C6-glucose tracing) analysis of the transmigrated neutrophils.

Results
CFMOD-recruited neutrophils contained ivacaftor (a HEMT drug), demonstrating exposure to the therapy. Compared to LTB4-recruited neutrophils, CFASN/CFMOD-recruited neutrophils showed increased AMP, GMP and intracellular and secreted metabolites related to citric acid cycle activity. 13C6-glucose flux indicated similar rates of extracellular glucose utilization in all transmigrated neutrophils, but higher total glycolysis to lactate in CFASN/CFMOD-transmigrated neutrophils.

Conclusion
Pathological metabolic adaptations of neutrophils following transmigration into CF airway fluid are not substantially altered by HEMT. Further studies are needed to assess the potential impact on functional adaptations by these cells.
Supported by NIH (R56 HL150658), Cystic Fibrosis Foundation (CAMMAR21F0, TIROUV19G0), I3 Teams Research Award (Emory), and CF@LANTA, a component of Emory University and Children’s Healthcare of Atlanta.
Developing a synbiotic biotherapy to prevent allergic responses to food
Authors: Hesser Lauren A , Maccio-Maretto Lisa , Hubbell Jeffrey , Nagler Cathryn 
Published: January 2023

Abstract
Over the past generation, the prevalence of food allergies has risen dramatically, but the development of treatments has lagged. The commensal gut microbiome is critically involved in regulating allergic responses to food. Our laboratory has described a humanized model of cow’s milk allergy (CMA) in which germ-free mice are colonized with feces from healthy or CMA infants and sensitized to the cow’s milk allergen b-lactoglobulin (BLG). The healthy infant microbiota and specifically a single Clostridial species, Anaerostipes caccae, protect against the development of anaphylaxis, while the CMA microbiota does not induce this protection. We isolated a novel sub-strain of A. caccae (A. caccae_lahuc) from the feces of a healthy infant, sequenced its genome, and characterized its growth on various substrates in vitro. A. caccae_lahuc produces high concentrations of butyrate, a key immunoregulatory molecule in the gut which we hypothesize is critical to its protective impact. A. caccae_lahuc engrafts readily into the dysbiotic CMA microbiota, but co-delivery with lactulose is required for measurable butyrate production in vivo. Lactulose undergoes primary degradation by bacteria in the CMA feces which release small metabolites that A. caccae_lahuc can ferment into butyrate. Preliminary data show that this novel synbiotic biotherapy (A. caccae_lahuc + lactulose) prevents allergic responses to BLG in CMA-colonized mice as measured by serum mMCPT-1 and core body temperature upon challenge, and type 2 cytokine production in BLG-stimulated splenocytes. Further exploration into the mechanisms behind this therapeutic effect will contribute toward the larger goal of developing bacterial biotherapeutics against food allergies.