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Snyder, E.

Publications and source records attributed to Snyder, E..

7 recordsLinked to original sources

Differential control of growth and identity by HNF4α isoforms in pancreatic ductal adenocarcinoma

BackgroundAlthough transcriptomic studies have stratified pancreatic ductal adenocarcinoma (PDAC) into clinically relevant subtypes, classical or basal-like, further research is needed to identify the transcriptional regulators of each subtype. Previous studies identified HNF4 as a key regulator of the classical subtype, but the distinct contributions of its isoforms (P1 and P2), which display dichotomous functions in normal development and gastrointestinal malignancies, remain unexplored. ObjectiveThe objective of this study is to investigate the role of HNF4 P1 and P2 isoforms in regulating growth and differentiation. DesignWe performed functional, transcriptomic, and epigenetic analysis after exogenous expression in HNF4-negative models or CRISPRi-mediated knockdown of endogenous isoforms. ResultsWe characterized the variable expression of P1 isoforms in HNF4-positive tumors. We demonstrate that P1 isoforms are less compatible with growth than P2 isoforms. Despite sharing a common DNA binding domain, we show that P1 isoforms are stronger transcriptional regulators. ConclusionsOur study characterizes the functional roles of HNF4 P1 and P2 isoforms in PDAC and highlights the necessity of considering different isoforms when studying molecular regulators.

cancer biology↗

Patho-transcriptomic analysis of invasive mucinous adenocarcinoma of the lung (IMA): comparison with lung adenocarcinoma with signet ring cell features (SRCC)

BackgroundInvasive mucinous adenocarcinoma (IMA) comprises [~]5% of lung adenocarcinoma. There is no effective therapy for IMA when surgical resection is not possible. IMA is sometimes confused with adenocarcinoma with signet ring cell features (SRCC) pathologically since both adenocarcinomas feature tumor cells with abundant intracellular mucin. The molecular mechanisms by which such mucin-producing lung adenocarcinomas develop remain unknown. MethodsUsing a Visium spatial transcriptomics approach, we analyzed IMA and compared it with SRCC patho-transcriptomically. Combining spatial transcriptomics data with in vitro studies using RNA-seq and ChIP-seq, we assessed downstream targets of transcription factors HNF4A and SPDEF that are highly expressed in IMA and/or SRCC. ResultsSpatial transcriptomics analysis indicated that there are 6 distinct cell clusters in IMA and SRCC. Notably, two clusters (C1 and C3) of mucinous tumor cells exist in both adenocarcinomas albeit at a different ratio. Importantly, a portion of genes (e.g., NKX2-1, GKN1, HNF4A and FOXA3) are distinctly expressed while some mucous-related genes (e.g., SPDEF and FOXA2) are expressed in both adenocarcinomas. We determined that HNF4A induces MUC3A/B and TM4SF4 and that BI 6015, an HNF4A antagonist, suppressed the growth of IMA cells. Using mutant SPDEF that is associated with COVID-19, we also determined that an intact DNA-binding domain of SPDEF is required for SPDEF-mediated induction of mucin genes (MUC5AC, MUC5B and AGR2). Additionally, we found that XMU-MP-1, a SPDEF inhibitor, suppressed the growth of IMA cells. ConclusionThese results revealed that IMA and SRCC contain heterogenous tumor cell types, some of which are targetable.

cancer biology↗

FoxA1/2-dependent epigenomic reprogramming drives lineage switching in lung adenocarcinoma

The ability of cancer cells to alter their identity is essential for tumor survival and progression. Loss of the pulmonary lineage specifier NKX2-1 within KRAS-driven lung adenocarcinoma (LUAD) enhances tumor progression and results in a pulmonary-to-gastric lineage switch that is dependent upon the activity of pioneer factors FoxA1 and FoxA2; however, the underlying mechanism remains largely unknown. Here, we show that FoxA1/2 reprogram the epigenetic landscape of NKX2-1-negative LUAD to facilitate a gastric identity. After Nkx2-1 deletion, FoxA1/2 mediate demethylation of gastric-defining genes through recruitment of TET3, an enzyme that induces DNA demethylation. H3K27ac ChIP-seq and HiChIP show that FoxA1/2 also control the activity of regulatory elements and their 3D interactions at gastric loci. Furthermore, oncogenic KRAS is required for the FoxA1/2-dependent epigenetic reprogramming. This work demonstrates the role of FoxA1/2 in rewiring the methylation and histone landscape and cis-regulatory dynamics of NKX2-1-negative LUAD to drive cancer cell lineage switching.

cancer biology↗

A newly-recognized population of residual neural crest cells in the adult leptomeninges is re-activated for vascular repair

The neural crest (NC) is a transient structure in vertebrate embryogenesis comprising highly migratory multipotent stem cells that give rise to a diverse array of cell types in organs throughout the body, including initiating neurovascular patterning. It is assumed that neural crest stem cells (NCSCs) disappear after development. Unexpectedly, using single-nucleus RNA-sequencing, we discovered residual quiescent NCSCs in the adult mouse meninges which are activated by injury and contribute to the brains homeostatic response. RNA velocity, pathway, and transcription factor analyses in a murine stroke model (combined with in vivo imaging) show that these adult NCSCs migrate towards the perivascular spaces of the infarct and undergo a perivascular stromal cell transition that is regulated by Ptp1b, Ghr, and Stat3. Loss- and gain-of-function experiments show that these "vestigial" NCSCs are required for restoring vascular endothelial barrier function via {beta}-catenin and Stat3 signaling. These findings suggest that, in the adult, an unexpected reservoir of cells -- once pivotal to embryogenesis and vascular morphogenesis -- are re-invoked for neurovascular repair.

neuroscience↗

Two RNA binding proteins, ADAD2 and RNF17, interact to form novel meiotic germ cell granules required for male fertility

Mammalian male germ cell differentiation relies on complex RNA biogenesis events, many of which occur in RNA binding protein (RBP) rich non-membrane bound organelles termed RNA germ cell granules. Though known to be required for male germ cell differentiation, little is understood of the relationships between and functions of the numerous granule subtypes. ADAD2, a testis specific RBP, is required for normal male fertility and forms a poorly characterized granule in meiotic male germ cells. This work aimed to define the role of ADAD2 granules in male germ cell differentiation and their relationship to other granules. Biochemical analyses identified RNF17, a testis specific RBP that forms meiotic male germ cell granules, as an ADAD2-interacting protein. Phenotypic analysis of Adad2 and Rnf17 mutant mice defined a shared and rare post-meiotic chromatin defect, suggesting shared biological roles. We further demonstrated ADAD2 and RNF17 are dependent on one another for granularization and together form a previously unstudied set of germ cell granules. Based on co-localization studies with well-characterized granule RBPs including DDX4 and PIWIL1, a subset of the ADAD2-RNF17 granules are likely components of the piRNA pathway. In contrast, a second, morphologically distinct population of ADAD2-RNF17 co-localize with the translation regulator NANOS1 and form a unique cup-shaped structure with distinct protein subdomains. This cup shape appears to be driven, in part, by association with the endoplasmic reticulum. Lastly, a double Adad2-Rnf17 mutant model demonstrated loss of ADAD2-RNF17 granules themselves, as opposed to loss of either ADAD2 or RNF17, is the likely driver of the Adad2 and Rnf17 mutant phenotypes. Together, this work identified a set of novel germ cell granules required for male fertility and sheds light on the relationship between germ cell granule pools. The example described here defines a new genetic approach to germ cell granule study. AUTHOR SUMMARYTo differentiate successfully, male germ cells tightly regulate their RNA pools. As such, they rely on RNA binding proteins, which often localize to cytoplasmic granules. The majority of studies have focused on a single granule type which regulates small-RNA biogenesis. Although additional granules have been identified, there is limited knowledge about their relationship to each other and exact functions. Here, we identify an interaction between two RNA binding proteins, ADAD2 and RNF17, and demonstrate mutants share a rare germ cell phenotype. Further, ADAD2 and RNF17 colocalize to the same germ cell granule, which displays two morphologically unique types. The first subset of ADAD2-RNF17 granules have similar morphologies to other characterized granules and likely play a role in the small-RNA pathway. The second granule type forms a unique shape with distinct protein subdomains. This second population appears to be closely associated with the endoplasmic reticulum. Genetic models further demonstrate the granules themselves, as opposed to the resident proteins, likely drive the mutant phenotypes. These findings not only identify a novel population of germ cell granules but reveal a new genetic approach to defining their formation and function during germ cell differentiation.

genetics↗

Transcriptional circuitry of NKX2-1 and SOX1 defines an unrecognized lineage subtype of small cell lung cancer

RationaleThe current molecular classification of small cell lung cancer (SCLC) based on expression of four lineage transcription factors still leaves its major subtype SCLC-A as a heterogeneous group, necessitating more precise characterization of lineage subclasses. ObjectivesTo refine the current SCLC classification with epigenomic profiles and to identify features of the re-defined SCLC subtypes. MethodsWe performed unsupervised clustering of epigenomic profiles on 25 SCLC cell lines. Functional significance was evaluated by cell growth, apoptosis and xenograft using CRISPR-Cas9-mediated deletion. The specific cistromic profiles by ChIP-seq and its functional transcriptional partners using co-immunoprecipitation followed by mass spectrometry were determined. Rb1fl/flTrp53fl/fl and Rb1fl/flNkx2-1fl/fl mouse models were engineered to explore the function of Nkx2-1 in tumor initiation and differentiation. H3K27ac profiles were analyzed to reveal 6 human SCLC specimen and 20 mice tumors epigenomic landscapes. Measurements and Main ResultsWe identified an epigenomic subclusters of the major SCLC-A subtype, named SCLC-A and SCLC-A{sigma}. SCLC-A was characterized by the presence of a super-enhancer at the NKX2-1 locus, which was observed in human SCLC specimens and a murine SCLC model. We found NKX2-1, a dual lung and neural lineage factor, is uniquely relevant in SCLC-A. We further found maintenance of this neural identity in SCLC-A is mediated by collaborative transcriptional activity with another neuronal transcriptional factor SOX1. ConclusionsWe comprehensively describe an additional epigenomic heterogeneity of the major SCLC-A subtype, and define SCLC-A subtype by the core regulatory circuitry representing NKX2-1 and SOX1 super-enhancers and their functional collaborations to maintain neuronal linage state.

molecular biology↗

Reciprocal regulation of pancreatic ductal adenocarcinoma growth and molecular subtype by HNF4α and SIX1/4

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy with a five-year survival of less than 5%. Transcriptomic analysis has identified two clinically relevant molecular subtypes of PDAC: Classical and Basal-like. The Classical subtype is characterized by a more favorable prognosis and better response to chemotherapy than the Basal-like subtype. The Classical subtype also expresses higher levels of lineage specifiers that regulate endodermal differentiation, including the nuclear receptor HNF4. Using in vitro and in vivo PDAC models, we show that HNF4 restrains tumor growth and drives tumor cells toward an epithelial identity. Gene expression analysis from murine models and human tumors shows that HNF4 activates expression of genes associated with the Classical subtype. Although HNF4 loss is not sufficient for complete conversion to the Basal-like subtype gene expression profile, HNF4 directly represses SIX4 and SIX1, mesodermal lineage specifiers expressed in the Basal-like subtype. Finally, HNF4-negative PDAC cells rely on expression of SIX4 and SIX1 for proliferation in vitro and in vivo. Overall, our data show that HNF4 regulates the growth and molecular subtype of PDAC by multiple mechanisms, including activation of the Classical gene expression program and repression of SIX4 and SIX1, which may represent novel dependencies of the Basal-like subtype.

cancer biology↗