title: Transcriptomic analysis of channel catfish stomach response to Aeromonas hydrophila infection correlated to skin integrity and fed state

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

summary: This study investigates the immune responses in the stomach of channel catfish (Ictalurus punctatus) under different feeding statuses and physical stress (fin-clipping) after infection with Aeromonas hydrophila. Transcriptomic analysis revealed early activation of Toll-like receptor (TLR) signaling and pro-inflammatory pathways in the fed groups, which led to significant tissue damage as observed in histopathological evaluations. Unfed groups showed delayed immune responses with less tissue damage but higher levels of apoptosis, particularly in the fin-clipped group. Histopathological examination at 2 hours post-challenge (HPC) revealed minimal to moderate edema in the lamina propria and submucosa across all treatment groups. By 4 HPC, mild to moderate edema was noted, accompanied by lymphoplasmacytic and granulocytic infiltration. At 8 HPC, multifocal hemorrhage and erosions in the superficial epithelium, along with moderate to severe transmural edema, were observed. These histological findings, particularly in the fed fin-clipped group, reflect the correlation between immune overactivation and tissue damage leading to higher mortality.

overall_design:
To determine how feeding and fin-clipping affect the stomach immune response and tissue damage in channel catfish during infection.
The experimental design included four treatment groups, each with 25 fish per replicate (6 replicates per group, n=150), for a total of 600 experimental fish including control groups.
Treatment was either mock using only sterile media or with Aeromonas hydrophila bacterium. The treatment groups included (1) fish subjected to an immersion challenge without fin clipping and fed on the day of the challenge (2) fish subjected to an immersion challenge with fin clipping and fed on the day of the challenge (3) fish subjected to an oral gavage challenge and fed on the day of challenge and (4) fish subjected to an oral gavage challenge but not fed on the day of the challenge.
Fish were sampled at 2, 4, and 8 hours post-challenge. At each time point, 6 fish per treatment group were euthanized, tissues were collected and immediately submerged in RNAlater, and later stored in an ultra cold freezer until processing for RNA sequencing.

first: Yesutor

last: Soku

first: Miles

last: Lange

first: Mohamed

last: Abdelrahman


title: A role for the plastidial GPT2 translocator in the modulation of lignin biosynthesis

status: Public on Aug 13 2025

city: College station

first: Wayne

last: Versaw

state: Texas

address: Nagle St

department: Biology

country: USA

institute: Texas A&M University

type: Expression profiling by high throughput sequencing

summary: GPT2 overexpression in A. thaliana reduced stem lignin content and guaiacyl and syringyl monolignol pools. Transcriptomic and metabolomic analyses revealed a regulatory link between GPT2 and HCT that influences flux between lignin, UV protectants and primary metabolism.

overall_design:
To invesigate the relationship between GPT2 expression and lignin biosynthesis, we examined transciptomic changes in HCT-RNAi (knockdown of HCT through silencing), gpt2-1 (mutant),35S GPT2 (overexpression) lines and compared them to wild type Col-0 lines. The model organism was A.thaliana.
We then performed RNA-seq analysis on three biological replicates of stem tissue from each genotype.
Differential seq analysis was performed using the RNA-seq data for comparison between wild type vs mutant (HCT-RNAi, gpt2-1) and wild type vs overexpression lines (35S GPT2)

first: Aditi

last: Subramani Raju

first: Versaw

last: Wayne

first: Dixon

last: Richard


title: Epidrug Screening Identifies Type I PRMT Inhibitors as Modulators of Lysosomal Exocytosis and Drug Sensitivity in Cancers

city: Istanbul

first: Hamzah

last: Syed

address: Rumelifeneri Yolu

department: School of Medicine

country: Turkey

institute: Koç University

summary: Epigenetic changes drive differential gene expression, contributing to oncogenic transformation and drug resistance. Lysosomes are crucial in cell signaling and the sequestration of toxins and chemotherapeutic agents. This sequestration followed by expulsion through lysosomal exocytosis is a factor in drug resistance. The epigenetic regulation of lysosomal exocytosis remains poorly understood. Our research focuses on this regulation, hypothesizing that epigenetic modifier drugs (epidrugs) capable of inhibiting lysosomal exocytosis and could serve as potential therapeutics. Additionally, we investigate their potential synergy with drugs known to be sequestered in lysosomes. To examine this concept, we screened approximately 150 epigenetic drugs targeting various reader, writer, or eraser proteins. These drugs were assessed for their combined cytotoxic effects with cisplatin, their impact on lysosomal exocytosis, and on lysosomal biogenesis. Our findings reveal that among the epidrugs showing synergy with cisplatin and further reducing cell viability in combination, two type I PRMT inhibitors, MS023 and GSK3368715, inhibited lysosomal exocytosis. Notably, neither of these drugs altered the expression of the CLEAR lysosomal biogenesis network of genes, suggesting the involvement of novel regulators in lysosomal functions. To explore the specific components of the trafficking machinery affected by PRMT inhibitors, we conducted an RNA-seq analysis, uncovering several differentially expressed genes (DEGs). In addition to previously described functions such as methylation activity, or DNA repair; these DEGs included those involved in vesicular trafficking, lysosomal enzyme activity and lysosome dynamics, offering potential insights into the mechanism of reduced exocytosis and identifying a novel mode for its regulation. Additionally, both inhibitors exhibited synergy with other drugs known to be sequestered in lysosomes, such as carboplatin, oxaliplatin, sunitinib, and doxorubicin, indicating that inhibition of lysosomal exocytosis may be a common phenomenon for such drugs. These findings underscore the potential of Type I PRMT inhibitors as therapeutic agents in cancer treatment. Consistently, analysis on the publicly available patient data revealed that lower levels of type I PRMTs (PRMT1 and 6) were associated with better patient response to these drugs, further suggesting their potential as drug candidates for combination therapy to enhance chemotherapy efficacy and improve cancer patient survival rates.

overall_design: To understand the molecular mechanisms underlying MS023-mediated inhibition of drug tolerance, we aimed to analyze the transcriptome of Du145 cells treated with MS023. We conducted gene expression profiling using RNA-seq data from both non-treated control (NT) and MS023-treated (MS) Du145 cells.

first: Baris

last: Sergi

first: Neslihan

last: Yuksel-Catal

first: Selahattin Can

last: Ozcan

first: Umamaheswar

last: Duvvuri

first: Kirill

last: Kiselyov

first: Ceyda

last: Acilan


title: Crotonate-activated histone H3K14 crotonylation enhances intestinal regeneration after injury [ChIP-seq]

city: Beijing

first: Ye-Guang

last: Chen

state: China

address: Haidian  District

country: China

institute: Tsinghua University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The intestinal epithelium undergoes rapid turnover driven by Lgr5+ intestinal stem cells (ISCs) at the crypt base, and can recover despite ISC loss during damage. However, the role of epigenetic modifications in regulating this regeneration remains unclear. In this study, we report that H3K14 crotonylation (H3K14cr), a vital histone modification mediated by the acyltransferase HBO1, is essential for intestinal regeneration. HBO1 ablation in the intestinal epithelium exacerbates dextran sulfate sodium (DSS)-induced colitis.

overall_design: To study how HBO1 regulates ISC and fetal genes expression, the control and HBO1 KO colonic crypts were subject to CUT&Tag and ChIP-seq with HBO1, H3K14ac and H3K14cr antibodies.Otherwise, the control and HBO1 KO mice were treated with 3% DSS, and the crypts were isolated at day 3 for ATAC-seq.

first: Yanhui

last: Xiao

first: Shicheng

last: Yu


title: Transcriptomic analysis of channel catfish intestine response to Aeromonas hydrophila infection correlated to skin integrity and fed state

first: Jason

last: Abernathy

summary: The study focuses on the intestinal immune responses of channel catfish (Ictalurus punctatus) under various feeding and fin-clipping conditions after infection with Aeromonas hydrophila. Transcriptomic data revealed significant activation of pathogen recognition pathways (TLR signaling and C-type lectins) and pro-inflammatory cytokines, particularly in the fed groups. Histopathological findings at 2 hours post-challenge (HPC) showed minimal to moderate expansion of the lamina propria by edema in the intestines of the treated groups. At 4 HPC, mild to moderate edema with lymphocytes and plasma cells was observed, indicating early immune cell infiltration. By 8 HPC, degenerative changes in the superficial epithelium and hemorrhage were evident, especially in the fed fin-clipped group, which correlates with increased mortality in this group. The unfed groups demonstrated delayed but sustained immune responses, marked by lower histological damage compared to the fed groups. These findings provide insights into how nutritional status and fin-clipping shape the intestinal immune response and tissue damage during infection.

overall_design:
To determine how feeding and fin-clipping affect the intestinal immune response and tissue damage in channel catfish during infection.
The experimental design included four treatment groups, each with 25 fish per replicate (6 replicates per group, n=150), for a total of 600 experimental fish including control groups.
Treatment was either mock using only sterile media or with Aeromonas hydrophila bacterium. The treatment groups included (1) fish subjected to an immersion challenge without fin clipping and fed on the day of the challenge (2) fish subjected to an immersion challenge with fin clipping and fed on the day of the challenge (3) fish subjected to an oral gavage challenge and fed on the day of challenge and (4) fish subjected to an oral gavage challenge but not fed on the day of the challenge.
Fish were sampled at 2, 4, and 8 hours post-challenge. At each time point, 6 fish per treatment group were euthanized, tissues were collected and immediately submerged in RNAlater, and later stored in an ultra cold freezer until processing for RNA sequencing.

first: Yesutor

middle: K

last: Soku

middle: W

middle: D


title: Multi-omic analysis reveals retinoic acid molecular drivers for fibrosis and regenerative repair in skin fibrosis [scATAC-seq]

city: Stanford

first: Jennifer

middle: Brigitta

last: Parker

state: CA

address: 257 Campus Drive

department: Surgery

institute: Stanford University

summary: In the skin, tissue injury results in fibrosis in the form of scars composed of dense extracellular matrix deposited by fibroblasts. The therapeutic goal of regenerative wound healing has remained elusive, in part because principles of fibroblast programming and adaptive response to injury remain incompletely understood. Here, we present a multimodal -omics platform for the comprehensive study of cell populations in complex tissue, which has allowed us to characterize the cells involved in wound healing using a bleomycin induced ifibrosis model. We employ a bleomycin skin models that recapitulates human tissue repair kinetics. Through integrated analysis of single cell chromatin landscapes and gene expression states, coupled with spatial transcriptomic profiling, we are able to impute fibroblast epigenomes with temporospatial resolution. This has allowed us to reveal potential mechanisms controlling fibroblast fate during migration, proliferation, and differentiation following skin injury, and thereby reexamine the canonical phases of wound healing. These findings have broad implications for the study of tissue repair in complex organ systems.

overall_design: Mouse wound tissue transcriptomes were profiles using single cell RNA sequencing, single cell ATAC sequencing, and Visium spatial transcriptomics. For single-cell RNA sequencing, wound cells were harvested at 3 timepoints over the course of wound healing (POD 12, 21, 28) and normal skin as a control. For single-cell ATAC sequencing and visium similiar time points were harvested. For single cell RNA sequencing, cells treated with a cyp26b1 inhibitor were also assessed referred to as POD 12 + TREATMENT.

first: Michael

last: Januszyk

first: Michelle

last: Griffin


title: Crotonate-activated histone H3K14 crotonylation enhances intestinal regeneration after injury [RNA-seq]

overall_design:
Part1:
We performed  gene expression analysis with RNA-seq data  from control and HBO1 KO small intestinal organoids. Otherwise,to study the function of HBO1 in intestinal regeneration, we analyzed RNA-seq data from control and HBO1 KO colonic epithelial cells  derived from DSS-treated mice.
Part2:
This study aims to characterize transcriptional dynamics during tissue damage and subsequent regeneration. Mice are treated with 3% DSS for 5 days, followed by normal drinking water. Colonic crypts were isolated at the indicated time points for bulk RNA-seq.


title: Multi-omic analysis reveals retinoic acid molecular drivers for fibrosis and regenerative repair in skin fibrosis

overall_design: Mouse wound tissue transcriptomes were profiled using single cell RNA sequencing, single cell ATAC sequencing, and Visium spatial transcriptomics. For single-cell RNA sequencing, wound cells were harvested at 3 timepoints over the course of wound healing (POD 12, 21, 28) and normal skin as a control. For single-cell ATAC sequencing and visium similiar time points were harvested. For single cell RNA sequencing, cells treated with a cyp26b1 inhibitor were also assessed referred to as POD 12 + TREATMENT.


title: Transcriptome-based screening in TARDBP/TDP-43 knock-in motor neurons identifies the NEDD8-activating enzyme inhibitor MLN4924 [RNA-Seq]

city: Montreal

first: Tomas

last: Durcan

state: QC

address: 3801 University Street

country: Canada

institute: McGill University

summary: A growing body of knowledge implicates perturbed RNA homeostasis in amyotrophic lateral sclerosis (ALS), a neurodegenerative disease that currently has no cure and few available treatments. Dysregulation of the multifunctional RNA-binding protein TDP-43 is increasingly regarded as a convergent feature of this disease, evidenced at the neuropathological level by the detection of TDP-43 pathology in most patient tissues, and at the genetic level by the identification of disease-associated mutations in its coding gene TARDBP. To characterize the transcriptional landscape induced by TARDBP mutations, we performed whole-transcriptome profiling of motor neurons differentiated from two knock-in iPSC lines expressing the ALS-linked TDP-43 variants p.A382T or p.G348C. Our results show that the TARDBP mutations significantly altered the expression profiles of mRNAs and microRNAs of the 14q32 cluster in MNs. Using mutation-induced gene signatures and the Connectivity Map database, we identified compounds predicted to restore gene expression toward wild-type levels. Among top-scoring compounds selected for further investigation, the NEDD8-activating enzyme inhibitor MLN4924 effectively improved cell viability and neuronal activity, highlighting a possible role for protein post-translational modification via NEDDylation in the pathobiology of TDP-43 in ALS.

overall_design:
To characterize the transcriptional changes induced by TARDBP mutations, we extracted total RNA from motor neurons differentiated from two knock-in iPSC lines expressing the ALS-linked TDP-43 variants p.A382T or p.G348C and their isogenic control iPSC line (AIW002-02).
We then performed differential gene expression analysis using data from RNA-seq of five independent differentiations (i.e., biological replicates) for each cell line.
We contrasted the isogenic control against each mutant cell lines individually and against both mutants combined.

first: Sarah

last: Lépine

first: Gilles

last: Maussion

first: Alexandria

last: Schneider

first: Angela

last: Nauleau-Javaudin

first: María José

last: Castellanos-Montriel

first: Georgina

last: Jiménez Ambriz

first: Dan

last: Spiegelan

first: Narges

last: Abdian

first: Anna Krystina

last: Franco-Flores

first: Ghazal

last: Haghi

first: Lale

last: Gursu

first: Mathilde

last: Chaineau

first: Thomas

middle: M


title: Transcriptome-based screening in TARDBP/TDP-43 knock-in motor neurons identifies the NEDD8-activating enzyme inhibitor MLN4924 [miRNA-Seq]

type: Non-coding RNA profiling by high throughput sequencing

overall_design:
To characterized the miRNA profiles induced by TARDBP mutations, we extracted total RNA from motor neurons differentiated from two knock-in iPSC lines expressing the ALS-linked TDP-43 variants p.A382T or p.G348C and their isogenic control iPSC line (AIW002-02) at four weeks post-plating of progenitors cells.
We then performed differential expression analysis using data from small RNA-seq of five independent differentiations (i.e., biological replicates) for each cell line.
We contrasted the isogenic control against each mutant cell lines individually and against both mutants combined.


title: Sex-specific role for 5-HT2A receptor in psychedelic-induced extinction of opioid rewarding properties

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

summary: Emerging evidence suggests that classical psychedelics may offer therapeutic potential for opioid use disorder (OUD) by alleviating key hallmarks such as altered reward processing and dependence. However, the mechanisms behind these effects remain unclear. Our data demonstrate that a single administration of the psychedelic psilocybin (PSI) reduces conditioned behavior and withdrawal induced by the opioid oxycodone (OXY) in male mice but not in females, and this effect is mediated via the 5-HT2A receptor (5-HT2AR). We show that the sex-specific attenuation of OXY preference is driven by 5-HT2AR activation in frontal cortex pyramidal neurons projecting to the nucleus accumbens (NAc). Additionally, PSI modulates epigenomic regulation following repeated OXY exposure and induces sex-specific NAc dendritic structural plasticity independently of 5-HT2AR. Notably, female frontal cortex and NAc show fewer changes at gene enhancer regions in response to PSI, repeated OXY, or combined PSI-OXY treatment compared to males, with the frontal cortex exhibiting more pronounced sex differences than the NAc at the epigenomic level. Together, these results provide novel insights into the neural and epigenetic mechanisms of psychedelic-induced plasticity in OUD, while also highlighting sex differences in PSI's modulation of reward pathways and its therapeutic potential.

overall_design: MOWChIP-seq (Zhu et al. Nature Protocols 14 (2019) 3366-3394) was performed on neuronal neclei extracted from mouse frontal cortex (FC) and nucleus accumbens (NAc) to investigate impact of psilocybin (PSI) treatment on epigenomic regulation following repeated oxycodone (OXY) administion in make and female mice. Mice received three separate administrations of OXY (3 mg/kg) or vehicle on consecutive days (days 1-3), with 24-hour intervals between doses, followed by a single dose of PSI (1 mg/kg) or vehicle (day 4), resulting in four distinct experimental groups: VEH-VEH, VEH-PSI, OXY-VEH, and OXY-PSI. On day 5, FC and NAc tissue samples were collected for H3K27ac profiling. Neuronal nuclei were extracted and isolated by FACS, followed by MOWChIP-seq on 10,000 nuclei per sample.

last: Hadlock


title: Diet-induced dyslipidemia leads to enhanced IFN-g production by mycolic acid-specific T cells

city: Chicago

first: Chyung-Ru

last: Wang

state: Illinois

address: 320 E Superior St

department: Microbiology and Immunology

institute: Northwestern University

summary: Diet-induced dyslipidemia, characterized by elevated plasma LDL-cholesterol levels, has been shown to affect host defense against infections, including Mycobacterium tuberculosis (Mtb). Although the impact of diet-induced dyslipidemia on conventional T cell functions is well studied, its influence on group 1-restricted T cells during Mtb infection is very limited. In this study, we generated a unique double-transgenic mouse model expressing human CD1 and mycolic acid (MA)-specific CD1b-restricted T cell receptor in a Rag-deficient and low-density lipoprotein receptor-deficient background to investigate how diet-induced dyslipidemia impacts functionality of MA-specific T cells and its effect on anti-Mtb immunity. While dyslipidemia augmented IFN-g production by MA-specific T cells, it paradoxically led to increased apoptosis and thus compromised their ability to restrict Mtb growth in vivo. These findings may elucidate the complex interplay between diet-induced dyslipidemia and lipid antigen-specific T-cell responses in the context of Mtb infection, offering insights that could inform potential therapeutic approaches addressing dyslipidemia-induced changes in T-cell functions.

overall_design: Human CD1 transgenic mice (hCD1Tg) and mycolic acid-specific CD1b-restricted TCR (DN1Tg) on the Rag-deficient background (DN1Tg/hCD1Tg/Rag-/-) were crossed with LDLR-/- mice to generate DN1Tg/hCD1Tg/Rag-/-/LDLR-/- mice. These mice were randomly assigned to two groups and fed with either a normal chow (NC) or a high-fat diet (HFD) for 10 weeks. Then, mycolic acid-specific T cells of lymph nodes from NC- and HFD-fed mice were activated by co-culturing with MA-pulsed hCD1Tg bone-marrow derived dendritic cells (BMDCs) for 48 hrs. Sorted mycolic acid-specific T cells were used for RNA sequencing.

first: Yen Lin

last: Lin

first: Chyung Ru


title: Vascular network-inspired diffusible scaffolds for engineering functional neural organoids

city: Bloomington

first: Feng

last: Guo

state: Indiana

address: 107 S Indiana Ave

institute: Indiana University

summary: Organoids, three-dimensional in vitro organ-like tissue cultures derived from stem cells, show promising potential for developmental biology, drug discovery, and regenerative medicine. However, the function and phenotype of current organoids, especially neural organoids, are still limited by insufficient diffusion of oxygen, nutrients, metabolites, signaling molecules, and drugs. Herein, we present Vascular network-Inspired Diffusible (VID) scaffolds to fully recapture the benefits of physiological diffusion physics for generating functional organoids and phenotyping their drug response. In a proof-of-concept application, the VID scaffolds, 3D-printed meshed tubular channel networks, support the successful generation of engineered human midbrain organoids almost without necrosis and hypoxia in commonly used well-plates. Compared to conventional organoids, these engineered organoids develop with more physiologically relevant features and functions including midbrain-specific identity, oxygen metabolism, neuronal maturation, and network activity. Moreover, these engineered organoids also better recapitulate pharmacological responses, such as neural activity changes to fentanyl exposure, compared to conventional organoids with significant diffusion limits. Combining these unique scaffolds and engineered organoids may provide insights for organoid development and therapeutic innovation.

overall_design: Engineered midbrain organoids, conventional midbrain organoids, and engineered midbrain organoids with 2-day 50nM fentanyl treatment on day 60 were analyzed by scRNAseq.

first: Hongwei

last: Cai

first: Chunhui

last: Tian

first: Lei

last: Chen

first: Kyle

last: McCracken

first: Jason

last: Tchieu

first: Mingxia

last: Gu

first: Ken

last: Mackie


title: Human Dicer hotspot mutation induces both loss and gain of miRNA function [sRNA-seq]

city: New York

first: Seungjae

last: Lee

state: NY

address: 430 East 67th St.

department: Department of Developmental Biology

institute: Sloan-Kettering Institute

summary: The core miRNA biogenesis enzyme Dicer sustains recurrent mutations in cancer, which specifically compromise catalysis by its RNase IIIb domain. These are proposed to act as selective hypomorphs, since Dicer-RNase IIIb cleaves the 5p arms of pre-miRNA hairpins. However, the lack of knockin models has hindered a full understanding of the consequences of Dicer hotspot mutations for miRNA biogenesis. Here, we generated Dicer-KO and Dicer-S1344L (homozygous and hemizygous) hESCs; the latter is a non-catalytic mutation in RNase IIIa that impairs RNase IIIb activity. Consistent with our previous work, Dicer-KO is cell lethal in hESCs. However, in contrast to the expectation that Dicer hotspot mutations confer cell advantages, Dicer-S1344L knockin hESCs were subviable and also required a conditional genetic strategy for isolation. Small RNA sequencing using spike-in normalization reveals two broad trends: ablation of miRNA-5p species, and selective changes in miRNA-3p species. Curiously, we recognized a directional upregulation of miRNA-3p passenger strands, indicating a broad strand switch. Activity assays and Argonaute profiling of the transcriptome confirm that these confer increased repression capacity. Finally, we used in vitro assays to show 3p arm-nicked pre-miRNAs preferentially load miRNA-3p species into Argonaute, compared to corresponding miRNA/passenger duplexes. Overall, Dicer hotspot mutations have unexpected neomorphic consequences on miRNAs, including both loss- and gain-of-function.

overall_design: To investigate the consequences of the Dicer cancer hotspot mutation, we generated CRISPR-Cas9 engineered Dicer-S1344L homozygous and hemizygous hESCs cells.

first: David

last: Jee

first: Dapeng

last: Yang

first: Robert

last: Rickert

first: Renfu

last: Shang

first: Danwei

last: Huangfu

first: Eric

middle: C

last: Lai


title: Human Dicer hotspot mutation induces both loss and gain of miRNA function [iCLIP]


title: Human Dicer hotspot mutation induces both loss and gain of miRNA function [RNA-seq]


title: Unveiling the molecular landscape of dental caries and its impact on ECM remodeling

city: Rio de Janeiro

first: Rodrigo

last: Jardim

state: RJ

address: Av. Brasil 4365

department: Oswaldo Cruz Institute

country: Brazil

institute: Oswaldo Cruz Foundation

summary: The rapid progression of caries lesions in dentin is facilitated by its reduced mineralization, high organic content, and tubular structure, contributing to ECM degradation through MMP activation in acidic conditions. This study investigates the expression of collagenases (MMP-2 and MMP-9) and their inhibitors (TIMP-1 and TIMP-2) in the pulp, predentin, and dentin of decayed teeth. RNA from these tissues was sequenced using Illumina® technology. Quality validation, read alignment to the human transcriptome, and differential gene expression analysis were performed. Gene Ontology and KEGG pathway analyses identified significant biological processes. Sequencing produced 16-37 million reads with 87.25%-88.08% alignment, identifying 1.01% of over 33,000 genes as differentially expressed. In decayed tissues, upregulated genes linked to detoxification and stress responses suggest adaptive mechanisms, while downregulated genes relate to energy metabolism and tooth development, indicating impaired enamel and dentin formation. Interaction network analysis underscores roles for proteins like EGFR and metallothioneins in acute-phase responses. Metabolic pathways involving ECM components underscore structural impacts of caries. MMP-2 is highly expressed in decayed predentin and dentin, while MMP-9 is reduced across all tissues. TIMP-1, predominantly in decayed dentin, aligns with its role as an MMP-9 inhibitor. TIMP-2, which inhibits MMP-2, shows elevated levels in both decayed and caries-free dentin, reflecting tissue-specific regulation. The expression of MMPs and TIMPs indicates a complex regulation of ECM degradation and repair. Upregulation of inflammatory and stress-related genes (SAA1, SAA2, ORM1, ORM2, SERPINA1), with the regulatory balance of MMPs and TIMPs, underscores their significant role in maintaining ECM integrity.

overall_design: Third molars were extracted from 18-year-old patients, clinically indicated for extraction, without active periodontal disease and without antibiotic use in the last three months. Three samples of dental tissue (pulp, predentin and dentin) were collected from healthy teeth and three from decayed teeth.

first: Simone

middle: G

last: Oliveira

first: Nelson

last: Kotowski

first: Alberto

last: Dávila

first: Hélio

middle: R

last: Sampaio-Filho

first: Karina

last: Ruiz

first: Flávio

middle: H

last: Aguiar


title: Multi-omic analysis reveals retinoic acid molecular drivers for fibrosis and regenerative repair in skin fibrosis [Spatial transcriptomics]

first: Jennifer

last: Parker

first: Michael

last: Januszyk

first: Michelle

last: Griffin


title: Tubular MYDGF slows the progression of chronic kidney disease by maintaining mitochondrial homeostasis

city: Jinan

first: Yang

last: Zhang

state: Shandong

address: 247 Beiyuan Street

department: Pharmacy

institute: The Second Hospital, Cheeloo College of Medicine

summary: Mitochondrial dysfunction is a key event in driving maladaptive repair of tubular epithelial cells during the transition from acute kidney injury to chronic kidney disease (CKD). Therefore, identifying the potential targets involved in mitochondrial dysfunction in tubular epithelial cells has clinical importance. Although our previous studies demonstrated that myeloid-derived growth factor (MYDGF) derived from podocyte attenuated glomerular injury by inhibiting mitotic catastrophe of podocyte, the function of MYDGF in tubular epithelial cells still keeps unknown. In this study, we found that MYDGF expression was significantly decreased in the cortex of kidney, especially in proximal tubules, from mice with CKD. Notably, the downregulation of MYDGF was further confirmed in renal tubules from CKD subjects. Tubule-specific deletion of MYDGF exacerbated kidney injury in mice with CKD. However, overexpression of MYDGF attenuated kidney fibrosis by remodeling mitochondrial homeostasis in tubular epithelial cells. Mechanistically, renal tubule MYDGF positively regulated the expression of isocitrate dehydrogenase 2 (IDH2), then restoring mitochondrial homeostasis and slowed the progression of CKD. Thus, our studies indicate that MYDGF derived from tubules may be an effective innovative therapeutic strategy for patients with CKD.

overall_design: The gene expression of 3 samples from the HK-2 cells with aristolochic acid treatment was compared to 3 NC samples by RNA sequencing. The gene expression of 3 samples from the HK-2 cells with aristolochic acid treatment was compared to 3  samples from the HK-2 cells with overexpression of MYDGF and aristolochic acid treatment by RNA sequencing.

first: Yu

middle: J

first: Min

last: Liu


title: Identification of unique mesenchymal subpopulations for regenerating follicular and interfollicular epithelia after devastating necrosis in the skin graft

city: Suita

first: Takashi

last: Shimbo

state: Osaka

address: 2-2 Yamadaoka

country: Japan

institute: Osaka university

summary: We investigated chronological changes of the skin graft in mice for 15 days at  single cell-transcriptomic levels. We found devastating necrotic changes in the dermal and epidermal tissues at post-operated day 3, (POD3), followed by significant regeneration processes of the follicular and interfollicular tissues after POD 6. Dermal papilla cells in the necrotic milieu exserted significant activation of Wnt signaling pathway and Sox2 and Fgf7 expressions, all of those are critical for follicular development in the fetal skin. We further identified a unique mesenchymal subpopulation, which expressed keratinocyte-specific genes, such as Krt5 and Epcam, as well as Irf6, a transcriptional factor to induce mesenchymal to epithelial transition (MET). Our data revealed significant contribution of the unique mesenchymal cell populations for the follicular and interfollicular epithelial regeneration after severe necrosis in the skin graft.

overall_design:
Skin from C57BL6/J neonatal mice were transplanted on the back of beta-actin-EGFP adult mice.
Mice were devided into three groups, which were the drug administrated group, saline administrated group and non-treated group. The transplanted skins were hervested at post-operative day (POD) 3,6,9,12,15. As the non-treated control, dorsal skins from postnatal day0 and 15 mice were also obtained. Each specimens were dissociated enzymatically, and then the cell suspensions were isolated by fluorescence-activated cell sorting (FACS) according to absence of dead cell stain. The sorted cells were analyzed using single cell RNA sequencing.

first: Tomomi

last: Kitayama

first: Yuya

last: Ouchi

first: Tomoya

last: Mori

first: Yoshikazu

last: Hirose


title: DNA glycosylases Ogg1 and Mutyh mediate gene expression of PRC2 targets important for memory formation (RNA-Seq)

city: Trondheim

first: Katja

last: Scheffler

address: Edvard Griegs Gate 8

department: Department of Neuromedicine and Movement Sciences

country: Norway

institute: Norwegian University of Science and Technology

summary: Base excision repair initiated by DNA glycosylases is known to preserve genomic integrity by removing damaged bases. Besides, DNA glycosylases Ogg1 and Mutyh were shown to alter the hippocampal transcriptome associated with cognition but independent of DNA damage repair. However, the underlying molecular mechanisms are not fully understood. Here, we combine transcriptomic and epigenomic analyses of the hippocampus in mice deficient in DNA glycosylases. We report that the combined deficiency of Ogg1 and Mutyh impairs spatial but not associative long-term memory. Mechanistically, Ogg1 and Mutyh modulate DNA methylation of polycomb repressive complex 2 (PRC2) target genes. We find that the occupancy of PRC2 and histone modifications associated with PRC2 activity depend on Ogg1 and Mutyh in neurons and glia. These epigenetic changes correlate with cell-type specificdifferences in gene expression of PRC2 targets. Our results uncover a novel role for Ogg1 and Mutyh beyond DNA repair in modulating the epigenome to control transcriptional responses in the brain important for memory formation.

overall_design: Transcriptomic and epigenetic analysis of WT and DNA glycosylase deficient (Ogg1-/-, Mutyh-/- and Ogg1xMutyh-/-) C57/BL6N mice in hippocampus. Bisulfite methylation sequencing of whole hippocampus DNA. RNA-sequencing of nuclear RNA from NeuN+ or NeuN- sorted hippocampal nuclei. ChIP-sequencing for PRC2 component Suz12 and two histone methylation markers (H4K4me3 and H3K27me3) from NeuN+ or NeuN- sorted hippocampal nuclei.

first: Andreas

last: Abentung

first: Teri

last: Sakshaug

first: Rabina

last: Dumaru

first: Nina-Beate

last: Liabakk

first: Mingyi

last: Yang

first: Junbai

last: Wang

first: Magnar

last: Bjørås


title: DNA glycosylases Ogg1 and Mutyh mediate gene expression of PRC2 targets important for memory formation (ChIP-Seq)


title: DNA glycosylases Ogg1 and Mutyh mediate gene expression of PRC2 targets important for memory formation (BiSulfite-Seq)

type: Methylation profiling by high throughput sequencing


title: In vivo cardiac reprogramming by delivery of PHF7 [snRNA-seq multiome]

city: Dallas

first: kenian

last: chen

state: TX

address: 5323 Harry Hines Boulevard

department: Population and Data Science

institute: UTsouthwestern

summary: Cellular reprogramming of cardiac fibroblasts to cardiomyocytes following myocardial infarction (MI) is an attractive strategy to redirect the fibrotic response of the non-regenerative adult heart to a more functional myocardium. Current reprogramming strategies are inefficient or require an excess of factors in adult and human cells due to staunch epigenetic barriers. Recently, we identified the epigenetic factor PHF7 as a potent activating factor of in vitro adult fibroblast reprogramming through modification of chromatin accessibility at cardiac super-enhancers. Here, we report the ability of PHF7 to activate adult fibroblast reprogramming alongside minimal co-factors in vitro, and the efficacy of these cocktails in vivo following MI in mice. Further, delivery of PHF7 as a single factor to the mouse heart following MI induced reprogramming and improved cardiac function. Deployment of single nuclear multi-omics revealed that PHF7 induced fundamental changes in chromatin structure by enhancing accessibility at CTCF binding sites and inhibiting Jun/Fos transcription factor activity to permit reprogramming in the injured heart. Together, these data support the potential for epigenetic factors like PHF7 to achieve in vivo reprogramming in isolation when utilized in the appropriate niche.

overall_design:
To investigate the effect of PHF7 cocktails on in vivo reprogramming we performed snRNA and snATAC sequencing on nuclei from mouse hearts that had undergone myocardial infarction (MI) and intramyocardial injection with retrovirus bearing control, PHF7, PHF7/TBX5 (PT), PHF7/Mef2c/Tbx5 (PMT) constructs.

Please note that each processed data was generated from both snATAC-seq and scRNA-seq samples, and is linked to the corresponding snATAC-seq sample records (GSE270267).

first: Glynnis

middle: A

last: Garry

first: Matthieu

last: dos Santos

first: Kenian

last: Chen

first: Wei

last: Tan

first: Lin

last: Xu

first: Eric

middle: N

last: Olson


title: In vivo cardiac reprogramming by delivery of PHF7 [snATAC-seq multiome]

overall_design: To investigate the effect of PHF7 cocktails on in vivo reprogramming we performed snRNA and snATAC sequencing on nuclei from mouse hearts that had undergone myocardial infarction (MI) and intramyocardial injection with retrovirus bearing control, PHF7, PHF7/TBX5 (PT), PHF7/Mef2c/Tbx5 (PMT) constructs.


title: Engineering a Microfluidic Platform to Cryopreserve Stem Cells: A DMSO-Free Sustainable Approach

city: London

first: Arghya

last: Paul

state: Ontario

address: Thompson Engineering Building

institute: The University of Western Ontario

summary: Human adipose-derived stem cells (hASCs) are cryopreserved traditionally using dimethyl sulfoxide (DMSO) as the cryoprotectant agent. DMSO penetrates cell membranes and prevents cellular damage during cryopreservation. However, DMSO is not inert to cells, inducing cytotoxic effects by causing mitochondrial dysfunction, reduced cell proliferation, and impaired hASCs transplantation. Additionally, large-scale production of DMSO and contamination can adversely impact the environment. A sustainable, green alternative to DMSO is trehalose, a natural disaccharide cryoprotectant agent that does not pose any risk of cytotoxicity. However, the cellular permeability of trehalose is less compared to DMSO. Here, a microfluidic chip is developed for the intracellular delivery of trehalose in hASCs. The chip is designed for mechanoporation, which creates transient pores in cell membranes by mechanical deformation. Mechanoporation allows the sparingly permeable trehalose to be internalized within the cell cytosol. The amount of trehalose delivered intracellularly is quantified and optimized based on cellular compatibility and functionality. Furthermore, whole-transcriptome sequencing confirms that less than 1% of all target genes display at least a twofold change in expression when cells are passed through the chip compared to untreated cells. Overall, the results confirm the feasibility and effectiveness of using this microfluidic chip for DMSO-free cryopreservation of hASCs.

overall_design: To evaluate the effect of designed microfluidic chip on hASCssqueezing. We passed hASCs through the microfluidic chip and subsequently, performed RNAseq of three replicates (and as control, three more replicates were analyzed using RNAseq where cells were not passed through the microfluidicchip), and differences in gene expressions were analyzed.

first: Saman

last: Modaresi

first: Settimio

last: Pacelli

first: Aishik

last: Chakraborty

first: Ali

last: Coyle

last: Luo

first: Irtisha

last: Singh


title: DNA glycosylases Ogg1 and Mutyh mediate gene expression of PRC2 targets important for memory formation

first: Katja

last: Scheffler

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

overall_design: Refer to individual Series


title: Next-generation sequencing to define the impact of Cxcl1 on murine MSC transcriptome and BM-PCa tumor microenvironment

city: Frederick

first: Leah

last: Cook

state: MD

address: 1050 Boyles St, Room 21-89

institute: National Cancer Institute-Frederick

summary: Purpose: Prostate cancer most frequently metastasizes to bone and is incurable. Metastatic prostate cancer cells thrive in bone through molecular regulation of surrounding bone stroma, including upregulation of CXCL8 (CXCL1 in mice) in MSCs. This study characterizes the changes in the bone marrow mesenchymal stem cells (MSCs) upon targeted deletion of Cxcl1 in murine MSC. It also characterized the changes in the tumor/stromal cells of tumors with Cxcl1 KO MSCs or control MSCs. These studies seek to determine the importance of MSC-derived CXCL1 in bone-metastatic prostate cancer.

overall_design: Cxcl1 was knocked down in murine bone marrow MSCs using stable lentiviral infection of Cxcl1-targeted or scrambled control shRNAs. RNA was collected for downstream bulk RNA-seq analyses. CRSIPR-Cas9 was used to generate Cxcl1 KO murine bone marrow MSCs. RNA was collected using Trizol reagent for downstream bulk RNA-seq analyses of Cxcl1 KO MSC and control MSC cell lines as well as tumor/stromal cells from an intratibial RM1 mouse prostate cancer model containing either Cxcl1 KO MSCs or control MSCs.


title: Non-activating ITGB3 mutation in β3 cytoplasmic region causes macrothrombocytopenia with impaired αIIbβ3/RhoA pathway

first: Daisuke

last: Motooka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: Almost all mutations of ITGA2B or ITGB3 identified in congenital macrothrombocytopenia induce constitutive activation of αIIbβ3. However, whether concomitant αIIbβ3 activation is essential for macrothrombocytopenia development remains unknown. Recently, we identified the β3(R734C) mutation that does not induce αIIbβ3 activation in macrothrombocytopenia. Here, we generated β3(R734C) knock-in (KI) mice and investigated the abnormalities in the platelet/megakaryocyte biology of KI mice and a family with β3(R734C)-related macrothrombocytopenia. Macrothrombocytopenia was observed in heterozygous β3(R734C) subjects with reduced expression of αIIbβ3. Compared to those in the wild-type (WT) mice, platelet counts decreased to 76 and 40% in heterozygous (Hetero) and homozygous (Homo) KI mice, respectively. Platelet αIIbβ3 expression was decreased in KI mice, and αIIbβ3 activation was not detected on non-stimulated KI platelets. Platelet aggregation, agonist-induced JON/A binding and P-selectin expression were impaired in KI mice. Platelet spreading on fibrinogen was also impaired in KI mice with ADP or thrombin stimulation. Additionally, filopodia and lamellipodia formation was impaired in fibrinogen-adhered megakaryocytes of KI mice. Moreover, RhoA activation was significantly impaired in fibrinogen-adhered megakaryocytes of KI mice. Proplatelet formation in KI mice was impaired with abnormal morphology. Platelet lifespan was shortened in Homo mice. Our data newly revealed that constitutive αIIbβ3 activation is not essential for the development of macrothrombocytopenia. We also showed that β3(R734C) mutation impairs the inside-out and outside-in signaling of αIIbβ3, and abnormal actin rearrangement and impaired RhoA activation may play major roles in leading to macrothrombocytopenia.

overall_design: To gain further understanding of β3(R734C) mutation, we performed a gene expression analysis using RNA-sequence (RNA-seq), using WT and β3(R734C) KI murine platelets. Putative differentially expressed genes generated by RNA-seq were identified (2 fold change cut-off).

first: Keiichi

last: Nakata

last: Okuzaki

first: Hirokazu

last: Kashiwagi


title: Investigating DDX41's Functional Role in Erythroid G-Quadruplex Dissolution

first: Peng

last: Ji

address: Ward Building Room 3-230/45, 303 E Chicago Avenue

department: Pathology

summary: To explore the functional role of DDX41 in the dissolution of G-quadruplexes, we conducted Cut&Run assays in both mouse erythroid cells and hematopoietic stem and progenitor cells (HSPCs). Initially, we harvested mouse bone marrow cells through PBS flushing. Subsequently, we isolated erythroid cells using Ter119 antibodies and purified HSPCs by selectively collecting lineage-negative cells. These cells were then subjected to Cut&Run assays, utilizing DDX41 antibodies and Bg4 antibodies. The DNA fragments obtained through this process were sonicated and sent for sequencing and subsequent analysis via NUseq.

overall_design: Mouse bone marrow cells were isolated, followed by the purification of erythroid cells and HSPCs for Cut&Run sequencing.

first: Bi

last: Honghao


title: Loss of TRIM21 drives UVB-induced systemic inflammation by regulating DNA-sensing pathways

city: Los Angeles

first: Lihong

last: Huo

address: 8700 Beverly Blvd, Los Angeles, CA 90048

institute: Cedars-Sinai

summary: This study investigated the mechanisms underlying photosensitivity in patients with systemic lupus erythematosus (SLE), focusing on the role of type I interferons (IFNs) and TRIM21, an autoantigen in SLE. Through experiments on mice exposed to ultraviolet light B (UVB), we demonstrate that TRIM21 deficiency leads to exacerbated systemic inflammation and IFN-driven responses following UVB exposure, mimicking aspects of SLE pathology. Specifically, we observe enhanced expression of IFN-stimulated genes (ISGs), increased levels of inflammatory chemokines, and elevated IgG deposition in the skin of UVB-exposed Trim21-/- mice. Mechanistic investigations reveal that TRIM21 restrains IFN induction by regulating the STING pathway, impacting the stability of proteins involved in RNA/DNA sensing and IFN responses. These findings shed light on the protective role of TRIM21 against UVB-induced systemic disease in SLE, offering insights into its potential as a therapeutic target to mitigate disease flares and activity in SLE patients.

overall_design: Eight-week-old wild-type (WT) and Trim21-/- mice were shaved dorsally prior to UVB exposure. Mice were allowed to move freely in their cage during UVB exposure and mice were treated with/without UVB 100 mJ/cm2 for one or three weeks.  spleens  were harvested following final UVB exposure to extract RNA for RNA sequencing

first: Gantsetseg

last: Tumurkhuu

first: Richard

last: Moore

first: Graziela

last: Perri

first: Caroline

last: Jefferies


title: Exploring DDX41's Functional Role in Bone Marrow through Single-Cell Analysis in WT and DKO Mice

summary: We conducted single-cell analysis of bone marrow cells from wild type (WT) and VavCre:Ddx41 fl/fl, cGAS-/- (DKO) mice to investigate DDX41's functional role in hematopoietic cell composition.

overall_design: Two mice were included, one wild-type and one DKO mouse

first: Honghao

last: Bi


title: In vivo cardiac reprogramming by delivery of PHF7

first: kenian

last: chen

overall_design: To investigate the global impact of PHF7 cocktails on reprogramming, we performed RNA sequencing using adult TTFs reprogrammed for 7 days following overexpression with retroviral constructs bearing Empty, PHF7 (P), TBX5 (T), PT, Mef2c+Tbx5 (MT), PMT, or Gata4 +MT (GMT) in biological triplicates.

first: Glynnis

last: Garry

first: Matthieu

last: dos Santos

first: Kenian

last: Chen

first: Wei

last: Tan

first: Lin

last: Xu

first: Eric

last: Olson


title: Silk-Ovarioids: establishment and characterization of a human ovarian primary cell 3D-model system

city: Solna

first: Tianyi

last: Li

address: Bioclinicum NKS J5:20, Solnavägen 30

department: Oncology-Pathology

country: Sweden

institute: Karolinska Institute

summary:
STUDY QUESTION
What is the best protocol to establish a long-term stable three-dimensional (3D) model for human primary ovarian cells?

SUMMARY ANSWER
We developed and characterized long-term cultured 3D models of primary ovarian somatic cells isolated from adult tissues, using Biosilk as a scaffold.

WHAT IS KNOWN ALREADY
In vitro models that mimic ovaries are crucial for elucidating the biological mechanisms underlying follicle activation and growth, hormonal activity, ovarian angiogenesis, damage in response to toxic exposures, and other biological mechanisms that enable the functionality of this complex organ. Three-dimensional (3D) systems are particularly relevant because they replicate heterogeneity and cell-cell communication among different ovarian cell types. However, complex models using human ovarian primary cells are yet to be developed.

STUDY DESIGN, SIZE, DURATION
Ovarian tissue samples were collected from five patients (age 26 ± 5 years) who underwent gender-affirming surgery. The cortex and medulla were separated and dissociated into single-cell suspensions using mechanical and enzymatic methods. Three approaches were tested to establish a 3D model culture system: matrix-free ovarian spheroids (MFOS), a Matrigel based three-layer gradient system (3LGS), and Biosilk scaffolds (Silk-Ovarioid). In parallel, paired controls from each patient and ovarian area were cultured in a standard 2D system for the same duration.

PARTICIPANTS/MATERIALS, SETTING, METHODS
The 3D culture systems were monitored every second day to detect signs of aggregation and growth. Freshly fixed tissue, as well as 2D and 3D-cultured samples were further processed for transcriptomic profiling after 42 days of culture using RNA sequencing. The culture of the 3D system was further characterized regarding its protein profile and steroid and cytokine production, through proteomics and liquid chromatography tandem mass spectrometry (LC-MS/MS), and Luminex platform, respectively. The key findings from the high-throughput assays were finally validated through RNA fluorescent in situ hybridization (RNA FISH) and immunofluorescent staining.

MAIN RESULTS AND THE ROLE OF CHANCE
The 3D model system MFOS (n = 120) and 3LGS (n = 18) failed to form aggregates capable of long-term maintenance in culture (MFOS: maximum of 15 days for both cortex and medulla; 3LGS: maximum of 11 days for medulla only). In contrast, we successfully established ovarian cortex- and medulla-derived 3D systems using Biosilk, termed Silk-Ovarioids (n = 120). Silk-Ovarioids were maintained for up to 42 days as free-floating culture without any signs of cell death, as confirmed by the absence of TUNEL, γ-H2A.X, and cleaved caspase 3 fluorescent signals. The presence of key ovarian somatic cell types, including granulosa, stromal, endothelial and perivascular cells, was confirmed by transcriptomics and proteomics in the majority of Silk-Ovarioids. Validation through RNA-FISH and immunostaining was performed using the following markers: AMHR2 for granulosa cells, PDGFRα for stromal cells, CLDN5 and GPIHBP1 for endothelial cells, GJA4/Cx37 and MCAM for perivascular cells. Notably, Silk-Ovarioids exhibited the formation of a pro-angiogenic hypoxic core, as evidenced by the transcriptomic and proteomic data and visualized by the expression of hypoxia markers MMP2 and PDGFRβ. This hypoxic environment led to development of vessel-like structures after 4-6 weeks of culture, which were positive for the angiogenic markers TGFBR2, BMP2 and PDGFα. The functionality of Silk-Ovarioids was further confirmed by the identification of de novo extracellular matrix secretion (Col1α1 and Lamα1), and by the detection of pro-angiogenic cytokines (e.g., IL-6, IL-8, and GM-CSF) and steroids (e.g., pregnenolone and epitestosterone) in the culture media.

LARGE SCALE DATA
The RNA-sequencing count matrix is deposited in Gene Expression Omnibus (GEO) with accession number GSE253571. Raw data is deposited in Swedish National Data Service (SND) with the DOI https://doi.org/10.48723/h8cm-bs19. Single cell RNA-seq data was downloaded from the ArrayExpress database at EMBL-EBI with the accession codes ‘E-MTAb − 8381’. The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD048710. The code used for the analysis can be found at https://github.com/tialiv/Silk-Ovarioid_project.

LIMITATIONS, REASONS FOR CAUTION
The ovarian samples were collected from patients undergoing androgen treatment, raising the concern that androgen exposure may alter the behaviour of cells in Silk-Ovarioids compared to those derived from androgen-unstimulated patients. Furthermore, the cell culture media used in this study was supplemented with fetal bovine serum and did not contain any supplement or growth factor that could be essential for the resemblance of Silk-Ovarioids to the tissue of origin.

WIDER IMPLICATIONS OF THE FINDINGS
The Silk-Ovarioids exhibited low intra-batch variability and long-term culture stability, underscoring their potential as a robust step towards developing a bioengineered, patient-specific artificial ovary. In addition, Silk-Ovarioids could be utilized as the first ovarian angiogenesis in vitro model, function as biological scaffold for in vitro folliculogenesis, and be used for toxicological and pharmacological studies targeting the ovaries.

overall_design:
In total 75 samples are included in the repository (36 samples from cortex and 39 from medulla). Among these samples, 29 tissue samples were used as reference in the comparision of 2D vs tissue and 3D vs tissue. 16 samples from 2D culture were used as the reference in the comparison of 3D vs 2D. The rest 30 samples were from 3D culture (Silk-Ovarioid).

**Raw data were deposited in Swedish National Data Service (DORIS) due to human data privacy concerns**

first: Valentina

last: Di Nisio

first: Zhijie

last: Xiao

first: Kiriaki

last: Papaikonomou

first: Anastasios

last: Damdimopoulos

first: Ákos

last: Végvári

first: Filipa

last: Lebre

first: Ernesto

last: Alfaro-Moreno

first: Mikael

last: Pedersen

first: Terje

last: Svingen

first: Roman

last: Zubarev

first: Ganesh

last: Acharya

first: Pauliina

last: Damdimopoulou

first: Andres

last: Salumets


title: Murine anaphylaxis to food requires cysteinyl leukotriene-mediated absorption of allergens in the gut

first: Slim

last: Fourati

address: 300 E Superior St

department: Medicine

summary: Food-specific IgE triggers life-threatening anaphylaxis; however, some people with food-specific IgE are asymptomatic upon allergen consumption. Using murine food allergy models, we discovered an unexpected pathway regulating the ability of food allergens to trigger anaphylaxis. C57BL/6 mice are uniquely resistant to anaphylaxis when challenged orally; we show that their gut barrier was impermeable to food allergens relative to anaphylaxis-susceptible strains, even prior to allergic sensitization. In a forward genetic screen, oral anaphylaxis resistance correlated with Dipeptidase1 (Dpep1) allelic variants. DPEP1 is expressed in intestinal epithelium and catabolizes leukotriene D4. Blocking DPEP1 with cilastatin enhanced allergen absorption in resistant mice. Conversely, pre-treatment of susceptible mice with a leukotriene synthesis inhibitor, zileuton, abrogated allergen absorption and subsequent oral anaphylaxis. Inhibiting leukotrienes may be a novel treatment for food allergy.

overall_design: 16S RNA-Sequencing of stool samples of N2-generation mice created by crossing C57BL/6 and C3H/HeJ mice together, and after 6 weeks of sensitization to peanut. Samples were collected from 6 mice suceptible and 12 mice resistant to oral analyphatic.

first: Adam

last: Williams

first: Mark

last: Adams


title: H3K36me3-coupled DNA Demethylation by DNMT3A Is Essential for Hypoxia-Induced EMT of Cancer Cells

city: Taipei

first: Che-Kun James

last: Shen

address: No. 128號, Section 2, Academia Rd, Nangang District

country: Taiwan

institute: Institute of Molecular Biology, Academia Sinica


title: Control of chloroplast integrity by the jasmonate signaling pathway is linked to growth-defense balance

city: Los Alamos

first: Leah

last: Johnson

state: NM

address: 3917 W Road

institute: Los Alamos National Laboratory

summary: The lipid-derived signal jasmonate (JA) controls growth-defense balance by modulating the abundance of JAZ proteins that repress MYC transcription factors. In Arabidopsis, the JAZ-MYC regulon also promotes JA-induced degreening of detached leaves under conditions of dark-induced starvation. These observations, together with the finding that JA biosynthesis and signaling mutants do not exhibit obvious defects in natural senescence, have confounded a satisfactory explanation of the physiological significance of JA-induced chlorosis. Using intact Arabidopsis plants grown under normal laboratory conditions, we manipulated JAZ abundance to investigate JA-induced degreening as a component of the leaf growth-defense syndrome. A jaz decuple mutant (jazD) lacking most JAZs exhibited strong growth-defense tradeoffs without visible symptoms of senescence. Further depletion of JAZ by treatment of jazD with coronatine recapitulated the major hallmarks of senescence, including the loss of chlorophyll and photosynthetic capacity, turnover of chloroplast proteins and lipids, and transition of chloroplasts to gerontoplasts. The data highlight the regulation of senescence by jasmonate signaling along the growth-defense continuum.

overall_design: To examine the transcriptional responses of jazD during coronatine-induced degreening, jazD were treated with coronatine or a mock (control/reference) solution and expression was examined over a 24 hour time course (0, 1, 3, 12, and 24 hours). Three replicates were sampled for each time point and treatment for 30 total samples. We performed treated versus untreated comparisons at each time point.

middle: Y

first: Gregg

last: Howe


title: Mimicking   gastric  bypass glucotonic effect: the role of atypical PKC activation and GLUT1

city: Seoul

first: UnHo

last: Kang

address: 15F, 241, Gangnam-daero, Seocho-gu

country: South Korea

institute: Arontier

summary: Bariatric surgery has demonstrated a significant therapeutic impact in reducing obesity and achieving euglycemia in diabetic patientspatients with diabetes. We previously demonstrated that iIntestinal glucotonic transformation, defined as increased intestinal serum glucose uptake and secretion into the lumen, has anplays a vital  important role in bypass surgeryies. Altered transcriptomes were evaluated in variable intestinal glucotonic models and big-data artificial  intelligence AI-based drug discovery systems. We found noted  that protein kinase C (PKC) activation mimics the intestinal transcriptome changes alterations observed in during intestinal glucotonic transformation. Among PKC subfamilies, atypical PKC promotes GLUT1- mediated  intestinal glucotonic transformation without inducing oncogenic proliferation. Intestinal aPKC activation through via the transposon expression vector induces serum glucose uptake into intestinal tissue and excretion into the lumeinal space. . Prostratin, a non-tumorigenic phorbol ester, was found observed to activate aPKC and induce a similar glucotonic effect. Taken together, our study results highlightCollectively, we identified  a a new chemical compound and target molecular pathways  that may provide a distinct and effective approach to to treating diabetes .

overall_design: To find the DEGs after PRKCZ overexpression, 3 mouse intestine samples with PRKCZ overexpression and 3 control mouse intestine samples were analysed.

first: Zhenyu

last: Hong

first: Mohamed

last: El-Agamy Farh

first: ChanWoo


title: H3K36me3-coupled DNA Demethylation by DNMT3A Is Essential for Hypoxia-Induced EMT of Cancer Cells [Bisulfite Sequencing]

summary: The epithelial-to-mesenchymal transition (EMT) and metastasis of the cancer cells are closely associated with epigenetic changes of chromatin and reprogramming of transcriptomes. The DNA methyltransferases DNMT3A and DNMT3B possess DNA demethylation/dehydroxymethylation activities. Here, we show, by a range of molecular/cellular approaches, that active DNA demethylation activity of DNMT3A is required for hypoxia-induced EMT of the primary colon carcinoma SW480 cells, its genome-wide DNA demethylation, and promoter DNA demethylation/transcriptional activation of the EMT genes TWIST1 and SNAIL1. DNMT3A also positively regulates hypoxia-induced TWIST1 activation in other types of cancer cells. Mechanistic analysis supports a regulatory model, in which hypoxia-induced H3K36me3 mark recruits DNMT3A to demethylate CpG in the hypoxia-responsive element (HRE), thereby facilitating HIF-1α binding and TWIST1 activation. This study demonstrates for the first time an in vivo functional role of the active DNA demethylation activity of DNMT3A and its potential as a novel therapeutic target of anti-cancer development.

overall_design: Compare the genome-wide methylation profile in SW480 cells under normoxia and hypoxia conditions.

first: Che-Kun

first: Biswanath

last: Chatterjee

first: Pritha

last: Majumder

first: Chen-Hsin

last: Yu

first: Hsin-Nan

last: Lin


title: Cockayne syndrome mice reflect human kidney disease and are defective in de novo NAD biosynthesis

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Cockayne Syndrome (CS) is a multi-system premature aging disorder caused by mutations in the genes involved in repairing DNA damage. CS patients display features including short stature, microcephaly, premature aging, neurodegeneration, photosensitivity, vision impairment, hearing loss, and bone and kidney abnormalities. Intracellular nicotinamide dinucleotide (NAD+) deprivation is one of the key molecular characteristics of CS patient-derived cells. NAD+ has critical roles in regulating cellular health, stress responses, and is important for maintaining renal homeostasis. While kidney dysfunction has been reported to be an important cause of death in CS patients, the molecular pathogenesis and potential linkage to NAD+ is not understood. In this study, we report kidney pathology in CS model mice, including renal atrophy, decreased glomerular filtration, and various types of lesions centering around the tubular epithelial cells. We further find that the NAD+ biosynthetic pathways are impaired in CS kidney from mice and in human cells.

overall_design: Comparative gene expression profiling analysis of kidney RNA-seq data for WT and CSA HO  and WT and CSBm/m mouse model.

first: Komal

last: Pekhale

first: Vinod

last: Tiwari

first: Tomasz

last: Kulikowicz

first: Christy

last: Bridges

first: Deborah

middle: L

last: Croteau

first: Jong-Hyuk

last: Lee

first: Vilhelm

last: Bohr


title: Lumbar 5 (L5) nerve compression affects adjacent DRGs and distal nerve

city: Shanghai

first: Jian

last: Zhou

address: No. 600, Yi Shan Road, Shanghai

institute: Shanghai Sixth People's Hospital

summary: Painful radiculopathy, mainly caused by physical damage to spinal nerve roots, brings algesia in their innervated areas. Intriguingly, the region of paresthesia is not always limited to the injured neuron-innervated area, and abnormal activation is also frequently observed in adjacent intact nerve segments. Since injured and uninjured nerve fibers comingle in one nerve trunk, we propose a hypothesis that the compression of the spinal nerve produces a degenerative environment at the distal end of the nerve, affecting the undamaged nerve fibers. We divided the rats into two groups: Compression of L5 spinal nerve in the experimental group and sham operation in the sham group. DRGs of L4, L5 and L6, femoral nerve and sciatic nerve were collected for RNA-seq. The results showed that L5 nerve compression resulted in inflammatory response in adjacent non-injured L4 DRG. The femoral nerve and sciatic nerve showed signs of nerve damage and repair. This suggests that injured nerve fibers can influence the properties of adjacent intact fibers through the nerve trunk which they converge.

overall_design: Rat L5 spinal nerve was wrapped with a cannula which internal diameter is 0.5mm for 3 days or 7 days. Then DRGs of L4, L5 and L6, femoral nerve and sciatic nerve were collected from rats for RNA seq.

first: Peng

last: Ding

first: Fang

last: Ye

first: Sihan

last: Tong


title: H3K36me3-coupled DNA Demethylation by DNMT3A Is Essential for Hypoxia-Induced EMT of Cancer Cells [ChIP-Seq]

first: Che-Kun James

last: Shen

overall_design: Compare the genome-wide enrichment profile of DNMT3A under normoxia and hypoxia conditions in SW480 cells.

first: Che-Kun


title: Leptin signalling promotes axonal regeneration in the peripheral and central nervous system

first: Jessica

middle: Sarah

last: Chadwick

address: Du Cane Road

department: Brain Sciences

country: United Kingdom

institute: Imperial College London


title: Leptin signalling promotes axonal regeneration in the peripheral and central nervous system [IFvAL RNA-seq]

summary: Axonal growth is limited or absent following peripheral or central nervous system injury respectively, inhibiting repair. The identification of novel growth-promoting molecular mechanisms is therefore a priority. In the search for dietary-dependent mechanisms that control neuronal regenerative ability, we found, via RNA sequencing, that growth-promoting intermittent fasting (IF) induced leptin expression in sensory neurons of the dorsal root ganglia (DRG). Surprisingly, leptin signalling, whose canonical function is to control energy homeostasis, was critical for the IF-dependent regenerative phenotype. In fact, neuronal conditional deletion of the leptin receptor significantly impaired the regenerative response elicited by IF. Overexpression of leptin in vivo in DRG neurons enhanced axonal regeneration following peripheral sciatic nerve crush (SNC) and central spinal cord injury. Lastly, RNA sequencing following leptin overexpression in DRG neurons showed a significant increase in regenerative gene expression and transcription after SCI, indicating a role for leptin in inducing a euchromatic, transcriptionally active environment that facilitates nervous system repair after injury.

overall_design: Mice underwent either ad libitum or 10 days of intermittent fasting diet. DRG were extracted and processed for RNA-seq.

first: Serger

last: Elizabeth

first: Siimone

last: Di Giovanni


title: Leptin signalling promotes axonal regeneration in the peripheral and central nervous system [LepvGFP RNA-seq]

overall_design: AAV-GFP or AAV-Leptin-GFP was injected bilaterally into the sciatic nerve 4 weeks prior to a dorsal column axotomy. 24 hours post-injury, DRG were extracted and a neruonal enriched population processed for RNA-seq

first: Franziska

last: Müller


title: Determinants of early-onset cachexia in transgenic mouse model of pancreatic cancer

city: Tainan City

first: Po-Hsien

middle: Joseph

last: Huang

address: 1 University Rd.

department: Biochemistry and Molecular Biology

institute: National Cheng Kung University

summary: Since the lack of understanding of signaling mechanisms in cancer cachexia progress, the exact time point of cachexia onset remains unpredictable. To determine the molecular phenotypes of single cells at the utmost approximated timepoint of cachexia onset, we hypothesized that the tumor microenvironment and circulating blood cells could serve as biomarkers of cachexia-onset to map out the determinants of muscle wasting in a mouse model of cancer cachexia. Depending on individual tumors, subcutaneous syngeneic implantation of xenografts derived from the transgenic KrasG12D/+;Trp53flox/flox;Pdx1-Cre mouse model of pancreatic cancer-induced early-onset cachexia (EOCX) and Pre-cachexia (PreCX) in individual recipient mice. To characterize the dominants of cachexia-onset, immediate fresh collection of samples and processing for single-cell RNA sequencing, allowed the analysis of gene expression in the subcutaneous xenografted tumors and the peripheral blood mononuclear cells (PBMC) at the single-cell level. Our dataset classified high-quality cells-- 29,885 PBMCs and 24,925 subcutaneous tumor cells into subtypes. By dissecting the differentially expressed markers genes of EOCX versus the PreCX, these markers may represent the determinants of cachexia in multiple cell types in circulating PBMCs and in tumors at the single-cell resolution.

overall_design: Analysis of scRNA-seq data to compare both PBMC and allograft samples for EOCX versus PreCX KPC mice to discover potential differentially expressed markers genes and biological mechanisms.

first: Yi-Ching

last: Wang

first: Li-Yun

first: Yin-Jer

last: Lu

first: Chia-Jung

last: Chang

first: Szu-Ying

last: Chen

first: Pei-Chia

last: Su

first: Kuan-Lin

first: Ting-Yi

last: Hsu

first: Miao-Neng

last: Hung

first: Ya-Na

last: Wu

first: Shang-Rung

first: Chih-Han

first: Daw-Yang

last: Hwang

first: Yan-Shen

last: Shan


title: Genetic and epigenetic gene inactivation coupling with KRAS activation in human gastric cancer [RNA-Seq]

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

summary: To confirm the differential regulation could occur in gastric epithelial cells as well as fibroblasts, RNA-seq analysis was performed in GES1 cells treated by pLKO lentiviral vectors expressing shRNA against non-target (shNON), TP53, and TGFBR2.

overall_design: Immortalized non-neoplastic gastric epithelial cells, GES1, were transfected with pLKO lentiviral vectors against non-target (shNON), TP53, and TGFBR2. GES1 cells were exposed to puromycin for 4 days for selection, and RNA was extracted. RNA-seq analysis was performed using NexSeq.

first: Keisuke

last: Matsusaka

first: Yasunobu

last: Mano

first: Masayuki

last: Urabe

first: Bahityar

last: Rahmutulla

first: Hiroyuki

last: Abe

first: Yasuyuki

last: Seto

last: Aburatani

first: Masashi

last: Fukayama

first: Atsushi

last: Kaneda


title: Expression Data from CD4+CD25+Nrp1+ regulatory T cells of Foxp3creCREBfl/fl mice

city: Aachen

first: Lin

last: Gan

address: Pauwelsstr. 30

department: IZKF

country: Germany

institute: University Hospital Aachen

summary:
Regulatory T cells (Tregs) are gatekeepers of immune homeostasis and characterized by expression of Foxp3, which maintains Treg identity. The transcriptional activator CREB critically stabilizes Foxp3 expression in vitro. Here we demonstrate that in mice with a Foxp3-specific knockout of CREB, Tregs show a reduced Foxp3 expression in vivo, but surprisingly enhanced expression of IL-13, IL-10, ST-2 and CREM. This rendered such Tregs highly suppressive in vitro and prevents disease activity in Th1 models like T cell mediated transfer colitis in an IL-10 dependent way. On the other hand, type 2 B cell responses were enhanced resulting in high IgE levels and susceptibility towards experimental asthma. Our data suggest that CREB expression in Tregs is important for the balance between Th1 and Th2 responses by regulating ST-2 and IL-10.
We used microarrays to detail the global programme of gene expression in CD4+CD25+Nrp1+ T cells of Foxp3creCREBfl/fl mice

overall_design: Genome-wide transcriptome analyses for Foxp3creCREBfl/fl and WT CD4+CD25+Nrp1+ T cells were performed in independent triplicates using Gene Chip® MTA 1.0 st arrays

first: Kim

last: Ohl

first: Bernd

last: Denecke

first: Klaus

last: Tenbrock


title: Microbial signals in primary and metastatic brain tumors

status: Public on Aug 12 2025

city: Houston

first: Nadim

last: Ajami

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

summary: Gliomas and brain metastases (BrM) are associated with poor prognosis, necessitating a deeper understanding of brain tumor biology and the development of effective therapeutic strategies. While our group and others have demonstrated microbial presence in various tumors, recent controversies regarding cancer-type-specific intra-tumoral microbiota emphasize the importance of rigorous, orthogonal validation. This prospective, multi-institutional study included a total of 243 samples from 221 patients, comprising 168 glioma and BrM samples and 75 non-cancerous or tumor-adjacent tissues. Using stringent fluorescent in situ hybridization, immunohistochemistry, and high-resolution spatial imaging, we detected intracellular bacterial 16S rRNA and lipopolysaccharides in both glioma and BrM samples, localized to tumor, immune, and stromal cells. Custom 16S and metagenomic sequencing workflows identified taxa associated with intra-tumoral bacterial signals in the tumor microenvironment; however, standard culture methods did not yield readily cultivable microbiota. Spatial analyses revealed significant correlations between bacterial 16S signals and anti-microbial and immunometabolic signatures at regional, neighborhood, and cellular levels. Furthermore, intra-tumoral 16S bacterial signals showed sequence overlap with matched oral and gut microbiota, suggesting a possible connection with distant communities. Together, these findings introduce microbial elements as a component of the brain tumor microenvironment and lay the foundation for future mechanistic and translational studies.

overall_design: Two glioma and brain metastasis tissue microarray slides (FFPE, 5 µm) were profiled using the NanoString GeoMx® Digital Spatial Profiler with the Immuno-Oncology Protein Atlas (>570 proteins) and Human Whole Transcriptome Atlas (~18,000 genes), supplemented with custom pan-microbial 16S rRNA probes. Morphology markers were Alexa Fluor 488–SYTO 13 (nuclei) and Alexa Fluor 594–anti-CD3 (TILs). ROIs (300 µm) from high- and low-TIL tumor regions (92 glioma, 90 brain metastases) were UV-cleaved and processed for RNA and protein libraries, pooled at a 2:1 molar ratio, and sequenced on an Illumina NovaSeq 6000 (2 × 27 bp, paired-end). Raw FASTQ files are provided for RNA (WTA + 16S) and protein; processed ROI-level count matrices include both raw and normalized counts.

first: Golnaz

last: Morad

first: Jennifer

last: Wargo


title: Epigenetic gene regulation during astrocyte development

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

institute: KAIST

summary: Numerous literatures report similar time points are important in astrocyte development and transition from neurogenesis to gliogenesis. However, these developmental time points have not been studied in the perspective of chromatin state and the resulting transcriptional changes. In addition, the characteristics of astrocyte in different developmental time point is still unclear. Therefore, we examined the transcriptome and open chromatin regions of astrocytes during its development.

overall_design: Examination of transcriptme and open chromatin regions during astrocyte development. This project contains mouse RNA-seq and ATAC-seq data during astrocyte development.

first: Seongwan

last: Park

first: Junghyun

last: Eom


title: Covalent pan-TEAD inhibitors block YAP activity and demonstrate brain penetrance in Hippo-dependent cancer models

city: Mississauga

first: James

last: Hawley

address: 7070 Mississauga Road

department: Computational Sciences

institute: Roche Canada

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

overall_design: Refer to individual Series


title: Covalent pan-TEAD inhibitors block YAP activity and demonstrate brain penetrance in Hippo-dependent cancer models [RNA-seq]

summary: TEAD proteins are a family of transcription factors that enable the oncogenic activity of deregulated Hippo signaling and are a promising therapeutic target in oncology. Targeting the lipid pocket of TEAD is an established path to inhibit the oncogenic activities of the cofactors YAP and TAZ. Here we present two covalent pan-TEAD inhibitors that bind to the lipid pocket, GNE-8025 and GNE-2181. GNE-8025 binds TEAD proteins covalently at a conserved cysteine residue to engage the lipid pocket and allosterically disrupt the interaction of TEAD proteins with YAP. GNE-2181 is a further optimized version of GNE-8025 with properties that enable brain penetrance in vivo. Both of these small molecules suppress the proliferation of YAP-driven tumor cells both in vitro and in vivo and increase activity of a broad range of inhibitors of the MAPK pathway. We demonstrate that these molecules have exceptional efficacy in Hippo-driven in vivo tumor models, including in a mouse model of brain metastases where GNE-2181 treatment significantly inhibits the growth of intracranial brain tumors. Altogether we present a next-generation class of TEAD inhibitors. The development of GNE-8025 and GNE-2181 is a significant advancement towards potent, specific, and effective Hippo-targeting cancer therapies.

overall_design: 200 000 cells per 6-well, treatment for 48 hours with compounds. Combination single treatment conditions: 1 uM compound + 0.01% DMSO. Final libraries were quantified using Agilent Technologies TapeStation 2200 system (High Sensitivity D1000 Cat# 5067- 5584).

first: Thijs

last: Hagenbeek

first: Jason

last: Zbieg

first: Russel

last: Smith

first: Luca

last: Gerosa

first: Christy

last: Ong

first: Consuelo

last: Torrini

first: Alissa

last: Guarnaccia

first: Sayantanee

last: Paul

last: Lacap

first: Nicole

last: Sodir

first: Marc

last: Hafner

first: Julien

last: Tremblay

first: Bryan

last: Chan

first: Vishal

last: Verma

first: Ramsay

last: Beveridge

first: Peter

last: Hsu

first: Gözde

last: Ulas

first: Lisha

last: Wang

first: Jim

last: Nonomiya

first: Shu

last: Chen

first: Victoria

last: Pham

first: Joshua

last: Webster

first: Jessica

last: Preston

first: Jeff

last: Hung

first: Jeffrey

last: Eastham

first: Debra

last: Dunlap

first: Wendy

last: Lee

first: Paul

last: Beroza

first: Naema

last: Nayyar

first: Scott

last: Martin

first: Eva

last: Lin

first: Julie

last: Weng

last: Foster

first: Francesc

last: Shanahan

first: Rina

last: Fong

first: Gladys

last: Boenig

first: Paola

last: Di Lello

first: Marta

last: Kubala

first: Thomas

last: Hunsaker

first: Mirunalini

last: Ravicahndran

first: Pablo

last: Saenz-Lopez Larrocha

last: Lau

first: Le

last: An

first: Elizabeth


title: Humanized antibody-drug conjugates for SSTR2-positive tumor treatment

city: COLUMBUS

first: Zhuoxin

last: Zhou

state: OH

address: Gateway Lofts Columbus, 2211 Dublin Rd

institute: Ohio State University

summary: Somatostatin receptor 2 (SSTR2) is overexpressed in neuroendocrine tumors (NETs) and meningiomas. The objective of this study was to develop an SSTR2-targeted therapy to treat both tumor types. We engineered and humanized an anti-SSTR2 monoclonal antibody (mAb) demonstrating strong cancer cell binding, internalization in cancer cells, and tumor specificity, as evidenced by flow cytometry, confocal microscopy, and live-animal imaging. Antibody-drug conjugates (ADCs) were generated by conjugating the SSTR2 mAb with potent payloads, including monomethyl auristatin F (MMAF) or mertansine (DM1). In vitro assessments revealed high cytotoxicity across diverse NET subtypes and meningioma cell lines. In vivo efficacy was confirmed in two mouse models, i.e. subcutaneous NET xenografts and intracranial meningioma xenografts, where treatment inhibited proliferation, induced apoptosis and cell death, exhibited minimal toxicity, and extended survival. The mechanism of action was further elucidated through bulk RNA sequencing post-treatment. These findings highlight the therapeutic potential of our humanized SSTR2 mAb for targeted payload delivery in NETs and meningiomas.

overall_design: CH157-MN cells were harvested three days after treatment with 100 nM hSSTR2-MMAF ADC. Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, Germantown, MD, USA). cDNA library construction and bulk RNA sequencing were performed at Novogene America (Sacramento, CA, USA) using the Illumina HiSeq™ X Ten platform.


title: Exosomal miR-193b-3p derived from Astrocytes Protects Cerebral BBB Integrity after Cerebral Ischemia‒Reperfusion via TRPM2 Inhibition

city: fuzhou

first: Huihong

last: Li

state: fujian

address: shangjie

institute: College of Rehabilitation Medicine, Fujian University of Traditional Chinese Medicine

summary: To detect the miRNAs that have undergone significant changes after cerebral ischemia-reperfusion and clarify which miRNAs play a role in this pathological process.

overall_design: Detect the content changes of miRNAs in the brain tissues of the sham operation group and the cerebral ischemia-reperfusion group.


title: mrRNA-directed DNA methylation enables selective mutant oncogene silencing therapy without exogenous proteins

first: Yifan

last: Guo

address: Dongan Road No.150

institute: Fudan university, Shanghai, China

summary: The outcome of recent demethylation therapy is limited by the unspecific hypomethylation of oncogenes. The mechanism underlying differential DNA methylation distribution in the same topological domain remains unclear. Here, we established an efficient framework based on heterogeneity across pan-cancers to systemically characterize DNA methylation regulatory boxes (mrBoxes). Through  plasmid-based functional motif interactome analysis assay, the role of mrBoxes on DNA methylation was validated. Moreover, the U1 small nuclear ribonucleoprotein A (SNPRA) was found to regulate the chromatin localization of DNMT1 to mrBox. In this process, long noncoding RNAs were identified to act as a bridge, connecting the targeted mrBox element and SNRPA/DNMT1 complex. Based on this regulatory model, we synthesized exogenous methylation-regulating RNA (mrRNA), which contains only the mrBox-recognizing and SNRPA/DNMT1 complex-binding motif. Furthermore, we developed a methylation-regulating therapy called “OncoMutation Silence”, which regulates the DNA methylation of mutated oncogenes through mrRNA. The efficacy and specificity of this therapy have been verified in tumors with KrasG12D mutation. Collectively, this study reveals mrBox-related regulatory model of DNA methylation, and provides mrRNA-based tumor therapy for silencing specific mutated oncogenes.

overall_design: ChIP-seq of DNMT1 dynamics in HEK293T cell lines treated with siZFPM2AS1 and siSNRPA

first: Yvan

first: Jie

last: Gu

first: Di

last: Ge

first: Ronghua

last: Liu


title: Disturbed LTB4 metabolism in ILC2 Aggravates Ulcerative Colitis via intercellular ATP accumulation

city: Shan Dong

first: Weijia

address: Shandong Province, Jinan City, Lixia District, Shandong University, Baotu Spring Campus

institute: Shandong University

summary: LTB4 biosynthesis is critically required for cytokine secretion by the group 2 innate lymphoid cell (ILC2), though its underlying regulatory mechanisms remain incompletely characterized. To investigate how LTB4 governs ILC2 functionality, we performed RNA sequencing on sorted murine colonic ILC2s treated with or without SC-57461A—an inhibitor targeting LTA4H, the key enzyme in LTB4 anabolism. This dataset delineates transcriptomic profiles of ILC2 with pharmacologically attenuated versus intact LTB4 synthesis. Here, we identify significant alterations in mitochondria-associated genes (including Fdps, Hmgcs1, and Acat3) upon suppression of LTB4 anabolism in ILC2. These genes encode proteins essential for mitochondrial function and are indispensable for ILC2 energy metabolism. These findings collectively demonstrate that LTB4 synthesis orchestrates mitochondrial functionality in ILC2, thereby modulating their bioenergetic capacity.RNA sequencing was performed for the SC-57461A- or vehicle-treated ILC2 sorted from the large intestine of C57BL/6 mice (n = 4 per group).

overall_design: Sorted large intestinal ILC2s from C57BL/6 mice were cultured in complete IMDM media containing IL-2 (10 ng/mL), IL-7 (10 ng/mL), IL-25 (10 ng/mL), and IL-33 (10 ng/mL) for 5 days, followed by treatment with SC-57461A for 16 hours. The SC-57461A- or vehicle-treated ILC2s were harvested by centrifugation and lysed for RNA extraction.

first: Xiuli

last: Zuo

first: Shiyang

first: Yanqing


title: PDZK1 Protects Against RPE Senescence by Targeting the 14-3-3ε-mTOR Axis to Attenuate Early Diabetic Retinopathy

city: Guangzhou

first: Junbiao

last: Zhang

state: Guangdong

address: No. 183, Zhongshan Avenue West

department: Ophthalmology

institute: The Third Affiliated Hospital of Southern Medical University

summary: In diabetic retinopathy (DR), hyperglycemia induces retinal pigment epithelium (RPE) cell senescence via downregulation of PDZK1. PDZK1 overexpression counteracts senescence by binding 14-3-3ε to modulate mTOR signaling, reducing oxidative stress and enhancing autophagy. Both genetic PDZK1 restoration and pharmacologic senolysis (Nutlin-3a) attenuate retinal senescence and ameliorate early DR pathology, establishing the PDZK1-14-3-3ε-mTOR axis as a therapeutic target

overall_design: Cells are maintained in DMEM with 10 % fetal bovine serum and 1 % penicillin–streptomycin at 37 °C in a humidified 5 % CO₂ incubator. At approximately 50 % confluence, cultures are transduced with PDZK1-overexpressing or control lentivirus (Tsingke) at MOI 10. After 48 h of transduction, 4 μg/ml puromycin is added for stable selection. Control and PDZK1-overexpressing cells are then exposed to 37.5 mM d-glucose for 48 h, after which total RNA is extracted for downstream analysis.

first: Jian

last: Zhao

first: Yanli

first: Lili

last: Wang

first: Chunxi

last: Huang

first: Wei

last: Chi

first: Meixia


title: EML4-ALK variant-specific genetic interactions shape lung tumorigenesis

city: Heidelberg

first: Data

last: Manager

address: Im Neuenheimer Feld 260

department: ODCF

institute: DKFZ

summary: Oncogenic fusions of EML4 and ALK occur in ~5% of lung adenocarcinomas. EML4-ALK variants have distinct breakpoints within EML4, but the functional differences among these variants remain poorly understood. Here we use CRISPR/Cas9 somatic genome editing to generate autochthonous mouse models of the two most common EML4-ALK variants and show that V3 is more oncogenic than V1. By employing multiplexed genome editing and quantifying the effects of 29 putative tumor suppressor genes on V1- and V3-driven lung cancer growth in vivo we show that many tumor suppressor genes have dramatically variant-specific effects on tumorigenesis. Pharmacogenomic analyses suggest that tumor genotype can also modify responses to therapy. Analysis of a large human EML4-ALK lung cancer cohort identified differences in the genomic landscape depending on the EML4-ALK variant. These findings demonstrate functional heterogeneity between EML4-ALK variants, suggesting that EML4-ALK variants behave more like distinct oncogenes than a uniform entity. More broadly, these findings highlight the dramatic impact of oncogenic fusions partner proteins and coincident tumor suppressor gene alterations on the biology of oncogenic fusion driven cancer.

overall_design: RNA-Seq profiling of sorted EGFP positive neoplastic cells from EML4-ALK V1 and V3-driven tumors that were either Setd2-proficient (sgNeo) or Setd2-deficient (sgSetd2).

first: Rocio

last: Sotillo

first: Oscar

last: Gonzalez-Velasco


title: Cellular Heterogeneity of HTII-280–Labeled Epithelial Cells in Healthy and Fibrotic Human Lungs

city: los angeles

first: Changfu

last: Yao

state: Ca

address: 8700 Beverly Blvd. AHSP Room A9401

department: Lung and Regenerative Medicine Institutes

institute: cedars-sinai medical center

summary: Previous work demonstrated that in idiopathic pulmonary fibrosis (IPF), the representation of AT2 cells is markedly reduced, accompanied by an increased presence of airway epithelial populations such as basal cells, — and newly identified pathological states including KRT5⁺KRT17⁻ /aberrant basaloid cells AT2 cells have been implicated as a potential source of both hyperplastic basal cells and KRT5⁺KRT17⁻ cells in IPF, based on findings from ex vivo lineage studies. The in vitro organoid culture studies often rely on in vitro organoid cultures of AT2 cells, which are typically isolated using HTII-280—a monoclonal antibody widely assumed to specifically label human AT2 cells. However, if the isolated HTII-280 populations are heterogeneous or contaminated, these lineage relationships may need to be reconsidered. To directly investigate the cellular composition of HTII-280–labeled cells in both healthy and fibrotic lungs, we performed scRNA-seq on fluorescence-activated cell sorting (FACS)–purified epithelial cells from the same sample, separating HTII-280⁺ and HTII-280⁻ fractions. Each population was independently labeled with TotalSeq anti-human Hashtag antibodies, then pooled at a 1:1 ratio for scRNA-seq analysis. In total, we profiled HTII-280⁺ and HTII-280⁻ epithelial cells from two healthy donor distal lung samples, two fibrotic IPF explants, and one non-fibrotic IPF explant.

first: Barry

last: Stripp


title: Gene Expression of mobPBSC After FVA3-Ang1 Priming

city: seoul

first: hyunju

last: seo

address: CMI, 71 Daehak-ro, Jongno-gu, Seoul, Republic of Korea

institute: seoul national niversity

summary: The FVA3-Ang1 priming strategy was evaluated with a dual focus—safety assessment via modifications in cell characteristics and enhancement of therapeutic efficacy through augmented angiogenic potential. Gene expression patterns were analyzed by total RNA sequencing of mobPBSCs collected from patients diagnosed with acute myocardial infarction.

overall_design: RNA sequencing profiling was performed on G-CSF–mobilized PBSCs from myocardial infarction patients, comparing cells treated with FVA3-Ang1 for 1 hour and 24 hours to untreated controls. Three controls and reference samples.


title: Uncovering gene regulatory differences between human and chimpanzee neural cells [RNA-seq]

city: Boston

first: Janet

last: Song

state: Massachusetts

address: 3 Blackfan St

institute: Boston Children's Hospital

summary: A major challenge in human evolutionary biology is to pinpoint the genetic differences that underlie phenotypic changes in the human lineage, such as increased neuron number and a prolonged period of neuronal maturation. Here, we used human-chimpanzee tetraploid cells to distinguish changes in gene expression due to cis-acting sequence variants that change local gene regulation, from trans expression changes due to species differences in the cellular environment, in neural progenitor cells and excitatory neurons. Using a CRISPR inhibition screen, transcription factor motif analyses, and downstream single-locus studies, we further characterized cis-acting gene regulatory differences, including changes to FOS, TNIK, FOSL2, and MAZ, that influence neurogenesis and neuronal maturation. This study identifies specific genomic changes that may contribute to human neural specializations and provides a general framework for understanding genetic differences that underlie human traits.

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens

overall_design:
We performed RNA-seq of human, chimpanzee, and human-chimpanzee neural progenitor cells and patterned induced neurons. We also performed single-locus CRISPR inhibition followed by RNAseq in human or chimpanzee cells.

***************************************************************
Raw files for human/patient samples are being made available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) for controlled access to the personally identifiable sequence data.
***************************************************************

first: Christopher

last: Walsh

first: Ava

last: Carter

first: Gabriel

last: Koreman

first: Michael

middle: E

last: Greenberg


title: A glycosylation-driven protein complex assembly governs mRNA homeostasis and ensures protein aggregates clearance in cells and organs

city: Hangzhou

first: Yulin

last: Chen

state: Not US or Canada

address: 88 Jiefang Rd, Shangcheng District

institute: The Second Affiliated Hospital of Zhejiang University School of Medicine

summary: Turnover of mRNA, governed by the dynamic balance between synthesis and degradation rates, is a critical mechanism for fine-tuning gene expression. This regulatory process is essential for maintaining mRNA abundance during key biological events, such as maternal mRNA clearance in the maternal-to-zygotic transition and synaptic plasticity during neuronal development. Despite its importance, the molecular mechanisms underlying mRNA turnover and degradation remain poorly understood. In this study, we identify O-GlcNAcylation as a pivotal regulator of mRNA degradation. Specifically, we demonstrate that O-GlcNAcylation of CNOT2 enhances the assembly of the CCR4-NOT complex and augments its ability to regulate the balance of autophagy-related mRNAs. This balance is crucial for maintaining cellular autophagy levels, thereby safeguarding cells from protein aggregation and ensuring cellular homeostasis. Furthermore, we provide evidence that this regulatory mechanism is indispensable for oocyte maturation and the formation of learning and memory. Our findings highlight the central role of O-GlcNAcylation in mRNA turnover regulation and its broader implications for cellular and organismal physiology.

overall_design: TAIL Iso-seq for Cnot2 knockdown HeLa cells as well as control cells.

first: Shixian

last: Lin


title: Covalent pan-TEAD inhibitors block YAP activity and demonstrate brain penetrance in Hippo-dependent cancer models [Quant-seq]

first: James

last: Hawley

overall_design: Total RNA was extracted using the Qiagen RNeasy 96 kit (Qiagen Cat#74181).  Library preparation for next generation sequencing was performed using QuantSeq 3’ mRNA-Seq V2 LibraryPrep Kit FWD (Lexogen Cat# 193.384) and UMI Second Strand Synthesis Module for QuantSeq (Lexogen Cat# 081.96) starting with 20-30 ng total RNA according to the manufacturer's instructions.  Final libraries were quantified using Agilent Technologies TapeStation 2200 system (High Sensitivity D1000 Cat# 5067- 5584).

first: Thijs

last: Hagenbeek

first: Jason

last: Zbieg

first: Russel

last: Smith

first: Luca

last: Gerosa

first: Christy

last: Ong

first: Consuelo

last: Torrini

first: Alissa

last: Guarnaccia

first: Sayantanee

last: Paul

first: Jennifer

last: Lacap

first: Nicole

last: Sodir

first: Marc

last: Hafner

first: Julien

last: Tremblay

first: Bryan

last: Chan

first: Vishal

last: Verma

first: Ramsay

last: Beveridge

first: Peter

last: Hsu

first: Gözde

last: Ulas

first: Lisha

first: Jim

last: Nonomiya

first: Shu

first: Victoria

last: Pham

first: Joshua

last: Webster

first: Jessica

last: Preston

first: Jeff

last: Hung

first: Jeffrey

last: Eastham

first: Debra

last: Dunlap

first: Wendy

last: Lee

first: Paul

last: Beroza

first: Naema

last: Nayyar

first: Scott

last: Martin

first: Eva

first: Julie

last: Weng

last: Foster

first: Francesc

last: Shanahan

first: Rina

last: Fong

first: Gladys

last: Boenig

first: Paola

last: Di Lello

first: Marta

last: Kubala

first: Thomas

last: Hunsaker

first: Mirunalini

last: Ravicahndran

first: Pablo

last: Saenz-Lopez Larrocha

last: Lau

first: Le

last: An

first: Elizabeth


title: Lysine-specific demethylase 1 regulates hematopoietic stem cell expansion and myeloid cell differentiation [ChIP-seq]

city: Freiburg im Breisgau

first: Heike L.

last: Pahl

address: Breisacher Str. 117

institute: University Hospital Freiburg

summary: The lysine-specific demethylase 1 (LSD1) regulates hematopoietic stem cell differentiation and has been identified as a therapeutic target in hematological disorders. LSD1 demethylates mono and dimethylated histones 3 at lysine 4 and 9. In addition, it acts as a scaffold for the formation of chromatin-modifying complexes that regulates the transcription of myeloid-lineage-specific genes in complex with GFI1, a transcriptional repressor. While both enzymatic and non-enzymatic functions of LSD1 have been well defined, the relative importance of these two functions in hematopoiesis remains incompletely understood. Here, we investigated the contribution of enzymatic and non-enzymatic functions of LSD1 to myelopoiesis. We show that myeloid differentiation is independent of the enzymatic functions of LSD1 but requires the non-enzymatic, scaffolding function, which directs GFI1 binding to target sequences. In absence of the LSD1 protein, GFI1 DNA binding is diminished and myeloid cell differentiation arrests at a granulocyte-macrophage-progenitor-like cell stage, which overexpresses Prtn3. We provide functional data implicating Prtn3 as an effector of the stem cell expansion and myeloid maturation block caused by the loss of LSD1.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: ChIP-seq of SPI1 and GFI1 was performed in THP1 cells. ChIP-seq of LSD1 and GFI1 was performed in Cas9-expressing K562 cells transduced with a non-targeting sgRNA (sg-NT) or an sgRNA against LSD1 (sg-LSD1). H3K4me1 RELACS ChIP-seq was performed on CD117+ cells isolated from two LSD1 ei mice and two LSD1 ei ctrl mice.


title: Tumor-Associated Schwann Cell Remodeling under Metabolic Stress via Lactate Sensing Orchestrates Pancreatic Ductal Adenocarcinoma Development.

city: Tianjin

first: xueying

last: Li

address: 94 Weijin Road, Nankai District

institute: Nankai University