title: Ectopic recruitment of the CTCF N-terminal domain with two proximal zinc-finger domains as a tool for 3D genome engineering [Hi-C]

first: Artem

last: Luzhin

summary: We developed a panel of chimeric proteins consisting of either full-length or truncated CTCF fused with programmable DNA-binding module dCas9 and fluorescent tracker EGFP. We found that the recruitment of a chimeric protein based on the CTCF N-terminal domain and two zinc-finger domains to the human HOXD locus leads to the de novo formation of a spatial contact with a nearby cohesin/CTCF-bound region anchoring several chromatin loops. This chimeric protein did not show binding to CTCF motifs and did not affect epigenetic and transcription profile of the locus. Recruitment of this chimeric protein is also able to restore chromatin loops, lost after deletion of an endogenous CTCF binding site. Together, our data indicate that the ectopic recruitment of CTCF N-terminal part could be an appropriate tool for the 3D genome engineering.

overall_design: ChIP-seq  and HiC-seq in K562 cells with full or truncated CTCF.

first: Eugenia

last: Tiukacheva

first: Sergey

last: Ulianov


title: Enterocyte dedifferentiation drives colonic regeneration following irradiation injury [scRNA-seq]

status: Public on Aug 16 2025

city: Beijing

first: Mengxian

last: Zhang

address: Beijing

country: China

institute: Tsinghua University

type: Expression profiling by high throughput sequencing

summary: The intestinal epithelium consistently exposes to various injuries and exhibits remarkable regenerative capacity. Although small intestinal regeneration has been extensively investigated, the mechanisms governing colonic regeneration remain poorly understood. Here, we identify irradiation-induced regenerative cells (IRECs), a previously unrecognized colonic enterocyte population, emerges following irradiation injury. IRECs, marked by the gene YuanShangCao (Ysc), undergo dedifferentiation and transition into a stem-like state, contributing to epithelial regeneration. IREC ablation severely impairs colonic repair. Mechanistically, YSC promotes colonic regeneration by preventing the lysosomal degradation of YAP. Furthermore, we demonstrate a critical role of p53 in colonic regeneration by inducing Ysc expression. Together, our findings define IRECs as an irradiation injury-induced enterocyte population that dedifferentiate into stem cells in colon epithelial repair and establish the p53-YSC-YAP axis plays a key role in this process, deepening the understanding of colonic diseases.

overall_design: In this study, leveraging a colon irradiation injury model coupled with single-cell sequencing, we identified a population of irradiation-induced Ysc+ cells. Through RNA velocity analysis and lineage tracing experiments, we demonstrated that these cells are a population of colonic absorptive enterocytes capable of dedifferentiation. They are activated by p53 and play a crucial role in colon regeneration, thereafter we call them irradiation-induced regenerative cells (IRECs). Further, we revealed that as the marker of IRECs, Ysc plays an important role in epithelial injury repair. Organoids deficient of Ysc were found to be more sensitive to irradiation damage, and the colonic injury repair capacity was impaired in mice lacking Ysc. Mechanistically, Ysc can affect lysosome function and activating YAP signaling by inhibiting its lysosomal degradation.

first: Ye-guang

last: Chen

first: Zeyu

last: Zang

first: Wanlu

last: Song


title: Molecular Portraits of Social Adversity in Breast Cancer

status: Public on Aug 15 2025

city: Miami

first: Aristeidis

middle: G

last: Telonis

state: FL

address: 1550 NW 10th Ave

country: USA

institute: University of Miami

type: Non-coding RNA profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Comprehensive transcriptome analysis of the neural stem cell and brain  in control and NSC-specific (P)RR deficienct mice.

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

country: Japan

institute: University of Toyama

summary: (Pro)renin receptor [(P)RR] is a single-pass transmembrane protein and is widely expressed in mammalian tissues. (P)RR acts as a component of the vacuolar ATPase in lysosomes, contributing to the degradation function and autophagy. Mutations in the (P)RR-coding ATP6AP2 have been reported to cause clinical conditions such as X-linked parkinsonism with spasticity. However, our understanding of the role of (P)RR in the whole brain development remains incomplete. We generated mice with neural stem cell (NSC)-specific (P)RR deficiency (CKO). CKO mice exhibited significant brain atrophy during mid-gestation, leading to perinatal lethality. Fetal CKO brains showed lateral ventricular enlargement with malformation of neocortex and ganglionic eminence (GE) from mid-gestation. CKO brains showed massive apoptosis of neuroblasts and other cell types along with microglial activation at E15. We found that CKO NSCs showed reduced proliferation in the primary neurosphere state, while it was recovered after passage, suggesting that (P)RR is not essential for NSCs self-renewal. We also show that cells in the CKO neocortex showed normal proliferation at E15.  In this study, to understand the molecular basis of ATP6AP2-mediated neural stem cell development, we performed a comprehensive analysis of gene expression changes in neural stem cells and whole brain of (P)RR CKO micec using the next-generation RNA sequencing (RNA-seq).

overall_design: mRNA profiles of  whole brain and neural stem cell were generated by RNA sequencing using the Illumina NexSeq 500 (Illumina).

first: Misuzu

last: Hashimoto


title: Single-Cell RNA Sequencing and Spatial Transcriptomics Reveal Unique Subpopulations of Infiltrating Macrophages and Dendritic Cells Following AKI

city: Birmingham

first: Kyle

middle: Hartley

last: Moore

state: Alabama

department: Division of Nephrology

institute: University of Alabama at Birmingham

summary: Kidney infiltrating macrophages (KIMs) and kidney dendritic cells (KDCs) are strongly associated with inflammation and fibrosis in acute kidney injury (AKI). Contrary to kidney resident macrophages (KRMs), which are self-renewing and present in the kidney prior to injury, KIMs are bone-marrow derived F4/80int, CD11bhigh macrophages that infiltrate the kidney during AKI. Here, we combined single-cell RNA sequencing (scRNAseq), spatial transcriptomics, and cellular indexing of transcriptomes and epitopes (CITE)-sequencing to elucidate temporal, spatial, and transcriptional characteristics of unique subpopulations of KIMs and KDCs in AKI. scRNAseq revealed three KIM, two KDC, and one proliferative macrophage subpopulation. All 6 clusters were localized in unique, spatially constrained microenvironments and their locations were dynamically regulated following bilateral ischemic reperfusion injury. We showed that a specific Arginase 1-specific KIM cluster infiltrates the kidney cortex at day 1 post-ischemia. We also identified a macrophage subpopulation that expresses genes specific to cell proliferation that resides in the cortex in uninjured states and in the medulla at day 6 during the reparative phase of AKI. Gene ontology analysis revealed functional characteristics that distinguish each KIM and KDC population. By day 28 post-ischemia, the transcriptional profiles of KIMs significantly upregulate C1q, Cd81, and Cd74, markers normally limited to KRMs in quiescence and early AKI. Because KIMs and KDCs are profoundly involved in AKI, it is paramount we understand their dynamics—temporally and spatially— and identify their key genes and surface protein markers to develop macrophage-specific therapeutics aimed towards targeting kidney disease.

overall_design: Quiescent (uninjured) and mice that received BIRI (Days 1, 6, and 28). scRNA sequencing, CITE-sequencing

first: Arin

middle: L

last: Melkonian

first: Matthew

middle: D

last: Cheung

first: Elise

middle: N

last: Erman

middle: H

first: Jeremie

middle: M

last: Lever

first: Yanlin

last: Jiang

first: Zhengqin

last: Yang

first: Brittany

last: Lasseigne

first: Anupam

last: Agarwal

first: James

middle: F

last: George


title: scRNA-seq Analysis of Dmp1cre-DTAki/wt and wt skin

city: Shanghai

first: Junjie

last: Gao

address: 600 Yishan Road

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: Utilizing the 10X Genomics Cell Ranger (Pipeline Version 3.1.0) platform, this study investigates the impact of osteocyte ablation on skin aging. Skin and bone share significant structural and molecular homology, including compositional architecture, cellular origins, and signaling pathways. Both tissues exhibit parallel degenerative changes during natural aging and under pathological conditions, characterized by collagen depletion leading to osteoporosis and skin atrophy. Through scRNA-seq analysis of skin following osteocyte knockout, our research provides novel insights into the regulatory role of osteocytes in skin aging.

overall_design: Dorsal skin samples were harvested from 8-week-old wild-type (WT) and osteocyte-ablated mice (Dmp1cre-DTAki/wt), followed by subcutaneous fat removal and single-cell dissociation. Single-cell RNA sequencing (scRNA-seq) was subsequently performed for comprehensive transcriptomic profiling.


title: sRNA-seq of Aspergillus fumigatus expressing a pksP or pabA inverted-repeat transgene

city: Jena

middle: George

last: Blango

address: Adolf-Reichwein-Str. 23

department: Junior Resaerch Group RNA Biology of Fungal Infections

country: Germany

institute: Leibniz Institute for Natural Product Research and Infection Biology

summary: The RNA interference (RNAi) pathway has evolved numerous functionalities in eukaryotes, with many on display in Kingdom Fungi. RNAi can regulate gene expression, facilitate drug resistance, or even be altogether lost to improve virulence potential in some fungal pathogens. In the WHO fungal priority pathogen, Aspergillus fumigatus, the RNAi system is known to be intact and functional. To extend our limited understanding of A. fumigatus RNAi, we performed a sRNA-seq to assess sRNAs produced in several RNAi knockouts and a wild type strain expressing a 1200 nt inverted-repeat transgene with complementarity to the pksP gene. We also performed the experiment with a wild-type expressing an IRT with complementarity to pabA. The transgenes harbor a 500-bp inverted repeat.  We included an uninduced and induced wild type strain with no inverted-repeat transgene as a control. All conditions were performed in mycelium grown for 24 hours in liquid culture.

overall_design: Small RNA profiling analysis of Aspergillus fumigatus RNAi  knockouts (𝚫dclA, 𝚫dclB) and wild type expressing a 1200 nt inverted-repeat transgene with complementarity to the pksP or pabA (wt only) gene, using 24-h-mycelium.

first: Xiaoqing

last: Pan

first: Schrettenbrunner

last: Lukas

first: Abdulrahman

middle: A

last: Kelani


title: RNA-seq analysis of 2851 Knockdown with and without ATC

city: CHANDIGARH

first: KHUSHBOO

last: MEHTA

address: SECTOR 39A

country: India

institute: CSIR IMTECH

summary: We have performred RNA-seq analysis of 2851 Knockdown  to investigate the role of this gene in maintaning the homoeostasis of bacterium. RNA was extracted from exponentially growing mycobacterial cells in Middlebrook 7H9 media. For cells with ATC and without ATC, re-suspended in media , and finally the cells were grown further for 0.4-0.6OD at 37°C. After incubation cells were combined with 40 ml of 5 M guanidinium thiocyanate solution containing 1% β-mercaptoethanol and 0.5% Tween 80. Cells were pelleted by centrifugation, and lysed by re-suspending in 1 ml Trizol (Ambion) in the presence of Lysing Matrix B (100 µm silica beads; MP Bio) using a FastPrep-24 bead beater (MP Bio) at a speed setting of 6.0 for 30 seconds. The procedure was repeated for 2-3 cycles with incubation on ice in between pulses. Next, cell lysates were centrifuged at 13000 rpm for 10 minutes; supernatant was collected and processed for RNA isolation using Direct-ZolTM RNA isolation kit (ZYMO) as per manufacturer’s recommendation. Following extraction, RNA was treated with DNAse I (Promega) to degrade contaminating DNA, and integrity was assessed using a Nanodrop (ND-1000, Spectrophotometer). RNA samples were further checked for intactness of 23S and 16S rRNA using formaldehyde-agarose gel electrophoresis, and Qubit fluoremeter (Invitrogen). RNA integrity was checked using Agilent 2200 Tape Station system (Agilent Technologies). Library construction, RNA-sequencing and data analysis have been carried out by Medgenome Labs Private Limited , India. The main purpose of this study is to understand how mycobacteria can sense acidic stress conditions and mount an appropriate stress response.

overall_design: RNA sequencing profile for bacterial culture grown of 2851 knockdown with and without ATC

first: Khushboo

last: Mehta

first: Partha

last: Paul

first: Dibyendu

last: Sarkar


title: A stem cell model identifies two alternative cell fates in CBFA2T3::GLIS2-driven acute megakaryoblastic leukemia initiation (ATAC-seq)

city: Vienna

first: Florian

last: Halbritter

address: Zimmermannplatz 10

country: Austria

institute: St. Anna Children's Cancer Research Institute (CCRI)

type: Genome binding/occupancy profiling by high throughput sequencing

summary: CBFA2T3::GLIS2 (CG) is an oncogenic fusion protein found in high-risk pediatric acute megakaryoblastic leukemia (AMKL). To gain insight into its leukemogenic mechanism, we developed a disease model based on genetically modified human induced pluripotent stem cells. We found that in this model CG expression disrupts myeloid differentiation via two alternate paths: either by delaying differentiation of aberrant megakaryocytes (aMK) or by locking aberrant megakaryocyte progenitors (aMKP) in a proliferative state akin to AMKL tumor cells. We defined the gene-regulatory networks characterizing both cell states by single-cell transcriptome and epigenome analysis and observed that CG sustains aMKP self-renewal along with cooperators like GATA2 and ERG, while repressing differentiation factors such as SPI1, CEBPA, NFE2, and LYL1. In contrast, in aMKs, CG downregulated drivers of self-renewal and upregulated most but not all lineage-specific differentiation factors. Our findings may contribute to strategies selectively targeting the aMKP state in CG-AMKL patients.

overall_design: We established a new hiPSC lines harboring an endogenous conditional CG allele and equipped with a degradation tag.  We generated gene expression (RNA-seq, scRNA-seq), chromatin (ChIP-seq, ATAC-seq), and multimodal (scRNA-seq+scATAC-seq) profilings in longitudinal fashion (early = Day 12-13, intermediate = Day 22-25, longterm = Day 72-115 ) for a comprehensive benchmark and characterization of our model.

first: Mohamed

middle: R

last: Shoeb

first: Dagmar

last: Schinnerl

first: Lisa

middle: E

last: Shaw

first: Matthias

last: Farlik

first: Sabine

last: Strehl

first: Klaus

last: Fortschegger


title: Ectopic recruitment of the CTCF N-terminal domain with two proximal zinc-finger domains as a tool for 3D genome engineering [RNA-seq]

city: Moscow

first: Artem

last: Luzhin

address: Vavilova 34/5

country: Russia

institute: Institute of Gene Biology RAS

first: Eugenia

last: Tiukacheva

first: Sergey

middle: V

last: Ulianov


title: Effect of K14Q MOTS-c treatment on cast immobilization-induced skeletal muscle atrophy

city: Los Angeles

first: Hiroshi

last: Kumagai

state: CA

address: 3715 McClintock Ave

institute: University of Southern California

summary: To understand the effect of K14Q MOTS-c treatment on cast immobilization-induced skeletal muscle atrophy, we injected K14Q MOTS-c into casted mice.

overall_design: Male C57BL/6J mice at 10 wk of age were obtained and assigned to one of the immobilization and K14Q MOTS-c treated group (15 mg/kg/day MOTS-c injection for 8 days, twice a day intraperitoneal injection, n = 8). Hindlimb immobilization was performed by using casting and the casting material was attached to both hinds. After eight days of hindlimb immobilization, mice were euthanized and gastrocnemius muscle was collected under anesthesia with isoflurane for RNA-seq.We then performed gene expression profiling analysis using data obtained from RNA-seq. The RNA-seq data in non-iimobilization control, immobilization control, and immobilization and WT MOTS-c treatment are depositted in GSE212709.


title: A stem cell model identifies two alternative cell fates in CBFA2T3::GLIS2-driven acute megakaryoblastic leukemia initiation (ChIP-seq)


title: Ectopic recruitment of the CTCF N-terminal domain with two proximal zinc-finger domains as a tool for 3D genome engineering [CHIP-seq]


title: Molecular Portraits of Social Adversity in Breast Cancer [RRBS]

first: Aristeidis

last: Telonis

summary: Neighborhood disadvantage (ND) is associated with shorter breast cancer (BCa) survival. Although studies have identified that ND is associated with alterations in DNA methylation (DNAme) or gene expression, a comprehensive study integrating DNAme with coding (mRNA) and non-coding (miRNA, tRNA) transcriptomic data to understand how the epigenome regulates key biological pathways is lacking. DNAme, mRNA, miRNA, and tRNA-derived fragment data were analyzed from 80 ER+/HER2- BCa samples from Hispanic White women with no significant differences in genetic ancestry, BMI, smoking, alcohol, Oncotype DX scores, and stage. We analyzed the association between objective ND [Area Deprivation Index (ADI)], subjective ND [Neighborhood Social Environment Adversity Survey (NSEAS)], DNAme, coding, and non-coding data to understand how the epigenome regulates key biological pathways among women living in ND. The cohort was divided into neighborhood advantage (NA, ADI<5; n=55, 69%) and ND (ADI≥5; n=25, 31%). In tumors from ND, calcium signaling and cell adhesion pathways were hypermethylated, immune-related pathways hypomethylated, immune response genes upregulated, and estrogen response genes downregulated. Small RNA analysis showed differential expression of miRNA isoforms and tRNA-derived fragments related to ND. Subjective ND correlated with epigenetic changes in calcium signaling, cell adhesion, and metabolic pathways, along with upregulation of proliferative and stemness pathways. We discovered novel associations between ND and epigenomic regulation of key clinically relevant oncogenesis pathways associated with aggressive biology, such as estrogen response pathways. These findings lay the foundation for multi-institutional studies to validate our findings and guide future treatment and cancer control interventions.

overall_design: Primary breast ER+/HER2- tumors were collected and homogenized. RNA and DNA were extracted for RNA sequencing and enhanced reduced representation bisulfite sequencing, respectively.

first: Aristeidis G.

first: Maria Eugenia

last: Figueroa

first: Neha

last: Goel


title: Transcriptomic analysis identifies injury-responsive fibroblast populations as potential mediators of Wnt-dependent spinal cord regeneration

city: Salt Lake City

first: Samuel

last: Alper

state: UT

department: Neurobiology

institute: University of Utah

summary: In humans and other mammals, spinal cord injury (SCI) can lead to a permanent loss of sensory and motor function, due to the inability of damaged neurons and axons to regenerate. However, other vertebrate species including zebrafish exhibit complete spinal cord regeneration and functional recovery after SCI. Wnt signaling is required for neurogenesis and axon regrowth in a larval zebrafish SCI model, but the genes regulated by this pathway and the cell types that express them remain largely unknown. In this study, we used bulk RNA-sequencing (RNAseq) to identify candidate genes regulated by Wnt signaling that are expressed after SCI. Using this unbiased screen, we identified multiple genes previously unassociated with SCI in larval zebrafish. Our data reveal potential  novel gene targets and cell populations that may play important roles in spinal cord regeneration.

overall_design: Wild Type larval (AB) zebrafish were subjected to full mechanical transection of the spinal cord at the level of the anal pore at 5 days post fertilization. After a 6hr recovery period, larvae were continuously incubated in 35µm of the wnt antagonist, IWR-1 in 0.25% DMSO. Control larvae were treated with 0.25% DMSO alone. Fresh treatment solutions were added each day after injury until sacrifice and fixation at 8 days post fertilization/3 days post injury. 20 animals were cut to remove a chunk of spinal cord, 1-2 segments caudal and rostral to the injury site, and ventrally, along the notochord. We used the Invitrogen Recover All Total Nucleic Acid Isolation Kit for FFPE to extract the RNA from the tissue samples. This process was repeated for three biological replicates per treatment condition.

first: Richard

last: Dorsky

first: Deeptha

last: Vasudevan


title: Molecular Portraits of Social Adversity in Breast Cancer [smallRNA-Seq]


title: Effect of BMP signaling levels on foregut specification during directed differentiation of BU3 NGPT human induced pluripotent stem cells

city: Boston

first: Pushpinder

last: Bawa

state: Massachusetts

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

summary: To investigate the dose dependent effects of BMP signaling on foregut organ domain specification, we treated hiPSC derived definitive endoderm  with 0μM, 1μM or 2μM of BMP inhibitor DSM during days 3-6 of directed differentiation. We then preformed gene expression analysis of D6 samples between the 3 treatment groups using data generated from the RNA seq

overall_design: Differential gene expression analysis of iPC derived foregut treated with differential concentrations of BMP inhibitor Dorsomorphin

first: Jake

last: Le Suer

middle: S

first: Feiya

last: Wang

first: Finn

middle: J

last: Hawkins


title: Molecular Portraits of Social Adversity in Breast Cancer [RNA-Seq]


title: Hog1/p38 regulates the integrated stress response (ISR) and global transcriptomic changes in C. neoformans during oxidative stress.

city: Buffalo

first: David

last: Goich

state: NY

address: 955 Main St

institute: The State University of New York at Buffalo

summary: Cryptococcus neoformans is an opportunistic fungal pathogen that is responsible for an estimated 112,000 deaths per year. We studied the role of the Hog1/p38 and Gcn2 signal transduction pathways during adaptation of C. neoformans to oxidative stress, a physiologically relevant stressor during infection. Using a combination of molecular assays and RNA-sequencing analysis in Hog1-, Gcn2- and double-deleted mutants, we identify shared targets of these pathways, and investigate a negative feedback loop that regulates induction of the integrated stress response (ISR). We found that simultaneous loss of Hog1 and Gcn2 profoundly impacts the ability of C. neoformans to tolerate oxidative stress. We also show that Hog1 regulates induction of the ISR, and that the Hog1 and Gcn2 pathways converge on repression of abundant, pro-growth mRNA, a key step in translatome reprogramming. Our results establish Hog1 and Gcn2 as key regulators of the response to oxidative stress, and demonstrate that the interplay between these pathways is critical for ROS tolerance in C. neoformans. More broadly, our results demonstrate the extent to which signaling via Hog1/p38 and Gcn2 are linked, and point to extensive recalibration of the cellular signaling apparatus when one of these pathways is disrupted.

overall_design: RNA-seq profiling of WT, hog1∆, gcn2∆, and hog1∆gcn2∆ strains of Cryptococcus neoformans H99 before and after 1 hr of treatment with 2mM H2O2.

first: Julia

last: Furfaro

first: John

middle: C

last: Panepinto


title: The human U5 snRNP assembly factor, AAR2, regulates gene expression dependent on the PRPF8 protein

city: Berlin

first: Marco

last: Preussner

address: Takustrasse 6

institute: FU berlin

summary: Small nuclear ribonucleoprotein complexes (snRNPs) represent the main subunits of the spliceosome. While the assembly of snRNP core particles has been well characterized, the incorporation of snRNP-specific proteins and the mechanisms of snRNP recycling after splicing are less well characterized. Furthermore, little is known about how targeted down-regulation of snRNP assembly factors impacts gene expression. U5 snRNP assembly in yeast requires the Aar2 protein, but the role of the human AAR2 homolog has not yet been investigated in detail. Here, we report a crystal structure of human AAR2 in complex with the RNase H-like domain of the U5-specific PRPF8 protein and in vitro interaction studies of AAR2 with U5 proteins, revealing similarities and differences in the interaction patterns compared to yeast Aar2p. Based on the structure, we probed the importance of interacting regions and residues, and designed AAR2 variants that failed to stably bind PRPF8 in vitro. SiRNA-mediated aar2 knock-down affected the expression levels of many genes. These effects were reversed by expressing siRNA-resistant PRPF8-binding AAR2 variants, but not by a phospho-mimetic AAR2 variant defective in PRPF8 binding. Our results reveal an unexpected role of an snRNP assembly factor in adjusting gene expression levels.

overall_design: HeLa cells were transfected with siRNA CTRL or with siAAR2 for 72 hours. RNA was hybridized to Affymetrix HTA2.0 arrays.

first: Gert

last: Weber

first: Florian

last: Heyd

first: Markus

last: Wahl


title: Hypoxic injury triggers maladaptive repair in human kidney organoids

city: Clayton

first: Laura

last: Perlaza-Jimenez

state: Victoria

address: 15 Innovation Walk

country: Australia

institute: Monash University


title: RNA-seq analysis of various strains of Mycobacterium tuberculosis under glycerol and acetate at acidic Ph

first: KHUSHBOO

last: MEHTA

address: SECTOR 39 A CHANDIGARH

summary: We have performred RNA-seq analysis of WT  under gycerol and acetate at acidic pH to investigate the role of PhoP in maintaning the pH homoeostasis of bacterium. RNA was extracted from exponentially growing mycobacterial cells in Middlebrook 7H9 media. For acid stress, cells at OD600 of 0.6 were pelleted, washed twice with 7H9 medium buffered with 100 mM MOPS or 2N HCl for pH 7.0 or pH 4.5, respectively, re-suspended in media of indicated pH, and finally the cells were grown further for 2 hours at 37°C. After incubation cells were combined with 40 ml of 5 M guanidinium thiocyanate solution containing 1% β-mercaptoethanol and 0.5% Tween 80. Cells were pelleted by centrifugation, and lysed by re-suspending in 1 ml Trizol (Ambion) in the presence of Lysing Matrix B (100 µm silica beads; MP Bio) using a FastPrep-24 bead beater (MP Bio) at a speed setting of 6.0 for 30 seconds. The procedure was repeated for 2-3 cycles with incubation on ice in between pulses. Next, cell lysates were centrifuged at 13000 rpm for 10 minutes; supernatant was collected and processed for RNA isolation using Direct-ZolTM RNA isolation kit (ZYMO) as per manufacturer’s recommendation. Following extraction, RNA was treated with DNAse I (Promega) to degrade contaminating DNA, and integrity was assessed using a Nanodrop (ND-1000, Spectrophotometer). RNA samples were further checked for intactness of 23S and 16S rRNA using formaldehyde-agarose gel electrophoresis, and Qubit fluoremeter (Invitrogen). RNA integrity was checked using Agilent 2200 Tape Station system (Agilent Technologies). Library construction, RNA-sequencing and data analysis have been carried out by Medgenome Labs Private Limited , India. The main purpose of this study is to understand how mycobacteria can sense acidic stress conditions and mount an appropriate stress response.

overall_design: RNA sequencing profile for bacterial culture grown under acetate and glycerol at acidic pH

first: Khushboo

last: Mehta

first: Partha

last: Paul

first: Dibyendu

last: Sarkar


title: Dynamic chromatin accessibility and transcription in salt-tolerant heterosis of Brassica napus

city: Wuhan

first: Junlin

last: Chen

address: No.1, Shizishan Street

institute: Huazhong Agricultural University

summary: Three Brassica napus materials (2063A, B409 and HZ62)growth in Hoagland nutrient solution with 220 mM/L NaCl condition for  0 h, 1 h, 3 h, 6 h, 12 h, 24 h and 48 h post salt stress

overall_design: Samples were collected from the three materials (2063A, B409 and HZ62) during salt stress treatments at a concentration of 1.25% NaCl at the following time points: 0 h, 1 h, 3 h, 6 h, 12 h, 24 h and 48 h post salt stress, and all samples underwent ATAC-seq and mRNA-seq.


title: Hypoxia Triggers Signatures of Maladaptive Repair in Human Kidney Organoids [bulk RNA-seq]

summary: Chronic kidney disease (CKD) affects over half of all adults over 70 and 13% of the global population. The development of renal fibrosis is strongly correlated with loss of kidney function during CKD and involves cellular injury, excessive production of extracellular matrix proteins and inflammation. Current treatments focus on controlling blood pressure, controlling diabetes, and steroid therapies; however, we have no treatments to suppress renal fibrosis. Because hypoxia plays a key role in the development and progression of CKD, we have developed a new model of induced pluripotent stem cell-derived kidney organoids to study in vitro the development of fibrosis in a human model.

overall_design: Eighteen-day old kidney organoids are exposed to hypoxic conditions (1% O2) for 48h. To assess the development of maladaptive repair following acute injury, kidney organoids are afterwards placed back into normoxic conditions (21% O2) for an extra 5 days. Comparative gene expression profiling analysis of bulk RNA-seq data of kidney organoids on day 20 and day 25 of development for both injury and control groups.

first: Ana

middle: B

last: Nunez-Nescolarde

first: Mehran

last: Piran

last: Nikolic-Paterson

first: Alexander

last: Combes


title: Hypoxic injury triggers maladaptive repair in human kidney organoids [scRNA-seq]

summary: Reduction in blood supply to the kidneys occurs to certain extent during acute kidney injury (AKI). Individuals who suffered AKI are at risk of developing chronic kidney disease (CKD) through a maladaptive repair process. Currently, the lack of a reliable research model that allows the characterization of the maladaptive regeneration during such transition, impedes the development of effective therapies. Here, we present the first human kidney organoid model that physiologically and morphologically resembles the AKI and the maladaptive regeneration. Kidney organoids were generated from human induced pluripotent stem cells. After 18 days of grow the organoids were under hypoxic conditions for 2 days to simulate AKI. Organoids were collected at day 20 to assess hypoxic injury, and after a 5-day recovery in normoxic conditions to assess maladaptive repair. The transcriptome, proteome and metabolome were profiled. Gene expression analysis of day 20 hypoxic organoids identified signatures of injury, cell death (necroptosis and ferroptosis), cell cycle arrest and changes in metabolism. The maladaptive repair phenotype was supported by enrichment of pathways associated with inflammatory signals, oxidative stress, and tissue remodelling. Specific genes associated with kidney injury and disease such as GDF15, MMP7, ICAM1, TGFB1, CCN1, C3 and S100A8/9 were upregulated. Single-cell RNA sequencing localized expression of maladaptive repair genes and activation of TNF and JAK-STAT signalling pathways specific to tubular epithelial cells. Dysregulation in metabolic pathways such as glycolysis and gluconeogenesis, amino acid and lipid metabolisms were conserved in this model. Altogether, these results support the use of kidney organoids as a model of AKI and early CKD that can be used for biomarker validation, elucidation of pathological mechanisms, and drug screening.

overall_design: The objective of this study involved evaluating the capacity of human iPSC-derived organoids to model the transition from AKI to CKD, including maladaptive repair. Hypoxia is involved in the pathophysiology of both AKI and CKD, here, we take a holistic approach and analyzed the transcriptome, proteome, and metabolome of organoids cultured under transient hypoxia, with findings validated against patients and animal models. We used three different cell lines to demonstrate reproducibility in different genetic backgrounds. We then used a single cell line as a representative for further investigation. All the experiments were performed using at least three replicates to demonstrate biological reproducibility. We performed quality controls for every differentiation and randomly assigned kidney organoids for experiment and control groups.

last: Perlaza-Jiménez

first: Deanna

last: Deveson

first: Chris

last: Burlow

first: Joel

last: Steele

first: Han-Chung

last: Lee

first: Ralf

last: Schittenhelm


title: Transactivation of EGF receptor in intestinal epithelial cells by 2’-fucosyllactose mediates prevention of colitis in adulthood

city: Nashville

first: Fang

last: Yan

state: TN

address: 2215 Garland Ave., Light hall, Lab No.  1035

institute: Vanderbilt University Medical Center

summary: 2’-fucosyllactose (2’-FL) is a unique oligosaccharide in human milk. We previously reported that 2’-FL protected intestinal integrity, modulated the gut microbial metabolism, and ameliorated intestinal inflammation in adult mice. This study aimed to elucidate mechanisms underlying the direct effects of 2’-FL on intestinal epithelial cells (IECs) for preventing colitis in adulthood. We found that 2’-FL transactivated EGFR in a colonic epithelial cell line, which required 2’-FL-stimulated release of HB-EGF from the cell membrane. Further, findings of 2’-FL-stimulated ADAM17 kinases activity on the cell surface and docking site of 2’-FL to the metalloprotease domain of ADAM17 suggest that 2’-FL could enhance ADAM17 shedding activity for releasing HB-EGF. Remarkably, apoptosis and disruption of tight junction induced by a proinflammatory cytokine and oxidative stress were mitigated by 2’-FL in wild-type, but not EGFR knock-out cell line and colonoids. By using the murine model of colonic injury and colitis induced by DSS, 2’-FL treatment prevented colitis, decreased epithelial apoptosis, and preserved intestinal barrier in wild-type adult mice. These effects were diminished in mice with EGFR deletion in IECs. This study demonstrates a novel mechanism underlying the direct transactivation of EGFR in IECs by 2’-FL that mediates protection of IECs during intestinal inflammation in adulthood.

overall_design: To elucidate if 2’-FL has direct effects on protecting IECs in colitis in adulthood. Established YAMC cells were treated with 2'-FL at 20 μg/ml for 6 hours.Total RNA was isolated for RNA-seq analysis.

first: Kaur

last: Harpreet

first: Ali

last: SyedAzmal

first: Yan

last: Fang


title: The Unique Role of Intracellular Perinuclear β1-Adrenergic Receptors in Defining Signaling Compartmentation and Pathological Cardiac Remodeling.

status: Public on Aug 14 2025

city: Palo Alto

first: Michael

middle: Seth

last: Kapiloff

state: California

address: 1651 Page Mill Road, Room 2112

institute: Stanford University

summary: The purpose of this RNA-seq analysis is to determine if peri-nuclear expression of the Nb80 nanobody or ICL3-9 pepducin affects gene expression in cutlured adult cardiomyocytes

overall_design: Comparison of  RNA-seq datasets for adenovirus-transduced cultured adult cardiomyocytes expressing either peri-nuclear localized Nb80,  ICL3-9, or control mCherry-nesprin fusion proteins in the absence or presence of acute norepineprhine stimulation. Experiment was performed using 3 different primary cardiomyocyte preparations.

first: Jinliang

last: Li


title: A stem cell model identifies two alternative cell fates in CBFA2T3::GLIS2-driven acute megakaryoblastic leukemia initiation (RNA-seq)

first: Florian

last: Halbritter

first: Mohamed

last: Shoeb

first: Dagmar

last: Schinnerl

first: Lisa

last: Shaw

first: Matthias

last: Farlik

first: Sabine

last: Strehl

first: Klaus

last: Fortschegger


title: Skeletal muscle RNA sequencing in Japanese population

first: Hiroshi

last: Kumagai

summary: Skeletal muscle samples were collected from Japanese males and females to understand gene expression patterns in the Japanese population.

overall_design: Skeletal muscle samples were collected from 23 males (25.7 ± 7.5 years old) and 25 females (24.9 ± 7.0 years old).

first: Noriyuki

last: Fuku

first: Eri

last: Miyamoto-Mikami

first: Hirofumi

last: Zempo

first: Mizuki

last: Takaragawa


title: C. elegans tissue after diet that includes nuclear and cystolic derived bovine thymus extract

city: Kannapolis

first: Robert

last: Reid

state: NC

address: 150 Research Campus Drive, Suite 3333

department: Bioinformatics and Genomics

institute: UNC Charlotte

summary: This study explores the effects of bovine derived thymus protomorphogen extracts added to c. elegans diet over their lifespan. We investigate the effects of life span, aging and immune response through changes in gene expression.

overall_design: C. elegan gene expression was measured after the L4 stage under 4 diferent experimental supplement conditons (control, Dessicated Thymus extract, Cytoplamsic Thymus Gland Extract and Nuclear Thymus Gland Extract)

first: Bassem

last: El-Khodor

first: Natalia

last: Surzenko

first: Franziska

last: Pohl


title: Effects of imiquimod on macrophages by transcriptomic analysis

city: Chengdu

first: Hongzhi

last: He

address: No.14,3Rd Section Of Ren Min Nan Rd.

institute: West China School/Hospital of Stomatology, Sichuan University

summary: Imiquimod is a small-molecule immunomodulator with anti-tumor effects, and its anti-tumor activity mainly relies on its immunomodulatory capacity, including activating dendritic cells， T cells, natural killer cells, and promoting the migration of antigen-presenting cells. In this study, we pretreated mouse bone marrow-derived macrophages (BMDMs) with imiquimod for 24 hours and conducted transcriptomic analysis to explore the mechanism by which imiquimod regulates macrophages to exert anti-tumor effects. We found that imiquimod pretreatment of macrophages upregulated multiple signaling pathways, with the most significant being immune regulation-related signaling pathways. Notably, pathways such as the NF-κB pathway, Toll-like receptor (TLR) pathway were significantly upregulated. We infer that imiquimod activates TLR pathway and the downstream NF-κB pathway, promoting the polarization of macrophages to a pro-inflammatory phenotype and exerting anti-tumor effects.

overall_design: Mouse macrophages were extracted from bone marrow and pretreated with dimethylsulfoxide (DMSO, as negative control), imiquimod, and lipopolysaccharides (LPS, as positive control) in three replicate, respectively. After 24h pretreatment, each group of cells is collected and proceeds for RNA sequencing.

first: Bolei

last: Li

first: Lei

last: Cheng


title: Effects of crizotinib on gene expression profiles of cultured hematopoietic stem and progenitor cells (HSPCs)  derived from MDS mice

city: Hachioji

first: Hiroki

last: Kobayashi

state: Tokyo

institute: Tokyo University of Pharmacy and Life Sciences

summary: Myelodysplastic syndromes are characterized by bone marrow (BM) failure due to ineffective hematopoiesis. However, the underlying mechanisms of ineffective hematopoiesis, in which clonal expansion coexists with accelerated cell death, remain to be elucidated. Recently, we established the CBLΔE8/9/RUNX1S291fs mice (MDS mice), which develope a variety of MDS phenotypes including defects in megakaryocyte (MK) maturation. We identified crizotinib as a potent inducer of MK maturation. RNA-Seq of cultured HSPCs derived from the mice revealed that crizotinib increased the expression levels of MK and platelet-related genes.

overall_design: To investigate effects of crizotinib on gene expression profiles in megakaryocyte progenitors derived from MDS mice, MDS mice were generated. Hematopoietic stem and progenitor cells (HSPCs) were isolated from the mice, cultured in the presence of thrombopoietin, and treated with DMSO (dimethyl sulfoxide) or crizotinib for 48 h. Gene expression profiling analysis of RNA-seq data for DMSO-treated cells and crizotinib-treated cells was performed.

first: Hironori

last: Harada


title: Myeloid-mesenchymal crosstalk drives ARG1-dependent profibrotic metabolism via ornithine in lung fibrosis

city: San Francisco

first: Javier

last: Gomez Ortega

address: 513 Parnassus Ave.

institute: UCSF

summary: Single-cell RNA sequencing (scRNA-seq) was performed to investigate fibroblast–myeloid cell crosstalk in lung fibrosis. The dataset includes murine lung macrophage–fibroblast cocultures or fibroblast monocultures, with macrophages derived from WT mice and fibroblasts from either WT or fibroblast-specific P2rx4 knockout (Pdgfrb-Cre: P2rx4 f/f) mice 7 days after bleomycin injury. Cells were captured using the Fluent Biosciences PIPseq platform. Data include gene–cell count matrices and support the study “Myeloid–mesenchymal crosstalk drives ARG1-dependent profibrotic metabolism via ornithine in lung fibrosis” (Yadav et al., 2025).

overall_design: Lungs were isolated after 7 days after bleomycin injury. Macrophages were obtained by positive selection by binding to CD11b microbeads and passing through MACS columns (130-049-601, Miltenyi Biotech). Isolated CD11b+ macrophages were cultured in DMEM supplemented with 10% FBS, 1% penicillin-streptomycin, and 20 ng/ml M-CSF (315-02, Peprotech) for 2 days. Primary mouse lung fibroblasts were freshly isolated after magnetic bead-based negative selection of epithelial cells (118204, Biotin anti-mouse CD326 Epcam, Clone: G8.8, BioLegend), endothelial cells (102404, Biotin anti-mouse CD31, clone: 390), immune cells (103104, Biotin anti-mouse CD45, clone: 30-F11, BioLegend), pericytes and smooth muscle cells (134716, Biotin anti-mouse CD146, clone: ME-9F1, BioLegend), and red blood cells (116204, Biotin anti-mouse Ter119, clone: TER-119, BioLegend) with biotinylated antibodies and Dynabeads (MyOne Streptavidin T1, 65601, Thermo Fisher Scientific). Fibroblasts were cultured for 5 days prior to trypsinization and addition to macrophages for coculture at a 1:1 ratio in DMEM complete media for 5 further days.

first: Preeti

last: Yadav

last: Gómez Ortega

first: Prerna

last: Dabral

first: Whitney

last: Tamaki

first: Charles

last: Chien

first: Kai-chun

last: Chang

first: Nivedita

last: Biswas

first: Sixuan

last: Pan

first: Julia

last: Nilsson

first: Xiaoyang

last: Yin

first: Aritra

last: Bhattacharyya

first: Kaveh

last: Boostanpour

first: Tanay

last: Jujaray

first: Jasper

last: Wang

first: Tatsuya

last: Tsukui

first: Christopher

last: Molina

first: Vincent

last: Auyeung

first: Dean

last: Sheppard

first: Baosheng

first: Mazharul

last: Maishan

last: Taenaka

first: Michael

last: Matthay

first: Rieko

last: Muramatsu

first: Lenka

last: Maliskova

first: Arnab

last: Ghosh

first: Walter

last: Eckalbar

first: Ari

last: Molofsky

first: Stanley

first: Trever

middle: G

last: Bivona

first: Adam

last: Abate

first: Allon

last: Wagner

first: Satish

middle: K

last: Pillai

first: Paul

last: Wolters

first: Kevin

last: Tharp

first: Mallar

last: Bhattacharya


title: Transcriptome profiling of FGL2-stimulated enteric neural crest cells to investigate metabolic dysregulation in Hirschsprung disease pathogenesis

city: Jinan

first: Jichang

last: Han

state: Shandong

address: 107 Wenhua Xi Road

department: Department of Pediatric Surgery

institute: Qilu hospital of Shandong University

summary: This dataset comprises bulk RNA sequencing data from primary mouse enteric neural crest cells (ENCCs) stimulated with fibrinogen-like protein 2 (FGL2) or left untreated as controls. ENCCs were isolated from embryonic day 14–15 C57BL/6J mice and cultured under defined conditions to ensure >95% expression of P75 and nestin markers. Following FGL2 stimulation, total RNA was extracted, and sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina. Paired-end sequencing (2 × 150 bp) was performed on the Illumina NovaSeq 6000 platform. The study aims to identify transcriptional changes and signaling pathway alterations induced by FGL2 in ENCCs, providing insights into the role of FGL2-mediated metabolic dysregulation in the pathogenesis of Hirschsprung disease.

overall_design:
Primary ENCCs were obtained from gut tissues of C57BL/6J mouse embryos at gestational day 14–15. Cells were cultured in complete mouse ENCC medium until reaching 80–90% confluence and confirmed to express P75 and nestin in >95% of cells by immunofluorescence. Cells were randomly assigned to two groups:
FGL2-treated group – ENCCs stimulated with recombinant FGL2 protein.
Control group – ENCCs cultured under identical conditions without FGL2.
Three biological replicates were included per group. Total RNA was extracted using TRIzol reagent, and RNA quality was assessed on an Agilent 2100 Bioanalyzer. Poly(A)+ mRNA was enriched, fragmented, and reverse-transcribed to cDNA. Libraries were constructed using the NEBNext Ultra RNA Library Prep Kit and sequenced (paired-end, 2 × 150 bp) on an Illumina NovaSeq 6000.


title: TGF-β1 promotes wound healing after ionizing radiation through the TGFβ-SMAD canonical signaling pathway

city: beijing

first: Zhihong

last: Song

address: Taiping Road 27

institute: Beijing Institute of Basic Medical Sciences

summary:
Objective: Ionizing radiation (IR) therapy, commonly used in cancer treatment, has detrimental effects on the skin. When combined with surgical resection, IR leads to persistent wounds and forms a significant side effect, making wound healing difficult. This study aimed to understand the mechanisms underlying IR-induced wound damage and develop treatment methods.
Approach: A mouse model of IR was created by exposing mice to 7Gy of radiation after skin excision. The temporal changes of epidermal stem cells (EPSCs) and wound healing were examined. RNA-seq analysis was performed on skin tissues to investigate regulatory mechanisms during the healing process. Topical application of TGFβ was used to assess its impact on wound healing.
Results: Mice in the IR group exhibited prolonged wound healing time, and the healing rate was significantly reduced. IR exposure decreased Ki67+/K14+ cells (proliferating EPSCs), reduced the expression levels of K14 and K15. The RNA-seq results revealed a significant decrease in epidermal stem cell-related genes following IR. Additionally, the TGFβ-SMAD pathway exhibited temporal changes during the wound healing process, while pre-treatment with TGFβ1 significantly promotes the healing of IR-induced wounds.
Innovation: TGF-β1 activated the TGFβ-SMAD pathway and promotes wound healing after ionizing radiation.
Conclusions: These findings indicate that IR diminishes the population of epidermal stem cells (EPSCs), thereby impeding the healing process by disrupting the TGFβ-Smad pathway. However, the external application of TGFβ1 to the wound area effectively improves IR-induced skin damage and exhibits promising therapeutic effects. These findings provide intervention targets and agents for the clinical applications.

overall_design: To investigate the molecules involved in wound healing after IR, we employed RNA-seq analysis to examine the gene expression changes in the control and IR groups at 3, 6, 9 day post-injury.


title: Transcriptomic profiling of aganglionic and ganglionic colon segments from Hirschsprung disease patients

summary: This dataset contains bulk RNA sequencing data from paired aganglionic and ganglionic colonic tissue specimens obtained from three pediatric patients diagnosed with Hirschsprung disease (HSCR, OMIM 142623). RNA was extracted and sequenced to investigate transcriptomic alterations and signaling pathway dysregulation associated with HSCR pathogenesis. Raw paired-end FASTQ files generated by Illumina NovaSeq 6000 sequencing are provided for each sample, enabling downstream analyses of differential gene expression between diseased and unaffected intestinal segments.

overall_design: Colonic tissue samples were collected from three pediatric HSCR patients during surgical resection. For each patient, paired specimens were obtained from the aganglionic segment (designated as “X”) and the ganglionic segment (designated as “K”). The paired samples from patients 1, 2, and 3 are labeled as HSCR-1 (X-1, K-1), HSCR-2 (X-2, K-2), and HSCR-3 (X-3, K-3).  Total RNA was extracted using the Trizol reagent kit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. RNA quality was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and verified using RNase-free agarose gel electrophoresis. Eukaryotic mRNA was enriched using Oligo(dT) beads, fragmented, and reverse transcribed into cDNA using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #7530, New England Biolabs, Ipswich, MA, USA). Purified double-stranded cDNA was end-repaired, A-tailed, ligated to Illumina sequencing adapters, purified with AMPure XP Beads (1.0X), and PCR-amplified.  The resulting cDNA libraries from colon tissue were sequenced using the Illumina NovaSeq 6000 platform (paired-end, 150 bp) by Beijing igeneCode Biotech Co., Ltd. (Beijing, China). Raw data are provided for all six tissue samples to facilitate downstream transcriptomic analysis.


title: Pressure Points: Endothelial Responses to Hemodynamic Stress in Health and Pulmonary Arterial Hypertension

city: Seattle

first: Samuel

last: Rayner

state: WA

address: 850 Republican Street

department: Medicine

institute: University of Washington

summary:
Background: Hemodynamic forces exert a profound influence on endothelial cell signaling and, when abnormal, contribute centrally to human vascular disease. Pulmonary arterial hypertension (PAH) is characterized by both hemodynamic derangement and pulmonary arterial endothelial cell (PAEC) dysfunction. Despite importance in disease initiation and progression, the combined effects of shear and pressure forces on PAEC biology remain incompletely understood, particularly in the context of PAH.
Methods: PAECs obtained at explant from controls and from patients with idiopathic or congenital heart disease-associated PAH (CHD-PAH) were cultured in a custom resistor-coupled microfluidic platform and exposed to static, low (3 dyne/cm²), or high (20 dyne/cm²) shear stress under either low or elevated (60 mmHg) pressure. After 24 hours, we assessed cellular morphology and performed systems-level transcriptomic analysis via bulk RNA sequencing, incorporating analyses of PAH subtype and donor sex.
Results: PAECs (n=18 donors) aligned with flow under high, but not low, shear, and alignment was not significantly altered by disease state or pressure. Shear stress fundamentally reorganized the PAEC transcriptome and the “dose-response” to increasing shear differed across biological pathways in six statistically significant patterns. Increasing shear led to divergence in transcription between control and PAH cells, particularly in pathways involved in immune activation, stress signaling, and vascular remodeling, with subtype differences also observed. Pressure alone had modest effects on transcription, though CHD-PAH PAECs especially displayed pressure-induced stress and inflammatory signaling. We identified sexual dimorphism in the endothelial shear response, noting male cells under shear enriched for pathways involved in proliferation and inflammation and female cells enriched for lipid metabolism and stress responses.
Conclusions: Shear and pressure forces profoundly influence PAEC transcription, with responses shaped by disease state, PAH subtype, and sex. These findings highlight the need for further investigation into mechanosensitive pathways in PAH as potential targets for novel therapies.

overall_design: Pulmonary arterial endothelial cells (PAECs) from control subjects and individuals with idiopathic pulmonary arterial hypertension (IPAH) or congenital heart disease-associated PAH (CHD-PAH) were seeded into microfluidic culture chambers, grown to confluence overnight under gentle, intermittent flow, and then exposed to defined combinations of pressure and shear stress for 24 hours. Pressure and shear stress were set by varying the length of a resistor channel and adjusting the flow rate of perfused culture media. After 24 hours RNA was collected and sequenced. Sequencing was performed in two batches: batch 1 contained pressure and shear stress as variables, batch 2 contained shear stress alone as a variable, with no manipulation of pressure

first: Kellen

last: Hirsch

first: Christian

last: Mandrycky

first: Sina

last: Gharib

first: Ying

last: Zheng


title: RNA-Sequencing of HEK293 During Adeno-Associated Virus Production [EXPB]

city: Bielefeld

first: Niklas

last: Kraemer

address: Alte Verler Strasse 1

institute: Sartorius Xell GmbH

summary: Recombinant viral vectors such as adeno-associated viruses (AAV) have emerged as a key tool in gene therapy applications. Despite extensive research efforts aimed at increasing production yields, the intricate molecular mechanisms that govern the synthesis of viral vectors within host cells remain largely unknown. The interplay between viral replication and cellular biosynthetic processes is complex and not fully understood, which poses challenges for effective manipulation. This study uses transcriptomics and RNA sequencing to investigate the cellular processes underlying viral vector production. Transcriptomics examines RNA molecules and their role in gene expression and has become invaluable in modern biological research. The advent of cost-effective, high-throughput sequencing technologies enables the comprehensive analysis of transcriptomes, providing valuable insights into gene regulation and cell signalling pathways.  This study takes a strategic approach to deciphering the cellular mechanisms involved in viral vector production by utilising RNA-Seq data from a commercially available HEK293 suspension cell line. This study emphasises the importance of data-driven methodologies in advancing cell line development and optimising viral vector production.

overall_design: The RNA-Seq dataset comprises samples collected from commercially available HEK293 suspension cell line. The experimental design involved transfecting these cell lines with a two-plasmid system and a polymer-based transfection reagent to facilitate viral vector synthesis. Samples were harvested 18 hours after transfection to capture the gene expression profiles in these conditions. For reference purposes, untransfected cultures were also sampled at the same time. These cultures received PBS instead of plasmid DNA and the transfection reagent.


title: RNA-Sequencing of HEK293 During Adeno-Associated Virus Production [EXPA]

overall_design: The RNA-Seq dataset comprises samples collected from a commercially available HEK293 suspension cell line. The experimental design involved transfecting these cell lines with a two-plasmid system and a polymer-based transfection reagent to facilitate AAV synthesis. Samples were harvested 18 hours after transfection to capture the gene expression profiles in these conditions. For reference purposes, untransfected cultures were also sampled at the same time. These cultures received PBS instead of plasmid DNA and the transfection reagent.


title: Non-severe burn injury leads to sustained molecular changes in the brain in a murine model

city: East victoria Park

first: Amira

last: Allahham

state: Perth, WA

address: 2/88 Dane st.

institute: Fiona Wood Foundation

summary: Background: Paediatric burn patients, including those with non-severe burns, have an increased risk of admission to hospital for mental health conditions for many years after the burn, even in children too young at the time of the burn to remember the incident. This study aimed to investigate the long-term physiological impact of non-severe burn injuries and non-burn trauma (NBT) on the brain in mice to understand whether there is a sustained impact of such injuries on the brain that may be linked to the increased mental health morbidity observed in patients.                                 Methods: Mice were exposed to either a non-severe burn injury, an excision injury of the same size (equivalent non-burn trauma), or a sham procedure. Behavioural tests were conducted at multiple timepoints to measure anxiety and depression-like behaviour. Mice were euthanised three months after the injury, and plasma and brain tissue, including the hippocampus and prefrontal cortex, were isolated and examined using RNA sequencing, mass spectrometry and nuclear magnetic resonance (NMR) to identify transcriptomic and metabolomic changes.                                         Results: A significant change in behaviour was observed with an increase in sucrose consumption three months after injury in the burn group compared to sham. Significant changes in the transcriptome were identified in some brain regions at 3 months after burn trauma compared to the sham group. Differentially expressed genes associated with inflammatory and immune functions were identified in the burn group compared to controls. Significant changes were also observed in the lipid profile and tryptophan catabolites in the brain after burn trauma compared to sham.                                            Conclusion: Sustained changes in the transcriptome and metabolome were identified in a mouse model of non-severe burns, supporting a likely sustained pro-inflammatory environment in the brain after this type of injury. The potential link between these changes and the poor long-term mental health outcomes observed in paediatric burn patients requires further investigation.

overall_design: This study investigated transcriptomic changes in the brain after burn injury by investigating three intervention groups: burn injury, excision injury, and sham, where RNA sequencing was done on three brain regions including the hippocampus, the frontal cortex and the piriform cortex. Two batches of hippocampus (n=14, n= 15) and frontal cortex (n=15, n=13) were analyzed along with one batch of piriform cortex (n=14). We performed gene and gene pathway analysis on these samples comparing the different intervention groups within the same region with batch corrections for the hippocampus and frontal cortex.

first: Nutan

last: Chaudhari

first: Sarah

last: Walsh

first: Blair

middle: Z

last: Johnson

first: Andrew

last: Stevenson

first: Samantha

last: Lodge

first: Drew

last: Hall

first: Zhenjun

last: Deng

first: Rongchang

last: Yang

first: Monique

last: Ryan

first: Phillip

last: Melton

first: Jennifer

last: Rodger

first: Fiona

last: Wood

first: Luke

last: Whiley

first: Mark

last: Fear


title: IRF5 siRNA Nano-Immunotherapy: Restoring Macrophage Efferocytosis in Atherosclerosis

city: chengdu

first: zeng

last: wanqin

state: chengdu

address: No17 renming

institute: Sichuan University

summary: We observe that the siIRF5 nano-immunotherapeutics were efficiently taken up by lesional macrophages, particularly Cd11c+ and Trem2hi macrophages, and enhanced their phagocytic clearance of apoptotic cells by efficiently silencing IRF5 expression within these macrophage subsets in atherosclerotic plaques. This resulted in remarkable therapeutic efficacy, as evidence by reduction of necrotic core area and enhancement of plaque stability in two independent ApoE-/- murine models of atherosclerosis. Mechanistically, single-cell RNA sequencing analysis revealed that siIRF5 nano-immunotherapeutics increased the pro-efferocytic receptors while decreasing the expression of pro-inflammatory genes associated with cytokine and chemokine pathways in lesional macrophages.

overall_design: We conducted single-cell RNA sequencing (scRNA-seq) to explore the molecular impact of ZnDPA@siIRF5 treatment on lesional macrophages in the aorta.


title: ASD gene Bcl11a regulates subcellular RNA localization, associative circuitry, and social behavior

city: Cambridge

first: Dustin

middle: Eliot

last: Tillman

state: MA

address: 7 Divinity Ave, Bauer Laboratory 103

department: Stem Cell and Regenerative Biology, Center for Brain Science

institute: Harvard University

summary: Precise, area-specific connectivity of interhemispheric callosal projection neurons (CPN) in the cerebral cortex is critical for sensory, associative, and behavioral functions. CPN circuitry, which connects and integrates the two cerebral hemispheres via the corpus callosum, is centrally implicated in autism spectrum disorder (ASD) and intellectual disability (ID). Though transcriptional controls regulating CPN subtype and areal development have progressively become partially understood, downstream subcellular mechanisms and molecular machinery that implement precise and diverse CPN circuitry is essentially unknown. Here, we identify that the highly penetrant ASD/ID risk gene Bcl11a/Ctip1 is critical developmentally for appropriate and precise areal targeting of CPN associative projections, and that its deletion both strikingly reshapes these projections, and causes dramatic disruption to circuit-specific subcellular growth cone (GC) molecular machinery and social behavior and cognition in mice. CPN-specific embryonic deletion of Bcl11a causes loss of correct homotopic targeting in the contralateral cortex, re-routes a substantial proportion of their axonal projections through the evolutionarily older anterior commissure, and induces strikingly aberrant, but specific and precise, projections to the basolateral amygdala in adult mice. Importantly, bilateral deletion of Bcl11a from CPN alone results in abnormal social behavior and working memory. Mechanistically, we identify dysregulation of the CPN axonal GC-localized transcriptome in Bcl11a nulls, due to either aberrant transcription or trafficking of individual transcripts. These molecular mis-localizations disrupt axon guidance and CPN-specific associative circuitry formation, causing disease-related behavior.  Together, this work identifies critical functions for Bcl11a in CPN axonal connectivity, development of functional associative-social circuitry, regulation of subtype-specific subcellular molecular machinery in vivo, revealing novel GC-localized transcripts that regulate precise axonal targeting and circuit formation. These results elucidate development and ASD/ID disease-related circuit disruption of CPN, and the importance of understanding circuit-specific subcellular– e.g. soma vs. GC– localization of RNA and protein molecular machinery by neurons.

overall_design: Comparative gene expression profiling and variant calling analysis of RNA-seq data for CPN somata and GCs that are wild-type, Bcl11a-heterozygous, or Bcl11a-null.

first: Omer

last: Durak

first: Ji-Yoon

last: Kim

first: Yasuhiro

last: Itoh

first: Marit

last: Wettstein

first: Luciano

last: Custo Greig

first: Jeffrey

middle: D

last: Macklis


title: RNA seq analysis of MEK inhibitor in combination with 5-azacitidine treated Shp2E76K/+ driven JMML mice

city: Indianapolis

first: Santhosh Kumar

last: Pasupuleti

state: Indiana

department: Pediatrics

institute: Indiana University School of Medicine

summary: Juvenile myelomonocytic leukemia (JMML) is a rare myelodysplastic and myeloproliferative neoplasm of childhood. Excessive proliferation of monocytes into the liver, spleen, lungs, and skin is frequently observed at presentation. Hematopoietic stem cell transplantation (HSCT) is the only curative therapy with a probability of event-free survival at 5-years of approximately 50%. The molecular hallmark of JMML is hyperactivation of the Ras/MAPK signaling pathway with the most common cause being mutations in the gene PTPN11, encoding the protein tyrosine phosphatase SHP2. Current therapeutic strategies in JMML include using MEK inhibitors such as trametinib and PD0325901 (PD-901) or the hypomethylating agent, 5-azactidine, but none of these are curative as monotherapy. In this study, utilizing a gain of function (GOF) Shp2E76K/+ murine model of JMML, we showed that the combination of PD-901 and 5-azacitidine reduced leukocytosis, monocytosis, and splenomegaly and reversed thrombocytopenia. Importantly, this drug combination significantly reduced leukemic hematopoietic stem and progenitor cells (HSC/Ps) in the Shp2E76K/+ mice.

overall_design: To explain the mechanism of action of MEK inhibitor, PD0325901 (PD-901) in combination with hypomethylating agent, 5-azactidine treatment on Shp2E76K/+ driven JMML mice, total RNA was isolated form the BM cells of 4 different drug treatment groups (Group 1: Vehicle, Group 2: PD-901, Group 3: 5-azacitidine, and Group 4: Combo). RNA-sequencing (RNA-seq) was performed on samples from 3 independent mice from each group.

first: Santhosh

first: Reuben

last: Kapur

first: Sheng

last: Liu

first: Jun

last: Wan


title: Succinate preserves CD8+ T cell fitness to augment anti-tumor immunity

city: Suzhou

first: Lin

last: Wang

address: No. 100. Chongwen Road

institute: Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College

summary: The tricarboxylic acid cycle intermediate succinate accumulates in tumors harboring succinate dehydrogenase (SDH) mutations. Despite evidence that succinate modulates CD8+ T cell cytotoxicity, its influence on T cell differentiation trajectories remains poorly understood. Here we reveal that SDHB-deficient tumors exhibit enriched tumor-specific CD8+ T cell infiltration and enhanced responsiveness to PD-L1 blockade.

overall_design: Detect the primary mouse cells cultured in vitro, the CD8+ T cells sorted from tumor-bearing mice, and the CD8+ T cells sorted from bacteria-loaded mice


title: ATF3 Overexpression Induces Cardiac Hypertrophy and Electrical Dysfunction through Enhanced Proliferation in Zebrafish

city: Seoul

first: Jung-Woong

address: 84 Heuksuk-ro Dongjak-ku

department: Life Science

country: South Korea

institute: Chung-Ang University

summary: Activating transcription factor 3 (ATF3) is a key regulator of gene expression in response to physiological stress across various tissues. Although its abnormal expression has been linked to cardiac dysfunction, the precise mechanisms by which ATF3 influences cardiac pathology remain unclear, with conflicting findings in the literature. To address this, we developed a cardiac-specific ATF3-expressing zebrafish line, Tg (myl7:ATF3), using the zebrafish model as a well-established vertebrate system for cardiovascular research. Compared to wild-type (WT) siblings, Tg (myl7:ATF3) zebrafish exhibited significant pathophysiological changes, including cardiac hypertrophy and features resembling hypertrophic cardiomyopathy (HCM). Histological analysis revealed increased fibrotic scarring, sarcomere disorganization, and elevated expression of heart failure gene markers (nppa and nppb). Notably, electrocardiogram (ECG) measurements showed that ATF3 overexpression led to symptoms resembling Long QT Syndrome (LQTS), indicating electrical dysfunction. Transcriptome analysis further revealed downregulation of apoptosis-related genes and upregulation of proliferation-related genes in transgenic zebrafish hearts. These findings suggest that stress-induced ATF3 expression contributes to cardiac hypertrophy through enhanced cardiomyocyte proliferation, providing novel insights into its role in cardiovascular disease progression.

overall_design: Cardiac tissue samples were collected from a transgenic zebrafish line with cardiac-specific overexpression of ATF3 (Tg(myl7:ATF3)) and age-matched wild-type (WT) siblings. RNA samples were harvested at two developmental stages—4 months post-fertilization (mpf) and 12 mpf—to investigate both early and progressive effects of ATF3 overexpression. Each group included three biological replicates. QuantSeq 3' mRNA sequencing was performed to evaluate transcriptomic changes associated with ATF3-induced cardiac hypertrophy and dysfunction. Wild-type samples serve as controls.


title: Prevalent mesenchymal drift in aging and disease is reversed by partial reprogramming [RNA-seq]

city: San Diego

first: William

last: Tu

address: 5510 Morehouse Dr

institute: Altos Labs

summary: The loss of cellular and tissue identity is a hallmark of aging and numerous diseases, but the underlying mechanisms are not well understood. Our analysis of gene expression data from over 40 human tissues and 20 diseases reveals a pervasive upregulation of mesenchymal genes across multiple cell types, along with an altered composition of stromal cell populations, denoting a “mesenchymal drift” (MD). Increased MD correlates with disease progression, reduced patient survival, and an elevated mortality risk, whereas suppression of key MD transcription factors leads to epigenetic rejuvenation. Notably, Yamanaka factor-induced partial reprogramming can markedly reduce MD before dedifferentiation and gain of pluripotency, rejuvenating the aging transcriptome at the cellular and tissue levels. These findings provide mechanistic insight into the underlying beneficial effects of partial reprogramming and offer a framework for developing interventions to reverse age-related diseases using the partial reprogramming approach.

overall_design: RNA-seq of dox induced OSK and OCT4YR mutant+SK expression in human fibroblasts from an aged donor (GM00731, 96yr male).

first: Jinlong

middle: Y

last: Lu

first: Juan Carlos

last: Izpisua Belmonte


title: Prevalent mesenchymal drift in aging and disease is reversed by partial reprogramming [scRNA-seq]

overall_design: 10x Genomics scRNA-seq of human fibroblasts from a young (GM23815, 22yr) and aged donor (GM00731, 96yr) treated with Sendai virus OSKM for up to 10 days.


title: Tissue and cellular spatiotemporal dynamics in colon aging [scRNA-seq]

city: Columbia

first: Aidan

last: Daly

state: SC

address: 2230 Rembert Street

institute: New York Genome Center

summary: Tissue structure and molecular circuitry in the colon can be profoundly impacted by systemic age-related effects, but many of the underlying molecular cues remain unclear. Here, we built a cellular and spatial atlas of the colon across three anatomical regions and 11 age groups, encompassing ~1,500 mouse gut tissues profiled by spatial transcriptomics and ~400,000 single nucleus RNA-seq profiles. We developed a new computational framework, cSplotch, which learns a hierarchical Bayesian model of spatially resolved cellular expression associated with age, tissue region, and sex, by leveraging histological features to share information across tissue samples and data modalities. Using this model, we identified cellular and molecular gradients along the adult colonic tract and across the main crypt axis, and multicellular programs associated with aging in the large intestine. Our multi-modal framework for the investigation of cell and tissue organization can aid in the understanding of cellular roles in tissue-level pathology.

overall_design: snRNA-seq profiling of colon tissue from C57BL/6J mice ranging in age from 0d to 2yr

first: Francesco

last: Cambuli

first: Tarmo

last: Aijo

first: Britta

last: Lotstedt

first: Nemanja

last: Marjanovic

first: Sara

last: Fernandez

first: Olena

last: Kuksenko

first: Matthew

last: Smith-Erb

first: Daniel

last: Domovic

first: Nicholas

last: van Wittenberghe

first: Eugene

last: Drokhlyansky

first: Gabriel

last: Griffin

first: Hemali

last: Phatnani

first: Richard

last: Bonneau

first: Aviv

last: Regev

first: Sanja

last: Vickovic


title: Microbial Bile acid metabolite, 3-oxo-LCA, prohibits colorectal cancer progression

city: Madison

first: TING

last: FU

state: Wisconsin

address: Attn: TING FU LAB, Suite/Rm:, 777 HIGHLAND AVE, RENNEBOHM HALL, ZN 3, MADISON, WI 53705-2222, United States

institute: University of Wisconsin-Madison

summary: Objective: Bile acids (BAs) not only influence gut microbiome composition but are also metabolized by gut bacteria to form various microbial BAs. Among these, 3-oxo-lithocholic acid (-oxo-LCA) and isoalloLCA have been reported to modulate host immunity, suppress intestinal pathogens, and provide anti-aging benefits. However, their specific effects on intestinal epithelial cells (IECs) and their role in colorectal cancer (CRC) progression remain unclear. Design: To investigate the impact of 3-oxo-LCA on intestinal tumorigenesis, we examined its effects on the growth of mouse and human CRC cell lines (CT26, MC38, HCT116), as well as on primary mouse intestinal organoids and patient-derived CRC organoids (PDCOs). Additionally, we evaluated its role in vivo using APCMin/+ mice and multiple  CRC models, including syngeneic CT26 and MC38 models, as well as HCT116 and PDX-derived xenografts in NSG (immunodeficient) mice. Results: Our findings show that 3-oxo-LCA is a potent FXR agonist that restores FXR signaling both in vitro and in vivo. This results in reduced growth of CRC cell lines and suppression of intestinal stem cell (ISC)’s proliferation in both mouse organoids and PDCOs. In APCMin/+ mice, 3-oxo-LCA reduced BA levels, enhanced gut barrier function, decreased tumor burden, and blocked tumor initiation. Furthermore, it significantly inhibited tumor progression in syngeneic and xenograft mouse models and promoted apoptosis within the tumors, enhancing cancer cell death. Conclusion: These results underscore the therapeutic potential of 3-oxo-LCA as a novel FXR agonist for CRC treatment, with its ability to inhibit tumorigenesis and progression by modulating epithelial cell proliferation and inducing apoptosis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HCT116 Xenograft Mouse model treated with Vehicle and 3-oxo-LCA.

first: Fei

last: Sun

first: Ke

last: Wang

first: Xingchen

last: Dong

first: Henry

last: Morocho

first: Alisa

last: Hui

first: Chunmiao

last: Cai

first: Jonathan

last: Sze

first: Brian

last: Low

first: Shirsa

last: Udgata

first: Cheri

last: Pasch

first: Tao

last: Huan

first: Dustin

last: Deming

first: Qiyun

last: Zhu

first: Jiaoyang

last: Jiang

first: Ting

last: Fu


title: ATAC-seq  revealing  chromatin accessibility and novel motifs linked to corneal fibrosis

first: Rajiv

last: Mohan

state: Missouri

address: 1520 East Rollins University of Missouri

department: Department of Veterinary Medicine and Surgery

institute: University of Missouri

summary: Dysregulation of wound healing cascade often results in corneal fibrosis. Increasingly evidence suggest the role of epigentics as one of the regulatory mechanisms that drive corneal fibrosis. The present study investigated epigenetic modulation caused by alkali-induced corneal fibrosis in rabbit model by employing ATAC-Seq to identify transcription factors and gene regulatory elements that drive the disease pathology. We observed a extensive epigenomic reprogramming characterized by reduced chromatin accessibility, promoter-to-enhancer regulatory shifts and selective activation of fibrosis-associated transcriptional networks in the fibrotic corneas. Key known (Sp1, KLF9, NFY, KLF4, and ETV4) and de novo motifs shwoing similarity to KLF17, NRF, and ETV6  were identified that could serve as potential epigenetic tragets for further evaluation as therapeutic approach in treating corneal fibrosis.

overall_design: ATAC seq profiling to explore diferences in the genome-wide chromatin accessibitlity in fibrotic and. naïve corneas

first: Swati

last: Sood

first: Rajnish

last: Kumar

first: Nishant

last: Sinha


title: Tissue and cellular spatiotemporal dynamics in colon aging

first: Aidan

last: Daly

overall_design: ST RNA-seq profiling of colon tissue from C57BL/6J mice ranging in age from 0d to 2yr

first: Francesco

last: Cambuli

first: Tarmo

last: Aijo

first: Britta

last: Lotstedt

first: Nemanja

last: Marjanovic

first: Sara

last: Fernandez

first: Olena

last: Kuksenko

first: Matthew

last: Smith-Erb

first: Daniel

last: Domovic

first: Nicholas

last: van Wittenberghe

first: Eugene

last: Drokhlyansky

first: Gabriel

last: Griffin

first: Hemali

last: Phatnani

first: Richard

last: Bonneau

first: Aviv

last: Regev

first: Sanja

last: Vickovic


title: Gene editing in hematopoietic stem cells by co-delivery of Cas9/sgRNA ribonucleoprotein and templates for homology-directed repair in ‘all-in-one’ lentivirus-derived nanoparticles

city: Aarhus C

first: Jacob

middle: Giehm

last: Mikkelsen

address: Hoegh-Guldbergs Gade 10

country: Denmark

institute: Aarhus University

summary: Repair of double-strand DNA breaks generated by site-directed endonucleases, like Cas9, is the hallmark of gene editing based on homology-directed repair (HDR). HDR uses an exogenous DNA template to restore the cleaved DNA sequence and can facilitate specific gene corrections as well as insertion of genes or partial cDNA sequences. For CRISPR/Cas-directed gene editing, co-administration of the Cas9/single guide RNA (sgRNA) ribonucleoprotein (RNP) complex and a DNA template typically involves two different delivery strategies or different types of vehicles. This requires exquisite timing of delivery and may potentially challenge safety and therapeutic applicability. There is a need therefore for technologies that can ferry complete editing tool kits into cells. Here, we demonstrate the use of lentivirus-derived nanoparticles (LVNPs) to transport both RNP complexes and vector RNA, which upon reverse transcription serves as donor for HDR-directed repair. These ‘all-in-one’ LVNPs support targeted gene insertion with reduced off-target effects relative to nucleofection procedures. We show potent editing in the HBB gene in human erythroid progenitor cells as well as HDR-directed editing in hematopoietic stem and progenitor cells. Our findings mark a first step toward using a single virus-derived vehicle for delivering a full HDR gene editing kit.

overall_design: HUDEP-2 cells homozygous for the sickle cell disease variant are treated with lentivirus-derived nanoparticles that deliver Cas9, sgRNA targeting the hemoglobin beta gene and a homology donor for correction of the mutation. Paired end sequencing of amplicons spanning the edited region is analyzed in CRISPResso2 with the untreated sample as reference sample.


title: RNA Sequencing of macrophages harboring redox-diverse Mycobacterium tuberculosis.

city: Bengaluru

first: Amit

last: Singh

state: KARNATAKA

address: Sir CV Raman Road

department: Microbiology and Cell Biology

institute: Indian Institute of Science

summary: The ability of Mycobacterium tuberculosis (Mtb) to tolerate antibiotics is a major impediment in the treatment of tuberculosis. This antibiotic tolerance is influenced by the host cells in which the bacteria reside, as Mtb senses host cues, and the bacterial response can provide an enhanced ability to withstand anti-TB drugs. Previouslyt, we have shown that Mtb exhibits redox heterogeneity in terms of its mycothiol redox potential (EMSH) giving rise to three broad subpopulations  EMSH-reduced, EMSH-basal, and EMSH-oxidized Mtb specifically inside the macrophages. Among these, the EMSH-reduced Mtb exhibit enahnced tolerance to several anti-TB drugs while the EMSH-basal and EMSH-oxidized subpopulations  are more susceptible. In this study, we explored the transcriptomic level differences between macrophages that harbor the antibiotic tolerant Mtb and those harboring antibiotic susceptible Mtb to get a mechanistic understanding of host factors that influence drug tolerance in intracellular Mtb.

overall_design: RNA-Seq of bone marrow-derived macrophages harboring different Mtb subpopulations 24 hours post infection. The study involves four different subpopulations- uninfected, bystanders, macrophages harboring EMSH-reduced Mtb, EMSH-oxidized Mtb.  All samples are assessed in biological triplicates.

first: Vikas

last: Yadav

first: Sarthak

last: Sahoo

first: Nitish

last: Malhotra

first: Mohit

last: Jolly

first: Aswin Sai Narain

last: Seshasayee


title: Role of ADAR1 on transcriptional output in cancer cells

city: Shanghai

first: Zhibo

last: Shao

institute: Fudan University Shanghai Cancer Center

summary: The loss of ADAR1 significantly reduced ribosome production, decreased tumor translational efficiency, and impaired the translation of oncogenic pathways.

overall_design: RNA-Seq and Ribo-seq were performed in control siRNA and ADAR1 siRNA MDA-MB-231 cells.

first: Xuliren

last: Wang

first: Qi

last: Zhang

first: Jiong

last: Wu


title: Identification of a new subpopulation of myonuclei during skeletal muscle hypertrophy

city: Paris

first: Léa

last: Delivry

address: 24 rue faubourg Saint-Jacques

country: France

institute: Cochin Institute

summary: We have employed a single nucleus sequencing approach using 10x Genomics snRNA-seq to study the process of skeletal muscle hypertrophy. We examined the plantaris muscle of control adult mice (Ctl) and adult mice after 7 days of induced overload (7OV). This study highlights a new subpopulation of myonuclei in the muscles of control and hypertrophied mice.

overall_design: We used 3 mice model : C57bl6N (WT), ROSAmTmG;PAX7CREert2/+ (mTmG) and HSA-Cre-ERT2:RhoAflox/flox (Mut). The plantaris muscle underwent compensatory surgery and were removed 7 days later with the control plantaris muscles. Nuclei were sorted by Fluorescence-activated cell sorting (FACS) with DAPI and analyzed using snRNA-seq.

first: Pascal

last: Maire

first: Athanassia

last: Sotiropoulos


title: Population and functional diversity of aged lymph node stromal cells during viral infection

city: Chicago

first: Justin

last: Richner

address: 835 S. Wolcott AVe

institute: University of Illinois Chicago

summary: Aging correlates with delayed and blunted adaptive immune responses following infection and vaccination leading to increased susceptibility to infectious diseases. Lymph node stromal cells (LNSC) are a diverse and rare population of fibroblast and endothelial cell subsets that assist in LN structure and immunological function. The negative impact of aging on the function of hematopoietic immune cells has been described; however, the contribution of aging to LNSC function has not been elucidated. Here, we utilized single cell RNA sequencing (scRNA-seq) to investigate adult and aged LNSC transcriptional dynamics during an acute West Nile virus infection to gain in vivo insight into the active immune response in these rare and diverse cellular subsets. We identified three major LNSC subsets as well as 15 individual stromal cell types present in adult and old LNs. Overall, the adult and aged LNSC response to WNV is characterized by the robust activation of antiviral signaling pathways, including expression of interferon stimulated genes. Population dynamics of LNSCs from adult and old LNs were largely similar, although aged LNs were found to be enriched in fibroblast subsets, including TRC and MedRC. Infection induced metabolic reprograming of the LNSC subsets in the adult setting; however, this reprogramming was dampened in the aged setting. Collectively, these studies demonstrate that aged LNSCs do not display age-related impairments in antiviral signatures; however, age-related changes influence the aged LN immune response. The data presented here is the first to examine age-dependent LNSC dynamics during viral infection on the single cell level.

overall_design: Lymph nodes were harvested and digested from adult and old mice. These mice were either naïve or 2 days post West Nile viral (WNV-Kunjin) infection. Lymph node stromal cells (LNSCs) were then isolated from lymph node suspensions using a magnetic microbead-based separations, based on the absence of CD45 expression and presence of CD31 and/or gp38 expression. The resulting LNSCs were then analyzed using single cell RNA sequencing (scRNA-seq). Adult LNSC scRNA-seq experiments were performed in duplicate, whereas the old LNSC scRNA-seq  experiment contains a single replicate.

first: Allison

last: Bennett

first: Maria

middle: P

last: Zappia

first: Mark

last: Sanborn

first: Michelle

first: Jalees

first: Maxim

last: Frolov

middle: M


title: Expression data from HEK-293 cells with and without small hepatitis delta antigen (S-HDAg) overexpression

city: Heidelberg

first: Angga

last: Prawira

address: Im Neuenheimer Feld 344

department: Molecular Virology

institute: University Hospital Heidelberg

summary:
Hepatitis delta virus (HDV) enters hepatocytes via the receptor NTCP and requires the SHDAg for efficient replication by host RNA polymerase II (Pol II). During replication, SHDAg reportedly binds to Pol II as an elongation factor and thus promotes the transition from the promoter-proximal pausing to the elongation state.
Here, we are interested in looking at the potential of S-HDAg as a global regulator of Pol II-mediated transcription in the presence and absence of the Mediator kinases CDK8/19

overall_design: SHDAg or an empty vector was stably transduced in HEK-293-NTCP wild-type and CDK8/19 dKO cell lines by lentivirus. Stable cell lines were subsequently infected with 10 MGE of HDV or with DMEM medium only. At 5 days post-infection, cells were harvested for RNA extraction and subjected to the human Clariom S assay, ThermoFisher.

first: Prawira

last: Angga

first: Ni

last: Yi


title: In-utero rescue of neurological dysfunction in a mouse model of Wiedemann-Steiner syndrome [CUT&Run]

city: Reykjavik

first: Tinna

last: Reynisdottir

state: Ísland

address: Sturlugata 8

country: Iceland

institute: University Of Iceland

summary: Wiedemann-Steiner syndrome (WDSTS) is a rare genetically determined cause of intellectual disability primarily caused by heterozygous loss of function variants in the gene encoding the histone methyltransferase KMT2A. Prior studies have shown successful postnatal amelioration of disease phenotypes for several related Mendelian disorders of the epigenetic machinery, including Rett, Rubinstein-Taybi and Kabuki syndromes. To explore whether the neurological phenotype in WDSTS is treatable in-utero, we created a novel mouse model carrying a loss of function variant in between two LoxP sites. Kmt2a+/LSL mice demonstrate core features of WDSTS including growth retardation, craniofacial abnormalities, and hypertrichosis as well as hippocampal memory defects. This mouse model offers a strategy to systematically explore the therapeutic window in WDSTS. The neurological phenotypes show rescue upon breeding to a nestin-Cre, which restores KMT2A levels in-utero. Together, our data provide a novel mouse model to explore the therapeutic window in WDSTS. Our work suggests that WDSTS has a window of opportunity extending at least until the mid-point of in-utero development, making WDSTS an ideal candidate for future therapeutic strategies.

overall_design: To explore the effects of Kmt2a loss and its in-utero malleability on a chromatin level, we performed a CUT&RUN of the H3K4me1 mark in mNPCs.

first: Kimberley

last: Anderson

first: Andrew

last: Brinn

first: Katie

last: Franklin

first: Juan

last: Ouyang

first: Cat

last: Lutz

first: Asbjorg

middle: O

last: Snorradottir

first: Valerie

last: DeLeon

first: Aamir

middle: R

last: Zuberi

first: Hans

middle: T

last: Bjornsson


title: BMAL1 represses transposable elements independently of CLOCK in pluripotent cells [ssRNA-seq]

city: Granada

first: Ivan

middle: Fernández

last: Rengel

address: Avenida de la Ilustración 114

country: Spain

institute: GENyO

summary: Genome profiling of BMAL1,TRIM28 and H3K9me3 analyzed by ChIP-seq in JM8+/+ and Bmal1-/- mESCs. Genome profiling of FlagBMAL1 in mESCs. High throughput capture chromosome conformation analysis (Hi-C) in  JM8+/+ and Bmal1-/- mESCs. mRNA-seq analysis of JM8+/+ and Clock-/- mESCs

first: Amador

last: Gallardo

last: Fernandez-Rengel

first: Guillermo

last: Peris

first: David

last: Landeira


title: In-utero rescue of neurological dysfunction in a mouse model of Wiedemann-Steiner syndrome

overall_design: To evaluate rescue of transcriptional abnormalities caused by heterozygous Kmt2a-deficiency and in-utero rescue of the effect in a homogenous cell population, we dissected the hippocampus from newborn pups (P0) and cultured mouse neuronal progenitor cells (mNPCs). We performed RNA-sequencing  to identify gene expression changes between Kmt2a+/+ and Kmt2a+/LSL NPCs and the reversal in Nes-Cre+/-Kmt2a+/LSL.

middle: J


title: Bronchoalveolar lavage of healthy human adults after LPS exposure

city: Denver

first: Camille

last: Moore

state: CO

address: 1400 Jackson St.

institute: National Jewish Health

summary: Rationale: Macrophages are both drivers of dysregulated inflammation and essential for healthy repair following acute lung injury. Distinct subsets of human macrophages have been associated with lung pathology but whether unique cellular programs are causally linked to disease or merely represent a conserved response to tissue damage is unknown. Objectives: We sought to identify the transcriptional heterogeneity and cellular programing of airspace macrophages (AM) during normal lung repair in a human model of self-resolving acute lung injury. Methods: Fifteen subjects underwent bronchoscopic lavage before and at a pre-assigned time point after endobronchial exposure to bacterial endotoxin. Cells from lavage were subjected to single-cell RNA sequencing and a longitudinal assessment of AM programing during resolution of inflammation and lung repair was performed. Measurements and Main Results:  We identify transcriptionally distinct subsets of AM present at all time points, in all subjects.  We focus on two populations that increase following inflammation, one which aligns closely with classical circulating monocytes (MoAM) and one with interstitial macrophages (IMAM). Comparison of subset-specific markers to those identified in disease states reveals that IMAM express many so-called “pathogenic” macrophage markers during both health and inflammation.  Conclusions: By applying a uniform inflammatory stimulus to healthy adults and examining BAL cells obtained at precise time points following inflammation, we construct a time-resolved kinetic of AM transcriptional programing during inflammation and normal lung repair. Our data suggest that IMAM are similar to cells identified at increased frequency in disease states and may reflect a conserved cellular response to tissue injury.

overall_design: scRNA-seq was performed on bronchoaelveolar lavage samples collected from healthy adults following lipopolysaccharide (LPS) exposure. Samples were collected 1-5 days post-exposure with 2-4 replicates per timepoint (total n=15) Each sample was collected from a participant with a corresponding baseline BAL sample available under GEO accesssion GSE151928

first: Shannon

middle: A

last: McManus

first: Elizabeth

last: Wynn

first: Jazalle

last: McClendon

first: William

last: Janssen

first: Kara

last: Mould


title: BMAL1 represses transposable elements independently of CLOCK in pluripotent cells [ChIP-seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for BMAL1, TRIM28 and H3K9me3 in JM8 WT and Bmal1-/- mESCs. ChIP-seq for FLAG in FLAG-BMAL1 expressing mESCs

first: Efres

last: Belmonte Reche


title: Microbial signals in primary and metastatic brain tumors [CosMx]

status: Public on Aug 13 2025

city: Houston

first: Nadim

last: Ajami

state: TX

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

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

overall_design: Spatial molecular imaging was conducted using the CosMx SMI Platform (NanoString Technologies, Seattle, WA) using the 6K Discovery panel and a custom panel of bacterial probes. This experiment was performed on two tissue microarrays (TMA) from glioma patients (n= 18) and brain metastasis patients (n=9), 39 fields of view per TMA.

first: Golnaz

last: Morad

first: Jennifer

last: Wargo


title: Targeting superenhancer-driven PRKCN mediated mTOR-IRF4 signaling as a potential strategy against multiple myeloma

city: suzhou

first: Koukou

last: Tang

address: xietang

institute: Soochow universiy

summary: Multiple myeloma (MM) remains incurable, necessitating development of novel therapeutic targets. Deregulated PRKCN contributes to development of solid tumors, while its role in MM remains elusive. In present, we identified PRKCN as a superenhancer-driven gene abundantly expressed in MM. PRKCN was transactivated by NF-κB signaling intrinsically existing or exogenously provoked, nominating PRKCN as a novel NF-κB target gene. Constitutive or inducible knockdown of PRKCN significantly impaired cell growth and tumorigenicity, while overcoming drug resistance and triggering apoptosis. The growth-inhibition elicited by PRKCN depletion was considerably rescued by IRF4 overexpression, supporting PRKCN functioned through IRF4. Intriguingly, IRF4 reciprocally transactivated PRKCN, thereby forming a positive feedback loop. Furthermore, PRKCN favored IRF4 expression by activating mTORC1/C2 signaling, which was associated with direct and extensive interaction with mTOR. Unexpectedly, although PRKCN could directly phosphorylate mTOR in vitro, it modulated mTOR-IRF4 axis and MM cell growth independently of intrinsic kinase activity yet requiring phosphorylation of activation loop. Noteworthily, targeting PRKCN with an orally bioavailable inhibitor suppressed the growth of cell lines together with primary samples and overcame drug resistance in vitro, and also elicited robust efficacy in a cell line-derived xenograft and a patient-derived xenograft, which was connected with mitigated activation loop phosphorylation of PRKCN and mTOR-IRF4 axis. Collectively, our study delineates PRKCN function that links NF-κB signaling and mTOR-IRF4 axis orchestrating cell growth and survival, providing the proof-of-concept for potentially targeting PRKCN to antagonize MM.

overall_design: RNA-seq profiling of MM.1S cells and PRKCN knockdown derivative at Day3

first: Yang

last: Xu

first: Chengcheng

last: Fu

first: Depei

last: Wu

first: Jianhong

last: Chu