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Lay SummaryWe demonstrate low rates of breakthrough coronavirus disease 2019 (COVID-19) infection and mild course of illness following severe acute respiratory syndrome coronavirus 2 vaccination in a large cohort of inflammatory bowel disease patients. Residence in southern United States and lower median anti-receptor binding antibody level were associated with development of COVID-19.

Context.— Clinical testing for tumor cell-free DNA (cfDNA) has evolved rapidly, but no practice guidelines exist. Objective.— To summarize cfDNA laboratory practices based on self-reporting and assess preanalytical, analytical, and postanalytical trends that may influence the quality, accuracy, and consistency of cfDNA testing. Design.— Data were derived from the College of American Pathologists cfDNA proficiency testing program submitted by 101 participating laboratories from 2018 to 2019. Results.— Most laboratories performing clinical circulating tumor DNA testing are commercial/nonhospital (71.2%; 72 of 101) and international (77.2%; 78 of 101) laboratories. Commercial laboratories had higher monthly test volumes than hospital-based laboratories (median, 36 versus 7–8) and tended to have larger gene panels (median, 50 versus 11 genes) when panel-based testing was offered. The main clinical indications include therapy selection and treatment/disease monitoring. Plasma is the most commonly accepted specimen, which is predominantly collected in cell-stabilizing tubes. Equal proportions of laboratories use next-generation sequencing (NGS) and non-NGS methods to assess key genes, including EGFR, BRAF, KRAS, NRAS, and IDH1. Most laboratories reported a lower limit of detection (LLOD) of 0.5%, variant allele frequency or less, which did not differ by method, NGS or non-NGS, except for EGFR. Sixty-five percent (17 of 26) of laboratories using the US Food and Drug Administration (FDA)-approved non-NGS EGFR assay report analytical sensitivities higher than 0.5%, as compared to 15% (16 of 104) of laboratories using an alternative NGS or non-NGS method. There is also a wider range in LLODs obtained for the FDA-approved EGFR assay than nonapproved assays. Conclusions.— These results highlight emerging practice trends and serve as a foundation to initiate future practice recommendations.

Abstract Alveolar macrophages (AMs) are major lung tissue-resident macrophages capable of proliferating and self-renewal in situ. AMs are vital in pulmonary antimicrobial immunity and surfactant clearance. The mechanisms regulating AM compartment formation and maintenance remain to be fully elucidated currently. In this study, we have explored the roles of mitochondrial transcription factor A (TFAM)–mediated mitochondrial fitness and metabolism in regulating AM formation and function. We found that TFAM deficiency in mice resulted in significantly reduced AM numbers and impaired AM maturation in vivo. TFAM deficiency was not required for the generation of AM precursors nor the differentiation of AM precursors into AMs, but was critical for the maintenance of AM compartment. Mechanistically, TFAM deficiency diminished gene programs associated with AM proliferation and self-renewal and promoted the expression of inflammatory genes in AMs. We further showed that TFAM-mediated AM compartment impairment resulted in defective clearance of cellular debris and surfactant in the lung and increased the host susceptibility to severe influenza virus infection. Finally, we found that influenza virus infection in AMs led to impaired TFAM expression and diminished mitochondrial fitness and metabolism. Thus, our data have established the critical function of TFAM-mediated mitochondrial metabolism in AM maintenance and function.

INTRODUCTION: Although an additional coronavirus disease 2019 vaccine dose for immunocompromised persons has been recommended in some countries, further data to guide vaccination strategies for patients with inflammatory bowel disease (IBD) are urgently needed. We sought to identify factors affecting initial humoral immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines among patients with IBD. METHODS: In this prospective cohort of SARS-CoV-2 immunized patients with IBD, we evaluated associations between participant age, sex, vaccine type, medication use, and the presence of a detectable antireceptor binding domain antibody and quantitative antibody level. RESULTS: In total, 1,909 participants were included (1,123, 692, and 94 received BNT162b2, mRNA-1273, and Ad26.COV2.S, respectively) of whom 96% achieved a positive antibody response. On multivariable analysis, factors associated with lack of antibody response were older age ( P = 0.043), BNT162b2 vs mRNA-1273 (odds ratio [OR] 2.1, 95% confidence interval [CI] 1.0–3.9), and combination therapy with anti-TNF and 6MP, azathioprine, or methotrexate (OR 4.2, 95% CI 2.4–7.3). The use of 5-aminosalicylate or sulfasalazine (OR 0.3, 95% CI 0.1–0.8) and ustekinumab (OR 0.2, 95% CI 0.05–0.8) was associated with decreased odds of lacking antibody response. DISCUSSION: Most patients with IBD mount an initial response to SARS-CoV-2 vaccination; however, older patients and those treated with anti-TNF and immunomodulator have blunted responses and may benefit the most from an additional vaccine dose. Patients treated with other classes of immunosuppressive medications have more robust initial immune responses to vaccination. These data should inform key decisions about patient selection for additional coronavirus disease 2019 vaccine doses in patients with IBD.

Abstract Background Severe acute respiratory syndrome coronavirus 2 vaccination is recommended for all individuals with inflammatory bowel disease (IBD), including those on immunosuppressive therapies; however, little is known about vaccine safety and efficacy in these patients or the impact of vaccination on IBD disease course. Methods We evaluated coronavirus disease 2019 (COVID-19) vaccine–related adverse events (AEs) and the effect of vaccination on IBD disease course among participants in the PREVENT-COVID (Partnership to Report Effectiveness of Vaccination in populations Excluded from iNitial Trials of COVID) study, a prospective, observational cohort study. Localized and systemic reactions were assessed via questionnaire. Disease flare was defined by worsening IBD symptoms and change in IBD medications. Outcomes were stratified by vaccine type and IBD medication classes. Results A total of 3316 individuals with IBD received at least 1 COVID-19 vaccine. Injection site tenderness (68%) and fatigue (46% dose 1, 68% dose 2) were the most commonly reported localized and systemic AEs after vaccination. Severe localized and systemic vaccine-related AEs were rare. The mRNA-1273 vaccine was associated with significantly greater severe AEs at dose 2 (localized 4% vs 2%, systemic 15% vs 10%; P < .001 for both). Prior COVID-19 infection, female sex, and vaccine type were associated with severe systemic reactions to dose 1, while age <50 years, female sex, vaccine type, and antitumor necrosis factor and vedolizumab use were associated with severe systemic reactions to dose 2. Overall rates (2%) of IBD flare were low following vaccination. Conclusions Our findings provide reassurance that the severe acute respiratory syndrome coronavirus 2 vaccine is safe and well tolerated among individuals with IBD, which may help to combat vaccine hesitancy and increase vaccine confidence.

Fatty acids (FAs) not only are a key component of cellular membrane structure, but also have diverse functions in biological processes. Recent years have seen great advances in understanding of how FA metabolism contributes to adaptive immune response. Here, we review three key processes, FA biosynthesis, FA oxidation and FA uptake, and how they direct T and B cell functions during immune challenges. Then, we will focus on the relationship between microbiota derived FAs, short‐chain FAs, and adaptive immunity. Along the way, we will also discuss the outstanding controversies and challenges in the field.

Abstract Introduction: Immune checkpoint receptor (ICR) blockade has emerged as an effective anti-tumour modality, but only in a subset of cancer patients. Moreover, in Multiple myeloma (MM), single-agent activity has not been observed, highlighting the need to better understand the mechanism of action of this class of drugs. We recently showed that combinatorial ICR blockade using αLAG3 and αPD-1 delays disease progression and improves survival in the transplantable Vκ*MYC model of MM (Croucher et al. ASH 2018). However, despite this being a controlled study with genetically-homogeneous tumours, anti-tumour immune responses were heterogeneous, with only a subset of mice demonstrating a delay in tumour progression (17/29 mice, response rate = 58.6%). Thus, using this model, we set out to define mechanisms underlying variability in response to ICR blockade. Methods: We established a cohort of mice by engrafting 5-week-old C57BL/6 mice with Vκ12598 cells via tail vein injection. Treatment with αLAG3/αPD-1 or Ig-control was initiated 1-week post-engraftment and bone marrow (BM) samples were collected 3 weeks after the start of treatment. Following FACS-enrichment of T cells and plasma cells (PCs), single cell suspensions were subjected to matched single-cell gene expression (5' scRNA-seq) and T cell receptor (TCR)/B cell receptor (BCR) profiling (10x Genomics). Results: Samples were selected for profiling based on response to treatment, with responders (n=4) defined by significantly lower disease burden compared to non-responders (n=3) and control-treated mice (n=5), as measured by serum M-protein and %PCs in BM/spleen at sacrifice. Unsupervised clustering of scRNA-seq data from PCs (n=3,318 cells) identified no gene expression or BCR repertoire differences between control and treated, or between responder and non-responder samples, supporting that variability in response was not related to malignant Vκ12598 cells themselves. Across all samples, a statistically significant difference was not detected between the total number of unique TCR sequences (clonotypes) comparing control-treated (351-2369), non-responders (1185-2327) and responders (1378-1698), with no overlapping TCR sequences between top clonotypes. Evaluation of TCR repertoire diversity revealed that αLAG3/αPD-1 treatment induces clonal T cell expansion in control versus treated mice, but this was not significantly different between responders and non-responders. Analysis of paired scRNA-seq data (n=21,520 cells) revealed that expanded T cells from αLAG3/αPD-1-treated mice occupy a different cell state in responder vs. non-responder mice. We speculate that underlying differences in the TCR repertoire may dictate the downstream phenotype of expanded, anti-tumour T cells in mice treated with combinatorial αLAG3/αPD-1. Tumour control following treatment was associated with clonal expansion of T cells expressing genes related to cytoxicity and activation (Ccl5, Ifng, Fasl, Gzmb), whereas tumour progression was associated with clonal expansion of proliferative T cells (Cdkn3, Birc5, Ccna2, Aurka, Mki67). Although T cell proliferation is typically a phenotype ascribed to effector T cells, recent studies have similarly observed this proliferative cell state in dysfunctional T cells within melanoma tumours. Moreover, emerging evidence supports suppression of T cell proliferation by CDK4/6 inhibitors as a means to augment anti-tumour activity of ICR-based therapy. Thus, studies exploring whether reversal of the observed proliferative T cell state can restore response to αLAG3/αPD-1 treatment in non-responding Vκ12598 mice are ongoing and will be reported. Conclusions: ICR inhibitors demonstrate significant activity in some cancers, however many patients fail to respond and a similarly promising level of efficacy has not been achieved in MM. Studies aimed at unraveling the mechanisms of response and resistance to ICR inhibitors are therefore needed to improve the utility of this class of drugs for all patients. Our approach of using paired single-cell gene expression and TCR repertoire profiling has enabled identification of molecular cell states specifically in expanded T cells of responder vs. non-responder mice. In turn, our work nominates novel mechanisms that may be used as potential biomarkers for anti-tumour immune responses as well as potential targets to augment responses to ICR blockade therapy. Disclosures Chesi: Abcuro: Patents & Royalties: Genetically engineered mouse model of myeloma; Novartis: Consultancy, Patents & Royalties: human CRBN transgenic mouse; Pfizer: Consultancy; Pi Therapeutics: Patents & Royalties: Genetically engineered mouse model of myeloma; Palleon Pharmaceuticals: Patents & Royalties: Genetically engineered mouse model of myeloma. Bergsagel: GSK: Consultancy, Honoraria; Genetech: Consultancy, Honoraria; Janssen: Consultancy, Honoraria; Oncopeptides: Consultancy, Honoraria; Novartis: Consultancy, Honoraria, Patents & Royalties: human CRBN mouse; Pfizer: Consultancy, Honoraria; Celgene: Consultancy, Honoraria. Sebag: Janssen: Research Funding; Bristol Myers-Squibb: Consultancy, Honoraria; Takeda: Consultancy, Honoraria; Novartis: Consultancy, Honoraria; Amgen: Consultancy, Honoraria; Sanofi: Consultancy, Honoraria; Karyopharm Therapeutics: Consultancy, Honoraria. Trudel: BMS/Celgene: Consultancy, Honoraria, Research Funding; Amgen: Honoraria, Research Funding; Janssen: Honoraria, Research Funding; GlaxoSmithKline: Consultancy, Honoraria, Research Funding; Roche: Consultancy; Sanofi: Honoraria; Pfizer: Honoraria, Research Funding; Genentech: Research Funding.