IntroductionShrimp is a common but understudied food allergen with relatively high rates of emergency department visits. Here we report the shrimp OIT outcomes in the MOTIF (NCT03504774) clinical trial and discuss some of the challenges with performing this study.MethodsIn this phase 2 clinical trial, 12 shrimp allergic participants aged 7–55 years (median age 21.5 years) were enrolled to receive shrimp OIT. Shrimp OIT was performed up to a maintenance dose of 1,000 mg shrimp protein by week 28 with desensitization to shrimp assessed by double-blind placebo-controlled food challenge at week 52 followed by switching to avoidance and assessing sustained unresponsiveness (SU) at week 58. The primary endpoint was the change in CD28 in CD4+ allergen specific (CD154+) T-cells at baseline and 52 weeks.ResultsShrimp OIT induced desensitization to a cumulative 4,043 mg shrimp protein in 58.3% (7/12) of the intention to treat and 87.5% (7/8) of the per protocol group after 52 weeks of shrimp OIT. Most shrimp OIT participants who remained in the study after desensitization (87.5%, 7/8) achieved SU. Although adverse events were common during shrimp OIT (75%), most were mild (Bock grade 1, 88%) and there were no severe (Bock grade 3+) reactions or use of epinephrine. No significant differences in CD28 expression were observed after shrimp OIT.ConclusionsShrimp OIT is safe and effective for the treatment of shrimp allergy. Most participants were successful and achieved SU after 6 weeks of avoidance.

Oral immunotherapy (OIT) is the only U.S. Food and Drud Administration-approved treatment for peanut allergy. Peanut-reactive (pr) CD4+ T cells are pivotal in peanut allergy pathogenesis and OIT-induced desensitization. However, the underlying pr CD4+ T cell immune mechanisms leading to sustained unresponsiveness after OIT discontinuation are largely unknown. We analyzed single-cell RNA and protein immunophenotypes and T cell receptor repertoires of pr CD4+ T cells from a phase 2 peanut OIT trial cohort. We identified increased cytotoxicity-related phenotypes and type 1 helper cytotoxic T lymphocyte-like cell clonal expansion during OIT, while type 2 helper T (TH2) cell-related phenotypes and TH2-like cell clonal expansion decreased. OIT participants achieving sustained unresponsiveness were distinguished by lower baseline TH2-related phenotypes, elevated post-OIT cytotoxicity-related pr effector T cell gene signatures and higher CD39 expression in pr regulatory T cells. These findings clarify OIT-induced CD4+ T cell tolerance mechanisms and can guide effective allergen-specific OIT strategies. Peanut oral immunotherapy reshapes T cell responses, suppressing allergy-associated type 2 helper T cells and boosting cytotoxic type 1 helper T cells, offering clues to long-term tolerance.

BackgroundWe designed an oral immunotherapy (OIT) clinical trial for cashew allergy to further our understanding of immunological responses with treatment, including changes in allergen-specific T cells. This information can further assist with the design of efficacious and safe treatments.MethodsParticipants were built up to and maintained on 1 g of cashew flour protein. Double-blind, placebo-controlled food challenges (DBPCFCs) were conducted before and after dosing completion (week 52) and 6 weeks after dosing discontinuation (week 58). Desensitization (DS) and sustained unresponsiveness (SU) were defined as tolerating DBPCFC to a cumulative dose of 2043 mg of the allergen at weeks 52 and 58, respectively. ClinicalTrials.gov, number NCT03504774.ResultsWe enrolled 40 cashew allergic participants. In the Intent-to-treat (ITT) population, both the DS and SU rate to cashew was 65% (26/40). Among cashew-reactive cells, CRTH2+ CD4+ T cells decreased at week 52 and week 58 compared to baseline. Additionally, we also saw reduced baseline expression of cytokines TARC, EGF and IP10 among participants that achieved SU at 4043mg compared to those who achieved SU at 2043mg.ConclusionCashew OIT have efficacy and safety outcomes similar to other published OIT studies. Reductions in pathogenic allergen-specific T cell populations may contribute to the immune mechanisms underlying tolerance achieved towards cashew post-treatment.Clinical trial registrationClinicalTrials.gov, identifier NCT03504774.

Despite the success of peanut oral immunotherapy (OIT), there is little insight into the safety, efficacy, and immune underpinnings of OIT to treat cashew or shrimp allergy. Cashew or shrimp allergic participants aged 7-55 years were enrolled in the phase 2 clinical trial - MOTIF (NCT03504774) and underwent cognate allergen-specific OIT to a maintenance dose of 1,000 mg until week 52. Oral food challenge (OFC) at weeks 52 and 58 evaluated desensitization and sustained unresponsiveness (SU) respectively to a cumulative allergen dose of 2043 mg. We examined immune changes in allergen-reactive CD4+ T cells and plasma at baseline, week 52, and week 58 using flow cytometry and Luminex. We enrolled 40 cashew and 12 shrimp allergic participants, of whom 25 cashew-treated (62.5%) and 7 shrimp-treated (58.3%) participants completed and passed week 58 OFC. Overall, cashew and shrimp OIT was safe with only mild (90%) or moderate (10%) adverse events, with gastrointestinal symptoms (31%) being the most common. OIT induced a significant increase in allergen-specific IgG4 at week 52 (q < 0.1). A trend of downregulation of Th2 and Th1 surrogate marker CRTH2 and CXCR3-expressing allergen-reactive CD4+ T cells was evident in cashew- and shrimp-treated participants respectively at week 52. Higher baseline plasma levels of TARC, EGF, and IP10 implied a lower likelihood of SU. Cashew and shrimp OIT could safely desensitize allergic study participants to respective allergen protein. Mechanistic analyses confirm readouts linked to successful desensitization and offer potential biomarkers for predicting SU that warrant further investigation.

IntroductionInnate lymphoid cells (ILCs) are enriched at mucosal surfaces where they respond rapidly to environmental stimuli and contribute to both tissue inflammation and healing. MethodsTo gain insight into the role of ILCs in the pathology and recovery from COVID-19 infection, we employed a multi-omics approach consisting of Abseq and targeted mRNA sequencing to respectively probe the surface marker expression, transcriptional profile and heterogeneity of ILCs in peripheral blood of patients with COVID-19 compared with healthy controls. ResultsWe found that the frequency of ILC1 and ILC2 cells was significantly increased in COVID-19 patients. Moreover, all ILC subsets displayed a significantly higher frequency of CD69-expressing cells, indicating a heightened state of activation. ILC2s from COVID-19 patients had the highest number of significantly differentially expressed (DE) genes. The most notable genes DE in COVID-19 vs healthy participants included a) genes associated with responses to virus infections and b) genes that support ILC self-proliferation, activation and homeostasis. In addition, differential gene regulatory network analysis revealed ILC-specific regulons and their interactions driving the differential gene expression in each ILC. DiscussionOverall, this study provides mechanistic insights into the characteristics of ILC subsets activated during COVID-19 infection.

Food insecurity impacts approximately 23% of the US population and poses a significant challenge for those dealing with food allergies, due to increased costs and difficulties associated with obtaining allergy-friendly food. The COVID-19 pandemic further exacerbated these challenges, amplifying the burden roughly 6-fold.

BACKGROUND:Conventional basophil activation tests (BATs) measure basophil activation by the increased expression of CD63. Previously, fluorophore-labeled avidin, a positively-charged molecule, was found to bind to activated basophils, which tend to expose negatively charged granule constituents during degranulation. This study further compares avidin versus CD63 as basophil activation biomarkers in classifying peanut allergy. METHODS:Seventy subjects with either a peanut allergy (N = 47), a food allergy other than peanut (N = 6), or no food allergy (N = 17) were evaluated. We conducted BATs in response to seven peanut extract (PE) concentrations (0.01-10,000 ng/mL) and four control conditions (no stimulant, anti-IgE, fMLP (N-formylmethionine-leucyl-phenylalanine), and anti-FcεRI). We measured avidin binding and CD63 expression on basophils with flow cytometry. We evaluated logistic regression and XGBoost models for peanut allergy classification and feature identification. RESULTS:Avidin binding was correlated with CD63 expression. Both markers discriminated between subjects with and without a peanut allergy. Although small by percentage, an avidin+ /CD63- cell subset was found in all allergic subjects tested, indicating that the combination of avidin and CD63 could allow a more comprehensive identification of activated basophils. Indeed, we obtained the best classification accuracy (97.8% sensitivity, 96.7% specificity) by combining avidin and CD63 across seven PE doses. Similar accuracy was obtained by combining PE dose of 10,000 ng/mL for avidin and PE doses of 10 and 100 ng/mL for CD63. CONCLUSIONS:Avidin and CD63 are reliable BAT activation markers associated with degranulation. Their combination enhances the identification of activated basophils and improves the classification accuracy of peanut allergy.

The majority of lung cancer patients are diagnosed with metastatic disease. This study identified a set of 73 microRNAs (miRNAs) that classified lung cancer tumors from normal lung tissues with an overall accuracy of 96.3% in the training patient cohort (n = 109) and 91.7% in unsupervised classification and 92.3% in supervised classification in the validation set (n = 375). Based on association with patient survival (n = 1016), 10 miRNAs were identified as potential tumor suppressors (hsa-miR-144, hsa-miR-195, hsa-miR-223, hsa-miR-30a, hsa-miR-30b, hsa-miR-30d, hsa-miR-335, hsa-miR-363, hsa-miR-451, and hsa-miR-99a), and 4 were identified as potential oncogenes (hsa-miR-21, hsa-miR-31, hsa-miR-411, and hsa-miR-494) in lung cancer. Experimentally confirmed target genes were identified for the 73 diagnostic miRNAs, from which proliferation genes were selected from CRISPR-Cas9/RNA interference (RNAi) screening assays. Pansensitive and panresistant genes to 21 NCCN-recommended drugs with concordant mRNA and protein expression were identified. DGKE and WDR47 were found with significant associations with responses to both systemic therapies and radiotherapy in lung cancer. Based on our identified miRNA-regulated molecular machinery, an inhibitor of PDK1/Akt BX-912, an anthracycline antibiotic daunorubicin, and a multi-targeted protein kinase inhibitor midostaurin were discovered as potential repositioning drugs for treating lung cancer. These findings have implications for improving lung cancer diagnosis, optimizing treatment selection, and discovering new drug options for better patient outcomes.

Oral Immunotherapy (OIT) is a promising emerging therapy which facilitates desensitization; however, the amount of allergen that can be tolerated during accidental ingestions following OIT is unknown. The objective of this study is to summarize findings from four OIT trials to better understand predictors and the likelihood that participants were able to achieve ten times their initial dose. Data from double blind placebo-controlled food challenges from four IRB-approved research cohorts that included multi-allergen immunotherapy with adjunct omalizumab or single allergen immunotherapy were summarized. A cutoff of success was defined as being able to ingest ten times the initial cumulative ingested dose following OIT. Mixed effect models were used to examine predictors of successful desensitization while controlling for omalizumab and study with a cut of statistical significance at p<0.05. Data was analyzed from 211 participants (ages u=10.63, [4,53]). A mean value of 2.13g was ingested at 10X cut off following OIT. Participants were able to ingest doses ranging from 25mg to 12000mg of an allergen post-OIT. Forty-one (17.45%) participants failed to increase their dose by 10X. Number of allergens (u=2.33, p=0.0162) and omalizumab (p=0.0186) were found to be positively associated with cutoff for success. However, weight, age, and sex were not significantly associated with success. These findings indicate that across studies, participants are likely to be successfully desensitized to 10 times their initial dose during food challenges, offering robust protection against accidental ingestions. Further investigation is necessary to understand factors behind successful as well as unsuccessful outcomes.

Background: The global epidemiology of asthma among COVID-19 patients presents striking geographic differences defining high and low [asthma and COVID-19] co-occurrence prevalence zones (1). The objective of the present study was to compare asthma prevalence among hospitalized COVID-19 patients in major global hubs across the world with the application of common inclusion criteria and definitions. Methods: We built a network of six academic hospitals in Stanford (Stanford University)/USA, Frankfurt (Goethe University), Giessen (Justus Liebig University) and Marburg (Philipps University)/Germany, and Moscow (Clinical Hospital 52 in collaboration with Sechenov University)/Russia. We collected clinical and laboratory data for patients hospitalized due to COVID-19. Comorbidities reported were based on the 2020 International Classification of Diseases-10th Revision codes. Results: Asthmatics were overrepresented among hospitalized COVID-19 patients in Stanford and underrepresented in Moscow and Germany as compared to the prevalence among adults in the local community. Asthma prevalence was similar among ICU and hospital non-ICU patients, which implied that the risk for developing severe COVID-19 was not higher among asthmatics. The number of males and comorbidities was higher among COVID-19 patients in the Stanford cohort, and the most frequent comorbidities among these asthma patients were other chronic inflammatory airway disorders such as chronic obstructive pulmonary disease (COPD). Conclusion: Observed disparity in COVID-19-associated risk among asthmatics across countries and continents is connected to varying prevalence of underlying comorbidities, particularly COPD. Public health policies in the future will need to consider comorbidities with an emphasis on COPD for prioritization of vaccination and preemptive treatment.

This figure shows the signal pathway of TLR1, TLR2, and TLR6. TLR1 and TLR6, each of which forms a heterodimer with TLR2, initiate MAPK or NFκB pathway through TAK1. MyD88: myeloid differentiation factor88, TRAF: TNF receptor-associated factor, IRAK: 　IL-1R associated kinase, TAK: TGFβ-activated kinase, TAB: TAK1-binding protein, MAPK: mitogen-activated protein kinase.

Although oral immunotherapy (OIT) is an effective treatment option for food allergy it can be complicated by persistent gastrointestinal (GI) reactions. The impact of GI symptoms on the outcome of OIT is not known. Data from 2 IRB-approved clinical research trials at our research center utilizing single allergen immunotherapy with a maintenance dose of 1000 mg and 4000 mg were reviewed. Persistent gastrointestinal (GI) symptoms were defined as having >= 4 days of symptoms a week for 2 consecutive weeks. A total of 58 participants in the 1000 mg maintenance group and 116 participants in the 4000 mg group were analyzed. Persistent GI symptoms were reported by 13.8% (n=8) in the 1000 mg and 11.9% (n=14) in the 4000 mg maintenance groups. Withdrawal rates were not statistically different among those with GI symptoms (n=5) and those without (n=35) across both maintenance groups. For participants who successfully reached maintenance, time to maintenance (TTM) was longer in those with GI symptoms compared to those without in both groups, however it only reached statistical significance in the 4000 mg maintenance group with a median time of 62.3 weeks in those with GI symptoms compared to 54.2 weeks in those without (p=0.008). Persistent GI symptoms did not increase withdrawal rates in trials involving OIT, however TTM was longer and reached significance in the group with a higher maintenance dose. Shared decision making and close monitoring is required to manage GI symptoms with OIT but can lead to successful outcomes in clinical trials.

This table shows the association of each SNP and clinical outcome in TRIBE. The association between SNP and clinical outcome in FIRE-3 is also demonstrated when there are statistically significant associations in TRIBE.

The incidence and prevalence of food allergy (FA) is increasing. While several studies have established the safety and efficacy of early introduction of single allergens in infants for the prevention of FA, the exact dose, frequency, and number of allergens that can be safely introduced to infants, particularly in those at high or low risk of atopy, are still unclear. This 1-year pilot study evaluated the safety of the early introduction of single foods (milk, egg, or peanut) vs. two foods (milk/egg, egg/peanut, milk/peanut) vs. multiple foods (milk/egg/peanut/cashew/almond/shrimp/walnut/wheat/salmon/hazelnut at low, medium, or high doses) vs. no early introduction in 180 infants between 4–6 months of age. At the end of the study, they were evaluated for plasma biomarkers associated with food reactivity via standardized blood tests. Two to four years after the start of the study, participants were evaluated by standardized food challenges. The serving sizes for the single, double, and low dose mixtures were 300 mg total protein per day. The serving sizes for the medium and high dose mixtures were 900 mg and 3000 mg total protein, respectively. Equal parts of each protein were used for double or mixture foods. All infants were breastfed until at least six months of age. The results demonstrate that infants at either high or low risk for atopy were able to tolerate the early introduction of multiple allergenic foods with no increases in any safety issues, including eczema, FA, or food protein induced enterocolitis. The mixtures of foods at either low, medium, or high doses demonstrated trends for improvement in food challenge reactivity and plasma biomarkers compared to single and double food introductions. The results of this study suggest that the early introduction of foods, particularly simultaneous mixtures of many allergenic foods, may be safe and efficacious for preventing FA and can occur safely. These results need to be confirmed by larger randomized controlled studies.

Supplementary Table 1. Summary of EMT-related SNPs Supplementary Table 2A. Association between baseline characteristics and clinical outcomes in the bevacizumab cohort Supplementary Table 2B. Association between baseline characteristics and clinical outcomes in the cetuximab cohort Supplementary Table 3. Association between TWIST1 rs2285682 and clinical outcomes in KRAS wild-type and mutant subgroups among the bevacizumab cohort Supplementary Table 4. Association between EMT-related SNPs and clinical outcomes stratified by gender in the bevacizumab cohort Supplementary Table 5. Association between TWIST1 rs2285682 and clinical outcomes in the cetuximab cohort

The safety and efficacy of food oral immunotherapy (OIT) has been extensively studied, however long-term maintenance OIT studies are limited. To better understand the durability of OIT long-term, larger studies on compliance, quality of life (QOL), and burden of treatment (BOT) are needed. Participants and caregivers who participated in food OIT clinical trials at Stanford University completed three IRB approved surveys: food allergy long-term follow up questionnaire (FALTFU), food allergy quality of life questionnaire (FAQOL), and burden of treatment questionnaire (BOT). FAQOL scores at baseline and study completion were compared using a Wilcoxon signed rank test. BOT was measured on a 1 to 7 scale (1=extremely positive, 7=extremely negative). 186 participants completed FALTFU questionnaires. 120 (69%) were children (0-12 years). Compliance rates were 79% for multi-food OIT (n=77) and 61% for single-food OIT (n=109, p=0.016). Younger children (0-12 years) were more compliant vs older children and adults (80% vs 52%, p<0.001). 104 (65%) continued peanut, 40 (78%) continued cashew, and 36 (69%) continued walnut. Multi-food OIT participants reported worse baseline FAQOL vs single-food OIT participants (p=0.034). Multi-food OIT participants reported significant improvement of FAQOL after study completion (p<0.001) but single-food OIT participants did not (p=0.055). Younger children reported positive or extremely positive more frequently on BOT vs older children and adults (82% vs 57%, p=0.001). This is the largest, long-term OIT follow up study to date to assess compliance, QOL, and BOT. The majority of participants continued OIT long-term. Positive treatment perception and improved QOL were seen among all participants.