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Cbl-b is a negative regulator of T cell activation, and in murine models, a lack of Cblb results in resistance of T effector (Teff) cells to T regulatory (Treg) cells, a feature of T cells in many autoimmune diseases. Here, we used trackable gene editing approaches to knock out CBLB in primary human CD4+ T cells. We found that CBLB-knockout (CBLB-KO) CD4+ T cells were hyperproliferative and produced excessive amounts of IL-2. CBLB-KO CD4+ T cells were resistant to Treg suppression in vitro, which was partially reversed by blockade of IL-2. RNA-sequencing and puromycin incorporation assays demonstrated that CBLB-KO CD4+ T cells can overcome Treg suppression on the transcriptional and translational levels, resulting in the overproduction of cytokines to drive the proliferation and activation of Teff cells. These findings highlight a potential mechanism of Teff resistance in human autoimmune disease and the power of gene editing primary T cells to explore disease mechanisms.

Objectives This study seeks to comprehensively analyze the impact of smoking history on outcomes after endoscopic transsphenoidal hypophysectomy (TSH) for pituitary adenoma. Design This was a retrospective study. Setting This study was done at the tertiary care center. Participants Three hundred and ninety-eight adult patients undergoing TSH for a pituitary adenoma. Main Outcome Measures Clinical and tumor characteristics and operative factors were collected. Patients were categorized as never, former, or active smokers, and the pack-years of smoking history was collected. Years since cessation of smoking was obtained for former smokers. Specific outcomes included postoperative cerebrospinal fluid (CSF) leak, length of hospitalization, 30-day return to the operating room, and 30-day readmission. Smoking history details were comprehensively analyzed for association with outcomes. Results Any history of smoking tobacco was associated with return to the operating room (odds ratio [OR] = 2.67, 95% confidence interval [CI]: 1.05–6.76, p = 0.039), which was for persistent CSF leak in 58.3%. Among patients with postoperative CSF leak, any history of smoking was associated with need for return to the operating room to repair the CSF leak (OR = 5.25, 95% CI: 1.07–25.79, p = 0.041). Pack-years of smoking was positively associated with a return to the operating room (OR = 1.03, 95% CI: 1.01–1.06, p = 0.048). In all multivariable models, all negative outcomes were significantly associated with the covariate: occurrence of intraoperative CSF leak. Conclusion This is the first study to show smoking may have a negative impact on healing of CSF leak repairs after TSH, requiring a return to the operating room. This effect appears to be dose dependent on the smoking history. Secondarily, intraoperative CSF leak as covariate in multivariable models was significantly associated with all negative outcomes.

Regulatory T cells (Tregs) suppress the activation and subsequent effector functions of CD4 effector T cells (Teffs). However, molecular mechanisms that enforce Treg-mediated suppression in CD4 Teff are unclear. We found that Tregs suppressed activation-induced global protein synthesis in CD4 Teffs prior to cell division. We analyzed genome-wide changes in the transcriptome and translatome of activated CD4 Teffs. We show that mRNAs encoding for the protein synthesis machinery are regulated at the level of translation in activated CD4 Teffs by Tregs. Tregs suppressed global protein synthesis of CD4 Teffs by specifically inhibiting mRNAs of the translation machinery at the level of mTORC1-mediated translation control through concerted action of immunosuppressive cytokines IL-10 and TGFβ. Lastly, we found that the therapeutic targeting of protein synthesis with the RNA helicase eIF4A inhibitor rocaglamide A can alleviate inflammatory CD4 Teff activation caused by acute Treg depletion in vivo. These data show that peripheral tolerance is enforced by Tregs through mRNA translational control in CD4 Teffs.

Recruitment of regulatory T cells (T regs ) to tumors is a hallmark of cancer progression. Tumor-derived factors, such as the cytokine thymic stromal lymphopoietin (TSLP), can influence T reg function in tumors. In our study, we identified a subset of T regs expressing the receptor for TSLP (TSLPR + T regs ) that were increased in colorectal tumors in humans and mice and largely absent in adjacent normal colon. This T reg subset was also found in the peripheral blood of patients with colon cancer but not in the peripheral blood of healthy control subjects. Mechanistically, we found that this T reg subset coexpressed the interleukin-33 (IL-33) receptor [suppressor of tumorigenicity 2 (ST2)] and had high programmed cell death 1 (PD-1) and cytotoxic lymphocyte–associated antigen 4 (CTLA-4) expression, regulated in part by the transcription factor Mef2c. T reg -specific deletion of TSLPR, but not ST2, was associated with a reduction in tumor number and size with concomitant increase in T H 1 cells in tumors in chemically induced mouse models of colorectal cancer. Therapeutic blockade of TSLP using TSLP-specific monoclonal antibodies effectively inhibited the progression of colorectal tumors in this mouse model. Collectively, these data suggest that TSLP controls the progression of colorectal cancer through regulation of tumor-specific T reg function and represents a potential therapeutic target that requires further investigation.

To compare isometric hamstring strength deficits, knee laxity, functional outcomes, and patient-reported outcomes between patients who underwent anterior cruciate ligament (ACL) reconstruction with doubled semitendinosus and gracilis tendon autograft (ST/G) versus quadrupled semitendinosus autograft (ST), at a minimum follow-up of 1-year postoperatively.Patients who underwent ACL reconstruction with ST/G or ST hamstring autografts were retrospectively identified. Isometric hamstring strength was tested with a hand-held dynamometer at 30, 60, and 90° of knee flexion. Anterior knee laxity was assessed using a KT-1000 arthrometer. Functional outcomes were collected using the single-leg hop test and single-leg squat test. Side-to-side differences were determined and compared between the ST/G and ST groups. Patient-reported outcomes were collected on all patients.Eighty-four patients who underwent ST/G (n = 34) or ST (n = 50) autograft ACL reconstruction were recruited to participate in this study. There was no difference in knee laxity between the groups. Side-to-side hamstring strength deficits increased with increased flexion angles. At 90° of flexion, the ST/G group had a significantly greater flexion strength deficit compared with the ST group (37.8 ± 15.1% vs 24.7 ± 12.5%, P.001). Aside from a significant difference in the KOOS pain Score (P .045), no other significant differences in functional or patient reported outcomes between the groups were identified.Patients who underwent ACL reconstruction with ST/G compared with ST autograft have a significantly greater isometric flexion strength deficit at 90° of flexion. Future investigations are required to determine the clinical relevance of this difference and whether specialized therapy protocols can mitigate this deficit.Level III, retrospective comparative study.

Significance The Rab5 GTPase functions in early endosome (EE) fusion in the endocytic pathway. Here, we propose that RAB5B also has a noncanonical vesicular fusion function in the regulated secretion pathway that produces mature surfactant proteins SP-B and SP-C in the lung. This function was revealed from investigation of a proband with interstitial lung disease suggestive of a surfactant dysfunction disorder who carried a de novo Asp136His variant in the RAB5B gene. Our modeling in C. elegans provided information on the genetic and cell biological mechanism, and analyses of proband and normal lung biopsies suggested a function for RAB5B and EEs in surfactant protein processing/trafficking. This work indicates that RAB5B p.Asp136His causes a surfactant dysfunction disorder.

Individuals with Down syndrome show cellular and clinical features of dysregulated aging of the immune system, including a shift from naïve to memory T cells and increased incidence of autoimmunity. However, a quantitative understanding of how various immune compartments change with age in Down syndrome remains lacking. Here we performed deep immunophenotyping of a cohort of individuals with Down syndrome across the lifespan, selecting for autoimmunity-free individuals. We simultaneously interrogated age- and sex-matched healthy controls and people with type 1 diabetes as a representative autoimmune disease. We built an analytical software, IMPACD (Iterative Machine-assisted Permutational Analysis of Cytometry Data), that enabled us to rapidly identify many features of immune dysregulation in Down syndrome shared with other autoimmune diseases. We found quantitative and qualitative dysregulation of naïve CD4(+) and CD8(+) T cells in individuals with Down syndrome and identified interleukin (IL)-6 as a candidate driver of some of these changes, thus extending the consideration of immunopathologic cytokines in Down syndrome beyond interferons. We used immune cellular composition to generate three linear models of aging (immune clocks) trained on control participants. All three immune clocks demonstrated advanced immune aging in individuals with Down syndrome. One of these clocks, informed by Down syndrome-relevant biology, also showed advanced immune aging in individuals with type 1 diabetes. Orthologous RNA sequencing-derived immune clocks also demonstrated advanced immune aging in individuals with Down syndrome. Together, our findings demonstrate an approach to studying immune aging in Down syndrome which may have implications in the context of other autoimmune diseases.

Human islet antigen reactive CD4+ memory T cells (IAR T cells) play a key role in the pathogenesis of autoimmune type 1 diabetes (T1D). Using single-cell RNA sequencing (scRNA-Seq) to identify T cell receptors (TCRs) in IAR T cells, we have identified a class of TCRs that share TCRα chains between individuals ("public" chains). We isolated IAR T cells from blood of healthy, new-onset T1D and established T1D donors using multiplexed CD154 enrichment and identified paired TCRαβ sequences from 2767 individual cells. More than a quarter of cells shared TCR junctions between 2 or more cells ("expanded"), and 29/47 (~62%) of expanded TCRs tested showed specificity for islet antigen epitopes. Public TCRs sharing TCRα junctions were most prominent in new-onset T1D. Public TCR sequences were more germline like than expanded unique, or "private," TCRs, and had shorter junction sequences, suggestive of fewer random nucleotide insertions. Public TCRα junctions were often paired with mismatched TCRβ junctions in TCRs; remarkably, a subset of these TCRs exhibited cross-reactivity toward distinct islet antigen peptides. Our findings demonstrate a prevalent population of IAR T cells with diverse specificities determined by TCRs with restricted TCRα junctions and germline-constrained antigen recognition properties. Since these "innate-like" TCRs differ from previously described immunodominant TCRβ chains in autoimmunity, they have implications for fundamental studies of disease mechanisms. Self-reactive restricted TCRα chains and their associated epitopes should be considered in fundamental and translational investigations of TCRs in T1D.

SUMMARYIncreased protein synthesis is a hallmark of lymphocyte activation. Regulatory T cells (Tregs) suppress the activation and subsequent effector functions of CD4 effector T cells (Teffs). However, molecular mechanisms that enforce Treg-mediated suppression in CD4 Teff are not fully clear. Control of CD4 Teff activation by Tregs has largely been defined at the transcriptional level, which does not reflect changes in post-transcriptional control. We found that Tregs suppressed activation-induced global protein synthesis in CD4 Teffs prior to cell division. We analyzed genome-wide changes in the transcriptome and translatome of activated CD4 Teffs using two independent approaches. We show that mRNAs encoding for the protein synthesis machinery are regulated at the level of translation in activated Teffs. Strikingly, Tregs suppressed global protein synthesis of CD4 Teffs by specifically inhibiting mRNAs of the translation machinery at the level of mTORC1-mediated translation control. Lastly, we found that the RNA helicase eIF4A inhibitor rocaglamide A (RocA) can suppress CD4 Teff activation in vitro to alleviate inflammatory CD4 Teff activation caused by acute Treg depletion in vivo. These data provide evidence that peripheral tolerance is enforced by Tregs through mRNA translational control in CD4 Teffs. Therefore, therapeutic targeting of the protein synthesis machinery can be expected to mitigate inflammatory responses invoked by Treg loss of function.

Eosinophilic esophagitis (EoE) is an allergic inflammatory disease of the esophagus that occurs in both children and adults. Previous studies of affected tissue from pediatric cohorts have identified prominent signatures of eosinophilia and type 2 inflammation. However, the details of the immune response in adults with EoE are still being elucidated. To determine whether EoE in adults shares inflammatory profiles with those observed in children, we performed RNA sequencing of paired human esophageal biopsies and blood samples from adults with EoE or gastroesophageal reflux disease. Unbiased analysis of differentially expressed genes in tissue revealed a strong IFN signature that was significantly enriched in EoE patients as compared with patients with gastroesophageal reflux disease. Both type I and type II IFN–responsive genes were upregulated in adult biopsies, but not in blood. A similar increase in expression of IFN gene sets was observed in pediatric EoE biopsies as compared with non-EoE samples, and in public pediatric and adult RNA-sequencing data. Finally, we found that human peripheral CD4+ T cells from children with EoE produce IFN-γ upon activation with EoE-causal allergens. Together, this work identifies a conserved IFN signature in pediatric and adult EoE, highlighting a role for non–type 2 inflammatory networks in the disease process in humans.

In data independent acquisition (DIA) mass spectrometry, precursor scans are interleaved with wide-window fragmentation scans, resulting in complex fragmentation spectra containing multiple co-eluting peptide species. In this setting, detecting the isotope distribution profiles of intact peptides in the precursor scans can be a critical initial step in accurate peptide detection and quantification. This peak detection step is particularly challenging when the isotope peaks associated with two different peptide species overlap—or interfere—with one another. We propose a regression model, called Siren, to detect isotopic peaks in precursor DIA data that can explicitly account for interference. We validate Siren’s peak-calling performance on a variety of data sets by counting how many of the peaks Siren identifies are associated with confidently detected peptides. In particular, we demonstrate that substituting the Siren regression model in place of the existing peak-calling step in DIA-Umpire leads to improved overall rates of peptide detection.

Kaposi’s Sarcoma associated Herpesvirus (KSHV), an oncogenic, human gamma-herpesvirus, is the etiological agent of Kaposi’s Sarcoma the most common tumor of AIDS patients world-wide. KSHV is predominantly latent in the main KS tumor cell, the spindle cell, a cell of endothelial origin. KSHV modulates numerous host cell-signaling pathways to activate endothelial cells including major metabolic pathways involved in lipid metabolism. To identify the underlying cellular mechanisms of KSHV alteration of host signaling and endothelial cell activation, we identified changes in the host proteome, phosphoproteome and transcriptome landscape following KSHV infection of endothelial cells. A Steiner forest algorithm was used to integrate the global data sets and, together with transcriptome based predicted transcription factor activity, cellular networks altered by latent KSHV were predicted. Several interesting pathways were identified, including peroxisome biogenesis. To validate the predictions, we showed that KSHV latent infection increases the number of peroxisomes per cell. Additionally, proteins involved in peroxisomal lipid metabolism of very long chain fatty acids, including ABCD3 and ACOX1, are required for the survival of latently infected cells. In summary, novel cellular pathways altered during herpesvirus latency that could not be predicted by a single systems biology platform, were identified by integrated proteomics and transcriptomics data analysis and when correlated with our metabolomics data revealed that peroxisome lipid metabolism is essential for KSHV latent infection of endothelial cells., Author summary Kaposi’s Sarcoma herpesvirus (KSHV) is the etiologic agent of Kaposi’s Sarcoma, the most common tumor of AIDS patients. KSHV modulates host cell signaling and metabolism to maintain a life-long latent infection. To unravel the underlying cellular mechanisms modulated by KSHV, we used multiple global systems biology platforms to identify and integrate changes in both cellular protein expression and transcription following KSHV infection of endothelial cells, the relevant cell type for KS tumors. The analysis identified several interesting pathways including peroxisome biogenesis. Peroxisomes are small cytoplasmic organelles involved in redox reactions and lipid metabolism. KSHV latent infection increases the number of peroxisomes per cell and proteins involved in peroxisomal lipid metabolism are required for the survival of latently infected cells. In summary, through integration of multiple global systems biology analyses we were able to identify novel pathways that could not be predicted by one platform alone and found that lipid metabolism in a small cytoplasmic organelle is necessary for the survival of latent infection with a herpesvirus.

Previous literature reviews or meta-analysis based studies on game-assisted learning have provided important results, but few studies have considered the importance of learning theory, and coverage of papers after 2007 is scant. This study presents a systematic review of the literature using a meta-analysis approach to provide a more comprehensive analysis and synthesis of relevant studies based on four orientations of learning theories and principles: behaviorism, cognitivism, humanism, and constructivism. Major findings of this study include that the majority of published studies were not based on learning theory and the development of learning theory orientations has prompted more studies to focus on constructivism and humanism than on behaviorism and cognitivism. In addition, most studies adopted a descriptive approach, followed by experimental methods and surveys, and most presented positive outcomes. These findings not only advance understanding of game-assisted learning from the important perspective of learning theory, but also provide useful insights for researchers and educators in issues related to game-assisted learning.