A conformational sensor based on genetic code expansion reveals an autocatalytic component in EGFR activation.

Epidermal growth factor receptor (EGFR) activation by growth factors (GFs) relies on dimerization and allosteric activation of its intrinsic kinase activity, resulting in trans-phosphorylation of tyrosines on its C-terminal tail. While structural and biochemical studies identified this EGF-induced allosteric activation, imaging collective EGFR activation in cells and molecular dynamics simulations pointed at additional catalytic EGFR activation mechanisms. To gain more insight into EGFR activation mechanisms in living cells, we develop a Förster resonance energy transfer (FRET)-based conformational EGFR indicator (CONEGI) using genetic code expansion that reports on conformational transitions in the EGFR activation loop. Comparing conformational transitions, self-association and auto-phosphorylation of CONEGI and its Y845F mutant reveals that Y845 phosphorylation induces a catalytically active conformation in EGFR monomers. This conformational transition depends on EGFR kinase activity and auto-phosphorylation on its C-terminal tail, generating a looped causality that leads to autocatalytic amplification of EGFR phosphorylation at low EGF dose

HLA-DP on Epithelial Cells Enables Tissue Damage by NKp44+ Natural Killer Cells in Ulcerative Colitis

Background & aims: Ulcerative colitis (UC) is characterized by severe inflammation and destruction of the intestinal epithelium, and is associated with specific risk single nucleotide polymorphisms in HLA class II. Given the recently discovered interactions between subsets of HLA-DP molecules and the activating natural killer (NK) cell receptor NKp44, genetic associations of UC and HLA-DP haplotypes and their functional implications were investigated.Methods: HLA-DP haplotype and UC risk association analyses were performed (UC: n = 13,927; control: n = 26,764). Expression levels of HLA-DP on intestinal epithelial cells (IECs) in individuals with and without UC were quantified. Human intestinal 3-dimensional (3D) organoid cocultures with human NK cells were used to determine functional consequences of interactions between HLA-DP and NKp44.Results: These studies identified HLA-DPA1∗01:03-DPB1∗04:01 (HLA-DP401) as a risk haplotype and HLA-DPA1∗01:03-DPB1∗03:01 (HLA-DP301) as a protective haplotype for UC in European populations. HLA-DP expression was significantly higher on IECs of individuals with UC compared with controls. IECs in human intestinal 3D organoids derived from HLA-DP401pos individuals showed significantly stronger binding of NKp44 compared with HLA-DP301pos IECs. HLA-DP401pos IECs in organoids triggered increased degranulation and tumor necrosis factor production by NKp44+ NK cells in cocultures, resulting in enhanced epithelial cell death compared with HLA-DP301pos organoids. Blocking of HLA-DP401-NKp44 interactions (anti-NKp44) abrogated NK cell activity in cocultures.Conclusions: We identified an UC risk HLA-DP haplotype that engages NKp44 and activates NKp44+ NK cells, mediating damage to intestinal epithelial cells in an HLA-DP haplotype-dependent manner. The molecular interaction between NKp44 and HLA-DP401 in UC can be targeted by therapeutic interventions to reduce NKp44+ NK cell-mediated destruction of the intestinal epithelium in UC

HLA-DP on Epithelial Cells Enables Tissue Damage by NKp44⁺ Natural Killer Cells in Ulcerative Colitis

Background &amp; Aims: Ulcerative colitis (UC) is characterized by severe inflammation and destruction of the intestinal epithelium, and is associated with specific risk single nucleotide polymorphisms in HLA class II. Given the recently discovered interactions between subsets of HLA-DP molecules and the activating natural killer (NK) cell receptor NKp44, genetic associations of UC and HLA-DP haplotypes and their functional implications were investigated. Methods: HLA-DP haplotype and UC risk association analyses were performed (UC: n = 13,927; control: n = 26,764). Expression levels of HLA-DP on intestinal epithelial cells (IECs) in individuals with and without UC were quantified. Human intestinal 3-dimensional (3D) organoid cocultures with human NK cells were used to determine functional consequences of interactions between HLA-DP and NKp44. Results: These studies identified HLA-DPA1∗01:03-DPB1∗04:01 (HLA-DP401) as a risk haplotype and HLA-DPA1∗01:03-DPB1∗03:01 (HLA-DP301) as a protective haplotype for UC in European populations. HLA-DP expression was significantly higher on IECs of individuals with UC compared with controls. IECs in human intestinal 3D organoids derived from HLA-DP401pos individuals showed significantly stronger binding of NKp44 compared with HLA-DP301pos IECs. HLA-DP401pos IECs in organoids triggered increased degranulation and tumor necrosis factor production by NKp44+ NK cells in cocultures, resulting in enhanced epithelial cell death compared with HLA-DP301pos organoids. Blocking of HLA-DP401–NKp44 interactions (anti-NKp44) abrogated NK cell activity in cocultures. Conclusions: We identified an UC risk HLA-DP haplotype that engages NKp44 and activates NKp44+ NK cells, mediating damage to intestinal epithelial cells in an HLA-DP haplotype–dependent manner. The molecular interaction between NKp44 and HLA-DP401 in UC can be targeted by therapeutic interventions to reduce NKp44+ NK cell–mediated destruction of the intestinal epithelium in UC.</p

Dynamic regulation of autocatalytic EGFR activation

The dynamics of epidermal growth factor receptor (EGFR) signaling emerge from its recursive interactions with protein tyrosine phosphatases (PTPs) and autocatalytic receptor activation thereby determining cellular behavior including proliferation, migration and differentiation. The autocatalytic activation of EGFR causes an amplification of EGFR phosphorylation in response to extracellular signals, but its trade-off is spontaneous activation at high receptor densities even in the absence of ligand. Structural and molecular dynamics studies identified an allosteric activation mechanism upon EGF-induced receptor activation, but the molecular basis of autocatalytic EGFR activation remains unclear. To better understand autocatalysis we developed a Förster Resonance Energy Transfer (FRET)-based, conformational EGFR indicator (CONEGI) using genetic code expansion to monitor the conformational state of the tyrosine kinase domain (TKD) in living cells and relate it to EGFR activity. We show that EGFR monomers can adopt an active conformation that is stabilized upon Y845 phosphorylation. Since Y845 is an auto-phosphorylation site this creates a positive feedback loop generating an autocatalytic amplification mechanism. To counteract autonomous, autocatalytic EGFR activation in the absence of ligand, intrinsic and extrinsic safeguard mechanisms are required. Intrinsic auto-inhibitory structural features can be overcome by thermal conformational fluctuations allowing a sub-population of EGFR to adopt an active conformation. This autonomous, autocatalytic EGFR activity is counterbalanced by a spatial cycle that suppresses phosphorylation of Y845 on EGFR monomers by vesicular recycling through perinuclear areas with high PTP1B activity. EGF-binding induces receptor dimerization and phosphorylation of the c-Cbl docking Y1045 leading to receptor ubiquitination that targets EGFR for degradation in lysosomes. The re-routing regulates EGFR signaling response by the transit-time to late endosomes where it is switched-off by high PTP1B activity. This ubiquitin-mediated switch from a suppressive cycle to a unidirectional trafficking mode is a uniquely suited solution to suppress spontaneous activation while maintaining responsiveness to EGF

In vitro co-culture of human intestinal organoids and lamina propria-derived CD4+ T cells

Summary: Crosstalk between immune cells and intestinal stem cells (ISCs) in vivo plays a critical role in tissue homeostasis and inflammation; however, in vitro models based on primary cells recapitulating this interaction were lacking. Here, we provide a detailed protocol for an autologous in vitro long-term 3D co-culture system of human intestinal CD4+ T cells and ISCs to study T cell-intestinal epithelial cell interactions during tissue development and inflammation.For complete details on the use and execution of this protocol, please refer to Schreurs et al. (2019)

Human Fetal TNF-α-Cytokine-Producing CD4+ Effector Memory T Cells Promote Intestinal Development and Mediate Inflammation Early in Life

Although the fetal immune system is considered tolerogenic, preterm infants can suffer from severe intestinal inflammation, including necrotizing enterocolitis (NEC). Here, we demonstrate that human fetal intestines predominantly contain tumor necrosis factor-α (TNF-α)+CD4+CD69+ T effector memory (Tem) cells. Single-cell RNA sequencing of fetal intestinal CD4+ T cells showed a T helper 1 phenotype and expression of genes mediating epithelial growth and cell cycling. Organoid co-cultures revealed a dose-dependent, TNF-α-mediated effect of fetal intestinal CD4+ T cells on intestinal stem cell (ISC) development, in which low T cell numbers supported epithelial development, whereas high numbers abrogated ISC proliferation. CD4+ Tem cell frequencies were higher in inflamed intestines from preterm infants with NEC than in healthy infant intestines and showed enhanced TNF signaling. These findings reveal a distinct population of TNF-α-producing CD4+ T cells that promote mucosal development in fetal intestines but can also mediate inflammation upon preterm birth

Human Fetal TNF-α-Cytokine-Producing CD4 + Effector Memory T Cells Promote Intestinal Development and Mediate Inflammation Early in Life

Although the fetal immune system is considered tolerogenic, preterm infants can suffer from severe intestinal inflammation, including necrotizing enterocolitis (NEC). Here, we demonstrate that human fetal intestines predominantly contain tumor necrosis factor-α (TNF-α) + CD4 + CD69 + T effector memory (Tem) cells. Single-cell RNA sequencing of fetal intestinal CD4 + T cells showed a T helper 1 phenotype and expression of genes mediating epithelial growth and cell cycling. Organoid co-cultures revealed a dose-dependent, TNF-α-mediated effect of fetal intestinal CD4 + T cells on intestinal stem cell (ISC) development, in which low T cell numbers supported epithelial development, whereas high numbers abrogated ISC proliferation. CD4 + Tem cell frequencies were higher in inflamed intestines from preterm infants with NEC than in healthy infant intestines and showed enhanced TNF signaling. These findings reveal a distinct population of TNF-α-producing CD4 + T cells that promote mucosal development in fetal intestines but can also mediate inflammation upon preterm birth. The fetal immune system is considered anti-inflammatory; nonetheless, preterm infants are at risk for necrotizing enterocolitis (NEC), a severe intestinal inflammatory disease. Schreurs et al. demonstrate that fetal TNF-α + CD4 + T cells promote gut development early in life. However, in preterm babies these TNFα + CD4 + T cells can mediate intestinal inflammation, providing a potential mechanism for NEC