Mass spectrometric identification of immunogenic SARS-CoV-2 epitopes and cognate TCRs.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections elicit both humoral and cellular immune responses. For the prevention and treatment of COVID-19, the disease caused by SARS-CoV-2, it has become increasingly apparent that T cell responses are equally if not more important than humoral responses in mediating recovery and immune protection. One major challenge in developing T cell-based therapies for infectious and malignant diseases has been the identification of immunogenic epitopes that can elicit a meaningful T cell response. Traditionally, this has been achieved using sophisticated in silico methods to predict putative epitopes deduced from binding affinities. Our studies find that, in contrast to current convention, "immunodominant" SARS-CoV-2 peptides defined by such in silico methods often fail to elicit T cell responses recognizing naturally presented SARS-CoV-2 epitopes. We postulated that immunogenic epitopes for SARS-CoV-2 are best defined empirically by directly analyzing peptides eluted from the naturally processed peptide-major histocompatibility complex (MHC) and then validating immunogenicity by determining whether such peptides can elicit T cells recognizing SARS-CoV-2 antigen-expressing cells. Using a tandem mass spectrometry approach, we identified epitopes derived from not only structural but also nonstructural genes in regions highly conserved among SARS-CoV-2 strains, including recently recognized variants. Finally, there are no reported T cell receptor-engineered T cell technology that can redirect T cell specificity to recognize and kill SARS-CoV-2 target cells. We report here several SARS-CoV-2 epitopes defined by mass spectrometric analysis of MHC-eluted peptides, provide empiric evidence for their immunogenicity, and demonstrate engineered TCR-redirected killing.

Hypoxia acts as an environmental cue for the human tissue-resident memory T cell differentiation program.

Tissue-resident memory T cells (TRM) provide frontline defense against infectious diseases and contribute to antitumor immunity; however, aside from the necessity of TGF-ß, knowledge regarding TRM-inductive cues remains incomplete, particularly for human cells. Oxygen tension is an environmental cue that distinguishes peripheral tissues from the circulation, and here, we demonstrate that differentiation of human CD8+ T cells in the presence of hypoxia and TGF-ß1 led to the development of a TRM phenotype, characterized by a greater than 5-fold increase in CD69+CD103+ cells expressing human TRM hallmarks and enrichment for endogenous human TRM gene signatures, including increased adhesion molecule expression and decreased expression of genes involved in recirculation. Hypoxia and TGF-ß1 synergized to produce a significantly larger population of TRM phenotype cells than either condition alone, and comparison of these cells from the individual and combination conditions revealed distinct phenotypic and transcriptional profiles, indicating a programming response to milieu rather than a mere expansion. Our findings identify a likely previously unreported cue for the TRM differentiation program and can enable facile generation of human TRM phenotype cells in vitro for basic studies and translational applications such as adoptive cellular therapy.

Halstead Category Test sensitivity to neurocognitive deficits in prenatal alcohol exposed and cognitively impaired children.

Objective: The Halstead Category Test (HCT) has been demonstrated to be sensitive to executive dysfunction in adults and children. Children with a history of significant prenatal alcohol exposure (PAE) typically show deficits in executive functions in such areas as abstract reasoning, concept formation abilities, and cognitive flexibility. However, earlier research has not taken into account the demographic variables of age, sex, and ethnicity.Methods: Three groups of psychiatrically hospitalized children ages 9-17 years were included: Children with a history of PAE (n = 295); children with cognitive impairment but no suspected history of PAE (n = 201); and children without suspected cognitive impairment (n = 317). All children completed a series of neuropsychological tests including the HCT and the Wechsler Intelligence Scale for Children-IV (WISC-IV).Results: Children with a history of PAE and cognitively impaired children with no history of PAE produced significantly more HCT errors across all ages than the cognitively unimpaired group. There were no significant effects of ethnicity or gender. Age and Working Memory Index were negatively correlated with HCT errors.Conclusion: The findings support the use of the HCT as a sensitive measure of executive functions in both PAE and non-PAE cognitively impaired children with no evidence of gender and ethnic bias. Use of the HCT is indicated in future research to measure improvement in executive functioning among children with a history of PAE facilitated by education, rehabilitation, and other forms of training and treatment.