Biology subjects

Yamashita, H.

Publications and source records attributed to Yamashita, H..

18 recordsLinked to original sources

bioRxiv2026

Genomic insights into polyketide toxin synthesis and algal symbiosis using high-quality genome sequences of the early divergent hexacorallian genus Palythoa (Cnidaria, Zoantharia)

Palytoxin, first isolated from Palythoa toxica, is among the most potent marine toxins known. Despite decades of biochemical investigation, genetic bases underlying its potential biosynthesis in Palythoa remain unresolved. Here we present four high-quality genome assemblies of Palythoa species, including Palythoa cf. toxica, and integrate these with a chromosome-scale genome assembly of P. caribaeorum. Performing comparative genomic analyses, we screened for candidate genes potentially involved in palytoxin biosynthesis and examined patterns of genome evolution. Unexpectedly, we identified only two classes of ketosynthase (KS) domain-containing genes in Palythoa: fatty acid synthases (FAS) and bacterial-like polyketide synthases (PKSs). Contrasting other anthozoans, animal FAS-like PKS (AFPK) genes common to all Palythoa species were not detected. We found no evidence for lineage-specific expansion of PKS genes unique to Palythoa, suggesting that if palytoxin/palytoxin-like molecule biosynthesis is host-encoded, it may involve functional modification or co-opting pre-existing FAS and/or bacterial-like PKS pathways. Comparative analyses revealed expansions of gene families associated with transport and binding functions in Palythoa, potentially reflecting molecular adaptations linked to their sand-incorporating body structure. We identified TPT1 and CLEC4A as rapidly evolving genes in multiple Palythoa species, consistent with possible roles in growth regulation and host-microbe interactions. Additionally, comparison between azooxanthellate and zooxanthellate species revealed mutations within conserved protein domains of LePin, which has been implicated in cnidarian endosymbiosis, suggesting lineage-specific modifications associated with symbiotic state. This study establishes a foundation for zoantharian genomic research, provides insights into lineage-specific genomic signatures, and advances molecular and evolutionary biological knowledge of this ecologically important group.

genomics↗

bioRxiv2026

Possible Novel Sulfolipid Utilization Pathway in Giant Clams and Other Aquatic Invertebrates: Implications for Photosymbiosis and Sulfur Cycling

Photosymbiosis with dinoflagellates of the family Symbiodiniaceae enables giant clams to thrive in oligotrophic coral reef environments. However, mechanisms by which clams utilize algal-derived biomolecules remain largely unexplored. Using newly available genome resources for photosymbiotic bivalves (Tridacna and Fragum), we conducted a comparative genomic analysis to identify positively selected genes from these photosymbiotic bivalve lineages, that are potentially involved in symbiotic adaptations. Among candidate genes, we focused on sulfoquinovosidase (SQase), an enzyme that hydrolyzes sulfoquinovose (SQ) from sulfoquinovosyl diacylglycerol (SQDG), a sulfur-containing sulfolipid abundant in photosynthetic membranes. Although SQDG degradation has been characterized in bacteria, the distribution and role of SQase in animals have not been systematically examined. We found that possibly functional SQase homologs are widely distributed among aquatic invertebrates, but are largely absent in terrestrial taxa. In silico predictions showed that most animal SQases possess signal peptides and enter the secretory pathway, with lineage-specific gains and losses of membrane association, suggesting functional diversification. Transcriptomic analyses further demonstrated that SQase is predominantly expressed in digestive organs in diverse taxa, whereas in giant clams, it is also highly expressed in the outer mantle, the tissue primarily involved in harboring symbionts enriched in SQDG. Together, these results suggest that in aquatic invertebrates, SQase functions as a digestive enzyme for algal-derived sulfolipids and that photosymbiotic bivalves have expanded its deployment to tissues specialized for symbiosis. Our findings uncover a previously unrecognized metabolic interface between photosymbiosis and sulfur utilization in aquatic invertebrates, with broader implications for host-symbiont interactions and marine sulfur cycling.

zoology↗

bioRxiv2025

Genomic insights into photosymbiosis in giant clams: Comparisons with coral strategies

Giant clams are representative bivalves in coral reef ecosystems that host photosynthetic dinoflagellates extracellularly and rely on their photosynthates, functioning as "solar-powered animals." Unlike corals, which harbor intracellular dinoflagellates, molecular mechanisms and evolutionary history underlying this symbiosis remain largely unknown. Here, we integrated chromosome-scale genome assembly, transcriptome profiling, and bleaching experiments involving Tridacna crocea to explore the genetic basis of extracellular symbiosis. Signals associated with sterol transport by Niemann-Pick disease type C2 (NPC2) transporters and carbon-concentrating mechanisms suggest that giant clams share some nutrient exchange strategies with corals. Strikingly, the nitrate transporter NRT2, a "plant-like" gene previously thought to be absent in animals, represents an unexpected evolutionary retention that enables nitrate-based nutrient supply, highlighting a fundamental divergence from coral symbiosis. Together, our findings reveal both conserved and distinct molecular strategies of photosymbiosis in reef-dwelling marine invertebrates and provide insights into evolution and ecological resilience of coral reef ecosystems.

zoology↗

bioRxiv2025

The increase in cell volume and nuclear number of the koji-fungus Aspergillus oryzae contributes to its high enzyme productivity

While the ratio of nuclei to cell volume is well regulated, it remains largely unexplored in multinucleate organisms. The koji-fungus Aspergillus oryzae, traditionally used in Japanese brewing and fermentation for over a thousand years, is now widely utilized in modern biotechnology as a host for enzyme production. We discovered that, over time in culture, hyphae become thicker, resulting in a tenfold increase in cell volume, and the number of nuclei in hyphal cells also increases tenfold, exceeding 200. The increase in cell volume and nuclear number is unique among the investigated Aspergillus species and correlates with its high enzyme production capabilities. Since nuclear number and cell volume are correlated, both must increase simultaneously for either to expand. Our analyses identified genetic factors and nutritional environmental signals involved in each of these increases. Increases in nuclear number and cell volume were also observed in other fungi bred for industrial use. This study not only deepens our understanding of the evolutionary processes that promote high enzyme productivity through fungal breeding, but also provides insights into the molecular mechanisms regulating cell volume and nuclear number in multinucleate organisms.

microbiology↗

bioRxiv2024

Recent codon preference reversals in the Drosophila melanogaster lineage

We employ fine-scale population genetic analyses to reveal dynamics among interacting forces that act at synonymous sites and introns among closely related Drosophila species. Synonymous codon usage bias has proven to be well-suited for population genetic inference. Under major codon preference, translationally superior "major" codons confer fitness benefits relative to their less efficiently and/or accurately decoded synonymous counterparts. Our codon family and lineage-specific analyses expand on previous findings in the Drosophila simulans lineage; patterns in naturally occurring polymorphism demonstrate fixation biases toward GC-ending codons that are consistent in direction, but heterogeneous in magnitude, among synonymous families. These forces are generally stronger than fixation biases in intron sequences. In contrast, population genetic analyses reveal unexpected evidence of codon preference reversals in the Drosophila melanogaster lineage. Codon family-specific polymorphism patterns support reduced efficacy of natural selection in most synonymous families but indicate reversals of favored states in the four codon families encoded by NAY. Accelerated synonymous fixations in favor of NAT and greater differences for both allele frequencies and fixation rates among X-linked, relative to autosomal, loci bolster support for fitness effect reversals. The specificity of preference reversals to codons whose cognate tRNAs undergo wobble position queuosine modification is intriguing. However, our analyses reveal prevalent dinucleotide preferences for ApT over ApC that act in opposition to GC favoring forces in both coding and intron regions. We present evidence that changes in the relative efficacy of translational selection and dinucleotide preference underlie apparent codon preference reversals.

evolutionary biology↗

bioRxiv2023

AtMYB50 regulates root cell elongation by upregulating PECTIN METHYLESTERASE INHIBITOR 8 in Arabidopsis thaliana

Plant root development is regulated by several signal transduction pathways. Among them, plant phytohormones, like auxin and cytokinin, are well characterized for their molecular mechanisms of action. Reactive oxygen species (ROS) play important roles as signaling molecules in controlling root development. Under these signal transduction pathways, the gene regulatory network, which is controlled by transcription factors, is the key to regulating root growth. We have previously reported an important transcription factor, UP BEAT1 (UPB1), that regulates ROS homeostasis at the root tip, further controlling the transition from cell proliferation to differentiation. Although UPB1 directly regulates the expression of several peroxidases that control ROS homeostasis, UPB1 still targets genes other than peroxidases. This indicates that UPB1 may regulate root growth through different ROS signals. Here, we investigated the function of the transcription factor MYB50, a direct target of UPB1, in Arabidopsis thaliana. We then examined whether UPB1 regulates MYB50 expression in the roots using an induction expression system and imaging of multiple fluorescent proteins. We also performed RNA-Seq analysis using MYB50 estradiol induction lines and ChIP-seq analysis to identify the MYB50 regulatory gene network. Integrating these analyses with UPB1 regulatory network revealed that MYB50 regulates the expression of PECTIN METHYLESTERASE INHIBITOR 8 (PMEI8). These data suggest that MYB50 is a new root growth regulator under the UPB1 gene regulatory network, which differs from the control of ROS homeostasis. Our study presents a model including a new transcriptional network under MYB50 into UPB1 regulatory root growth system and will provide novel insights into the cell elongation controlled by pectin modification.

plant biology↗

bioRxiv2023

Deciphering transcriptomic signatures explaining the phenotypic plasticity of non-heading lettuce genotypes under artificial light conditions

Elucidating the mechanisms and pathways involved in genotype-environment (GxE) interactions and phenotypic plasticity is critical for improving plant growth. Controlled environment agricultural systems allow growers to modulate the environment for particular genotypes. In this study, we evaluated the effects of interactions among 14 genotypes and four artificial light environments on leaf lettuce phenotypes and dissected the underlying molecular mechanism via transcriptome-based modeling. Variations in morphological traits and phytochemical contents in response to artificial light treatments revealed significant GxE interactions. The appropriate genotype and artificial light combinations for maximizing phenotypic expression were determined on the basis of a joint regression analysis and the additive main effect and multiplicative interaction model for these GxE interactions. Transcriptome-based regression modeling explained approximately 50%-90% of the GxE variations. Further analyzes indicated Red Lettuce Leaves 4 (RLL4) regulates UV-B and blue light signaling through the effects of the HY5-MBW pathway on flavonoid biosynthesis and contributes to natural variations in the light-responsive plasticity of lettuce traits. Our study represents an important step toward elucidating the phenotypic variations due to GxE interactions in non-heading lettuce under artificial light conditions. HighlightsO_LISeveral morphological characteristics of lettuce genotypes were altered by different light wavelengths. C_LIO_LIA defective RLL4 allele (rll4) induces the expression of downstream genes related to UV-B and blue light signaling through activation of the HY5-MBW pathway, which enhances phytochemical accumulation in lettuce. C_LIO_LIGxE analyzes identified the ideal genotype and artificial light combinations for individual phenotypes. C_LIO_LITranscriptome-based modeling explained approximately 50%-90% of the GxE variations. C_LI

plant biology↗

bioRxiv2023

Smart utilization of betaine lipids in giant clam Tridacna crocea

The giant clam Tridacna crocea inhabits shallow tropical seas with poorly nourished water and severe sun irradiation. They harbor symbiotic algae "zooxanthellae" (dinoflagellate family Symbiodiniaceae) in the mantle tissue and are thought to thrive in this extreme environment by utilizing photosynthetic products from the algae. However, there is no measure of the detailed metabolic flow between the host and symbiont to evaluate one of the most successful symbiotic relationships in nature. Here, we employed liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based lipidomics and Fourier-transform ion cyclotron resonance MS imaging on T. crocea tissues, revealing a unique lipid composition and localization with their symbiont algae. We discovered that the non-phosphorous microalgal betaine lipid diacylglycerylcarboxy-hydroxymethylcholine (DGCC) was present in all tissues and organs of T. crocea to approximately the same degree as phosphatidylcholine (PC). The fatty acid composition of DGCC was similar to that of PC, which is thought to have physiological roles similar to that of DGCC. MS imaging showed co-localization of these lipids throughout the clam tissues. Glycerylcarboxy-hydroxymethylcholine (GCC), the deacylated derivative of DGCC, was found to be a free form of DGCC in the clams and was isolated and characterized from cultured Symbiodiniaceae strains that were isolated from giant clams. These results strongly suggest that giant clams have evolved to smartly utilize DGCCs, phosphorus-free polar lipids of symbiont algae, as essential membrane components to enable them to thrive in oligotrophic coral reef milieu.

zoology↗

bioRxiv2022

Manipulating the 3D organization of the largest synthetic yeast chromosome

Whether synthetic genomes can power life has attracted broad interest in the synthetic biology field, especially when the synthetic genomes are extensively modified with thousands of designer features. Here we report de novo synthesis of the largest eukaryotic chromosome thus far, synIV, a 1,454,621-bp Saccharomyces cerevisiae chromosome resulting from extensive genome streamlining and modification. During the construction of synIV, we developed megachunk assembly combined with a hierarchical integration strategy, which significantly increased the accuracy and flexibility of synthetic chromosome construction and facilitated chromosome debugging. In addition to the drastic sequence changes made to synIV by rewriting it, we further manipulated the three-dimensional structure of synIV in the yeast nucleus to explore spatial gene regulation within the nuclear space. Surprisingly, we found few gene expression changes, suggesting that positioning inside the yeast nucleoplasm plays a minor role in gene regulation. Lastly, we tethered synIV to the inner nuclear membrane via its hundreds of loxPsym sites and observed transcriptional repression of the entire chromosome, demonstrating chromosome-wide transcription manipulation without changing the DNA sequences. Our manipulation of the spatial structure of the largest synthetic yeast chromosome shed light on higher-order architectural design of the synthetic genomes. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC="FIGDIR/small/487066v2_ufig1.gif" ALT="Figure 1"> View larger version (64K): org.highwire.dtl.DTLVardef@18bf586org.highwire.dtl.DTLVardef@1a471d5org.highwire.dtl.DTLVardef@12d7690org.highwire.dtl.DTLVardef@1c32510_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIDe novo synthesis of the largest eukaryotic chromosome, synIV C_LIO_LISynIV shows similar 3D structure to wild-type IV, despite thousands of changes made to it C_LIO_LI"Inside-out" repositioning of synIV in nucleus shows minor transcriptional changes C_LIO_LIMultipoint tethering synIV to inner nuclear membrane represses transcription of whole chromosome C_LI

synthetic biology↗

bioRxiv2022

Dimerization processes for light-regulated transcription factor Photozipper visualized by high-speed atomic force microscopy

Dimerization is critical for transcription factors (TFs) to bind DNA and regulate a wide variety of cellular functions; however, the single-molecular mechanisms remain to be completely elucidated. Here, we used high-speed atomic force microscopy (HS-AFM) to observe the dimerization process for a photoresponsive TF Photozipper (PZ), which consists of light-oxygen-voltage-sensing (LOV) and basic-region-leucine-zipper (bZIP) domain. HS-AFM visualized not only the oligomeric states of PZ molecules forming monomers and dimers under controlled dark-light conditions but also the domain structures within each molecule. Successive AFM movies captured the dimerization process for an individual PZ molecule and the monomer-dimer reversible transition during dark-light cycling. The high-resolution AFM images of the domain structures in PZ molecules demonstrated that the bZIP domain entangled under dark conditions was loosened owing to light illumination and fluctuated around the LOV domain. These observations revealed the role of the bZIP domain in the dimerization processes of a TF.

biophysics↗

bioRxiv2021

Intratumoral Heterogeneity Promotes Collective Cancer Invasion Through NOTCH1 Variation

Cellular and molecular heterogeneity within tumors has long been associated with the progression of cancer to an aggressive phenotype and a poor prognosis. However, how such intratumoral heterogeneity contributes to the invasiveness of cancer is largely unknown. Here, using a multidisciplinary approach, we investigate the interaction between molecular subtypes within bladder microtumors and the corresponding effects on their invasiveness. Our results reveal heterogeneous microtumors formed by multiple molecular subtypes possess enhanced invasiveness compared to individual cells, even when both cells are not invasive individually. To examine the molecular mechanism of intratumoral heterogeneity mediated invasiveness, live single cell biosensing, RNA interference, and CRISPR-Cas9 gene editing approaches were applied to investigate and control the composition of the microtumors. An agent-based computational model was also developed to evaluate the influence of NOTCH1 variation on DLL4 expression within a microtumor. The data indicate that variation in NOTCH1 expression can lead to upregulation of DLL4 expression within the microtumor and enhancement of microtumor invasiveness. Overall, our results reveal a novel mechanism of heterogeneity mediated invasiveness through intratumoral variation of gene expression. Summary statementThis study reveals a mechanism that Notch1 variation, instead of the average value, promotes the invasiveness of microtumor, providing a link between intratumoral heterogeneity and collective cancer invasion.

cancer biology↗

bioRxiv2020

Loss of the Pioneer Factor FOXA1 Results in Genome-wide Epigenetic Reprogramming and activation of Interferon-Response Genes including CD274/PD-L1

Forkhead Box A1 (FOXA1) is a pioneer transcription factor critical in epigenetic regulation of chromatin and cell fate determination. Reduced FOXA1 expression is an independent predictor of poor overall survival in bladder cancer patients. However, the impact of FOXA1 loss on chromatin epigenetics in bladder cancer is unknown. Therefore, we determined the impact of FOXA1 knock out (KO) on epigenetic modification of chromatin and associated gene expression. We identified 8,230 differentially expressed genes following FOXA1 KO. Surprisingly, Gene Set Enrichment Analysis (GSEA) identified IFN[a]/{gamma} gene expression signatures as enriched following FOXA1 KO. FOXA1 KO induced both increased and decreased numbers of histone 3 lysine 27 acetylation (H3K27ac) sites throughout the genome. As expected, the majority of differences in H3K27ac across genomic areas in FOXA1 KO cells is mapped to intergenic and intronic regions where enhancers reside. In addition, a subset of differential H3K27ac levels were also mapped to proximal promoters and within gene bodies. Integrated analysis of RNA/ChIP-seq data shows changes in gene expression that are mirrored by differences in H3K27ac. Motif analysis of DNA sequence enriched for H3K27ac identified significant increases in transcription factor binding motifs including the interferon sensitive response element (ISRE) and interferon response factors such as IRF1. Moreover, we identified increased H3K27ac of regulatory elements as being associated with several upregulated interferon sensitive genes (ISGs) in FOXA1 KO cells, including CD274/PD-L1. Western blotting and Q-RT-PCR confirmed upregulation of CD274/PD-L1 following FOXA1 KO. Analysis of TCGA data confirmed an inverse relationship between FOXA1 and CD274 in bladder cancer, as well as in other cancers. In summary, we provide evidence of widespread epigenetic reprogramming after FOXA1 KO in bladder cancer cells. Additionally, we provide evidence that FOXA1 KO-induced epigenetic changes contribute to activation of a global interferon-dominant expression signature, including the immune checkpoint target CD274/PD-L1 in a cancer cell-intrinsic manner.

cancer biology↗

bioRxiv2020

In situ measurement of intracellular thermal conductivity using heater-thermometer hybrid diamond nanosensor

Understanding heat dissipation processes at nanoscale during cellular thermogenesis is essential to clarify the relationships between the heat and biological processes in cells and organisms. A key parameter determining the heat flux inside a cell is the local thermal conductivity, a factor poorly investigated both experimentally and theoretically. Here, using a nanoheater/nanothermometer hybrid based on a polydopamine shell encapsulating a fluorescent diamond nanocrystal, we measured the intracellular thermal conductivity of HeLa cell with a spatial resolution of about 200 nm. Its mean value of 0.11 Wm-1K-1 determined for the first time is significantly smaller than that of water. Bayesian analysis of the data strongly supports the existence of variation of the intracellular thermal conductivity of about 40%. These results present a major milestone towards understanding the intracellular heat transfer phenomena at nanoscale.

cell biology↗

bioRxiv2020

Subtype-specific epigenomic landscape and 3D genome structure in bladder cancer

Muscle-invasive bladder cancers have recently been characterized by their distinct expression of luminal and basal genes, which could be used to predict key clinical features such as disease progression and overall survival. For example, FOXA1, GATA3, and PPARG have been shown to be essential for luminal subtype-specific regulation and subtype switching, while TP63 and STAT3 are critical for basal subtype bladder cancer. Despite these advances, the underlying epigenetic mechanism and 3D chromatin architecture for subtype-specific regulation in bladder cancers remains largely unknown. Here, we determined the genome-wide transcriptome, enhancer landscape, TF binding profiles (FOXA1 and GATA3) in luminal and basal subtypes of bladder cancers. Furthermore, we mapped genome-wide chromatin interactions by Hi-C in both bladder cancer cell lines and primary patient tumors, for the first time in bladder cancer. We showed that subtype-specific transcription is accompanied by specific open chromatin and epigenomic marks, at least partially driven by distinct TF binding at distal-enhancers of luminal and basal bladder cancers. Finally, we identified a novel clinically relevant transcriptional factor, Neuronal PAS Domain Protein 2 (NPAS2), in luminal bladder cancers that regulates other luminal-specific genes (such as FOXA1, GATA3, and PPARG) and affects cancer cell proliferation and migration. In summary, our work shows a subtype-specific epigenomic and 3D genome structure in urinary bladder cancers and suggested a novel link between the circadian TF NPAS2 and a clinical bladder cancer subtype.

genomics↗

bioRxiv2019

Affinity of rhodopsin to raft enables the aligned oligomer formation from dimers: Coarse-grained molecular dynamics simulation of disk membranes

The visual photopigment protein rhodopsin (Rh) is a typical G protein-coupled receptor (GPCR) that initiates the phototransduction cascade in retinal disk membrane of rod-photoreceptor cells. Rh molecule has a tendency to form dimer, and the dimer tends to form rows, which is suggested to heighten phototransduction efficiency in single-photon regime. In addition, the dimerization confers Rh an affinity for lipid raft, i.e. raftophilicity. However, the mechanism by which Rh-dimer raftophilicity contributes to the organization of the higher order structure remains unknown. In this study, we performed coarse-grained molecular dynamics simulations of a disk membrane model containing unsaturated lipids, saturated lipids with cholesterol, and Rh-dimers. We described the Rh-dimers by two-dimensional particle populations where the palmitoyl moieties of each Rh exhibits raftophilicity. We simulated the structuring of Rh in a disk for two types of Rh-dimer, i.e., the most and second most stable Rh dimers, which exposes the raftophilic regions at the dimerization-interface (H1/H8 dimer) and two edges away from the interface (H4/H5 dimer), respectively. Our simulations revealed that only the H1/H8 dimer could form a row structure. A small number of raftophilic lipids recruited to and intercalated in a narrow space between H1/H8 dimers stabilize the side-by-side interaction between dimers in a row. Our results implicate that the nano-sized lipid raft domains act as a "glue" to organize the long row structures of Rh-dimers.

biophysics↗

bioRxiv2019

The local state of chromatin compaction at transcription start sites controls transcription levels

A defined amount of transcript is produced from transcription start sites (TSSs) of each gene, suggesting that the binding frequency of RNA polymerase varies among genes. However, what structure in chromatin controls this frequency remains elusive. We established a method to fractionate chromatin according to its degree of three-dimensional compaction. Nucleosomes were evenly detected through all of the fractions, but histone H1 was more highly enriched in the more compact chromatin fractions. Similarly, HP1 and MBD2b were more abundant in more compact chromatin, while the levels of tri-methylated H3 (Lys9) and 5-methyl cytosine subtly increased. Via genome-wide analyses, nearly the entire genome was found to exist in compact chromatin without variations between repeat and non-repeat sequences; however, active TSSs were rarely found in compact chromatin. Based on a correlation between weak compaction and RNA polymerase binding at TSSs, it appears that local states of chromatin compaction determine transcription levels.

molecular biology↗

bioRxiv2019

Gene Cascade Finder: A tool for identification of gene cascades and its application in Caenorhabditis elegans

Obtaining a comprehensive understanding of the gene regulatory networks, or gene cascades, involved in cell fate determination and cell lineage segregation in Caenorhabditis elegans is a long-standing challenge. Although RNA-sequencing (RNA-Seq) is a promising technique to resolve these questions, the bioinformatics tools to identify associated gene cascades from RNA-Seq data remain inadequate. To overcome these limitations, we developed Gene Cascade Finder (GCF) as a novel tool for building gene cascades by comparison of mutant and wild-type RNA-Seq data along with integrated information of protein-protein interactions, expression timing, and domains. Application of GCF to RNA-Seq data confirmed that SPN-4 and MEX-3 regulate the canonical Wnt pathway during embryonic development. Moreover, lin-35, hsp-3, and gpa-12 were found to be involved in MEX-1-dependent neurogenesis, and MEX-3 was found to control the gene cascade promoting neurogenesis through lin-35 and apl-1. Thus, GCF could be a useful tool for building gene cascades from RNA-Seq data.

genomics↗

bioRxiv2018

Repression of Transcription Factor AP-2 Alpha by Peroxisome Proliferator Activated Receptor Gamma Reveals a Novel Transcriptional Circuit in basal-squamous Bladder Cancer

The discovery of bladder cancer transcriptional subtypes provides an opportunity to identify high risk patients, and tailor disease management. Recent studies suggest tumor heterogeneity contributes to \"plasticity\" of molecular subtype during progression and following treatment. Nonetheless, the transcriptional drivers of the aggressive basal-squamous subtype remain unidentified. As PPAR{gamma} has been repeatedly implicated in the luminal subtype of bladder cancer, we hypothesized inactivation of this transcriptional master regulator during progression results in increased expression of basal-squamous specific transcription factors (TFs) which act to drive aggressive behavior. We initiated a pharmacologic and RNA-seq-based screen to identify PPAR{gamma}-repressed, basal-squamous specific TFs. Hierarchical clustering of RNA-seq data following treatment of a panel of human bladder cancer cell lines with a PPAR{gamma} agonist identified a number of TFs regulated by PPAR{gamma} activation, several of which are implicated in urothelial and squamous differentiation. One PPAR{gamma}-repressed TF implicated in squamous differentiation identified is Transcription Factor Activating Protein 2 alpha (TFAP2A). We show TFAP2A and its paralog TFAP2C are overexpressed in basal-squamous bladder cancer and in squamous areas of cystectomy samples, and that overexpression is associated with increased lymph node metastasis and distant recurrence, respectively. Biochemical analysis confirmed the ability of PPAR{gamma} activation to repress TFAP2A, while PPAR{gamma} antagonist studies indicate the requirement of a functional receptor. In vivo tissue recombination studies show TFAP2A and TFAP2C promote tumor growth in line with the aggressive nature of basal-squamous bladder cancer. Our findings suggest PPAR{gamma} inactivation, as well as TFAP2A and TFAP2C overexpression cooperate with other TFs to promote the basal-squamous transition.

cancer biology↗