The study of genetic diversity has a rich history, as it serves as the foundation upon which evolutionary processes act. Numerous methods have been developed to quantify genetic variation within and among populations. While some methods focus solely on allele frequencies, others assess branching patterns within phylogenetic clades without considering genetic distances. Here we introduce the Proportional Diversity Likelihood Ratio Statistic (PLR), a novel method that integrates genetic distances with phylogenetic tree structure to provide a comprehensive measure of genetic diversity. This method evaluates the likelihood of observed genetic data under models with constrained and unconstrained diversity, offering a robust statistical framework for testing hypotheses about genetic differentiation. The PLR approach is broadly applicable, from assessing immune repertoire diversity, such as B-cell diversity before and after vaccination, to evaluating tumor genetic diversity before and after treatment. By combining genetic distance and tree topology, PLR enables deeper insights into evolutionary dynamics and population structure. We demonstrate the use of this approach on SARS-CoV-2 sequences from two different time frames and found that diversity maybe waning. Moreover, we applied PRL to chronic lymphocytic leukemia (CLL) data, revealing that with temporally order sequences from with treatment we do not see a significant drop in diversity.

Long-lived humoral memory is key to durable immunity against pathogens yet remains challenging to define due to heterogeneity among antigen-reactive B cells. We addressed this gap through longitudinal sampling over the course of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mRNA vaccinations with or without breakthrough infection. High-dimensional phenotypic profiling performed on ∼72 million B cells showed that receptor-binding domain (RBD) reactivity was associated with five distinct immunoglobulin G (IgG) B cell populations. Two expressed the activation marker CD71, both correlated with neutralizing antibodies, yet the one lacking the memory marker CD27 was induced by vaccination and blunted by infection. Two were resting memory populations; one lacking CD73 arose early and contributed to cross-reactivity; the other, expressing CD73, arose later and correlated with neutralizing antibodies. The fifth, a rare germinal center-like population, contributed to recall responses and was highly cross reactive. Overall, robust and distinct responses to booster vaccination overcame the superiority of hybrid immunity provided by breakthrough infection.

Asthma is a genetically complex inflammatory airway disease associated with more than 200 SNPs. However, the functional effects of many asthma-associated SNPs in lung and airway epithelial samples are unknown. Here, we aimed to conduct expression quantitative trait loci (eQTL) analysis using a meta-analysis of nasal and lung samples. We hypothesize that incorporating cell type proportions of airway and lung samples enhances eQTL analysis outcomes. Nasal brush (n = 792) and lung tissue (n =1,087) samples were investigated separately. Initially, a general eQTL analysis identified genetic variants associated with gene expression levels. Estimated cell type proportions were adjusted based on the Human Lung Cell Atlas. In addition, the presence of significant interaction effects between asthma-associated SNPs and each cell type proportion was explored and considered evidence for cell type-associated eQTL. In nasal brush and lung parenchyma samples, 44 and 116 asthma-associated SNPs were identified as eQTL. Adjusting for cell type proportions revealed eQTL for an additional 17 genes (e.g., FCER1G, CD200R1, and GABBR2) and 16 genes (e.g., CYP2C8, SLC9A2, and SGCD) in nose and lung, respectively. Moreover, we identified eQTL for nine SNPs annotated to genes such as VASP, FOXA3, and PCDHB12 displayed significant interactions with cell type proportions of club, goblet, and alveolar macrophages. Our findings demonstrate increased power for identifying eQTL among asthma-associated SNPs by considering cell type proportion of the bulk RNA-sequencing data from nasal and lung tissues. Integration of cell type deconvolution and eQTL analysis enhances our understanding of asthma genetics and cellular mechanisms, uncovering potential therapeutic targets for personalized interventions.

The role of the chronic obstructive pulmonary disease (COPD) susceptibility gene hedgehog (Hh) interacting protein (HHIP) in lung tissue damage and abnormal repair in COPD is incompletely understood. We hypothesized that dysregulated HHIP expression affects cigarette smoke-induced epithelial damage and repair within the epithelial-mesenchymal trophic unit. HHIP expression was assessed in lung tissue and airway epithelial cells (AECs) from patients with COPD and non-COPD controls. The effect of HHIP overexpression was assessed on cigarette smoke extract (CSE)-induced changes in epithelial plasticity genes, for example, cadherin 1 (CDH1, encoding E-cadherin) in human bronchial epithelial cells (16HBE) cells, and on epithelial-mesenchymal interactions during alveolar repair as modeled by organoid formation using distal lung-derived mesenchymal stromal cells (LMSCs) and EpCAM+ epithelial cells. We observed no abnormalities in HHIP protein levels in the lung tissue of patients with COPD, whereas the expression of HHIP was significantly lower in COPD-derived AECs compared with the control. HHIP overexpression in 16HBE cells attenuated the CSE-induced reduction in CDH1 expression. Furthermore, overexpression of HHIP significantly suppressed Sonic hedgehog-induced GLI1 expression in control but not COPD-derived LMSCs and resulted in the formation of more and larger organoids, which was not observed for COPD-derived LMSCs. This defect was accompanied by lower expression of the growth factor FGF10 upon HHIP overexpression in COPD compared with control-derived LMSCs. Together, our data suggest a protective role of HHIP in CSE-induced airway epithelial responses and a supportive role in alveolar epithelial regeneration, which may be impaired in COPD.NEW & NOTEWORTHY We show that overexpression of HHIP protected from cigarette smoke-induced epithelial-to-mesenchymal transition and promoted epithelial regeneration via epithelial-mesenchymal cross talk in non-COPD controls. Thus, the lower expression of HHIP in airway epithelial cells from patients with COPD may contribute to abnormal epithelial repair in both proximal and distal parts of the lungs of patients with COPD.

Extracellular matrix (ECM) remodeling has been associated with chronic lung diseases. However, information about specific age -associated differences in lung ECM is currently limited. In this study, we aimed to identify and localize age-associated ECM dif-ferences in human lungs using comprehensive transcriptomic, proteomic, and immunohistochemical analyses. Our previously identified age-associated gene expression signature of the lung was re-analyzed limiting it to an aging signature based on 270 control patients (37-80 years) and focused on the Matrisome core geneset using geneset enrichment analysis. To validate the age-associated transcriptomic differences on protein level, we compared the age-associated ECM genes (false discovery rate, FDR < 0.05) with a profile of age-associated proteins identified from a lung tissue proteomics dataset from nine control patients (49-76 years) (FDR < 0.05). Extensive immunohistochemical analysis was used to localize and semi-quantify the age-associated ECM differences in lung tissues from 62 control patients (18-82 years). Comparative analysis of transcriptomic and proteomic data identified seven ECM proteins with higher expression with age at both gene and protein levels: COL1A1, COL6A1, COL6A2, COL14A1, FBLN2, LTBP4, and LUM. With immunohistochemistry, we demonstrated higher protein levels with age for COL6A2 in whole tissue, parenchyma, airway wall, and blood vessel, for COL14A1 and LUM in bronchial epithelium, and COL1A1 in lung pa-renchyma. Our study revealed that higher age is associated with lung ECM remodeling, with specific differences occurring in defined regions within the lung. These differences may affect lung structure and physiology with aging and as such may increase susceptibility to developing chronic lung diseases. NEW & NOTEWORTHY We identified seven age-associated extracellular matrix (ECM) proteins, i.e., COL1A1, COL6A1, COL6A2 COL14A1, FBLN2, LTBP4, and LUM with higher transcript and protein levels in human lung tissue with age. Extensive immunohis-tochemical analysis revealed significant age-associated differences for COL6A2 in whole tissue, parenchyma, airway wall, and vessel, for COL14A1 and LUM in bronchial epithelium, and COL1A1 in parenchyma. Our findings lay a new foundation for the investigation of ECM differences in age-associated chronic lung diseases.

Background Myelodysplastic neoplasms (MDS) and acute myeloid leukemia (AML) exhibit a dynamic and diverse mutational landscape, especially during disease progression. Mutations in the splicing factors SF3B1 and U2AF1 drive overexpression of a highly active long isoform of interleukin-1 receptor-associated kinase 4 (IRAK4), triggering inflammation, oncogenesis and survival of cancer cells through activation of NFκB and other signaling pathways. NFκB target genes CCL4, IL1β and IER3 are highly expressed in patients with AML and MDS and associated with poor prognosis. Emavusertib is a potent oral inhibitor of IRAK4 and FLT3 with efficacy in pre-clinical leukemia models. Here, we describe our insights from RNA sequencing (RNA-seq) applied to clinical samples from the ongoing TakeAim Leukemia trial. Methods In the Phase I/IIa of the TakeAim Leukemia trial (NCT04278768), patients with relapsed/refractory (R/R) AML or higher-risk MDS were treated with emavusertib. RNA-seq was performed on mononuclear cells from bone marrow, or peripheral blood, from 26 AML and 16 MDS patients, including 24 paired samples. The read depth ranged from 10.4–120 million reads and% reads aligned ranged from 67%-92%. Quality control was performed with FASTQC V0.11.8 and low-quality reads were removed using Trimgalore V0.6.3. Raw counts were normalized to total number of reads by calculating log2CPM (Counts Per Million). Results MDS patients that responded to emavusertib had decreased gene expression levels of the NFκB target genes IL1β and IER3 (P≤0.05, respectively) compared to non-responders. A decrease in CCL4 expression was also observed (N.S.). Pathway analysis demonstrated significant downregulation of the Heme Metabolism, G2M Checkpoint, and E2F Targets pathways in on-treatment samples (FDR p-value <0.005 for all, normalized enrichment score= -3.39, -1.97 & -2.17, respectively). Notably E2F2 was decreased in on-treatment samples compared to baseline samples with a log2FC of ~1.3. Conclusions RNA-seq pathway analysis indicates that inhibition of IRAK4 downregulates genes relevant to the development and pathophysiology of AML/MDS. Previous clinical research supports our findings describing IL1β and IE3 as important markers in the prognosis of AML/MDS. In addition, we observed that emavusertib downregulates pathways associated with heme metabolism, proliferation and cell cycle regulation (including E2F associated genes) that could translate into improved disease outcomes. Ongoing studies will attempt to identify treatment response biomarkers. Future research will examine the correlations of gene expression with mutational profiles, splicing factor mutations, emavusertib dose regimens, and use of proteomics technologies to assess targeted kinase phosphorylation levels (e.g. IRAK4, NFκB) and quantification of soluble markers. Trial Registration Trial Registration NCT04278768 Ethics Approval The protocol and related documents were approved by the applicable regional review boards, ethics committees, or both, and all samples used in the analysis were from patients who provided written informed consent.

Background: Seralutinib is an inhaled small-molecule kinase inhibitor which selectively targets PDGFRα/β, CSF1R, and c-KIT signalling implicated in PAH pathobiology. Higher lung than plasma exposure and extended lung target engagement (TE) in preclinical studies suggest that pharmacodynamic activity in the human lung is expected at the dose levels studied. We evaluated changes in exploratory peripheral biomarkers of TE and mechanism of action in PAH subjects. Methods: In a phase 1b multicenter, randomized, placebo-controlled study, subjects with PAH were randomized 3:1 to receive inhaled seralutinib up to 90 mg BID or placebo for 14 days. Whole blood and serum samples were collected at screening and Day 14 for biomarker analysis: pre-treatment, 5 minutes, and 2 hours post-treatment. A novel whole blood CSF1R internalization assay was developed to assess TE. Epigenetic immunoprofiling assays and RNAseq were performed. Results: Eight subjects received seralutinib (n=6) or placebo (n=2). Seralutinib was well tolerated at doses up to 90 mg BID. Seralutinib inhibited CSF1R internalization at 5 min but not 2 hrs post-inhalation relative to baseline, consistent with its short half-life in peripheral circulation. Transcriptomics data at Day 14 identified treatment-associated shifts in 779 genes. An epigenetic signal suggestive of increasing FOXP3+ Tregs:CD4+ T cells following treatment was also observed. Conclusion: Preliminary biomarker findings support TE and downstream effects in the periphery that suggest target modulation by seralutinib in PAH patients. Seralutinib is being actively evaluated as a treatment for PAH in a currently recruiting phase 2 study (NCT04456998).

Clostridioides (Clostridium) difficile infection, the leading cause of healthcare-associated diarrhea, represents a significant burden on global healthcare systems. Despite being a global issue, information on C. difficile from a global perspective is lacking. The aim of this study is to model the global phylogeography of clinical C. difficile. Using samples collected from the MODIFY I and II studies (NCT01241552, NCT01513239), we performed whole-genome sequencing of 1501 clinical isolates including 37 novel sequence types (STs), representing the largest worldwide collection to date. Our data showed ribotypes, multi-locus sequence typing clades, and whole-genome phylogeny were in good accordance. The clinical C. difficile genome was found to be more conserved than previously reported (61% core genes), and modest recombination rates of 1.4–5.0 were observed across clades. We observed a significant continent distribution preference among five C. difficile clades (Benjamini-Hochberg corrected Fisher’s exact test P < 0.01); moreover, weak association between geographic and genetic distance among ribotypes suggested sources beyond healthcare-related transmission. Markedly different trends of antibiotic susceptibility among lineages and regions were identified, and three novel mutations (in pyridoxamine 5′-phosphate oxidase family protein: Tyr130Ser, Tyr130Cys, and a promoter SNP) associated with metronidazole-reduced susceptibility were discovered on a nim-related gene and its promotor by genome-wide association study. Toxin gene polymorphisms were shown to vary within and between prevalent ribotypes, and novel severe mutations were found on the tcdC toxin regulator protein. Our systematic characterization of a global set of clinical trial C. difficile isolates from infected individuals demonstrated the complexity of the genetic makeup of this pathogenic organism. The geographic variability of clades, variability in toxin genes, and mutations associated with antibiotic susceptibility indicate a highly complex interaction of C. difficile between host and environment. This dataset will provide a useful resource for validation of findings and future research of C. difficile.

To identify candidate causal genes of asthma, we performed a genome-wide association study (GWAS) in UK Biobank on a broad asthma definition (n = 56,167 asthma cases and 352,255 controls). We then carried out functional mapping through transcriptome-wide association studies (TWAS) and Mendelian randomization in lung (n = 1,038) and blood (n = 31,684) tissues. The GWAS reveals 72 asthma-associated loci from 116 independent significant variants (P GWAS < 5.0E-8). The most significant lung TWAS gene on 17q12-q21 is GSDMB (P TWAS = 1.42E-54). Other TWAS genes include TSLP on 5q22, RERE on 1p36, CLEC16A on 16p13, and IL4R on 16p12, which all replicated in GTEx lung (n = 515). We demonstrate that the largest fold enrichment of regulatory and functional annotations among asthma-associated variants is in the blood. We map 485 blood eQTL-regulated genes associated with asthma and 50 of them are causal by Mendelian randomization. Prioritization of druggable genes reveals known ( IL4R , TSLP , IL6 , TNFSF4 ) and potentially new therapeutic targets for asthma.

Human rhinoviruses (RVs) are the primary aetiological agent of the common cold. Generally, the associated infection is mild and self-limiting, but may also be associated with bronchiolitis in infants, pneumonia in the immunocompromised and exacerbation in patients with pulmonary conditions such as asthma or chronic obstructive pulmonary disease. Viral infection accounts for as many as two thirds of asthma exacerbations in children and more than half in adults. Allergy and asthma are major risk factors for more frequent and severe RV-related illnesses. The prevalence of RV-induced wheezing will likely continue to increase given that asthma affects a significant proportion of the population, with allergic asthma accounting for the majority. Several new respiratory viruses and their subgroups have been discovered, with various degrees of relevance. This review will focus on RV infection in the context of the epidemiologic evidence, genetic variability, pathobiology, clinical studies in the context of asthma, differences with other viruses including COVID-19 and current treatment interventions.

Emphysema, a component of chronic obstructive pulmonary disease (COPD), is characterized by irreversible alveolar destruction that results in a progressive decline in lung function. This alveolar destruction is caused by cigarette smoke, the most important risk factor for COPD. Only 15%-20% of smokers develop COPD, suggesting that unknown factors contribute to disease pathogenesis. We postulate that the aryl hydrocarbon receptor (AHR), a receptor/transcription factor highly expressed in the lungs, may be a new susceptibility factor whose expression protects against COPD. Here, we report that Ahr-deficient mice chronically exposed to cigarette smoke develop airspace enlargement concomitant with a decline in lung function. Chronic cigarette smoke exposure also increased cleaved caspase-3, lowered SOD2 expression, and altered MMP9 and TIMP-1 levels in Ahr-deficient mice. We also show that people with COPD have reduced expression of pulmonary and systemic AHR, with systemic AHR mRNA levels positively correlating with lung function. Systemic AHR was also lower in never-smokers with COPD. Thus, AHR expression protects against the development of COPD by controlling interrelated mechanisms involved in the pathogenesis of this disease. This study identifies the AHR as a new, central player in the homeostatic maintenance of lung health, providing a foundation for the AHR as a novel therapeutic target and/or predictive biomarker in chronic lung disease.

Respiratory syncytial virus (RSV) causes respiratory illness in children, immunosuppressed individuals and the elderly. However, the viral factors influencing the clinical outcome of RSV infections remain poorly defined. Defective viral genomes (DVGs) can suppress virus replication by competing for viral proteins and by stimulating antiviral immunity. We studied the association between detection of DVGs of the copy-back type and disease severity in three RSV A-confirmed cohorts. In hospitalized children, detection of DVGs in respiratory samples at or around the time of admission associated strongly with more severe disease, higher viral load and a stronger pro-inflammatory response. Interestingly, in experimentally infected adults, the presence of DVGs in respiratory secretions differentially associated with RSV disease severity depending on when DVGs were detected. Detection of DVGs early after infection associated with low viral loads and mild disease, whereas detection of DVGs late after infection, especially if DVGs were present for prolonged periods, associated with high viral loads and severe disease. Taken together, we demonstrate that the kinetics of DVG accumulation and duration could predict clinical outcome of RSV A infection in humans, and thus could be used as a prognostic tool to identify patients at risk of worse clinical disease. Clinical outcomes of respiratory syncytial virus A infection are associated with kinetics of defective viral genome accumulation in humans.

RATIONALE: The genes that influence the pathophysiology of COVID-19 have yet to be identified. Association analysis has found genetic loci for COVID-191. We used integrative genomics (IG) to combine gene expression and proteomic information with COVID-19 susceptibility loci in order to identify candidate genes for this disease. METHODS: For these analyses we used the COVID-19 Host Genetics Initiative genome-wide association (GWA) meta-analysis version 4 (COVID-19 positive versus COVID-19 negative), the Lung eQTL study2 (n=1,038), eQTLGen3 study (n=31,784) and the INTERVAL4 study (n=3,301). We conducted two IG methods (Bayesian Colocalization [coloc] and Summary Based Mendelian Randomization) to link gene and protein expression in lung and blood tissues with COVID-19 susceptibility loci. We identified the most consistently colocalized gene and conducted a Mendelian Randomization (MR) to assess the causal association of its protein ('exposure') with COVID-19 susceptibility ('outcomes'). Significant MR was set as P&lt;0.05. RESULTS: The expression of 6 genes in lung and 12 in blood colocalized with COVID-19 susceptibility loci. SMR results demonstrated that the expression levels of 6 genes in lung tissue and 5 in blood were associated with COVID-19. Out of the candidate genes identified, two (ABO and SLC6A20) were within previously identified loci (Figure 1). Based on the SMR we found that the expression of SLC6A20 in lung was associated with a higher risk of COVID-19. Novel discovered associations included ERMP1, FCER1G, and CA11, genes which have been previously linked with respiratory diseases (i.e.: asthma) and host immune responses (i.e.: neutrophil and eosinophil counts). COVID-19 susceptibility also colocalized with plasma protein levels of ABO. Based on MR, ABO demonstrated a significant causal association (P = 2.10 × 10-5) with the risk of COVID-19 with increased levels of this protein in plasma associated with an increased risk of COVID-19. The top variant in the MR test (rs505922) was in complete linkage disequilibrium with the variant responsible for the blood O genotype, conferring reduced risk. CONCLUSIONS: This multi-omics approach led to the discovery of novel genes associated with COVID-19. We found that the ABO protein is a causal risk factor for COVID-19, with blood group O being protective against COVID-19. REFERENCES: 1. Ellinghaus, D. et al. N. Engl. J. Med. (2020). 2. Hao, K. et al. PLoS Genet. (2012). 3. Ṽsa, U. et al. bioRxiv. (2018). 4. Sun, B. B. et al. Nature. (2018) .

3085 Background: GB1275 is a first-in-class CD11b modulator that reduced myeloid-derived suppressor cells (MDSCs) and tumor associated macrophages (TAMs) at the tumor site, repolarized M2 immunosuppressive TAMs to an M1 phenotype, and increased tumor infiltration of activated CD8+ T cells in preclinical models. When combined with an anti-PD-1 antibody or chemotherapy, these immunomodulatory effects translated into potent anti-tumor effects and prolonged survival in orthotopic PDAC models [Panni RZ, et al. Sci Transl Med. 2019 Jul 3;11(499)]. This ongoing first-in-human study consists of dose escalation of GB1275 monotherapy (Regimen A), GB1275 + pembrolizumab (Regimen B), and GB1275 + nab-paclitaxel + gemcitabine (Regimen C), followed by Phase 2 expansion in newly diagnosed metastatic pancreatic, MSS colorectal, and PD-L1-positive gastric/GEJ cancers. Here we report interim results of the dose escalation portion of the trial. Methods: The dose escalation phase is based on a standard oncology phase 1, 3+3 design. Cohorts of 3 to 6 patients (pts) with histologically confirmed locally advanced/metastatic pancreatic, esophageal, gastric, MSS colorectal, prostate, or breast cancer were sequentially assigned to ascending dose levels of GB1275 taken orally twice daily (BID) in 1 of 3 regimens: Regimen A was initiated first; Regimen B commenced after completion of the first two cohorts of Regimen A, and Regimen C will be initiated when Regimen A is completed. Dose escalation was based on assessment of safety including dose-limiting toxicity (DLT). Serial blood and tumor samples were collected for pharmacokinetic (PK) and biomarker analyses. Results: As of January 21, 2020, 13 pts were treated, with 3 each in Regimen A (GB1275 100mg, 200 mg and 400 mg BID) dose levels and 4 in Regimen B with GB1275 100 mg BID + pembrolizumab. No DLTs have been reported. GB1275 treatment-related adverse events were reported in 5 pts; all were Grade 1 in severity. Preliminary PK analyses showed a mean elimination half-life of ~7 hours. Reduction in peripheral MDSCs was observed in the majority of pts with serial samples. Biomarker analysis in serial tumor tissue is ongoing. Conclusions: Preliminary data show minimal treatment-related toxicities with the studied regimens. PK data support BID dosing. Dose escalation is ongoing. Updated data will be presented. Clinical trial information: NCT04060342 .

Cell entry of SARS-CoV-2, the novel coronavirus causing COVID-19, is facilitated by host cell angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2). We aimed to identify and characterize genes that are co-expressed with ACE2 and TMPRSS2, and to further explore their biological functions and potential as druggable targets. Using the gene expression profiles of 1,038 lung tissue samples, we performed a weighted gene correlation network analysis (WGCNA) to identify modules of co-expressed genes. We explored the biology of co-expressed genes using bioinformatics databases, and identified known drug-gene interactions. ACE2 was in a module of 681 co-expressed genes; 10 genes with moderate-high correlation with ACE2 (r>0.3, FDR<0.05) had known interactions with existing drug compounds. TMPRSS2 was in a module of 1,086 co-expressed genes; 31 of these genes were enriched in the gene ontology biologic process 'receptor-mediated endocytosis', and 52 TMPRSS2-correlated genes had known interactions with drug compounds. Dozens of genes are co-expressed with ACE2 and TMPRSS2, many of which have plausible links to COVID-19 pathophysiology. Many of the co-expressed genes are potentially targetable with existing drugs, which may accelerate the development of COVID-19 therapeutics.

Abstract Background: Tumor influx of CD11b-expressing myeloid-derived suppressor cells (MDSCs) and M2 tumor-associated macrophages (TAMs) creates an immunosuppressive tumor microenvironment associated with resistance to anti-PD-1 antibody therapy. GB1275 is a novel, first-in-class, CD11b modulator that, in vivo, reduced MDSCs and TAMs at the tumor site, repolarized M2 immunosuppressive TAMs to an M1 phenotype, and increased tumor infiltration of activated CD8+ T cells. In combination with an anti-PD-1 antibody or chemotherapy, these immunomodulatory effects translated into potent anti-tumor effects and prolonged survival in orthotopic PDAC models. We hypothesize that GB1275-based therapy can alleviate myeloid cell-mediated immunosuppression and improve cancer treatment outcomes. Methods: This is an open-label, first-in-human study comprising phase 1 dose escalation of GB1275 monotherapy (Regimen A) and GB1275 plus pembrolizumab (Regimen B) in patients with previously treated, locally advanced or metastatic PDA, esophageal, gastric/GEJ, triple negative breast, castration-resistant prostate, or microsatellite-stable colorectal cancer (MSS CRC), and GB1275 plus nab-paclitaxel and gemcitabine (Nab-P+Gem) (Regimen C) in mPDAC. This is followed by phase 2 expansion in three disease cohorts: 1) newly diagnosed stage IV mPDAC (GB1275+Nab-P+Gem), 2) MSS CRC (GB1275+pembrolizumab), and 3) PD-L1+ gastric/GEJ cancer (GB1275+pembrolizumab). Patients are enrolled in Regimen A initially, with Regimen B commencing after completion of the first few cohorts of Regimen A. Regimen C will initiate when Regimen A is completed. Eligible patients are ≥18 years of age, with histologically confirmed locally advanced/metastatic tumor specified and ECOG 0-1 PS; prior immunotherapy is permissible during Regimen A and B dose escalation, but not Regimen C or during the expansion phase. Patients are excluded for untreated or symptomatic CNS metastasis, prior myeloid targeting treatment or other prohibited medications, or a history of clinically significant cardiovascular disease. Patients with active autoimmune disease requiring systemic therapy will be excluded from Regimen B and from expansion cohorts 2 and 3. Primary objectives for phase 1 are to determine the maximum tolerated dose/recommended phase dose and pharmacokinetic profile of GB1275 alone and combination with pembrolizumab, and safety in combination with Nab-P+Gem, and for phase 2, to assess efficacy.Statistical Considerations: A 3+3 design is used for the dose escalation phase and Simon's 2-stage design for the expansion phase. Adverse events are graded per CTCAE v5.0, responses per RECIST v1.1. This study is open for recruitment (NCT04060342). Citation Format: Andrea Wang-Gillam, Drew W. Rasco, Wungki Park, Eileen O'Reilly, Wells Messersmith, David G. DeNardo, Vineet Gupta, Lei Zhou, Anna Galkin, Debbie Slee, Laura L. Carter, David Nickle, Rebecca Tran, Jack Li, Beatrice Ferguson, Marya F. Chaney, Luisa Salter-Cid, Jakob Dupont, Johanna C. Bendell. A phase 1/2 study of GB1275, a first-in-class CD11b modulator, as monotherapy and with an anti-PD-1 antibody in specified advanced solid tumors or with chemotherapy in metastatic pancreatic cancer (KEYNOTE-A36) [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr CT247.

BACKGROUND:Asthma is a complex disease with multiple phenotypes that may differ in disease pathobiology and treatment response. IL33 single nucleotide polymorphisms (SNPs) have been reproducibly associated with asthma. IL33 levels are elevated in sputum and bronchial biopsies of patients with asthma. The functional consequences of IL33 asthma SNPs remain unknown. OBJECTIVE:This study sought to determine whether IL33 SNPs associate with asthma-related phenotypes and with IL33 expression in lung or bronchial epithelium. This study investigated the effect of increased IL33 expression on human bronchial epithelial cell (HBEC) function. METHODS:Association between IL33 SNPs (Chr9: 5,815,786-6,657,983) and asthma phenotypes (Lifelines/DAG [Dutch Asthma GWAS]/GASP [Genetics of Asthma Severity & Phenotypes] cohorts) and between SNPs and expression (lung tissue, bronchial brushes, HBECs) was done using regression modeling. Lentiviral overexpression was used to study IL33 effects on HBECs. RESULTS:We found that 161 SNPs spanning the IL33 region associated with 1 or more asthma phenotypes after correction for multiple testing. We report a main independent signal tagged by rs992969 associating with blood eosinophil levels, asthma, and eosinophilic asthma. A second, independent signal tagged by rs4008366 presented modest association with eosinophilic asthma. Neither signal associated with FEV1, FEV1/forced vital capacity, atopy, and age of asthma onset. The 2 IL33 signals are expression quantitative loci in bronchial brushes and cultured HBECs, but not in lung tissue. IL33 overexpression in vitro resulted in reduced viability and reactive oxygen species-capturing of HBECs, without influencing epithelial cell count, metabolic activity, or barrier function. CONCLUSIONS:We identify IL33 as an epithelial susceptibility gene for eosinophilia and asthma, provide mechanistic insight, and implicate targeting of the IL33 pathway specifically in eosinophilic asthma.

Macrophage migration inhibitory factor (MIF) is a cytokine found to be associated with chronic obstructive pulmonary disease (COPD). However, there is no consensus on how MIF levels differ in COPD compared to control conditions and there are no reports on MIF expression in lung tissue. Here we studied gene expression of members of the MIF family MIF , D-Dopachrome Tautomerase ( DDT ) and DDT-like ( DDTL ) in a lung tissue dataset with 1087 subjects and identified single nucleotide polymorphisms (SNPs) regulating their gene expression. We found higher MIF and DDT expression in COPD patients compared to non-COPD subjects and found 71 SNPs significantly influencing gene expression of MIF and DDTL . Furthermore, the platform used to measure MIF (microarray or RNAseq) was found to influence the splice variants detected and subsequently the direction of the SNP effects on MIF expression. Among the SNPs found to regulate MIF expression, the major LD block identified was linked to rs5844572, a SNP previously found to be associated with lower diffusion capacity in COPD. This suggests that MIF may be contributing to the pathogenesis of COPD, as SNPs that influence MIF expression are also associated with symptoms of COPD. Our study shows that MIF levels are affected not only by disease but also by genetic diversity (i.e. SNPs). Since none of our significant eSNPs for MIF or DDTL have been described in GWAS for COPD or lung function, MIF expression in COPD patients is more likely a consequence of disease-related factors rather than a cause of the disease.