title: Gene expression profile  of WT and mdig/mina53 KO MDA-MB 231 breast cancer cells [RNA-Seq]

city: Stony Brook

first: Fei

last: Chen

state: New York

address: Lauterbur Drive Stony Brook, NY 11794

institute: Stony Brook Cancer Center

summary: The mineral dust-induced gene (mdig, also called as MINA or RIOX2) is upregulated in breast cancer and predicts poor overall survival of breast cancer patients. Our studies suggested the anti-metastasis feature of mdig in regulating the cell motility of breast cancer cells. Here we studied the transcriptomic profile of human triple negative breast cancer cells MDA-MB-231 that were knocked out for mdig via CRISPR-Cas 9 gene editing. Our analysis identified distinct transcriptomic profiles in mdig knockout cells, where genes  associated with epithelial-mesenchymal transition (EMT) and TGF-β pathways were upregulated

overall_design: Wildtype type (WT) and mdig knockout (KO) MDA-MB-231 cells were subjected to RNA-Sequencing

first: Chitra

last: Thakur


title: Chromatin accessibility landscapes define stromal cell identities across tissues

status: Public on Jan 20 2026

city: Toronto

first: Amin

last: Nooranikhojasteh

state: ON

address: 101 College Street

country: Canada

institute: Princess Margaret Cancer Centre

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Chromatin accessibility landscapes are pivotal in regulating gene expression and maintaining cellular identity across diverse tissues. Using single-cell ATAC sequencing (scATAC-seq), we profiled chromatin accessibility across nine murine organs, encompassing 51,248 cells, to decipher the cis-regulatory mechanisms underlying tissue-specific and cell type-specific functions. Our analysis uncovered 28 major cell types with distinct chromatin accessibility signatures, revealing conserved and unique regulatory patterns. We identified transcription factor (TF) motifs associated with these regions, highlighting TF dynamics in cell differentiation and organ-specific functions. Additionally, we demonstrated that chromatin accessibility can trace stromal cells, including endothelial cells and fibroblasts, back to their tissue of origin, offering new insights into tissue-specific epigenomic landscapes. This innovative approach of leveraging epigenomic features to trace cells of origin represents a significant advancement, providing valuable insights into both normal and pathological states where identifying the tissue of origin is critically important.

overall_design: Single cell chromatin accessibility (scATAC-Seq) profiles from nine mouse organs. Experiments were performed according to the Chromium Single Cell ATAC reagent kit v1.1 user guide (10x Genomics, CG000209 Rev F)

first: Elias

last: Orouji


title: MRTFA-SRF driven gene expression promotes cellular stiffness by controlling cytoplasmic Ca2+ and K+ levels in cancer cells II

city: CHICAGO

first: Ekrem Emrah

last: Er

state: IL

address: 909 S  WOLCOTT AVE

department: Physiology and Biophysics

country: USA

institute: The University of Illinois at Chicago

type: Expression profiling by high throughput sequencing

summary: Cellular stiffness, the inverse of compliance, is a biophysical property of cells that fundamentally impacts homeostatic functions and pathological states and understanding how these properties are controlled can provide novel insights into tissue homeostasis and disease mechanisms. A prominent regulator of cellular stiffness is the filamentous actin (F-actin) cytoskeleton that forms aligned stress fibers during cellular contraction. It has been recently shown that F-actin polymerization and the subsequent cortical stiffening of cancer cells is regulated by the myocardin-related transcription factor A (MRTFA) and this results in dramatic changes in the ability of cancer cells to evade anti-tumor immune surveillance. However, the precise mechanism by which MRTFA regulated cortical stiffness remained unknown. Here, we demonstrate that cancer cell stiffening occurs as a consequence of MRTFA binding to its cofactor serum response factor (SRF). Specifically, MRTFA-SRF promotes the expression of Ca2+ and K+ handling genes and the flux of these ions are critically needed for cortical stiffening. Finally, we show the results of a series of rigorous gain-of-function and loss-of-function studies that reveal the large conductance K+ channel auxiliary subunit, KCNMB1, as an MRTFA-SRF target that regulates cell stiffness and F-actin organization. Collectively, these findings point to previously unrecognized MRTFA-SRF targets in cellular stiffness, including a novel druggable ion channel. Here, we test the efficacy of 2 BK channel activators (NS,BMS) under high K+ conditions and how they may affect cancer cell transcriptional changes.

overall_design: 150k AT-3 or E0771 cells were seeded for 24hr in a 6well dish, then treated with the listed treatments for 24hr. RNA was then extracted and submitted for sequencing.

first: Alexa

middle: M

last: Gajda

first: Mark

middle: A

last: Sanborn

first: Ekrem

middle: E


title: Beta cell-derived cholecystokinin drives obesity-associated pancreatic adenocarcinoma development [CUT&RUN]

city: New Haven

first: Mandar

middle: Deepak

last: Muzumdar

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

summary: Pancreatic endocrine-exocrine crosstalk plays a key role in normal physiology and disease and can be altered by host metabolic states, such as obesity. Classically, endocrine islet beta (β) cell secretion of insulin is thought to promote the development of obesity-associated pancreatic adenocarcinoma (PDAC), an exocrine cell-derived tumor. Here, we show that β cell expression of the peptide hormone cholecystokinin (CCK) is necessary and sufficient for obesity-associated PDAC progression in mice and that CCK expression – rather than insulin – correlates strongly with enhanced tumorigenesis. Single-cell RNA-sequencing, in silico latent-space archetypal and trajectory analysis, and experimental lineage tracing in vivo reveal that obesity induces the expansion of postnatal immature β cells, which adapt to express CCK via stress-responsive JNK/cJun signaling. Finally, obesity perturbs CCK-dependent peri-islet exocrine cell transcriptional states and enhances islet-proximal tumor formation. These results define endocrine-exocrine CCK signaling as a bona fide driver of obesity-associated PDAC development and uncover new avenues to target the endocrine pancreas to subvert exocrine tumorigenesis.

overall_design: Min6 cells were plated (2.5 million) and grown for 3 days prior to treatment with the JNK inhibitor SP600125 (20 uM, Med Chem Express) or DMSO (control) for 48 hours. 550,000 cells were harvested per reaction and condition. Cells were processed using the CUTANA ChIC/CUT&RUN Kit (14-1048), JUN/cJun CUTANA CUT&RUN antibody (SKU:13-2019), and positive (anti-H3K4Me3) and negative (IgG) control antibodies from the kit following the manufacturer’s protocol. Library preparation was performed by the Yale Center for Genome Analysis followed by sequencing to a depth of 30 million paired-end 150 bp reads (2x150) per sample on NovaSeq (Illumina).

first: Cathy

middle: C

last: Garcia

first: Aarthi

last: Venkat

first: Daniel

last: McQuaid

first: Sherry

middle: S

last: Agabiti

first: Alexander

last: Tong

first: Boby

last: Mathew

first: Rebecca

middle: L

last: Cardone

last: Starble

first: Christian

middle: F

last: Ruiz

first: Christy

last: Zheng

first: Akin

last: Sogunro

first: Jeremy

middle: B

last: Jacox

first: Ken

middle: H

last: Loh

first: Richard

middle: G

last: Kibbey

first: Smita

last: Krishnaswamy

middle: D


title: MeCP2 gene dosage-dependent neurodevelopmentally restricted defects arise by SWI/SNF-mediated aberrant activation of cell fate-determining bivalent genes [RNA-Seq]

city: Milan

first: Michal

last: Kubacki

address: Via Olgettina 58

country: Italy

institute: San Raffaele Scientific Institute

summary: Increased dosage of genes encoding for chromatin factors is thought to inevitably alter gene transcriptional output, leading to cellular dysfunctions. However, a mechanistic understanding of the molecular processes in action and their consistency across different cell types is still lacking. A prototypical gene in this context is MECP2, as its overexpression determines severe neurological deficits in MECP2 duplication syndrome (MDS) and its dosage is considered a crucial safety risk factor in gene therapy for Rett syndrome (RTT). However, in MDS patients, MECP2 dysregulation arises at the embryonic stage while in RTT gene therapy, MECP2 is delivered into the mature brain. Despite these important implications, the molecular consequences of increased MECP2 gene dosage have yet to be fully elucidated. Surprisingly, we found that MeCP2 overexpression induced profound transcriptional alterations in neural progenitor cells (NPCs) while it had minimal or no effects in both mouse and human neurons. Consequently, MeCP2 overexpression in NPCs, but not mature neurons, led to profound functional alterations. Mechanistically, we observed that both endogenous and overexpressed Mecp2 bind to the same CpG island repertoire. In NPCs, lower endogenous Mecp2 levels facilitated stronger deposition of the ectopic protein into CpG islands, driving the transcriptional activation of many developmental bivalent genes, deranging neuronal differentiation. We uncovered that this activation is mediated by the interaction with the SWI/SNF chromatin remodeling complex. Conversely, in neurons, where endogenous Mecp2 is highly expressed, ectopic protein expression leads to minimal CpG island binding and accelerate protein degradation. Our findings reveal that increased gene dosage-dependent effects are highly influenced by cell type, levels of proteins and their mechanisms of action. These results provide a framework to interpret the relationship between Mecp2 chromatin binding and transcriptional output and suggest that Mecp2 overexpression is expected to be well tolerated in gene therapy applications for RTT.

overall_design: This study was designed to investigate the cell-type and developmental-stage-specific consequences of Mecp2 overexpression. We used primary mouse Neuronal Progenitor Cells (NPCs) derived from E13.5 embryos and primary mouse Neurons (Ns) from E18.5 embryos, as well as human iPSC-derived neurons, to compare the effects of Mecp2/MECP2 overexpression versus an EGFP control. To assess the functional outcomes, we performed in vivo experiments using in utero electroporation in E13.5 mouse embryos and systemic AAV-PHP.eB vector delivery in adult mice. The molecular consequences of Mecp2 dosage were analyzed using a combination of high-throughput sequencing techniques: RNA-sequencing was used to profile transcriptional changes, CUT&Tag was employed to map the genomic binding of endogenous and exogenous Mecp2 and the chromatin remodeler Smarcb1, and 4f-SAMMY-seq was used to analyze global chromatin accessibility and organization.

first: Mirko

last: Luoni

first: Serena Gea

last: Giannelli

first: Francesca

last: Morosi

first: Claudia

last: Di Berardino

first: Angelo

last: Iannielli

first: Alessandro

last: Sessa

first: Gaia

last: Colasante

first: Emanuele Di Patrizio

last: Soldateschi

first: Chiara

last: Lanzuolo

first: Vania

last: Broccoli


title: Gene expression profile at single cell level of WT and mdig/mina53 KO MDA-MB 231 breast cancer cells

first: Fei

last: Chen

overall_design: Wildtype type (WT) and mdig knockout (KO) MDA-MB-231 cells were subjected to single cell RNA-Sequencing

first: Chitra

last: Thakur


title: TL1A-activated Tcells as upstream regulators of perianal fistulizing disease-associated changes in the rectum of Crohn's Disease patients [scRNA-seq]

city: Barcelona

first: Azucena

last: Salas

address: Rosselló, 149-153

department: Gastroenterology

country: Spain

institute: IDIBAPS

summary: Single-cell RNA sequencing revealed the increased abundance of some cell types, such as intestinal fibroblasts, in the CD-PFD rectal mucosa relative to CD. Within the stromal subset, the lamina propria S1 fibroblasts showed the highest number of differentially expressed genes (DEGs) between CD and CD-PFD patients, including an upregulation of TFPI2 and a downregulation of the TGFβ-responding gene CTGF. These changes were validated by bulk RNA analysis, where we also observed overexpression of the previously described PFD target genes MMP1 and MMP3. In vitro studies with intestinal fibroblasts confirmed the negative regulation by TGFβ of the PFD-signature, thus ruling out TGFβ as a driver of the PFD-associated fibroblast signature. Next, we investigated DEGs in the lymphoid compartment and identified lymphotoxin beta (LTB) as being upregulated in CD-PFD intestinal CD4+ T cells. LTB interacts with its receptor LTBR, which is expressed in stromal, epithelial and myeloid cells. Interestingly, LTB-LTBR interactions were increased in the CD-PFD group. In vitro studies in primary fibroblasts showed that LTB upregulates TFPI2, while it downregulates CTGF, thus reproducing the PFD-associated signature. Finally, we submitted the top 50 genes overexpressed by CD-PFD CD4+ T cells to the immune dictionary1, which identified TL1A as its most likely driver. In line with this, the TL1A receptor TNFRSF25 was overexpressed in CD-PFD CD4+ T cells. As a link between TL1A and LTB is not described in the literature, we stimulated anti-CD3-activated peripheral T cells with TL1A and observed the significant upregulation of LTa1b2, the functional form of LTB. Intriguingly, we also observed that while TNF can drive the PFD-associated signature in fibroblasts, it cannot induce LTa1b2 in T cells, suggesting that TNF and TL1A/LTB signalling are two independent but potentially complementary pathways in PFD. In summary, we propose a previously unrecognized TL1A-LTB axis as being responsible for inducing PFD-associated alterations in the rectal mucosa, and we hypothesise that inhibition of TL1A might be worth exploring in the context of perianal disease.

overall_design: Rectum biopsies from patients with Crohn's Disease (CD) with and without perianal fistulizing disease (PFD) were digested and processed for scRNA-seq analysis (10x Genomics). A total of 31 patients were included, with distinct clinical characteristics (active inflammation, remission, or uninvolved tissue).

first: Victoria

last: Gudiño

first: Jae-Won

last: Cho

first: Berta

last: Caballol

first: Angela

last: Sanzo-Machuca

first: Ana

last: Corraliza

first: Marisol

last: Veny

first: Livia

last: Genaro

first: Elisa

last: Melón-Ardanaz

first: Carme M

last: Masamunt

first: Miriam

last: Esteller

first: Agnès

last: Fernández-Clotet

first: Ingrid

last: Ordàs

first: Raquel

last: Franco-Leal

first: Elena

last: Ricart

first: Julià

last: Panés

first: Martin

last: Hemberg


title: NF-κB activation in astrocytes critically affects wound regeneration after traumatic brain injury II

city: Ulm

first: Bernd

last: Baumann

address: Albert-Einstein-Allee 11

country: Germany

institute: Ulm University

summary: Traumatic brain injury (TBI) is a complex condition in which multiple pathophysiological mechanisms influence the course of the disease. After the primary mechanical impact, neuroinflammatory reactions of glial cells along with infiltrating peripheral immune cells mainly determine the overall clinical outcome. However, these secondary processes and their molecular determinants promoting either beneficial or detrimental consequences are not well-defined. Here, we show that TBI-mediated NF-κB activation in astrocytes impairs their homeostatic functions and acts as a key regulator of multiple post-traumatic responses in mice. We determined striking deficits in CNS scar formation after TBI using a combination of NF-κB-reporter mice, conditional mouse models allowing astrocytic NF-κB modulation, and analysis of transcriptomic signatures. Importantly, the development of wound healing deficits depends on paracrine signaling of NF-κB-activated astrocytes and cross-responsive microglial cells.Our findings identify astrocytic NF-κB activation as a critical pathological amplification factor interfering with the restoration of CNS integrity at wound lesion sites.

overall_design: Wildtype mice were subjected to TBI/closed head injury (CHI). Tissue was taken from the insult area at day 3 post TBI or sham treatment and used for RNA sequencing. The was the identification of pathways prominently activated in response to TBI, as well as the analysis of NF-kappaB-associated activation patterns.

first: Heinrich

last: Wendt

first: Tabea

last: Hein

first: Thomas

last: Wirth


title: Characterization of gene expression in canine invasive urothelial carcinoma using a NanoString-based urine assay

city: West Lafayette

first: Sagar

last: Utturkar

state: IN

address: 201 S University St

department: Institute for Cancer Research

institute: Purdue University

summary: For human and canine invasive urothelial carcinoma (InvUC), there is growing interest in using the molecular characteristics of a tumor to guide individualized treatment strategies. The objective of this study was to use a noninvasive, urine-based method to characterize gene expression signatures in dogs with InvUC.

overall_design: RNA was isolated from canine InvUC tumor samples, urine sediment from dogs with InvUC, normal canine bladder mucosa, and normal canine urine sediment and queried using the nCounter Canine Immuno-Oncology Panel. Differential gene expression profiles were characterized for tissue and urine samples, and nCounter results were compared to bulk RNA-seq gene expression profiles. The effect of spiking normal urine with WBCs from the same dog was also assessed.

first: Ellen

last: Kuerbitz

first: Deepika

last: Dhawan

first: Mario

last: Sola

first: Alexander

middle: W

last: Enstrom

first: Lindsey

last: Fourez

first: Deborah

last: Knapp


title: NF-κB activation in astrocytes critically affects wound regeneration after traumatic brain injury

summary:
Traumatic brain injury (TBI) is a complex condition in which multiple pathophysiological mechanisms influence the course of the disease. After the primary mechanical impact, neuroinflammatory reactions of glial cells along with infiltrating peripheral immune cells mainly determine the overall clinical outcome. However, these secondary processes and their molecular determinants promoting either beneficial or detrimental consequences are not well-defined. Here, we show that TBI-mediated NF-κB activation in astrocytes impairs their homeostatic functions and acts as a key regulator of multiple post-traumatic responses in mice. We determined striking deficits in CNS scar formation after TBI using a combination of NF-κB-reporter mice, conditional mouse models allowing astrocytic NF-κB modulation, and analysis of transcriptomic signatures. Importantly, the development of wound healing deficits depends on paracrine signaling of NF-κB-activated astrocytes and cross-responsive microglial cells.
Our findings identify astrocytic NF-κB activation as a critical pathological amplification factor interfering with the restoration of CNS integrity at wound lesion sites.

overall_design: To further analyzed the impact of astrocytic IKK/NF-kappaB modulation on the post-traumatic transcriptome using an IKK2 gain-of-function (GoF) and IKK2 loss-of-function (LoF) mouse model


title: Beta cell-derived cholecystokinin drives obesity-associated pancreatic adenocarcinoma development

first: Mandar

last: Muzumdar

overall_design: Male 16 week-old wild-type (WT) C57/B6 mice (Stock #000664) and male C57/B6 mice fed a 60% kcal fat diet (Research Diets 12492) for 10 weeks (Stock #380050) starting at 6 weeks of age were obtained from JAX. Islets were isolated, pooled for each group (n=4 mice per group), and dispersed into single cells for single-cell RNA sequencing.

first: Cathy

last: Garcia

first: Aarthi

last: Venkat

first: Daniel

last: McQuaid

first: Sherry

last: Agabiti

last: Tong

first: Boby

last: Mathew

first: Rebecca

last: Cardone

last: Starble

first: Christian

last: Ruiz

first: Christy

last: Zheng

first: Akin

last: Sogunro

first: Jeremy

last: Jacox

first: Ken

last: Loh

first: Richard

last: Kibbey

first: Smita

last: Krishnaswamy


title: Disruption of ARID1B recruitment to the nuclear pore complex as a new anticancer therapeutic strategy [RNA-seq]

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

summary: Triple-negative breast cancer (TNBC), a highly aggressive subtype, currently lacks potent targeted therapies. ARID1B, a key SWI/SNF chromatin remodeling complex subunit, is linked to high-grade malignancies and poorer prognosis, making it a potential biomarker and therapeutic target. However, its function and regulation remain unclear. Here, we found that uncontrolled accumulation of ARID1B and its nuclear import promoted oncogenesis and drug resistance. ARID1B negatively regulates ARID1A, impairing SWI/SNF-mediated tumor suppression and enhancing tumor survival. Using protein complex purification and mass spectrometry, we identified KPNA2-KPNB1-RANBP2 as a critical protein cascade that facilitates ARID1B nuclear import. Replacing R1518, H1519, and D1522 residues on ARID1B with T1518, G1519, and G1522 attenuated the ARID1B-KPNA2 interaction, preventing recruitment of ARID1B to the nuclear pore complex. Pharmacological inhibition of KPNB1 suppressed ARID1B translocation, thereby limiting its nuclear levels. Our RNA-seq and ATAC-seq analyses indicated that KPNB1 inhibition also mimicked the effects of the SWI/SNF inhibitor on chromatin accessibility and gene expression, likely due to the reduced nuclear levels of ARID1B. In TNBC mouse models, ARID1B knockout significantly reduced tumor growth and enhanced PARP inhibitor efficacy. Collectively, our findings reveal that disrupting ARID1B nuclear translocation could be a new therapeutic strategy for TNBC.

overall_design: 1. To investigate the role of KPNB1 in breast cancer, we examined the effect of KPNB1 inhibition using importazole (IPZ) on chromatin accessibility and gene expression in MDA-MB-468 cellls. 2. To investigate whether KPNA2-KPNB1-RANBP2-mediated ARID1B nuclear translocation affects chromatin accessibility and gene expression through the SWI/SNF complex, we conducted RNA-seq and ATAC-seq analysis in MDA-MB-468 cells treated with BRM014 (BRMi). BRMi is a commonly used small-molecule inhibitor that selectively targets the BRG1/BRM ATPase activity of the SWI/SNF complex.

first: Olena

last: Odnokoz

first: Xiaodong

last: Lu

first: Jonathan

last: Zhao

first: Yong

last: Wan


title: Biomarkers that prospectively predict HIV-1 infection in high risk adults

city: Kilifi

first: Abdirahman

last: Abdi

state: Not US or Canada

address: Mombasa-Malindi Road

department: Bioscience

country: Kenya

institute: KEMRI-Wellcome Trust Research Programme

summary: We sequenced the RNA content of plasma-derived extracellular vesicles from a historical high risk HIV cohort at the Coast of Kenya. We found that an immunosuppresive transcriptional profile and the presence of Pegivirus C associate with HIV acquisition in this particular cohort.

overall_design: To determine circulating biomarkers that prospectively predict HIV-1 infection in high risk adults.

first: Kioko

last: Mwikali

first: Shaban

last: Mwangi

first: Eunice

last: Nduati


title: The PIDDosome controls cardiomyocyte polyploidization during postnatal heart development

city: Freiburg

first: Katharina

last: Moos

address: Breisacherstr. 153

department: Medical Faculty

institute: University of Freiburg

summary: The mammalian adult heart is a post-mitotic organ characterized by mainly polyploid cardiomyocytes (CMs). The post-mitotic status of polyploid adult CMs poses a clear limit to heart regeneration. Thus, understanding how polyploid CMs acquire this status is relevant to heart regeneration therapies. Here, we aim to unveil whether the PIDDosome, a multi-protein complex known to limit scheduled and accidental polyploidization events by activating p53, implements a CM-specific genetic program that controls CM polyploidization during heart development. Flow cytometric DNA content analysis coupled with image-based 3D volumetric measurements of CM nuclei showed that PIDDosome knockout animals harbor significantly more polyploid CMs compared to WT animals. This increased CM ploidy levels do not interfere with both cardiac structure and functional output in steady-state and is a cell-autonomous phenotype. During heart development, ploidy analyses revealed that the PIDDosome starts to shape CM ploidy status at postnatal day 7 (P7), reaching a plateau of its action at P14. Moreover, PIDDosome activation in CM is dependent on PIDD1 localization to the extra mother centrioles via the distal appendage protein ANKRD26. Interestingly, in opposite to prior observations the PIDDosome limits CM polyploidization in a p53-independent manner that still involves p21, as confirmed in genetic and nuclear RNAseq analysis. Together these results identify a new molecular machinery that controls proliferation of polyploid CMs postnatally, adding a set of new players that control the tightly regulated program of the terminal CM differentiation occurring in the postnatal heart.

overall_design: We performed bulk RNA-seq of both Casp2 deficient (XMLC2(+)Casp2(fl/fl)) and control (XMLC2(-)Casp2(fl/fl)) postnatal cardiomyocyte nuclei in mice. Cardiomyocytes were collected at postnatal days 1, 7 and 14. Four replicates were collected per postnatal day and genotype. To obtain sufficient RNA material, several hearts were pooled per replicate (P1: 15 hearts, P7: 6 hearts, P14: 2 hearts).

first: Marina

last: Leone

first: Nadine

last: Kinz

first: Felix

last: Eichin

first: David

last: Obwegs

first: Valentina

last: Sladky

first: Dario

last: Rizzotto

first: Claudia

last: Manzl

first: Etienne

last: Jacotot

first: Clarissa

last: Savko

first: Mark

last: Sussmann

first: Melanie

last: Boerries

first: Andreas

last: Villunger


title: Disruption of ARID1B recruitment to the nuclear pore complex as a new anticancer therapeutic strategy

first: Jindan

last: Yu

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: TAS1440, an LSD1 Inhibitor, Disrupts the INSM1-LSD1 Complex to Activate Tumor-Suppressive Pathways via Transcriptional Reprogramming in Neuroendocrine SCLC [ChIP-seq]

city: chiba

first: YINGBO

last: GONG

department: Medicine

country: Japan

institute: CHIBA University

summary: Small cell lung cancer (SCLC) is characterized by aggressive progression and limited treatment options, necessitating novel therapeutic strategies. Lysine-specific histone demethylase 1A (LSD1), a key epigenetic enzyme essential for maintaining the neuroendocrine phenotype, represses NOTCH and TGF-β signaling. Reactivation of these pathways suppresses proliferation and induces differentiation, underscoring LSD1's potential as a therapeutic target. However, the molecular mechanisms underlying LSD1 inhibition and chemoresistance drivers remain poorly understood. Here, through structure-based engineering, we developed TAS1440, a potent histone H3-competitive LSD1 inhibitor designed to enhance specificity and reduce off-target effects. Unlike covalent inhibitors, which bind irreversibly to the FAD cofactor in LSD1, TAS1440 non-covalently targets the histone H3-binding pocket, improving safety and efficacy. TAS1440 demonstrated superior anti-proliferative activity in SCLC-A cells with high INSM1 and ASCL1 expression. In xenograft models, TAS1440 achieved over 70% tumor growth inhibition with minimal toxicity, highlighting its potential for SCLC. Mechanistically, integrated studies revealed that TAS1440 exerts dual mechanisms: direct inhibition of LSD1 enzymatic activity and disruption of LSD1-repressive complexes, thereby altering the histone modification landscape and activating transcription factors such as INSM1 and SMAD2. These actions coordinately reprogram tumor-suppressive pathways, including TGF-β and NOTCH signaling, positioning TAS1440 as an effective epigenetic therapy for SCLC. Importantly, Loss of LSD1 enzymatic activity and INSM1 knockout abrogated TAS1440’s effects, elucidating its mechanism of action and uncovering potential resistance pathways. These findings establish TAS1440 as a next-generation LSD1 inhibitor with dual actions on transcriptional regulation and epigenetic reprogramming. TAS1440 holds significant promise as a targeted therapy for SCLC, particularly for the SCLC-A subtype with high INSM1 expression.

overall_design: To identify the transcription factors involved in LSD1 inhibitor-dependent changes in histone modifications, we performed ChIP-seq (H3K4me1, H3K4me2, H3K4me3 and H3K27ac) using the NCI-H1417 cell line.

first: Takumitsu

last: Machida

first: Yingbo

last: Gong

first: Sayaka

last: Tsukioka

first: Atsushi

last: Onodera

first: Akitoshi

last: Nakayama

first: Naoko

last: Hashimoto

first: Takahiro

last: Fuchigami

first: Satoshi

last: Yamashita

first: Tatsuya

last: Suzuki

first: Ryo

last: Hatanaka

first: Yasuo

last: Kodama

first: Shuichi

last: Ohkubo

first: Tomoaki

last: Tanaka


title: Paneth cell SIRT1 regulates intestinal tissue homeostasis

city: RTP

first: Xiaojiang

last: Xu

state: North Carolina

address: 111 T. W. Alexander Dr.,

institute: NIEHS

summary: Intestinal epithelial homeostasis is maintained by a complex interplay between different epithelial cells, gut microorganisms, and immune cells. Disruption of this interplay contributes to inflammatory and immune diseases associated with gut microbiome dysbiosis. A genetic factor that modulates the interactions between gut epithelium, microbiota and immune cells is sirtuin 1 (SIRT1), the most conserved mammalian NAD+-dependent protein deacetylase. We and others have shown that deficiency of intestinal epithelial SIRT1 leads to intestinal inflammation, disruption of gut microbial composition, and altered susceptibility to environmentally induced colitis. Recently we generated a Paneth-cell specific SIRT1 KO mouse model (SIRT1 PKO). Similar to mice with SIRT1 deficiency in whole intestinal epithelium, SIRT1 PKO mice had increased abundance as well as hyperactivation of Paneth cells in vivo and in cultured intestinal organoids. Single-cell RNA-seq of whole intestinal cell populations confirmed that deletion of Paneth cell SIRT1 significantly increases the abundance of Paneth cells. This increase was accompanied with an elevated abundance of intestinal stem cells, transition amplifying cells, and enterocytes. Consistently, SIRT1 PKO mice were able to better maintain their intestinal epithelial integrity during aging and were protected from chemically induced colitis compared to control mice. Deletion of SIRT1 in Paneth cells further induced profound alterations in gut microbiota. Using microbiota-depleted mice and fecal transplantation, we demonstrate that Paneth cell SIRT1 deficiency ameliorates colitis through the gut microbiota. Collectively, our findings uncover an unanticipated function of Paneth cell SIRT1 in conferring sensitivity of the gut epithelium to stress.

overall_design: The single cells from the small intestine of young mice were prepared as described above. The resulting single cell suspension from three pairs of young (2-3 months old) and 2 pairs of aged (12-14 months old) female mice was combined and stained for PI. Flow cytometry sorted live single cells were used for generating scRNA-seq libraries.

first: Alicia

last: Wellman

first: Xiaoling

last: Li


title: Oligodendrocyte precursor cell regulates microglial transition to neuroprotective phenotype by BMP4 driven acquisition of disease associated state in Alzheimer’s disease

city: Daegu

first: Jaemyung

last: Jang

address: 61, Cheomdan-ro, Dong-gu

country: South Korea

institute: Korea Brain Research Institute

summary: Alzheimer's disease (AD) is a progressive and irreversible neurodegenerative disorder characterized by cognitive decline and memory loss. Oligodendrocyte precursor cells (OPCs) reciprocally communicate with microglia in a context-dependent manner probably for immune surveillance, extending beyond their initial function as progenitor cells. In this study, we showed that late-OPC, also known as committed oligodendrocyte precursors (COPs), markedly upregulated expression of Bmp4 in response to Amyloid-β (Aβ). Selective Bone morphogenetic protein 4 (Bmp4) knock-out in OPCs of AD mouse model led to impairment of microglial clustering around Aβ plaque and Aβ phagocytosis, resulting in a substantial increase of Aβ deposition alongside dystrophic neurites. Mechanistically, Mothers against decapentaplegic homolog (Smad) signaling pathway, activated by Bmp4 derived from late-OPC, directly induced Triggering receptor expressed on myeloid cells 2 (Trem2) expression in microglia. This molecular cascade was required for robust acquisition of the disease-associated microglia (DAM) transcriptome, ultimately contributing to the development of neuroprotective DAM at early stage of amyloid deposition, prior to severe neuronal loss. Late-OPC sourced Bmp4 dependent appearance of DAM facilitated microglial barrier for Aβ plaque compaction, thereby insulating toxic Aβ species from adjacent neurites. Notably, intracerebroventricular administration of adeno-associated virus (AAV) carrying Bmp4 to AD mouse enhanced Trem2 expression of microglia around Aβ plaque, resulting in acceleration of plaque compaction. Consequently, this intervention alleviated synaptic damage and memory loss. Taken together, our findings strongly suggest that OPC-specific Bmp4 drives a molecular cascade to turn microglia into protective phenotype, providing a theoretical basis for a novel therapeutic strategy to target AD onset.

overall_design: To uncover how oligoednrocyte precurosor cells sourced Bmp4 is involved amyloid pathology, we performed Single-cell RNA sequencing (scRNA-seq) of cortex  from 5xFAD;PdgfraCreERT2;Bmp4+/+  and 5xFAD;PdgfraCreERT2;Bmp4-/-  mice.

first: Soonbong

last: Baek

first: Jong-Pil

last: Kim

first: Seungeun

last: Yeo

first: Hyun

middle: J

last: Jung

first: Youngshik

last: Choe


title: TFRC-RNA interactome revealed the expression and alternative splicing regulation of genes associated with IgAN in human renal tubule mesangial cells

city: Harbin

first: Jiansi

address: Xuefu Road No.246

country: China

institute: Harbin Medical University


title: TFRC-RNA interactome revealed the expression and alternative splicing regulation of genes associated with IgAN in human renal tubule mesangial cells [RIP-seq]

summary: IgA nephropathy (IgAN), characterized by the aberrant deposition of IgA immune complexes, is the most common primary glomerular disease (PGD) which progresses to renal failure. As a receptor of IgA and potential RNA binding protein (RBP), transferrin receptor1(TFRC) plays a key part in IgAN. However, the molecular mechanism of TFRC in the development of IgAN remains unclear. In the current study, TFRC was overexpressed in human renal tubular mesangial cells (HRMCs), followed by RNA-sequencing (RNA-seq) and improved RNA immunoprecipitation sequencing (iRIP-seq) to analyze and identify potential RNA targets at the transcription and alternative splicing (AS) levels regulated by TFRC. TFRC regulates the expression levels of genes positively associated with cell cycle and proliferation. The AS genes regulated by TFRC were enriched in mRNA splicing and DNA repair, consistent with the global AS profile changes by TFRC overexpression (TFRC-OE). Meanwhile, reverse transcription quantitative polymerase chain reaction (RT-qPCR) was conducted to validate TFRC-regulated genes potentially associated with IgAN, including CENPH, FOXM1, KIFC1, TOP2A, FABP4, ID1, KIF20A, ATF3, H19, IRF7, and H1-2 at the expression level and CYGB, MCM7, and HNRNPH1 at the AS level. In addition, iRIP-seq data were analyzed to identify TFRC-bound RNA targets. TFRC regulates the expression and AS levels of a subset of genes by binding to their transcripts, thus playing an important role in IgAN. We validated several TFRC-bound RNA targets with important functions in cell proliferation, including RCC1 and RPPH1. In conclusion, the molecular targets of TFRC were identified in HRMCs, and TFRC may play a key role in IgAN development by binding to RNAs or indirectly regulating genes’ transcriptomic levels, including the expression and AS, further extending the knowledge of the mechanism of TFRC as a clinical therapeutic target.

overall_design: We speculated that TFRC may regulate the signaling pathways in GMCs through binding to RNAs. Thus, we overexpressed TFRC in human renal mesangial cells (HRMCs) and performed RNA-sequencing (RNA-seq) and improved RIP sequencing (iRIP-seq) experiments to identify RNA targets and investigate the underlying regulatory mechanisms, further investigating TFRC’s novel functions in IgAN progression

first: Jian-Si

first: Xiao

last: Chen

first: Ailing

last: Luo

first: Dong


title: Projection-defined amygdala neurons encode emotional memory through distinct transcriptomic programs

status: Public on Jan 19 2026

city: Shanghai

first: Yang

last: Yang

address: 393 Middle Huaxia Road, Pudong, Shanghai

institute: ShanghaiTech University

summary: The amygdala is crucial for emotional memory, but the molecular programs that enable its distinct circuits to encode different memory features remain unclear. Combining single-cell RNA sequencing with retrograde tracing, we investigated transcriptomic dynamics of amygdala neurons projecting to nucleus accumbens (NAc) or auditory/temporal association cortex (AuC/TeA) during formation and long-term retention of fear and reward memories. We found that memory engages pathway-specific transcriptional programs of synaptic genes determined by valence, temporal stage, and projection target. Notably, the AMY→AuC/TeA pathway, previously considered a fear circuit, showed robust modulation during reward memory retention, and chemogenetic silencing confirmed its essential role in reward memory. Projection-defined neurons are transcriptionally and functionally heterogeneous: some subpopulations encode a single feature of emotional memory, such as an AMY→NAc subpopulation for reward memory formation and retention, and an AMY→AuC/TeA subpopulation for retention of fear and reward memories. Most subpopulations, however, encode multiple features via largely non-overlapping gene programs. We further identified Dcn as a selective marker for an AMY→NAc subpopulation preferentially recruited during fear memory formation. Our findings reveal a principle of projection-, valence-, and time-dependent transcriptional programming, demonstrate how subpopulations multiplex memory features via dynamic gene networks, and provide a comprehensive resource for dissecting amygdala function.

overall_design: We utilized stereotaxic viral injections to retrogradely label Amygdala (AMY) neurons projecting to the Nucleus Accumbens (AMY→NAc) and the Auditory Cortex/Temporal Association Cortex (AMY→AuC/TeA). Labeled mice were then trained using fear and reward conditioning paradigms (CS-US pairing), and the amygdala was dissected for scRNA-seq analysis at 2 hours or 5 days post-conditioning, representing the phases of memory formation and retention, respectively.  A control group was subjected only to the conditioned stimulus (CS, sound only, no US) and sampled 2 hours post-exposure.

first: Lu

last: Zhang

first: Dongling

last: Guo

first: Xiangjia

last: Zhu


title: Modeling Spastic Paraplegia 4 using Human Corticospinal Motor Neuron enriched Cortical Organoids Uncovers Genotype–Phenotype Distinctions and HDAC6-Targetable Pathology

city: Philadelphia

first: Liang

last: Qiang

state: PA

address: 2900 Queen Lane room183

institute: Drexel University

summary: Spastic Paraplegia 4 (SPG4), the most common form of Hereditary Spastic Paraplegia, causes progressive gait deficiency due to corticospinal tract degeneration. SPG4 results from mutations in the SPAST gene, which encodes spastin, a microtubule-severing AAA-ATPase. To dissect genotype–phenotype relationships, we generated isogenic human induced pluripotent stem cell lines carrying either a SPAST missense (SPASTWT/C448Y) or truncation (SPASTWT/S245X) mutation and differentiated them into motor cortical organoids. These models revealed mutation-specific patterns of aberrant neuronal activity, microtubule hypoacetylation and axonal degeneration. We identified mutant M1-spastin-induced hyperactivation of histone deacetylase 6 (HDAC6), a major tubulin deacetylase as the key pathogenic culprit. Pharmacological inhibition of HDAC6 with Tubastatin A restored microtubule acetylation and rescued axonal degeneration in organoids, with corresponding improvements in corticospinal tract integrity and gait defects in SPG4 transgenic mice. Our study uncovers HDAC6 hyperactivation as a targetable mechanism for SPG4 and verifies human organoids as a platform for therapeutic discovery.

overall_design: The generated corticospinal motor neuron enriched cortical organoids were dissociated and processed using 10X genomics, 3' NEXT-GEM kit. The wild-type organoids sc-RNAseq data was used to identify the different cell-populations.

first: Neha

last: Mohan

first: Skandha

last: Ramakrishnan

first: Xiaohuan

last: Sun

first: Ying

first: Theresa

last: Connors

first: Victor

last: Chai

first: Emanuela

last: Piermarini

first: Peter

last: Baas

first: James

last: Cai

first: Mei

last: Liu


title: TAS1440, an LSD1 Inhibitor, Disrupts the INSM1-LSD1 Complex to Activate Tumor-Suppressive Pathways via Transcriptional Reprogramming in Neuroendocrine SCLC [RNA-seq]

first: YINGBO

last: GONG

overall_design:
To study the transcriptional signatures and the effects of the LSD1 inhibitors in SCLC cell lines, we sequenced the bulk RNA of the 22 SCLC cell lines under DMSO/LSD1 inhibitors treatment.
To elucidate whether the TAS1440-dependent dissociation of INSM1 from the LSD1 complex is crucial for inhibition of cell growth, we established NCI-H1417 and NCI-H146 cells lacking INSM1 using the CRISPR/Cas9 system. We then sequenced NCI-H1417 and NCI-H146 cells lacking INSM1 under DMSO/TAS1440 treatment.

first: Takumitsu

last: Machida

first: Yingbo

last: Gong

first: Sayaka

last: Tsukioka

first: Atsushi

last: Onodera

first: Akitoshi

last: Nakayama

first: Naoko

last: Hashimoto

first: Takahiro

last: Fuchigami

first: Satoshi

last: Yamashita

first: Tatsuya

last: Suzuki

first: Ryo

last: Hatanaka

first: Yasuo

last: Kodama

first: Shuichi

last: Ohkubo

first: Tomoaki

last: Tanaka


title: IL11 organizes a macrotrabecular structure with immune evasion in aggressive hepatocellular carcinoma

city: Bunkyo-ku

first: Shu

last: Shimada

state: Tokyo

address: 1-5-45 Yushima

department: Department of Molecular Oncology

institute: Tokyo Medical and Dental University

summary: BACKGROUND & AIMS: Molecular characteristics and tumor microenvironment of aggressive hepatocellular carcinoma (HCC) remains uncertain, and therapeutic strategies effective for aggressive HCC have not been determined. We have established a syngeneic mouse model of aggressive HCC to elucidate therapeutic targets. METHODS: A mouse HCC model was generated from 3H3, a hepatoma cell line of C57BL/6 mouse origin, following Trp53 knockout and MYC overexpression (3H3PM), which are major genetic alterations in aggressive human HCC. Immunohistochemical analysis of 104 human HCC tissues was performed for validation. RESULTS: The 3H3PM cells demonstrated abnormal cell cycle regulation, and exhibited highly tumorigenic and metastatic phenotypes in immunocompetent C57BL/6 mice. The histological features of the grafted tumors were similar to those of aggressive human HCC; a predominant macrotrabecular pattern and a distinctive structure of cell clusters surrounded by endothelial cells, namely macrotrabecular-massive (MTM) HCC and vessels encapsulating tumor clusters (VETC), as well as T cell depletion. Gene expression analysis indicated that interleukin-11 (IL11) was specifically upregulated in aggressive mouse and human HCC, and Il11 knockout (Il11-KO) disrupted the MTM/VETC structure and recruited T cells in the 3H3PM tumors. Treatment with anti-PD-1 antibody successfully eliminated tumors of the Il11-KO 3H3PM cells, but not the 3H3PM cells alone. CONCLUSION: We created a syngeneic mouse model recapitulating aggressive human HCC with the MTM/VETC structure and the immune-suppressive microenvironment by Trp53 knockout and MYC overexpression. IL11 contributed to MTM/VETC formation and T cell exclusion in the aggressive HCC phenotype, and the combination of IL11 inhibition and immune checkpoint blockade may act in synergy to promote anti-tumor effects in aggressive HCC.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the 3H3P cells and the 3H3PM subclones.


title: RecQ dysfunction contributes to social and depressive-like behavior and aldolase activity changes in mice [Metabolic]

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary:
The RecQ helicase family plays a vital role in maintaining genome stability, including DNA replication, recombination, and DNA repair. In human cells, there are five RecQ helicases: RECQL1, Bloom syndrome (BLM), Werner syndrome (WRN), RECQL4, and RECQL5. Dysfunction or absence of RecQ proteins is associated with genetic disorders, tumorigenesis, premature aging, and neurodegeneration. The biological importance of RecQ helicases is well established; However, it is still unknown the potential outcomes after DNA damage, and there is no systematic study yet to compare the behavioral changes amongst various RecQ-deficient mice. In this study, we investigated the effects of IR treatment on three RecQ-deficient mouse models (Recql1, Wrn and Recql4). Here we provided evidence that RecQ dysfunction impaired social ability and induced depressive-like behavior in mice, with or without irradiation stress, while abnormal cognitive behaviors only existed in RecQ-deficient mice without IR treatment, suggesting RecQ proteins contribute to mood and cognition. Furthermore, transcripts and metabolomics analysis revealed significant alterations in the RecQ-deficient mice, especially after IR treatment. Particularly, pathways related to neuronal and microglia functions, DNA damage repair, cell cycle, and reactive oxygen response were downregulated in the RecQ4 and Wrn mice. In addition, increased DNA damage responses were found in RecQ-deficient mice. Notably, two genes, Aldolase Fructose-Bisphosphate B (Aldob) and NADPH Oxidase 4 (Nox4), were differentially expressed in RecQ-deficient mice. Our finding suggested that RecQ dysfunction contributes to social and depressive-like behaviors in mice, and that aldolase activity may be associated with these changes, representing it as a potential therapeutic intervention.
To understand what metabolism-related gene expression changes are induced by γ-irradiation in the WT,  RecQ1, WRN, RecQ4 deficient mice. They were exposed the whole body with γ-irradiation (IR, 6 Gy), thereafter prefrontal cortex tissues were collected from each mouse and subjected to RNA isolation.

overall_design: We analyzed a total of 33 samples of mouse prefrontal cortex either exposed with γ-irradiation (IR) or not as follows: WT_vehicle (n=4), RecQ4_vehicle (n=4),  WRN_vehicle (n=3), RecQ1_vehicle (n=4), WT_IR (n=5), RecQ4_IR (n=5), WRN_IR (n=3), and RecQ1_IR (n=5). Analysis employed nCounter Advanced Analysis suite of tools.

first: Vilhelm

last: Bohr


title: RECQL dysfunction contributes to social and depressive-like behavior and aldolase activity changes in mice [Neuroinflammation]

summary:
The RecQ helicase family plays a vital role in maintaining genome stability, including DNA replication, recombination, and DNA repair. In human cells, there are five RecQ helicases: RECQL1, Bloom syndrome (BLM), Werner syndrome (WRN), RECQL4, and RECQL5. Dysfunction or absence of RecQ proteins is associated with genetic disorders, tumorigenesis, premature aging, and neurodegeneration. The biological importance of RecQ helicases is well established; However, it is still unknown the potential outcomes after DNA damage, and there is no systematic study yet to compare the behavioral changes amongst various RecQ-deficient mice. In this study, we investigated the effects of IR treatment on three RecQ-deficient mouse models (Recql1, Wrn and Recql4). Here we provided evidence that RecQ dysfunction impaired social ability and induced depressive-like behavior in mice, with or without irradiation stress, while abnormal cognitive behaviors only existed in RecQ-deficient mice without IR treatment, suggesting RecQ proteins contribute to mood and cognition. Furthermore, transcripts and metabolomics analysis revealed significant alterations in the RecQ-deficient mice, especially after IR treatment. Particularly, pathways related to neuronal and microglia functions, DNA damage repair, cell cycle, and reactive oxygen response were downregulated in the RecQ4 and Wrn mice. In addition, increased DNA damage responses were found in RecQ-deficient mice. Notably, two genes, Aldolase Fructose-Bisphosphate B (Aldob) and NADPH Oxidase 4 (Nox4), were differentially expressed in RecQ-deficient mice. Our finding suggested that RecQ dysfunction contributes to social and depressive-like behaviors in mice, and that aldolase activity may be associated with these changes, representing it as a potential therapeutic intervention.
To understand what Neuroinflammation-related gene expression changes are induced by γ-irradiation in the WT,  RecQ1, WRN, RecQ4 deficient mice. They were exposed the whole body with γ-irradiation (IR, 6 Gy), thereafter prefrontal cortex tissues were collected from each mouse and subjected to RNA isolation.


title: TFRC-RNA interactome revealed the expression and alternative splicing regulation of genes associated with IgAN in human renal tubule mesangial cells [RNA-seq]

first: Jiansi

last: Li

first: Jian-Si

first: Xiao

last: Chen

first: Ailing

last: Luo

first: Dong


title: NAT10 Promotes Tubular Epithelial Cell Senescence in Cisplatin-Induced Acute Kidney Injury by Regulating DDX17

city: Wuhan

first: Yuting

last: Zhu

state: Hubei

address: 1277 Jiefang Avenue

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: Acute kidney injury (AKI) is a severe clinical syndrome with high morbidity and mortality, yet its pathogenesis remains incompletely understood, and effective therapeutic strategies are still lacking. In this study, we observed significant upregulation of N-acetyltransferase 10 (NAT10) in the tubular epithelial cells of Cisplatin-induced AKI. Lentivirus-mediated knockdown of NAT10 or treatment with NAT10 inhibitor Remodelin, ameliorated Cisplatin-induced renal dysfunction and tubular injury. Importantly, NAT10 inhibition markedly attenuated cellular senescence in Cisplatin-induced AKI, as evidenced by reduced senescence-associated β-galactosidase (SA-β-gal) activity, downregulation of senescence markers (p53, p21, and γ-H2A.X), and decreased levels of senescence-associated secretory phenotype (SASP) factors (IL-1β, IL-6, and TNF-α). Mechanistically, co-immunoprecipitation assay suggested that NAT10 interacted with DDX17 to regulate its expression. Knockdown or inhibition of NAT10 reduced the protein expression of DDX17 in Cisplatin-injured kidneys. While silencing DDX17 could inhibit Cisplatin-induced senescence in HK-2 cells. Furthermore, we demonstrated that the effects of NAT10 on Cisplatin-induced tubular injury and senescence was dependent on DDX17. Our study revealed a novel mechanism by which NAT10 promoted Cisplatin-induced renal tubular cell senescence via DDX17 upregulation, suggesting that targeting the NAT10/DDX17 signaling axis may offer a potential therapeutic strategy for AKI.

overall_design: Cisplatin-induced HK-2 cells transfected with either negative control siRNA or NAT10 siRNA

first: Chun

last: Zhang


title: Outer membrane vesicles of carbapenem-resistant Acinetobacter baumannii derive enhanced inflammatory response

city: Suzhou

first: Yang

last: Yang

address: NO. 899, Pinghai Road

institute: the First Affiliated Hospital of Soochow University

summary: Carbapenem-resistant Acinetobacter baumannii (CRAB) is a critical nosocomial pathogen with limited treatment options. Although antibiotic resistance in CRAB is well-characterized, its interactions with host immunity and the contribution of outer membrane vesicles (OMVs) to pathogenesis remain poorly understood. We examined a clinical CRAB isolate and compared it with the reference strain A19606. Antimicrobial susceptibility testing revealed complete resistance of CRAB to commonly used antibiotics in clinical practice, while A19606 remained susceptible to most agents. In murine intranasal infection models and bone marrow-derived macrophages, CRAB induced significantly stronger activation of inflammatory signaling pathways and elevated levels of pro-inflammatory cytokines relative to A19606. Transcriptomic analysis of infected lung tissue identified differentially expressed genes, enriched for inflammatory response pathways. proteomics showed upregulated proteins in CRAB related to secretion systems. OMVs characterization revealed that CRAB-derived OMVs highly enriched in proteins associated with periplasmic and outer membrane spaces, and more potent in triggering macrophage inflammatory signaling. CRAB displays expansive antibiotic resistance and enhanced pro-inflammatory potential mediated in part by unique OMVs properties. Targeting OMVs formation or host immune modulation may represent effective strategies for combating CRAB infections.

overall_design: Mice were uninfected with 1 × 107 CFU of CRAB or A19606 for 6 h (n = 3), lungs were harvested and prepared for RNA-sequencing.

first: Nana

last: Tang

first: Yuanyuan

last: Zeng

first: Jianjie

first: Jiajia

last: Wang

first: Zeyi

last: Liu

first: Jian-an

last: Huang


title: MYC modulates TOP2A diffusion to promote substrate detection and activity.

city: Solna

first: Vladislav

last: Kuzin

state: Stockholm

address: Solnavägen 9

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Institute


title: A dorsal hippocampus-prodynorphinergic dorsolateral septum-to-lateral hypothalamus circuit mediates contextual gating of feeding

city: Cambridge

first: Mukund

last: Raj

state: Massachusetts

address: 415 Main St

institute: Broad Institute of MIT and Harvard

summary: Contextual encoding in the dorsal hippocampus (DHPC) may recruit hypothalamic feeding modules to calibrate eating across environments, but mechanistic instantiation of cells and circuits that undergird these processes is limited. Single-cell transcriptomics and transsynaptic tracing of the dorsolateral septum (DLS) identified an evolutionarily conserved Prodynorphin (Pdyn)-expressing subpopulation of Somatostatin (Sst)-expressing inhibitory neurons that receives dense dorsal, but not ventral, hippocampal inputs. Circuit optogenetics, electrophysiology, and in vivo calcium imaging demonstrated that DLS(Pdyn) neurons inhibit GABAergic neurons of the lateral hypothalamic area (LHA), exhibit context-dependent neural responses to food rewards and aversive stimuli, and confer contextual and internal state-dependent calibration of feeding. Viral deletion of Pdyn in the DLS impaired context-dependent food reward consumption, suggesting a role for Dynorphin/Kappa opioid receptor signaling in these processes. Together, our findings highlight how ancient LHA feeding circuits integrate DHPC input through DLS(Pdyn) inhibitory neurons to link context with regulation of food consumption.

overall_design: Lateral septum tissue was collected from adult male C57BL/6J littermates and single-nucleus RNA sequencing was performed using the 10X Genomics (v.3) kit and using NextSeq or NovaSeq4000 (Illumina).

first: Travis

last: Goode

first: Mollie

middle: X

last: Bernstein

first: Michael

last: Totty

first: Jason

last: Alipio

first: Cinzia

last: Vicidomini

first: Devesh

last: Pathak

first: Antoine

last: Besnard

first: Delara

last: Chizari

first: Nina

last: Sachdev

last: Kritzer

first: Ain

last: Chung

first: Xin

last: Duan

first: Evan

last: Macosko

first: Stephanie

last: Hicks

first: Larry

last: Zweifel

first: Amar

last: Sahay


title: Propranolol overcomes vemurafenib resistance in melanoma by upregulating CDK11 and inducing cell cycle arrest

city: Changsha

first: Yijing

last: He

address: Xiangya road

institute: Central South University

summary: Acquired resistance to the BRAF inhibitor vemurafenib remains a major obstacle in melanoma therapy. Drug repurposing offers a promising strategy to overcome such resistance. Here, we investigated the β-blocker propranolol as a sensitizer to vemurafenib in resistant melanoma. Using vemurafenib-resistant cell lines (A375-VR and patient-derived P-8-VR), we found that propranolol restored vemurafenib sensitivity both in vitro and in vivo. RNA sequencing revealed that propranolol significantly upregulated CDK11A and CDK11B. Functional studies demonstrated that knockdown of CDK11 attenuated the pro-apoptotic and cell cycle arrest effects of propranolol and vemurafenib. Mechanistically, propranolol induced G1/S phase arrest and apoptosis without affecting MAPK or AKT pathway reactivation. In a xenograft model, the combination of propranolol and vemurafenib significantly suppressed tumor growth and improved survival. Our study identifies CDK11 upregulation as a novel mechanism by which propranolol reverses vemurafenib resistance, supporting the clinical potential of this drug combination in resistant melanoma.

overall_design: Libraries were prepared with the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) and sequenced on an Illumina HiSeq 2000 platform (paired-end 150 bp). Raw reads were aligned to the human reference genome (GRCh37/hg19) using TopHat (v1.3.3).


title: MOLECULAR SIGNATURE OF IN UTERO HYPERTHERMIA ON THE MAMMARY FAT PAD OF NEWBORN HEIFERS

city: Madison

first: Jimena

last: Laporta

state: Wisconsin

address: 1675 Observatory Dr Madison

department: Department of Dairy Science

institute: University of Wisconsin Madison

summary: This study investigated the effects of in utero heat stress on the microstructure and transcriptomic profile of the mammary fat pad in Holstein heifers at birth. Calves were gestated under either heat stress (iuHS; n = 6) or cooling conditions (iuCL; n = 6) during the last 54 ±5 days of gestation in a subtropical summer. At birth, mFP samples were collected for histologic and transcriptomic analysis. Compared to iuCL heifers, iuHS calves exhibited a higher number of small adipocytes and fewer large adipocytes in their mammary fat pads. Transcriptomic analysis revealed 122 differentially expressed genes (FDR < 0.01, |Log₂FC| ≥ 1.5) in iuHS mFP, including 40 upregulated and 82 downregulated. Downregulated genes were involved in fatty acid synthesis, adipocyte hypertrophy, metabolic regulation, and adipogenesis suppression (ACACA, ALMS1, PPARGC1A, SMAD2); while upregulated genes were associated with thermogenesis and cAMP/PKA signaling (GNB1, AKAP14, PRKACA), lipogenesis (PLD2), extracellular matrix remodeling (THBS4), and insulin resistance/adipocyte remodeling (FOXO6, ARVCF, LIMK2). Functional enrichment predicted activation of pathways related to cell death, inflammation, and oxidative stress, and inhibition of prolactin and gap junction signaling, and several key intracellular cascades (e.g., PI3K/AKT, MAPK, STAT3, ILK, ERK5). Nuclear receptors (ESR1), transcription factors (FOXO1, ATF4, HMG), and growth factors (EGF, BMP4) were predicted to be inactivated in iuHS mFP, indicating a coordinated suppression of cell differentiation, lipid metabolism, hormone/nutrient sensing, and stress adaptation.

overall_design: RNA sequencing of uterus under heat stress on the  transcriptomic profile of the mammary fat pad Holstein heifers at birth. Calves were gestated under either heat stress (iuHS; n = 6) or cooling conditions (iuCL; n = 6) during the last 54 ± 5 days of gestation in a subtropical summer.

first: Maverick

last: Guenther

first: Bethany

last: Dado-Senn

first: Madison

middle: N

last: Myers

first: Jayasimha

middle: R

last: Daddam

first: G

last: Andres Contreras

first: Zhou

last: Zheng

first: Geoffrey

last: Dahl


title: Rapid production of precisely edited cattle and mice via a single AAV delivered miniature IscB#/ωRNA# [dataset 1]

city: Hohhot

first: Lei

last: Yang

state: Inner Mongolia Autonomous Region

address: 24 Zhaojun Rd.

department: State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock

institute: Inner Mongolia University

summary: Utilising adeno-associated virus (AAV) to deliver CRISPR/Cas has enhanced the generation of knock-out mice, but single-AAV delivery of Cas and homology-directed-repair (HDR) templates in livestock remains a challenge. Here, we introduce all-in-one AAV vectors containing shortened IscB#, the progenitor of Cas9, along with either miniature ωRNA#, or ωRNA# with a large HDR-template. Encouragingly, we efficiently generated knock-out and knock-in cattle and mice by infecting zygotes with AAV::IscB#/ωRNA#-HDR without costly micromanipulators.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: The novel strategy to generate genetically modified mice and ruminant cattle by transduction of engineered IscB and its ωRNA (termed IscB#-ωRNA#) components into pre-implantation embryos via co-culture with adeno-associated viruses (AAVs).


title: Codonopsis pilosula polysaccharides mitigates Brucella abortus outer membrane protein 19-induced uterine damage via macrophage adhesion and calcium signaling

first: xuxu

last: wang

address: Jinshan Campus, Inner Mongolia Medical University, Jinshan Economic and Technological Development Zone, Tumed Left Banner

department: School of Public Health

institute: Inner Mongolia Medical University

summary: Brucellosis is a zoonotic disease caused by the Brucella species. Its pathogenesis is closely linked to bacterial evasion of macrophage-mediated killing, induction of a pro-inflammatory cytokine storm, and immune-mediated pathological damage. Accumulating evidence indicates that Codonopsis pilosula polysaccharides (CPPS) inhibits inflammatory signaling, enhances macrophage phagocytosis, and exerts immunomodulatory effects across multiple organs. However, the therapeutic potential of CPPS against brucellosis remains largely unexplored.

overall_design:
This study aimed to explore the effects of CPPS on inflammatory response induced by Brucella outer membrane protein 19 (OMP19). In vivo, CPPS significantly alleviated tissue damage and HMGB1 expression in the mouse uterus induced by OMP19. In vitro, CPPS inhibited the SYK/FAK/AKT phosphorylation, PKC activation, and Wnt-1 signaling pathway transduction. Additionally, CPPS also modulated the cytokine profile, downregulating pro-inflammatory cytokines (TNF-α, IL-6) while increasing anti-inflammatory IL-10 levels. Furthermore, CPPS decreased the levels of paxillin and E-cadherin, and reduced the intracellular calcium ion (Ca²⁺) concentration. Collectively, these findings indicate that CPPS mitigates OMP19-triggered uterine damage by regulating macrophage adhesion and calcium-dependent signaling, highlighting its potential as a therapeutic agent against brucellosis.
Control: Untreated (mouse primary peritoneal macrophages)
CPPS+OMP: Stimulated with CPPS and OMP19 (mouse primary peritoneal macrophages)
OMP: Stimulated with OMP19 (mouse primary peritoneal macrophages)


title: Metabolic reprogramming regulates histone lactylation during zebrafish caudal fin regeneration

city: Lisobon

first: António

last: Jacinto

address: Campus de Campolide

country: Portugal

institute: NIMSB - NOVA Institute for Medical Systens Biology

summary: Tissue regeneration relies on precise molecular mechanisms controlling cell fate transitions, with cell metabolism emerging as a key regulator. Lactate-derived histone lactylation has recently been identified as an important epigenetic modification involved in the regulation of gene expression across various biological processes. In this study, we report an increase in global histone lactylation and H3K18Lac levels in the mesenchyme and osteoblasts of the zebrafish caudal fin, during the early stages of regeneration. Our findings demonstrate that this epigenetic modification is functionally regulated by increased lactate levels, while inhibition of glycolysis and lactate production significantly reduces histone lactylation. These results suggest that metabolic reprogramming, in response to caudal fin injury, regulates histone lactylation, potentially modulating gene expression essential for cell plasticity and proliferation. This study expands our understanding of how metabolic-epigenetic interactions influence regenerative processes, providing valuable insights for the development of novel therapeutic strategies to enhance tissue repair.

overall_design: RNA-seq profiling of zebrafish caudal fin regenerating tissue treated with Galloflavin or Vehicle (DMSO) and collected 24h after amputation.

first: Jorge

last: Borbinha

first: Raquel

last: Lourenço

first: Ana

last: Brandão

first: Daniel

last: Ribeiro

last: Carvalho

first: Rune

last: Matthiesen


title: A beneficial environment promotes immune resilience through epigenetic regulation

city: München

first: Thomas

middle: M

last: Conlon

address: Ingolstädter Landstraße 1

institute: Helmholtz Zentrum München

summary: Environmental factors are often detrimental; however, certain environments enhance immune resilience. Notably, children raised on traditional farms show reduced allergies and asthma prevalence. Here, we investigated how a beneficial environment, using farm dust (FD) extract, influenced lung immune function in OVA-induced allergic inflammation. FD-exposure reduced allergic lung inflammation and increased monocyte-derived macrophage (MDM) recruitment. scRNA-seq revealed that FD-exposed MDMs had altered gene expression, including dampened Ccl8 and MHCII expression, impairing eosinophil recruitment and antigen presentation. RNA-seq and ATAC-seq confirmed FD-induced epigenetic reprogramming ex-vivo, on bone marrow-derived macrophages. This modulation, seen in both human and murine cells, relied on HDAC activity sustained by PPARγ signaling. These findings suggest that beneficial environmental exposures can reprogram immune cells and may offer a novel strategy for asthma prevention.

overall_design: ATAC-seq profiling of mouse BMDM and BMDC treated with 100 µg/ml FD or PBS twice over a 24-hour period then incubated with 10 ng/ml LPS for 6 hours

first: Markus

last: Klotz

first: Guilherme

last: Dragunas

first: Sirui

last: Chen

first: Deepesh

last: Dhakad

first: Ali

last: Önder Yildirim


title: Methylation-based cellular deconvolution of triple-negative breast cancer DNA reveals prognostic immune signature

city: Sydney

first: Sarah

last: Williams

state: NSW

address: 384 Victoria St, Darlinghurst

country: Australia

institute: The Garvan Institute of Medical Research

type: Methylation profiling by genome tiling array

summary: In triple negative breast cancer (TNBC), immune infiltration is now recognised as playing an important role in prognosis. DNA methylation, due to its cell-type specificity, offers a promising approach for quantifying immune cell abundance as a biomarker for risk stratification. Here, we used EpiDISH, a DNA methylation-based cellular deconvolution method, to estimate immune cell proportions from genome-wide methylation data across three independent cohorts, including TNBC patients. We show that increased immune cell percentage in TNBC patients specifically, was associated with longer disease-specific survival, highlighting the potential of DNA methylation-based estimates of cell composition for prognosis in TNBC.

overall_design: TNBC samples were obtained as FFPET blocks from archives of Hunter Area Pathology Service, John Hunter Hospital, Newcastle, Australia, University of Queensland and Garvan Institute of Medical Research

first: Ruth

last: Pidsley

first: Clare

last: Stirzaker


title: Haploinsufficiency of MBD5 and MBD6 impairs mitochondrial respiration through chromatin-mediated gene regulation [MBD6]

city: Kanazawa

first: Shin-ichi

last: Horike

state: Ishikawa

address: 13-1 Takaramachi

department: Research Center for Experimental Modeling of Human Disease

institute: Kanazawa University

summary: Autism spectrum disorder (ASD) is a highly heritable neurodevelopmental disorder, yet the molecular mechanisms linking ASD-associated genes to cellular dysfunction remain incompletely understood. Among methyl-CpG binding domain (MBD) proteins, MBD5 and MBD6 are recurrently disrupted in individuals with ASD, but their functional roles in neuronal cells are poorly defined. Here, we investigated the consequences of MBD5 and MBD6 haploinsufficiency using human neuroblastoma SH-SY5Y cells.  We established MBD5- and MBD6-heterozygous SH-SY5Y cell lines by genome editing and performed genome-wide transcriptome analysis. Microarray profiling revealed widespread transcriptional dysregulation, with predominant gene upregulation, suggesting that both proteins function mainly as transcriptional repressors. Notably, a shared subset of downregulated genes included multiple mitochondrial-related genes, such as COX17, COX4I2, DHRS2, MCUB, and PDK1. Quantitative real-time PCR validated these expression changes. Analysis of public ChIP-seq datasets further demonstrated co-localization of MBD5, MBD6, and components of the BAP1 complex at the COX17 promoter, suggesting direct regulation through a chromatin-associated mechanism.  Functionally, MBD5 and MBD6 haploinsufficiency impaired mitochondrial respiration, as evidenced by reduced basal and ATP-linked oxygen consumption rates without changes in mitochondrial content. Consistently, heterozygous cells showed severe growth defects under galactose conditions and a compensatory shift toward glycolytic metabolism.  Together, these findings identify a previously unrecognized chromatin–mitochondria regulatory axis linking MBD5 and MBD6 haploinsufficiency to mitochondrial dysfunction, providing mechanistic insight into ASD pathogenesis.

overall_design: Comaprison between control SH-SY5Y cells and MBD6-heterozygous SH-SY5Y cells. There are two biological replicates for each conditions.

first: Makiko

last: Meguro-Horike

first: Keiko

last: Iwata

first: Hideo

last: Matsuzaki


title: CGRP signaling Links Tumor-Associated Pain to Immune Evasion in Oral Squamous Cell Carcinoma

city: Kingston

first: Sebastien

last: Talbot

state: ON

address: 18 Stuart st

department: DBMS

institute: Queen's University

summary: Peripheral sensory nerves are thought to contribute to solid tumor growth, particularly in oral squamous cell carcinoma (OSCC); however, the link between pain and immunosuppression remains unresolved. Here, using a prospective observational study, we demonstrate an inverse relationship between OSCC-induced pain mediated by calcitonin gene-related peptide (CGRP)-expressing nerves and tumor-associated immunity. Bulk RNA sequencing of tumor-innervating sensory neurons from mice revealed differential regulation of genes associated with excitability, neurotransmission, and axonal sprouting. Using a gain-of-function approach with persistent stimulation of peptidergic afferents, we show that sensory neurons promote oral tongue tumor growth and limit the activation of effective anti-tumor immune responses via efferent CGRP release. Conversely, loss-of-function approaches—including local ablation of nociceptive nerves and systemic CGRP receptor antagonism—slowed tumor growth and improved anti-tumor immunity. Targeting CGRP may therefore represent a therapeutic strategy in OSCC to reduce pain and improve treatment response.

overall_design: Retrogradely labeled trigeminal ganglion (TG) neurons were isolated from sham and tumor-bearing mice by fluorescence-activated cell sorting. Briefly, bilateral TGs were harvested, dissociated, and cell viability was assessed by microscopy. DiI⁺ neurons were sorted directly into 500 µL TRIzol reagent and stored at −80 °C until RNA extraction. Gating was established using TG neurons from naïve mice and DiI-injected sham controls.  Bulk RNA sequencing was performed to compare gene expression between MOC1 tumor-bearing and sham control mice (n = 11 total; 6 MOC1 and 5 sham). RNA extraction, library preparation, and sequencing were carried out at the IRIC Genomics Platform (Université de Montréal). RNA integrity was verified using an Agilent Bioanalyzer. Poly(A)⁺ RNA was enriched from total RNA, and libraries were prepared using the KAPA RNA HyperPrep Kit with poly(A) selection according to the manufacturer’s instructions. Libraries were sequenced on an Illumina NextSeq 500 to generate single-end reads over 75 sequencing cycles (maximum read length 1 × 85 nt).  Reads were trimmed with Trimmomatic v0.35 and aligned to the mouse reference genome GRCm38 (mm10) using STAR v2.7.1a with strand-specific parameters. Gene-level quantification was performed using STAR and RSEM.  Differential expression analysis was conducted in R using DESeq2, with significance determined using Benjamini–Hochberg adjusted p-values (padj < 0.05). Significant genes were annotated with gene symbols and exported for downstream analyses. Data visualization included volcano plots (ggplot2, ggrepel) and heatmaps of z-score–normalized expression for significant genes, with rows annotated by −log10(padj) and columns labeled by condition. Expression of selected genes (e.g., Trpv1, Calca, and Ngfr) was compared between groups using box plots; statistical testing used Wilcoxon rank-sum tests with Benjamini–Hochberg correction. Principal component analysis (PCA) was performed on rlog-transformed counts to assess sample clustering and overall variance, and visualized using ggplot2 and plotly. All analyses were performed in R to support reproducibility.

first: Amin Reza

last: Nikpoor

first: Maryam

last: Ahmadi

first: Nicole

last: Scheff


title: RNA-seq profiling of ADAM10 inhibition in DLD-1 and SW620 colorectal cancer cell lines

city: Brooklyn

first: Pargol

last: Mashati

state: New York

address: 2100 Bedford ave, BSB 2-95

institute: SUNY Downstate

summary: This study examines the transcriptomic effects of ADAM10 inhibition in two human colorectal cancer cell lines, DLD-1 and SW620. Cells were treated with vehicle control or the conformation-specific ADAM10 monoclonal antibody 1H5 for 48 hours, followed by extraction of total RNA and paired-end RNA sequencing. The dataset enables comparative analysis of ADAM10-regulated pathways across different CRC genetic backgrounds, including alterations in Notch and EGFR signaling, metabolic gene programs, and other pathways associated with tumor progression.

overall_design: Total RNA was extracted from human colorectal cancer cell lines DLD-1 and SW620 following treatment with either vehicle control or the ADAM10-targeting monoclonal antibody 1H5 (40 μg/mL) for 48 hours. Cells were cultured under standard conditions, and RNA isolation was performed using a column-based extraction method. RNA-seq was conducted to characterize global transcriptional changes induced by ADAM10 inhibition across two colorectal cancer genetic backgrounds and to identify regulated pathways related to Notch signaling, EGFR signaling, and cancer metabolism.


title: A beneficial environment promotes immune resilience through epigenetic regulation [scRNA-seq]

first: Thomas

last: Conlon

overall_design: Farm dust (FD) was collected from 9 traditional European cow farms (EUC) in Southern Germany and Austria that did not house sheep. Dust was collected from stables by sweeping settled dust from ledges, windowsills, and other, higher shelves (at least 1 m above ground) to obtain dry airborne dust. Animals were sensitized to ovalbumin (OVA) on days 0, 7, and 14 by intraperitoneal injection of 10 μg OVA emulsified in 1.0 mg aluminum hydroxide  and diluted to 200 μL with PBS. Subsequently, mice were challenged on days 26, 27 and 28 with intranasal administration of 100ug OVA. FD administration was carried out via intranasal administration of 25 μL from a 100ug/ml stock solution of FD extract on days 0, 2, 5, 7, 9, 12, 14, 16, 19, 21, 23 and 26, for a total of 12 administrations. 24h after the last challenge wit OVA, mice were deeply anesthetized in MMF, exsanguinated via the hepatic artery, and one whole lung was processed for scRNAseq.

first: Theodoros

last: Kapellos

first: Yuexin

first: Herbert

last: Schiller

first: Zeynep

last: Ertrüz

first: Ali Önder

last: Yildirim


title: AtNUDT11 mediated dpCoA-RNA-seq defines epitranscriptomicdpCoA capped RNA

city: Beijing

first: Han

last: Wang

address: No.5 Yiheyuan Road

institute: Peking University

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Mithramycin Alters EWS::FLI1 DNA Binding and RNA Polymerase II Processivity to Inhibit Nascent Transcription

city: Ann Arbor

first: Patrick

last: Grohar

state: MI

address: 1600 Huron Pkwy

institute: University of Michigan Medical School

summary: Although many DNA binding natural products exert their effects through non-specific mechanisms, a therapeutic opportunity exists for a subset of these compounds that alter the expression or activity of specific driver oncogenes in specific cell contexts. In this study, we integrate CUT&Tag with Global Run-On Sequencing (CUT, Tag, and GRO) to show that the minor groove binding compound, mithramycin (MMA), inhibits the Ewing sarcoma oncogenic driver, the EWS::FLI1 transcription factor. MMA causes either an increase or decrease in EWS::FLI1 binding to chromatin at downstream target response elements to poison nascent transcription. The reversal of EWS::FLI1 activity is limited by non-specific effects of the drug on RNAPII processivity but can be optimized by continuous administration at low concentration to cause more precise reversal of the oncogenic transcriptome and striking Ewing sarcoma xenograft regressions. The activity in vivo is further improved with a less-toxic second-generation analog, AIT-102.

overall_design: GROseq data of nascent RNA immunoprecipitated using an anti-BrDU antibody following incubation with PBS solvent control or mithramycin at either 20 nmol/L for 72 hours or 100 nmol/L for 18 hours.

first: Rebecca

last: Kaufman


title: Hairy Vetch–Based Green Manure Improves Yield and Grain Appearance Quality in High-Yielding Japanese Rice Cultivars with Lodging Resistance Conferred by Functionally Weak GA20ox alleles

city: Tsukuba

first: Hirofunmi

last: Fukuda

state: Ibaraki

address: 1-31-1 Kannondai

institute: National Agriculture and Food Research Organization (NARO)

summary: Green manure is widely advocated as a sustainable alternative to chemical fertilizers in crop systems, yet the mechanisms underlying its yield benefits remain unclear. Moreover, vigorous vegetative growth under green manure can elevate lodging risk, undermining yield and harvest efficiency. Here, we describe mechanisms by which hairy vetch–based green manure enhances yield and evaluate the practical value of deploying functionally weak alleles of gibberellin 20-oxidase (GA20ox) in this management context. We conducted field comparisons of green manure and conventional chemical fertilization to evaluate effects on rice productivity, grain appearance quality, and canopy physiology. Green manure significantly increased grain yield and grain appearance quality in the leading Japanese cultivar ‘Koshihikari’, accompanied by higher lodging. By contrast, high-yielding cultivars homozygous for a single-copy GA20ox1 allele and/or a non-functional GA20ox2 allele maintained superior lodging resistance under green manure treatment while improving yield and grain appearance quality, indicating an effective combination of its treatment and genotypes. Physiologically, green manure increased chlorophyll index during vegetative growth and at the reproductive stage, and nitrogen (N) concentration on the whole plant. Furthermore, green manure increased flag-leaf width and tiller number; these canopy changes were associated with reduced panicle temperature at the ripening stage. Green manure treatment induced upregulation of OsNADH-GOGAT2, a known gene associated with increased N loading to grains, and more grain storage proteins, providing a positive link to improved grain appearance quality. Collectively, this study demonstrates that integrating hairy vetch with functionally weak GA20ox alleles can enhance productivity and grain appearance quality while mitigating lodging risk. This sheds light on the importance of aligning green-manure treatment with targeted allelic selection to stabilize performance across intensive-farming systems and reduce chemical fertilizer dependency.

overall_design: RNA-seq on the first fully expanded leaf (from the top) of ‘Koshihikari’ grown under chemical fertilizer or hairy vetch–based green manure, sampled at 47 days after transplanting (2023) and 38 days after transplanting (2024).

first: Hirofumi

first: Toshihiro

last: Sakamoto

first: Akari

first: Daisuke

last: Ogawa


title: Haploinsufficiency of MBD5 and MBD6 impairs mitochondrial respiration through chromatin-mediated gene regulation

first: Shin-ichi

last: Horike

overall_design: Comaprison between control SH-SY5Y cells and MBD5-heterozygous SH-SY5Y cells. There are two biological replicates for each conditions.

first: Makiko

last: Meguro-Horike

first: Keiko

last: Iwata

first: Hideo

last: Matsuzaki


title: TRMT6 mitigates susceptibility and progression of DSS-induced colitis multifacetedly via translational regulation

city: Hangzhou

first: Aiwei

last: Wu

state: Zhejiang

address: 2318 Yuhangtang Road

department: School of Basic Medical Sciences

institute: Hangzhou Normal University


title: TRMT6 mitigates susceptibility and progression of DSS-induced colitis multifacetedly via translational regulation [16S rRNA-seq]

summary: The intestinal epithelium, a self-renewing single-cell layer, acts as a physical barrier isolating gut microbiota from deeper tissues. In human IBD and experimental IBD mouse models, this barrier is compromised, causing microbial infiltration and inflammation. However, the pathogenesis of IBD remains to be fully understood. Our research shows that the absence of TRMT6 in the mouse gut impairs the intestinal mucosal barrier, increasing susceptibility to DSS-induced colitis. Mechanically, loss of TRMT6 in intestinal epithelial cells disrupts m¹A modification-mediated translational control and impairs MYC protein synthesis–a deficiency that inhibits epithelial cell proliferation and differentiation. Further multi-omics analyses suggest that TRMT6 deficiency may be associated with perturbations in intestinal lipid metabolism, nutrient absorption, metabolite homeostasis, and gut microbiota composition–changes that could collectively contribute to the acceleration of colitis progression. In summary, TRMT6 is crucial for maintaining small intestinal mucosal barrier function, offering insights into how its deficiency may drive gastrointestinal inflammation in IBD. Given the critical role of TRMT6 in maintaining intestinal homeostasis, our findings highlight its potential as a therapeutic target for IBD treatment.

overall_design: 16s rRNA gene sequencing of stool samples from WT (n=3) and Trmt6-/- (n=3) DSS-induced colitis mice to investigate the changes in gut microbiota (GM) composition.

first: Xianli

last: Zhang

first: Yanting

last: Du

first: Yuefang

last: Ye

first: Xueqing

last: Zhong

first: Chengsong

last: Cai

first: Guodong

last: Li

first: Hu

first: Liquan

last: Hong


title: A pivotal contribution of proteostasis failure and mitochondria dysfunction to Chromosomal Instability-induced microcephaly [2]

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

institute: IRB Barcelona

summary: Mosaic variegated aneuploidy (MVA), a rare human congenital disorder that causes microcephaly, is characterized by extensive abnormalities in chromosome number and caused by mutations in genes involved in accurate mitotic chromosome segregation. Here we generated a Drosophila model of microcephaly caused by depletion of a single spindle assembly checkpoint (SAC) gene in the neural stem cell (NSC) compartment to characterize the cellular mechanisms underlying this disease. We present evidence that loss of stemness of NSCs – compromised identity and proliferative capacity - is the underlying cause of the disease and results in a reduced number of neurons and glial cells. We show that loss of stemness is a consequence of the accumulation overtime of an unbalanced number of gains and losses of more than one chromosome, rather than a direct consequence of chromosomal instability-induced DNA damage or the production of simple aneuploidies. We unravel a contribution of proteostasis failure, most probably as a consequence of the imbalance in the whole protoeome, and mitochondria dysfunction to the negative impact of complex aneuploidies on stem cell identity. We identify autophagy activation -either directly or through TOR depletion –, overexpression of Radical Oxygen Species scavengers, or restoration of mitochondria proteostasis as genetic interventions capable of dampening the deleterious effects of aneuploidy on NSC identify and brain development

overall_design: The samples used for this study are late L3 larvae from Drosophila melanogaster. For the control, we have used C(1)DX/Y and C(2L)SH1 larvae, raised at 25ºC and dissected 5 days after egg laying (AEL). For the experimental condition, we have used C(1)DX/X and C(2L)SH1/+ larvae, respectively, raised at 25ºC and dissected 8 days AEL. 3 replicates from different days were performed and 3 brains were dissected per each genotype and per replicate. All the larvae used were females.

last: Stephan-Otto Attolini

first: Marco

last: Milan

first: Amanda

last: González


title: GLASS-OD primary – recurrent oligodendrogliomas

city: Rotterdam

first: Youri

last: Hoogstrate

address: Wytemaweg 80

department: Neurology

country: Netherlands

institute: Erasmus MC

summary: Background: Treatment decisions in IDH-mutant oligodendrogliomas are shaped by tumor aggressiveness, underscoring the need for objective grading of these malignant brain tumors. Material and Methods: We collect 302 primary and recurrent resections from oligodendrogliomas and perform Ki-67 staining, proteomics and DNA methylation profiling. Results & conclusion: During tumor progression, DNA methylation of oligodendrogliomas changes along a continuum. This continuum is linked to increased epigenetic aging, methylation of transcription factors and Ki-67+ cell density, and to large scale DNA demethylation. Demethylation correlates with CpGs flanking sequences preferred by TET enzymes. We confirm these findings in previously profiled astrocytomas, indicating IDH-mutant gliomas progress along a shared epigenetic axis. We develop an objective DNA methylation based prognostic continuous grading coefficient (CGCψ) that capturs these changes and outperformed WHO grading for oligodendrogliomas. Our findings underscore the potential of DNA methylation-based grading to more accurately reflect tumor biology and inform clinical decision-making in IDH-mutant gliomas.

overall_design:
Primary – Recurrent Oligodendroglioma pairs were collected as part of the GLASS-OD initiative. Validation set samples were not selected to be resected more than once.
The resection number is in the sample identifier: patient_id-R[surgery_number]
Sample identifiers ending with 2, 3, 4, or 5 (up to five brain surgeries...) are recurrent

first: Pim

last: French


title: Brief exposure to oral antibiotics has age-dependent effects on morphine reward and gene expression in the medial prefrontal cortex of adolescent and adult mice_2

city: Winston-Salem

first: Rebecca

last: Hofford

state: NC

address: 115 S Chestnut St

department: Translational Neuroscience

institute: Wake Forest School of Medicine

summary: Adolescence is a critical period for the initiation of problematic drug use, which significantly increases the risk of developing substance use disorders later in life. This heightened vulnerability is partly attributed to the immaturity of the prefrontal cortex, a brain region both essential for decision-making and implicated in drug reward. During adolescence, peripheral systems, such as the gut microbiome, also undergo substantial changes. Emerging evidence suggests that disruptions to the gut microbiome can influence gene expression and drug reward behaviors in rodent models. In this study, we investigated the effects of oral antibiotics on morphine reward and prefrontal cortical gene expression in adolescent and adult mice. Using oral antibiotics to transiently disrupt the microbiome, we found that short-term antibiotic exposure reduced morphine place preference specifically in adolescent mice. In a separate cohort, we observed that antibiotic treatment altered the transcriptomic response to morphine in the medial prefrontal cortex across all age groups. Notably, the transcriptomic changes induced by antibiotics and morphine were age-specific, with distinct gene expression patterns observed in adolescents compared to adults. These findings establish a foundation for future research into the role of the gut microbiome in opioid reward and highlight potential gene pathways underlying age-dependent differences in opioid sensitivity.

overall_design: Female C57BL/6J wild type mice adolescent (start PND 25) or adult (start PND 55) given oral antibiotics (Abx) or remained on water and were given injections (s.c.) of saline or morphine (15 mg/kg) for 5 days.

first: Jonathon

middle: P

last: Sens

first: Ava

last: Shipman

first: Violet

last: Kimble

first: Christina

last: Coric

first: Katherine

last: Meckel

first: Drew

last: Kiraly


title: Targeted citrullination enables p53 binding to non-canonical sites [ChIP-seq]

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: TP53 encodes for the transcription factor p53, which binds to a diverse set of target genes in response to stress.  Activation of p53 results in highly specific transcriptional responses, but the regulation of promoter selectivity by p53 is poorly understood.  Here we report that sequence-specific binding of p53 is regulated by its target gene and binding partner PADI4.  PADI4 enzymatically converts peptidyl-arginine to peptidyl-citrulline in a process known as citrullination.  We show p53 is citrullinated in vitro at the C-terminus by PADI4, and we confirm two citrullination events in vivo (R306, R363).  ChIP-seq reveals that PADI4 expression causes a redirection of p53 away from canonical binding sites to target genes associated with the ETS transcription factor and the interferon response.  Chromatin profiling using citrullination-specific p53 antibodies supports this conclusion.  These findings link citrullination to p53 function and illustrate how chromatin modifiers like PADI4 can redirect the p53 transcriptional response.

overall_design: Chromatin immunoprecipitation followed by DNA-sequencing (ChIP-seq) of H3K27ac and p53 in HCT116 cells transfected with a tetracycline-inducible system to induce PADI4 or it's catalytically dead mutant (D350A) expression. Cells were either treated with vehicle (untreated), nutlin, or the combination of nutlin and doxycyline for 24 hours.

first: Alexandra

last: Indeglia

first: Andrea

last: Valdespino

first: Giulia

last: Pantella

first: Sarah

last: Offley

first: Connor

last: Hill

first: Alessandro

last: Gardini

first: Maureen E.

last: Murphy


title: Evolutionarily divergent transcriptomic programs in ovarian folliculogenesis across mice, monkeys and humans

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

summary: Understanding the mechanisms for human ovarian folliculogenesis is fundamental to reproductive biology and medicine. Here, we investigated transcriptomic dynamics in individual oocytes and their associated granulosa cells (GCs) during folliculogenesis in mice, monkeys and humans. Unlike mouse oocytes, which exhibited stage-specific, stepwise transcriptomic maturation, monkey and human oocytes showed minimal transcriptomic changes until the secondary follicle stage and could be broadly categorized as either immature or mature. In all three species, most highly variable genes (HVGs) during oocyte growth displayed monotonic up- or downregulation, with limited overlap in HVGs across species. GCs exhibited similarly species-specific transcriptomic trajectories. Correspondingly, intercellular communication pathways, including ligand–receptor signaling, gap junctions, and metabolic coupling between oocytes and GCs, demonstrated substantial species-specific differences. Nonetheless, X-chromosome dosage compensation and repression of evolutionarily young transposons were conserved across species. We established in vitro culture systems supporting preantral to antral follicle development in monkeys and humans, revealing relatively normal oocyte transcriptome maturation but aberrant GC profiles. By delineating interspecies differences in folliculogenesis, this study provides a framework for understanding human ovarian development and advancing its in vitro reconstruction.

overall_design:
Expression profiling by high throughput sequencing
gene expression datasets for oocytes and granulosa cells

first: Baku

last: Nakakita

first: Ken

last: Mizuta

first: Yoshitaka

last: Katou

first: Hidetaka

last: Tasaki

first: Tomonori

last: Nakamura

first: Chizuru

last: Iwatani

first: Hideaki

last: Tsuchiya

first: Ikuo

last: Kawamoto

first: Tomoyuki

last: Tsukiyama

first: Xun

last: Chen

first: Guillaume

last: Bourque

first: Junko

last: Otsuki

first: Mikiya

last: Nakatsuka

first: Akihito

last: Horie

first: Masaki

last: Mandai

first: Mitinori

last: Saitou

first: Hiroshi

last: Ohta


title: TRMT6 mitigates susceptibility and progression of DSS-induced colitis multifacetedly via translational regulation [RNA-seq]

first: Aiwei

last: Wu

overall_design: RNA-seq of intestinal tissue of WT (n=3) and Trmt6-/- (n=3) DSS-induced colitis mice.

first: Xianli

last: Zhang

first: Yanting

last: Du

first: Yuefang

last: Ye

first: Xueqing

last: Zhong

first: Chengsong

last: Cai

first: Guodong

last: Li

first: Hu

last: Wang

first: Liquan

last: Hong


title: Bulk RNAseq of BMDM-T cells co-culture system with or without tumor antigen and IL-1beta or IL-18

city: Chengdu

first: Ziqi

state: Sichuan

address: No. 17, Block 3, Southern Renmin Road

department: National Clinical Research Center for Geriatrics,

institute: West China Hospital, Sichuan University

summary: To investigate the transcriptome changes of BMDM-T cell co-culture system, spleen lyphocytes were cultured with WT or Tmem175-/- BMDMs in 1640 supplied with FBS, m-CSF, and IL-2 for 48 hours. Tumor antigens, IL-1beta (500 pg/ml), or IL-18 (500 pg/ml) were added during the co-culture period. At the end of the culture, cells were harvested for RNA seq.

overall_design: Spleen lymphocytes from B16-F10-OVA tumor bearing mice were cultured with WT or Tmem175-/- BMDMs, which were used as control groups. The experiment groups were treated with B16-F10-OVA tumor cell antigen. For further interventions, IL-1beta (500 pg/ml), or IL-18 (500 pg/ml) were added during the co-culture period.

first: Lei

last: Chen


title: Midgut cell atlas of four important mosquito species and the key factors associated with DENV infection

city: Wuhan

first: Han

last: Xia

state: Hubei

department: Key Laboratory of pathogenic Viruses and Biosafety

institute: Wuhan Institute of Virology, CAS

summary: Mosquitoes serve as medically significant vectors for transmitting various arboviruses. The mosquito midgut is both the digestive organ and primary infection site via viral bloodmeals, and the midgut cells show heterogeneity on virus-vector interactions. Rapidly developed single-cell RNA sequencing (scRNA-seq) technologies allow to characterize midgut physiology and viral infection dynamics at cellular solution. At present, scRNA-seq studies about mosquito midgut cell atlas are still limited and lack established protocols for cellular isolation. Therefore, we developed and employed a compatible microwell-based scRNA-seq protocol on four important mosquito species including Aedes aegypti, Aedes albopictus, Culex pipiens pallens and Culex tritaeniorhynchus and successfully established their midgut cell atlases pre- and post-bloodmeal. Further, we performed scRNA-seq experiments on DENV-infected Ae. aegypti to characterize the viral infection dynamics at single-cell solution.

sample_organism:
Aedes aegypti
Aedes albopictus
Culex tritaeniorhynchus
Culex pipiens pallens

overall_design: To establish midgut cell atlas of four medically important mosquitoes including Aedes aegypti, Aedes albopictus, Culex pipiens pallens and Culex tritaeniorhynchus, we developed and applied a compatible microwell-based scRNA-seq protocol to the female mosquitoes. We performed scRNA-seq experiments on the midgut samples of the four mosquito species at 7 days with only glucose solution to establish their midgut cell atlas. To decipher the transcriptional changes following the uninfectious bloodmeal, we utilized scRNA-seq experiments on both Aedes aegypti and Culex tritaeniorhynchus, respectively. Further, to characterize the dynamics of mosquito midgut post-infection, we performed scRNA-seq experiments on the DENV-infected Aedes aegypti.