title: Multi-omic analysis of guided and unguided forebrain organoids reveal differences in cellular composition and metabolic profiles

city: Cambridge

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

institute: MRC Laboratory of Molecular Biology

summary: Neural organoids are invaluable model systems for studying neurodevelopment and neurological diseases. For this purpose, reproducible differentiation protocols are needed that minimize inter-organoid variability whilst generating neural organoids that physiologically resemble the brain area of interest. Currently, two main approaches are used: guided where the differentiation towards neuroectoderm and subsequently specific CNS regions is driven by applying extrinsic signalling molecules and unguided where the intrinsic capability of pluripotent stem cells to generate neuroectoderm without external signalling is promoted. Despite the importance for the field, the resulting differences between these models have not been directly investigated. To obtain an unbiased comparison, we performed a multi-omic analysis of forebrain organoids generated using a guided and unguided approach focusing on proteomic, lipidomic and metabolomic differences. Furthermore, we characterised differences in phosphorylation and sialylation states of proteins, two key post-translational modifications (PTMs) in neurodevelopment, and performed single cell transcriptomics (scRNAseq). The multi-omic analysis revealed considerable differences in neuronal, synaptic and glial content, indicating that guided forebrain organoids contain a larger proportion of neurons, including GABAergic interneurons, and synapses whereas unguided organoids contain significantly more glial progenitors and choroid plexus. Furthermore, substantial differences in mitochondrial and metabolic profiles were identified, pointing to increased levels of oxidative phosphorylation and fatty acid β-oxidation in unguided forebrain organoids and a higher reliance on glycolysis in guided forebrain organoids. Overall, our study comprises a thorough description of the multi-omic differences arising when generating guided and unguided forebrain organoids and provide an important resource for the organoid field studying neurodevelopment and disease.

overall_design: Single cell RNA-seq was performed using the Parse Evercode technology on human forebrain organoids.  Organoids were either: i) "guided" towards neuroectoderm or ii) were considered "unguided" and left to generate into neuroectoderm without external signalling.  Organoid samples were taken in triplicate at day 20 and day 40 for both guided and unguided organoids.

first: Marie

middle: S

last: Øhlenschlæger

first: Pia

last: Jensen

first: Jesper

last: Havelund

first: Magdalena

last: Sutcliffe

first: Sofie

last: Elmkvist

first: Lucrezia

last: Criscuolo

middle: W

first: Lene

last: Jakobsen

first: Jonathan

last: Brewer

first: Nils

last: Færgeman

first: Madeline

last: Lancaster

first: Martin

last: Larsen

first: Helle

last: Bogetofte


title: Deletion of CD177 exacerbates acute pancreatitis-associated lung injury and colonic barrier dysfunction in a mouse model of acute pancreatitis

status: Public on Mar 04 2026

city: Beijing

first: Li

last: Ji

address: No.1 Shuaifuyuan

department: Department of Gastroenterology

country: China

institute: Peking Union Medical College

type: Expression profiling by high throughput sequencing

summary: We aimed to investigate how Cd177 deletion affected AP-associated lung injury, colonic barrier dysfunction, and changes in gut microbiota. After a mouse model of AP was established, measurement of amylase and lipase, histopathological examination and intestinal mucosa-protein detection were conducted.

overall_design: The lung and colon tissues were subjected to perform RNA sequencing between wild-type and Cd177 knock-out (KO) mice.

first: Qingwei

last: Jiang

first: Guorong

last: Chen

first: Yangyang

last: Xiong

first: Liang

last: Gong

first: Kai

last: Song

first: Zhengyang

last: Fan

first: Ziying

last: Han

first: Jiaming

last: Qian

first: Dong

last: Wu


title: Dissecting the Role of Myf6 in Facilitating Fibroblast Conversion into Myogenic Progenitor and Differentiated Cells

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Transcriptional Control of Male-specific Pathway in Temperature-dependent Sex Determination

city: Harbin

first: li

middle: jia

last: meng

state: Harbin

address: Northeast Forestry University

institute: Northeast Forestry University

summary: Temperature-dependent sex determination (TSD), wherein the incubation temperature of embryos dictates the sex of the offspring, is a phenomenon documented across diverse reptilian species. In the accompanying study, we demonstrated the thermal switch mechanism within thermosensitive steroidogenic cells (TSSCs) that triggers the male development pathway in turtles. However, the transcriptional regulatory mechanisms linking TSSCs' cold sensitivity with pre-Sertoli cell specification remain elusive. Herein, we elucidate the regulatory schema governing the male determination pathway, including Ca2+-induced aldosterone synthesis in TSSCs and subsequent aldosterone-driven transcriptional modulation in pre-supporting cells. Aldosterone-bound NR3C1, a master regulator of male determination pathway, activates DMRT1 gene expression, culminating in pre-Sertoli specification. Therefore, our findings suggest a conserved male-specific pathway in turtles.

overall_design: Gonads' single cells were dissected from embryos at stage 15 (as common starting point), stage 16, 17, 19, 21 for FTP, and stage 15_5, 16_5, 17, 19, 21 for MTP.

first: Yin-Zi

last: Ye

first: Jiameng

last: Li

first: Weiming

first: Xiaonan

last: Fu

first: Shilong

last: Yang

first: Wei-Guo

last: Du


title: Dissecting the Role of Myf6 in Facilitating Fibroblast Conversion into Myogenic Progenitor and Differentiated Cells [CUT&Run]

summary: Conversion of fibroblasts into skeletal muscle cells by overexpression of the transcription factor MyoD has been widely employed over past decades in a multitude of experimental settings. However, the potential of additional myogenic regulatory factors such as Myf5, Myf6 and Myog to elicit a myogenic conversion has been significantly less studied. To address this disparity, we set out to investigate the role of MRFs in fibroblast conversion into skeletal muscle stem and differentiated cells. Surprisingly, we found that Myf6, a transcription factor associated with postnatal late-stage myogenesis, efficiently converted fibroblasts into myotubes alone, or alternatively into expandable Pax7-expressing induced myogenic progenitor cells (iMPCs) in the presence of defined small molecules. To investigate reprogramming dynamics in a tightly regulated system, we generated an inducible Myf6 overexpression transgenic mouse model, which enabled dissection of transcription and epigenetic dynamics unique to iMPC formation. Mechanistically, we characterized the chromatin binding of Myf6, as well as its protein binding partners, during iMPC reprogramming and conventional transdifferentiation, revealing shared and different targets and binding partners. To further investigate its role, we surprisingly found that endogenous Myf6 is dispensable for iMPC formation by MyoD and small molecules. In accordance with this observation, we demonstrated that subjecting MyoD-KO fibroblasts to reprogramming with Myf6 and small molecules gave rise to expandable MyoD-KO iMPCs, indicating that MyoD is similarly dispensable for iMPC formation and self-renewal. Multi-omics analyses of Myf6-derived MyoD-KO iMPCs uncovered upregulated genes that compensated for the lack of MyoD, whose downregulation during iMPC production mitigated Pax7 expression, highlighting their roles as reprogramming regulators. Collectively, these results illustrate a redundancy between MRFs’ function in myogenic cellular conversions, highlighting an unexpected potency for Myf6 in the induction of a muscle stem cell fate in vitro.

overall_design: Mouse embryonic fibroblasts (MEFs) were transduced with lentiviruses encoding for doxycycline-inducible HA-tagged Myf6 overexpression (LV[Exp]-Neo-TRE>mMyf6[NM_008657.3]/HA/HA/HA). Transduced cells were then treated with doxycycline (dox) and/or Forskolin/RepSox/CHIR99021 (F/R/C) for 24h and subjected to CUT&RUN to investigate Myf6 binding.

first: Giada

last: Bacchin

first: Alison

middle: R

last: Swearingen Pashos

first: João

middle: P

last: Agostinho de Sousa

first: Adhideb

last: Ghosh

first: Falko

last: Noé

first: Justin

last: Brumbaugh

first: Ori

last: Bar-Nur


title: Age-dependent autophagy impairment risks Alzheimer’s disease due to ULK1 reduction

city: Guangzhou

first: Lipeng

last: Mao

state: Guangdong

address: No.601, West Huangpu Avenue

department: Department of Microbiology and Immunology

institute: Jinan University

summary: Why age is the primary driver of the most common dementia-Alzheimer’s disease (AD)? Autophagy plays fundamental roles in cellular homeostasis, metabolic energetics, and in maintaining cellular resilience such as via eliminating damaged mitochondria. It is proposed that impaired autophagy leads to compromised catabolic degradation of amyloid beta (Aβ) and Tau pathologies, the disease-defining pathologies of AD; however, molecular mechanisms on whether and if yes, why reduced autophagy during ageing and its contribution to AD, especially in human samples, are largely elusive.   By using serum and CSF samples from a healthy ageing cohort (n = 22 with 4-year follow up samples) and an AD cohort (n = 391), we show that the abundance of ULK1 protein in serum and CSF decreases with increasing age and is extremely lower in AD patients than in age-matched controls.  In a large number of postmortem human brain samples (n = 72), expression of ULK1 in entorhinal cortical and hippocampal neurons in AD patients is significantly lower than in neurons from cognitive normal controls. To investigate whether ULK1 reduction is a bystander or cause/risk of AD, we generated a ubiquitously ULK1-ov mouse model and an AAV-based CA1 neuronal ULK1-ov mouse model in Aβ-bearing background; ULK1 overexpression stimulates autophagic and phagocytic degradation of Aβ, improves mitochondrial quality, thereby delaying progressive cognitive loss. Similarly, in hTau.P301S mice, overexpression of ULK1 inhibits Tau pathology and inhibits memory loss; mechanistically, ULK1 upregulation increases autophagy which increases cellular NAD+, leading to the inhibition of acetylated Tau174 (a cause of Tau pathology) through the NAD+/SIRT1 axis. ULK1 is likely a druggable target for AD as small molecule activators of ULK1 antagonize AD progression which is dependent on PINK1- and FUNDC1-related mitophagy. We propose age-dependent autophagy impairment risks AD due to ULK1 reduction, opening a new window for anti-AD therapeutics.

overall_design: Total RNA was isolated from hippocampal tissues from WT, 5xFAD, 5xFAD;Ulk1OV and Ulk1OV mice. Agarose gel electrophoresis was applied to check RNA integrity and DNA contamination; RNA purity (as well as concentration) was checked by the NanoPhotomerer spectrophotometer (IMPLEN) and Bioanalyzer 2100 system (Agilent Technologies). Then cDNA libraries were constructed using ≥ 800 ng RNA per sample with the Illumina's NEBNext® UltraTM RNA Library Prep Kit following manufacturer’s recommendations. The effective concentration of the library was determined to be at least 2nM. Next-generation sequencing data (performed by the company Novogene, China) were obtained and analyzed. FastQC and trim galore were used to filter raw sequence data and the removal of adapters, N-containing reads, and low-quality reads (reads below Q20).

first: Jun-ping

last: Pan

first: Ping-jie

last: Wang

first: Jianying

last: Zhang

first: Li-peng


title: Psmd13, a proteosome regulatory subunit for co-transcriptional miR-29a processing during neurogenesis [miRNA-seq]

city: Melbourne

first: Diji

last: Kuriakose

address: Clayton

country: Australia

institute: Monash University

type: Non-coding RNA profiling by high throughput sequencing

summary: miR-29a plays a critical role in neuronal development and is associated with neurodegenerative diseases, but its regulatory mechanisms remain unclear. To identify genes that influence miR-29a expression, we utilized the genetically diverse Collaborative Cross (CC) mouse strains and conducted expression profiling and Quantitative Trait Loci (QTL) analysis. A significant QTL on chromosome 7 was identified, and ten candidate genes were mapped within this region. RNAi-mediated knockdown experiments revealed that Psmd13 and Nap1l4 significantly increased miR-29a expression, implicating these genes as upstream regulators. Further investigation in mouse neural precursor cells (mNPCs) demonstrated that Psmd13 knockdown enhanced neuronal differentiation, as indicated by increased βIII-tubulin-positive cells, and miR-29a inhibition also promoted this process. Co-immunoprecipitation experiments showed that Psmd13 interacts with Dicer, modulating miR-29a levels through a differentiation-dependent mechanism. Chromatin immunoprecipitation sequencing (ChIP-seq) revealed co-binding of Psmd13 and Dicer at key genomic loci, including miR-29a, influencing chromatin accessibility and transcriptional regulation. Notably, proteasome inhibition using MG132 decreased Psmd13 and Dicer levels, leading to downregulation of miR-29a and impaired neuronal differentiation. These findings suggest that Psmd13 and Dicer coordinate to regulate miR-29a biogenesis and neuronal differentiation, highlighting the proteasome's essential role in maintaining neurodevelopmental homeostasis.

overall_design: Genome-wide co-localization of Psmd13 and Dicer at active miR loci during neurogenesis


title: tRNA m1A modification enhances anti-tumor immunity in macrophages by promoting translation of key interferon associated genes [TAMs bulk RNA-seq]

city: anonymity

first: anonymity

last: anonymity

state: anonymity

address: anonymity

department: anonymity

institute: anonymity

summary: Tumor-associated macrophages (TAMs) play a crucial role in tumor progression through their recruitment, polarization, and interaction with T cells in the tumor microenvironment (TME). However, the mechanisms underlying the post-transcriptional and translational regulation of TAMs in the TME remain largely unknown. In this study, we investigate the role of tRNA N1-methyladenosine (m1A) modification in controlling the behavior of macrophages in response to TME stimuli. We demonstrate that the m1A “writer” enzymes TRMT61A is highly enriched in the anti-tumoral and phagocytotic TAM subset, and TRMT61A is rapidly downregulated in macrophages upon stimulation with multiple TME components. Macrophage-specific knockout of TRMT61A leads to increased infiltration of TAMs, impaired CD8+ T cell function, and enhanced tumor growth. To further explore the biological effects of m1A deficient macrophages, we performed RNA sequencing analysis of TRMT61A-KO and WT TAMs derived from tumor bearing Trmt61af/fLysmCre and Trmt61af/f mice. The Gene ontology (GO) and Gene set enrichment analysis (GSEA) documented that the interferon response and the STAT1/IL-12 signaling pathway were impaired in TAMs upon TRMT61A deletion, indicating that TRMT61A is critical for macrophages to control interferon responses and exert anti-tumor effect in the TME.

overall_design: RNA samples of TRMT61A-KO and WT TAMs derived from tumor bearing Trmt61af/fLysmCre and Trmt61af/f mice after 14 days of tumor injection were collected by FACS sorting, and then RNA purification, reverse transcription, library construction and sequencing were performed according to the manufacturer's instructions (Illumina).


title: ST2 Signaling Regulates Innate Immune Response in Kidney Injury

city: Charlottesville

first: Vikram

last: Sabapathy

state: Virginia

address: 1340 Jefferson Park Ave., Pinn Hall, Room No: 4043

department: Center for Immunity, Inflammation and Regenerative Medicine

country: USA

institute: University of Virginia

summary: IL-33/ST2 signaling plays a crucial role in macrophage function during kidney injury. Using myeloid cell-specific ST2 knockout mice, the study revealed that ST2 deficiency attenuates renal damage in acute IRI but exacerbates it in chronic IRI. RNAseq and functional assays showed that ST2 is critical for macrophage-mediated efferocytosis and mitochondrial metabolism. The findings highlight the importance of IL-33/ST2 signaling in regulating macrophage activity and maintaining tissue homeostasis during renal injury.

overall_design: Bulk RNAseq analysis of bone marrow derived macrophages  from ST2-/- and wildtype (ST2+/+) controls.

first: Rahul

last: Sharma


title: High resolution multi-scale profiling of embryonic germ cell-like cell derivation reveals pluripotent state transitions in humans [RNA-Seq]

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

summary: Primordial germ cells (PGCs) are the embryonic precursors of the gametes. In mice and rats, PGCs can readily acquire pluripotency in vitro by forming embryonic germ cells (EGCs). To date, a comparable in vitro system has not been established in humans, despite the fact that human PGCs (hPGCs) readily undergo pluripotent conversion in the context of germ cell tumorigenesis. Here we report that hPGC-like cells (hPGCLCs) undergo conversion to human embryonic germ-like cells (hEGCLCs) upon exposure to the same inductive signals previously used to derive mouse EGCs. This defined, feeder-free culture system allows efficient derivation of human EGCLCs which  can be expanded and maintained in standard human pluripotent stem cell medium. hEGCLCs are transcriptionally similar to human pluripotent stem cells (hPSCs) and can differentiate into all three germ layers, as well as giving rise to PGCLCs once more - demonstrating the interconvertibility of pluripotent states. This is also evident at the epigenetic level,  as the initial DNA demethylation that occurs in hPGCLCs is largely reversed in hEGCLCs, restoring DNA methylation to the level observed in hPSCs. This new in vitro model captures the transition from the pluripotent stem cell state to a germ cell identity and back again, and therefore represents a highly tractable system to study pluripotent and epigenetic transitions, including those which occur during human germ cell tumorigenesis.

overall_design: We established a definer and feeder free protocol to reprogram hPGCLCs to EGCLCs and performed gene expression profiling analysis at different time points.

first: Sarah

last: Stucchi

first: Lessly

last: Sepulveda-Rincon

first: Camille

last: Dion

first: Giuseppe

last: Testa

first: Harry

middle: G

last: Leitch


title: Low-molecular weight heparins possess different effects on lung cancer cells in vitro and on cancer patient survival.

city: Hannover

first: Stephan

last: Immenschuh

state: Deutschland

address: Carl-Neuberg-Str. 1

department: Institute for Transfusion Medicine and Transplant Engineering

country: Germany

institute: Hannover Medical School

summary: The risk factors leading to cancer-associated thromboembolism include the patient’s gender, age, cancer type and stage, comorbidities, and therapies. Low-molecular-weight heparins (LMWH) are administrated for the prophylaxis and/or treatment of cancer and comorbid diseases associated with thrombosis. The effects of LMWH on cancer cells and overall patient survival remain controversial.

overall_design: Lung cancer cells (n=9) exposed to LMWH (tinzaparin) were studied for viability, proliferation, lipid droplet and colony formation. We generated transcriptome data from four of the cell lines. In a retrospective cohort of 2302 NSCLC patients (1089 received LMWH and 1213 did not) from the lung cancer registry at Thorax Clinic Heidelberg we assessed effects of tinzaparin, enoxaparin and other LMWHs on overall survival using a Cox regression model.

first: Julia

last: Held

first: Marc

middle: A

last: Schneider

first: Beatriz

last: Martinez-Delgado

first: Bin

last: Liu

first: David

last: DeLuca

first: Elena

last: Korenbaum

first: Tobias

last: Welte

first: Sabina

last: Janciauskiene

first: Thomas

last: Muley


title: tRNA m1A modification in macrophages promotes translation of interferon pathway genes to enhance CD8+ T cell-mediated anti-tumor immunity [CAR-iMACs RNA-seq]

first: anonymity

last: anonymity

summary: The involvement of tRNA m1A modification in the anti-tumoral tumor-associated macrophages (TAMs) has been validated in our study that macrophage-specific knockout of m1A “writer” enzymes TRMT61A leads to increased infiltration of TAMs, impaired CD8+ T cell function, and enhanced tumor growth. Since we observed that tumor-derived components suppresses tRNA m1A modification in macrophages, we sought to identify which component in the TME induces the down-regulation of tRNA m1A modification. Here, we performed bulk RNA-seq using TRMT61AOE-CAR-iMACs and CAR-iMACs to ensure the effect of human Trmt61a overexpression on CAR-iMACs. Kyoto encyclopedia of genes and genomes (KEGG) analysis showed that signal transduction is the most up-regulated pathway in CAR-iMACs after human Trmt61a overexpression.

overall_design: RNA samples of TRMT61AOE-CAR-iMACs and CAR-iMACs were collected, and then RNA purification, reverse transcription, library construction and sequencing were performed according to the manufacturer's instructions (Illumina).


title: RNA-seq of the central amygdala of rats with painful diabetic neuropathy

status: Public on Mar 03 2026

city: Hefei

first: xiaomin

last: nie

address: 17 Lujiang Road

institute: The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China

summary: Painful diabetic neuropathy (PDN) is a debilitating complication of diabetes, yet its central nervous system pathogenesis remains poorly understood. We investigated transcriptomic alterations in the central amygdala (CeA) in a diabetic rat model exhibiting neuropathic pain behavior. Male Sprague-Dawley rats were intraperitoneally injected a single dose of streptozotocin to induce diabetes. Six weeks following administration, the development of neuropathic pain was confirmed by the von Frey filament test. Subsequently, RNA sequencing of the CeA tissues identified 157 differentially expressed genes. This RNA sequencing dataset of the CeA in a neuropathic pain-exhibiting diabetic rat model provides insights into central nervous system adaptations in PDN and highlights potential molecular targets for therapeutic intervention.

overall_design: Male Sprague-Dawley rats were administered a single intraperitoneal dose of 60 mg/kg STZ to induce diabetes. Six weeks post-injection, neuralgia was confirmed in diabetic rats through a significant reduction in the withdrawal threshold in the von Frey test. Transcriptomic analysis of the central amygdala was performed on the rats with painful diabetic neuropathy compared with the non-diabetic controls.

first: Xiaomin

last: Nie


title: PARP1 Suppression Drives ROS Resistance in Aneuploid Cancer Cells

city: New York City

first: Ze

last: Chen

state: New York

address: 430 East 29th Street

department: Microbioloy

institute: NYU Grossman School of Medicine

summary: Aneuploidy—defined as gains and losses of chromosomes—is frequently observed in cancer and has been implicated in promoting tumor progression and metastasis. However, the molecular mechanisms underlying this phenomenon remain poorly understood. By generating new models of aneuploidy, we found that aneuploidy confers remarkable resistance to reactive oxygen species (ROS)-mediated cell death. This resistance is a general consequence of aneuploidy, independent of the specific chromosomes gained or lost. Mechanistically, Poly(ADP-Ribose) Polymerase 1 (PARP1) is suppressed in aneuploid cells, which inhibits PARP1-mediated cell death after ROS (parthanatos). We validated aneuploidy-associated PARP1 suppression across 15 cell models and human tumors, with pronounced effects in metastatic tumors. Importantly, decreased PARP1 levels promote tumor metastasis while increased PARP1 suppresses it. Through a genome-wide CRISPR screen and functional validation, we identified the transcription factor CCAAT/enhancer-binding protein beta (CEBPB) as a critical mediator of PARP1 downregulation and ROS resistance in aneuploid cells. Furthermore, we found that lysosomal dysfunction serves as the upstream mediator of CEBPB activation in aneuploid cells. We propose that aneuploidy-driven CEBPB activation promotes PARP1 suppression, fostering ROS resistance and cancer progression.

overall_design: To study the impact of aneuploidy on gene expression, we generated two aneuploidy models. In the acute aneuploidy model (Fig. 1A), immortalized human colon epithelial cells (hCECs) with TP53 knockout (TP53KO) were treated with MPS1/TTK inhibitors (reversine or AZ3146; MPS1i) for 24–30 hours to induce chromosome missegregation, then collected 3 days after inhibitor washout. To examine aneuploidy effects over a longer timeframe, we developed a chronic aneuploidy model in which reversine-treated TP53KO hCECs were expanded into 55 single-cell-derived isogenic clones with varying aneuploidy levels, as assessed by whole-genome sequencing. RNA-seq was performed on some clones to characterize their transcriptional profiles.

first: Pan

last: Cheng

first: Angela

last: Mermerian-Baghdassarian

first: Yufeng

last: Wang

first: Helberth M.

last: Quysbertf

first: Pradeep Singh

last: Cheema

first: Joseph C.

last: Mays

first: Xin

last: Zhao

first: Lizabeth

last: Katsnelson

first: Sally

last: Mei

first: Rohini

last: Shrivastava

first: Mirna

last: Bulatovic

first: Jiehui

last: Deng

first: Markus

last: Schober

first: Kwok-Kin

last: Wong

first: Teresa

last: Davoli


title: Transcriptomic Analysis of Control and p16INK4a Knockout Mice Hearts

city: Shanghai

first: tingting

middle: ting

last: Yang

address: 333 Nan Chen Road, Shanghai

institute: Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair

summary: This RNA-sequencing was performed to determine the differentially expressed mRNA in αMHC-Cre driven cardiomyocyte-specific knockout of p16INK4a mice after aging

overall_design: Transcriptomic profiling was performed using RNA-seq analysis of total RNA extracted from hearts of ~6 months and ~20 months post αMHC-Cre driven cardiomyocyte-specific knockout of p16INK4a（p16KO）and p16INK4a flox (Control) mice. Four groups were set in this animal experiment (n=4 per group): (1) Control_Young; (2) p16KO_Young ; (3) Control_Old; (4) p16KO_Old. The mRNA expression profiling analyses were performed using data obtained from RNA-seq of 4 different groups.

first: Junjie

last: Xiao

first: Anthony

last: Rosenzweig

first: Tingting

first: Qiulian

last: Zhou

first: Yihua

last: Bei


title: Comparison of transcriptomic profile of the murine B16F1-GFP-M melanoma cells with the derived dormant B16F1-GFP-D, B16F1-GFP-DB#1, B16F1-GFP-DB#2, B16F1-GFP-DB#3 melanoma cells - Part2

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

summary: Cancer patients after successful therapy contain nested in their organs and/or circulating in the systemic fluids tumor cells that remain asymptomatic for an extended period of time. They stay dormant with no apparent immediate potential to develop into a clinically manifested tumor until activated by yet not well defined mechanisms. We previously developed tumor dormancy model of murine melanoma, a cancer with a high potential of phenotype plasticity to adapt to micro-environmental changes, in which to investigate cellular quiescence and related factors as a potential mechanism of tumour dormancy. In this study,  to explore molecular mechanism responsible for cellular dormancy, we performed a comparative transcriptome analysis of dormant B16F1-GFP-D and derived dormant brain metastasis (DB) with maternal B16F1-GFP-M cells.

overall_design: Transcriptomic profiling of myeloïde and melanoma cell lines in the context of dormancy.

first: Thierry

last: Idziorek

first: Yasmine

last: Touil


title: Electromagnetic exposure changes human Schwann cells motility and transcriptomic profile of hearing-loss related genes

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

summary: Schwann cells (SCs) are glial cells of the peripheral nervous system with functional plasticity in physio-pathological conditions, as injury, and oncotransformation. Interestingly, human SCs seem to develop, mature, and respond differently to other species to environmental challenges. Recently, concerns raised about the expansion of environmental electromagnetic fields (EMF) and the increasing incidence of vestibular schwannoma (VS). We previously demonstrated that SCs respond to EMF by acquiring a state prone to oncotransformation. However, the biodependence of such transformation on the species (rodents versus human) deserves clarification. Here, we obtained and characterized human SCs, showing that EMF affects proliferation, migration, and transcriptomic profile. The expression of motility proteins increased, while those of cell-to-cell adhesion proteins decreased. The functional clustering of genes differentially expressed matched with those involved in hearing loss. In summary, we provide insights into the effects of chronic EMF on human SCs, highlighting its potential role in VS onset.

overall_design: RNA-Seq was performed on hSCs exposed to EMF or control cells, which were not exposed to EMF. For each condition, experiments were done in triplicate to performstatistics for differential expression studies

first: Tasnim

last: Mohamed

first: Alessandra

last: Colciago

first: Alessandro

last: Faroni

first: Adam

last: Reid

first: Valerio

last: Magnaghi


title: SGI-7079 as a novel type I FLT3 inhibitor overcomes resistance to gilteritinib and quizartinib mediated by ITD and TKD mutations in acute myeloid leukemia

first: Peihong

last: Wang

address: No. 1, Panfu Road

department: Department of Hematology

institute: Guangzhou First People's Hospital

summary: FLT3-ITD mutations are among the most frequent mutations in acute myeloid leukemia (AML) and are associated with poor prognosis and high relapse rates. Despite the extensive use of existing FLT3 inhibitors, resistance caused by secondary TKD mutations remains a major challenge. Therefore, the development of next-generation FLT3 inhibitors with broad-spectrum activity and sensitivity to drug-resistant mutations is of considerable clinical value. In this study, we systematically evaluated the antileukemic activity of a novel type I FLT3 inhibitor, SGI-7079, within the context of FLT3-ITD mutations and drug-resistant secondary mutations. SGI-7079 notably inhibited the proliferation of AML cell lines harboring FLT3-ITD mutations and multiple drug-resistant secondary mutations, such as D835Y/V/F, Y842C, and F691L, in vitro. Mechanistically, SGI-7079 was bound stably to the FLT3 protein, as indicated by molecular docking and CETSA analyses; inhibited FLT3 phosphorylation and downstream STAT5, AKT, and ERK signaling; and induced G1-phase arrest and apoptosis. In mouse models harboring FLT3-ITD mutations, SGI-7079 greatly reduced leukemia burdens, mitigated histopathological abnormalities, and prolonged median survival. Notably, SGI-7079 effectively overcame gilteritinib resistance driven by FLT3-ITD-F691L mutations in vivo and exhibited effectiveness against quizartinib-resistant FLT3-ITD-D835Y mutations. Importantly, SGI-7079 demonstrated notable inhibitory activity in primary AML cells from FLT3-ITD-positive patients, with effectiveness surpassing that of approved agents gilteritinib and quizartinib. In summary, this study is the first to demonstrate that SGI-7079 provides broad-spectrum and potent inhibitory activity across diverse FLT3 mutation contexts, showing remarkable advantages against drug-resistant mutations, especially F691L, and exhibits high potential for clinical translation.

overall_design: To systematically elucidate the transcriptional regulatory mechanisms of SGI-7079 in FLT3-ITD-mutant AML cells, RNA sequencing (RNA-seq) analysis of MV4-11 and MOLM13 cells was performed. Total RNA was extracted from cells treated with 10 nM SGI-7079 for 24 hours, after which RNA quality and integrity were assessed. After library construction, paired-end sequencing was conducted on the Illumina NovaSeq 6000 platform. The raw sequencing data were subjected to quality control, and adapter sequences and low-quality reads were removed. Clean high-quality reads were aligned to the human reference genome (hg38), and gene quantification was performed using featureCounts. Differential expression analysis was performed using DESeq2 with thresholds of |log₂Fold Change| > 1 and FDR < 0.05. Differentially expressed genes (DEGs) were further annotated using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses to identify key biological processes and pathways potentially regulated by SGI-7079.

first: Zhiwei

last: Zhong

first: Miner

last: Xie

first: Shiyang

first: Jiajun

last: He

first: Jiaqi

last: Fan

first: Xiaoqing

last: Bai

first: Tingfen

last: Deng

first: Caixia

first: Wei

first: Shunqing


title: ETV1 activates a rapid conduction transcriptional program in rodent and human cardiomyocytes [RNA-Seq]

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

summary: ETV1 (ER81) was identified as a highly enriched transcription factor in rapidly conducting atrial and His-Purkinje cardiomyocytes. Previous work has shown that ETV1 is a critical factor in determining fast conduction physiology in the heart. High-throughput sequencing project aims to uncover ETV1-dependent gene networks in cardiomyocytes, and transcriptomic changes in the left atrium under cardiac pressure overload. These results provide insight into the role of ETV1 in the establishment of rapid conduction zones in the heart.

overall_design: Constriction of the transverse thoracic aorta was performed on 2 month-old C57BL/6J male mice. After 2 weeks of the procedure, whole left appendage tissues were harvested and total RNAs were extracted using the RNeasy kit (Qiagen) according to the manufacture's protocol. Sequencing libraries were prepared using the TruSeq RNALibrary Prep Kit v2. (Illumina) according to the manufacture's protocol.

first: Akshay

last: Shekhar

first: Deven

last: Narke

first: David

last: Park


title: Acute depletion of Cited2 in embryonic stem cells disrupts gene networks controlling self-renewal, homeostasis, and early cell fate commitment

city: Faro

first: Rui Sotero

last: Rodrigues Machado

address: Campus de Gambelas

country: Portugal

institute: Universidade do Algarve

summary: Cited2 is a transcriptional regulator essential for embryonic development and cellular homeostasis. Studies in vertebrate models highlight its critical roles in heart, placental, neural tube, and hematopoietic development. In humans, CITED2 variants are associated to congenital heart disease. Functionally, Cited2 interacts with the transcriptional co-regulators p300/CBP and modulates the activity of multiple transcription factors. In embryonic stem cells (ESC), Cited2 supports pluripotency, self-renewal, and differentiation potential. Here, we performed comparative transcriptomic analysis after acute Cited2 depletion in mouse ESC to define its role in maintaining self-renewal, lineage competence, and cell survival. Loss of Cited2 rapidly destabilized the pluripotency network and induced aberrant activation of developmental gene programs. Nodal/Activin pathway targets, including key regulators of mesoderm, cardiac, and neural development, were markedly downregulated, consistent with Cited2-null embryonic phenotypes. Cited2 depletion also altered the expression of genes involved in DNA damage response, immune signaling, and apoptosis, correlating with the increased γH2AX accumulation and p53-dependent viability loss observed. Comparison with p300- and CBP-depletion datasets revealed minimal overlap, supporting a largely p300/CBP-independent role for Cited2 in ESC. These results position Cited2 as a core regulator preserving ESC identity, genomic stability, and proper lineage engagement during early differentiation.

overall_design: 12 samples analyzed, 4 conditions with 3 replicates each. Used as reference sample is condition Day_0_ETOH_treated.

first: Leonardo

last: Mendes-Silva

first: Sara

last: Brigida

first: Marlene

last: Trindade

first: João

middle: M

last: Santos

first: Lucas

last: Rougier

first: Rui

last: Machado

first: Ana

middle: L

last: Escapa

first: Agapios

last: Sachinidis

first: Jessica

last: MacDonald

first: José

last: Bragança


title: Effect of eIF5B silencing on KSHV-reactivated human iSLK.219 cells from 0-72 Hours reactivation

city: Miami

first: Yuande

last: Tan

address: 1120 NW 14th Street

department: UNM Comprehensive Cancer Center

institute: Miami University

summary: Kaposi’s Sarcoma (KS) Herpesvirus (KSHV) is the etiological agent of KS, an AIDS-defining illness. Recent studies have demonstrated that even during normoxic conditions, KSHV facilitates replication by modulating hypoxia-inducible factors (HIFs), creating a hypoxia-like environment that promotes cellular transformation. KSHV lytic viral genes are favored for protein synthesis during infection by upregulating HIF2α and utilizing the hypoxic eIF4E2 translation initiation complex in oxygen-replete conditions. This translation initiation plasticity (TRIP) links viral replication strategies to angiogenic signaling and oncogenicity. However, the molecular basis of this plasticity remains poorly understood. This study reveals that viral inhibition of eukaryotic initiation factor 2 (eIF2) induces the use of another alternative initiation factor, eIF5B, which canonically mediates delivery of initiator methionine during hypoxia. Specifically, our transcriptomic analyses reveals that the mRNA landscape in KSHV-infected cells depleted of eIF5B mirrors that of uninfected hypoxic cells, highlighted by differential gene expression of pathways involved in hypoxia and glycolysis.

overall_design: KSHV-harboring iSLK.219 cells were transfected with either control or eIF5B siRNA for 24 hours, followed by lytic induction by addition of doxycycline and collection of mRNAs of both groups at 0, 24, 48 and 72 hours post-reactivation.  Bulk-RNA sequencing was performed on  three biological replicates over the course of KSHV infection.

first: Christian

last: McDonald

first: Yuan-De

first: Enrique

last: Mesri

first: Noula

last: Shembade


title: Interleukin-6: A Phenotype-Agnostic Therapeutic Target for Mucus Plugs in Type 2 and Non-type 2 Asthma

city: BeiJing

first: Chun

last: Chang

address: 49 North Huayuan Road

institute: Peking University Third Hospital

summary: Airway mucus plugs are prevalent in both type 2 (T2) and non-T2 asthma phenotypes, contributing to treatment resistance. Current biologics predominantly target T2 pathways. In our cross-sectional study of 321 patients with asthma, chest CT showed mucus plugs were prevalent in both T2 and non-T2 asthma (33.2% vs 20%, P = 0.034) and across all severities (mild-to-moderate: 27.0%; severe: 60.7%; P = 0.001). Patients with mucus plugs had higher rates of severe asthma (17.7% vs 4.9%, P < 0.001) and elevated serum and sputum IL-6 (P = 0.004; P < 0.001). Multivariable regression identified sputum IL-6 as an independent risk factor for mucus plugs (OR 4.84; 95%CI, 1.63–24.5; P = 0.020). In vivo and in vitro studies demonstrated that anti-IL-6/IL-6R treatment significantly reduced periodic acid-Schiff scores (2.80 ± 0.84 vs 4.60 ± 0.55, P = 0.004) and mucin 5 subtype AC/B expression via the PI3K mTOR signaling pathway. We further observed that 2 of 3 patients with mucus plugs exhibited significant resolution following tocilizumab treatment. These findings indicate that mucus plugs are a common feature across asthma inflammatory phenotypes and are associated with increased disease severity. IL-6 pathway inhibition offers a phenotype agnostic therapeutic strategy for mucus plug resolution in asthma.

overall_design: This translational study employed a three-part design: first, a cross-sectional analysis of 321 asthma patients using chest CT and cytokine profiling to identify sputum IL-6 as an independent risk factor for mucus plugs; second, mechanistic validation in murine asthma models and human bronchial epithelial cells demonstrating that IL-6 drives mucin overproduction via the PI3K-mTOR pathway; and third, a retrospective evaluation showing mucus plug resolution in two of three patients treated with the IL-6 receptor antagonist tocilizumab.

first: Qiao

last: Yixian

first: Li

last: Zemin

first: Xi

last: Hanxu

first: Liu

last: Kexin

last: Meijiao

first: Sun

last: Lina

last: Yongchang

first: Aili

last: Abudureyimujiang

first: Chang

last: Chun


title: Retrotransposon-driven co-transcriptional chromatin remodelling rewires Ash2l isoform usage to prime developmental promoters [ChIP-seq]

first: Folkert

last: van Werven

address: 1 Midland Road

institute: Francis Crick Institute

summary: Transcription start site (TSS) selection diversifies the transcriptome and proteome, yet the mechanisms and functional consequences of alternative TSSs in development remain poorly understood. Here, we show that the chromatin regulator ASH2L undergoes developmentally regulated alternative TSS switching in differentiating mouse cells, generating distinct mRNA and protein isoforms: a full-length ASH2L and a truncated form lacking an intrinsically disordered region (IDR). In pluripotent stem cells, transcription from the upstream TSS is driven by a mouse-specific retrotransposon element that suppresses transcription from the downstream TSS through a transcription interference mechanism involving SETD2-directed histone H3 lysine 36 methylation. The resulting upstream-driven, stem cell–specific truncated ASH2L isoform primes developmental-gene promoters for histone H3 lysine 4 methylation, establishing a chromatin state required for embryogenesis and motor neuron differentiation. We propose that co-option of a mouse-specific retrotransposon drives a switch in Ash2l TSS and protein isoforms to control developmental timing and cell fate decisions.

overall_design: ChIP-seq H3K4me3, and ASH2L in CRISPRi control, gRNA TSS1, gRNA TSS2

first: Eleanor

last: Elgood Hunt

first: Claudia

last: Vivori

first: Richard

last: Mitter


title: Retrotransposon-driven co-transcriptional chromatin remodelling rewires Ash2l isoform usage to prime developmental promoters [Timecourse]

overall_design: mESCs (HM-1) cells were differentiated to spinal cord motor neurons in 7 day time course. Cells were lifted and resuspended in N2B27 (49% DMEM/F12-/- (Gibco), 49% Neurobasal (Gibco), 1X N2 (Gibco), 1X B27 (Gibco), 0.05 mM 2-Mercaptoethanol (Gibco), 2mM L-Glutamine (Gibco)) with bFGF (10 ng/ml, Bio-Techne, 3139-FB-025) before 85,000 cells were plated on Geltrex- (or Matrigel-) coated 6-well plates in N2B27 with bFGF (10 ng/ml). 48 hours later the media was changed to N2B27 with bFGF (10ng/ml), CHIR99021 (5μM, Axon MedChem, 1386), SB 431542 (10uM, Cambridge Bioscience S0400) and DMH1 (2uM, Cambridge Bioscience, 16679). 20 hours later, the media was changed to N2B27 with 100 nM RA (Sigma Aldrich, R2625) and 100 nM SAG (Merck, 566660). After this, the media was replaced every 24 hours for up to 7 days of total differentiation. Treatment with 10 µg/ml notch inhibitor DBZ (Tocris 4889) occurred from day 5 onwards.  We have performed Poly(A)-TSS-seq, TT-TSS-seq, TTchem-seq, RNA-seq, in duplicates, 14 samples per approach.


title: Adipocytes signal to recruit specific mRNAs from surrounding cells to restore expression deficits [RNA-Seq]

city: St. Louis

first: Clair

last: Crewe

address: 660 S Euclid Avenue

institute: Washington Univeristy in St. Louis

summary: Extracellular vesicles (EVs) are nano-sized, membrane-delimited, particles released by cells that carry signaling macromolecules. A major pathway of EV production is potentiated by neutral sphingomyelinase 2 (SMPD3/nSMAse2), an enzyme that generates ceramide from sphingomyelin. In our attempt to study this pathway in adipocytes of male mice, we discovered that the elimination of SMPD3 from adipocytes in vivo triggers a signal to surrounding immune cell-like preadipocytes to release EVs that carry SMPD3 mRNA. This results in a widespread increase in SMPD3 mRNA in purified null adipocytes without a change in the transcripts of other enzymes involved in ceramide metabolism. These results point to a fundamental, novel, and selective mechanism by which specific mRNA molecules are acquired from the microenvironment to a level that can restore expression of mRNA and protein in a cell that is depleted of the corresponding genetic information.

overall_design: After 2 weeks on doxycycline diet to induce SMPD3 knockout, subcutaneous white adipose tissue (sWAT) control and ad-SMPD3KO mice were harvested. sWAT was dissocited with collagenase into single cells and live cells were sorted by FACS.

first: Christy

last: Gliniak

first: Toshiharu

last: Onodera

first: Shiuhwei

last: Chen

first: Jan-Bernd

last: Funcke

first: May-Yun

last: Wang

first: Snigdha

last: Tiash

first: Yun-Ling

last: Pai

first: Marjori

last: Russo

first: Saket

last: Patel

first: Ze

last: Yu

first: Yi-Cian

last: Zheng

first: Chao

last: Xing

first: Laurent

last: Gautron

first: Chun-Kan

first: Chen

last: Liu

first: Philipp

middle: E

last: Scherer


title: Gene expression microarrays of ADCY9-deficient human pancratic islets

city: Malmö

first: Jones

middle: K

last: Ofori

address: Jan Waldenströms gata 35

department: Department of Clinical Sciences

country: Sweden

institute: Lund University

summary:
Adcy9-deficiency impairs stimulus-secretion coupling in β-cells
To characterize the mechanisms underlying the dysfunction caused by ADCY9-deficiency, we performed global transcriptomic analyses in human islets

overall_design: Total RNA was extracted from human islets after silencing ADCY9 using siADCY9 from human islets(N=5 donors)

first: Ofori

last: Jones

first: Ling

last: Charlotte


title: Gene expression microarrays of ONECUT2-overexpression in human pancratic islets

summary:
ONECUT2-overexpression impairs stimulus-secretion coupling in β-cells
To characterize the mechanisms underlying the dysfunction caused by ONECUT2-overexpression , we performed global transcriptomic analyses in human islets

overall_design: Total RNA was extracted from human islets after overexpression ONECUT2 in human islets (N=6 donors)


title: The establishment of cell-type specific gene regulation in the sea urchin embryo [scRNA-seq, bulk RNA-seq]

city: Bergen

first: Jonas

middle: Maurice

last: Brandenburg

address: Thormolensgatan 55

department: Michael Sars Centre

country: Norway

institute: University of Bergen

summary: Cell-fate commitment in metazoan development relies on precise gene regulatory programs. This study presents a comprehensive single-cell atlas of gene expression (scRNA-seq), nascent transcription (scSLAM-seq), and chromatin accessibility (scATAC-seq) in the purple sea urchin, Strongylocentrotus purpuratus, from early cleavage to pluteus larva stages. Our findings reveal a dynamic regulatory landscape with extensive usage of distal and intronic regulatory elements, which often exhibit cell-type-specific motifs and accessibility profiles that closely track gene expression. We identify a major wave of zygotic genome activation (ZGA) at the 128-cell stage, coinciding with the loss of developmental plasticity, alongside evidence of restricted, lineage-specific gene activation preceding widespread ZGA. Motif analysis highlights distinct regulatory grammars for these early accessible regions. Regulatory element usage largely clusters by germ layer, indicating shared accessibility among related cell types. We delve into the regulatory intricacies of neurons and skeletogenic cells. Sea urchin neurodevelopment proceeds through three distinct lineages, utilizing transcription factors with conserved roles in mammalian neurogenesis. Surprisingly, skeletogenic cells show significant transcriptional and regulatory diversity across their subpopulations, and we identify novel genes associated with calcification. This research offers unprecedented insights into the dynamic regulatory genome of a non-chordate deuterostome, highlighting both conserved principles of gene regulation and unique features that underscore the sea urchin’s importance as a model for understanding developmental and evolutionary genomics in ecologically critical marine species.

overall_design: scRNA-seq (coupled with scSLAM-seq) of purple sea urchin (Strongylocentrotus purpuratus) embryos from cleavage stages through gastrulation to pluteus stage. Processed by 10x Genomics 3' scRNA-seq. Bulk RNA sequencing was used to obtain SNP profiles of each experimental cross and allowed to demultiplex the scRNA-seq dataset.

first: Alexandra

last: Trinks

first: Dominika

last: Voijtasova

first: Anna

last: Monaco

first: William

last: Chang

first: Roberto

last: Arsie

first: Marian

last: Hu

first: Amro

last: Hamdoun

first: Chloe

last: Jenniches

first: Markus

last: Landthaler

first: Nils

last: Blüthgen

first: David

last: Garfield


title: E1A transactivation through superinfection turns iPSC-derived macrophages from a quiescent to a productive adenovirus cell state

city: Zurich

first: Maarit

last: Suomalainen

address: Winterthurerstrasse 190

department: DMLS

institute: University of Zurich

summary: Macrophages are a first line defense against pathogens. Human adenovirus C5 (AdV-C5) infection is inefficient in human iPSC-derived macrophages, partially due to poor activity of the enhancer/promoter (e/p) of the virus immediate early gene E1A. The E1A proteins are needed to activate other viral transcription units and to rewire the host cell for efficient virus replication. The E1A restriction can be overcome by coinfection of the wt virus together with a non-replicating AdV in which the E1A e/p has been replaced by the cytomegalovirus immediate early e/p (AdV-C5-CMV-E1A virus). We report here bulk RNA-seq results from noninfected iPSC-derived macrophages (NI samples), single wild type AdV-C5 (wt samples) and wt and AdV-C5-CMV-E1A coinfections (wtCMV samples) at 12 h and 27 h (marked as 24 h in the files) post infection. All samples had three technical replicates.

overall_design: Bulk RNA-Seq of noninfected, AdV-C5 wild type (wt)-infected and AdV-C5 wt and AdV-C5-CMV-E1A (wtCMV) coinfected human iPSC-derived macrophages. Samples collected at 12h and 27h (file names 24h) post infection. All samples had three technical replicates

first: Walther

last: Haenseler

first: Urs

middle: F

last: Greber


title: Single-cell RNA-seq of tumor samples from six advanced HGSOC patients across treatment stages (pre-NACT, post-NACT and platinum-sensitive recurrence)

city: Beijing

first: Yumei

last: Wu

address: Dongcheng District, Qi-he-lou Street No.17

institute: Department of Gynecological Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University

summary: High-grade serous ovarian cancer (HGSOC) is characterized by pronounced cellular heterogeneity and dynamic changes during treatment and recurrence. In this study, we collected 10 tumor samples from six patients with advanced-stage HGSOC and performed single-cell RNA sequencing (scRNA-seq) to profile the tumor ecosystem across different treatment stages, including pre-neoadjuvant chemotherapy (pre-NACT), post-neoadjuvant chemotherapy (post-NACT), and platinum-sensitive recurrence. Single-cell libraries were prepared using the 10x Genomics platform followed by high-throughput sequencing. This dataset provides a resource for investigating transcriptional heterogeneity and cellular composition changes associated with treatment and recurrence in advanced HGSOC.

overall_design:
Single-cell RNA-seq was performed on 10 tumor specimens from six advanced-stage HGSOC patients across three clinical stages (pre-NACT, post-NACT, and platinum-sensitive recurrence) using the 10x Genomics platform to characterize cellular heterogeneity and treatment-associated changes.
Submitters state that raw FASTQ files are not available due to human subject privacy considerations and institutional data-sharing restrictions.

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************


title: tRNA m1A modification enhances anti-tumor immunity in macrophages by promoting translation of key interferon associated genes [BMDMs bulk RNA-seq]

city: anonymity

first: anonymity

last: anonymity

address: anonymity

institute: anonymity

summary: The involvement of tRNA m1A modification in the anti-tumoral tumor-associated macrophages (TAMs) has been validated in our study that macrophage-specific knockout of m1A “writer” enzymes TRMT61A leads to increased infiltration of TAMs, impaired CD8+ T cell function, and enhanced tumor growth. Since TRMT61A-derived tRNA m1A modification mainly enhances translation efficiency, we reasoned that the loss of TRMT61A in macrophages would result in the downregulation of a group of protein levels without affecting their mRNA levels. To assess the impact of TRMT61A deficiency on mRNA transcript levels in macrophages, we collected TRMT61A-KO and WT BMDMs derived from Trmt61af/fLysmCre and Trmt61af/f mice to perform bulk RNA sequencing. Of total 22173 genes, the mRNA expression of 22054 genes remain unchanged in macrophages upon TRMT61A deletion, suggesting that TRMT61A did not contribute to mRNA transcriptional regulation in macrophages.

overall_design: RNA samples of TRMT61A-KO and WT BMDMs derived from Trmt61af/fLysmCre and Trmt61af/f mice were collected, and then RNA purification, reverse transcription, library construction and sequencing were performed according to the manufacturer's instructions (Illumina).


title: SCD1 and SCD5 Modulate PARP-Dependent DNA Repair via Fatty Acid Desaturation in Glioblastoma

city: Boston

first: Hayk

last: Mnatsakanyan

state: MA

address: 149 13th Street Charlestown

department: Neurology

institute: Massachusetts General Hospital

summary: Glioblastoma (GBM) relies on fatty acid metabolism to sustain its aggressive growth. While the role of stearoyl-CoA desaturase-1 (SCD1) in GBM is established, the function of its brain-enriched isoform, SCD5, remains unexplored. Here, we demonstrate that SCD5 is essential for glioblastoma stem cell (GSC) maintenance and genomic stability, with elevated expression in GSCs that declines upon differentiation, underscoring its role in tumor initiation. Through shotgun lipidomics, 13C metabolic flux analysis, and functional genomics, we reveal that SCD1 and SCD5 play non-redundant roles in fatty acid desaturation, with SCD5 preferentially desaturating C18:0 and uniquely contributing to sphingolipid remodeling. Genetic silencing of either isoform disrupts cell cycle progression, impairs DNA damage repair, and reduces GSC viability, while SCD5 knockdown significantly extends survival in orthotopic GBM models. Mechanistically, loss of SCD activity or saturated fatty acid accumulation triggers PARP1 hyperactivation and subsequent degradation, depleting RAD51 to compromise homologous recombination and induce parthanatos. These findings uncover a lipid-mediated vulnerability in GBM, linking fatty acid desaturation to PARP1-dependent genome integrity. Targeting SCD5 may offer a novel therapeutic strategy to eliminate therapy-resistant GSCs and enhance the efficacy of genotoxic or immunotherapeutic interventions.

overall_design: RNA-seq profile of glioma stem cells (GSCs; Mayo120) after 4 days of control, stearoyl-CoA desaturase (SCD1), or SCD5 knockdown.

first: Christian E.

last: Badr


title: Cost adjusted hierarchical defense strategies enables stratified oxidative stress tolerance

city: Mumbai

first: Amitesh

last: Anand

state: Maharashtra

address: Homi Bhabha Road

department: DBS

country: India

institute: TIFR

summary: Organisms employ diverse adaptive strategies to withstand environmental stresses, yet how bacteria tailor their responses to different magnitudes of the same stressor remains poorly understood. This question is particularly salient for oxidative stress, which varies substantially across physiological niches and exerts distinct selection pressures on colonizing bacterial populations. Here, we used four separate adaptive laboratory evolution (ALE) of Escherichia coli across multiple paraquat concentrations and genetic backgrounds to dissect how cells adapt to varying levels of superoxide stress. Integrating multi-omic analyses with tailored genome-scale metabolic modeling, we identify two fundamentally distinct tolerance strategies based on flux control and cellular resource optimization. Under low superoxide stress, reducing paraquat influx suffices to maintain redox balance. In contrast, higher stress levels activate an energetically demanding program involving enhanced ROS defenses and active efflux. We further show that these flux regulatory responses interface with metabolic repair systems to enable additional fitness gains. Together, our findings reveal how E. coli differentially engages modular stress-response programs depending on stress magnitude, offering generalizable insights into the principles governing dynamic bacterial adaptation.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Adaptive laboratory evolution (ALE) of Escherichia coli was performed across multiple paraquat concentrations and genetic backgrounds, followed by multi-omics analysis and validation experiments.

first: Anjali V.

last: Patil

first: Jiao

last: Zhao

first: Snehal V.

last: Khairnar

first: Sonali

last: Srivastava

first: Laurence

last: Yang


title: Overcoming Menin inhibitor resistance in AML cells with combinations including BET proteins and dual BRG1/BRM inhibitor [ChIP-seq]

city: Houston

first: Xiaoping

last: Su

state: Texas

address: 7300 Brompton St, Apt 5633

institute: MD Anderson Cancer Center

summary: Menin inhibitors (MI) disrupt the binding of Menin to MLL1 leading to repression of MLL1 or MLL1-fusion protein (FP) target genes, including reduced levels of HOXA9 and MEIS1 in AML with mtNPM1 or MLL1-r. While MIs are relatively well-tolerated and induce clinical remissions, these are often short-lived due to development of resistance followed by AML relapse. Through repeated shocks with the MI SNDX-50469, a precursor tool compound to revumenib, followed by recovery, we developed MI-resistant (MITR) AML MV4-11 and OCI-AML3 cells. Present studies show that, compared to MI-sensitive parental cells, MITR cells exhibit an altered epigenome, transcriptome and proteome, without Menin mutations. Through a CRISPR screen, novel druggable MI co-enrichments were identified and targeted, including BRD4, SMARCA4, and CREBBP. Co-treatment with the MI and the SMARCA4/SMARCA2 (BRG1/BRM) inhibitor FHD-286 or the BET proteins inhibitor OTX015 (birabresib), synergistically induced in vitro lethality in MITR and MI-resistant AML cells expressing the mutant Menin (M327I), as well as in patient-derived (PD) AML cells with MLL1r or mtNPM1 that exhibited ex vivo resistance to MI. Compared to each drug alone, co-treatment with SNDX-5613 (revumenib) and FHD-286 or OTX015 and FHD-286 significantly reduced the in vivo AML burden and improved survival of the immune depleted mice, without inducing significant toxicity, in the xenograft models of MITR and MI-resistant PD MLLr AML cells. These findings highlight novel, targeted, drug combinations that overcome MI resistance in AML cells with MLL1r or mtNPM1.

overall_design: Paired end ChIP-Seq of MLL1 rearranged and mutant NPM1 expressing AML samples treated with Menin inhibitor SNDX-50469 for 16 hours.

first: Warren

last: Fiskus

first: Kapil

last: Bhalla


title: Targeting BMP and TAZ/TEAD mechanotransduction pathways impairs AML chemoresistance

city: Lyon

first: Kevin

last: Geistlich

address: 28 rue Laennec

institute: CRCL

summary: Despite extensive research and intensive use of chemotherapies in clinics, the 5-year overall survival of Acute Myeloid Leukemia (AML) patients does not exceed 20%. The clonal expansion of leukemic blasts leads to modifications of the bone marrow physical properties, including increased extracellular matrix stiffening, upregulation of intramedullary pressure and reduction of the space available for cells. These biomechanical modifications are speculated to alter therapeutic response and cause treatment resistance. This project aims to decipher the role of mechanotransduction pathways in specially the Hippo pathway in resistant AML.

overall_design: The AML cell line used, ML2 (RRID:CVCL_1418) was cultured in RPMI 1640 with 10% fetal bovine serum (FBS). Resistant cells were permanently cultured with Cytarabine (ara-C) or venetoclax at 1 µM. Stable ML2-R were transduced with lentivirus shCtl or dual shYAP/TAZ names shTAZ#1 and shTAZ#2 (constructs generously given by Rob Bremner lab) including a EGFP marker and sorted by cytometry.

first: Sylvain

last: Lefort

first: Nicolas

last: Lespinasse

first: Lea

last: Barral

first: Véronique

last: Maguer-Satta


title: Overcoming Menin inhibitor resistance in AML cells with combinations including BET proteins and dual BRG1/BRM inhibitor [RNA-seq]

overall_design: Paired end targeted mRNA Seq of cultured and patient-derived AML cells sensitive or resistant to Menin inhibitor treatment for 16 hours


title: Long-read isoform sequencing reveals Aroclor1260-induced isoform expression in mouse liver

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: Long-term exposure to polychlorinated biphenyls (PCBs) including the mixture of PCBs in Aroclor1260 (Ar1260) results in metabolic dysfunction-associated steatotic liver disease (MASLD) in mice and humans. Previously, we reported that chronic (34 wks.) exposure of normal low fat diet (LFD)-fed male mice to Ar1260 resulted in twelve hepatic RNA modifications. We confirmed the downregulation NRF2 (Nfe2l2) network pathway associated with human liver diseases. Proteomic analysis of these same liver samples identified Ar1260 exposure-associated changes in protein abundance including altered selenoproteins: GPX4 and SELENBP2 were increased and SELENOS and SELENOF were reduced.  Alternative splicing (AS) has been implicated in MASLD. Here we used long-read isoform sequencing (IsoSeq) to and differential transcript usage (DTU) to specific DTU gene differences depending on the severity of liver injury with Ar1260.

overall_design: Three sample groups (low fat diet + DMSO control, low fat diet + Ar1260 treatment + low NAFLD Activity Score (< 3.0), low fat diet + Ar1260 treatment + high NAFLD Activity Score (>3.0)) with four replicates per group.

first: Belinda

middle: J

last: Petri

first: Kelli

last: Piell

first: Banrida

last: Wahlang

first: Julia

middle: H

last: Chariker

middle: C

first: Matthew

last: Cave

first: Carolyn

last: Klinge


title: PAF1C-driven restoration of RNAPII elongation after DNA damage occurs independently of transcription-associated histone mark deposition

city: Leiden

first: Martijn

middle: S.

last: Luijsterburg

state: zuid-holland

address: Einthovenweg 20

department: Human Genetics

country: Netherlands

institute: LUMC

summary: DNA lesions block the progression of RNA polymerase II (RNAPII) during transcription, impeding gene expression and threatening genome integrity. When RNAPII stalls on transcription-blocking lesions, the transcription-coupled DNA repair pathway is activated to remove the DNA damage. Following DNA repair, efficient transcription restart depends on the PAF1 elongation complex (PAF1C). PAF1C contributes to deposition of transcription-associated histone marks, including H2B-K120Ub, H3K4me3 and H3K79me. These marks are enriched at actively transcribed genes and have been associated with regulation of post-repair transcription restart. Here, we show that the H2B-K120 E3 ubiquitin ligase RNF20/RNF40, the H3K4-methyltransferase SET1/COMPASS complex, and the H3K79-methyltransferase DOT1L are dispensable for transcription restart. Moreover, levels of H2B-K120Ub and H3K4me3 do not correlate with transcription restoration following DNA damage. Additionally, we observe that, unlike PAF1, the dissociable PAF1C subunit RTF1, while stimulating H2B-K120Ub and H3K4me3, does not play a role in transcription restart. Together, these data suggest that transcription restoration after DNA damage is stimulated by the PAF1C elongation complex, independently of transcription-associated histone mark deposition.

overall_design: To study how the recovery of transcription after DNA damage correlates with transcription-associated histon mark deposition, we performed ChIP-seq for ubH2B before and after UV-C irradiation in WT RPE1 cells

first: Janne

last: van Schie

first: Bram

last: de Groot


title: Transciptomic analysis of lungs  from mice with selective expression of hACE2 in ATII and club cells after SARS-CoV-2 infection

city: San Antonio

first: Yidong

last: Chen

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: To define the contribution of type II alveolar epithelial cells (ATII) and club cells in SARS-CoV-2-induced lung immunopathology and protective immune responses, we generated mice with selective expression of hACE2 in ATII and club cells, respectively.  Our results indicate that SARS-CoV-2 infection elicits a robust immune response dominated by T cell and macrophage activation, primarily driven by infection of ATIIs, with club cells playing a more limited but complementary role.

overall_design: Mice with selective expression of hACE2 on type II alveolar epithelial cells (hACE-ATII) and club cells (hACE2-Club) were intratracheally infected with 1x105 PFU of WA1/US 2020 SARS-CoV-2 and analyzed at day 5. The total RNA from the lungs was isolated using Qiagen RNeasy RNA purification kit. The quality of RNA samples was assessed using Agilent 2100 Bioanalyzer (Agilent Technologies, CA). Samples were prepared and processed for RNA sequencing libraries using the NEBNext Ultra II Directional RNA Library Prep Kit with mRNA isolation module for Illumina following the manufacturer’s instructions (New England Biolabs, MA). The sequencing libraries were pooled and sequenced using the NovaSeq 6000 system (Illumina, CA) with 100 bp paired-end sequencing module. The sequence reads were aligned to the mouse reference transcript (build mm9) using HiSAT (v2.1.0), with default parameters. The alignment (BAM) files were processed with Stringtie (v2.1.3b) to quantify the expression level of genes as expected counts and normalized expression as FPKM (Fragments per kilobase of transcript per million mapped reads). The read counts were further analyzed using the R/Bioconductor based DESeq (v1.36.0) package to identify the differentially expressed genes between different cell sorting criterion.

first: Austin

middle: W

last: Todd

first: Alexei

middle: V

last: Tumanov

first: Ekaterina

last: Koroleva

first: Zhao

last: Lai


title: Fetal growth restriction leads to prolonged nephrogenesis and persistent developmental gene dysregulation in the adult kidney

city: Charlottesville

first: Jennifer

last: Charlton

address: 409 Lane Rd. Room 2035

institute: University of Virginia

summary: Introduction: Low birthweight is a risk factor for chronic kidney disease (CKD), in part due to an associated low nephron number, but the mechanisms leading to increased risk are not well understood. Low birthweight and growth restriction can be modeled in mice using gestational low protein (LP). Using this model, here we sought to 1) identify a potential window for therapeutic intervention to prevent future CKD in LP animals, 2) understand the transcriptional impact of LP on adult kidneys, and 3) clarify the mechanistic connection between low nephron endowment and predisposition to disease in LP animals. We hypothesized that gestational LP-induced growth restriction would lead to shorter nephrogenesis and altered gene expression in adulthood. Methods: At the initiation of pregnancy, CD-1 dams received a normal protein (NP, 18%) or LP (8%) diet. Offspring were euthanized on postnatal days (PN) 2-7 (n=2-7/day). Kidneys were stained with Periodic acid–Schiff (PAS). Immunofluorescence was used to assess SIX2 (progenitor cells), JAG1 (nascent nephron patterning), and LEF1 (Wnt signaling). At 6 weeks, mice underwent transdermal glomerular filtration rate (GFR) measurement. Ex vivo kidneys underwent histologic evaluation, bulk RNA sequencing, and cationic ferritin- enhanced MRI to quantify glomerular number (Nglom). Results: LP mice had protracted nephrogenesis extending to PN5-6, compared to NP mice that had completed nephrogenesis by PN3-5. Adult LP mice had fewer glomeruli, and LP males had lower GFR and more ATG compared to NP males. LP mice did not have evidence of glomerular hypertrophy. In LP males, the following genes were downregulated: Gfr1, Pax8, Fgf10, Dvl1, and Aldh1a1. Foxd1, Hif1an, Egln3, and Fzd7 were upregulated in the LP males. LP females exhibited upregulation of Etv5 and Osr2 and downregulation of Gata3, Mgp, and Trpv6 with no overlap of dysregulated genes between the sexes. Conclusions: LP offspring exhibit prolonged nephrogenesis and a reduced nephron endowment in adulthood. In males, this is characterized by a suppressed retinoic acid–GDNF–Wnt axis, while both sexes show persistent dysregulation of developmental genes. Together, these findings identify the late gestational and early postnatal periods as critical therapeutic windows. Targeting these molecular pathways during active nephrogenesis may offer a strategy to mitigate the programmed risk of CKD in growth-restricted offspring.

overall_design: One whole kidney from the following animals group: LP, M n=5, LP, F n=5, NP, M n=5, and NP, F n=3, were disassociated and RNA was isolated for bulk RNA-Sequencing (RNA-Seq).

first: Sage

last: Timberline

first: Rachel

last: Dailey

first: Wyatt

last: Johnson

first: Ayyappa

last: Kameshwar

first: Jaya

last: Isaac

first: Kimberly

last: deRonde

first: Mark

last: Conaway

first: Aleksandra

last: Cwiek

first: Kevin

last: Bennett

first: Edwin

last: Baldelomar

first: Teng

last: Li

first: Teresa

last: Wu

middle: R

last: Hoch

first: Meredith

middle: P

last: Schuh

first: Shalini

last: Indugula

first: Masako

last: Suzuki

last: Reidy


title: DHODH regulates mitochondrial bioenergetics, methylation cycle, and DNA repair in Prostate Adenocarcinoma

first: Arun

last: Sreekumar

address: One Baylor Plaza

department: Molecular and Cell Biology

institute: Baylor College of Medicine

summary: African American (AA) men exhibit disproportionately high incidence rates of prostate cancer (PCa) and a greater propensity for aggressive disease progression. Although epidemiological studies have delineated various risk factors, the precise molecular mechanisms driving the unique tumor biology and clinical disparities in AA men remain poorly characterized. Our prior investigations employing in situ analyses of clinical PCa tissues revealed increased uracil incorporation and elevated pyrimidine damage, indicative of heightened DNA repair activity, particularly within AA prostate tumours. Notably, dihydroorotate dehydrogenase (DHODH), a critical enzyme involved in de novo pyrimidine biosynthesis, was significantly overexpressed in PCa, specifically in epithelial cells, with the highest expression observed in patient-derived tumours from AA patients. Through comprehensive gain and loss-of-function experiments across multiple PCa cell lines integrating transcriptomic profiling, DNA methylation sequencing, and metabolomics we demonstrate that DHODH centrally orchestrates mitochondrial bioenergetics, one-carbon metabolism, methylation pathways, and DNA repair mechanisms. Functionally, modulation of DHODH expression directly influenced cellular proliferation, migration, and metastatic potential in vivo, accompanied by alterations in base excision repair (BER)-mediated DNA damage. Collectively, our findings position DHODH as a pivotal metabolic and epigenetic regulator with critical implications for PCa aggressiveness and racial disparities. This work establishes DHODH as a promising therapeutic target, potentially addressing unmet clinical needs and improving outcomes specifically for AA prostate cancer patients.

overall_design: RNA seq profling of genetically modified MDA-PCA-2B cellines (NT, DHODH-Knock Down 1, DHODH-Knock Down 2 and DHODH Knock2-Down-Rescue).


title: NFIX-mediated transcriptional regulation in skeletal muscle cells

city: Shanghai

first: Shuang

last: Liu

address: No.274 Zhijiang Middle Road

department: orthopedics

institute: Shanghai Municipal Hospital of Traditional Chinese Medicine

summary: Skeletal muscle plays a central role in voluntary movement and possesses remarkable regenerative capacity following injury. NFIX, a member of the Nuclear Factor I (NFI) family of transcription factors, is essential for skeletal muscle development and regeneration. Despite its increasing importance, the molecular mechanisms by which NFIX mediates transcriptional regulation in skeletal muscle remain unclear. In this study, we performed siRNA-mediated knockdown of NFIX in human immortalized skeletal muscle cells and conducted RNA-seq analysis.

overall_design: To identify genes whose expression is controlled by NFIX, we performed high-throughput RNA sequencing (RNA-seq) in human immortalized skeletal muscle cells following small interfering RNA (siRNA)–mediated depletion of NFIX or a scrambled control. Cells were maintained as proliferating myoblasts and harvested concurrently 36 hours after transfection, and transcript levels were compared between NFIX-depleted and control groups to define NFIX-dependent transcriptional programs.

first: Chunchun

last: Xue

first: Lingxing

first: Xiaofeng

first: Jie

last: Shen

first: He

last: Song


title: TOX3 in hypothalamic POMC-lineage cells regulates energy balance via the PTEN-AKT signaling axis

city: Chengdu

first: Qin

last: Tang

state: Select...

address: 37 Guoxue Xiang, Wuhou District, Chengdu, Sichuan Province, China

institute: West China Hospital of Sichuan University

summary: Obesity and its associated metabolic disorders, including type 2 diabetes and fatty liver disease, represent a growing global health burden. Although the hypothalamus is well-established as the central regulator of energy homeostasis through specialized neuronal circuits, the molecular mechanisms governing these pathways remain incompletely elucidated. In this study, we identify thymocyte selection-associated high mobility group box 3 (TOX3) as a critical metabolic regulator in pro-opiomelanocortin (POMC) neurons of the arcuate nucleus. By employing cell-type-specific genetic manipulation in murine models, we establish that conditional TOX3 ablation in POMC neurons exacerbates diet-induced obesity and metabolic dysfunction, while its overexpression in these neurons confers robust metabolic benefits. Mechanistically, TOX3 enhances POMC neuronal function via a novel post-translational regulatory mechanism involving PTEN proteasomal degradation, leading to potentiated AKT signaling. This central modulation drives sympathetic activation of adipose tissues, resulting in enhanced lipid mobilization and energy expenditure. Notably, TOX3 exhibits striking neuronal specificity, as both loss- and gain-of-function manipulation in agouti-related peptide (AgRP) neurons produce negligible metabolic consequences. Our work identifies previously unrecognized physiological roles of TOX3 in POMC neurons that are essential for maintaining energy homeostasis, thereby revealing novel therapeutic opportunities for metabolic disorders.

overall_design: Hypothalamus from three Pomc-cre;Ai9 or PTKO;Ai9 male mice fed an HFD for 16 weeks were pooled per experimental sample. Single-cell suspensions were prepared using the Adult Brain Dissociation Kit (Miltenyi Biotec, #130-107-677) according to the manufacturer’s instructions. Briefly, freshly dissected hypothalamus was rinsed in ice-cold Dulbecco’s PBS (D-PBS) and subsequently transferred into gentleMACS C Tubes (Miltenyi Biotec, #130-093-237) containing the enzymatic digestion mixture. Tissue dissociation was performed using the gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec, #130-096-427). The resulting cell suspension was filtered through a 70 μm nylon mesh and centrifuged at 300 × g for 10 minutes at 4°C, followed by removal of cellular debris and erythrocytes. The pelleted cells were resuspended in D-PBS, and cell viability was assessed using 7-aminoactinomycin D (7-AAD; Beyotime Biotechnology, #C1053S, Shanghai, China). Fluorescence-activated cell sorting was conducted using a BD FACSAria SORP cell sorter (BD Biosciences) at the Flow Cytometry Core Facility. tdTomato-positive cells were selectively collected for subsequent RNA sequencing analysis, which was performed by Shi-Bio Technology (Wuhan, China).

first: Juan

last: Pang

first: Jinhang

last: Zhang

first: Qinhui

first: Jiahui

first: Ailin

first: Ying

last: Xu

first: Haiying

first: Haifeng

last: Zeng

first: Xiandan

last: Jing

last: Yang

first: Yimin

last: Xiong

first: Zijing

first: Yining

first: Yanping

first: Li

last: Mo

first: Jinhan

last: He


title: 3D chromosome remodeling in B-cell development and acute lymphoblastic leukemia [HiChIP]

city: New York

first: Yohana

last: Ghebrechristos

address: 550 1st Ave.

department: Pathology

institute: NYU Grossman School of Medicine

summary: The identification of molecular subgroups of pediatric B-cell acute lymphocytic leukemia (B-ALL) has proven to be a powerful tool in both understanding disease pathogenesis and treatment stratification. Several studies have suggested that aberrant transcription factor (TF) function and epigenetic regulation can explain the differences between distinct B-ALL subtypes. However, the organization of the 3D genome across leukemia subtypes and comparison with healthy B-cell progenitors remains unclear. Here we use in situ Hi-C and RNA-seq to profile early human B-cell progenitors from healthy bone marrow donors and B-ALL patient samples harboring prognostically relevant structural variations, including ETV6::RUNX1, KMT2A::AFF1 and BCR::ABL. We show that B-ALLs undergo subtype-specific changes in 3D genome organization that in part reflect the differentiation stage of the disease. We demonstrate that B-ALL blasts also acquire distinct aberrant chromatin configurations that allow expression of oncogenic drivers compared to normal progenitors. One such driver, the transcription factor ERG, displays increased interactivity and expression in ETV6::RUNX1 B-ALL, and directly regulates B-cell progenitor survival and differentiation. Overall, these results underscore the essential role of 3D nuclear organization in human acute leukemia.

overall_design: Primary pediatric B ALL  samples were used to study  the 3D chromosome architecture across subtypes of B ALL as well as healthy progenitors at various stages of B cell differentiation. The B ALL cell line REH was used to create a model to test the impact of ERG, a transcription factor, on 3D remodeling. Using the CRISPR Cas9 system, a REH_sgROSA control and sgERG cell lines were created and Hi-ChIP for H3K27 acetylation was performed.

first: Nikki

middle: A

last: Evensen

first: Romane

last: Cathelin

first: Soobeom

last: Lee

first: Finnegan

last: Clark

first: Nestor

last: Saiz

first: Stanley

last: Clarke

first: Matthew

middle: T

last: Witkowski

first: Ziyan

last: Lin

first: Sonali

last: Narang

first: Hua

last: Zhou

first: Elizabeth

last: Raetz

first: David

last: Teachey

first: Timothée

last: Lionne

first: Aristotelis

last: Tsirigos

first: William

last: Carroll

first: Iannis

last: Aifantis


title: Recurrent DNA Break Clusters Regulated by Polymerase Theta Are Essential for Replication Stress Induced Copy Number Variation [ [dataset 2]

city: Heidelberg

first: Pei-Chi

last: Wei

state: Baden-Württemberg

address: Im Neuenheim Feld 280

department: Structural and functional genomics

institute: German Cancer Research Center

summary: Copy number variation (CNV) is a form of genetic alteration that has been strongly implicated in the pathogenesis of a wide range of neurological disorders. Replication stress is a common cause of CNV. Despite the prevailing model that CNV arises from DNA double strand breaks (DSBs), there has been no assay that directly perturbs presumed DSB sources and measures CNV output. In this article, we identified a subset of recurrent DNA break clusters (RDC) as a causal factor for CNV formation. In murine neural progenitor cells under replication stress, mapping the formation of CNVs revealed their exclusive location in RDC regions that contain actively transcribed genes. CRISPR/Cas9-mediated transcriptional suppression demonstrated that CNV formation depends on transcription-mediated RDCs, but is independent of elevated replication timing. We found that polymerase theta (Pol θ), a  protector against CNV formation,  plays a critical but context dependent role upstream of RDC. Chemically inhibiting the polymerase activity of Pol θ reduced end filling and micro-homology-mediated joining in XRCC4/P53-deficient cells. Conversely, Pol θ inhibition led to elevated DSB density at RDC-containing loci in wild-type neural stem and progenitor cells, suggesting its role in preventing transcription-replication conflict. These results underscore the role of RDCs in driving genome heterogeneity, and suggest their potential involvement in the pathogenesis of various conditions including neuropsychiatric disorders and cancer.

overall_design: This collection includes the following assays to measure the linear interactions between transcription and replication, as well as recurrent DNA breaks at nucleotide resolutions in mouse neural progenitor cells. We appiled global run-on sequencing (GRO-seq) to determine nascent transcription quantity and transcription direction. Replicaiton timing was determined by two-fraction Repli-seq, and DNA breaks were mapepd with Linear Amplification-mediated, High Throughput Genome-wide Translocation Sequencing (LAM-HTGTS). There are three majojr expeirmental groups in this submission. First, to test if transcription activity is indispensible for recurrent DNA break clusters formation and affecting replication timing, we performed GRO-seq for parental (Nxp010), and four promoter-enhancer (pe-del) deleted ES cell derived NPC (ESC-NPC) cell lines (Nxp010-18-4, Nxp010-38-3, Nxp010-n29j6, Nxp010-n48j18). We also performed LAM-HTGTS using bait on chr6 or chr14 to the same cell lines treated with low-dose aphidicolin or with the solution control (DMSO). The second experiment group is the effect of polQ inhibitor treatment for Xrcc4-/-p53-/- ESC-NPCs. In this group, we performed LAM-HTGTS to cells treated with aphidicolin along, PolQ inhibitor alone (ART558), APH plus ART558, or untreated. Three chromosomal baits (Chr6, chr8, chr12) were used. Replication timing for APH or APH+ART558-treated cells were measured by two-fraction Repli-Seq. The third experimental group concerns PolQ inhibition in wild-type neural stem/progenitor cells. We captured DNA breaks genome-wider in wild-type primary isolated neural stem/progenitor cells with two chromosomal baits (Chr6 and CHr14). Cells treated with APH alone or in combination with ART558 were analyzed.

first: Corazzi

last: Lorenzo

first: Ionasz

last: Vivien

first: Wei

last: Pei-Chi

first: Ing

last: Alex

first: Marx

last: Anna

first: Tausch

last: Nathan

first: Benedetto

last: Sarah

first: Di Muzio

last: Giulia

first: Ding

last: Boyu

first: Giaisi

last: Marco

first: Hoefer

last: Thomas


title: Recurrent DNA Break Clusters Regulated by Polymerase Theta Are Essential for Replication Stress Induced Copy Number Variation [dataset 1]


title: Derivation of elephant induced pluripotent stem cells [short-read RNA-seq]

first: Evan

middle: Michael

last: Appleton

address: 75 Kneeland St.

institute: Colossal Biosciences

summary:
The crisis of biodiversity loss in the present era requires new tools for studying non-model organisms. Elephants are both an endangered species and excellent models for studying complex phenotypes including body size, social behavior, and longevity. Here we report here the first derivation of (Elephas maximus) induced pluripotent stem cells (emiPSCs). We achieved emiPSCs using two approaches: (1) a two-step process of chemical-media induction and colony selection followed by overexpression of elephant transcription factors; and (2) a one-step process with the same transgenes but without the chemical induction step and including an additional HRAS mutant transgene, HRASG12V. For both protocols, we inhibited TP53 expansion genes, which are hypothesized to confer unique cancer resistance in elephants. To confirm their reprogrammed state, we generated a functional genomics catalog of the modified cells with RNA-seq, ATAC-seq, and single-molecule direct RNA-sequencing. While these emiPSCs are transgene-dependent, we inactivated them to differentiate emiPSCs into all three germ layers via tri-lineage differentiation, embryoid body generation, and direct differentiation into putative cell types from all three layers. These methods will open new frontiers for cellular
models of non-model organisms, including for genetic rescue and conservation.

overall_design: Short-read sequencing of elephant induced pluripotent stem cells

first: Nataly

last: Korover

first: Kyunghee

last: Hong

first: Xochitl

last: Ambriz-Peña

first: Yoshiaki

last: Tanaka

first: Asaf

last: Ashkenazy-Titelman

first: Cody

last: Rasmussen-Ivey

first: Cristina

last: Rodriguez-Caycedo

first: Ketaki

last: Bhide

first: Hao

last: Bai

first: Ana

last: Queiroz

first: Jorgen

last: Nelson

first: Grishma

last: Rathod

first: Miles

last: Morgan

first: Anthony

last: Mastracci

first: Theodore

middle: M

first: Gregory

last: Knox

first: Brody

last: McNutt

first: Nandini

last: Malviya

first: Kairui

last: Zhang

first: Amanda

last: Kowalczyk

first: Austin

last: Bow

first: Bryan

last: McLendon

first: Jaroslav

last: Slamecka

first: Krista

last: Ryon

first: Jackie

last: Proszynski

first: Nadia

last: Houerbi

first: Ashley

middle: S

last: Kleinman

first: Chi-Lam

last: Poon

first: Wendy

last: Kiso

first: Matt

last: James

first: In-Hyun

last: Park

first: Charles

last: Gray

first: Virginia

last: Pearson

first: Christopher

last: Mason

first: Brandi

last: Cantarel

first: Karl

last: Koehler

first: Beth

last: Shapiro

first: James

last: Kehler

first: Ben

last: Lamm

first: George

last: Church

first: Eriona

last: Hysolli


title: Adipocytes signal to recruit specific mRNAs from surrounding cells to restore expression deficits [scRNA-Seq]

city: St. Louis

first: Clair

last: Crewe

address: 660 S Euclid Avenue

institute: Washington Univeristy in St. Louis

summary: Extracellular vesicles (EVs) are nano-sized, membrane-delimited, particles released by cells that carry signaling macromolecules. A major pathway of EV production is potentiated by neutral sphingomyelinase 2 (SMPD3/nSMAse2), an enzyme that generates ceramide from sphingomyelin. In our attempt to study this pathway in adipocytes of male mice, we discovered that the elimination of SMPD3 from adipocytes in vivo triggers a signal to surrounding immune cell-like preadipocytes to release EVs that carry SMPD3 mRNA. This results in a widespread increase in SMPD3 mRNA in purified null adipocytes without a change in the transcripts of other enzymes involved in ceramide metabolism. These results point to a fundamental, novel, and selective mechanism by which specific mRNA molecules are acquired from the microenvironment to a level that can restore expression of mRNA and protein in a cell that is depleted of the corresponding genetic information.

overall_design: After 2 weeks on doxycycline diet to induce SMPD3 knockout, subcutaneous white adipose tissue (sWAT) control and ad-SMPD3KO mice were harvested. sWAT was dissocited with collagenase into single cells and live cells were sorted by FACS.

first: Christy

last: Gliniak

first: Toshiharu

last: Onodera

first: Shiuhwei

last: Chen

first: Jan-Bernd

last: Funcke

first: May-Yun

last: Wang

first: Snigdha

last: Tiash

first: Yun-Ling

last: Pai

first: Marjori

last: Russo

first: Saket

last: Patel

first: Ze

last: Yu

first: Yi-Cian

last: Zheng

first: Chao

last: Xing

first: Laurent

last: Gautron

first: Chun-Kan

first: Chen

last: Liu

first: Philipp

middle: E

last: Scherer


title: Transcriptomic analysis of KLRG1+CD127- CD8 T cells in the liver following treatment with anti-CD137 agonistic antibody

first: Yidong

summary: We have employed bulk RNA sequencing approach to study cells associated with hepatotoxicity caused by treatment with anti-CD137 agonistic antibody.  We found that the treatment-induced CD11c+KLRG1+ and CD11c-KLRG1+ CD8 T cells were main producers of IFNγ in the liver, suggesting their pathogenic role in the hepatotoxicity. Transcriptomic analysis revealed differential gene expression of inhibitory receptor NKG2A, activating receptor NKG2D, granzyme A, and adhesion molecule Ly6C in the CD11c+ population. This study represents the analysis of CD11c+ and CD11c- populations of KLRG1+CD127- CD8 T cells in the liver following anti-CD137 agonistic antibody treatment.

overall_design: Bulk RNA-Seq analysis of 8 samples. C57BL/6 mice were treated with αCD137 antibody on day 0, 3 and 6 and single cell suspensions were isolated from the livers on day 8. Intrahepatic CD11c+KLRG1+CD127- and CD11c-KLRG1+CD127- CD8 T cells were sorted using BD FACSAria cell sorter (n=4/group).  CD8 T cells were defined as live CD45+MHCII-NK1.1-TCRβ+CD8α+CD4-.

first: Sergey

last: Shein

first: Anna

last: Korchagina

first: Li-Ju

first: Zhao

last: Lai

first: Yang-Xin

last: Fu

first: Ekaterina

last: Koroleva

first: Alexei

last: Tumanov


title: A comparative analysis of 2D and 3D in vitro models for hepatocellular carcinoma research

city: Botucatu

first: Guilherme

middle: Ribeiro

last: Romualdo

state: SP

address: Rua Dr José Barbosa de Barros, 1486

country: Brazil

institute: UNESP

summary: The tumor microenvironment (TME) influences hepatocellular carcinoma (HCC) behavior and disease progression. Cell-cell dynamics of non-parenchymal components, such as hepatic stellate cells (HSC), are key factors in understanding HCC onset and progression. This study established mono- and co-culture in vitro HCC models in both 2D and 3D configurations to investigate HCC cell behavior at both functional and transcriptional levels. Human HCC C3A cells were co-cultured with human HSC LX2 cells or alone in ultra-low attachment plates to form spheroids (3D) or in a transwell system (2D). In the 2D model, the paracrine signaling of HSC-HCC cells promoted colony formation and HCC cells motility compared to the C3A monolayer, showing a pro-inflammatory transcriptomic signature thought a positive regulation of canonical NF-κB pathway. Regarding the 3D model, co-culture spheroids exhibited higher cell viability, enhanced angiogenesis, migration, and extracellular matrix (ECM)-related transcriptomic hallmarks compared to C3A monoculture. Regardless of the model configuration, co-culture setups shared 74 genes, including invasion- and metastasis-related, and angiogenesis functional annotation, indicating a “LX2 signature” in C3A cells. The 2D vs. 3D comparison revealed that the 3D setup enriched proliferation-related genes in C3A spheroids compared to monolayers, whilst co-culture spheroids showed cholesterol, angiogenesis, migration and ECM annotations compared to co-culture transwell model. These findings reinforce the importance of HSC as key microenvironmental cellular components in HCC and highlight how cellular dynamics modify HCC cell behavior in vitro.

overall_design: RNA-Seq profile of unexposed C3A cells (HB-8065, ATCC) and LX2. 48h of contact with LX2 or spheroids and 48h after spheroid formation

first: Letícia

last: Valente

first: Luana

last: Riechelmann-Casarin


title: Microglial Fructose Metabolism Is Essential for Glioblastoma Growth

city: Chicago

first: Shashwat

last: Tripathi

state: Illinois

address: 302 e Huron St

department: Neurosurgery

institute: Northwestern

summary: Glioblastoma (GBM) is most common and aggressive primary brain tumor in adults, for which standard of care hasn’t changed in twenty years. GBM tumor associated macrophages (TAMCs), consisting of infiltrating myeloid cells from the periphery and resident microglia cells, are pro-tumorigenic, promoting tumor growth. Fructose is one of the most abundant metabolites in the GBM tumor microenvironment (TME), as well as in the healthy central nervous system (CNS). In the CNS and GBM, microglia are the predominant expressors of the fructose transporter GLUT5. Mice lacking the GLUT5 transporter (GLUT5-KO) survive significantly longer after orthotopic implantation of two glioma cell lines than wildtype mice, which is not due to dietary fructose or peripherally derived TAMCs. Investigation of the TME showed that GLUT5-KO mice have more highly activated and inflammatory innate and adaptive immune compartments. Microglia cultured in fructose have a decreased phagocytic ability and exhibit decreased inflammatory capacity due to the polyol pathway promoting redox homeostasis.

overall_design: Murine scRNA brain samples from wildtype and Glut5 knockdown mice. CT-2A tumor cells were implanted intracranially, and the resulting tumor was removed after 14 days and digested into single-cell suspension using the adult brain dissociation kit (Miltenyi) according to the manufacturers instructions. CD45+ cells were isolated via magnetic bead isolation (Miltenyi) and submitted to the Northwestern University NUseq facility core for single cell library preparation and sequencing. AOPI fluorescent staining was used to determine cell number and viability Nexcelom Cellometer Auto2000 with. Sixteen thousand cells were loaded into the Chromium Controller (10X Genomics, PN-120223) on a Chromium Next GEM Chip K (10X Genomics, PN-1000127), and processed to generate single cell gel beads in the emulsion (GEM) according to the manufacturer’s protocol. The cDNA and library were generated using the Chromium Next GEM Single Cell 5’ Reagent Kits v2 (10X Genomics, PN-1000283) according to the manufacturer’s manual. The multiplexed libraries were pooled and sequenced on Illumina HiSeq 4000 sequencer with paired-end 50 kits using the following read length: 28 bp Read1 for cell barcode and UMI and 91 bp Read2 for transcript.


title: Sequence-specific RNA recognition drives Restrictor-mediated termination of extragenic transcription

city: Milano

first: Gaurav

last: Mandana

address: Via Adamello 16

institute: European Institute of Oncology

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

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Catalytic Activity of ADAR1 Governs Ribosome Biogenesis

first: Zhibo

last: Shao

institute: Fudan University Shanghai Cancer Center

summary: Wild-type and STAT1-knockout T47D cells transfected with control or ADAR1 siRNAs

overall_design: Comparing transcriptomic changes induced by ADAR1 knockdown in WT versus STAT1-KO backgrounds.

first: Xuliren

last: Wang

first: Qi

last: Zhang

first: Jiong

last: Wu


title: Heat stress triggers nuclear invagination and spatial compartmentalization of protein metabolism

city: guagnzhou

first: tang

last: guorun

address: xingang

institute: Sun Yat-sen University

summary: Heat stress is a common challenge for cells, causing multiple types of cellular damage while triggering complex stress responses, including the classical heat shock response. However, the subcellular coordination of these stress responses remains poorly understood. In this study, we identify reversible nuclear morphological changes under heat stress, characterized by kidney-shaped invaginations. These nuclear invaginations are associated with intermediate filament collapse and the regional clustering of organelles. Through immunofluorescence imaging and proteomic analysis, we further reveal that nuclear invagination region function as "protein metabolism hotspots", where both protein translation and degradation are enhanced. Moreover, this compartmentalization is not only essential for cellular adaptation and recovery from heat stress but also correlates with the differential heat tolerance across cell lines. Our findings highlight a previously unappreciated mechanism by which cells spatially reorganize protein metabolism to optimize stress responses, providing new insights into heat stress adaptation.

overall_design: RNA-seq profling of HEK293T cells under three conditions: untreated wild-type, heat shock treatment (43°C for 1 hour), and recovery after heat shock (37°C for 1, 6, 18 hours)

first: Zhihao

first: Yuantao

last: Qiu

first: Yifeng

last: Huang

first: Yelin

last: Lan

first: Yuli

last: Zhao

first: Fu

first: Chenlong

first: Guorun

last: Tang

first: Jingyun

last: Ji

first: Zhang

first: Guanzheng

last: Luo