Biology subjects

Matsui, A.

Publications and source records attributed to Matsui, A..

18 recordsLinked to original sources

bioRxiv2026

Mapping AMPA and NMDA receptors at mouse brain hippocampal synapses by cryo-ET

AMPA and NMDA receptors are fundamental to synaptic transmission through the detection of released neurotransmitter. These ion channels open in response to glutamate binding, resulting in depolarization of the postsynaptic membrane and influx of calcium. Receptor localization plays a key role in synaptic strength, and changes in receptor number and location underpin synaptic plasticity, learning and memory. Here we apply receptor subunit-specific antibody fragments and multiplexed gold nanoparticle conjugates, together with cryo-electron tomography (cryo-ET), to elucidate the in-situ molecular organization of AMPA and NMDA receptors at hippocampal synapses in adult mouse brain tissue. AMPA receptors are predominantly found in densely packed liquid-like clusters, with interspersed NMDA receptors and adjacent NMDA receptor clusters. By direct localization of individual receptors, we provide molecular-resolution insight into the distribution of AMPA and NMDA receptors across the synapse, at peri and extrasynaptic sites, and within endocytosed vesicles. Visualization of multiple presynaptic vesicle fusion events suggests that receptors are near, but not always directly adjacent to, transmitter release sites. By mapping AMPA and NMDA receptors, and glutamate release sites, we provide receptor-resolution insight into the structure and function of brain hippocampal synapses.

neuroscience↗

bioRxiv2026

Programmable gold nanoparticle conjugates enable precise AMPA receptor localization at brain synapses by cryo-ET

Cryo-electron tomography (cryo-ET) is a powerful approach to image cells, organelles, viruses and molecular assemblies. However, resolving smaller complexes and molecules is challenging and presents a roadblock to the broad application of cryo-ET. Gold nanoparticles (AuNPs) have been used to localize otherwise unidentifiable molecules and complexes in tomograms but are typically tethered to the target of interest via a flexible linker. As a result, the position of the AuNP does not directly define the location of the target. Here we attach AuNPs to Fab antibody fragments via cysteine residues on defined elements of secondary structure and show that the AuNPs are rigidly bound to the Fab. We use these Fab-AuNP conjugates to locate AMPA receptors and probe their conformation upon desensitization with sub nanometer resolution in tomograms derived from brain slice lamella. By harnessing small, homogeneous AuNPs with precise conjugation to a Fab, we have developed reagents that enable direct investigation of conformational states of previously unidentifiable biomolecules and complexes in tomograms.

biochemistry↗

bioRxiv2025

Brain insulin signaling restores deficits in striatal dopamine release in overweight male mice with preexisting low D2-receptor expression

Obesity is characterized by insulin resistance, motivational impairments, and, in some cases, reduced availability of dopamine D2 receptors in the brain. However, whether the low D2 receptor levels represent a predisposing factor or a consequence of obesity, and how these processes are mechanistically linked, remains unclear. Here, we directly tested this causal relationship by selectively reducing D2 receptor density in striatal neurons. Male, but not female, mice with a low density of striatal D2 receptors consumed more food, gained more weight, and developed metabolic features of peripheral insulin resistance despite being maintained on standard chow. Motivational deficits preceded weight gain, manifesting as delayed circadian locomotor onset, reduced physical activity, and diminished effort to obtain food. In the brain, male mice with low D2 receptor density showed reduced dopamine release capacity and age-dependent alterations in brain insulin sensitivity. Prior to weight gain, brain insulin responses were blunted compared to those of controls, in which insulin potentiates dopamine release and enhances striatal acetylcholine signaling. Once overweight, however, these mice exhibited brain insulin hypersensitivity, with insulin strongly restoring dopamine release capacity. Together, these findings demonstrate that low striatal D2 receptor density predisposes male mice to an obesity-like phenotype through early dopaminergic dysfunction that precedes weight gain and is later compensated by insulin hypersensitivity in the brain.

neuroscience↗

bioRxiv2025

Pathological Angiogenesis Precedes the Onset of Aortic Dissection

Aortic dissection (AD) is a severe, life-threatening disease that occurs abruptly1. Although remodeling and inherent vulnerability of the aortic media, as observed in heritable connective tissue disorders such as Marfan syndrome, have been implicated in the onset of AD, the precise pathological mechanisms underlying the non-heritable form, which accounts for most cases, remains largely unknown2. Here, using hyperacute AD patient-derived samples, we show that pathological angiogenesis within the aortic media precedes the onset of dissection. Integrating single-cell transcriptomic analysis of aortic medial endothelial cells with high-resolution imaging revealed temporal changes preceding dissection. Hypoxic alterations in the media triggered osteochondrogenic changes in smooth muscle cells, promoted hydroxyapatite deposition, and induced angiogenesis via VEGF secretion from AD-specific CD14+CD68+CD163+MRC1(CD206)neg-low macrophages. Atomic force microscopy revealed that these processes culminated in the formation of a soft capillary layer, potentially concentrating stress on this region and contributing to AD onset. H&E staining of archived specimens revealed that non-heritable AD can be classified into angiogenic or non-angiogenic subtypes, with more than half exhibiting the former. In contrast, acute AD cases associated with Marfan syndrome typically exhibit a non-angiogenic pattern, suggesting distinct underlying mechanisms. This study reports angiogenesis as a key pathological driver in non-heritable AD and highlight potential targets for early diagnosis, prevention, and treatment.

pathology↗

bioRxiv2025

Neuronal feedback loop in the suprachiasmatic nucleus generates robust circadian rhythms

The central circadian clock of the suprachiasmatic nucleus (SCN) is a network consisting of various types of neurons and glial cells, but its mechanism remains elusive. Here, by monitoring cellular calcium rhythms in vivo in vasoactive intestinal polypeptide (VIP)-deficient mice, we show that arginine vasopressin (AVP) neurons intrinsically oscillate with a short period and that VIP amplifies and delays the AVP neuronal rhythm to lengthen its period to [~]24 hours. Consistently, the circadian behavior period is shortened and lengthened by VIP receptor disruption and neurotransmission blockade of AVP neurons, respectively. VIP and other neurons occasionally exhibit weak, unstable, long-period calcium rhythms only when AVP neuronal oscillation is attenuated. Together with our previous finding that AVP neurons act as the primary pacesetter cells of the SCN ensemble rhythm, our results indicate that the feedback neuronal circuit of AVP cellular oscillator and VIP peptide signaling is crucial for the robust circadian rhythm.

neuroscience↗

bioRxiv2025

GABAergic network from AVP neurons to VIP neurons in the suprachiasmatic nucleus sets the activity/rest time of the circadian behavior rhythm

The central circadian clock of the suprachiasmatic nucleus (SCN) is a network composed of multiple types of {gamma}-aminobutyric acid (GABA)-ergic neurons and glial cells. However, the precise role of GABAergic transmission in the SCN remains unclear. In this study, we investigated the GABAergic regulation from arginine vasopressin (AVP)-producing neurons in the SCN shell to vasoactive intestinal polypeptide (VIP)-producing neurons in the SCN core. Blocking GABA release from AVP neurons by a vesicular GABA transporter (Vgat) gene deletion lengthened the activity time (the interval between the onset and offset of locomotor activity) and shortened the duration of high Ca2+ activity in VIP neurons to match the behavioral rest time. Conversely, eliminating functional GABAA receptors (GABAAR) in VIP neurons by in vivo genome editing reduced locomotor activity level and the activity time, and lengthened the high Ca2+ duration in VIP neurons. Optogenetic activation of AVP neurons in vivo increased Ca2+ in VIP neurons during the night. A similar Ca2+ response of VIP neurons to AVP neuronal activation was also observed in SCN slices and was inhibited by a GABAAR antagonist, gabazine. Importantly, gabazine application alone raised the baseline Ca2+ in VIP neurons, suggesting a tonic depression of these neurons by GABA. Moreover, AVP neuronal activation decreased Ca2+ in non-AVP neurons located between AVP- and VIP-rich regions in the SCN. These results suggest that GABA from AVP neurons disinhibits VIP neurons indirectly by suppressing other intermediate GABA neurons to set the behavior activity/rest time precisely.

neuroscience↗

bioRxiv2025

Inhibiting B-cell-mediated Immunosuppression to Enhance the Immunotherapy Efficacy in Hepatocellular Carcinoma

BackgroundImmunotherapy is efficacious in hepatocellular carcinoma (HCC), but the benefits are limited to a minority of patients. Most HCC patients show resistance to immune checkpoint blockade (ICB). Agonists of the stimulator of interferon genes (STING), potent immune stimulators, showed limited effectiveness. Using preclinical models, we studied the mechanisms of resistance to ICB and STING agonism. MethodsMurine HCA-1 and RIL-175 HCCs were orthotopically grown in mice with underlying liver fibrosis, to mimic the presentation of human HCC. Established tumors were treated with a STING agonist (BMS-986301) or anti-PD1 ICB, and mice were followed to evaluate safety and efficacy, as well as the mechanisms of treatment resistance by RNA sequencing, flow cytometry, and immunofluorescence, B-cell depletion and T-cell immunoglobulin and mucin domain 1 (TIM-1) ICB. ResultsUnbiased analyses of transcriptomic data from murine HCC tissues from ICB-treated mice showed an increased abundance of intratumoral CD8+ T cells and B cells. STING agonism alone showed efficacy in the ICB-responsive RIL-175 HCC model but more limited efficacy in the ICB-resistant HCA-1 model. STING agonism increased circulating IL-10 and intratumoral infiltration by B-cells, including TIM-1+ B cells, and promoted the formation of tertiary lymphoid structure (TLS)-like structures, especially in the peritumoral areas. Strikingly, adding B cell depletion to ICB or STING agonism treatment significantly increased survival. Interestingly, unlike ICB, STING agonism also had a pronounced anti-metastatic activity. In addition, the combination of STING agonism and TIM-1 blockade augmented B cell differentiation and antigen presentation in vitro and improved the anti-tumor effects in murine HCC in vivo. This approach decreased the number of TIM-1+ B cells in the tumor and shifted B cells to higher expression of CD86 and MHC class II, enhancing the antigen presentation capability and further boosting the antitumor efficacy of CD8+ cytotoxic T cells. ConclusionOur findings demonstrate that B cells are associated with ICB- and STING-mediated therapy resistance, and that depleting B-cells or targeting TIM-1 enhances both innate and acquired therapeutic efficacy in HCC.

cancer biology↗

bioRxiv2024

Cryo-electron tomographic investigation of native hippocampal glutamatergic synapses

Chemical synapses are the major sites of communication between neurons in the nervous system and mediate either excitatory or inhibitory signaling [1]. At excitatory synapses, glutamate is the primary neurotransmitter and upon release from presynaptic vesicles, is detected by postsynaptic glutamate receptors, which include ionotropic AMPA and NMDA receptors [2, 3]. Here we have developed methods to identify glutamatergic synapses in brain tissue slices, label AMPA receptors with small gold nanoparticles (AuNPs), and prepare lamella for cryo-electron tomography studies. The targeted imaging of glutamatergic synapses in the lamella is facilitated by fluorescent pre- and postsynaptic signatures, and the subsequent tomograms allow for identification of key features of chemical synapses, including synaptic vesicles, the synaptic cleft and AuNP-labeled AMPA receptors. These methods pave the way for imaging brain regions at high resolution, using unstained, unfixed samples preserved under near-native conditions.

biochemistry↗

bioRxiv2023

Combined blockade of CXCR4 and PD-1 enhances intratumoral dendritic cell activation and immune responses against HCC

Immune checkpoint inhibitors (ICIs) have transformed systemic therapy for unresectable hepatocellular carcinoma (HCC). Nevertheless, their efficacy is limited to a small percentage of patients, leaving an opportunity for enhancement through synergistic combination therapies. We tested here the combined blockade of programmed death receptor 1 (PD-1) and CXCR4, a receptor for CXCL12 and a key mediator of immunosuppression in the tumor microenvironment in orthotopic grafted and autochthonous models of HCC. We evaluated tumor growth and survival outcomes and examined the underlying mechanisms using immunofluorescence, flow cytometry, RNA-sequencing, and transgenic mice experiments. Combined anti-CXCR4/PD-1 therapy had a robust impact on tumor growth and significantly prolonged survival in all murine preclinical models. The combination treatment successfully reprogrammed antigen-presenting cells, revealing the role of conventional type 1 dendritic cells (cDC1s) in the tumor microenvironment. Moreover, DC reprogramming enhanced anti-cancer immunity by facilitating CD8 T-cell accumulation and activation in the HCC tissue. The effectiveness of the anti-CXCR4 antibody/ICI combination treatment was compromised entirely in Batf3-KO mice deficient in cDC1 cells. Thus, combined ICI therapy with an anti-CXCR4 antibody has the potential to augment the anti-cancer effects and improve survival outcomes in HCC via reprogramming intra-tumoral cDC1 cells.

cancer biology↗

bioRxiv2023

Preventing NK cell activation in the damaged liver induced by cabozantinib/PD-1 blockade increases survival in hepatocellular carcinoma models

Combining multikinase inhibitors with immune checkpoint blockade improves tumor control in hepatocellular carcinoma (HCC), but survival benefits remain inconsistent. To define this discordance, we integrated COSMIC-312 with orthotopic and autochthonous murine HCC models with or without liver fibrosis. In patients treated with cabozantinib plus atezolizumab, baseline liver function stratified overall survival but not progression-free survival, indicating uncoupling of tumor control from survival. In contrast, sorafenib outcomes tracked with both endpoints, supporting a treatment-specific effect rather than a purely prognostic effect of liver status. In murine HCC models, cabozantinib plus PD-1 blockade induced comparable tumor regression regardless of liver condition, but improved survival only in mice with preserved liver function, whereas fibrotic hosts developed hepatotoxicity. Immune profiling revealed compartment-specific remodeling, with enhanced cytotoxic T-cell programs in tumors but expansion of NK-lineage innate lymphocytes with ILC1-like features in fibrotic liver. Depletion of NK1.1-positive cells reduced liver injury and restored survival without compromising antitumor efficacy, whereas CD4-positive or CD8-positive T-cell depletion did not protect from hepatotoxicity. Transcriptomic, single-cell, adoptive-transfer, and human in vitro studies supported a model in which the fibrotic liver niche promotes NK-to-ILC1-like reprogramming, hepatocyte stress signaling, and TNF/TRAIL-associated epithelial injury. Consistently, cabozantinib and nivolumab showed liver-predominant remodeling of CD56-positive innate lymphocyte-enriched populations in human HCC samples, and ex vivo TGF-beta induced ILC1-like phenotypic changes in human NK cells. These findings identify liver fibrosis as a host determinant that can limit the survival benefit of multikinase inhibitor immunotherapy by promoting innate immune-mediated hepatotoxicity despite preserved tumor control in HCC. One Sentence SummaryLiver fibrosis limits the survival benefit of multikinase inhibitor immunotherapy in hepatocellular carcinoma by promoting innate immune-mediated hepatotoxicity despite preserved tumor control.

cancer biology↗

bioRxiv2023

Reprogramming Intrahepatic Cholangiocarcinoma Immune Microenvironment by Chemotherapy and CTLA-4 Blockade Enhances Anti-PD1 Therapy

Intrahepatic cholangiocarcinoma (ICC) has limited therapeutic options and a dismal prognosis. Anti-PD-L1 immunotherapy combined with gemcitabine/cisplatin chemotherapy has recently shown efficacy in biliary tract cancers, but responses are seen only in a minority of patients. Here, we studied the roles of anti-PD1 and anti-CTLA-4 immune checkpoint blockade (ICB) therapies when combined with gemcitabine/cisplatin and the mechanisms of treatment benefit in orthotopic murine ICC models. We evaluated the effects of the combined treatments on ICC vasculature and immune microenvironment using flow cytometry analysis, immunofluorescence, imaging mass cytometry, RNA-sequencing, qPCR, and in vivo T-cell depletion and CD8+ T-cell transfer using orthotopic ICC models and transgenic mice. Combining gemcitabine/cisplatin with anti-PD1 and anti-CTLA-4 antibodies led to substantial survival benefits and reduction of morbidity in two aggressive ICC models, which were ICB-resistant. Gemcitabine/cisplatin treatment increased the frequency of tumor-infiltrating lymphocytes and normalized the ICC vessels, and when combined with dual CTLA-4/PD1 blockade, increased the number of activated CD8+Cxcr3+IFN-{gamma}+ T-cells. Depletion of CD8+ but not CD4+ T-cells compromised efficacy. Conversely, CD8+ T-cell transfer from Cxcr3-/- versus Cxcr3+/+ mice into Rag1-/- immunodeficient mice restored the anti-tumor effect of gemcitabine/cisplatin/ICB combination therapy. Finally, rational scheduling of the ICBs (anti-CTLA-4 "priming") with chemotherapy and anti-PD1 therapy achieved equivalent efficacy with continuous dosing while reducing overall drug exposure. In summary, gemcitabine/cisplatin chemotherapy normalizes vessel structure, increases activated T-cell infiltration, and enhances anti-PD1/CTLA-4 immunotherapy efficacy in aggressive murine ICC. This combination approach should be clinically tested to overcome resistance to current therapies in ICC patients. One Sentence SummaryImmune microenvironment reprogramming by chemotherapy and priming using CTLA-4 blockade render ICCs responsive to anti-PD-1 immunotherapy.

cancer biology↗

bioRxiv2022

IFNA pathway drives the more aggressive phenotype of KRASG12D-mutant pancreatic ductal adenocarcinomas via IFNAR1/STAT3 activation

Activating mutations of KRAS play critical roles in the initiation and progression of pancreatic ductal adenocarcinoma (PDAC). Accumulating evidence indicates that distinct KRAS alleles associate with different prognoses, but the underlying mechanisms are not known. We established isogenic KRAS mutants (KRASG12D, KRASG12V, and KRASWT) using a KRASG12R patient-derived PDAC cell line by CRISPR/Cas9 knock-in. We used these isogenic cell lines, a collection of characterized human PDAC patient-derived cell lines, and murine PDAC models to study the role of these KRAS alleles in vitro and in vivo. We verified that the growth of KRASG12D cells is more aggressive compared to KRASG12V isogenic cells in vitro and in vivo using orthotopic mouse models. Signal transducer and activator of transcription (STAT) activation was the most significant difference between KRASG12D and KRASG12V isogenic PDACs. Furthermore, activation of interferon-alpha (IFNA)/IFNA receptor (IFNAR)1/STAT3 signaling in the cancer cells mediated the more aggressive phenotype of KRASG12D PDACs. Conversely, inhibition of IFNAR1 in patient-derived PDAC cells suppressed tumor growth. Finally, IFNAR1 blockade was also effective in murine PDAC models and induced a significant increase in survival when combined with immune checkpoint blockade therapy. We conclude that the IFNA pathway and IFNAR1/STAT3 axis contribute to a more aggressive tumor progression in human KRASG12D PDACs and that IFNAR1 inhibition is a potential therapeutic target for overcoming resistance to immunotherapy in PDAC. One Sentence SummaryIFNA pathway drives the more aggressive phenotype of KRASG12D-mutant pancreatic ductal adenocarcinomas via IFNAR1/STAT3 activation.

cancer biology↗

bioRxiv2022

Inflammasome targeting with an NLRP3 agonist therapy is feasible but ineffective in murine hepatocellular carcinoma models with liver damage

Co-inhibition of programmed cell death receptor-1 (PD-1) and vascular endothelial growth factor receptor (VEGFR) pathway has shown efficacy in hepatocellular carcinoma (HCC). NLRP3 is a component of the inflammasome involved in the initiation, development, and progression of multiple cancers. We examined whether adding an NLRP3 agonist to dual PD-1/VEGFR inhibitors is feasible and can address treatment resistance in orthotopic HCC in mice with underlying liver damage. Mice with established tumors were treated with an NLRP3 agonist alone, combination of anti-VEGFR2 or the multikinase inhibitor regorafenib with anti-PD1 antibodies, or their combination. In all models tested, NLRP3 agonist therapy showed acceptable toxicity but no effect on tumor growth delay, disease morbidity, or survival. Pharmacodynamic analyses confirmed the effects of NLRP3 agonist therapy on inflammasome, evidenced by a significant elevation in plasma levels of pro-inflammatory cytokines such as IL-1{beta}. However, these changes were not detectable in tumor tissues, where we detected increased expression of immunosuppressive markers IL-6, KC/GRO, CCL9, and IL-18, and immune checkpoint molecules (PD1, PD-L1, and CTLA-4) after NLRP3 agonist therapy. Thus, modulation of the inflammasome with a novel NLRP3 agonist was feasible in mice with orthotopic HCC and liver damage but did not enhance efficacy when combined with anti-PD1/VEGFR therapies.

immunology↗

bioRxiv2022

Leucine-Rich Repeat Kinase 2 limits dopamine D1 receptor signaling in the striatum and biases against heavy persistent alcohol drinking

The transition from hedonic alcohol drinking to problematic drinking is a hallmark of alcohol use disorder that occurs only in a subset of drinkers. This transition is known to require long-lasting changes in the synaptic drive and the activity of striatal neurons expressing dopamine D1 receptor (D1R). The molecular mechanisms that generate vulnerability in some individuals to undergo the transition are less understood. Here, we report that the Parkinsons-related protein leucine-rich repeat kinase 2 (LRRK2) modulates striatal D1R function to affect the behavioral response to alcohol and the likelihood that mice transition to heavy, persistent alcohol drinking. Deletion of the Lrrk2 gene specifically from D1R-expressing neurons potentiates D1R signaling at the cellular and synaptic level, enhancing alcohol-related behaviors and drinking. Mice with cell-specific deletion of Lrrk2 are more prone to heavy alcohol drinking and consumption is insensitive to punishment. These findings identify a novel role for LRRK2 function in the striatum in promoting resilience against heavy and persistent alcohol drinking.

neuroscience↗

bioRxiv2021

Neurexins in serotonergic neurons regulate serotonin transmission and complex mouse behaviors

Extensive serotonin (5-HT) innervation throughout the brain corroborates 5-HTs modulatory role in numerous cognitive activities. Volume transmission is the major mode for 5-HT transmission but mechanisms underlying 5-HT signaling are still largely unknown. Abnormal brain 5-HT levels and function have been implicated in autism spectrum disorder (ASD). Neurexin (Nrxn) genes encode presynaptic cell adhesion molecules important for the regulation of synaptic neurotransmitter release, notably glutamatergic and GABAergic transmission. Mutations in Nrxn genes are associated with neurodevelopmental disorders including ASD. However, the role of Nrxn genes in the 5-HT system is poorly understood. Here, we generated a mouse model with all three Nrxn genes disrupted specifically in 5-HT neurons to study how Nrxns affect 5-HT transmission. Loss of Nrxns in 5-HT neurons reduced the number of serotonin neurons in the early postnatal stage, impaired 5-HT release, and decreased 5-HT release sites and serotonin transporter expression. Furthermore, 5-HT neuron-specific Nrxn knockout reduced sociability and increased depressive-like behavior. Our results highlight functional roles for Nrxns in 5-HT neurotransmission, 5-HT neuron survival, and the execution of complex behaviors.

neuroscience↗

bioRxiv2021

Molecular structure and conformation of stereocilia tip-links elucidated by cryo-electron tomography

Mechanosensory transduction (MT), the conversion of mechanical stimuli into electrical signals, underpins hearing and balance and is carried out within hair cells in the inner ear. Hair cells harbor actin-filled stereocilia, arranged in rows of descending heights, where the tips of stereocilia are connected to their taller neighbors by a filament composed of protocadherin 15 (PCDH15) and cadherin 23 (CDH23), deemed the tip-link. Tension exerted on the tip-link opens an ion channel at the tip of the shorter stereocilia, thus converting mechanical force into an electrical signal. While biochemical and structural studies have provided insights into the molecular composition and structure of isolated portions of the tip-link, the architecture, location and conformational states of intact tip-links, on stereocilia, remains unknown. Here we report in situ cryo-electron microscopy imaging of the tip-link in mouse stereocilia. We observe individual PCDH15 molecules at the tip and shaft of stereocilia and determine their stoichiometry, conformational heterogeneity, and their complexes with CDH23. The PCDH15/CDH23 complexes occur in clusters, frequently with more than one copy of PCDH15 at the tip of stereocilia, suggesting that tip-links might consist of more than one copy of the PCDH15/CDH23 heterotetramer and by extension, might include multiple MT complexes.

neuroscience↗

bioRxiv2021

A high resolution single molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis

BackgroundAccurate and comprehensive annotation of transcript sequences is essential for transcript quantification and differential gene and transcript expression analysis. Single molecule long read sequencing technologies provide improved integrity of transcript structures including alternative splicing, and transcription start and polyadenylation sites. However, accuracy is significantly affected by sequencing errors, mRNA degradation or incomplete cDNA synthesis. ResultsWe present a new and comprehensive Arabidopsis thaliana Reference Transcript Dataset 3 (AtRTD3). AtRTD3 contains over 160k transcripts - twice that of the best current Arabidopsis transcriptome and including over 1,500 novel genes. 79% of transcripts are from Iso-seq with accurately defined splice junctions and transcription start and end sites. We developed novel methods to determine splice junctions and transcription start and end sites accurately. Mis- match profiles around splice junctions provided a powerful feature to distinguish correct splice junctions and remove false splice junctions. Stratified approaches identified high confidence transcription start/end sites and removed fragmentary transcripts due to degradation. AtRTD3 is a major improvement over existing transcriptomes as demonstrated by analysis of an Arabidopsis cold response RNA-seq time-series. AtRTD3 provided higher resolution of transcript expression profiling and identified cold- and light-induced differential transcription start and polyadenylation site usage. ConclusionsAtRTD3 is the most comprehensive Arabidopsis transcriptome currently available. It improves the precision of differential gene and transcript expression, differential alternative splicing, and transcription start/end site usage from RNA-seq data. The novel methods for identifying accurate splice junctions and transcription start/end sites are widely applicable and will improve single molecule sequencing analysis from any species.

plant biology↗

bioRxiv2021

HOXB7 induces oncogenic transformation in NMuMG cells via JAK2-STAT3 signaling

The homeobox family genes are often dysregulated in a various cancer type. Particularly HOXB7 amplification and overexpression correlate with poor prognosis in various cancer such as gastric, pancreatic, and lung cancers. Moreover, HOXB7 is known to contribute to cancer progression by promoting epithelial to mesenchymal transition, anti-cancer drug resistance, and angiogenesis. In this study, we show that HOXB7 is coamplified with ERBB2 in a subset of breast cancer patients and HOXB7 expression correlates with poor prognosis in HER2-positive breast cancer patients. This clinical observation is supported by the following results: HOXB7 overexpression in an immortalized murine mammary gland epithelial cell line NMuMG induces cellular transformation in vitro, tumorigenesis and lung metastasis through the activation of JAK-STAT signaling.

cancer biology↗