Biology subjects

Aster, J. C.

Publications and source records attributed to Aster, J. C..

11 recordsLinked to original sources

bioRxiv2024

The follicular lymphoma and chronic lymphocytic leukemia proliferative microenvironment at single-cell resolution

Adaptive immune responses occur lymph nodes (LNs) in a microenvironment established by resident stromal cells. LNs are also a site of proliferation of chronic lymphocytic leukemia (CLL), a B cell cancer that alters LN structure in a stereotypic manner. To deeply characterize reactive and CLL LNs, we developed a single-cell RNA sequencing pipeline. We find that proliferation of CLL cells in proliferation centers (PCs), a CLL-specific niche, begins with transient upregulation of MYC, subsequent downregulation of which may limit CLL growth. PCs contain a distinct fibroblast population expressing CCL19 while CLL cells express the CCL19 receptor CCR7, providing a recruitment mechanism for CLL cells to PCs. Using informatic, spatial, and in situ analyses to identify ligand-receptor pairs involving PC CLL cells and nearby immune and stromal cells, we observe that PCs are enriched for macrophages expressing BAFF, the integrin X{beta}2 heterodimer, and Galectin9, factors implicated in cell growth, adhesion, and immunosuppression. The most common predicted interactions in PCs involve CD74 and ligands such as MIF, and we find that CD74 blockade consistently inhibits CLL cell growth in culture. Our work highlights key features of the CLL proliferative niche and provides a roadmap for identifying vulnerabilities and new therapeutic strategies.

pathology↗

bioRxiv2024

Notch induces transcription by stimulating release of paused RNA Pol II without increasing chromatin accessibility

Notch proteins undergo ligand-induced proteolysis to release a nuclear effector that influences a wide range of cellular processes by regulating transcription. Despite years of study, however, how Notch induces the transcription of its target genes remains unclear. Here, we comprehensively examined the response to human Notch1 across a time course of activation using high-resolution genomic assays of chromatin accessibility and nascent RNA production. Our data reveal that Notch induces target gene transcription primarily by releasing paused RNA polymerase II (RNAPII). Moreover, in contrast to prevailing models suggesting that Notch acts by promoting chromatin accessibility, we found that open chromatin was established at Notch-responsive regulatory elements prior to Notch signal induction, through SWI/SNF-mediated remodeling. Together, these studies show that the nuclear response to Notch signaling is dictated by the pre-existing chromatin state and RNAPII distribution at the time of signal activation.

genomics↗

bioRxiv2024

Structural Requirements for Activity of Mind bomb1 in Notch Signaling

Mind bomb 1 (MIB1) is a RING E3 ligase that ubiquitinates Notch ligands, a necessary step for induction of Notch signaling. The structural basis for binding of the JAG1 ligand by the N-terminal region of MIB1 is known, yet how the ankyrin (ANK) and RING domains of MIB1 cooperate to catalyze ubiquitin transfer from E2[~]Ub to Notch ligands remains unclear. Here, we show that the third RING domain and adjacent coiled coil region of MIB1 (ccRING3) drives MIB1 dimerization and that ubiquitin transfer activity of MIB1 relies solely on RING3. We report x-ray crystal structures of a UbcH5B-ccRING3 complex as a fusion protein and of the ANK region. Directly tethering the N-terminal region to ccRING3 forms a minimal MIB1 protein, which is sufficient to induce a Notch response in receiver cells. Together, these studies define the functional elements of an E3 ligase needed for ligands to induce a Notch signaling response.

biochemistry↗

bioRxiv2023

Temporal Dynamics and Stoichiometry in Notch Signaling - from Notch Synaptic Complex Formation to NICD Nuclear Entry

Mammalian Notch signaling occurs when binding of Delta or Jagged to Notch stimulates proteolytic release of the Notch intracellular domain (NICD), which enters the nucleus to regulate target gene expression. To determine the temporal dynamics of events associated with Notch signaling under native conditions, we fluorescently tagged Notch and Delta at their endogenous genomic loci and visualized them upon pairing of receiver (Notch) and sender (Delta) cells as a function of time after cell contact. At contact sites, Notch and Delta immediately accumulated at 1:1 stoichiometry in synapses, which resolved by 15-20 min after contact. Synapse formation preceded entrance of the Notch extracellular domain into the sender cell and accumulation of NICD in the nucleus of the receiver cell, which approached a maximum after [~]45 min and was prevented by chemical and genetic inhibitors of signaling. These findings directly link Notch-Delta synapse dynamics to NICD production with unprecedented spatiotemporal precision.

cell biology↗

bioRxiv2023

Molecular Mechanism of PP2A/B55α Inhibition by IER5

PP2A serine/threonine phosphatases are heterotrimeric complexes that execute many essential physiologic functions. These activities are modulated by additional regulatory proteins, such as ARPP19, FAM122A, and IER5. Here, we report the cryoelectron microscopy structure of a complex of PP2A/B55 with the N-terminal structured region of IER5 (IER5-N50), which occludes a surface on B55 used for substrate recruitment, and show that IER5-N50 inhibits PP2A/B55 catalyzed dephosphorylation of pTau in biochemical assays. Mutations of full-length IER5 that disrupt its PP2A/B55 interface interfere with co-immunoprecipitation of PP2A/B55. These mutations and deletions that remove the nuclear localization sequence of IER5 suppress cellular events such as KRT1 expression that depend on association of IER5 with PP2A/B55. Querying the Alphafold2 predicted structure database identified SERTA domain proteins as high-confidence PP2A/B55-binding structural homologs of IER5-N50. These studies define the molecular basis of PP2A/B55 inhibition by IER5-family proteins and suggest a roadmap for selective pharmacologic modulation of PP2A/B55 complexes.

biochemistry↗

bioRxiv2023

A novel cryopreservation and biobanking strategy to study lymphoid tissue stromal cells in human disease

Non-hematopoietic lymph node stromal cells (LNSCs) regulate lymphocyte trafficking, survival, and function for key roles in host defense, autoimmunity, alloimmunity, and lymphoproliferative disorders. However, study of LNSCs in human diseases is complicated by a dependence on viable lymphoid tissues, which are most often excised prior to establishment of a specific diagnosis. Here, we demonstrate that cryopreservation can be used to bank lymphoid tissue for the study of LNSCs in human disease. Using human tonsils, lymphoid tissue fragments were cryopreserved for subsequent enzymatic digestion and recovery of viable non-hematopoietic cells. Flow cytometry and single-cell transcriptomics identified comparable proportions of LNSC cell types in fresh and cryopreserved tissue. Moreover, cryopreservation had little effect on transcriptional profiles, which showed significant overlap between tonsils and lymph nodes. The presence and spatial distribution of transcriptionally defined cell types was confirmed by in situ analyses. Our broadly applicable approach promises to greatly enable research into the roles of LNSC in human disease.

immunology↗

bioRxiv2022

A Spatiotemporal Notch Interaction Map from Membrane to Nucleus

Notch signaling relies on ligand-induced proteolysis to liberate a nuclear effector that drives cell fate decisions. The location and timing of individual steps required for proteolysis and movement of Notch from membrane to nucleus, however, remain unclear. Here, we use proximity labeling with quantitative multiplexed mass spectrometry to monitor the microenvironment of endogenous Notch2 after ligand stimulation in the presence of a gamma secretase inhibitor and then as a function of time after inhibitor removal. Our studies show that gamma secretase cleavage of Notch2 occurs in an intracellular compartment and that formation of nuclear complexes and recruitment of chromatin-modifying enzymes occurs within 45 minutes of inhibitor washout. This work provides a spatiotemporal map of unprecedented detail tracking the itinerary of Notch from membrane to nucleus after activation and identifies molecular events in signal transmission that are potential targets for modulating Notch signaling activity.

molecular biology↗

bioRxiv2020

IER5, a DNA-damage response gene, is required for Notch-mediated induction of squamous cell differentiation

Notch signaling regulates normal squamous cell proliferation and differentiation and is frequently disrupted in squamous cell carcinomas, in which Notch is a key tumor suppressive pathway. To identify the direct targets of Notch that produce these phenotypes, we introduced a conditional Notch transgene into squamous cell carcinoma cell lines, which respond to Notch activation in 2D culture and in organoid cultures by undergoing differentiation. RNA-seq and ChIP-seq analyses show that in squamous cells Notch activates a context-specific program of gene expression that depends on lineage-specific regulatory elements, most of which lie in long- range enhancers. Among the direct Notch target genes are multiple DNA damage response genes, including IER5, which is regulated by Notch through several enhancer elements. We show that IER5 is required for Notch-induced differentiation in squamous carcinoma cells and in TERT-immortalized keratinocytes. Its function is epistatic to PPP2R2A, which encodes the B55 subunit of PP2A, and IER5 interacts with B55 in cells and in purified systems. These results show that Notch and DNA-damage response pathways converge in squamous cells and that some components of these pathways promote differentiation, which may serve to eliminate DNA-damaged cells from the proliferative pool in squamous epithelia. Crosstalk involving Notch and PP2A may enable Notch signaling to be tuned and integrated with other pathways that regulate squamous differentiation. Our work also suggests that squamous cell carcinomas remain responsive to Notch signaling, providing a rationale for reactivation of Notch as a therapeutic strategy in these cancers. ImpactOur findings highlight context-specific crosstalk between Notch, DNA damage response genes, and PP2A, and provide a roadmap for understanding how Notch induces the differentiation of squamous cells.

cancer biology↗

bioRxiv2020

Varying co-factor requirements for MAML1-dependent transcription at different Notch-responsive target genes

Mastermind proteins are required for transcription of Notch target genes, yet the molecular basis for mastermind function remains incompletely understood. Previous work has shown that Notch can induce transcriptional responses by binding to promoters, but more often by binding to enhancers, with HES4 and DTX1 as representative mammalian examples of promoter and enhancer responsiveness, respectively. Here, we show that mastermind dependence of the Notch response at these loci is differentially encoded in Jurkat T-ALL cells. Knockout of Mastermind-like1 (MAML1) eliminates Notch responsive activation of both these genes, and reduced target gene expression is accompanied by a decrease in H3K27 acetylation, consistent with the importance of MAML1 for p300 activity. Add-back of defined MAML1 constructs in knockout cells identifies residues 151-350 of MAML1 as essential for expression of either Notch-responsive gene. Fusion of the Notch-binding region of MAML1 to the HAT domain of p300 rescues expression of HES4 but not DTX1, suggesting that an additional activity of MAML1 is needed for gene induction at a distance. Together, these studies establish the functional importance of the MAML1151-350 region for Notch-dependent transcriptional induction, and reveal differential requirements for MAML1-dependent recruitment activities at different Notch responsive loci, highlighting the molecular complexity of NTC-stimulated transcription.

molecular biology↗

bioRxiv2019

A Germinal Center-Associated Microenvironmental Signature Reflects Malignant Phenotype and Outcome of Diffuse Large B-cell Lymphoma

Diffuse large B-cell lymphoma (DLBCL) is the most common B-cell malignancy with varying prognosis after the gold standard rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP). Several prognostic models have been established by focusing primarily on characteristics of lymphoma cells themselves including cell-of-origin, genomic alterations, and gene/protein expressions. However, the prognostic impact of lymphoma microenvironment and its association with characteristics of lymphoma cells are not fully understood. Using highly-sensitive transcriptome profiling of untreated DLBCL tissues, we here assess the clinical impact of lymphoma microenvironment on the clinical outcomes and pathophysiological, molecular signatures in DLBCL. The presence of normal germinal center (GC)-microenvironmental cells, including follicular T cells, macrophage/dendritic cells, and stromal cells, in lymphoma tissue indicates a positive therapeutic response. Our prognostic model, based on quantitation of transcripts from distinct GC-microenvironmental cell markers, clearly identified patients with graded prognosis independently of existing prognostic models. We observed increased incidences of genomic alterations and aberrant gene expression associated with poor prognosis in DLBCL tissues lacking GC-microenvironmental cells relative to those containing these cells. These data suggest that the loss of GC-associated microenvironmental signature dictates clinical outcomes of DLBCL patients reflecting the accumulation of \"unfavorable\" molecular signatures.

cancer biology↗

bioRxiv2019

Molecular basis for feedback inhibition of Notch signaling by the Notch regulated ankyrin repeat protein NRARP

The Notch regulated ankyrin repeat protein (NRARP) is a negative feedback regulator of Notch signaling in higher organisms. The molecular basis for NRARP function, however, has remained elusive. Mass spectrometry-based proteomic studies show that human NRARP associates with the core Notch transcriptional activation complex (NTC), containing the RBPJ transcription factor, the Notch intracellular domain (NICD), and a Mastermind-like co-activator. Binding of NRARP is direct, requires both RBPJ and NICD, and is independent of Mastermind-like proteins or DNA. The X-ray structure of an NRARP/RBPJ/NOTCH1/DNA complex, determined to 3.75 [A] resolution, reveals a non-canonical mode of binding in which NRARP extends the NOTCH1 ankyrin-repeat stack by three additional repeats. Mutations of NRARP residues at the binding interface disrupt entry into complexes and suppress feedback inhibition in signaling assays. These studies establish the structural basis for NTC engagement by NRARP and provide insight into its mechanism of feedback inhibition of Notch signaling.

biochemistry↗