title: PAL-AI reveals genetic determinants that control poly(A)-tail length during oocyte maturation, with relevance to human infertility

status: Public on Jun 26 2025

city: Cambridge

first: David

last: Bartel

address: 455 Main Street

institute: Whitehead Institute

summary: In oocytes of mammals and other animals, gene regulation is mediated primarily through changes in poly(A)-tail length. Here, we introduce PAL-AI, an integrated neural network machine-learning model that accurately predicts tail-length changes in maturing oocytes of frogs and mammals. We show that PAL-AI learned known and previously unknown sequence elements and their contextual features that control poly(A)-tail length, enabling it to predict tail-length changes resulting from 3ʹ-UTR single-nucleotide substitutions. It also predicted tail-length-mediated translational changes, allowing us to nominate genes important for oocyte maturation. When comparing predicted tail-length changes in human oocytes with genomic datasets of the All of Us Research Program and gnomAD we found that genetic variants predicted to disrupt tail lengthening are under negative selection in the human population, thereby linking mRNA tail lengthening to human female fertility.

overall_design: Sythetic mRNA reporter libraries with random and mutagenesis 3'-UTR sequences were injected into frog oocytes. Poly(A)-tail lengths were measured to at different developmental stages to examine the concordance between experimentally determined effects and PAL-AI predicted effects.

first: Kehui

last: Xiang


title: Large-Scale CRISPR Screening in Primary Human 3D Gastric Organoids Enables Comprehensive Dissection of Gene-Drug Interactions

city: Dallas

first: Jin

last: Chen

state: TX

address: 5323 Harry Hines Blvd

country: USA

institute: UT Southwestern Medical Center

type: Expression profiling by high throughput sequencing

summary: Investigating gene-drug interactions is critical for advancing personalized medicine by revealing how genetic variations shape individual responses to medications. To achieve this goal, it is essential to develop a robust human functional genomics system that can accurately recapitulate normal physiology and disease while effectively accounting for the complexity and heterogeneity among individuals. We explored this potential in primary 3D human gastric organoids by implementing a wide range of large-scale CRISPR-based genetic screens, including CRISPR knockout, CRISPR interference (CRISPRi), CRISPR activation (CRISPRa), and single-cell CRISPR screens. Our cisplatin sensitization screens targeting 1,952 DNA-binding proteins identified numerous known genes associated with DNA repair pathways, along with previously unrecognized cisplatin sensitization loci. Individual validation of top hits further confirmed the robustness of the screening results. Furthermore, using multiplexed single-cell CRISPR screens to simultaneously extract individual sgRNAs and single-cell transcriptomes, we uncovered a convergence within DNA repair pathways in cisplatin-treated organoids compared to cisplatin-naïve organoids. These methods distinguished high-dimensional synergistic effects between sgRNAs and drug perturbations by leveraging each cell's gene expression profiles, improving the resolution to link genotypes with drug response phenotypes in organoids. Finally, we identified TAF6L as a novel cisplatin sensitization gene. Mechanistically, TAF6L is crucial for the proliferation of cell recovery following cisplatin-induced DNA damage response. In summary, diverse CRISPR-based functional genomics platforms can be successfully applied to human organoids, revealing new gene-drug interactions with implications for human disease.

overall_design: In order to investigate the feasibility of pooled single-cell screening in primary human 3D organoids, we performed CRISPRi and CRISPRa CROP-seq (Perturb-Seq) in an inducible CRISPR/dCas9-KRAB-engineered human gastric organoid lines.

first: Yuan-Hung

last: Lo


title: MUC1-C IS ESSENTIAL FOR ESTABLISHING AND RECALLING INFLAMMATORY MEMORY OF OSIMERTINIB RESISTANCE IN NSCLC CELLS [H1975_vs_H1975-OR]

city: Fukuoka

first: Naoki

last: Haratake

state: Please Select

address: 3-1-1 Maidashi, Higashi-ku

country: Japan

institute: Graduate School of Medical Sciences, Kyushu University

summary: MUC1-C is necessary for establishing and recalling resistance of NSCLC cells to osimertinib by driving an inflammatory memory responseThe oncogenic MUC1-C protein functions as a master regulator of NSCLC cell resistance to osimertinib by unclear mechanisms. We report that MUC1-C-mediated regulation of STAT1 and the interferon (IFN) type I/II pathways is necessary for establishing osimertinib resistance. Studies of osimertinib-resistant NSCLC cells selected for growth in the absence of drug further demonstrate that revertant cells are dependent on MUC1-C for recalling resistance to osimertinib. We show that establishing and recalling osimertinib resistance is dependent on activation of the MUC1 gene at (i) a proximal enhancer-like signature 1 (pELS-1) by MUC1-C and STAT1 and (ii) a pELS-2 by MUC1-C, JUN/AP-1 and PBAF. The MUC1 pELS regions function as memory domains for activation of MUC1-C and downstream STAT1 and IFN stimulated genes in conferring osimertinib resistance. Of clinical relevance, we report that the MUC1-C-driven inflammatory responses are induced in patient-derived, osimertinib-resistant MGH170 NSCLC cells with MET amplification. Our results further demonstrate that MGH170 cells are dependent on the MUC1-C-induced inflammatory response for resistance to the osimertinib and combination of osimertinib with the MET inhibitor capmatinib. These findings indicate that MUC1-C is necessary for establishing and recalling resistance of NSCLC cells to osimertinib by driving an inflammatory memory response.

overall_design:
Comparison between H1975, which is sensitive to osimertinib, and H1975-OR, which has become a resistance due to long-term exposure to osimertinib (H1975 vs H1975-OR).
Treatment of H1975 = None
Treatment of H1975-OR = Osimertinib


title: Identification of multiple genomic alterations and prediction of neoantigens from circulating tumor cells at the single-cell level

city: ShangHai

first: Da

last: Lin

address: No. 650 Songjiang Road

country: China

institute: Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China

summary: Circulating tumor cells (CTCs) are linked to cancer progression and poor prognosis, offering valuable genetic insights into tumors. Accurate detection of genomic alterations in CTCs is essential for improving cancer diagnosis and treatment. To address this, we develop Uniform Chromosome Conformation Capture (Uni-C), a method for profiling 3D chromatin architecture and genomic alterations at the single-cell level. Using Uni-C, we analyze CTCs from pancreatic cancer patient-derived xenograft (PDX) and spontaneous tumor mouse models. In the PDX model, integrating data from seven CTCs captures 88.7% of SNPs and INDELs, and 75.0% of structural variants present in tumor tissue. These findings indicate that variants detected in CTCs reflect tumor genomic features. Notably, we observe chromatin conformation differences between mitotic and interphase CTCs, suggesting potential markers of cell vitality. In the spontaneous tumor model, we identify driver gene mutations in CTCs and predict neoantigens, advancing early cancer detection and treatment strategies.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Role of ATF4 in regulation of kidney gene expressions, signaling pathways and functions [human RCC4]

status: Public on Jun 25 2025

city: New York

first: Genomics-core-facility

last: WCM

state: NY

address: 1300 York Ave.

institute: Weill Cornell Medicine

summary: Activating transcription factor 4 (ATF4) is a transcription factor that mediates the response to stress at the cellular, tissue, and organism level. We deleted the gene encoding ATF4 in the kidney proximal tubules of the wild type (WT) and TRACK (TRAnsgenic model of Cancer of the Kidney (TRACK)) mice by using a temporal and cell type-specific approach. We show that ATF4 plays a major role in regulating the transcriptome and proteome, which, in turn, influences the metabolome and kidney functions. ATF4 deletion changed transcripts of some transporters responsible for nutrient uptake and waste excretion. It modulates metabolisms of fatty acid and glucose in the mouse model of ccRCC. It also changes metabolism in RCC4 cells. These data indicate that ATF4 plays an important role in regulation of kidney functions.

overall_design: RNA seq profiling of cortices from mice of wild type, ATF4 KO, TRACK and TRACK-ATF4, profiing of parental RCC4 cells and RCC4 ATF4 KO cells.

first: Lorraine

last: Gudas

first: Yuling

last: Chi

first: Eduardo Mere

last: Del Aguila


title: Role of ATF4 in regulation of kidney gene expressions, signaling pathways and functions [mouse]


title: Transcription factors SP5 and SP8 drive primary cilia formation in mammalian embryos [scRNA-seq]

first: Yinwen

last: Liang

email: liangy@mskcc.org, liangyinwen@gmail.com

state: New York

address: 1275 york avenue

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

summary: Although specific transcription factors (TFs) are known to regulate cell fate decisions, the degree to which they can stimulate formation of specific cell organelles is less clear. We used a multiomics comparison of the transcriptomes of ciliated and unciliated embryonic cells to identify TFs up-regulated in ciliated cells. We also used conditional genetics in mouse embryos and stem cells and found that the TFs SP5 and SP8 regulate cilia formation and gene expression. In embryos lacking Sp5 and Sp8, primary and motile cilia were shorter than normal and reduced in number across cell types, contributing to situs inversus and hydrocephalus. Moreover, expression of SP8 was sufficient to induce primary cilia in unciliated cells. This work will facilitate the study of cilia assembly using stem cell models and promote further understanding of human ciliopathies.

overall_design: To investigate transcriptome differences of Sp8 GOF and control yolk sac tissue, we performed scRNA-seq analysis of yolk sac tissue of E8.5 mouse embryos.2 yolk sac tissues pooled for each library, 2 replicates per genotype. For each libarry, 2 embryos at E8.5 stages were dissected out and dissassoicated into single cells, sorted for lvie cell and loaed for single cell sequencing.

first: Alexandra L

last: Joyner


title: Transcriptomic response of ethanol extract of Jakyakgamcho-tang (JGT-E) in C2C12 myotube

city: Daejeon

first: Su-Jin

last: Baek

address: 1672, Yuseong-daero

country: South Korea

institute: KOREA INSTITUTE of ORIENTAL MEDICINE

summary: Whole transcriptomic analysis in C2C12 myotube cells was conducted, comparing cells treated with a vehicle control to those treated with three different concentrations of JGT-E. All experiments were performed in triplicate.

overall_design: Total whole transcritome profiles treated with vehicle and JGT-E in C2C12 myotubes

first: Aeyung

last: Kim

first: Sang-Min

last: Park


title: Integrated Metagenomics and Transcriptomics Analysis Reveals Pathways Associated with Oral Periapical Lesions Formation and Progression

city: Sharjah

first: Rifat

last: Hamoudi

state: Sharjah

address: M32 Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, , Sharjah

department: Clinical Sciences

country: United Arab Emirates

institute: University of Sharjah

summary: Periapical abscesses, radicular cysts, and periapical granulomas are among the most frequently identified pathological lesions in the alveolar bone. Although many studies have investigated bacterial metagenomics in periapical abscesses, little is known about the genome mining of abundant bacteria of periapical lesions and its correlation to human transcriptome. This study aims to explore the enriched metabolic environment of periapical lesions associated with microbial diversity and their role in lesion progression. Bacterial DNA and human RNA were isolated from periapical lesions and healthy pulp tissue and sequenced using next-generation sequencing. Bacterial sequences were then analyzed to identify secondary metabolites, pathogenic proteins, and their associated metabolic pathways. Integrated bacterial and human metabolic pathways indicated similar pathways in each lesion. Among these pathways, inflammatory response, humoral immune response, and hemopoiesis were enriched in abscesses. NABA matrisome associated, neutrophil degranulation, and P73 pathway were enriched in cysts. Meanwhile, response to bacterium, regulation of immune effector process, and positive regulation of response to external stimulus were enriched in granulomas. In conclusion, this study is the first to elucidate the interplay between microbial and human metabolic activity. These findings have significant clinical implications for the early diagnosis, prevention, and treatment of periapical lesions.

overall_design:
By comparing the metabolic pathways of the bacterial metagenome with those of the human transcriptome, we investigated the correlation between the bacterial metagenome and the human transcriptome in periapical abscesses, radicular cysts, and periapical granulomas.
DNA and RNA were isolated from from periapical abscesses, radicular cysts, and periapical granulomas. To analyze the bacterial communities, the Ion 16S™ Metagenomics Kit was employed, which amplifies multiple hypervariable regions of the 16S rRNA gene. For host gene expression analysis, the Ion AmpliSeq™ Transcriptome Human Gene Expression Kit was utilized, enabling the simultaneous measurement of over 20,000 human RefSeq genes. For bacterial metagenomics, 30 patient samples were included and for human transcriptome, 16 patient samples were included.
The identified metabolic pathways of bacterial metagenome and human transcriptome were identified and compared.

first: Alaa

last: Altaie

first: Thenmozhi

last: Venkatachalam

first: Kiran

last: Patil

first: Farah

last: Al-Marzooq

first: Surendra

last: Rawat

first: Ali

last: Al-Qabbani

first: Mohammed

last: Alsaegh

first: Lakshman

last: Samaranayake

first: Sameh

last: Soliman


title: Integrated Single-Cell and Spatial Transcriptomics Uncover Distinct Cellular Subtypes Involved in Neural Invasion in PDAC [TCR-Seq]

city: shenzhen

first: Minmin

last: Chen

state: GuangDong

address: Gaoke Innovation Center, Guangqiao Road, Guangming District, Shenzhen

institute: Shenzhen bay lab

summary: This study aims to explore the role of nerves in tumor biology, particularly focusing on their function and the impact of the neural microenvironment in cancer invasion. Utilizing multi-omics technologies, we have mapped the spatial transcriptomic landscape of nerve-associated cells in pancreatic ductal adenocarcinoma (PDAC). By analyzing tissue samples with varying degrees of neural invasion, we have uncovered the complex interactions between tumor cells, immune cells, and neurons, providing new insights into the mechanisms underlying nerve-tumor interactions. This research lays the groundwork for future studies in cancer neuroscience and potentially advances the development of novel therapeutic strategies.

overall_design:
We generated scTCR-seq data from PDAC patients to investigate Neural Invasion, including blood, tumor and normal tissue.

***************************************************************
Raw data were deposited in the Genome Sequence Archive (GSA) with the accession number HRA008568.
***************************************************************

first: Min-Min

first: Qinhang

last: Gao

first: Huiheng

last: Ning

first: Kang

first: Yang

first: Chaoqun

last: Liu

first: Linnan

last: Zhu

first: Wei

last: Zhou

first: Jieying

last: Pan

first: Lusheng

last: Wei

first: Dingwen

last: Zhang

first: Min

last: Yu

first: Qingling

first: Rufu

first: Zemin


title: MUC1-C IS ESSENTIAL FOR ESTABLISHING AND RECALLING INFLAMMATORY MEMORY OF OSIMERTINIB RESISTANCE IN NSCLC CELLS [H1975-RT_vs_H1975-OR]

first: Naoki

last: Haratake

overall_design:
Comparison between H1975-OR, the osimertinib-resistant cell line, and H1975-RT cells, which had osimertinib removed for a longer period from H1975-OR and moderately regained sensitivity (H1975-OR vs H1975-RT).
Treatment of H1975-OR = Osimertinib
Treatment of H1975-RT = None


title: Changes of gene expression in DRG tissue after pathologic pain

city: Guangzhou

first: Xiao-Long

address: 106 Zhongshan 2nd Road

institute: Guangdong Provincial People’s Hospital

summary: To identify common mechanisms and targets regulating different types of pathological pain, we established models for neuropathic pain induced by spinal nerve ligation (SNL), inflammatory pain induced by complete Freund's adjuvant (CFA), chemotherapy pain induced by paclitaxel (PTX), and bone cancer pain induced by Lewis lung carcinoma (LLC) cells. We then collected dorsal root ganglion (DRG) tissues from mice for RNA-seq analysis.

overall_design: Dorsal root ganglion mRNA profiles of CFA, SNL, PTX, LLC mice were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: ManXiu

last: Xie

first: RenChun

last: Lai

first: YiBin

last: Xiao

first: ShiYu

last: Zuo

first: XiaoLong


title: Transcription factors SP5 and SP8 drive primary cilia formation in mammalian embryos [ChIP-seq]

first: Yinwen

last: Liang

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Chromatin Immunoprecipitation DNA-sequencing (ChIP-seq) for H3K4me3 and FLAG in Sp8 overexpression (iSp8-3xFLAG) EpiSC cells.

first: Richard

last: Koche

first: Alexandra

middle: L

last: Joyner


title: Transcription factors SP5 and SP8 drive primary cilia formation in mammalian embryos

overall_design: To investigate transcriptome differences of ciliated cell types versus unciliated visceral endoderm lineage cell types in yolk sac tissue, we performed scRNA-seq analysis of yolk sac tissue of E8.75 mouse embryos.3 yolk sac tissues from 3 embryos at E8.75 stages were dissected out and dissassoicated into single cells, multiplexed and pooled for single cell sequencing.


title: DynaTag for efficient mapping of transcription factors in low-input samples and at single-cell resolution

city: Cologne

first: Robert

last: Hänsel-Hertsch

department: CMMC

country: Germany

institute: University of Cologne

summary: Systematic discovery of transcription factor (TF) landscapes in low-input samples and at single cell level is a major challenge in the fields of molecular biology, genetics, and epigenetics. Here, we present cleavage under Dynamic targets and Tagmentation (DynaTag), enabling robust mapping of TF-DNA interactions using a physiological salt solution during sample preparation. DynaTag uncovered occupancy alterations for 15 TFs in stem cell and cancer tissue models. We highlight changes in TF-DNA binding for NANOG, MYC, and OCT4, during stem-cell differentiation, at both bulk and single-cell resolutions. DynaTag surpasses CUT&RUN and ChIP-seq in signal-to-background ratio and resolution. Furthermore, using tumours of a small cell lung cancer model derived from a single female donor, DynaTag reveals increased chromatin occupancy of FOXA1, MYC, and the mutant P53 (p.R248Q) at enriched gene pathways (e.g. epithelial-mesenchymal transition), following chemotherapy treatment. Collectively, DynaTag represents a significant technological advancement, facilitating precise characterization of TF landscapes across diverse biological systems and complex models.

overall_design: DynaTag of various TFs in murine embryonic stem cells, differentiated epiblast like cells.

first: Pascal

last: Hunold

first: Giulia

last: Pizzolato

first: Nadia

last: Heramvand

first: Laura

last: Kaiser

last: Barbiera

first: Olivia

last: van Ray

first: Roman

last: Thomas

first: Julie

last: George

first: Martin

last: Peifer


title: Spatial transcriptomics dataset of primary tumours from MDA-MB-231 xenograft model

status: Public on Jun 24 2025

city: Darlinghurst

first: Shabarni

last: Gupta

state: NSW

address: Precinct Loading Dock,, West Street (off Burton Street)

country: Australia

institute: Garvan Institute of Medical Researc

summary: Identifying functionally important cell states and structure within heterogeneous tumors remains a significant biological and computational challenge. Current clustering or trajectory-based models are ill-equipped to address the notion that cancer cells reside along a phenotypic continuum. We present Archetypal Analysis network (AAnet), a neural network that learns archetypal states within a phenotypic continuum in single-cell data. Unlike traditional archetypal analysis, AAnet learns archetypes in simplex-shaped neural network latent space. Using pre-clinical models and clinical breast cancers, AAnet resolves distinct cell states and processes, including cell proliferation, hypoxia, metabolism and immune interactions. Primary tumor archetypes are recapitulated in matched liver, lung and lymph node metastases. The dataset here comprises of the 10X genomics based spatial transcriptomics (Visium) on MDA-MB-231 xenografts to perform archetypal analysis and understand spatial aspects of tumour hetegeneity. scRNAseq datasets from matched models and metastasis is projected onto this spatial transcriptomics data to understand the spatial dependencies and characteriostics of these archetypes in the manuscript.

overall_design: In an MDA-MB-231 mouse model, single-cell RNA-sequencing and spatial RNA-sequencing data were collected for primary tumors, and single-cell RNA-sequencing was collected for lymph node, liver, and lung metastases. Dataset here presents the spatial transcriptomics profile of the two primary tumours used in this study.

first: Aarthi

last: Venkat

first: Scott

middle: E

last: Youlten

first: Beatriz

middle: P

last: San Juan

first: Carley

middle: A

last: Purcell

first: Matthew

last: Amodio

first: Daniel

last: Neumann

first: John

middle: G

last: Lock

first: Anton

last: Westacott

first: Cerys

middle: S

last: McCool

middle: B

last: Burkhardt

first: Andrew

last: Benz

first: Annelie

last: Mollbrink

first: Joakim

last: Lundeberg

first: David

last: van Dijk

first: Jeff

last: Holst

first: Leonard

middle: D

last: Goldstein

first: Sarah

last: Kummerfeld

first: Smita

last: Krishnaswamy

first: Christine

last: Chaffer


title: KAT6A Chimeras Forms a Self-Reinforcing Epigenetic Module with NURF and MLL/COMPASS in AML [ChIPMNase]

city: Wuhan

first: Yin

last: Zhinang

state: Hubei

address: Donghu road 185

institute: Wuhan University

summary: KAT6A-CBP (K/C) and KAT6A-P300 (K/P) fusions are recurrent genetic alterations in acute myeloid leukemia(AML) that are associated with poor prognosis. The large size of these fusion proteins has posed challenges in developing preclinical models, limiting mechanistic studies. To address this, we employed a domain-focused truncation strategy to generate de novo murine models of K/C and K/P fusions, which faithfully recapitulate the morphological, immunophenotypic, and transcriptomic features of KAT6A-rearranged AML. Genomic profiling revealed that KAT6A fusions preferentially localize to H3K4me2/3-marked regions and interact with the Nucleosome Remodeling Factor (NURF), a critical H3K4me2/3 reader. Disrupting NURF-chromatin interactions impaired K/C recruitment to target loci and disrupted MLL/COMPASS-mediated H3K4me2 deposition, thereby establishing an epigenetic regulatory module involving KAT6A chimeras, NURF, and MLL/COMPASS. Concurrently, CBP/P300 inhibition reduced histone acetylation, chromatin accessibility, and genomic targeting of the module. Therapeutically, NURF inhibition induced cell cycle arrest and suppressed leukemia proliferation, while CBP/P300 inhibition promoted leukemia differentiation. Both strategies demonstrated promising efficacy in K/C murine models, with superior effects observed with combined NURF and CBP/P300 inhibition. These findings uncover a self-reinforcing epigenetic module centered on histone reader proteins and modifying enzymes, providing mechanistic insights into KAT6A-rearranged AML and identifying promising combinatorial therapeutic vulnerabilities.

overall_design:
RNA-seq profiling of MPs and c-Kit-enriched HSPCs, K/C-III leukemia cells, and K/P-III leukemia cells.
RNA-seq profiling of K/C-III leukemia cells treated with 2 μM A485 or BZ1 for 6 or 12 hours.
RNA-seq profiling of K/C-III leukemia cells treated with 0.5 μM A485 and 1 μM BZ1 combination for 6 hours.
CUT&RUN analysis of KAT6A variants (NT1, NT2, fusions), Pol II, and histone modifications in HEK293T cells.
CUT&RUN analysis of KAT6A mutants (NT1, ΔWH1, ΔMYST, G657E) in HEK293T cells.
CUT&RUN analysis of KAT6A and BPTF in HEK293T cells expressing KAT6A-NT1 with either BPTF knockdown or GFP knockdown.
CUT&RUN profiling of K/C-III, BPTF, SMARCA1, and histone modifications (H3K4me2/3, H3K27ac) in murine K/C-III leukemia cells.
CUT&RUN profiling of K/C-III, BPTF, and MLL in murine K/C-III leukemia cells following 6-hour treatment with 2 μM BZ1.
CUT&RUN profiling of K/C-III and H3K27ac in murine K/C-III leukemia cells following 6-hour treatment with 2 μM A485.
ChIP-seq analysis of Pol II, WDR5, H3K4me1, and H3K4me2 in murine K/C-III leukemia cells treated with 2 μM BZ1 for 6 hours.
ChIP-seq analysis of BPTF, MLL, and Pol II in murine K/C-III leukemia cells treated with 2 μM A485 for 6 hours.
ATAC-seq analysis of murine K/C-III leukemia cells treated with 2 μM A485 or BZ1 for 6 hours.
ChIP-MNase analysis of H3K4me2 in HEK293T cells expressing K/C-III, treated with 2 μM BZ1 for 6 or 12 hours.

first: Kaiwei

last: Liang


title: KAT6A Chimeras Forms a Self-Reinforcing Epigenetic Module with NURF and MLL/COMPASS in AML [ChIP-Seq]


title: Transcription factors SP5 and SP8 drive primary cilia formation in mammalian embryos [ATAC-seq]

first: Yinwen

overall_design: Examination of chromatin accessibility profile in Yolk sac mesoderm, Yolk sac viseral endoderm and Gut viseral endoderm cells obtained from fluorescence-activated cell sorting of E8.75 (12 somite) Afp-GFP/+ embryos.

first: Richard

last: Koche

first: Alexandra

last: Joyner


title: KAT6A Chimeras Forms a Self-Reinforcing Epigenetic Module with NURF and MLL/COMPASS in AML [RNA-Seq]

overall_design:
RNA-seq profiling of MPs and c-Kit-enriched HSPCs, K/C-III leukemia cells, and K/P-III leukemia cells.
RNA-seq profiling of K/C-III leukemia cells treated with 2 μM A485 or BZ1 for 6 or 12 hours.
RNA-seq profiling of K/C-III leukemia cells treated with 0.5 μM A485 and 1 μM BZ1 combination for 6 hours.


title: ARABIDOPSIS HOMOLOG OF THRITORAX impact the lateral root development by epigenetic regulation of targets involved in root system architecture.

city: Cuernavaca

first: Gustavo

last: Rodriguez-Alonso

state: Morelos

address: Av.Universidad 2001, Col. Chamilpa

department: Biología Molecular de Plantas

country: Mexico

institute: Instituto de Biotecnología

summary: The chemical modifications of histones between others process are important to modify the chromatin structure and permit the access to DNA. The ARABIDOPSIS HOMOLOG OF TRITHORAX1 (ATX1/SDG27) is a known regulator of floral development which encodes a histone methyltransferase (H3K4me). ATX1 is directly involved in the H3K4 trimethylation which is associated with maintenance of transcriptionally active chromatin state. To study the ATX1 role in lateral root development, we performed a root phenotypic analysis of atx1setm mutant, and the transcriptome profiling (using RNA-seq approach). The atx1setm mutant express the catalytically inactive form of the ATX1 protein (that maintains its structural integrity) in the atx1-1 (null mutant) background. Here, we showed that the primary root and lateral root (LR) primordium (LRP) development in the atx1setm mutant are abnormal, and the phenotype is stronger compared to the atx1-1 mutant. We identified ATX1-activated genes involved in the LR development like PEROXIDASE35 (PER35), AGAMOUS LIKE14 (AGL14), HOMEOBOX PROTEIN 21 (ATHB21), KIDARI (KDR) and USUALLY MULTIPLE ACIDS MOVE IN AND OUT TRANSPORTERS 20 (UMAMIT20). Here, we studied PEROXIDASE 35 gene whose expression is promoted by ATX1 activity. Interestingly, in the per35 mutant the primary root growth was greater compared to Wt and the LRP morphogenesis was abnormal with a phenotype like that found in atx1setm mutant. The data suggest that PER35 gene is a new player related to lateral root primordium morphogenesis in Arabidopsis thaliana.

overall_design: RNA-seq was done for whole roots of two biological replicates from the atx1setm and the Wt genotype (10 days-post-germination seedlings). Two biological replicates per genotype

first: Selene

last: Napsucialy-Mendivil.

last: Rodríguez-Alonso.

first: Joseph

last: Dubrovsky.


title: RNA Pol I activity is required for meiotic chromatin organization and the H3K4me3 gradient essential for oogenesis, independent of ribosome synthesis [ATAC-Seq]

city: Austin

first: Elif

last: Sarinay Cenik

address: 2500 Speedway

department: Molecular Biosciences

institute: University of Texas at Austin

summary: Oogenesis requires extensive and dynamic chromatin remodeling that primes gene promoters for later transcriptional activation during embryonic development. Here, we uncover a pivotal, non-canonical role for RNA Polymerase I (Pol I) in driving these chromatin state transitions during Caenorhabditis elegans oogenesis. Using the auxin-inducible degron system to selectively deplete either Pol I catalytic subunits or ribosome assembly factors, we disentangle the consequences of impaired nucleolar integrity from reductions in ribosome biogenesis. Strikingly, although disrupting ribosome assembly caused minimal effects on oocyte production, loss of Pol I activity led to widespread changes in chromatin accessibility, a dampening of the distal-proximal H3K4me3 gradient required for oogenesis, reduced synapsis, and elevated ATM/ATR phosphorylation, resulting in fewer but significantly larger oocytes. Despite their promoters becoming more accessible, oogenesis genes did not show large changes in steady-state mRNA, consistent with transcriptional repression prior to fertilization. Instead, Pol I depletion prematurely remodeled oogenic chromatin, through a misdirection of H3K4me3 deposition towards promoters normally primed for zygotic genome activation. These findings reveal an epigenetic gating function for nucleolar integrity in oocyte maturation: Pol I preserves three-dimensional chromatin organization and maintains proper spatiotemporal regulation of histone modifications, independent of ribosome production. Given the evolutionary conservation of nucleolar dynamics and histone modifications during gametogenesis, our work suggests that nucleolar stress, whether from environmental factors, aging, or genetic disorders, could broadly compromise fertility by disrupting oogenic chromatin priming.

overall_design: Chromatin accessibility data from dissected gonads of auxin-inducible degron strains used to deplete an RNA Pol I subunit (RPOA-2) or ribosome assembly chaperone (GRWD-1). L4 stage animals were treated with 1 mM auxin (IAA) or EtOH control for 18 hours before germline dissection and ATAC-seq. Each replicate includes 20 gonads.

first: Raquel

last: Mejia-Trujillo

first: Qiuxia

last: Zhao

first: Ayesha

last: Rahman

first: Trevor

middle: F

last: Freeman


title: KAT6A Chimeras Forms a Self-Reinforcing Epigenetic Module with NURF and MLL/COMPASS in AML [ATAC-Seq]


title: KAT6A Chimeras Forms a Self-Reinforcing Epigenetic Module with NURF and MLL/COMPASS in AML [CUT&Run]


title: RNA Pol I activity is required for meiotic chromatin organization and the H3K4me3 gradient essential for oogenesis, independent of ribosome synthesis [RNA-seq]

overall_design:
Gene expression data from dissected gonads of auxin-inducible degron strains used to deplete an RNA Pol I subunit (RPOA-2) or ribosome assembly chaperone (GRWD-1). L4 stage animals were treated with 1 mM auxin (IAA) or EtOH control for 18 hours before germline dissection and RNA-seq. Each replicate includes 20 gonads.
Gene expression data from dissected gonads of auxin-inducible degron strains used to deplete a ribosome assembly chaperone (TSR-2). L4 stage animals were treated with 1 mM auxin (IAA) or EtOH control for 18 hours before germline dissection and RNA-seq. Each replicate includes 20 gonads.


title: Removal of promoter DNA methylation by epigenome editing reverses HBG silencing [ATAC-seq]

city: Sydney

first: Merlin

last: Crossley

address: UNSW

department: BABS

institute: University of New South Wales

summary: Beta-hemoglobinopathies caused by mutations in adult-expressed HBB can be treated by re-activating the adjacent paralogous genes HBG1 and HBG2 (HBG), which are normally silenced perinatally. Although HBG expression is induced by global demethylating drugs, their mechanism is poorly understood and toxicity limits their use. We identified the DNMT1-associated maintenance methylation protein UHRF1 as a mediator of HBG repression in a genome-wide screen. Loss of UHRF1 in the adult-type erythroid cell line HUDEP2 caused global demethylation and HBG activation that was reversed upon localized promoter re-methylation. Conversely, targeted demethylation of the HBG promoters activated their genes in HUDEP2 or primary CD34+ cell-derived erythroblasts. Mutation of MBD2, a CpG-methylation reading component of the NuRD complex, to impair methylation sensitivity recapitulated the effects of promoter demethylation. Our studies demonstrate that localized CpG-methylation at the HBG promoters facilitates developmental silencing and identify a targeted therapeutic approach for b-hemoglobinopathies via epigenomic editing.

overall_design: ATAC-seq experiments were performed inCD34+ derived erythroidblast cells treated with NT sgRNA or UHRF1 sgRNA1, or targeted by TETv4 dTETv4 with gRNAs targeting HBG promoter

first: Ruopeng

last: Feng

first: Yichao

last: Li

first: Mitchell J

last: Weiss


title: Role of ATF4 in regulation of kidney gene expressions, signaling pathways and functions

first: Genomics-core-facility

last: WCM

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

overall_design: Refer to individual Series


title: Removal of promoter DNA methylation by epigenome editing reverses HBG silencing [RNA-seq]

overall_design: RNA-seq experiments were performed in human CD34+ derived CD235a+ erythroid cells treated with NT or UHRF1gRNA1+Cas9. RNA-seq was also performed after transfection of HUDEP-2 cells with TETv4 and sgRNAs 1-6 targeting HBG and in a mutant MBD2 Y178F HUDEP-2 cell line.

first: Henry

middle: W

last: Bell

first: Manan

last: Shah

first: Kate

last: Quinlan

first: Mithcell

middle: J


title: Cut&Run of freshly isolated quiescent muscle stem cells (MuSCs) for H3K27me3 and Cut&Run of myoblasts for REST/NRSF

city: Montreal

first: Vahab

middle: D.

last: Soleimani

state: Quebec

address: 3755 Chem. de la Côte-Sainte-Catherine

department: Lady Davis Institute for Medical Research

country: Canada

institute: Jewish General Hospital

summary: The maintenance of cell lineage and cell fate are essential for the function of adult stem cells. Despite this, the epigenetic mechanisms that regulate muscle stem cell (MuSC) identity are not well understood. In this study, we performed Cut&Tag of the activating histone marks H3K4me3 and H3K27ac on freshly isolated quiescent MuSCs and found that a large number of genes without transcription still maintained the permissive mark H3K4me3 but lacked the marker of active enhancers, H3K27ac. These genes included those that are essential for non-myogenic lineage determination. We found that many of the genes that were not transcribed but enriched for H3K4me3, were also enriched for the RE-1 binding motif, the motif recognized by the repressive transcription factor REST. Using a genetic mouse model where REST is conditionally knocked out of MuSCs, we further investigated the role of REST in the maintenance of quiescent MuSC cell identity. Investigation of the transcriptome and chromatin accessibility of WT and REST deficient MuSCs determined that the loss of REST results in the gain of expression of key genes of several non-myogenic tissues, particularly neuronal genes.  Additionally, the loss of REST led to the dramatic reduction of the MuSC pool and the induction of muscle atrophy.  The unstable cell identity caused by the genetic deletion of REST results in the MuSCs undergoing apoptosis and is the main driver of the observed loss of the MuSC pool. Together, the data presented in this study establishes a novel function of the transcription factor REST, where it safeguards the identity and myogenic lineage of MuSCs, through the repression of alternative lineages.

overall_design: For Cut&Run of H3K27me3 on MuSCS, 45000 MuSCs (ITGA7+/VCAM1+/CD11b-/CD45-/CD31-/Ly6a-) were isolated by Fluorescence Activated Cell Sorting (FACS) from 3 WT (C57BL/6)  male mice (6 weeks old). MuSCs were sorted directly into 2%FBS in PBS and Cut&Run was performed using the commercially available Cut&Run Kit (Epicypher, 14-1048) according to the manufacturer’s guidelines with the H3K27me3 primary antibody (Cell Signalling, Cell Signalling, C36B11). Cut&Run for REST/NRSF was performed on low passage cultured myoblasts. Briefly, 100 000 cells were isolated by FACS and cells were cultured for 1 week in growth media. Cells were then trypsinized, washed and Cut&Run was performed using the commercially available Cut&Run Kit (Epicypher, 14-1048) according to the manufacturer’s guidelines with the anti-REST antibody (Milllipore, 17-641). All Cut&Run libraries were prepared with Cut&Run Library Prep Kit (Epicypher, 14-1001) according to the manufacturer’s guidelines and the samples were sequenced on NovaSeq6000 Sprime Paired End (PE) 150 bp.


title: Removal of promoter DNA methylation by epigenome editing reverses HBG silencing [CUT&RUN]

overall_design: CUT&RUN experiments were performed inCD34+ derived erythroidblast cells treated with NT sgRNA or UHRF1 sgRNA1, or targeted by TETv4 dTETv4 with gRNAs targeting HBG promoter


title: Polyclonality and Metabolic Heterogeneity in a Colorectal Tumor Model

city: GIF-SUR-YVETTE

first: Jacques

last: Montagne

address: 1 AVENUE DE LA TERRASSE

country: France

summary: The monoclonal origin of cancer is widely accepted, although numerous studies suggest that some are of polyclonal origin. Loss-of checkpoints in transformed cells gives rise to carcinomas comprising a wide diversity of cell types that fulfill distinct, even complementary, metabolic functions, contrasting with a hypothetical monoclonal origin. Here, using a Drosophila intestinal tumor model, we show that, despite an identical genetic background, these tumors 1), comprise a conserved set of different metabolic-specialized clusters; 2), are always polyclonal and derive from several clones characterized by distinct metabolic specificity; 3) depend on motility of the founder clones for their growth; 4) share metabolic needs similar to those of human cancers. In summary, our study indicates that, in this model, tumor formation always requires assembly between founder clones potentially providing distinct cellular functions, as visualized by their metabolic heterogeneity. Thus, this polyclonal assembly would constitute a critical step of tumor progression.

overall_design: To investigate metabolism in tumors, single and group of 6 tumors were dissected and sequenced. Tumorous flies were heat-shocked at 37°C for 2-hrs 2-3 days after adult eclosion. At least 21-dpi flies were selected based on GFP fluorescence through the abdomens. Tumors were dissected on ice in Ringer buffer, rinsed twice ice-cold Ringer baths and the extracellular matrix was digested by gentle pipetting for 3-5 minutes with 20µL 5X Trypsin (PAN BIOTECH P10-022100) twice diluted. Efficient digestion was promptly checked under fluorescent dissecting microscope. Consequently, for each sample, 1X Ringer buffer was added up to 1.5mL and each tube was filtered through 30µm filters (Sysmex CellTrics). Tubes were centrifugated for 4 minutes at 1000G, at 4°C; 1mL of supernatant was discarded and the same volume of fresh 1X Ringer buffer was added. A second centrifugation (4 minutes, 1000G, 4°C) was done and after carefully removing all supernatant, pellets were gently resuspended in 30µL 1X Ringer buffer for sequencing. The whole sample preparation procedure did not exceed 20 minutes. Cell suspension were loaded into the Chromium Controller using a Chromium Next GEM Single Cell 3’ v3.1 kit (10x Genomics) to generate a droplet emulsion. cDNA were purified and libraries were prepared, according to the manufacturer recommendations. Single cell libraries were sequenced on a NextSeq 2000 Intrument (Illumina) using a P2-100 cycles kit. FastQ files were analyzed using the Cell Ranger software (10X Genomics, version 6.0.1), including alignment, filtering and quantitation of reads on the Drosophila genome r6.42 and generation of feature-barcode matrices. We used the Seurat R pipeline 10 for sample quality control and analysis. The R script used to evaluate sample quality, generate clusters, umaps, heatmaps and GO analysis is available at: https://github.com/Pdelam/Delamotte-et-al.-2024.git

first: Pierre

last: Delamotte

first: Mickaël

last: Poidevin

first: Yan

last: Jazczyszyn

first: Arnaud

last: Le Rouzic


title: RNA-seq profilling of wild type C57BL/6 Tac mice at E15.5 days post conception.

status: Public on Jun 23 2025

first: Simone

last: Sanna-Cherchi

address: 1150 St.Nicholas Ave

department: Department of Medicine, Nephrology

institute: Columbia University

summary: To better understand the molecular underpinnings of nephrogenesis at key developmental stages, we performed a bulk gene expression profiling in mouse kidneys at embryonic day 15.5 (E15.5) to identify genes essential for normal kidney development and to provide insights to the mechanisms underlying congenital anomalies of the kidney and urinary tract.

first: Max

last: Werth

first: Qing Xue

last: Liu

first: Jeremiah

last: Martino


title: Co-translational ribosome pairing enables native assembly of misfolding-prone subunits

city: Heidelberg

first: Günter

last: Kramer

address: Im Neuenheimer Feld 329

institute: Center for Molecular Biology of Heidelberg University (ZMBH)

summary: Protein complexes are pivotal to most cellular processes. Emerging evidence indicates that pairs of ribosomes ubiquitously drive the synchronized synthesis and assembly of two protein subunits into homodimeric complexes1-5. These observations suggest protein folding mechanisms of general importance enabled by contacts between nascent chains6,7 – which have thus far rather been considered detrimental8,9. However, owing to their dynamic and heterogeneous nature, the folding of interacting nascent chains remains unexplored. Here, we show that co-translational ribosome pairing allows their nascent chains to ‘chaperone each other’, thus enabling the formation of coiled-coil homodimers from subunits that misfold individually. We developed an integrated single-molecule fluorescence and force spectroscopy approach to probe the folding and assembly of two nascent chains extending from nearby ribosomes, using the intermediate filament lamin as a model system. Ribosome proximity in early translation stages was found to be critical: when interactions between nascent chains are inhibited or delayed, they become trapped in stable misfolded states that are no longer assembly-competent. Conversely, early interactions allow the two nascent chains to nucleate native-like quaternary structures that grow in size and stability as translation advances. We conjecture that protein folding mechanisms enabled by ribosome cooperation are more broadly relevant to intermediate filaments and other protein classes.

overall_design: Screening of nascent chain dimerization in two human cell lines (HEK293-T and U2OS cell lines). Disome selective profiling was performed as previously described (Bertolini et.al 2021) with modifications concerning crosslinking and salt concentrations, by using a low salt lysis buffer (150 mM KCl) with or without crosslinkers (lysis buffer supplemented with 2.5 mM BS3 and 20 mM EDC).

first: Florian

last: Wruck

first: Jaro

last: Schmitt

first: Katharina

last: Till

first: Kai

last: Fenzl

first: Matilde

last: Bertolini

first: Frank

last: Tippmann

first: Alexandros

last: Katranidis

first: Bernd

last: Bukau

first: Sander

last: Tans


title: Murine hematopoietic progenitor cell lines with erythroid and megakaryocyte potential

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: Red blood cells and platelets derive from bi-potential bone marrow megakaryocyte-erythroid progenitors, but their study is constrained by cell scarcity and limited experimental systems. Here we show that conditional expression of a virally transduced, regulated form of Hoxa7 enables expansion of murine cells resembling megakaryocyte-erythroid progenitors (Hoxa7-TPO), which undergo erythro-megakaryocytic differentiation upon Hoxa7 inactivation. The close relationship of Hoxa7-TPO cells to megakaryocyte-erythroid progenitors is supported by genetic and phenotypic analyses, and mature Hoxa7-TPO-derived red blood cells and platelets are largely indistinguishable from their primary counterparts. Genetic knock-out studies in Hoxa7-TPO cells recapitulate the key function of Klf1 and Nfe2 in red blood cell and platelet development, respectively, while disruption of the von Willebrand receptor gene Gp1ba recapitulates features of human Bernard-Soulier syndrome. Hence, we developed a versatile experimental system for expansion and differentiation of megakaryocyte-erythroid progenitors to study red blood cell and platelet development and model human diseases.

overall_design: Comparing non-differentiated Hoxa7-TPO cells (CD41-) with in vitro differentiated, Hoxa7-TPO-derived megakaryocytes (CD41+) or in vivo differentiated reticulocytes (Ter119+).

first: Ruiqiong

last: Wu

first: Vanessa

last: Redecke

first: Zhijun

last: Ma

first: Marco

last: Marchetti

first: Mortimer

last: Poncz

first: Peng

last: Xu

first: Yong

last: Cheng

first: Conroy

last: Field

first: Kimberly

last: Queisser

first: Faraz

last: Salehi

first: Hyun Sook

last: Ahn

first: Mitchell

last: Weiss

first: Hans

last: Häcker


title: Large-Scale CRISPR Screening in Primary Human 3D Gastric Organoids Enables Comprehensive Dissection of Gene-Drug Interactions [ATAC-seq]

city: Houston

first: Mo-Fan

last: Huang

address: 6431 Fannin Street

department: Integrative Biology and Pharmacology

institute: University of Texas Health science center

summary: Investigating gene-drug interactions is critical for advancing personalized medicine by revealing how genetic variations shape individual responses to medications. To achieve this goal, it is essential to develop a robust human functional genomics system that can accurately recapitulate normal physiology and disease while effectively accounting for the complexity and heterogeneity among individuals. We explored this potential in primary 3D human gastric organoids by implementing a wide range of large-scale CRISPR-based genetic screens, including CRISPR knockout, CRISPR interference (CRISPRi), CRISPR activation (CRISPRa), and single-cell CRISPR screens. Our cisplatin sensitization screens targeting 1,952 DNA-binding proteins identified numerous known genes associated with DNA repair pathways, along with previously unrecognized cisplatin sensitization loci. Individual validation of top hits further confirmed the robustness of the screening results. Furthermore, using multiplexed single-cell CRISPR screens to simultaneously extract individual sgRNAs and single-cell transcriptomes, we uncovered a convergence within DNA repair pathways in cisplatin-treated organoids compared to cisplatin-naïve organoids. These methods distinguished high-dimensional synergistic effects between sgRNAs and drug perturbations by leveraging each cell's gene expression profiles, improving the resolution to link genotypes with drug response phenotypes in organoids. Finally, we identified TAF6L as a novel cisplatin sensitization gene. Mechanistically, TAF6L is crucial for the proliferation of cell recovery following cisplatin-induced DNA damage response. In summary, diverse CRISPR-based functional genomics platforms can be successfully applied to human organoids, revealing new gene-drug interactions with implications for human disease.

overall_design: In order to investigate TAF6L-associated chromatin accessibility, we established TAF6L knockdown, TAG6L-GFP overexpression and their control human gastric organoid lines followed by ATAC-seq analyses.

first: Yuan-Hung

last: Lo

first: Hudson

middle: T

last: Horn

first: Wei-Chieh

last: Yu

first: Qing

last: Liu

first: Madeline

last: Tomaske

first: Martina

last: Tower

first: Antonia

last: Dominguez

first: Michael

middle: C

last: Bassik

first: Dung-Fang

last: Lee

first: Lei

last: Qi

first: Jonathan

last: Weissman

first: Jin

last: Chen

first: Calvin

last: Kuo


title: Effect of ASC-J9 on gene expression of murine bone marrow-derived macrophages

city: Zhuhai

first: Guanmin

last: Jiang

address: No.52 Meihua East Road, Xiangzhou District, Zhuhai, Guangdong Province, China

department: Department of Clinical Laboratory

institute: the Fifth Affiliated Hospital of Sun Yat-sen University

summary: The Androgen receptor (AR) in prostate cancer cells acts as a central transcription factor, playing a crucial role in maintaining tumour cell survival and the production of prostate-specific antigen (PSA).To investigate the effect of AR on macrophage gene phenotype, mouse bone marrow-derived macrophages (BMDMs) treated with the AR-degrading agent ASC-J9 in presence of conditioned media (CM) derived from RM1 mouse prostate cancer cells (RM1 CM) was collected for RNA sequencing (RNA-seq). Differential expressed genes (DEGs) analysis showed that compared to DMSO-treated macrophages, ASC-J9-treated macrophages had lower expressions of Trem2 and Trem1, anti-inflammatory M2-like macrophage markers Cd163 and Arg1 expression, pro-migratory factors Ccl2 and Ccl8, but had higher expressions of pro-inflammatory M1-like macrophage markers Cd86 and Tnf, suggesting that AR may be associated with macrophage phenotypic differentiation.

overall_design: RNA-seg profiling of C57BL/6J wildtype or TREM2 knockout (TREM2 KO) mouse bone marrow-derived macrophages treated with 10 μM ASC-J9 or DMSO for 48 h.

first: Qiaohua

last: Wang


title: Epigenetic enigma: reinstating normalcy at a naïve chromosomal locus by suppressing an oncogenic lncRNA transgene

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH

type: Methylation profiling by high throughput sequencing


title: Cytokine exposure of human macrophages induces disease-associated microglia transcriptional signatures

city: New York

first: Anna

last: Podlesny-Drabiniok

address: 1 Gustave Levy Place

institute: Icahn School of Medicine at Mount Sinai

summary: Myeloid cells including brain-resident macrophages (microglia) and peripheral macrophages play a crucial role in various pathological conditions, including neurodegenerative diseases such as Alzheimer's disease (AD). They adapt to extracellular stimuli by acquiring various transcriptional states. Understanding of how these states are regulated is limited due to a lack of tools that enable robust reprogramming toward disease-associated phenotypes. In this study, we investigated the effects of a cytokine mix, including interleukin-4 (IL-4), colony stimulating factor 1 (CSF1/M-CSF), interleukin 34 (IL-34) and transforming growth factor beta (TGFβ), on human THP-1 macrophages to elucidate their potential reprogramming towards disease-associated phenotypes and subsequential functional changes. Our results indicate that treatment with the cytokine mix led to significant transcriptomic changes, driving human THP-1 macrophages towards a transcriptional state reminiscent of disease-associated microglia (DAM) and lipid-associated macrophages (LAM) collectively referred to as DLAM. Transcriptome profiling revealed gene expression changes related to oxidative phosphorylation, lysosome function, and lipid metabolism. Single-cell RNA sequencing revealed the activation of DLAM-like transcriptional responses across multiple cell clusters. Functional assays demonstrated alterations in macrophage motility, phagocytosis, lysosomal activity, and metabolic and energetic profiles. Our findings provide insights into the cytokine-mediated reprogramming of macrophages towards disease-relevant states, highlighting their role in neurodegenerative diseases and potential for therapeutic development.

overall_design: Human THP-1 monocytic leukemia line was differentiated to macrophages and treated with 1) three factors (3F): IL34, MCSF, TGFb; 2) IL4; 3) mix of 3F and IL4 (MIX): IL34, MCSF, TGFb, IL4. Control THP-1 macrophages were not treated (NT). Concentration of each cytokine in every treatment IL34 100ng/ml, TGFb 50ng/ml, MCSF 25ng/ml, IL4 20ng/ml

first: Tulsi

last: Patel

first: Carmen

last: Romero-Molina

first: Yiyuan

first: Alison

last: Goate

first: Edoardo

last: Marcora


title: CGRP-Related Neuropeptide Adrenomedullin 2 Promotes Tissue-Protective ILC2 Responses and Limits Intestinal Inflammation

first: Jazib

last: Uddin

address: 413 E 69th Street, BB-709

department: Medicine

institute: Weill Cornell Medicine

summary: Neuro-immune circuits regulate innate and adaptive immunity at barrier surfaces, however the differential impact of these circuits on proinflammatory versus tissue-protective responses remains poorly defined. We identify that enteric neurons produce CGRP-related adrenomedullin 2 (ADM2), and identify a previously unrecognized role for the ADM2-ADM2 receptor pathway in promoting intestinal tissue-protective functions of group 2 innate lymphoid cells (ILC2s). Genomic or ILC2-intrinsic deletion of ADM2 receptor subunits resulted in a significant reduction in tissue-protective ILC2 responses, defective amphiregulin (AREG) production and increased susceptibility to intestinal damage and inflammation. Conversely, therapeutic delivery of recombinant ADM2 elicited tissue-protective AREG production in ILC2s and limited intestinal inflammation. Expression of genes encoding human ADM2 receptor (CALCRL and RAMP3) was altered in IBD patients and associated with reduced expression of AREG in ILC2s. Collectively, these findings identify that the ADM2-ADM2 receptor pathway can promote tissue-protective functions of ILC2s in the context of intestinal damage and inflammation.

overall_design: Expression profiling by high throughput sequencing

first: David

last: Artis


title: Large-Scale CRISPR Screening in Primary Human 3D Gastric Organoids Enables Comprehensive Dissection of Gene-Drug Interactions [RNA-seq]

first: Mo-Fan

last: Huang

overall_design: In order to investigate TAF6L-associated gene expression, we established TAF6L knockdown, TAG6L-GFP overexpression and their control human gastric organoid lines followed by RNA-seq analyses.

first: Yuan-Hung

last: Lo

first: Hudson

last: Horn

first: Wei-Chieh

last: Yu

first: Qing

last: Liu

first: Madeline

last: Tomaske

first: Martina

last: Tower

first: Antonia

last: Dominguez

first: Michael


title: Epigenetic enigma: reinstating normalcy at a naïve chromosomal locus by suppressing an oncogenic lncRNA transgene [WGS]

first: Songjoon

summary: Maintaining genome integrity is crucial for the proper functioning and development of organisms. One intriguing aspect of genome integrity is the formation and function of neocentromeres at non-centromeric sites. The centromere-specific protein CENP-A plays a vital role in centromere identification and function. However, in many cancers, CENP-A is often found to be ectopically misplaced when overexpressed. Moreover, the deposition of CENP-A at the centromere depends on the transcription of centromeric non-coding RNAs. Consequently, ectopic CENP-A is found at transcriptionally active and frequent breakpoint regions. To further explore the ectopic CENP-A localization, we engineered a stable ectopic CENP-A site at a naïve chromosome by overexpressing a non-centromeric oncogenic lncRNA capable of recruiting CENP-A to its transcription site. We tracked cells carrying the stable transgene to understand the stability and longevity of the induced ectopic CENP-A site and the harboring chromosome. Our findings revealed that the induced epigenetic memory was eventually lost by suppression of the transgene through competing epigenetic silencing mechanisms. This epigenetic restoration naturally reversed the ectopic CENP-A level to its previous levels at the engineered site. Our observations suggest that cells may have evolved failsafe mechanisms to prevent neocentromere formation at ectopic sites unless otherwise favored by selection involving multiple components.

overall_design: The metastatic colorectal cancer cell line SW480 wild type and stable SW480 cells expressing the lncRNA PCAT2 transgene cassette were employed in this work. ChIP, immunoblotting, quantitative real-time PCR, immunofluorescence, and DNA-FISH analysis were used on these two cell lines to investigate the levels of various epigenetic marks, lncRNAs,and gene expression, and the localization of CENP-A nucleosomes in non-centromeric regions. The DNA methylation profile ofthe same two cell lines wasalso studied using next-generation sequencing.

first: Arunkumar

last: Ganesan

first: Sikder

last: Sweta

first: Baek

last: Songjoon

first: Dalal

last: Yamini


title: Obese individuals exhibit distinct temporal gene expression dynamics in response to influenza vaccination

first: Megan

last: Hockman

address: 50 South Drive

department: NIAID

institute: National Institutes of Health

summary: The effectiveness of the seasonal influenza vaccine varies between individuals. Specific risk groups with comorbidities, such as the obese, have an increased risk of infection even when vaccinated. It has been proposed that a heightened baseline inflammatory state and alterations in adaptive immune cell populations in obese individuals may adversely impact immune response to pathogens and vaccines. Therefore, understanding differences in vaccine response in obese individuals is critical for the development of improved influenza vaccine design and strategies. Previously, we identified a transcriptomic signature prior to seasonal influenza vaccination that is predictive of an individual’s response to the influenza vaccine. To understand the dynamics of the host response following vaccination we studied systemic gene expression from whole blood collected from 163 vaccinated individuals on days 3, 7, and 28 post-vaccination. Gene expression profiles were compared between high and low vaccine responders in both obese and non-obese groups. We detected characteristic changes in gene expression over time, with a peak at day 7 post-vaccination. A large subset of genes associated with the adaptive immune response exhibited significantly different expression in high- and non- vaccine responders. Distinct gene sets presented differing temporal patterns in different weight and response groups, indicative of molecular processes impacting the immune response to vaccination.

overall_design: Comparative gene expression profiling of humans after influenza vacination.

first: Julia

last: Matthews

last: Carlock

first: Ted

last: Ross

last: Gresham

first: Elodie

last: Ghedin


title: Epigenetic enigma: reinstating normalcy at a naïve chromosomal locus by suppressing an oncogenic lncRNA transgene [Bisulfite-Seq]

last: Baek


title: The keratin-associated protein epiplakin is down-regulated in psoriasis

status: Public on Jun 22 2025

city: Vienna

first: Hannes

last: Kühtreiber

state: Vienna

address: Lazarettgasse 14

department: Department of Dermatology

country: Austria

institute: Medical University Vienna

summary: Epiplakin (EPPK1) is a protein that specifically interacts with keratin filaments in the epidermis. It helps to stabilize this filament network when the cells are under stress. In the present study we investigated how EPPK1 is regulated during the process of keratinocyte differentiation and in psoriasis, an inflammatory skin disease in which this process is disturbed. Here, we analyzed single-cell RNA sequencing (scRNA-seq) data from psoriatic patients and performed comparative analyses with wild-type and Eppk1 knockout mice.

overall_design: Murine skin samples were obtained from wild-type and Eppk1 knockout mice, as previously described (Spazierer et al., Mol Cell Biol. 2006;26(2):559–568. doi:10.1128/MCB.26.2.559-568.2006), and subjected to single-cell RNA sequencing (scRNA-seq).

last: Mildner

first: Peter

last: Fuchs


title: PIEZO2 mechanoreceptor-expressing fibroblasts in keloids cause short-term recurrence after surgical resection

status: Public on Jun 20 2025

city: chiba city

first: Masahiro

last: Kiuchi

state: chiba

address: cyuoku inohana1-8-1

institute: Chiba univercity

summary: Keloids are characterized by persistent scar tissue growth that causes abnormal sensory perceptions due to mechanical stress. But the molecular dysfunction and disease-specific cells that fashion keloid pathophysiology are still not evident. Here, we found a distinct subpopulation of fibroblasts with enhanced expression of PIEZO2 in the dermal layer of keloid patients experiencing dysesthesia, including pain and pressure-tactile itch. The PIEZO2-expressing fibroblasts exhibited a keloid-typical phenotype marked by increased extracellular matrix production signaling and higher levels of collagens such as COL1A1, COL1A2, and COL3A1 compared with other fibroblasts. Notably, patients with higher PIEZO2 expression tend to experience keloid recurrence more quickly after keloidectomy (4/5 vs. 0/5, p = 0.047) than those with lower PIEZO2 expression. Thus, the PIEZO2-positive fibroblasts are indicative cells that most accurately reflect the keloid characteristics, suggesting the driving role for the persistent growth of Keloids.

overall_design: According to the supplier's manual, total RNA purification was performed using an RNeasy Plus Kit (QIAGEN) with an RNase-free DNase Set (QIAGEN) described in our previous study 9. In brief, twenty 4um-thick thin sections were cut from cryopreserved skin tissue using a cryostat, dissolved in Lysis Buffers in the RNAeasy Kit to extract total RNA.  The quality and amount of the RNA in each sample were evaluated using Experion (Bio-Rad, Hercules, CA, USA) and NanoDrop (Thermo Fisher Scientific), respectively. RNA-seq analysis was performed by Operon biotechnology.

first: Shinsuke

last: Akita

first: Sanae

last: Ikehara

first: Kota

last: Kokubo

first: Kazuhiko

last: Azuma

first: Syouta

last: Ohki

first: Joceline

last: Kadarman

first: Yohei

last: Hosokawa

first: Yoshihiro

last: Akimoto

first: Yosuke

last: Inaba

first: Hideki

last: Hanaoka

first: Nobuyuki

last: Mitsukawa

first: Kiyoshi

last: Hirahara

first: Toshinori

last: Nakayama

first: Yuzuru


title: HIF1α Mediates Circadian Regulation of Skeletal Muscle Metabolism and Substrate Preference in Response to Time-of-Day Exercise

status: Public on Jun 21 2025

city: Copenhagen

first: Ali

last: Altintas

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

summary: The regulation of metabolism in peripheral tissues is mediated by pathways that are under circadian control. a bidirectional relationship is evident between the circadian clock and hypoxia-inducible factor-1 α (HIF1α), which is specific to time-of-day exercise. To elucidate the role of HIF1α in driving the divergences in the systemic and skeletal muscle metabolic responses to exercise, a skeletal muscle-specific HIF1α knockout (KO) mouse model was generated. Metabolic phenotyping alongside global transcriptomic profiling was conducted under basal conditions or in response to an acute exercise bout in HIF1α KO and wild-type (WT) mice at the early rest phase (ZT3) or early active phase (ZT15). Our findings demonstrate that HIF1α is dispensable for the metabolic response to exercise at ZT15, but required for an elevation in glycolytic metabolism in response to exercise at ZT3. Specifically, the loss of HIF1α alters the fate of glucose with a shift towards mannose-6-phosphate production observed at ZT3. In addition, the loss of HIF1α alters the transcriptional profile of skeletal muscle specifically at ZT3 with a shift towards oxidative metabolism. HIF1α contributes to regulating the time-of-day exercise response by driving a shift in substrate preference primarily towards glucose oxidation while sparing fatty acid oxidation. This comprehensive metabolic phenotyping of HIF1α KO mice demonstrates that the contribution of HIF1α to the regulation of time-of-day metabolism is dependent on metabolic status and energetic stressors.

overall_design:
To determine the role of skeletal muscle HIF1α in mediating the transcriptional responses to time-of-day, a skeletal muscle-specific HIF1α knockout mouse was generated (HIF1α KO). Skeletal muscle specific HIF1α knock out and wild type mice were subjected to 60 min treadmill running (16 m/min, 5 % incline) or a sham treatment at zeitgeber time (ZT) 3 and ZT 15. RNA sequencing was performed on gastrocnemius tissue of mice 3 hr following the treatment.

The sample 'ko_3_ex_44' (GSM8647977), also referred to as '0156_44' in the GSE282641_rawCounts.txt.gz file, was excluded from downstream analysis due to low coverage.

first: Ehrlich

middle: M

last: Amy

first: MacGregor

last: Kirstin

first: Ashcroft

last: Stephen

first: Small

last: Lewin

first: Altintas

last: Ali

first: Chibalin

middle: V

last: Alex

first: Mattanovich

last: Matthias

first: Stocks

last: Ben

first: Moritz

last: Thomas

first: Treebak

last: Jonas

first: Zierath

middle: R

last: Juleen


title: CBFβ-SMMHC-driven leukemogenesis requires enhanced RUNX1-DNA binding affinity in mice

first: Yaqiang

last: Cao

state: Maryland

address: 9000 Rockville Pike

department: System Biology Center

institute: NHLBI

summary: The leukemia fusion gene CBFB-MYH11 requires RUNX1 for leukemogenesis, but the underlying mechanism is unclear. By in vitro studies, we found that CBFβ-SMMHC, the chimeric protein encoded by CBFB-MYH11, could enhance the binding affinity between RUNX1 and its target DNA. Increased RUNX1-DNA binding was also observed in myeloid progenitor cells from mice expressing CBFβ-SMMHC. Moreover, only CBFβ-SMMHC variants able to enhance the DNA binding affinity by RUNX1 could induce leukemia in mouse models. Significant transcriptomic changes, affecting genes associated with inflammatory response and target genes of CBFA2T3, were observed in mice expressing leukemogenic CBFβ-SMMHC variants. Finally, we show that CBFβ-SMMHC could not induce leukemia in mice with a Runx1-R188Q mutation, which reduces RUNX1 DNA binding but not affecting its interaction with CBFβ-SMMHC or its sequestration to cytoplasm by CBFβ-SMMHC. Our data suggest that enhancing RUNX1-target DNA binding affinity is an important mechanism of leukemogenesis by CBFβ-SMMHC.

overall_design: ChIC-seq, RNA-seq and scRNA-seq were used to study the DNA binding preference and gene expression changes caused by CBFβ-SMMHC or RUNX1 variants or mutations during leukemogenesis.

first: Tao

last: Zhen

first: Tongyi

last: Dou

first: Yun

last: Chen

first: Guadalupe

last: Lopez

first: Ana

last: Menezes

first: Xuefeng

last: Wu

first: John

last: Hammer

first: Jun

last: Cheng

first: Lisa

last: Garrett

first: Stacie

last: Anderson

first: Martha

last: Kirby

first: Stephen

last: Wincovitch

first: Bayu

last: Sisay

first: Abdel

last: Elkahloun

first: Di

first: Lucio

last: Castilla

first: Wei

last: Yang

first: Jiansen

last: Jiang

first: Keji

last: Zhao

first: Pu

last: Liu


title: CUT&Tag in Bacteria Reveals Unconventional G-Quadruplex Landscape in Mycobacterium tuberculosis in Response to Oxidative Stress

city: Padova

first: Ilaria

middle: Rebecca

last: Maurizio

address: Via Gabelli, 63

department: Molecular Medicine

country: Italy

institute: University of Padova

summary:
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, remains a global health threat due to increasing drug resistance and high mortality rates. To combat tuberculosis effectively, novel therapeutic targets are urgently needed. G-quadruplexes (G4s) represent promising candidates for this purpose. In this study, we successfully apply the cleavage under targets and tagmentation (CUT&Tag) technique for the first time in bacteria, mapping the G4 landscape in Mtb under standard and oxidative stress conditions, the latter mimicking the environment Mtb faces within macrophages. We validate the CUT&Tag protocol using an antibody against the RNA polymerase β-subunit, confirming its association with actively transcribed genes. Employing the anti-G4 antibody BG4, we discover that Mtb G4s, unlike their eukaryotic counterparts, predominantly locate within gene coding sequences and consist of two-guanine tract motifs. Notably, oxidative stress increases G4 formation, correlating with reduced gene expression.
Our findings provide the first evidence of G4 formation in Mtb cells and suggest their potential role in bacterial survival within macrophages. This study demonstrates the successful application of CUT&Tag in bacteria and unveils an unconventional G4 landscape in Mtb, offering new insights into bacterial stress response mechanisms and potential therapeutic targets.

overall_design: G4 ChIP-seq has been applied to the Mycobacterium tuberculosis genome. Two experimental conditions were tested, exponential growth and oxidative stress treatement. Each experiment consisted of three biological replicas.

first: Emanuela

last: Ruggiero

first: Irene

last: Zanin

first: Marta

last: Conflitti

first: Giulia

last: Nicoletto

first: Roberta

last: Provvedi

first: Sara

middle: N

last: Richter


overall_design: RNA Polymerase- and G4-CUT&Tag was applied to the Mtb genome for the first time. Two conditions were tested, exponential growth and oxidative stress treatment. Each experiment consisted of three biological replicas.


title: Fibroblasts expressing PIEZO2 mechanoreceptor in keloids possibly cause alloknesis and short-term recurrence after surgical resection [RNA-seq]

city: Yachiyo-City

first: Kota

last: Kokubo

state: Chiba

address: Yachiyodai-minami 1-10-12

department: Department of Immunology

institute: Chiba University

summary: Keloids are scar tissue that can develop under tensile stress and manifest the tactile itch called alloknesis due to the heterogeneous course.  But the molecular and cellular mechanisms underlying the pathology of keloid have been still unknown.  Here, we found that unique fibroblast subpopulation that have dense-core granules with enhanced expression of PIEZO2 in the dermal layer of keloid tissue with alloknesis, a pressure-tactile itch. PIEZO2-expressed fibroblasts showed enhanced expression of COL1A1, COL1A2 and COL3A1. Gene expression profile analysis of fibrous disease tissues could distinguish the keloid cases by higher PIEZO2, which correlated with collagen COL1A1, COL1A2, and COL3A1 gene expression, not only from the keloid cases with lower PIEZO2 expression but also from the lymphedema cases where massive fibroblast proliferation appears. Notably, patients with the keloid accompanied by higher expression of PIEZO2 showed a significantly shorter time to recurrence after keloidectomy in patients with the keloids (4/5 vs. 0/5, p = 0.047). Thus, a unique subset of PIEZO2-positive fibroblasts may be involved in a keloid pathology and be a potent therapeutic target for the intractable keloids.

overall_design: RNA sequencing was performed using skin tissue cells from one keloid skin case.

first: Shinsuke

last: Akita

first: Sanae

last: Ikehara

first: Masahiro

last: Kiuchi

first: Kazuhiko

last: Azuma

first: Syouta

last: Ohki

first: Joceline

last: Kadarman

first: Yoshihiro

last: Akimoto

first: Komei

last: Baba

first: Yohei

last: Hosokawa

first: Kiyoshi

last: Hirahara

first: Nobuyuki

last: Mitsukawa

first: Toshinori

last: Nakayama

first: Yuzuru


first: Ilaria

last: Maurizio

overall_design: RNA-seq has been performed in triplicate on Mycobacterium tuberculosis cultures upon exponential growth phase and after oxidative stress treatment.

first: Emanuela

last: Ruggiero

first: Irene

last: Zanin

first: Marta

last: Conflitti

first: Giulia


title: MGA directly recruits SETDB1/ATF7IP for histone H3K9me3 on meiosis-related genes in mouse embryonic stem cells.

status: Public on Jun 19 2025

city: Hidaka

first: Akihiko

last: Okuda

state: Saitama

address: 1397-1 Yamane

department: Division of Biomedical Sciences, Research Center for Genomic Medicine

institute: Saitama Medical University

summary: Many of meiosis-related genes in mouse embryonic stem cells (ESCs) bear substantial amounts of trimethylated lysine 9 of histone H3 (H3K9me3) modification. However, how meiosis-related genes in ESCs acquire this histone modification is totally obscure. We hypothesize that the specific functional domain termed FAM of MGA that is the scaffolding component of PRC1.6, one of atypical subtypes of PRC1 is directly involved in the deposition of this histone modification by recruiting SETDB1 via its interaction with ATF7IP. To address the hypothesis, we generated ESCs producing MGA that lacks FAM domain and examined effects of the mutation on global expression profile and H3K9me3 levels by RNA- and ChIP-sequence analyses, respectively. We also generated ESCs producing mutant ATF7IP lacking its FNIII domain that is considered to be crucial for the interaction with MGA in our hypothesis to assess the role of the domain for the deposition of H3K9me3 by ChIP-seq analyses.

overall_design: Mouse ESCs producing MGA that lacks FAM domain or ATF7IP that lacks of FNIII domain were generated by means of lenti virus-mediated CRISPR-Cas9 system. Fragmented chromatins were prepared from these genetically manipulated- and parental-ESCs and used for ChIP-sequence analyses to elucidate the effect of removal of these domains on the magnitude/distribution of H3K9me3 modification in ESCs. Mouse ESCs producing the MGA mutant and their control counterparts were also used for RNA-seq analyses to examine the effect of removal of the FAM domain from MGA on global expression profile.

first: Kousuke

last: Uranishi

first: Masataka

last: Hirasaki

first: Ayumu

last: Suzuki


title: Fibroblasts expressing PIEZO2 mechanoreceptor in keloids possibly cause alloknesis and short-term recurrence after surgical resection [scRNA-seq]

first: Kota

last: Kokubo

overall_design: single cell RNA sequencing (scRNA-seq) was performed using a total of 10,000 skin tissue cells from three keloid skin cases and one normal skin cases. The data for keloid patients No. 1-3 were obtained from specimens case 11-13.

first: Shinsuke

last: Akita

first: Sanae

last: Ikehara

first: Masahiro

last: Kiuchi

first: Kazuhiko

last: Azuma

first: Syouta

first: Joceline


title: Identification of replicative aging and inflammatory aging signatures via whole-genome CRISPRi screens

city: seattle

first: xueqiu

last: lin

state: wa

address: 1100 Fairview Ave N

institute: FRED HUTCHINSON CANCER CENTER

summary: Aging is one of the greatest risk factors for chronic diseases. Research on aging at the cellular level, especially in adult stem cells, is conducive to a comprehensive understanding of the molecular processes of aging. We performed multiple systematic genome-wide CRISPR interference (CRISPRi) screenings in human primary mesenchymal stem cells (MSC) derived from adipose tissues. Notably, we identified potential novel regulators in the progress of MSC senescence in terms of both replicative senescence and inflammatory induced senescence. Combining the functional genomic data with 405 GWAS datasets, including 50 aging-related studies, we observed that the inflammatory aging signatures identified from the CRISPRi screenings were significantly associated with diverse aging processes, suggesting novel signatures to analyze and predict aging status and aging-related disease. These novel signatures verified from the comprehensive functional genomics and genetic datasets may provide targets to interfere with the aging process as well as to improve cell therapy products.

overall_design: The goals of this study were (i) to identify novel senescence-promoting genes in adult stem cells, (ii) to characterize novel senescence-promoting genes in a specific inflammatory milieu(iii) and to decipher the inflammatory aging process by comparing two solid screening platforms (IL-6 minus and IL6 plus), thus highlight the biomarker for  pathological aging and therapeutic potential of MSC by manipulating the senescence-promoting genes.


title: Mitochondrial respiration is necessary for CD8 T cell proliferation and cell fate

city: Chicago

first: Rogan

last: Grant

state: IL

address: 303 E Superior St, Simpson Querrey Biomedical Research Center 5-522

department: Pulmonary and Critical Care Medicine

institute: Northwestern University

summary: CD8 T cell proliferation and memory formation are linked to changes in metabolism, which has important implications for improving CD8 T cell fitness in therapies against chronic infections and cancer. The mitochondrial electron transport chain (ETC) is essential for antigen-specific CD8 T cell proliferation. Mitochondrial ETC function is linked to the generation of ATP, production of metabolites to sustain proliferation, and signaling molecules including reactive oxygen species (ROS), which determine T cell function and fate. However, it is not fully understood which mitochondrial ETC functions are necessary for CD8 T cell proliferation in vivo. Here we report that impairing mitochondrial complex III function, which diminishes respiration, proton pumping linked to ATP production, and superoxide production, decreases CD8 T cell proliferation and memory formation. CD8 T cells lacking functional mitochondrial complex III also exhibit an exhausted-like phenotype following acute stimulation. The expression of Ciona intestinalis alternative oxidase (AOX), which accepts electrons from coenzyme Q, thus compensating for the loss of mitochondrial complex III function without generating ROS or proton pumping, restores respiration, proliferation and largely prevents the exhausted phenotype in vitro and in vivo. However, AOX did not sustain memory CD8 T cells, suggesting mitochondrial complex III ROS is necessary for optimal memory formation. These findings demonstrate that the primary function of the mitochondrial ETC in CD8 T cells is enabling respiration to sustain proliferation and memory formation as well as to prevent an exhausted phenotype.

overall_design: Bulk RNA-seq profiling of CD8+ T cells, with and without mitochondrial complex III function (or with partial rescue of function with AOX).Cells were either: 1) Isolated 40dpi LCMV armstrong infection. 2) Adoptively transferred into naive wildtype mice then isolated 7dpi LCMV armstrong infection. or 3) Isolated and activated overnight in vitro.

first: Steinert

last: Elizabeth

first: Bruza

last: Beatriz

first: Danchine

last: Veronika

first: Grant

last: Rogan

first: Vasan

last: Karthik

first: Kharel

last: Arjun

first: Zhang

last: Yuqi

first: Cui

last: Weguo

first: Szibor

last: Marten

first: Weinberg

last: Samuel

first: Chandel

last: Navdeep


title: Selective remodelling of the adipose niche in obesity and weight loss [snRNA-Seq]

city: London

first: William

middle: Robert

last: Scott

address: Hammersmith Hospital, Du Cane Road

department: Institute of Clinical Sciences

country: United Kingdom

institute: Imperial College London

summary: Weight loss significantly improves metabolic and cardiovascular health in people with obesity. Adipose tissue remodelling is central to these varied and important clinical effects. However surprisingly little is known about the underlying mechanisms, presenting a barrier to treatment advances. Here we report a spatially resolved single nucleus atlas (171,247 cells, 70 people) investigating the cell types, molecular events and regulatory factors that reshape human adipose tissues, and thus metabolic health, in obesity and therapeutic weight loss. We discover selective vulnerability to senescence in metabolic, precursor and vascular cells and reveal senescence is potently reversed by weight loss. We define gene regulatory mechanisms and tissue signals that may drive a degenerative cycle of senescence, tissue injury and metabolic dysfunction. We find that weight loss reduces adipocyte hypertrophy and biomechanical constraint pathways, activating global metabolic flux and bioenergetic substrate cycles that may mediate systemic improvements in metabolic health. In the immune compartment, we demonstrate that weight loss represses obesity-induced macrophage infiltration but does not completely reverse activation, leaving these cells primed to trigger potential weight regain and worsen metabolic dysfunction. Throughout, we map cells to tissue niches to understand the collective determinants of tissue injury and recovery. Overall, our complementary single nucleus and spatial datasets offer unprecedented insights into the basis of obese adipose tissue dysfunction and its reversal by weight loss, and a key resource for mechanistic and therapeutic exploration.

overall_design: Single nucleus RNA (snRNAseq) sequencing was carried out in subcutaneous abdominal adipose tissue (AT) from 25 people with obesity before and after marked weight loss (paired samples), and in 26 healthy lean controls. 2 lean samples were removed during quality control. All molecular phenotyping was carried out after overnight fast. The weight loss interval was a minimum of 5 months (median 7, range 5 to 18 months). Median percentage weight loss was 22% (range 13 to 33%). AT samples were obtained intraoperatively from morbidly obese individuals (BMI>35kg/m2) undergoing laparoscopic bariatric surgery (gastric bypass or gastric sleeve) and healthy controls (BMI<26kg/m2) undergoing non-bariatric laparoscopic abdominal surgery. Subcutaneous AT was collected from abdominal surgical incision sites. Follow up subcutaneous AT samples were collected from the peri-umbilical region using needle biopsy at >5 months after weight loss intervention. Whole AT samples were snap frozen at collection and stored at -80C for future use. Participants were unrelated, between 20-70 years of age, from a multi-ethnic background, and free from systemic illnesses not related to obesity. People with treated T2D were excluded because of potential effects of hypoglycaemic medications on AT metabolism. All participants gave informed consent. The study complies with all relevant ethical regulations and was approved by the London – City Road and Hampstead Research Ethics Committee, United Kingdom (reference 13/LO/0477).

first: Antonio

last: Miranda

first: Liam

last: McAllan

first: Guianfranco

last: Mazzei

first: Ivan

last: Andrew

first: Iona

last: Davies

first: Meryem

last: Ertugrul

first: Julia

last: Kenkre

first: Hiromi

last: Kudo

first: Joana

last: Carrelha

first: Bhavik

last: Patel

first: Sophie

last: Newton

first: Weihua

last: Zhang

first: Alice

last: Pollard

first: Amy

last: Cross

first: Oliver

last: McCallion

first: Mikyung

last: Jang

first: Ka Lok

last: Choi

first: Scarlett

last: Brown

first: Yasmin

last: Rasool

first: Marco

last: Adamo

first: Mohamed

last: Elkalaawy

first: Andrew

last: Jenkinson

first: Borzoueh

last: Mohammadi

first: Majid

last: Hashemi

first: Robert

last: Goldin

first: Laurence

last: Game

first: Joanna

last: Hester

first: Fadi

last: Issa

first: Dylan

last: G Ryan

first: Patricia

last: Ortega

first: Ahmed

last: Ahmed

first: Rachel

middle: L

last: Batterham

first: John

last: Chambers

first: Jaspal

last: Kooner

first: Damir

last: Baranasic

first: Michela

last: Noseda

first: Tricia

last: Tan


title: Selective remodelling of the adipose niche in obesity and weight loss [Xenium]

first: William

last: Scott

overall_design: Spatial transcriptomics was carried out in subcutaneous abdominal AT from 4 people with obesity before and after marked WL (paired samples), and in 4 healthy lean controls. All molecular phenotyping was carried out after overnight fast. AT samples were obtained intraoperatively from morbidly obese individuals (BMI>35kg/m2) undergoing laparoscopic bariatric surgery (gastric bypass or gastric sleeve) and healthy controls (BMI<26kg/m2) undergoing non-bariatric laparoscopic abdominal surgery. Subcutaneous AT was collected from abdominal surgical incision sites. Follow up subcutaneous AT samples were collected from the peri-umbilical region using needle biopsy at >5 months after weight loss intervention. Whole AT samples were snap frozen at collection and stored at -80C for future use. Participants were unrelated, between 20-70 years of age, from a multi-ethnic background, and free from systemic illnesses not related to obesity. People with treated T2D were excluded because of potential effects of hypoglycaemic medications on AT metabolism. All participants gave informed consent. The study complies with all relevant ethical regulations and was approved by the London – City Road and Hampstead Research Ethics Committee, United Kingdom (reference 13/LO/0477).

first: Antonio

last: Miranda

first: Liam

last: McAllan

first: Guianfranco

last: Mazzei

first: Ivan

last: Andrew

first: Iona

last: Davies

first: Meryem

last: Ertugrul

first: Julia

last: Kenkre

first: Hiromi

last: Kudo

first: Joana

last: Carrelha

first: Bhavik

last: Patel

first: Sophie

last: Newton

first: Weihua

last: Zhang

first: Alice

last: Pollard

first: Amy

last: Cross

first: Oliver

last: McCallion

first: Mikyung

last: Jang

first: Ka Lok

last: Choi

first: Scarlett

last: Brown

first: Yasmin

last: Rasool

first: Marco

last: Adamo

first: Mohamed

last: Elkalaawy


title: PCK1 loss contributes to kidney disease progression by altering mitochondrial fitness through its cataplerotic function [snRNA-seq_PCK1KO]

status: Public on Jun 18 2025

city: Bellinzona

first: Anna

last: Rinaldi

address: Zorzi

country: Switzerland

institute: EOC

summary: Metabolic alterations are recognized as key features of kidney injury, but their causal role in kidney repair remains a topic of debate. We investigate the role of PCK1, an enzyme involved in gluconeogenesis and cataplerosis, i.e. the removal of TCA intermediates from the mitochondrial matrix, in kidney disease. We demonstrate that PCK1 loss leads to injured mitochondria with decreased respiration and TCA metabolites accumulation. This results in inflammation, tubular injury and impaired tubule repair. We show that maintaining PCK1 expression in models of acute and chronic kidney disease preserves renal structure and function by improving TCA metabolite clearance. Restoration of PCK1 enhances mitochondrial health, reducing the progression to fibrosis. In humans, we confirm the correlation between PCK1 loss, mitochondrial injury as well as a failed tubule repair phenotype.  We further observe the accumulation of TCA metabolites consistent with disrupted cataplerosis in chronic kidney disease. Our findings establish the maintenance of cataplerosis as an important factor of tubular physiology and repair and PCK1 as causal and potential therapeutic targets in this process.

overall_design: We characterized by single nucleus RNA sequencing (snRNAseq) kidney specimens obtained from 6 transgenic POD-ATTAC mouse model, 3 PCK1_WT, and 3 PCK1_KO.

first: Delal

last: Dalga

last: Faivre

first: David

last: Jaques

first: Aurelie

last: Huber

first: Gregoire

last: Arnoux

first: Arnaud

last: Lyon

first: Lena

last: Berchtold

first: Joseph

last: Rutkowski

first: Quentin

last: Gex

first: Deborah

last: Paolucci

first: Mario

last: Kreuzfeld

first: Thomas

last: Cagarelli

first: Belen

last: Ponte

first: Alban

last: Longchamp

first: Solange

last: Moll

first: Pietro

last: Cippà

last: Verissimo

last: deSeigneux


title: Unique nigral and cortical pathways implicated by epigenomic and transcriptional analyses in a rotenone rat model of Parkinson’s disease [RNA-Seq]

first: Maria

last: Tsalenchuk

address: Maurice Wohl Clinical Neuroscience Institute, 5 Cutcombe Road

institute: King's College London

summary: Pesticide exposure is increasingly recognised as a potential environmental factor contributing to the onset of idiopathic Parkinson’s disease, yet the molecular mechanisms underlying this connection remain unclear. This study aims to explore how pesticide exposure disrupts key brain regions involved in Parkinson’s disease pathology by reshaping gene expression and epigenetic landscapes. Using the  well established rotenone rat model of the disease, we used H3K27ac ChIP-sequencing and RNA-sequencing to profile active regulatory elements and transcriptional activity in the substantia nigra and cortex. We identified widespread transcriptomic and epigenetic differences which are consistent across the assays. Our results indicate there is a strong immune response to rotenone localised to the substantia nigra and highlight an enrichment of immune-related motifs in this brain region, suggesting that the immune response is at least partially driven by gene regulatory mechanisms. We also noted an increase in C1q complement pathway activity in the substantia nigra. In contrast, we identified widespread dysregulation of synaptic function at the gene regulatory level in the cortex of these same rats. Our results highlight a role for gene regulatory mechanisms potentially mediating the effects of pesticide exposure, driving region-specific functional responses in the brain that may contribute to the pathology of Parkinson’s disease.

overall_design: To profile gene regulatory variation in the SN and cortex of rats exposed to rotenone compared to vehicle controls, we used RNA sequencing (RNA-seq) and H3K27ac chromatin immunoprecipitation (ChIP)-seq

first: Kyle

last: Farmer

first: Sandra

last: Castro

first: Abigail

last: Scherier

first: Yuqian

last: Ye

first: Timothy

last: Greenamyre

first: Emily

last: Rocha

first: Sarah

last: Marzi


title: PCK1 loss contributes to kidney disease progression by altering mitochondrial fitness through its cataplerotic function [snRNA-seq_Human]

first: Anna

last: Rinaldi

overall_design: We characterized by single nucleus RNA sequencing (snRNAseq) patient kidney biopsies obtained from 6 proteinuric nephropathies

first: Delal

last: Dalga

last: Faivre

first: David

last: Jaques

first: Aurelie

last: Huber

first: Gregoire

last: Arnoux

first: Arnaud

last: Lyon

first: Lena

last: Berchtold

first: Joseph

last: Rutkowski

last: Gex

last: Paolucci

first: Sophie


title: Revisiting NeuroD1-mediated Glia-to-Neuron Trans-differentiation Using Transgenic Mice

city: Shanghai

first: Fangbing

last: Chen

state: shanghai

address: Children’s Hospital of Fudan University Wanyuan Ro

institute: Fudan university

summary: Direct astrocyte-to-neuron conversion holds promise for in situ neuroregeneration to treat neurodegenerative diseases. However, commonly-used adeno-associated vectors carrying GFAP mini-promoters drive leaky expression of neurogenic factors in endogenous neurons, raising concerns about trans-differentiation validity. Developing inducible, lineage-traceable transgenic mice, we evaluate NeuroD1 effects on astrocyte-to-neuron conversion in spinal cord and brain injury models. Lineage-tracing and single-cell transcriptomics reveal that ectopic NeuroD1 expression promotes robust conversion of reactive astrocytes in lesion cores to neurons at the acute phase of injury, but not in peri-injury astrocytes.

overall_design: We performed spinal cord injury in iNeuroD1GFP adult mice at postnatal day 60 (P60) and administered TAM (100 mg/kg/day)44 from days post-injury (dpi) 5 to 8. At dpi10,spinal cords were rapidly extruded from iNeuroD1GFP mice (n=3) after anesthesia. Each cord was separated into lesion core and distal regions, and analyzed using snRNA-seq


title: PCK1 loss contributes to kidney disease progression by altering mitochondrial fitness through its cataplerotic function [snRNA-seq_PCK1KI]

overall_design: We characterized by single nucleus RNA sequencing (snRNAseq) kidney specimens obtained from 4 transgenic POD-ATTAC mouse model, 2 PCK1_WT, and 2 PCK1_KI.

first: Quentin

first: Deborah

first: Mario

last: Kreuzfeld

first: Thomas

last: Cagarelli

first: Belen

last: Ponte

first: Alban

last: Longchamp

first: Solange

last: Moll

first: Pietro

last: Cippà

last: Verissimo

last: deSeigneux


title: Evf2 enhancer lncRNA-enhancer gene guidance through direct RNA binding and RNP recruitment domains

first: Jhumku

last: Kohtz

state: Illinois

address: 303 E Chicago

department: Neurology

summary: During mouse embryonic brain development, the Evf2 ultraconserved enhancer lncRNA (e-lncRNA) guides the Dlx5/6UCE enhancer to ~129 sites across chr6.  However, previous work identified only 4 transcriptionally regulated targets associated with Evf2 enhancer-gene guided sites (EGGs), raising questions about the significance of the majority of Evf2-EGGs.  Here, single cell transcriptomics shows that Evf2-regulated EGGs on chr6 coincide with subpopulation-specific Evf2 transcriptional targets, revealing far greater alignment between EGGs and transcriptional effects than previously reported.  Evf2 regulation of EGGs to gene bodies (GB ±5kb) divides chr6 into short-range (<10Mb), highly activated and long/super long-range (10-129Mb), moderately repressed genes. However, chr6 clustering of Evf2 transcriptionally regulated targets in populations where Evf2 is first activated, supports that transcriptional outcomes of Evf2-EGGs are not limited to gene body guidance, but may result from EGGs as far as 3Mb, uncoupling shift distance from transcriptional effects.  Analysis of directly bound Evf2 RNA binding sites on chr6 (6 RBSs), divides chr6 into 4 regions, consistent with a role for RBS spacing in Evf2-EGG mediated, chromosome-spanning transcriptional regulation.  In addition to chr6 Evf2 RBSs, 141 genome-wide RBSs are identified, 69 exactly aligning (>25bp) with at least one RBS, In addition to chr6 Evf2 RBSs, 141 genome-wide RBSs are identified, 69 exactly aligning (>25bp) with at least one RBS.  RBS DNA identities are associated with transcription factor enrichment rather than DNA looping, as shown by HiCseq (chromosome capture of dual crosslinked) of E13.5GEs.  While 80/147 RBSs are involved in inter-or intra-chr interactions, RBS chromosomal domains are differentially enriched for intra- and inter-chromosomal interactions, and domain specific Evf2-regulated RNP binding. Together with heterogeneous Evf2 regulation of protein pool/condensates (PPCs) of diverse Evf2 ribonucleoproteins (RNPs) (Smarcc2, an RNA binding chromatin remodeler, and Nono, an RNA paraspeckle organizer, Sox2 (a homeodomain transcription factor), RNP recruitment at RBSs and transcriptional targets, we propose a model whereby direct e-lncRNA binding, combinatorial Evf2-RNP recruitment, and homeodomain transcription factor DNA motif recognition/binding/activity, enables multi-modal EGG selectivity and transcriptional outcomes.

overall_design: Transcriptional effects of the Evf2 enhancer long non-coding RNA (e-lncRNA) are studied by comparing E13.5 mouse brain ganglionic eminences (GEs) from mutant mice lacking Evf2 (Evf2TS/TS) and wildtypes (Evf2+/+).  E13.5 GEs are used in these studies to study the birthplace of embryonic interneurons.  scSeq: 10X genomics single cell sequencing platform was performed to determine gene expression at single cell resolution from mutant and wildtype E13.5GEs. ChIPseq : Cut&Run native chromatin immunoprecipitation sequencing method was performed E13.5GEs from mutant and wildtypes to determine the effects of Evf2 on binding by two Evf2 ribonucleoproteins -Smarcc2 and Nono binding genome-wide, using anti-Smarcc2 and anti-Nono and subtraction with anti-IgG profiles as a negative control.  ChIRP: Chromatin immunoprecipitation of RNA  (ChIRP) on glutaraldehyde crosslinked Evf1/2TSTS E13.5GEs (mice lacking both Evf2 and Evf1, alternatively spliced form) followed by probing with two sets of antisense oligo probes (odd or even probes against the Evf2 transcript).  GAPDH antisense oligo probes were used as a negative control.  Only overlapping odd and even probe binding regions absent from GAPDH peaks and absent  were considered to be Evf1/2 RNA binding sites.

first: Brian

last: Clark

first: Abhijit

last: Chakraborty

first: Ferhat

last: Ay


title: CRISPR engineering of armored CAR T cells enables tumor-restricted payload delivery with enhanced safety and efficacy

city: Perth

first: Jesse

middle: David

last: Armitage

state: WA

address: 35 Stirling Hwy, Crawley

department: School of Biomedical Sciences

institute: University of Western Australia

summary: The efficacy of chimeric antigen receptor (CAR) T cell therapy in solid tumors is limited by immunosuppression and antigen heterogeneity. To overcome these barriers, “armored” CAR T cells, which secrete proinflammatory cytokines, have been developed. However, their clinical application has been limited due to toxicities related to peripheral expression of the armoring transgene. Here, we developed a CRISPR knock-in strategy that leverages the regulatory mechanisms of endogenous genes to drive transgene expression in a tumor-localized manner. By screening endogenous genes with tumor-restricted expression, the NR4A2 and RGS16 promoters were identified to support the delivery of cytokines such as IL-12 and IL-2 directly to the tumor site, leading to enhanced anti-tumor efficacy and long-term survival of mice in both syngeneic and xenogeneic models. This was concomitant with improved CAR T cell polyfunctionality, activation of endogenous anti-tumor immunity, a favorable safety profile, and was applicable using CAR T cells from patients.

overall_design: Bulk RNA-seq profiling of human anti-LeY CAR T cells engineered to express IL-12 from the NR4A2 gene locus. Experiment includes n=2 Mock control, NR4A2/GFP control and NR4A2/IL12 CAR T cells.