title: Role of Importin alpha3 and importin beta 1 in the peripheral sensory neurons

city: Rehovot

first: Mike

last: Fainzilber

address: Dept. of Biomolecular Sciences

country: Israel

institute: Weizmann Institute of Science

summary:
Project 1: Overall, our work showed using three independent approaches that importin α3 mice have a lower basal sensitivity for noxious heat, show a delayed response to capsaicin-induced pain and recover faster with less pain from a neuropathic pain injury. The data further identified a novel role for an importin α3/c-FOS pathway in the transduction of pain signals. Finally, our preliminary drug screen suggest that two FDA-approved drugs, Sulmazole and Sulfamethizole could be used as new therapeutic to tackle acute and chronic pain.
Project 2: Here, we found that Importin beta 1 3’ UTR knockout embryonic neurons that were treated with NT3 grow longer neurites in DRG explants in two independent culturing regimes. RNA seq revealed a set of genes enriched in the importin beta 1 3’ UTR knockout with on commonality; almost all the candidate genes show a binding sequence for Krüppel-like factor (KLF6) transcription factor. In wild type DRG neurons, KLF6 protein is localized in the soma and in their terminals in “the growth cone” when treated with normal NT3 supplement. However, when NT3 concentration is lowered, KL6 is absent from the soma and from the growth cone. These results suggest a positive and direct link of NT3 to the expression of KLF6 in the growth-cone.

overall_design: There are in total 16 samples. 8 wts and 4 Importin alpha3 -/- and 4 importin beta 1 3'UTR ko samples. The 8 wts were used for both projects analyses due to gender bias effect.

first: Letizia

last: Marvaldi


title: ZNF865 (BLST) Regulates Human Cell Senescence and DNA Damage

status: Public on Nov 30 2025

city: Salt Lake City

first: Jason

last: Gertz

state: Utah

address: 2000 Circle of Hope

department: Oncological Sciences

country: USA

institute: University of Utah

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: ZNF865 (BLST) Regulates Human Cell Senescence and DNA Damage [ATAC-seq]

summary: Senescence has been shown to contribute to the progression of aging related diseases including degenerative disc disease (DDD). However, the mechanisms regulating senescence in the intervertebral disc (IVD) and other tissues/diseases remain poorly understood. Recently, in a CRISPRa genome-wide screen, our lab identified a previously uncharacterized zinc finger protein, ZNF865 (BLST), that regulates a wide array of genes related to protein processing, cell senescence and DNA damage repair. Here, we demonstrate that ZNF865 expression is correlated with age and disease state in human patient IVD samples and mouse IVD. Utilizing CRISPR-guided gene modulation, we show that ZNF865 is necessary for healthy cell function and is a critical protein in regulating senescence and DNA damage in intervertebral disc cells, with implications for a wide range of tissues and organs. We also demonstrate that downregulation of ZNF865 induces senescence and upregulation mitigates senescence and DNA damage in human nucleus pulposus (NP) cells. Importantly, upregulation of ZNF865 shifts the chromatin landscape and gene expression profile of human degenerative NP cells towards a healthy cell phenotype. Collectively, our findings establish ZNF865 as a novel modulator of genome stability and senescence and as a potential therapeutic target for mediating senescence/DNA damage in senescence related diseases and disorders.

overall_design: ATAC-seq was used to identify regions of differential chromatin accessibility in healthy (hNPC), degenerative (dhNPC), and degenerative with ZNF865 activation (ZNF865 VPR dhNPC) nucleus pulposis cells obtained from human donors.

first: Christian

last: Lewis

first: Hunter

last: Levis

first: Jacob

last: T. Polaski

first: Robby

last: D. Bowles


title: A reduced TBX5-dependent gene regulatory network links atrial fibrillation and heart failure [RNA-seq: Tbx5_LV_KO]

city: Chicago

first: Ivan

last: Moskowitz

state: IL

address: 900 East 57th Street, KCBD Room 5102

institute: Univeristy of Chicago

summary: Transcriptomic profiles of cardiac tissue from CD1 mice subjected to sham or transverse aortic constriction (TAC) surgery, a pressure-overload mouse model. Left atrial tissue was collected 9 days post-surgery, and RNA-seq was performed to identify differentially expressed genes between sham and TAC.

overall_design: RNA-seq profiling of left atrial tissue from sham vs. TAC, Day 9 post-surgery

middle: P

first: Sonja

last: Lazarevic

first: Carlos

last: Perez-Cervantes


title: A reduced TBX5-dependent gene regulatory network links atrial fibrillation and heart failure [HI-C]

summary: Atrial fibrillation (AF) and heart failure (HF) frequently co-occur and exacerbate each other's morbidity, yet the underlying molecular mechanisms remain incompletely understood. Here, we compared atrial gene regulatory networks across multiple mouse models of AF (Tbx5 cKO, Zfhx3 KO, Scn1b-null) and HF (TAC, AngII), revealing unexpected transcriptional and genomic convergence between Tbx5 cKO and HF models. Notably, Tbx5 was significantly downregulated in atrial tissue from both murine and human HF samples. We identified over 100 coordinately dysregulated Tbx5- and TAC-dependent transcription factor genes, with cell-type resolution achieved through single-cell transcriptomics. Loss of a TBX5-driven cardiomyocyte gene regulatory network—including Klf15, a transcriptional repressor of hypertrophy—was observed in both AF and HF models, while a shared disease-specific network emerged in activated fibroblasts, notably involving the pro-fibrotic regulator Sox9. These findings define a conserved TBX5-dependent atrial genomic injury response that may underlie the reciprocal pathophysiological relationship between AF and HF.

overall_design: Adult mouse ventricular fibroblasts (AMVFs) were isolated from male C57BL/6J mice using Langendorff perfusion and enzymatic digestion with collagenase type 2. Following isolation, fibroblasts were separated from cardiomyocytes by differential sedimentation and centrifugation, then cultured and passaged once before serum starvation for 18 hours. Cells were subsequently treated with either TGF-β1 (10 ng/mL) or vehicle control for 48 hours to model fibroblast activation. Genome-wide chromatin conformation was assessed using the Arima Genomics Hi-C+ protocol. Libraries were sequenced to approximately 1 billion paired-end reads per group and processed through HiC-Pro for alignment to the mm10 reference genome.

first: Thomas

last: Vondriska

first: Timothy

last: Mckinsey


title: A reduced TBX5-dependent gene regulatory network links atrial fibrillation and heart failure [RNA-Seq]

first: David

middle: S

last: Park

first: Junhua

last: Xiao


title: Arabidopsis thaliana gene expression in seedlings of mutants in exocyst subunits exo70B1, exo70B2 and exo70B1xexo70B2

city: Praha 6

first: Karel

last: Muller

address: Rozvojová 263

department: Lab. of hormonal regulations in plants

country: Czech Republic

institute: Institute of Experimenal Botany of the Czech Academy of Sciences

summary: Several mutants in plant exocyst vesicle-tethering complex have various phenotypes. We decided to look into the differential gene expression for subunits exo70B1, B2 and double B1xB2 mutant, which were found before to be mores susceptible toward Pseudomonas in young developmental stages. We uncovered both the quantitative and qualitative changes in gene expressions among the analysed mutant lines in comparison to WT. We discovered several interesting candidate genes involved in cell wall function, that would be worth of further more focused studies.

overall_design: The seven-day-old whole seedlings (ca 50 seedlings) grown on vertical plates (23oC, 16/8 light/dark) were used as a source of RNA, always as three replicates for each mutant line and WT.

last: Müller

first: Tamara

last: Pečenková

first: Matěj

last: Drs


title: Gradient-Based Regulation of Activin A Directs Multilineage Liver Organoid Development from Human Pluripotent Stem Cells

city: Lisboa

first: Alice

last: Borges

address: Av. Rovisco Pais

country: Portugal

institute: IBB

summary: Morphogen gradients critically regulate the coordinated emergence of endodermal and mesodermal lineages during liver bud formation, yet current human hepatic organoid models inadequately replicate these spatial cues. Here we demonstrate that precise modulation of Activin A concentrations within a dynamic 3D vertical-wheel bioreactor system enables the co-emergence and spatial organization of hepatic epithelium and septum transversum mesenchyme-like populations from human pluripotent stem cells. High Activin levels induce uniform definitive endoderm and enhanced hepatic maturation, whereas low levels promote epithelial tube–like structures encased by mesenchymal cells, recapitulating early liver diverticulum architecture. This gradient-based approach autonomously generates parenchymal and non-parenchymal hepatic lineages, providing a scalable platform to model human liver organogenesis and engineer ventral foregut–derived tissues.

overall_design: RNA-seq profiling of iPS-DF6-9-9T.B cells at Day0, Day3 and Day20 of 3D hepatic differentiation

first: João

last: Cotovio

middle: C

first: Diogo

middle: E

last: Nogueira

middle: A

last: Rodrigues

first: Joaquim

middle: M

last: Cabral

first: Tiago

middle: G

last: Fernandes


title: A reduced TBX5-dependent gene regulatory network links atrial fibrillation and heart failure

last: Moskowitz

type: Non-coding RNA profiling by high throughput sequencing


title: Bulk ATAC-seq analysis of human H1 ESCs differentiated into definitive endoderm and foregut endoderm with our without 2uM Retinoic Acid.

city: Cincinnati

first: Aaron

last: Zorn

state: OH

address: 240 Albert Sabin Way, Bld S

department: Developmental Biology

institute: Cincinnati Children's Hospital and Medical Center

summary: To examine the effect of a high pulse of Retinoic Acid (2uM) during a 24 hour temporal window (days5-6) on the accessible chromatin status of human H1 ESCs differentiated into foregut endoderm.

overall_design: Differentiation of definitive endoderm and foregut endoderm from human H1 ESCs: For differentiation, hESCs were plated as single cells in a Matrigel-coated 24-well dish using accutase (Stem Cell Technologies), at a density of 200,000 cells per well in mTesR1 with ROCK inhibitor Y-27632 (10uM; Stemgent). On the following day, hESCs were differentiated to DE as follows: cells were treated with Activin A (100ng/mL; Cell Guidance Systems) for three days (72hours) in RPMI 1640 media (Invitrogen) containing increasing concentrations of defined fetal bovine serum (dFBS; Invitrogen):  0% (day1), 0.2% (day2), and 2.0% (day3 onwards). In addition, BMP4 (50 ng/mL; R&D Systems) was added for 24 hours on the first day of DE induction. For foregut endoderm differentiation, cells were cultured in RPMI 1640 media with 2.0% dFBS and Noggin (200 ng/mL R&D Systems) for 72 hours (days4-6).  Retinoic acid (RA; 2 μM; Sigma Aldrich) was added for 24 hours from day5-6 to promote posterior foregut fate. Replicate wells were harvested for bulk ATAC-seq analysis after 72 hours (end of day 3) or further differentiated for 72 hours into foregut endoderm, with or without Retinoic Acid treatment for 24 hours (day5-6) and harvested at end of day 6 for bulk ATAC-seq.

first: Scott

last: Rankin

first: Jacek

last: Biesiada


title: The CUT&Tag assay was conducted on protoplasts that had been transiently transformed with OsDOF3-GFP and then sorted using a flow cytometer.

city: Shanghai

first: Han

last: Lu

address: No.220 Handan Road Shanghai

country: China

institute: Fudan university

summary: Crop production is persistently threatened by a multitude of destructive diseases. In rice, the Ca2+ sensor RESISTANCE OF RICE TO DISEASES1 (ROD1) is a key regulator of defense against major pathogens, including those causing blast, sheath blight, and bacterial blight. However, the molecular mechanisms underlying ROD1-mediated immune suppression remain largely elusive. Here, we characterize an immune signalling cascade comprising the B3-domain transcription factor OsVAL2, the DOF transcription factor OsDOF3, as well as their downstream target OsCSE encoding a caffeoyl shikimate esterase. We demonstrate that the OsVAL2-OsDOF3-OsCSE module promotes lignin deposition and cell wall fortification to confer broad-spectrum disease resistance. ROD1 interacts with and sequesters OsVAL2 in the cytoplasm, thereby preventing its nuclear translocation and subsequent initiation of this immune program. Our findings reveal a spatiotemporal regulatory mechanism that maintains immune homeostasis, highlighting the crucial role of cell wall remodelling in crop disease resistance.

overall_design: Protoplasts were isolated from 14-day-old hydroponically grown wild-type rice seedlings (TP309). These protoplasts were then transiently transformed with the OsDOF3-GFP construct. Approximately 200,000 GFP-positive cells were collected using fluorescence-activated cell sorting (FACS). After centrifugation, the cell pellets were harvested, and chromatin fragmentation was performed using the Vazyme TD904-C2 kit. The experimental group (OsDOF3_CUTTAG) was incubated with a GFP antibody, while the no-antibody control (OsDOF3_control_CUTTAG) was processed in parallel. Finally, libraries were constructed following the kit's protocol and sent for sequencing.

first: Yangxuan

last: Liu

first: Mingjun

last: Gao


title: Raw ChIP-seq data of OsVAL2 overexpression materials, using an anti-FLAG antibody.

overall_design: We germinated homozygous OsVAL2 overexpression materials (Ubi_OsVAL2_FLAG) using hydroponics. Leaves from 14-day-old seedlings were ground in liquid nitrogen. Subsequently, the chromatin was fragmented by sonication following standard ChIP-seq procedures, and 20 µl of this sample was aliquoted as the control group (OsVAL2_control_ChIP). DNA fragments immunoprecipitated with FLAG beads were used as the experimental group (OsVAL2_ChIP). The samples were then used for library construction, sequencing, and subsequent data alignment and analysis..


title: The Unique Efg1 Fungal Virulence Regulon in the Catheterized Bladder Environment.

city: Notre Dame

first: Alyssa

last: La Bella

state: IN

address: 278 Galvin Life Science

department: Biological Sciences

institute: University of Notre Dame

summary: Urinary catheterization, a common procedure in hospitals and nursing home facilities, is a primary driver of hospital-acquired infections (HAI). These devices frequently lead to catheter-associated urinary tract infections (CAUTIs), which often progress to severe complication, sepsis, and ultimately death. The fungus Candida albicans has emerged as the second most common causative agent of CAUTIs; yet, its pathogenesis is poorly understood, which complicates development of efficient treatments. Previously, we identified the transcription factor Efg1 as a critical virulence driver in C. albicans CAUTIs. However, its specific downstream targets within the unique bladder microenvironment remained unknown. This study identifies, for the first time, the complete Efg1 regulon that is active during growth in human urine. We confirmed the clinical relevance of this discovery, finding that many of these Efg1-regulated factors are present and significantly upregulated in catheter samples from patients with C. albicans infections. Furthermore, we characterized two of these key factors, ECE1 and EED1, validating their roles both in vitro in urine conditions and in vivo using a CAUTI mouse model. Identifying the tissue-specific downstream targets of Efg1 elucidates the precise mechanism of fungal CAUTI. This knowledge provides a new roadmap for developing targeted therapeutics, offering vital antimicrobial-sparing strategies to combat these life- threatening infections.

overall_design: RNA-seq profiling of C. albicans SC5314, SN250 efg1∆/∆, and SN250 EFG1 Complement from fibrinogen-urine or fibrinogen-YPD biofilms for 48 hours at 37 Celsius. RNA-seq profiling of C. albicans transcriptomes isolated from urinary catheters.

first: Nicholas

last: Gervais

first: Kurt

middle: N

last: Kohler

first: Chloe

middle: L

last: Obernuefemann

first: Ilse

middle: D

last: Jacobsen

first: Rebecca

last: Shapiro

first: Michael

last: Caparon

middle: J

last: Hultgren

first: Ana

last: Flores Mireles

first: Felipe

middle: H

last: Santiago Tirado


title: Arabidopsis thaliana gene expression in adult leaf tissue of mutants in exocyst subunits exo70B1, exo70B2 and exo70B1xexo70B2

first: Karel

last: Muller

summary: Several mutants in plant exocyst vesicle-tethering complex have various phenotypes. We decided to look into the differential gene expression for subunits exo70B1, B2 and double B1xB2 mutant, which were found before to be mores susceptible toward Pseudomonas in young developmental stages, but may develop enhanced resistance in later stages of development (especially exo70B1). We uncovered both the quantitative and qualitative changes in gene expressions among the analysed mutant lines in comparison to WT. We discovered several interesting candidate genes involved in stomatal and cell wall function, that would be worth of further more focused studies.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from A. thaliana leaf tissue from WT and mutants. exo70B1, exo70B2 and double exo70B1xB2

last: Müller

first: Tamara

last: Pečenková

first: Matěj

last: Drs


title: Transcriptomic Profiling of Escherichia coli Reveals Regulatory Roles of the 3′ UTR-Derived sRNA UhpU Under Various Growth Conditions

first: Chuan

last: Wang

address: 131 # Dong An Road

institute: Fudan University

summary: 1.To investigate the biological function and regulatory impact of the 3′ UTR-derived small RNA (sRNA) UhpU, we performed comparative transcriptomic analysis of wild-type and ΔuhpTU deletion strains during growth in M9CA medium supplemented with Glucose-6-phosphate as the sole carbon source.  2:To investigate the biological function and regulatory impact of the transcriptional repressor MprA, we performed transcriptomic analyses in Escherichia coli with short-term pulse expression of MprA during LB growth.

overall_design: 1. To assess the endogenous role of UhpU, RNA was isolated from wild-type and ΔuhpTU E. coli strains grown in M9CA +0.1% Glucose-6-phosphate medium to OD₆₀₀ ~0.4. Stranded RNA-seq libraries were prepared after DNase I treatment to compare transcriptomic differences attributable to the absence of UhpU under standard conditions. 2.The E. coli ygaH’-mprA sequence was cloned and expressed in a ΔmprA strain. Cultures were grown in LB medium to OD₆₀₀ ~1.0. MprA expression was induced with 0.2% L-arabinose for 10 minutes. RNA was extracted and processed as above, with the empty vector serving as a negative control.

first: Cheng

last: Bei

first: Qian


title: A reduced TBX5-dependent gene regulatory network links atrial fibrillation and heart failure [ncRNA-Seq]

first: Ivan

last: Moskowitz

overall_design: non-coding RNA-seq profiling of left atrial tissue from sham vs. TAC, Day 9 post-surgery

first: Sonja

last: Lazarevic

first: Carlos

last: Perez-Cervantes

first: David

last: Park

first: Junhua

last: Xiao


title: HIF-1α CUT&Tag binding profile reveals a multifaceted regulation of steroidogenesis

city: Dresden

first: Ben

last: Wielockx

address: Fetscherstrasse 74

country: Germany

institute: IKL, Carl Gustav Carus Universitätklinikum Dresden

summary: The production of steroid hormones by the adrenal cortex is essential for maintaining homeostasis in response to stress. Disruptions to this process have been linked to various diseases, including congenital defects in steroid synthesis, Cushing syndrome, and adrenal tumors. Therefore, proper regulation of steroid hormone levels is essential for maintaining physiological balance and overall health. Hypoxia is a key regulator of adrenal steroidogenesis acting via the stabilization of HIF-1α transcription factors. We recently identified HIF-1α as a regulator of adrenal steroidogenesis through its control of specific microRNAs (miRNAs) that target key steroidogenic enzymes. However, the mechanisms by which HIF-1α influences miRNA expression remain unclear. To address this, we used the Cleavage Under Targets & Tagmentation (CUT&Tag) technique to map HIF-1α binding sites across the genome in a murine adrenocortical cell line. Our analysis of the HIF-1α binding profile revealed putative binding sites not only in classic steroidogenic gene loci, including Cyp11a1, but also in miRNA loci involved in steroid regulation. Crucially, HIF-1α-bound regions included genes involved in miRNA biogenesis and function, such as nuclear microprocessor and cytoplasmic RNA-induced silencing complex (RISC) components. Subsequent analysis of hypoxic transcriptomic profiles demonstrated widespread repression of these miRNA biogenesis and function genes by hypoxia, that could be modulated by HIF-1α. Based on our previous identification of HIF-1α as a regulator of adrenal steroidogenesis, our current findings further support its dual role in directly controlling steroidogenic gene expression via both transcriptional and posttranscriptional mechanisms. These results reinforce the HIF pathway as a master regulator of steroid hormone output under hypoxic conditions.

overall_design: HIF-1α CUT&Tag samples prepared from murine adrenocortical Y-1 cells grown under standard culture conditions in control medium for 24 hours (2 replicates) or Y-1 cells grown under standard culture conditions in the presence of 1 mM DMOG (dimethyloxalylglycine) for 24 hours (2 replicates)

first: Barbara

middle: K

last: Stepien

first: Anupam

last: Sinha

first: Stephen

last: Ariyeloye

first: Anja

last: Krüger

first: Rafał

last: Bartoszewski


title: UVA irradiation promotes ROS-mediated formation of the common deletion in mitochondrial DNA

city: Zürich

first: Shana

last: Strula

address: Schmelzbergstrasse 9

country: Switzerland

institute: ETH Zürich

summary: Ultraviolet (UV) radiation from the sun causes adverse skin changes such as premature aging. UV-induced mitochondrial DNA (mtDNA) alterations, including deletions, contribute to photoaging and cellular dysfunction. The most frequent mtDNA rearrangement is the common deletion (CD), characterized by the loss of nearly one-third of the genome (4,977 bp). Although UV radiation exposure leads to CD formation, the molecular mechanisms initiating UV-induced CD remain poorly defined. In this study, we show that increasing UV doses increase CD levels in human skin fibroblasts. UVA exposure increased cellular reactive oxygen species (ROS) and mtDNA oxidation. Antioxidant preconditioning prevented UVA-induced CD accumulation, indicating a ROS-dependent mechanism. Conversely, UVB exposure induced cyclobutane pyrimidine dimers (CPDs) without affecting ROS, suggesting a ROS-independent pathway. Using a 3D full-thickness human skin model, we confirmed UVA-dependent CD formation in both epidermis and dermis. RNA-Seq analysis of UVA-exposed fibroblasts revealed upregulation of mitochondrial DNA replication genes and downregulation of mtDNA repair genes. Taken together, our findings provide insight into how UVA and UVB differ in their detrimental effects on mtDNA, with UVA impacting mtDNA maintenance and transcription via a ROS-dependent mechanism.

overall_design: BJ-5ta cells were exposed to a cumulative dose of 100 J/cm² UVA for 5 days. Each day the cells were exposed twice at 10 J/cm² with a 2 h recovery period in between.  On day 5, cells were harvested and RNA was extracted for RNA-Seq. The experiment was performed in 5 replicates per condition (UVA-exposed and control).

first: Gabriele

last: Fontana

first: Navnit

last: Singh

first: Nadezhda

last: Rotankova

first: Antonia

last: Eichelberg

first: Michela

last: Di Filippo

first: Michael

last: Mc Arthur

first: Franziska

last: Wandrey

first: Susanne

last: Heldmaier

first: Hans-Dietmar

last: Beer

last: Sturla

first: Hailey

last: Gahlon


title: Androgen receptor cell-autonomously regulates luminal cell plasticity and regeneration [scRNA-seq]

city: New York City

first: Dan

last: Li

state: NY

department: HOPP

institute: Memorial Sloan-Kettering Cancer Center

summary: Comparision of single cell transcriptomes of Intact, Ar knockout, castrated or DHT treated prostate cells after 2 weeks Ar knockout, 5 days and 14 days castration, 2 days and 14 days DHT treatment.

overall_design: Alive Ar knockout or castrated or DHT treated prostate cells were sorted by Fluorescence-activated cell sorting (FACS) according to DAPI and analyzed using scRNAseq. Each sample contains 3 different mice as biological replicates, each replicate was labelled with Biolegend TotalSeq™-C0301/C0302/C0303 Hashtags separately, and mixed as one sample for scRNA sequencing.

first: Yu

last: Chen


title: Macrophage heterogeneity and spatial localization in granulomas characterize early responses in Mycobacterium tuberculosis infected nonhuman primates.

city: Ithaca

first: Davide

last: Pisu

address: 930 Campus Road

department: Microbiology and Immunology

institute: Cornell University

summary: Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), is defined by granulomas—immune aggregates that either contain or support bacterial replication. Macrophages, fundamental components of these lesions, are crucial to TB pathogenesis, yet their phenotypic and functional diversity remains incompletely understood. Here, we used single-cell RNA sequencing and immunofluorescence to profile macrophages in lung tissue and granulomas from a nonhuman primate model of early TB. We identified transcriptionally distinct subsets, including embryonic-origin tissue-resident alveolar macrophages and monocyte-derived alveolar and interstitial macrophages, each with distinct spatial localization in granulomas. Tissue-resident alveolar macrophages and a subset undergoing epithelial-to-mesenchymal transition accounted for the highest frequency of Mtb-infected cells. Infected cells exhibited differential expression of immune- and migration-associated genes compared to uninfected counterparts, suggesting Mtb either induces or exploits these pathways as a survival strategy. These findings highlight macrophage heterogeneity as a major driver of differential susceptibility to Mtb and provide insights relevant to future immunomodulatory strategies.

overall_design: CITE-seq analysis of macrophages from granulomatous and non-granulomatous NHPs lungs infected with mCherry-positive Mtb. Cynomolgues macaques have been infected with mCherry-positve Mtb Erdman. 5 weeks post-infection animals have been necropsied and lung tissue sections from granuloma and non-granuloma regions cryopreserved with CellBanker2. Samples have then been thawed at 37C, processed with the GentleMacs tissue dissociator, stained with TotalSeq antibodies at 4C, sorted to enrich for macrophages and processed for CITE-seq. We used the standard 10X and commercially available Biolegend protocols to generate sequencing libraries.

first: Persis S

last: Sunny

first: Molly L

last: Nelson

first: Beth F

last: Junecko

first: Roopa

last: Venugopalan

first: Jake H

last: Borish

first: Pauline

last: Maiello

first: Charles A

last: Scanga

first: Philana Ling

last: Lin

first: Mark A

last: Rodgers

first: David G

last: Russell

first: Joshua T

last: Mattila

first: JoAnne L

last: Flynn


title: The fate of cell to cell transfer via tunnelling nanotubes in astroglia upon alpha synuclein protofibril treatment

city: Bengakuru

first: Sangeetha

last: Nath

state: Karnataka

address: MAHE Bengaluru, BSF Campus, Govindapura

department: Manipal Institute of Regenerative Medicine

country: India

institute: Manipal Academy of Higher Education

summary: Pathogenic aggregates of α-SYN can release from degenerating neurons, which can be taken up by surrounding neurons and glial cells. Neurodegenerative proteins induce biogenesis of f-actin-based intercellular membrane nanotubes (TNTs) and these TNTs facilitate inter-cellular transfer of prion proteins, viruses and cell organelles. Recent study from our lab reported, FAK-mediated regulation of Rho-associated kinases plays a significant role in actin membrane modulation, the biogenesis of TNTs, and successively proliferation. TNT-mediated cell-to-cell transfer not only accelerated degradation of α-SYN protofibrils, but helped cells to eliminate toxic dysfunctional mitochondria and curb ROS levels. In this study we observed the transfer of mitochondria through tunneling nanotubes and the fate in the transcription level expression. We hypothesize that the increase in ROS may induce the transfer of defective mitochondria and their clearance in the acceptor glial cells.

overall_design: The experimental setup involved treating U-87 MG, alpha-synuclein protofibrils at 1 μM, 37°C, 5% CO₂ for durations of 3, and 24 hours. Control is without the addition of alpha-synuclein protofibrils .

first: Sangeeta

last: NATH


title: Expresion data from yeast  (wild type strain and sus1 mutant) exposed to Congo Red (CR)

city: Madrid

first: Raul

last: Garcia

state: Madrid

address: Plaza Ramon y Cajal s/n

department: Microbiologia y Parasitologia

country: Spain

institute: Universidad Complutense de Madrid

summary: We did transcription profiling on the effect of SUS1 (global transcriptional regulator, component of SAGA, TREX-2 complexes) deletion in genes involved in Congo Red response (3 hours of treatment).

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Three biological samples for wild type strain and sus1 mutant were analyzed.  Two microarray experiments were carried out for each biological sample:  1. absence of the drug   2. presence of 30 microg/ml of Congo Red for two hours


title: CRISPR-Cas9 base editor screening identifies the spectrum of MEN1 mutations impacting menin inhibitors in clinical trials [RNA-Seq]

city: Boston

first: Scott

last: Armstrong

state: MA

address: 450 Brookline Ave

department: pediatric oncology

institute: Dana Farber Cancer Institute

summary: Menin inhibitors have entered clinical trials for KMT2A-rearranged and NPM1 mutant acute leukemias and are demonstrating promising activity. CRISPR-Cas9 base editor screening previously predicted several MEN1 mutations that have arisen in patients receiving SNDX-5613 and confer menin inhibitor resistance. The extent to which MEN1 mutations will impact each menin inhibitor is currently unknown. We leveraged advances in CRISPR-Cas9 base editing technology to predict the MEN1 mutation profile that will impact five different menin inhibitors in clinical trials. We found key similarities (M327) and differences (C334, E368, V372) in the profile of MEN1 mutations that affect each compound. The co-crystal structure of menin bound to each compound suggests resistance mechanisms related to how each menin inhibitor binds in the KMT2A binding pocket of menin. Our in vitro and in vivo validation suggests that the MEN1 mutations identified and validated with this approach are likely to arise and impact all menin inhibitors.

overall_design: A patient derived xenograft model was established from a patient who had AML with a KMT2A::EPS15 gene rearrangement. In the current experiment, two mice received vehicle control therapy, two mice received VTP-50469 (SNDX-5613 pre-clinical analogue) at a dose of 0.03% chow, and two mice received VTP-50469 0.1% chow. After 4 weeks of treatment of treatment, mice were euthanized, leukemia cells were obtained, and the mice were euthanized and RNA-sequencing was performed.

first: Wallace

last: Bourgeois

first: Florian

last: Perner


title: Infusible Extracellular Matrix Biomaterial Enhances and Expedites Cell-Specific Pro-Repair Following Acute Myocardial Infarction

city: La Jolla

first: Karen

last: Christman

state: California

address: 2880 Torrey Pines Scenic Drive

department: Shu Chien-Gene Lay Department of Bioengineering

institute: University of California San Diego

summary: Myocardial infarctions (MI) affect 805,000 people per year in the United States. To mitigate the pathological effects of MI, we have developed and investigated pro-reparative decellularized extracellular matrix (ECM) biomaterials: an intravascularly infusible ECM (iECM). However, no one has ever utilized single cell and spatially resolved transcriptomics to further probe how systemically administered infusible ECM can elicit pro-repair in an MI model. Thus, we utilize spatial transcriptomics and single nucleus RNA sequencing (snRNAseq) to further measure pro-repair in various cell types, and thus validate these findings with spectral flow cytometry.With iECM, we found pro-reparative macrophage activation, fibroblast remodeling, increased vasculature development, and cardioprotection. Thus, we depict the pro-reparative nature of decellularized ECM biomaterials on cardiac cell types and elucidate previously undiscovered therapeutic pathways, further demonstrating infusible ECM’s potential as an MI therapy.

overall_design: Gene expression profiling of 10x Genomic Chromium single nucleus RNA-Seq or Visium spatial transcriptomics from the left ventricular myocardium short axis sections  on injured Sprague Dawley female rats (225-250 g). Injuries include I/R (45 minutes of ischemia followed by reperfusion).

first: Joshua

last: Mesfin

first: Alexander

last: Chen

first: Maria

last: Karkanitsa

first: Justin

last: Yu

first: Quincy

last: Lyons

first: Van

last: Ninh

first: Emily

last: Gardner

first: Elyse

last: Wong

first: Sriya

last: Paleti

first: Colin

last: Luo

first: Zhenxing

last: Fu

first: Kevin

last: King


title: DNA methylation analysis of colonic epithelial cells from 5-AZA and DSS treated mice

city: London

first: Samuel

last: Asfaha

address: 1151 Richmond St

country: Canada

institute: Univeristy of Western Ontario

summary: Transposable elements (TEs) comprising nearly 50% of the genome are generally silenced by epigenetic mechanisms. Epigenetic anti-cancer drugs can lead to their re-expression, however, the role of TEs in tumorigenesis is unknown. Here, we demonstrate that TEs and their activation of a viral mimicry response plays an important tumor suppressive role in inflammation. We discovered that both patients and mice with colitis express TEs that lead to a viral mimicry response. Interestingly, this response inhibits stemness of cancer-initiating cells. Further activation of viral mimicry by DNA hypomethylation inhibits tumorigenesis. Conversely, knockout of the anti-viral signaling protein MAVS promotes tumorigenesis and reverses the anti-tumor effect of DNA hypomethylation, confirming a tumor suppressive role of viral mimicry. Consistent with this finding, patients with colitis-associated dysplasia show decreased expression of TEs and interferon-related genes. These findings suggest that activation of viral mimicry inhibits stemness and plays a key tumor suppressive role in inflammation.

overall_design: DNA methylation status was meaused of colonic epithelial cells isolated C57Bl6/J mice (n=3 in each group) treated with 5-AZA-2'-deoxycytidine and 2.5% dextran sodium sulfate. The mice received one dose of 5mg/kg 5-AZA-2'-deoxycytidine (5-AZA) or vehicle (saline) 2 days prior to DSS treatment for 5 days and the remaining two doses of 5-AZA, 5 and 10 days following the end of DSS treatment. 14 days post the end of DS, colonic epithelial cells were isolated from the colons of mice and bisulfite converted DNA were then hybridized to the Illumina Mouse Methylation BeadChip array.


title: Longitudinal Gene Expression Changes in PTSD Following Sub-Anaesthetic Oral Ketamine Administration

city: Birtinya

first: Nathan

last: Wellington

state: QLD

address: 12 Innovation Pkwy,

department: Thompson Institute

country: Australia

institute: University of the Sunshine Coast

summary: This study investigates the differential gene expression in response to sub-anaesthetic oral ketamine treatment of PTSD to identify key molecular markers in building a predictive profile in determining longer term treatment outcomes. This study highlights the utility of integrating gene expression data with clinical outcomes to elucidate a molecular profile receptive to ketamine’s sustained therapeutic effects.

overall_design: Building on clinical data gathered from the sub- anaesthetic Oral Ketamine Trial of PTSD (OKTOP) (Prince Charles Hospital (PCH) Human Research Committee ethics number: HREC/18/QPCH/288. USC ethics number: A181190), a six week open-label, dose-ranging clinical trial conducted between 2021 and 2024 by the Thompson Institute (QLD, Australia) we collected and processed blood samples from the same participants at Baseline (BAS), 1 Week post ketamine treatment (Week 7) and 4 weeks post ketamine treatment (Week 10) Twenty three Adult male and female participants, aged 18 and above, diagnosed with PTSD were recruited. Eligibility was confirmed using the Clinician-Administered PTSD Scale for DSM-5 (CAPS-5). Baseline assessments, including a physical examination, urinalysis, standard clinical blood tests, and medical history, were completed within 14 days prior to the ketamine treatment. Participants received a sub-anaesthetic dose of oral ketamine weekly, monitored by a psychiatrist and health clinician. The initial dose was set at 0.5 mg/kg and gradually increased by 0.1-0.5 mg/kg each week based on individual tolerance, with a maximum dose of 3.0 mg/kg. Samples were collected within 24 hours of post administration, processed into whole blood, serum, plasma, and peripheral blood mononuclear cells (PBMCs). RNA was extracted and 20 million RNA-Seq read was conducted through NovaSeq. Reads were QC’d, trimmed and mapped to GRCh38.p14 for differential expression analysis using CLC Genomics Workbench 25.0 (Qiagen).


title: Genome-wide Occupancy Changes of TgHDAC3 Before and After Deletion of Transcription Factor AP2XII-5

city: wuhan

first: xue

last: lilan

state: 请选择...

address: shizishan

institute: huazhong agriculture university

summary: Toxoplasma gondii is a ubiquitous protozoan parasite with a complex life cycle containing multiple developmental stages. The parasites have distinct gene expression patterns at different stages to enable stage specific life activities, but the underlying regulatory mechanisms are largely unknown. In this study, we identified a nuclear complex that controls the expression of developmentally regulated genes, especially merozoite specific genes. This complex consists of the AP2 family transcription factor AP2Ⅻ-5, the epigenetic factors MORC and HDAC3, as well as a novel AP2Ⅻ-5 interacting protein 1 (AIP1) that stabilizes this complex. At the tachyzoite stage when the parasites proliferate rapidly by asexual endodyogeny, AP2Ⅻ-5 binds to the promoter regions of developmentally activated genes and recruits MORC and HDAC3 to suppress their expression. When sexual commitment and merozoite development is triggered, the abundance of AP2Ⅻ-5 decreases and its suppression on target genes is relieved. In contrast to MORC and HDAC3, which regulate Toxoplasma development but are also essential for tachyzoite growth, AP2Ⅻ-5 and AIP1 are dispensable for tachyzoite proliferation in vitro. These data suggest that while MORC and HDAC3 have broad regulatory activities, forming a complex with AP2Ⅻ-5 and AIP1 enables them to specifically regulate gene expression during development.

overall_design: To determine the HDAC3 binding sites in the genomes of ME49 and ΔⅫ-5 strains using CUT&Tag.

first: Lilan

last: Xue

first: Bang

last: Shen


title: Development of CAR T cells Targeting U5 snRNP200 for the Treatment of Acute Myeloid and B-Lymphoid Leukemias

city: New York

first: Omar

last: Abdel-Wahab

state: New York

address: 1275 York Ave

department: Molecular Pharmacology Program

institute: Memorial Sloan Kettering Cancer Center

summary: Developing chimeric antigen receptor (CAR) T cells for acute myeloid leukemia (AML) has been challenging due to a lack of known AML-associated antigens which spare normal hematopoietic precursor cells. Here we reasoned that donor auto-antibodies from AML recipients cured following allogeneic transplant and responsible for graft-versus-leukemia effect could be engineered to create effective CAR-T cells. We generated CAR-T cells against one such antigen - U5 snRNP200, an RNA helicase localized to the surface of AML cells and absent from normal hematopoietic precursors. Anti-U5 snRNP200 CAR T cells were effective in human and syngeneic models of AML as well as B acute lymphoblastic leukemia (B-ALL), a setting where surface U5 snRNP200 was also present. IL-18 armoring augmented target antigen expression due to cell surface trafficking of U5 snRNP200 with CD32A. These data thereby identify a CAR-T cell platform which addresses prior limitations in tumor-selectivity and safety for patients with acute leukemias.

overall_design: We employed Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) and T-cell Receptor Sequencing (TCR-seq) to simultaneously capture gene expression, surface proteomes, and the T-cell receptor repertoire. The  TotalSeq-C Mouse Universal Cocktail (BioLegend) was applied to CD45.1+ endogenous blood cells as well as CD45.2+ RN2 leukemia, donor-derived T, and control or anti-U5 snRNP200 IL18-armored chimeric antigen receptor (CAR) T cells.

first: Takeshi

last: Fujino

first: Maxim

middle: I

last: Maron

first: Anthony

middle: F

last: Daniyan


title: Prior High Fiber Intake Impinges on the Cellular Responses of Mesenteric Adipose and Intestinal Tissues to Subsequent High Fat Feeding

city: Huddinge

first: Zhi

last: Peng

state: Stockholm

address: Blickagången 16

department: MedH

country: Sweden

institute: Karolinska Institutet

summary: Dietary modification by consuming plant-based food with high fiber content is a primary strategy to induce weight loss in obese individuals. However, long-term usage of such fiber-enriched dieting is challenging and rapid weight regain often occurs once the high-fat dietary habit resumes. Currently, how do adipose and intestinal tissues respond to a switch between high-fiber and high-fat diet remains unknown. Here, we applied C57BL/6J mice to chow diet (CD)/high-fiber diet (HfiD)-to-high-fat diet (HFD) switching paradigms and collected mesenteric white adipose tissue (mWAT), duodenum and colon tissue sections at different time points for single-nucleus profiling and spatially resolved transcriptomic analysis, respectively. We show that the progenitors and adipocytes of HfiD-fed mWAT are more sensitive to HFD-induced molecular changes. In addition, HfiD feeding prevents the subsequent HFD-induced expansion of immune-related enterocytes in duodenum and reverses the HFD-induced enterocyte-to-goblet cell conversion in colon. Moreover, HfiD-induced microbiome changes are mostly abrogated upon HFD feeding. Our results indicate that prior HfiD feeding can alter the cellular response of adipose and intestinal tissues to subsequent HFD feeding, which highlights the impact of dietary interventions with fiber-rich food for obesity treatment from a different perspective. Our data provide a spatiotemporal resource for future hypothesis-driven studies on the mechanisms of adipose and intestinal tissue plasticity in response to diet switches.

overall_design: To investigate how switch between HfiD and HFD shapes the intestinal and adipose tissues, we applied freshly weaned C57BL/6J male mice to either a control diet (CD) (AIN93G) or an HfiD (AIN93G supplemented with inulin for 5 weeks, before switching both groups to an HFD (AIN93G supplemented with 60 kcal% fat) and collected different cohorts of mice right before, 4 and 8 weeks after switching to HFD for analysis.

first: Meng

last: Xie


title: OSGEP-mediated tRNA t6A modifications promotes leukaemogenesis and mediates the reistance of cytarabine in AML

city: Guangzhou

first: XiaPing

last: Miao

state: GuangDong

address: 10 Luoxuan 3rd Road, Guangzhou International Biotech Island, Guangdong, China

institute: Guangzhou KingMed Center for Clinical Laboratory

summary: Emerging research highlights the role of RNA modifications, especially tRNA modifications, in the progression of human cancers, though the molecular mechanisms remain unclear. In this study, we uncovered that OSGEP which is the  tRNA N6-threonylcarbamoyladenosine (t6A) methyltransferase complex core component is significantly elevated in acute myeloid leukemia (AML) patients and correlates with poor prognosis. Impaired t6A modification upon OSGEP depletion led to decreased cell proliferation, induced cell cycle arrest, promoted apoptosis, and reduced cellular sensitivity to cytarabine. Furthermore, transcriptome and proteome profiling revealed that differentially expressed genes and proteins were enriched in cell cycle and apoptosis pathways. Our study demonstrates that OSGEP-mediated tRNA t6A modification plays a critical role in AML progression and cytarabine resistance, offering potential therapeutic targets for improving treatment outcomes in AML patients.

overall_design:
To investigate the role of OSGEP in AML, we first assessed the expression levels of OSGEP and tRNA t6A modification in AML cells.Then we established HL-60 cell lines in which each target gene has been knocked down by shRNA.
To investigate potential pathways related to cell proliferation, cell cycle, and apoptosis, we performed transcriptome and proteome analyses of OSGEP knockdown in HL-60 cells using RNA-seq and LC-MS/MS, respectively.

first: YaTing

last: Cheng

first: Tao

last: Chen

first: Heng

last: Dong

first: YuHuan

last: Meng

first: XuanRan

last: Tao

first: Kaimin

last: Li

first: RuiZe

last: Gong

first: TongMeng

last: Yan


title: A blueprint for local and distal glioblastoma invasion programs

city: Rehovot

first: Rony

last: Chanoch

state: Israel

address: Weizmann Institute of Science, 234 Herzl Street

institute: Weizmann Instititue

summary: Glioblastoma (GBM) invasion into brain parenchyma presents significant challenges for treatment but remains poorly understood. In this study, we combined single-cell RNA sequencing (scRNA-seq), spatial transcriptomics, and multiplexed imaging of orthotopic xenograft models to investigate GBM invasion. We first screened 20 patient-derived gliomasphere models for their distal (i.e., extending to the contralateral hemisphere) and local invasive potential in mice. We found that models with distal invasion potential are enriched with oligodendrocyte progenitor-like (OPC-like) cells, while models with only local invasion potential are enriched with mesenchymal-like (MES-like) cells. These patterns reflect predominantly peri-axonal vs peri-vascular invasion routes, respectively. Next, we analyzed the transcriptomes of invading cells within models (compared to tumor core) and identified novel programs associated with distal and local invasion. Thus, we decouple transcriptional features associated with invasion potential from those associated with the process of invasion. We validated our findings by spatial transcriptomics and multiplexed imaging, further describing the spatial niche of invasive cells. Taken together, our results provide a blueprint for the invasive potential of GBM cell states and of the programs associated with invasion across different scales.

overall_design: We developed a pooled in vivo system to simultaneously analyze the contralateral invasion capacity of multiple patient-derived GBM models. In this assay, we grew 20 GBM patient-derived gliomasphere models separately and pooled them for stereotaxic injection into the mouse brains (10 models per pool – [Pool #1, Pool #2] with 2 mice replicates). At symptom onset, the mice were euthanized, and brains were dissected under a stereomicroscope and separated into the primary injection site and the contralateral hemispheric invasion fractions. Malignant cells from each site were isolated by flow cytometry based on GFP expression and profiled by scRNA-seq using the 10X Genomics 3’ gene expression platform.To characterize the program expressed by locally-invading glioma, we employed fluorescent-guided microdissection and isolated around 200 malignant cells associated with vasculature within the ipsilateral hemisphere of two non-distally invasive models (MGG65 and MGG123). These cells were profiled by scRNA-seq using SS2, along with around 200 cells of the tumor core of each model.

last: Chanoch-Myers

first: Toshiro

last: Hara

first: Alissa C.

last: Greenwald

first: Itay

last: Tirosh

first: Mario L.

last: Suva


title: Podocyte Aging with and without Hypertension: A Comparative Study in Young and Middle-Aged Mice

city: Cleveland

first: Oliver

last: Wessely

address: 9500 Euclid Avenue/NC10

department: Cardiovascular and Metabolic Sciences

institute: Cleveland Clinic Foundation

summary: Recent studies show that acute injury to non-aged podocytes induces many similarities to healthy aged podocytes, such as decreased lifespan and health-span. Like healthy aged podocytes, injury to young mouse and human podocytes can induce a senescent phenotype. This begs the question if injury to young podocytes phenocopies a healthy middle-aged podocyte, and if the pathways underlying senescence and other injury responses overlap between injured young podocytes and healthy middle-aged podocytes. To address this knowledge gap we induced hypertension, a major cause of chronic kidney disease, in young mice (4m of age~20-year-old human) and in middle-aged mice (18m of age, ~55+ year old human) with deoxycorticosterone and high salt (DOCA) and compared outcomes to non-hypertensive healthy middle-aged mice. In both healthy middle-aged mice and in young mice with hypertension, the increase in age-related senescent genes p16 and p19, along with the stress-related senescent genes p21 and p53 were similar. Bulk RNA-sequencing of podocytes showed that the senescent associated secretory phenotype and individual genes from several aging gene sets were also similar between middle-aged mice and young mice with hypertension. Of the highest enriched Hallmark pathways in middle-aged podocytes, 95% were also enriched in young mice treated with DOCA. Gene set enrichment analysis of podocytes showed that 36 genes overlapped between middle-aged mice, and young and middle-aged mice given DOCA, while 119 genes identified were “DOCA-specific”. These results suggest that hypertension in young mice induces podocyte injury and an aging/senescent phenotype that is similar to the one of podocytes from healthy middle-aged mice.

overall_design: 18 months-old C57BL/6J mice were separated into two groups, (i) a treatment group of mice with Deoxycorticosterone Acetate Salt (DOCA) along with ad libitum access to saline water for 6 weeks and (ii) an untreated control group. Kidneys were removed from the mice at 19.5 months. Podocytes we isolated by MAC sorting and injury and senescence were assessed with mRNA sequencing.

first: Natalya

last: Kaverina

first: R

last: Schweickart

first: Christopher

last: Chaney

first: Jeffrey

middle: W

last: Pippin

first: Thomas

last: Carroll

first: Stuart

last: Shankland


title: OsMAINTENANCE OF MERISTEM LIKE 1 controls style number at high temperatures in rice

city: MILANO

first: Vittoria

middle: Francesca

last: Brambilla

state: MI

address: via Celoria 2

department: Department of Agricultural and Environmental Sciences

country: Italy

institute: Università degli Studi di Milano

summary: OsMAIL1 encodes for a rice protein of the Plant Mobile Domain (PMD) family and is strongly upregulated during floral induction in response to the presence of the florigens Heading date 3a (Hd3a) and RICE FLOWERING LOCUS T1 (RFT1). Although OsMAIL1 expression depends on the florigens, osmail1 null mutants do not show delay in flowering time, rather OsMAIL1 participates in ensuring successful reproduction. Indeed, when day temperatures reach 35°C (7°C higher than standard greenhouse conditions), osmail1 mutants show increased sterility due to abnormal pistil development with about half of the plants developing three styles topped by stigmas. OsMAIL1 expression correlates with that of carpel identity genes and RNA-seq of osmail1-1 mutant compared to the wt during inflorescence development showed that OsMAIL1 is required to activate carpel identity genes expression when floral meristems are about to be initiated. OsMAIL1 is a newly characterized rice gene that specifically controls carpel development under heat stress, ensuring plant female fertility in these conditions

overall_design: Transcriptome comparison between wild type and osmail1-1 rice plants, at two different timepoints (15SDs and 21SDs after induction)


title: Polyethylene Microplastics Breach Chorion Protection, Triggering Cardiotoxicity Across Aquatic Models

city: Yangsan-si

first: Hyerin

last: Lee

address: 49, Busandaehak-ro

country: South Korea

institute: Pusan National University

summary: Polyethylene microplastics are pervasive environmental pollutants that pose potential risks to aquatic organisms. This study investigates the effects of polyethylene microplastics on zebrafish (Danio rerio) embryo development, with a focus on whether the chorion, a protective barrier surrounding the embryo, is effective in blocking polyethylene penetration. Contrary to previous findings that suggested the chorion could prevent larger microplastics (>0.7 µm) from entering, our study demonstrates that polyethylene particles sized 1-4 µm can still negatively impact embryo development without dechorionation. Embryos were exposed to polyethylene at concentrations of 0.01, 0.1, and 1 mg/L, followed by RNA sequencing to assess gene expression changes. Despite no significant differences in survival, hatching, or body length between control and treated groups, a significant reduction in heart rate was observed at higher concentrations, indicating potential sub-lethal cardiotoxicity. Further, qRT-PCR validation confirmed significant downregulation of key heart development-related genes, particularly fbln1 and fn1b, in polyethylene-exposed embryos. Additionally, polyethylene exposure also impacted Daphnia magna, reducing heart rate and delaying growth. These findings highlight the ability of polyethylene microplastics to penetrate natural barriers such as the chorion and induce physiological and developmental changes. Our results emphasize the need for further research into the long-term effects of microplastic exposure on aquatic ecosystems.

overall_design: To confirm whether PE particles larger than the pore size of the zebrafish chorion truly have no effect on zebrafish embryos, PE was administered without dechorionating the embryos, followed by bulk RNA sequencing analysis.

first: Yejin

last: Kim

first: Yun Hak

first: Chang-kyu

last: Oh


title: Single Cell sequencing of human and porcine monononuclear immune cells in cystic fibrosis and healthy controls

city: Munich

first: Gianluca

last: Santamaria

state: Germany

address: Ismaninger Strasse 22

department: Department of Medicine I

institute: Klinikum rechts der Isar – Technical University Munich

summary: The study aimed to compare the gene expression profiles at a single cell level in peripheral blood (human&pig), lung-derived (pig), bone marrow (pig) mononuclear cells (MNC)  between subjects with cystic fibrosis (CF) and disease controls (WT).

sample_organism:
Homo sapiens
Sus scrofa

platform_organism:
Homo sapiens
Sus scrofa

overall_design: Cryopreserved MNC of four donors were pooled and then processed for generating single-cell RNA sequencing libriaries for each genotype, cell source and species.

first: Daniel

last: Reichart

first: Florian

last: Jaudas

first: Nikolai

last: Klymiuk


title: Reappraisal of Soft Tissue Myoepithelial Tumors by DNA Methylation Profiling Reveals an Epigenetically Distinct Group of Mostly Fusion-Driven Neoplasms

city: Memphis

first: Quynh

last: Tran

state: TN

address: 262 Danny Thomas Place, C4029, Mail Stop 250

department: Pathology

institute: St. Jude Children's Research Hospital

summary: Soft tissue myoepithelial tumors (METs) are diagnostically challenging tumors that require careful histologic and immunohistochemical characterization for accurate classification. Nearly half of METs show recurrent EWSR1 or FUS gene rearrangements with a diverse set of fusion partners. The diversity of fusion partners and lack of known driver abnormalities in many cases raise the question of whether METs represent a uniformly distinct tumor entity. To address this question, we performed careful histopathologic and molecular analysis, including DNA methylation profiling (DNA-MP) and fusion testing, on a cohort of 30 institutionally diagnosed METs from 29 patients. On histologic and immunophenotypic evaluation, 22 of 30 tumors diagnosed as MET fulfilled strict histologic and immunophenotypic criteria. Among those failing to meet criteria, most were reclassified as another tumor entity by DNA-MP. 7 tumors meeting criteria grouped with another sarcoma reference type by DNA-MP, with confirmation of the characteristic driver abnormality of that tumor in selected cases. The remaining tumors histologically “consistent” with METs (n = 15) formed a distinct epigenetic cluster, independent of other reference entities. Recurrent gene fusions were identified in 11 of 15 tumors in this epigenetically distinct group, including EWSR1::KLF15 (n= 4), EWSR1::PBX3 (n= 2), and EWSR1::POU5F1 (n = 1)  rearrangements. Clinicopathologic correlation suggests that EWSR1::KLF15 tumors are enriched in pediatric patients with aggressive histology. Our work shows that not all tumors meeting the strict morphologic and immunohistochemical diagnostic criteria for METs fall within one distinct epigenetic tumor group. Furthermore, DNA-MP provides a useful adjunct to other molecular testing to help distinguish METs from histologic mimics

overall_design: Herein, we report genome-wide methylation profiling, copy number analysis, and next generation sequencing of a cohort of 30 soft tissue tumors from 29 patients, all institutionally classified as "myoepithelial neoplasms" based on histologic and immunohistochemical analysis.

first: Brent Orr

last: Faizan Malik


title: Identification of lncRNA-up4 as an Enhancer of Influenza A Virus Replication through Negatively Regulating the Innate Immune Response

city: Fuzhou

first: Nelam

last: Sajjad

state: Fujian, China

address: 15 Shangxiadian road

department: Animal Science

institute: Fujian Agriculture and Forestry University

summary: Inflammation cause a critical role against immune response and activate the macrophages. Current studies have reported that long non coding RNAs (lncRNAs) regulate the gene expression by interacting with various biological molecules. Experimental research has provided insights into the functions of lncRNAs that have significant impact on host-virus dynamics, including response to IAV infections such as H9N2, WSN, and PR8.Given the global health threat posed by influenza A virus (IAV) and its association with severe pneumonia, we investigated the role of host lncRNAs in IAV infection and pathogenesis. RNA microarray analysis of chicken DF1 cells showed regulation changes in 2,118 lncRNAs following 12 hours of IAV infection (H9N2-VS-CON P-value<0.05 & |log2FC| >1). Notably, lncRNA-up4 exhibited significant up regulation post-IAV induction and was associated with IL-6, a critical cytokine involved in excessive inflammatory response to IAV. Functional analysis of lncRNA-up4 revealed that its depletion resulted in decreased viral NP protein accumulation and reduced IL-6, TNFα, IL-1β levels, while increasing IFN-β, MX1, and OAS-1 mRNA expression. Conversely, overexpression of lncRNA-up4 led to increase IL-6, TNF-α, IL-1β, and decreased IFN-β, MX1, and OAS-1 levels. In conclusion, lncRNA-up4 modulates cytokines activity and inflammatory responses, providing insights into its regulatory role in innate immunity and interferon response against H9N2 IAV. This research enhances our understanding of the lncRNA-up4 regulatory network and its potential implication in inflammatory diseases.

overall_design: to investigate the role of novel lncRNAs in chicken DF-1 cells during H9N2 infection

first: Wang

last: Song

first: Ji-long

last: Chen

first: Yang

last: Binxi


title: A functional subpopulation of human glioma associated macrophages linked to malignant glioma progression [scRNA-seq]

first: Kenny

last: Yu

department: Neurosurgery

summary: Malignant gliomas are progressive brain cancers with poor prognosis. Pro-tumorigenic glioma associated macrophages (GAM) have been implicated in disease progression however identification of pathogenic functional subsets is lacking. Macrophage functional specification is driven by transcription factor-associated gene regulatory networks, yet the core regulatory transcription factors that govern GAM functions remain unclear. Here we apply single cell RNA/ATAC sequencing to derive the imprint of the glioma tumor microenvironment on GAM transcriptional program specification and identify cell surface markers to prospectively isolate a functionally distinct subpopulation of GAMs in human samples present high grade tumors irrespective of IDH mutation status. This subset of GAMs, termed malignancy associated GAMs (mGAMs) spatially localize to hypoxic metabolic niches and possess a multitude of pro-tumorigenic functions. mGAMs also share somatic mutations with monocytes, suggesting a common bone marrow origin. mGAMs therefore represent a functional subset of GAMs in humans and a potential therapeutic target.

overall_design: Tumor tissue from glioma operations (IDH wildtype (wIDH, n=7), IDH mutant gliomas (mIDH, n=8), and normal brain control samples from the institutional rapid autopsy program (NB, n=2)) was collected immediately after resection for single-cell dissociation. A portion of the single-cell suspensions were then enriched for CD45+ cells by CD45-MACS enrichment.

first: Zaki

last: Abou-Mrad

first: Kristof

last: Törkenczy

first: Isabell

last: Schulze

first: Jennifer

last: Gantchev

first: Gerard

last: Baquer

first: Kelsey

last: Hopland

first: Evan

last: Bander

first: Umberto

last: Tosi

first: Cameron

last: Brennan

first: Nelson

last: Moss

first: Pierre-Jacques

last: Hamard

first: Richard

last: Koche

first: Caleb

last: Lareau

first: Nathalie

middle: Y

last: Agar

first: Taha

last: Merghoub

first: Viviane

last: Tabar


title: p53 regulates pluripotency of embryonic stem cells via microenvironmental fibronectin-integrin interaction

city: 沈阳市

first: Zonghua

last: Ma

state: 辽宁省

address: 辽宁省沈阳市东北大学浑南校区生命科学与健康学院

institute: Northeastern University

summary: Feeders make necessary contributions to maintaining pluripotency and have been widely used for culturing embryonic stem cells (ESCs).  Here, we showed p53 in feeders is required for ESC self-renewal. Following ablation of p53 in feeders, ESCs attenuated their pluripotent characteristics, with hyperactivation of ERK.  We established that p53 in feeders transcriptionally actives MMP-2 or -9, thereby promoting degradation of fibronectin, preventing its interaction with integrins in ESCs and subsequent activation of integrin/FAK/ERK pathway.  Based on these, we developed a new 2i or 1i system for ESC culture.  Moreover, treatment of human pluripotent stem cells, or tissue stem cells with a fibronectin-integrin inhibitor strongly increased Sox2 and Oct4 levels.  Our findings demonstrate a cross-cell function for p53 in regulating pluripotency, reveal a novel feeder-action mechanism beneficial for developing new stem cell culture conditions.

overall_design: For samples of Control and p53-defective feeders samples


title: A functional subpopulation of human glioma associated macrophages linked to malignant glioma progression [scATAC-seq]

first: Kenny

last: Yu

first: Zaki

last: Abou-Mrad

middle: S


title: A functional subpopulation of human glioma associated macrophages linked to malignant glioma progression

overall_design: Glioma-associated macrophages are thawed and stained for mGAM markers for Fluorescence-activated Cell Sorting (FACS). Sorted cells are then crosslinked in PBS with 1% formaldehyde for 10 min at room temperature, quenched with 0.125M glycine for 5 min and washed in PBS with protease inhibitors (Millipore Sigma, USA) three times before being snap frozen in cryotubes.

first: Kristof

last: Törkenczy

first: Isabell

last: Schulze


title: A functional subpopulation of human glioma associated macrophages linked to malignant glioma progression -RNA-seq

overall_design: Patient-derived PBMCs from non-glioma patients are sorted for CD14+ monocytes through magnetic-activated cell sorting (MACS) using CD14 MicroBeads (Miltenyi Biotech, Germany). These monocytes are then co-cultured alongside a previously established patient-derived GBM cell line, MSK-103. Following the initial three-day co-culture, hypoxia was induced by culturing the cells under 0.5% O2 for 4 hours. Cells from monocultures and co-cultures at normoxic and hypoxic conditions are then collected, stained for CD45 (BioLegend, USA) and sorted through FACS

first: Jennifer

last: Gantchev

first: Gerard

last: Baquer


title: Transcriptome analysis of the CA1 region of the rat hippocampus reveals the signature of experience-induced gene expression in the left and right hemispheres

city: Kanazawa

first: Azusa

last: Kubota

state: Ishikawa

address: 13-1 Takara-machi

department: Graduate School of Advanced Preventive Medical Sciences

country: Japan

institute: Kanazawa University

summary: We aimed to characterize experience-induced gene expression in lateralization and to assess the sensitivity of the left and right CA1 regions of the rat hippocampus to an enriched environment. RNA sequencing was performed on the left and right CA1 region tissues dissected from the rats, which lived in isolated or enriched conditions. Transcriptomic analysis was used to characterize the gene expression profiles of the left and right CA1 regions and to determine the effects of different environmental conditions. Hippocampal CA1 lateralization was observed at the gene expression level in both housing conditions.

overall_design: To investigate the left-right asymmetry of the rat hippocampal CA1 region at the level of gene expression exposed by environmental enrichment, we performed RNA-seq using both sides of hippocampal CA1 tissues, which were dissected from the rats lived in isolated or enriched conditions.

first: Kentaro

last: Kojima

first: Shinnosuke

last: Koketsu

first: Takayuki

last: Kannon

first: Takehiro

last: Sato

first: Kazuyoshi

last: Hosomichi

first: Yoshiaki

last: Shinohara

first: Atsushi

last: Tajima


title: The role of CBLL1 (HAKAI) component of the RNA methyltransferase complex in androgen signaling in breast cancer cells (MDA-MB-231)

city: Nottingham

first: Nigel

middle: P

last: Mongan

address: University Park

department: Biodiscovery Institute

country: United Kingdom

institute: University of Nottingham

summary: CBLL1, also known as HAKAI, plays a dual role in the METTL3-containing RNA m6A methyltransferase complex and as a regulator of e-cadherin protein expression. RNA methylation is known to play diverse functions in the regulation of mRNA processing, splicing, translation and stability. In this study we used siRNA to deplete CBLL1 in the MDA-MB-231 triple negative breast cancer cell line and the effect on global transcription determined.

overall_design: A smartpool of four siRNAs (Dharmacon) were used to deplete CBLL1 in cultured MDA-MB-231 breast cancer cells and the effect on global transcription relative to a non-targetting siRNA scramble control determined using RNA sequencing.

first: Jennie

last: Jeyapalan

first: Anna

last: Harris

first: Catrin

last: Rutland

first: Rachel

last: Thompson

last: Lothion-Roy


title: The role of CBLL1 (HAKAI) component of the RNA methyltransferase complex in basal and estrogen signaling in breast cancer cells (MCF-7)

summary: CBLL1, also known as HAKAI, plays a dual role in the METTL3-containing RNA m6A methyltransferase complex and as a regulator of e-cadherin protein expression. RNA methylation is known to play diverse functions in the regulation of mRNA processing, splicing, translation and stability. In this study we used siRNA to deplete CBLL1 in the MCF-7 breast cancer cell line and determined the effect on basal and estrogen regulated transcription

overall_design: A smartpool of four siRNAs (GE Dharmacon) were used to deplete CBLL1 in cultured MCF-7 breast cancer cells and the effect on basal and estrogen regulated transcription relative to a non-targetting siRNA scramble control determined using RNA sequencing.


title: Prior High Fiber Intake Impinges on the Cellular Responses of Mesenteric Adipose and Intestinal Tissues to Subsequent High Fat Feeding [Spatial Transcriptomics]

first: Zhi

last: Peng

first: Meng

last: Xie


title: m6A Reader IGF2BP3 Regulates Histone-to-protamine Replacement through RNA Translation Repression during Mouse Sperm Development

first: Zhenyi

last: Huang

address: ShaTaiNan Street 1023-1063,Baiyun

department: Development

institute: Southern Medical University

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

overall_design: Refer to individual Series

first: Dazhuang

last: Wang

first: Peiyan

last: Chen

first: Yichun

last: Zhou

first: Mei


title: IGF2BP3 Inhibits Translation in Round Spermatozoa

summary: To reveal the effects of IGF2BP3 on mouse spermatids at the post-transcriptional and translational levels, we performed RNA-seq and ribosome nascent-chain complex sequencing (RNC-seq) of spermatids from Igf2bp3+/- and Igf2bp3-/- mice after isolation. RNA-seq and RNC-seq sequencing showed that IGF2BP3 mainly plays a regulatory role in translational repression in spermatids.

overall_design: RNA-seq and RNC-seq of spermatids from Igf2bp3+/- and Igf2bp3-/- mouse testes by flow sorting. Three biological replicates per sample.

first: D

middle: Z

first: J

middle: X

last: Zhao

first: Y

middle: C

first: Z


title: Transcriptome-wide Identification of RNA Bound by IGF2BP3 in Mouse Testes by eCLIP-seq

summary: The knockout of IGF2BP3 affects the proper progress of spermatogenesis. We use Enhanced Crosslinking Immunoprecipitation Sequencing (eCLIP-seq) to find the targets bound by IGF2BP3 in the testis. After conducting joint analysis with the RNC-seq of knockout mice, we identified that changes in the downstream target genes of IGF2BP3 at the transcriptional and translational levels will damage the conversion of histones to protamines.

overall_design: eCLIP-seq in mouse testes with anti-IGF2BP3 or anti-IgG. Three biological replicates per sample.


title: A novel biallelic missense variant in the BTB domain of ZBTB24 leads to Immunodeficiency, Centromeric instability and Facial anomalies type 2 syndrome

city: Caserta

first: Francesco

last: Cecere

state: Caserta

address: Via A. Vivaldi, n. 43

department: DiStABiF

institute: University of Campania "Luigi Vanvitelli"

type: Methylation profiling by genome tiling array

summary: ZBTB24 is a member of a protein family that includes a Broad-Complex, Tramtrack, and Bric a Brac (BTB) domain, which functions in protein-protein interactions. ZBTB24, a transcription factor, binds its targets through its C-terminus zinc finger (ZF) domain. Biallelic ZBTB24 mutations lead to the rare autosomal recessive Immunodeficiency, Centromeric instability and Facial anomalies subtype 2 (ICF2) syndrome. The majority of the ICF2 patients have biallelic loss of function alleles. The remaining patients have missense variants in their ZF domain. As a consequence, one of ZBTB24’s targets, CDCA7, the gene responsible for ICF3, is not expressed in ICF2 patient cells. Similar to all subtypes of ICF syndrome, ZBTB24 pathogenic mutations lead to significant DNA hypomethylation throughout the genome.   Here we describe a patient with a homozygous variant with unknown significance (VUS), p.Val43Leu, in the BTB domain of ZBTB24. To examine the pathogenicity of this change, we determined DNA methylation levels and patterns in patient blood and lymphoblastoid cells (LCLs). We found significant hypomethylation throughout the patient’s genome, with a methylation pattern identical to that of other ICF2 patients, albeit with less severe hypomethylation. Importantly, the satellite repeats were significantly hypomethylated, a hallmark of ICF syndrome. We found that the p.Val43Leu change significantly reduces the protein’s stability, resulting in very low levels of CDCA7 expression in the patient-derived LCLs. Additionally ,the nuclear pattern of localization of ZBTB24 was disrupted due to this amino acid change. Thus, we demonstrate for the first time that biallelic missense variants in the BTB domain of ZBTB24, can disrupt the normal functionality of the protein and lead to ICF2 syndrome.

overall_design: DNA samples extracted from ICF2 patients (RZ, pV and pD) and Control LCLs, as well as RZ patient peripheral whole blood were subjected to methylation analysis using Infinium MethylationEPIC 850K Bead Chip Array. We assessed the methylation levels at both genome-wide and satellite repetitive elements

first: Maria

middle: R

last: Matarazzo

first: Sara

last: Selig

first: Ido

last: Han


title: scRNA-SEQ OF MECP2 AND MECP2T203M D30 cerebral organoids.

city: beijing

first: Zhihong

last: Song

address: Taiping Road 27

institute: Beijing Institute of Basic Medical Sciences

summary: To further systematically probe the contribution of different cell types for brain development in MECP2T203M organoids, we performed scRNA-seq (10X genomics) on day 30 cerebral organoids.

first: Haitao

last: Wu


title: Dissection by single-cell RNA-sequencing of the cellular composition of mouse salivary gland epithelia (wild-type and irradiated).

city: Nutley

first: Piero

last: Dalerba

state: NJ

address: 111 Ideation Way

department: Center for Discovery and Innovation (CDI)

institute: Hackensack Meridian Health

summary: The major salivary glands (SG) are exocrine glands responsible for the physiological production of saliva, a sero-mucinous fluid that plays a key role in the digestion and swallowing of food, the articulation of speech and the maintenance of oral hygene. Among the principal causes of SG dysfunction is radiation treatment of head-and-neck malignancies, which can cause severe damage to multiple cell-types within the SG epithelium, resulting in permanent loss of saliva production and substantial disability. The aim of this study is to analyze the cellular composition of the mouse SG epithelium using single-cell RNA-sequencing (scRNAseq) in order to: 1) gain a deeper understanding of the rich repertoire of different epithelial cell-types that coexist witin it; and 2) to elucidate whether different sub-types of epithelial cells display different radiosensitivity and are preferentially elimininated from SGs following radiotherapy. The dataset includes data from scRNAseq experiments performed on the epithelial compartment (Epcam+) of mouse adult sub-mandibular glands (C57BL/6J, female), either at baseline (wild type) or following stereotactic X-ray irradiation (30 Gy). In the specific case of wild-type mice, the dataset also includes data from a secind scRNAseq experiment performed on the basal compartment (Epcam+, Cd49f-high) of the sub-mandibular gland, which is postulated to contain a minority population of epithelial cells with stem-progenitor properties.

overall_design:
The cell populations included in the study were sorted by fluorescence activated cell sorting (FACS), starting from the SMG of adult (8-10 weeks) female C57BL/6J mice (The Jackson Laboratory: stock #000664). Each scRNAseq experiment was representative of 3 independent biological replicates (3 independent mice) that were sorted in parallel and labelled with oligonucleotide-tagged antibodies for CITE-seq applications, before being pooled. Mouse SMG were surgically dissected, mechanically disaggregated by mincing into small fragments and then dissociated into single-cell suspensions using DNAse-I (100 units/ml), Collagenase-III (200 units/ml), Hyaluronidase (100 units/ml) for 2 hours, followed by a brief digestion (5 minutes) with Trypsin (0.25%). Single-cell suspensions were stained with monoclonal antibodies against seven differentially expressed surface antigens (Epcam, Cd49f, Kit, Cd3, Cd16/Cd32, Cd31, Cd45) and sorted using a FACSAria-III machine (Becton Dickinson), after exclusion of dead cells (DAPI+), cell doublets (serial gating based on FSC-A vs. FSC-H and SSC-A vs. SSC-H profiles) and cells of non-epithelial lineages (Cd3+, Cd16/Cd32+, Cd31+, Cd45+). In the specific case of the scRNAseq experiment performed on irradiated SGs, the specimens were collected 90 days after selective stereotactic irradiation (30 Gy) of the left submandibular gland, performed under Computed Tomography (CT) guidance (2 Gy/minute) using a Small Animal Radiation Research Platform (SARRP; Xstrahl).
HTO barcode sequence hashtagged samples
TotalSeq™ - B0301 anti-mouse Hashtag 1 Antibody (BioLegend) ACCCACCAGTAAGAC replicate 1
TotalSeq™ - B0302 anti-mouse Hashtag 2 Antibody (BioLegend) GGTCGAGAGCATTCA replicate 2
TotalSeq™ - B0303 anti-mouse Hashtag 3 Antibody (BioLegend) CTTGCCGCATGTCAT replicate 3

last: Viragova

first: Pierangela

last: Palmerini


title: The METTL3:METTL14 RNA methyltransferase regulates gene expression in MDA-MB-231 breast cancer cells

first: Nigel

last: Mongan

summary: siRNAs targeting METTL3 and METTL14 were used to deplete METTL3 and METTL14 in MDA-MB-231 breast cancer cells and the effects on gene expression determined.

overall_design: MDA-MB-231 cells were maintained in in RPMI-1640 medium supplemented with 100 µg/mL penicillin, 100 µg/mL streptomycin, 1 mM sodium pyruvate and 10% fetal bovine serum (FBS).  siRNA-mediated functional depletion of METTL3 and METTL14 was performed in MDA-MB-231 breast cancer cells grown in phenol red-free RPMI-1640 medium supplemented with 1% penicillin-streptomycin, 2mM L-Glutamine and 1 mM sodium pyruvate and 10% FBS. ON-TARGETplus non-targeting control siRNAs (#D-001810-10-05, GE DharmaconTM) were employed as negative controls. Cells were transfected using DharmaFECT Transfection Reagent (GE DharmaconTM) and transfection was performed accoding to the manufacturer's instructions.The effect on global gene expression and alternative splicing was determined by RNA sequencing.

first: Jennie

last: Jeyapalan

first: Catrin

last: Rutland

first: Anna

middle: E

last: Harris

first: Jennifer

last: Lothion-Roy

first: Rachel

last: Thompson


title: bulkRNA-SEQ OF MECP2 AND MECP2T203M D30 cerebral organoids.

summary: To uncover the underlying molecular mechanisms of the low differentiation, we performed bulk RNA analysis to compare the transcriptomes of MECP2 and MECP2T203M organoids.


title: ATAC-SEQ OF MECP2 AND MECP2T203M D30 cerebral organoids.

summary: To evaluate whether chromatin accessibility was affected, we performed chromatin accessibility analysis of D30 cerebral organoids using ATAC-Seq.


title: MECP2 AND MECP2T203M D30 cerebral organoids


title: The effect of METTL3 RNA methyltransferase inhibition on breast cancer cell gene expression

summary: MCF-7 and MDA-MB-231 cells were treated with the STM2457 METTL3 RNA methyltransferase inhibitor. The effect on global gene expression and alternative splicing was determined.

overall_design: MCF-7 were maintained in phenol-red free RPMI-1640 medium supplemented with 100 µg/mL penicillin, 100 µg/mL streptomycin, 1 mM sodium pyruvate, and  10% charcoal “depleted” FBS. MCF-7 cells were either treated with vehicle (DMSO) or estradiol (10nM), alone or in combination with the STM2457 (10µM) METTL3 inhibitor.  MDA-MB-231 cells were maintained in in RPMI-1640 medium supplemented with 100 µg/mL penicillin, 100 µg/mL streptomycin, 1 mM sodium pyruvate and 10% fetal bovine serum (FBS). MDA-MB-231 cells were treated with either vehicle (DMSO) or STM2457 (10µM). Cells were treated twice over 6 days (day 0 and day 3) and RNA harvested on day 6. The effect on global gene expression and alternative splicing was determined by RNA sequencing.

middle: L


title: NAT10-mediated ac4C modification promotes neuroectoderm specification of human embryonic stem cells via acetylating NR2F1 mRNA to enhance translation efficiency [acRIP-seq]

city: Shanghai

first: Ji

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

summary: We use acRIP-seq to report the most comprehensive survey to date of mRNA in human embryonic stem cells (hESCs), neuroepithelial progenitors cells (NEP) and mesendoderm cells (ME)

overall_design: Examing 3 conditions, each with 2 replicates

first: Junbang

last: Ge


title: The METTL3 RNA methyltransferase regulates estrogen signalling in MCF-7 breast cancer cells

summary: siRNAs targeting METTL3 were used to deplete METTL3 in MCF-7 breast cancer cells and the effect on basal and estrogen regulated gene expression determined.

overall_design: A pool of siRNAs were used to deplete METTL3 in MCF-7 breast cancer cells and the effect on basal and estrogen regulated gene expression and alternative splicing determined using RNA sequencing.

first: Corinne

last: Woodcock

first: Lorraine

last: Gudas

first: Michael

last: Toss

first: Emad

last: Rakha

first: Rupert

last: Fray

middle: N


title: Cell-specific transcriptome for comparison of cell surface receptor expression

city: Hannover

first: Ralf

last: Gerhard

state: Lower Saxony

address: Carl-Neuberg-Str. 1

department: Institute of Toxicology

institute: Hannover Medical School

summary: All cells were kept under standard culture condition (HeLa: MEM medium; HT29: DMEM/F12 mix; Caco-2: ).

overall_design: After seeding, cells were kept in culture medium for 48 hours until 70% confluency. Differentiated Caco-2 cells were harvested after 14 days of culture when cells showed transepithelial electrical resistance as marker for formation of tight junctions and for polarization of cell monolayer. Whole transcriptomes of cells were analyzed for comparison of cell-specific expression of surface receptors that contribute to binding and uptake of bacterial toxins.


title: Spatial transcriptomics of bladder cancer with squamous differentiation

status: Public on Nov 29 2025

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

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

summary: We analyze the gene expression of bladder cancer with squamous differenciarion using spatial gene expression analysis techniques (Visium HD, 10x genomics).

overall_design: Formalin-fixed, paraffin-embedded (FFPE) sample of bladder cancer is analyzed with using the CytAssist Visium HD (10x genomics) spatial transcriptomics platform.

first: Ryuta

last: Watanabe

first: Shunsuke

last: Haga

first: Noriyoshi

last: Miura

first: Tadahiko

last: Kikugawa

first: Takashi

last: Saika


title: Mitochondrial fission mediates an evolutionarily conserved innate defense response against bacterial infection

city: Nouzilly

first: ronan

last: kapetanovic

address: Centre INRAE Val de Loire

country: France

institute: INRAE - UMR ISP 1282

summary: Animals must be able to engage pleiotropic immune defense mechanisms against microorganisms to survive infection. Here we reveal an unexpected function for mitochondrial fission in innate immunity, showing this process mediates host defense through antimicrobial lipid droplet production. Bacterial infection activates fission, enabling microbial clearance in mammalian macrophages and Caenorhabditis elegans. The mechanism involves the mitochondrial unfolded protein response (UPRmt), characterized by activation of Atf transcription factor family members in mouse (Atf5) and C. elegans (ATFS-1). Fission and the UPRmt initiate bacterial killing through inducible production of lipid droplets, organelles with antimicrobial properties. Salmonella enterica serovar Typhimurium blocks inducible fission but inhibiting the fusion-promoting enzyme histone deacetylase 6 (Hdac6) overcomes this host subversion, enabling bacterial clearance. We propose that mitochondrial fission has similarities to intracellular bacterial replication, forewarning the host of impending infection. Awakening this ancient pathway in bacterial pathogen-compromised cells could be exploited for host-directed anti-infective strategies.

overall_design: Mouse BMM activated with LPS for 6h before performing Cut&Run for ATF5, H3K27Ac and Control (DRP1)

first: Ronan

last: Kapetanovic

first: Syeda

last: Afroz

first: Ina

last: Kirmes

first: Divya

last: Ramnath

first: Stephan

last: Nothjunge

first: Karoline

middle: D

last: Raven

first: Bernhard

last: Keller

first: Grace

middle: M

last: Lawrence

first: Kaustav

last: Gupta

first: Melanie

last: Shakespear

first: Charles

last: Ferguson

first: Claudia

middle: J

last: Stocks

first: Nilesh

last: Bokil

first: James

last: Curson

first: Gabriele

last: Matthias

first: Tam

middle: T

last: Nguyen

first: Zeinab

middle: G

last: Khalil

first: Robert

last: Reid

first: Karl

middle: A

last: Hansford

first: Philip

last: Hansbro

first: Matthew

last: Cooper

first: Mark

last: Schembri

first: Marta

last: Bosch

first: Albert

last: Pol

first: Antje

last: Blumenthal

first: Kate

last: Schroder

first: David

last: Fairlie

first: Patrick

last: Parton

first: Steven

last: Zuryn

last: Sweet


title: The METTL14 component of the RNA methyltransferase complex influences estrogen signalling in MCF-7 breast cancer cells

first: Nigel

last: Mongan

summary: siRNAs targeting METTL14 were used to deplete METTL14 in MCF-7 breast cancer cells and the effect on basal and estrogen regulated gene expression determined.

overall_design: A pool of siRNAs were used to deplete METTL14 in MCF-7 breast cancer cells and the effect on basal and estrogen regulated gene expression and alternative splicing determined using RNA sequencing.

first: Anna

last: Harris

first: Jennifer

last: Lothion-Roy

first: Corinne

last: Woodcock

first: Rachel

last: Thompson

first: Lorraine

last: Gudas

first: Michael

last: Toss

first: Emad

last: Rakha

first: Catrin

last: Rutland

first: Rupert

last: Fray

first: Jennie

last: Jeyapalan


title: NAT10-mediated ac4C modification promotes neuroectoderm specification of human embryonic stem cells via acetylating NR2F1 mRNA to enhance translation efficiency

first: Ji

last: Wu


title: STING/MITA-CD38 axis in macrophages supports regulatory T cell survival and NSCLC progression.

city: Wuhan

first: Zhidong

last: Zhang

address: Donghu Road, No. 115, Wuchang District

institute: Wuhan University

summary: Mediator of IRF3 activation (MITA, also known as STING) is a cyclic GMP-AMP (cGAMP) receptor that activates type I interferon responses to inhibit tumorigenesis in tumor cells. However, the MITA agonists have limited antitumor efficacy in clinical trials. Here we show that MITA in macrophages promotes the survival of regulatory T cell (Treg) in the tumor microenvironment (TME) and the progression of non-small cell lung cancer (NSCLC) in the KRasG12D autochthonous NSCLC mouse models. Mechanistically, MITA-mediated activation of NF-B upregulates CD38 in monocyte-derived macrophages (MDMs) that metabolizes nicotinamide adenine dinucleotide (NAD) into niacinamide (NAM) and ADP-ribose in the TME. Inhibition of CD38 enzymatic activity or deletion of MITA or CD38 alone or simultaneously in macrophages results in the accumulation of NAD that induces apoptosis of Treg via the ART2-P2RX7 axis and enhances antitumor CD8+ T-cell responses in the TME. Importantly, pharmacological inhibition of CD38 sensitizes mice to the low-dose anti-CTLA4 therapy in the KRasG12D autochthonous NSCLC mouse models. These findings uncover a previously uncharacterized cGAMP-MITA-CD38 axis in MDMs that supports Treg survival and NSCLC progression and highlight potential therapeutic strategies for immune checkpoint blockade (ICB)-resistant cancers.

overall_design: Comparative gene expression profiling analysis of single cell RNA-seq data in immune cells sorted from tumor-burdened lungs of WTKL  and LYZKL mice {transferring the bone marrow cells from Tmem173fl/fl,  Tmem173fl/fl;Lyz2-Cre mice into the lethally irradiated KrasLSL-G12D/+Lkb1fl/fl (KL)  mice}.

first: Dandan

last: Lin

first: Bo

last: Zhong


title: Gut Microbiota Profiling of Lebanese Patients with Ulcerative Colitis and Healthy Controls: A Pilot Study

status: Public on Nov 27 2025

city: Beirut

first: Melhem

last: Bilen

address: Bliss street

department: Department of Experimental Pathology, Immunology and Microbiology

country: Lebanon

institute: American University of Beirut

summary: Ulcerative colitis (UC) is a chronic inflammatory disease of the colon, associated with gut microbiota dysbiosis. While global studies have explored this link, region-specific microbial profiles remain underreported. This pilot study aimed to characterize and compare, for the first time, the gut microbiota of Lebanese UC patients and healthy controls using 16S rRNA gene sequencing (V3–V4 region). Fecal samples from 11 UC patients and 11 healthy individuals were analyzed. Alpha and beta diversity metrics were computed, and gut microbial composition was assessed across taxonomic levels. Statistical comparisons used Mann-Whitney and Fisher’s exact tests. UC patients showed significantly reduced microbial diversity based on Faith’s Phylogenetic Diversity and Shannon index (p < 0.05), though evenness was unaffected. Beta diversity also revealed significant group-level dissimilarities (p < 0.05). At the phylum level, Bacteroidota was elevated in UC, while Bacillota and Actinomycetota were reduced. Genera such as Ruminococcus, Fusicatenibacter, Mediterraneibacter, Eubacterium, and Coprococcus were depleted in UC. Faecalibacterium, commonly reduced in UC, showed no significant difference. This first analysis of gut microbiota in Lebanese UC patients reveals a distinct microbial signature that partially diverges from global trends, supporting the need for region-specific microbiome studies and personalized microbiota-targeted therapies.

overall_design: Cross-sectional, observational, case-control pilot study using 16S rRNA gene sequencing.

first: Fayez

last: Yassine

first: Hassan

last: Abbas

first: Abdallah

last: Kurdi

first: Reem

last: Mansour

first: Fadi H

last: Mourad

first: Ghassan

last: Matar


title: Transfer RNA acetylation regulates in vivo mammalian stress signaling

city: Frederick

first: Colin

state: MD

department: RNA Biology Laboratory

country: USA

institute: NCI

summary: Transfer RNA (tRNA) modifications are crucial for protein synthesis, but their physiological roles remain poorly understood. Here we investigate the impact of N4-acetylcytidine (ac4C), a highly conserved tRNA modification, using a Thumpd1 knockout mouse model. We find that loss of Thumpd1-dependent tRNA acetylation leads to reduced levels of tRNALeu , increased ribosome stalling and collisions, and activation of eIF2α phosphorylation. Thumpd1 knockout mice exhibit growth defects and sterility. Remarkably, concurrent knockout of Thumpd1 and the stress-sensing kinase Gcn2 causes penetrant postnatal lethality, revealing a critical genetic interaction. Our findings demonstrate that a modification restricted to a single site within type II cytosolic tRNAs can regulate ribosome-mediated signaling in mammalian organisms. By providing insight into how tRNA modifications shape signaling and cell fate in response to stress, this work opens up novel strategies for therapeutic intervention and translational control.

overall_design: RNAseq


title: Identification of  pro- and anti-tumorigenic signals from the injury microenvironment following depletion of Nf1 in myelinating Schwann cells

city: Zürich

first: Salome

last: Stierli

address: Winterthurerstrasse 190

department: Institute of Anatomy

institute: University of Zurich

summary: The loss of Nf1 in mSC is not sufficient to induce tumourigenesis, however, we found that after sciatic nerve injury, Nf1- deficient mSCs formed neurofibromas specifically at the wound site (Ribeiro et al., 2013). Remarkably, in contrast to the tumorigenic behaviour of Nf1- deficient SCs at the wound site, they behaved and repaired normally in the distal stump. This indicated that whereas the normal nerve environment suppresses neurofibroma formation, the injury site of the nerve is a tumour- promoting environment, fostering the development of neurofibromas. Using bulk RNA seq, comparing the injury site with the distal stump of Nf1 KO vs Control nerve fragments, we identified TGFB as pro-tumorigenic microenvironmental signal that is highly expressed by pro-tumorigenic macrophages at the site of injury in Nf1-Ko mice.

overall_design: RNA seq profiling of regenerating nerve fragments of Nf1 KO and control mice at 14 days follwing nerve injury. 6 nerve fragments (each fragment had a size of 0.5mm) were combined from multiple mice for each sample. 3 independent samples were sequenced for each region and genotype of interest. Genotypes: P0-CreERT2:YFPfl/fl:Nf1+/+ (CTL) and P0-CreERT2:YFPfl/fl:Nf1fl/fl (loss of Nf1 im myelinating Schwann cells, Nf1 KO)

first: Alison

last: Lloyd

first: Alex

last: Power

first: Cristina

last: Venturini

first: Ilaria

last: Napoli


title: Ms4a7 expression in cDC1s determines cross-presentation and anti-tumor immunity

city: Beijing

first: Bowen

last: Xie

address: Chengfu Road, Haidian District

institute: Tsinghua University

summary: Type 1 conventional dendritic cells (cDC1s) capture antigens in peripheral tissues and migrate to draining lymph nodes (dLNs) to prime antigen-specific CD8+ T cells. How tumor antigens are processed for activating CD8+ T cell immunity are not well understood. Here, we found that Ms4a7 was selectively expressed in cDC1s after engulfing tumor antigens or exposed to exogenous antigens, and required for their cross-priming ability and migration to dLNs. Ms4a7-/- mice showed normal cDC1 development and turnover but failed to prime antigen-specific CD8+ T cells after infection or tumor development. In human cancers, MS4A7 specifically expressed in a subset of cDC1s which preferentially enriched in dLNs, playing a crucial role in patient survival. Our findings reveal a critical role of Ms4a7 in cDC1 migration, cross-presentation and anti-tumor CD8+ T cell responses.

overall_design: For in vitro samle: Flt3L-induced DCs (Day 9) were sorted as live B220-MHC II(high)CD11c(high)CD24+CD172α- (cDC1) and live B220-MHC II(high)CD11c(high)CD24-CD172α+ (cDC2). After treatment with or without LPS (100 ng/ml), cells were collected for RNA-seq and ATAC-seq. For in vivo sample: Tumors grown for 18 days were harvested and cDCs or other antigen presenting cells loaded with (GFP+) or without (GFP-) within TME and dLNs were sorted as as live CD45+TCRβ-MHC IIhighCD11high GFP+ (GFP+ cDCs), CD45+TCRβ-MHC IIhighCD11high GFP- (GFP- cDCs), CD45+TCRβ-MHC II+CD11c-GFP+ (GFP+ nAPCs, non-cDC APCs) and CD45+TCRβ-MHC II+CD11c-GFP- (GFP- nAPCs).

first: Xiaohong

last: Zhao

first: Tian


title: Transcriptome sequencing of normal intestinal mucosal tissues, paired primary CRC tissues and liver metastases lesions in participants of CRC

status: Public on Nov 26 2025

city: Guangzhou

first: Wen

last: Ni

state: Guangdong

address: No. 135, Xingang Xi Road

institute: SUN YAT-SEN UNIVERSITY

summary:
To investigate the key regulators in CRC progression, we carried out transcriptome sequencing in normal intestinal mucosal tissues, paired primary CRC tissues and liver metastases lesions in participants of CRC.
We then performed gene expression profiling analysis using data obtained from RNA-seq of tissues.

overall_design: Transcription profile of normal intestinal mucosal tissues, paired primary CRC tissues and liver metastases lesions in CRC participants.

first: Su

last: Yao

first: Jianming

last: Li


title: Sympathetic Neuron Hyperactivation Drives Hair Follicle Necrosis and T Cell Autoreactivity

status: Public on Nov 25 2025

city: Cambridge

first: Ya-Chieh

last: Hsu

state: MA

address: 7 Divinity Ave, sherman-fairchild

department: Stem Cell and Regenerative Biology

institute: Harvard University

summary: Stress profoundly affects health, but the mechanisms driving stress-induced tissue changes remain poorly understood. Here, we show that strong acute stress drives rapid hair loss and initiates autoimmunity. Under stress, hyperactivated sympathetic nerves release excessive norepinephrine, causing necrosis in rapidly dividing hair follicle transit-amplifying cells (HF-TACs) while sparing most hair follicle stem cells (HFSCs). This differential sensitivity to stress stems from differences in cell death genes, metabolic strategies, and calcium homeostasis. Together, these factors render HF-TACs more vulnerable to the sudden calcium surges triggered by norepinephrine. HF-TAC necrosis releases cellular debris that triggers macrophage clearance and dendritic cell activation, ultimately leading to the activation and amplification of autoreactive T cells that can attack the hair follicle. Our findings reveal mechanistically how stress causes immediate tissue damage in the highly proliferative HF-TACs via sympathetic nerve-induced necrosis, which in turn fuels the activation of a T cell-mediated response against the hair follicle.

overall_design: Cell type: FACS purified cells from mouse skin; 3 conditions: 12H, and 72H RTX treated vs control; 2 replicate for each condition.

first: Emily

last: Scott-Solomon

first: Shlomi

last: Brielle